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Pinheiro A, Borges JR, Côrte-Real JV, Esteves PJ. Evolution of guanylate binding protein genes shows a remarkable variability within bats (Chiroptera). Front Immunol 2024; 15:1329098. [PMID: 38357541 PMCID: PMC10864436 DOI: 10.3389/fimmu.2024.1329098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/16/2024] [Indexed: 02/16/2024] Open
Abstract
Background GBPs (guanylate binding proteins), an evolutionary ancient protein family, play a key role in the host's innate immune response against bacterial, parasitic and viral infections. In Humans, seven GBP genes have been described (GBP1-7). Despite the interest these proteins have received over the last years, evolutionary studies have only been performed in primates, Tupaia and rodents. These have shown a pattern of gene gain and loss in each family, indicative of the birth-and-death evolution process. Results In this study, we analysed the evolution of this gene cluster in several bat species, belonging to the Yangochiroptera and Yinpterochiroptera sub-orders. Detailed analysis shows a conserved synteny and a gene expansion and loss history. Phylogenetic analysis showed that bats have GBPs 1,2 and 4-6. GBP2 has been lost in several bat families, being present only in Hipposideidae and Pteropodidae. GBPs1, 4 and 5 are present mostly as single-copy genes in all families but have suffered duplication events, particularly in Myotis myotis and Eptesicus fuscus. Most interestingly, we demonstrate that GBP6 duplicated in a Chiroptera ancestor species originating two genes, which we named GBP6a and GBP6b, with different subsequent evolutionary histories. GBP6a underwent several duplication events in all families while GBP6b is present as a single copy gene and has been lost in Pteropodidae, Miniopteridae and Desmodus rotundus, a Phyllostomidae. With 14 and 15 GBP genes, Myotis myotis and Eptesicus fuscus stand out as having far more copies than all other studied bat species. Antagonistically, Pteropodidae have the lowest number of GBP genes in bats. Conclusion Bats are important reservoirs of viruses, many of which have become zoonotic diseases in the last decades. Further functional studies on bats GBPs will help elucidate their function, evolutionary history, and the role of bats as virus reservoirs.
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Affiliation(s)
- Ana Pinheiro
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - J. Ricardo Borges
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - João Vasco Côrte-Real
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU) München, Munich, Germany
| | - Pedro J. Esteves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal
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Fernandes AP, OhAinle M, Esteves PJ. Patterns of Evolution of TRIM Genes Highlight the Evolutionary Plasticity of Antiviral Effectors in Mammals. Genome Biol Evol 2023; 15:evad209. [PMID: 37988574 PMCID: PMC10709114 DOI: 10.1093/gbe/evad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
The innate immune system of mammals is formed by a complex web of interacting proteins, which together constitute the first barrier of entry for infectious pathogens. Genes from the E3-ubiquitin ligase tripartite motif (TRIM) family have been shown to play an important role in the innate immune system by restricting the activity of different retrovirus species. For example, TRIM5 and TRIM22 have both been associated with HIV restriction and are regarded as crucial parts of the antiretroviral machinery of mammals. Our analyses of positive selection corroborate the great significance of these genes for some groups of mammals. However, we also show that many species lack TRIM5 and TRIM22 altogether. By analyzing a large number of mammalian genomes, here we provide the first comprehensive view of the evolution of these genes in eutherians, showcasing that the pattern of accumulation of TRIM genes has been dissimilar across mammalian orders. Our data suggest that these differences are caused by the evolutionary plasticity of the immune system of eutherians, which have adapted to use different strategies to combat retrovirus infections. Altogether, our results provide insights into the dissimilar evolution of a representative family of restriction factors, highlighting an example of adaptive and idiosyncratic evolution in the innate immune system.
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Affiliation(s)
- Alexandre P Fernandes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Molly OhAinle
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
| | - Pedro J Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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Pinheiro A, de Sousa-Pereira P, Esteves PJ. The IgA of hares ( Lepus sp.) and rabbit confirms that the leporids IgA explosion is old and reveals a new case of trans-species polymorphism. Front Immunol 2023; 14:1192460. [PMID: 37600766 PMCID: PMC10435986 DOI: 10.3389/fimmu.2023.1192460] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Background Immunoglobulin A (IgA) is the mammalian mucosal antibody, providing an important line of defense against pathogens. With 15 IgA subclasses, the European rabbit has an extremely complex IgA system, strikingly more complex than most other mammals, which have only one IgA or, in the case of hominoids, two IgA subclasses. Similar to the two hominoid primate IGHA genes, the expansion of the rabbit IGHA genes appears to have begun in an ancestral lagomorph since multiple IgA copies were found by Southern blot analysis for the genera Sylvilagus, Lepus, and Ochotona. Results To gain a better insight into the extraordinary lagomorph IgA evolution, we sequenced, for the first time, expressed IgA genes for two Lepus species, L. europaeus and L. granatensis. These were aligned with the 15 rabbit IgA isotypes, and evolutionary analyses were conducted. The obtained phylogenetic tree shows that the Lepus IgA sequences cluster with and among the rabbit IgA isotypes, and the interspecies and intraspecies nucleotide genetic distances are similar. A comparison of the amino acid sequences of the Lepus and rabbit IgA confirms that there are two trans-species polymorphisms and that the rabbit and Lepus sequences share a common genetic pool. In fact, the main differences between the studied leporids IgAs reside in the characteristics of the hinge region. Conclusion The Lepus IgA sequences we have obtained strongly suggest that the great expansion of the leporid IGHA genes occurred in a common ancestral species and was then maintained in the descendants. A strong selective pressure caused the extraordinary expansion of the IGHA genes but then subsided, leading to the maintenance of the acquired polymorphisms in the descendants, with little subsequent divergence. This is a unique evolutionary pattern in which an ancient gene expansion has been maintained for approximately 18 million years.
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Affiliation(s)
- Ana Pinheiro
- Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto (CIBIO-UP), InBIO, Laboratório Associado, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Patrícia de Sousa-Pereira
- Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto (CIBIO-UP), InBIO, Laboratório Associado, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Pedro J. Esteves
- Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto (CIBIO-UP), InBIO, Laboratório Associado, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Centro de Investigação em Tecnologias de Saúde (CITS), CESPU, Gandra, Portugal
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Lopes AM, Almeida T, Diz S, Côrte-Real JV, Osório HC, Ramilo DW, Rebelo MT, da Fonseca IP, Esteves PJ, Alves PC, Santos N, Abrantes J. The potential role of scavenging flies as mechanical vectors of Lagovirus europaeus/GI.2. Virol J 2023; 20:103. [PMID: 37237382 DOI: 10.1186/s12985-023-02065-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
The European rabbit (Oryctolagus cuniculus) populations of the Iberian Peninsula have been severely affected by the emergence of the rabbit haemorrhagic disease virus (RHDV) Lagovirus europaeus/GI.2 (RHDV2/b). Bushflies and blowflies (Muscidae and Calliphoridae families, respectively) are important RHDV vectors in Oceania, but their epidemiological role is unknown in the native range of the European rabbit. In this study, scavenging flies were collected between June 2018 and February 2019 in baited traps at one site in southern Portugal, alongside a longitudinal capture-mark-recapture study of a wild European rabbit population, aiming to provide evidence of mechanical transmission of GI.2 by flies. Fly abundance, particularly from Calliphoridae and Muscidae families, peaked in October 2018 and in February 2019. By employing molecular tools, we were able to detect the presence of GI.2 in flies belonging to the families Calliphoridae, Muscidae, Fanniidae and Drosophilidae. The positive samples were detected during an RHD outbreak and absent in samples collected when no evidence of viral circulation in the local rabbit population was found. We were able to sequence a short viral genomic fragment, confirming its identity as RHDV GI.2. The results suggest that scavenging flies may act as mechanical vectors of GI.2 in the native range of the southwestern Iberian subspecies O. cuniculus algirus. Future studies should better assess their potential in the epidemiology of RHD and as a tool for monitoring viral circulation in the field.
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Affiliation(s)
- Ana M Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Unidade Multidisciplinar de Investigação Biomédica (UMIB), Universidade do Porto, Porto, 4050-313, Portugal
| | - Tereza Almeida
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Sílvia Diz
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - João V Côrte-Real
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU) München, Munich, Germany
| | - Hugo C Osório
- Centro de Estudos de Vectores e Doenças Infecciosas, Instituto Nacional de Saúde Doutor Ricardo Jorge, Marateca, Portugal
- Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - David W Ramilo
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-s-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Faculdade de Medicina Veterinária, Universidade Lusófona, Lisbon, Portugal
| | - Maria Teresa Rebelo
- CESAM - Centre for Environmental and Marine Studies, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Isabel Pereira da Fonseca
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-s-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
| | - Pedro J Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal
- CITS - Center of Investigation in Health Technologies, CESPU, 4585-116, Gandra, Portugal
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal
| | - Nuno Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
| | - Joana Abrantes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal.
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Neves F, Muñoz-Mérida A, Machado AM, Almeida T, Gaigher A, Esteves PJ, Castro LFC, Veríssimo A. Corrigendum: Uncovering a 500 million year old history and evidence of pseudogenization for TLR15. Front Immunol 2023; 14:1216338. [PMID: 37234170 PMCID: PMC10206515 DOI: 10.3389/fimmu.2023.1216338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/27/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fimmu.2022.1020601.].
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Affiliation(s)
- Fabiana Neves
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - André M. Machado
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Tereza Almeida
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Arnaud Gaigher
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Pedro J. Esteves
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- CITS - Center of Investigation in Health Technologies, CESPU, Gandra, Portugal
| | - L. Filipe C. Castro
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Ana Veríssimo
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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Neves F, Muñoz-Mérida A, Machado AM, Almeida T, Gaigher A, Esteves PJ, Castro LFC, Veríssimo A. Uncovering a 500 million year old history and evidence of pseudogenization for TLR15. Front Immunol 2022; 13:1020601. [PMID: 36605191 PMCID: PMC9808068 DOI: 10.3389/fimmu.2022.1020601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Toll like receptors (TLRs) are at the front line of pathogen recognition and host immune response. Many TLR genes have been described to date with some being found across metazoans while others are restricted to specific lineages. A cryptic member of the TLR gene family, TLR15, has a unique phylogenetic distribution. Initially described in extant species of birds and reptiles, an ortholog has been reported for cartilaginous fish. Methods Here, we significantly expanded the evolutionary analysis of TLR15 gene evolution, taking advantage of large genomic and transcriptomic resources available from different lineages of vertebrates. Additionally, we objectively search for TLR15 in lobe-finned and ray-finned fish, as well as in cartilaginous fish and jawless vertebrates. Results and discussion We confirm the presence of TLR15 in early branching jawed vertebrates - the cartilaginous fish, as well as in basal Sarcopterygii - in lungfish. However, within cartilaginous fish, the gene is present in Holocephalans (all three families) but not in Elasmobranchs (its sister-lineage). Holocephalans have long TLR15 protein sequences that disrupt the typical TLR structure, and some species display a pseudogene sequence due to the presence of frameshift mutations and early stop codons. Additionally, TLR15 has low expression levels in holocephalans when compared with other TLR genes. In turn, lungfish also have long TLR15 protein sequences but the protein structure is not compromised. Finally, TLR15 presents several sites under negative selection. Overall, these results suggest that TLR15 is an ancient TLR gene and is experiencing ongoing pseudogenization in early-branching vertebrates.
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Affiliation(s)
- Fabiana Neves
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,*Correspondence: Fabiana Neves,
| | - Antonio Muñoz-Mérida
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - André M. Machado
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Tereza Almeida
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Arnaud Gaigher
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany,Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Pedro J. Esteves
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal,CITS - Center of Investigation in Health Technologies, CESPU, Gandra, Portugal
| | - L. Filipe C. Castro
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Ana Veríssimo
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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Neves F, de Sousa-Pereira P, Melo-Ferreira J, Esteves PJ, Pinheiro A. Evolutionary analyses of polymeric immunoglobulin receptor (pIgR) in the mammals reveals an outstanding mutation rate in the lagomorphs. Front Immunol 2022; 13:1009387. [PMID: 36466819 PMCID: PMC9716071 DOI: 10.3389/fimmu.2022.1009387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/03/2022] [Indexed: 08/22/2023] Open
Abstract
BACKGROUND The transcytosis of polymeric immunoglobulins, IgA and IgM, across the epithelial barrier to the luminal side of mucosal tissues is mediated by the polymeric immunoglobulin receptor (pIgR). At the luminal side the extracellular ligand binding region of pIgR, the secretory component (SC), is cleaved and released bound to dimeric IgA (dIgA), protecting it from proteolytic degradation, or in free form, protecting the mucosa form pathogens attacks. The pIgR was first cloned for rabbit in early 1980's and since then has been described for all vertebrates, from fish to mammals. The existence of more than one functional pIgR alternative-spliced variant in the European rabbit, the complete pIgR as other mammals and a shorter pIgR lacking two SC exons, raised the question whether other lagomorphs share the same characteristics and how has the PIGR gene evolved in these mammals. RESULTS To investigate these questions, we sequenced expressed pIgR genes for other leporid genus, Lepus spp., and obtained and aligned pIgR sequences from representative species of all mammalian orders. The obtained mammalian phylogeny, as well as the Bayesian inference of evolutionary rates and genetic distances, show that Lagomorpha pIgR is evolving at a higher substitution rate. Codon-based analyses of positive selection show that mammalian pIgR is evolving under strong positive selection, with strong incidence in the domains excised from the rabbit short pIgR isoform. We further confirmed that the hares also express the two rabbit pIgR isoforms. CONCLUSIONS The Lagomorpha pIgR unique evolutionary pattern may reflect a group specific adaptation. The pIgR evolution may be linked to the unusual expansion of IgA genes observed in lagomorphs, or to neofunctionalization in this group. Further studies are necessary to clarify the driving forces behind the unique lagomorph pIgR evolution.
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Affiliation(s)
- Fabiana Neves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Patrícia de Sousa-Pereira
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - José Melo-Ferreira
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Pedro J. Esteves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal
| | - Ana Pinheiro
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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de Sousa-Pereira P, Lanning DK, Esteves PJ, Spoerry C, Woof JM, Pinheiro A. Rabbit IgA Hinges That Resist IgA1 Protease Action Provide Options for Improved IgA-Based Therapeutic Agents. Front Immunol 2022; 13:907342. [PMID: 35784276 PMCID: PMC9247829 DOI: 10.3389/fimmu.2022.907342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/23/2022] [Indexed: 11/18/2022] Open
Abstract
Immunoglobulin A provides a major line of defence against pathogens and plays a key role in the maintenance of the commensal microbiota in the intestinal tract. Having been shown to be more effective at tumour cell killing than IgG and strongly active against pathogens present in the mucosae, IgA antibodies have been attracting significant attention in recent years for use as therapeutic antibodies. To improve their therapeutic potential, bioengineered IgA forms with increased serum half-life and neutralizing abilities have been developed but the IgA hinge, which impacts susceptibility to bacterial proteases and ability to bridge between target and effector cells, has not yet been explored. The European rabbit has 15 IgA subclasses with exclusive hinge region motifs and varying lengths, constituting a unique model to evaluate the functional capabilities offered by incorporation of longer IgA hinges into immunoglobulins. Hinge regions from rabbit IgAs, featuring different lengths and sequences, were inserted into human IgA1 heavy chain to substitute the IgA1 hinge. These hinges did not appear to affect antigen binding nor the ability of the engineered chimeric IgA1 to bind and trigger FcαRI, as detected by IgA-mediated cell agglutination and release of superoxide by neutrophils. All rabbit hinge-human IgA1 hybrids were resistant to Clostridrum ramosum IgA protease enzyme digestion, as predicted by the lack of the cleavage site in the rabbit hinges. Some IgA1s featuring long rabbit hinges were cleaved by Neisseria meningitidis IgA1 protease cleavage type 1 or 2 enzymes, despite the lack of the predicted cleavage sites. More interestingly, the hybrid featuring the rabbit IgA15 hinge was not affected by any of the IgA proteases. The IgA15 hinge is longer than that found in human IgA1 and is composed by a unique motif with a stretch of nine consecutive Ser residues. These characteristics allow the preservation of a long hinge, with associated ability to bridge distantly spaced antigens and provide higher avidity binding, while remaining resistant to IgA protease degradation. The data suggest that the rabbit Cα15 hinge represents an interesting alternative hinge sequence for therapeutic human IgA antibodies that remains resistant to proteolytic cleavage.
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Affiliation(s)
- Patrícia de Sousa-Pereira
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus Agrário de Vairão, Vairão, Portugal
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Dennis K. Lanning
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Pedro J. Esteves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus Agrário de Vairão, Vairão, Portugal
- CITS—Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra, Portugal
| | - Christian Spoerry
- Department of Microbiology, Tumor and Cell Biology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Jenny M. Woof
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ana Pinheiro
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus Agrário de Vairão, Vairão, Portugal
- *Correspondence: Ana Pinheiro,
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9
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Águeda-Pinto A, Kraberger S, Everts A, Gutierrez-Jensen A, Glenn HL, Dalton KP, Podadera A, Parra F, Martinez-Haro M, Viñuelas JA, Varsani A, McFadden G, Rahman MM, Esteves PJ. Identification of a Novel Myxoma Virus C7-Like Host Range Factor That Enabled a Species Leap from Rabbits to Hares. mBio 2022; 13:e0346121. [PMID: 35352978 PMCID: PMC9040879 DOI: 10.1128/mbio.03461-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/23/2022] [Indexed: 01/04/2023] Open
Abstract
Myxoma virus (MYXV) is naturally found in rabbit Sylvilagus species and is known to cause lethal myxomatosis in European rabbits (Oryctolagus cuniculus). In 2019, an MYXV strain (MYXV strain Toledo [MYXV-Tol]) causing myxomatosis-like disease in Iberian hares (Lepus granatensis) was identified. MYXV-Tol acquired a recombinant region of ∼2.8 kb harboring several new genes, including a novel host range gene (M159) that we show to be an orthologous member of the vaccinia virus C7 host range family. Here, to test whether M159 alone has enabled MYXV to alter its host range to Iberian hares, several recombinant viruses were generated, including an MYXV-Tol ΔM159 (knockout) strain. While MYXV-Tol underwent fully productive infection in hare HN-R cells, neither the wild-type MYXV-Lau strain (lacking M159) nor vMyxTol-ΔM159 (deleted for M159) was able to infect and replicate, showing that the ability of MYXV-Tol to infect these cells and replicate depends on the presence of M159. Similar to other C7L family members, M159 was shown to be expressed as an early/late gene but was translocated into the nucleus at later time points, indicating that further studies are needed to elucidate its role in the nucleus. Finally, in rabbit cells, the M159 protein did not contribute to increased replication but was able to upregulate the replication levels of MYXV in nonpermissive and semipermissive human cancer cells, suggesting that the M159-targeted pathway is conserved across mammalian species. Altogether, these observations demonstrate that the M159 protein plays a critical role in determining the host specificity of MYXV-Tol in hare and human cells by imparting new host range functions. IMPORTANCE The coevolution of European rabbit populations and MYXV is a textbook example of an arms race between a pathogen and a host. Recently, a recombinant MYXV (MYXV-Tol) crossed the species barrier by jumping from leporid species to another species, causing lethal myxomatosis-like disease. Given the highly pathogenic nature of this new virus in hares and the incidences of other poxvirus cross-species spillovers into other animals, including humans, it is important to understand how and why MYXV-Tol was able to become virulent in a new host species. The results presented clearly demonstrate that M159 is the key factor allowing MYXV-Tol replication in hare cells by imparting new host range functions. These results have the potential to improve current knowledge about the virulence of poxviruses and provide a platform to better understand the new MYXV-Tol, rendering the virus capable of leaping into a new host species.
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Affiliation(s)
- Ana Águeda-Pinto
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Center for Immunotherapy, Vaccines and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ , USA
| | - Anne Everts
- Center for Immunotherapy, Vaccines and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Ami Gutierrez-Jensen
- Center for Immunotherapy, Vaccines and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Honor L. Glenn
- Center for Immunotherapy, Vaccines and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Kevin P. Dalton
- Instituto Universitario de Biotecnología de Asturias, Departamento de Bioquímica y Biología Molecular, Edificio Santiago Gascón, Universidad de Oviedo, Campus El Cristo, Oviedo, Spain
| | - Ana Podadera
- Instituto Universitario de Biotecnología de Asturias, Departamento de Bioquímica y Biología Molecular, Edificio Santiago Gascón, Universidad de Oviedo, Campus El Cristo, Oviedo, Spain
| | - Francisco Parra
- Instituto Universitario de Biotecnología de Asturias, Departamento de Bioquímica y Biología Molecular, Edificio Santiago Gascón, Universidad de Oviedo, Campus El Cristo, Oviedo, Spain
| | - Monica Martinez-Haro
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), CIAG del Chaparrillo, Ciudad Real, Spain
| | - José Alberto Viñuelas
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), CIAG del Chaparrillo, Ciudad Real, Spain
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ , USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Grant McFadden
- Center for Immunotherapy, Vaccines and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Masmudur M. Rahman
- Center for Immunotherapy, Vaccines and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Pedro J. Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- CITS—Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra, Portugal
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10
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Fernandes AP, Águeda-Pinto A, Pinheiro A, Rebelo H, Esteves PJ. Evolution of TRIM5 and TRIM22 in Bats Reveals a Complex Duplication Process. Viruses 2022; 14:v14020345. [PMID: 35215944 PMCID: PMC8879501 DOI: 10.3390/v14020345] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 12/29/2022] Open
Abstract
The innate immunological response in mammals involves a diverse and complex network of many proteins. Over the last years, the tripartite motif-containing protein 5 (TRIM5) and 22 (TRIM22) have shown promise as restriction factors of a plethora of viruses that infect primates. Although there have been studies describing the evolution of these proteins in a wide range of mammals, no prior studies of the TRIM6/34/5/22 gene cluster have been performed in the Chiroptera order. Here, we provide a detailed analysis of the evolution of this gene cluster in several bat genomes. Examination of different yangochiroptera and yinpterochiroptera bat species revealed a dynamic history of gene expansion occurring in TRIM5 and TRIM22 genes. Multiple copies of TRIM5 were found in the genomes of several bats, demonstrating a very low degree of conservation in the synteny of this gene among species of the Chiroptera order. Our findings also reveal that TRIM22 is often found duplicated in yangochiroptera bat species, an evolutionary phenomenon not yet observed in any other lineages of mammals. In total, we identified 31 TRIM5 and 19 TRIM22 amino acids to be evolving under positive selection, with most of the residues being placed in the PRYSPRY domain, known to be responsible for binding to the viral capsid during restriction in the primate orthologous TRIM proteins. Altogether, our results help to shed light on the distinctive role of bats in nature as reservoirs of viruses, many of which have become threatening zoonotic diseases through virus spillover in the last decades.
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Affiliation(s)
- Alexandre P. Fernandes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vila do Conde, Portugal; (A.P.F.); (A.Á.-P.); (A.P.); (H.R.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vila do Conde, Portugal
| | - Ana Águeda-Pinto
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vila do Conde, Portugal; (A.P.F.); (A.Á.-P.); (A.P.); (H.R.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vila do Conde, Portugal
| | - Ana Pinheiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vila do Conde, Portugal; (A.P.F.); (A.Á.-P.); (A.P.); (H.R.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vila do Conde, Portugal
| | - Hugo Rebelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vila do Conde, Portugal; (A.P.F.); (A.Á.-P.); (A.P.); (H.R.)
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vila do Conde, Portugal
- CIBIO/InBIO, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Pedro J. Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vila do Conde, Portugal; (A.P.F.); (A.Á.-P.); (A.P.); (H.R.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vila do Conde, Portugal
- CITS—Centro de Investigac¸ão em Tecnologias da Saúde, Instituto Politécnico de Saúde do Norte (IPSN), Cooperativa de Ensino Superior Politécnico e Universitário (CESPU), 4585-116 Gandra, Portugal
- Correspondence:
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11
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Águeda-Pinto A, Alves LQ, Neves F, McFadden G, Jacobs BL, Castro LFC, Rahman MM, Esteves PJ. Convergent Loss of the Necroptosis Pathway in Disparate Mammalian Lineages Shapes Viruses Countermeasures. Front Immunol 2021; 12:747737. [PMID: 34539677 PMCID: PMC8445033 DOI: 10.3389/fimmu.2021.747737] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/17/2021] [Indexed: 01/21/2023] Open
Abstract
Programmed cell death is a vital process in the life cycle of organisms. Necroptosis, an evolutionary form of programmed necrosis, contributes to the innate immune response by killing pathogen-infected cells. This virus-host interaction pathway is organized around two components: the receptor-interacting protein kinase 3 (RIPK3), which recruits and phosphorylates the mixed lineage kinase-like protein (MLKL), inducing cellular plasma membrane rupture and cell death. Critically, the presence of necroptotic inhibitors in viral genomes validates necroptosis as an important host defense mechanism. Here, we show, counterintuitively, that in different mammalian lineages, central components of necroptosis, such as RIPK3 and MLKL, are deleted or display inactivating mutations. Frameshifts or premature stop codons are observed in all the studied species of cetaceans and leporids. In carnivores’ genomes, the MLKL gene is deleted, while in a small number of species from afrotheria and rodentia premature stop codons are observed in RIPK3 and/or MLKL. Interestingly, we also found a strong correlation between the disruption of necroptosis in leporids and cetaceans and the absence of the N-terminal domain of E3-like homologs (responsible for necroptosis inhibition) in their naturally infecting poxviruses. Overall, our study provides the first comprehensive picture of the molecular evolution of necroptosis in mammals. The loss of necroptosis multiple times during mammalian evolution highlights the importance of gene/pathway loss for species adaptation and suggests that necroptosis is not required for normal mammalian development. Moreover, this study highlights a co-evolutionary relationship between poxviruses and their hosts, emphasizing the role of host adaptation in shaping virus evolution.
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Affiliation(s)
- Ana Águeda-Pinto
- CIBIO/InBio-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Luís Q Alves
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
| | - Fabiana Neves
- CIBIO/InBio-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Grant McFadden
- Center for Immunotherapy, Vaccines and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Bertram L Jacobs
- Center for Immunotherapy, Vaccines and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, AZ, United States.,School of Life Sciences Center for Immunotherapy, Vaccines and Virotherapy, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - L Filipe C Castro
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
| | - Masmudur M Rahman
- Center for Immunotherapy, Vaccines and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Pedro J Esteves
- CIBIO/InBio-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,CITS-Centro de Investigação em Tecnologias da Saúde, Instituto Politécnico de Saúde do Norte (IPSN), Cooperativa de Ensino Superior Politécnico e Universitário (CESPU), Gandra, Portugal
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12
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Velarde R, Abrantes J, Lopes AM, Estruch J, Côrte-Real JV, Esteves PJ, García-Bocanegra I, Ruiz-Olmo J, Rouco C. Spillover event of recombinant Lagovirus europaeus/GI.2 into the Iberian hare (Lepus granatensis) in Spain. Transbound Emerg Dis 2021; 68:3187-3193. [PMID: 34324796 DOI: 10.1111/tbed.14264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022]
Abstract
Viruses that affect lagomorphs have decades of reported history of spillover events. One of these viruses is the causative agent of the so-called rabbit or 'lagomorph' haemorrhagic disease (e.g. Lagovirus europaeus/GI.1 and L. europaeus/GI.2). In particular, L. europaeus/GI.2 has shown a great capacity to recombine with existing lagoviruses. In fact, it has replaced the former GI.1 genotype in the wild, and recently, an increase on spillover events has been detected among several lagomorph species including European and North American species of hares. In this study, we report for the first time the infection of a wild Iberian hare with GI.2 (RHDV2/b), potential shedding and associated histopathological alterations. We identify the recombinant GI.4P-GI.2 as causative of the infection and discuss plausible causes regarding the origin of the spillover event and its potential consequences for the Iberian hare wild populations, which is an endemic species of the Iberian Peninsula as well as an important game and prey species for many predators, including endangered species.
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Affiliation(s)
- Roser Velarde
- Wildlife Ecology & Health group (WEH) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Joana Abrantes
- Research Centre in Biodiversity and Genetic Resources (CIBIO), Research Network in Biodiversity and Evolutionary Biology (InBIO), University of Porto, Vairao, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Ana M Lopes
- Research Centre in Biodiversity and Genetic Resources (CIBIO), Research Network in Biodiversity and Evolutionary Biology (InBIO), University of Porto, Vairao, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS)/Unidade Multidisciplinar de Investigação Biomédica (UMIB), Universidade do Porto, Porto, Portugal
| | - Josep Estruch
- Wildlife Ecology & Health group (WEH) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - João V Côrte-Real
- Research Centre in Biodiversity and Genetic Resources (CIBIO), Research Network in Biodiversity and Evolutionary Biology (InBIO), University of Porto, Vairao, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Pedro J Esteves
- Research Centre in Biodiversity and Genetic Resources (CIBIO), Research Network in Biodiversity and Evolutionary Biology (InBIO), University of Porto, Vairao, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Ignacio García-Bocanegra
- Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), Departamento de Sanidad Animal, Universidad de Córdoba, Córdoba, Spain
| | - Jordi Ruiz-Olmo
- Departament d'Agricultura, Ramaderia, Pesca i Alimentació de la Generalitat de Catalunya, Barcelona, Spain
| | - Carlos Rouco
- Departmento de Botánica, Ecología y Fisiología Vegetal, Universdad de Córdoba, Cordoba, Spain.,Sociedad, Ecología y Gestión del Medio Ambiente, UCO-IESA, Unidad Asociada al CSIC, Córdoba, Spain
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13
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Almeida T, Ohta Y, Gaigher A, Muñoz-Mérida A, Neves F, Castro LFC, Machado AM, Esteves PJ, Veríssimo A, Flajnik MF. A Highly Complex, MHC-Linked, 350 Million-Year-Old Shark Nonclassical Class I Lineage. J Immunol 2021; 207:824-836. [PMID: 34301841 DOI: 10.4049/jimmunol.2000851] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 05/09/2021] [Indexed: 11/19/2022]
Abstract
Cartilaginous fish, or Chondrichthyes, are the oldest extant vertebrates to possess the MHC and the Ig superfamily-based Ag receptors, the defining genes of the gnathostome adaptive immune system. In this work, we have identified a novel MHC lineage, UEA, a complex multigene nonclassical class I family found in sharks (division Selachii) but not detected in chimaeras (subclass Holocephali) or rays (division Batoidea). This new lineage is distantly related to the previously reported nonclassical class I lineage UCA, which appears to be present only in dogfish sharks (order Squaliformes). UEA lacks conservation of the nine invariant residues in the peptide (ligand)-binding regions (PBR) that bind to the N and C termini of bound peptide in most vertebrate classical class I proteins, which are replaced by relatively hydrophobic residues compared with the classical UAA. In fact, UEA and UCA proteins have the most hydrophobic-predicted PBR of all identified chondrichthyan class I molecules. UEA genes detected in the whale shark and bamboo shark genome projects are MHC linked. Consistent with UEA comprising a very large gene family, we detected weak expression in different tissues of the nurse shark via Northern blotting and RNA sequencing. UEA genes fall into three sublineages with unique characteristics in the PBR. UEA shares structural and genetic features with certain nonclassical class I genes in other vertebrates, such as the highly complex XNC nonclassical class I genes in Xenopus, and we anticipate that each shark gene, or at least each sublineage, will have a unique function, perhaps in bacterial defense.
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Affiliation(s)
- Tereza Almeida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD; and
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD; and
| | - Arnaud Gaigher
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal
| | - Fabiana Neves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal
| | - L Filipe C Castro
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - André M Machado
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Pedro J Esteves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Ana Veríssimo
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD; and
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14
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Abstract
Several strands of evidence indicate the presence of marked similarities between human brain and testis. Understanding these similarities and their implications has become a topic of interest among the scientific community. Indeed, an association of intelligence with some semen quality parameters has been reported and a relation between dysfunctions of the human brain and testis has also been evident. Numerous common molecular features are evident when these tissues are compared, which is reflected in the huge number of common proteins. At the functional level, human neurons and sperm share a number of characteristics, including the importance of the exocytotic process and the presence of similar receptors and signalling pathways. The common proteins are mainly involved in exocytosis, tissue development and neuron/brain-associated biological processes. With this analysis, we conclude that human brain and testis share several biochemical characteristics which, in addition to their involvement in the speciation process, could, at least in part, be responsible for the expression of a huge number of common proteins. Nonetheless, this is an underexplored topic, and the connection between these tissues needs to be clarified, which could help to understand the dysfunctions affecting brain and testis, as well as to develop improved therapeutic strategies.
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Affiliation(s)
- Bárbara Matos
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Stephen J Publicover
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Luis Filipe C Castro
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Department of Biology, FCUP-Faculty of Sciences, University of Porto, Porto, Portugal
| | - Pedro J Esteves
- Department of Biology, FCUP-Faculty of Sciences, University of Porto, Porto, Portugal.,CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, Campus Agrico de Vairão, University of Porto, 4485-661 Vairão, Portugal
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
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15
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Carneiro M, Vieillard J, Andrade P, Boucher S, Afonso S, Blanco-Aguiar JA, Santos N, Branco J, Esteves PJ, Ferrand N, Kullander K, Andersson L. A loss-of-function mutation in RORB disrupts saltatorial locomotion in rabbits. PLoS Genet 2021; 17:e1009429. [PMID: 33764968 PMCID: PMC7993613 DOI: 10.1371/journal.pgen.1009429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/17/2021] [Indexed: 11/18/2022] Open
Abstract
Saltatorial locomotion is a type of hopping gait that in mammals can be found in rabbits, hares, kangaroos, and some species of rodents. The molecular mechanisms that control and fine-tune the formation of this type of gait are unknown. Here, we take advantage of one strain of domesticated rabbits, the sauteur d'Alfort, that exhibits an abnormal locomotion behavior defined by the loss of the typical jumping that characterizes wild-type rabbits. Strikingly, individuals from this strain frequently adopt a bipedal gait using their front legs. Using a combination of experimental crosses and whole genome sequencing, we show that a single locus containing the RAR related orphan receptor B gene (RORB) explains the atypical gait of these rabbits. We found that a splice-site mutation in an evolutionary conserved site of RORB results in several aberrant transcript isoforms incorporating intronic sequence. This mutation leads to a drastic reduction of RORB-positive neurons in the spinal cord, as well as defects in differentiation of populations of spinal cord interneurons. Our results show that RORB function is required for the performance of saltatorial locomotion in rabbits.
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Affiliation(s)
- Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- * E-mail: (MC); (LA)
| | | | - Pedro Andrade
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Samuel Boucher
- Labovet Conseil (Réseau Cristal), Les Herbiers Cedex, France
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - José A. Blanco-Aguiar
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Nuno Santos
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - João Branco
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Pedro J. Esteves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland, South Africa
| | - Klas Kullander
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Leif Andersson
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail: (MC); (LA)
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16
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Niedźwiedzka-Rystwej P, Tokarz-Deptuła B, Abrantes J, Esteves PJ, Deptuła W. B and T lymphocytes in rabbits change according to the sex and throughout the year. Pol J Vet Sci 2021; 23:37-42. [PMID: 32233300 DOI: 10.24425/pjvs.2020.132746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The European rabbit (Oryctolagus cuniculus) is a good model in biomedicine used in research on several human diseases. The reference values of B and T cells and their subpopu- lations are very important to understand how the adaptive immune system is responding to infectious agents. The aim of this study was to determine values of B and T cells and their subpopulations in Polish mixed-breed rabbits, considering seasons of the year and sex. The study was performed on 200 Polish mixed-breed rabbits and the percentage of B and T lymphocytes was measured cytometrically using mouse anti-rabbit antibodies. The study revealed that the season of the year and sex of the animals affected the percentage of B- and T-cells and their subpopulations in peripheral blood. Statistically significant values of CD19+ B-cells in spring and autumn, of T CD5+ cells in spring and winter, of T CD4+ in spring, summer, autumn and winter, of T CD8+ in winter and of T CD25+ in spring were noted. Generally the highest values were found mainly in warm part of the year, while the lowest in colder months. A statistical significance was also observed between males and females - changes were found in T CD4+ and T CD25+ lymphocytes in spring, T CD8+ cells in winter and higher percentage was generally obtained in females than in males. The only exception was the T CD5+ subpopulation in which no differences were observed between the sexes and throughout the year. This is the first paper on adaptive immune system cell values in the European rabbit of domestic breeds.
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Affiliation(s)
| | - B Tokarz-Deptuła
- Institute of Biology, University of Szczecin, Felczaka 3c, 71-412 Szczecin, Poland
| | - J Abrantes
- CIBIO/InBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - P J Esteves
- CIBIO/InBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, R. Campo Alegre s/n, 4169-007, Porto, Portugal
| | - W Deptuła
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
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17
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Almeida T, Gaigher A, Muñoz-Mérida A, Neves F, Castro LFC, Flajnik MF, Ohta Y, Esteves PJ, Veríssimo A. Cartilaginous fish class II genes reveal unprecedented old allelic lineages and confirm the late evolutionary emergence of DM. Mol Immunol 2020; 128:125-138. [PMID: 33126081 PMCID: PMC8010645 DOI: 10.1016/j.molimm.2020.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/22/2020] [Accepted: 10/03/2020] [Indexed: 12/16/2022]
Abstract
Cartilaginous fish (chimaeras, rays and sharks) are the most basal extant jawed vertebrates with an adaptive immune system based on the Major Histocompatibility Complex (MHC). Despite being a key taxon in the evolution of vertebrate adaptive immunity, no comprehensive characterization of MHC class II genes has been undertaken for the group. We performed extensive bioinformatic searches on a taxonomically diverse dataset of transcriptomes and genomes of cartilaginous fish targeting MHC class II sequences. Class IIα and IIβ sequences were retrieved from all taxa analyzed and showed typical features of classical class II genes. Phylogenetic trees of the immunoglobulin superfamily domain showed two divergent and remarkably ancient lineages of class II genes in Selachians (sharks), originating >350 million years ago. Close linkage of lineage-specific pairs of IIα and IIβ genes was found, confirming previous results, with genes from distinct lineages segregating as alleles. Nonclassical class II DM sequences were not retrieved from these data and classical class II sequences lacked the conserved residues shown to interact with DM molecules, supporting claims that the DM system arose only in the lobe-finned fish lineage leading to tetrapods. Based on our search methods, other divergent class II genes are unlikely in cartilaginous fish.
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Affiliation(s)
- Tereza Almeida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Department of Biology, Faculty of Sciences - University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal; Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
| | - Arnaud Gaigher
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Fabiana Neves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - L Filipe C Castro
- Department of Biology, Faculty of Sciences - University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal; CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
| | - Pedro J Esteves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Department of Biology, Faculty of Sciences - University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Ana Veríssimo
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
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18
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Abrantes J, Lopes AM, Lemaitre E, Ahola H, Banihashem F, Droillard C, Marchandeau S, Esteves PJ, Neimanis A, Le Gall-Reculé G. Retrospective Analysis Shows That Most RHDV GI.1 Strains Circulating Since the Late 1990s in France and Sweden Were Recombinant GI.3P-GI.1d Strains. Genes (Basel) 2020; 11:E910. [PMID: 32784857 PMCID: PMC7464634 DOI: 10.3390/genes11080910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/27/2020] [Accepted: 08/06/2020] [Indexed: 12/27/2022] Open
Abstract
Recombination is one of the major sources of genetic variation in viruses. RNA viruses, such as rabbit hemorrhagic disease virus (RHDV), are among the viruses with the highest recombination rates. Several recombination events have been described for RHDV, mostly as a consequence of their genomic architecture. Here, we undertook phylogenetic and recombination analyses of French and Swedish RHDV strains from 1994 to 2016 and uncovered a new intergenotypic recombination event. This event occurred in the late 1990s/early 2000s and involved nonpathogenic GI.3 strains as donors for the nonstructural part of the genome of these recombinants, while pathogenic GI.1d strains contributed to the structural part. These GI.3P-GI.1d recombinant strains did not entirely replace GI.1d (nonrecombinant) strains, but became the dominant strains in France and Sweden, likely due to a fitness advantage associated with this genomic architecture. GI.3P-GI.1d (P stands for polymerase) strains persisted until 2013 and 2016 in Sweden and France, respectively, and cocirculated with the new genotype GI.2 in France. Since strains from the first GI.2 outbreaks were GI.3P-GI.2, we hypothesize that GI.3P-GI.1d could be the parental strain. Our results confirm the outstanding recombination ability of RHDV and its importance in the evolution of lagoviruses, which was only revealed by studying complete genomic sequences.
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Affiliation(s)
- Joana Abrantes
- CIBIO/InBio-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.M.L.); (P.J.E.)
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Ana M. Lopes
- CIBIO/InBio-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.M.L.); (P.J.E.)
- Instituto de Ciências Biomédicas Abel Salazar/Unidade Multidisciplinar de Investigação Biomédica, Universidade do Porto, 4050-313 Porto, Portugal
| | - Evelyne Lemaitre
- Unité de Virologie, Immunologie, Parasitologie, Aviaires et Cunicoles, Laboratoire de Ploufragan-Plouzané-Niort, Agence nationale de sécurité sanitaire, de l’alimentation, de l’environnement et du travail (Anses), 22440 Ploufragan, France; (E.L.); (C.D.)
| | - Harri Ahola
- Department of Microbiology, National Veterinary Institute (SVA), Ulls väg 2B, SE75189 Uppsala, Sweden; (H.A.); (F.B.)
| | - Fereshteh Banihashem
- Department of Microbiology, National Veterinary Institute (SVA), Ulls väg 2B, SE75189 Uppsala, Sweden; (H.A.); (F.B.)
| | - Clément Droillard
- Unité de Virologie, Immunologie, Parasitologie, Aviaires et Cunicoles, Laboratoire de Ploufragan-Plouzané-Niort, Agence nationale de sécurité sanitaire, de l’alimentation, de l’environnement et du travail (Anses), 22440 Ploufragan, France; (E.L.); (C.D.)
| | - Stéphane Marchandeau
- Unité Petite Faune Sédentaire et Espèces Outre-Mer, Direction de la Recherche et de l’Appui Scientifique, Office Français de la Biodiversité (OFB), 44300 Nantes, France;
| | - Pedro J. Esteves
- CIBIO/InBio-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.M.L.); (P.J.E.)
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Aleksija Neimanis
- Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), Ulls väg 2B, SE75189 Uppsala, Sweden
| | - Ghislaine Le Gall-Reculé
- Unité de Virologie, Immunologie, Parasitologie, Aviaires et Cunicoles, Laboratoire de Ploufragan-Plouzané-Niort, Agence nationale de sécurité sanitaire, de l’alimentation, de l’environnement et du travail (Anses), 22440 Ploufragan, France; (E.L.); (C.D.)
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19
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Águeda-Pinto A, Kraberger S, Lund MC, Gortázar C, McFadden G, Varsani A, Esteves PJ. Coinfections of Novel Polyomavirus, Anelloviruses and a Recombinant Strain of Myxoma Virus-MYXV-Tol Identified in Iberian Hares. Viruses 2020; 12:E340. [PMID: 32244962 PMCID: PMC7150814 DOI: 10.3390/v12030340] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/11/2020] [Accepted: 03/17/2020] [Indexed: 12/24/2022] Open
Abstract
Viruses are ubiquitous in nature; however, very few have been identified in the Leporid species. In the fall of 2018, an outbreak of myxomatosis in Iberian hares (Lepus granatensis) was reported in Spain and a novel recombinant myxoma virus strain (MYXV-Tol) was identified. To investigate variability within the recombinant region of the MYXV-Tol and identify any potential viral coinfections, samples (ear, eyelid or vaginal) of Iberian hares were collected from Spain and analyzed. The presence of the recombinant region of the MYXV-Tol was confirmed in six out of eleven samples analyzed. Additionally, a polyomavirus (family Polyomaviridae), representing a putative new species, and anelloviruses (family Anelloviridae) belonging to two putative species were identified, some as coinfection with the recombinant MYXV-Tol. The two polyomavirus genomes were identified in two hares and share >99% genome-wide identity. Based on the analysis of their large T-antigen, the new polyomavirus clusters in a distant clade from other mammals sharing <64% amino acid identity. A total of 14 anelloviruses were identified, which share 63-99% genome-wide identity. Overall, our results show a coinfection of different DNA viruses in the studied samples and raise awareness regarding the extensive unsampled diversity of viruses in hares.
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Affiliation(s)
- Ana Águeda-Pinto
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal;
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
- Center for Immunotherapy, Vaccines, and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; (S.K.); (G.M.)
| | - Simona Kraberger
- Center for Immunotherapy, Vaccines, and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; (S.K.); (G.M.)
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Michael C. Lund
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Christian Gortázar
- SaBio Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo, 28005 Ciudad Real, Spain;
| | - Grant McFadden
- Center for Immunotherapy, Vaccines, and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; (S.K.); (G.M.)
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life sciences, Arizona State University, Tempe, AZ 85287, USA;
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7701, South Africa
| | - Pedro J. Esteves
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal;
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
- CITS—Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, 4585-116 Gandra, Portugal
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20
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Almeida T, Esteves PJ, Flajnik MF, Ohta Y, Veríssimo A. An Ancient, MHC-Linked, Nonclassical Class I Lineage in Cartilaginous Fish. J Immunol 2020; 204:892-902. [PMID: 31932500 PMCID: PMC7002201 DOI: 10.4049/jimmunol.1901025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/05/2019] [Indexed: 01/08/2023]
Abstract
Cartilaginous fishes, or chondrichthyans, are the oldest jawed vertebrates that have an adaptive immune system based on the MHC and Ig superfamily-based AgR. In this basal group of jawed vertebrates, we identified a third nonclassical MHC class I lineage (UDA), which is present in all species analyzed within the two major cartilaginous subclasses, Holocephali (chimaeras) and Elasmobranchii (sharks, skates, and rays). The deduced amino acid sequences of UDA have eight out of nine typically invariant residues that bind to the N and C termini of bound peptide found in most vertebrae classical class I (UAA); additionally, the other predicted 28 peptide-binding residues are perfectly conserved in all elasmobranch UDA sequences. UDA is distinct from UAA in its differential tissue distribution and its lower expression levels and is mono- or oligomorphic unlike the highly polymorphic UAA UDA has a low copy number in elasmobranchs but is multicopy in the holocephalan spotted ratfish (Hydrolagus colliei). Using a nurse shark (Ginglymostoma cirratum) family, we found that UDA is MHC linked but separable by recombination from the tightly linked cluster of UAA, TAP, and LMP genes, the so-called class I region found in most nonmammalian vertebrates. UDA has predicted structural features that are similar to certain nonclassical class I genes in other vertebrates, and, unlike polymorpic classical class I, we anticipate that it may bind to a conserved set of specialized peptides.
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Affiliation(s)
- Tereza Almeida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD 21201; and
| | - Pedro J Esteves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD 21201; and
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD 21201; and
| | - Ana Veríssimo
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Porto, Portugal
- Virginia Institute of Marine Science, William & Mary, Gloucester Point, VA 23062
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21
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Águeda-Pinto A, Lemos de Matos A, Pinheiro A, Neves F, de Sousa-Pereira P, Esteves PJ. Not so unique to Primates: The independent adaptive evolution of TRIM5 in Lagomorpha lineage. PLoS One 2019; 14:e0226202. [PMID: 31830084 PMCID: PMC6907815 DOI: 10.1371/journal.pone.0226202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 11/21/2019] [Indexed: 02/07/2023] Open
Abstract
The plethora of restriction factors with the ability to inhibit the replication of retroviruses have been widely studied and genetic hallmarks of evolutionary selective pressures in Primates have been well documented. One example is the tripartite motif-containing protein 5 alpha (TRIM5α), a cytoplasmic factor that restricts retroviral infection in a species-specific fashion. In Lagomorphs, similarly to what has been observed in Primates, the specificity of TRIM5 restriction has been assigned to the PRYSPRY domain. In this study, we present the first insight of an intra-genus variability within the Lagomorpha TRIM5 PRYSPRY domain. Remarkably, and considering just the 32 residue-long v1 region of this domain, the deduced amino acid sequences of Daurian pika (Ochotona dauurica) and steppe pika (O. pusilla) evidenced a high divergence when compared to the remaining Ochotona species, presenting values of 44% and 66% of amino acid differences, respectively. The same evolutionary pattern was also observed when comparing the v1 region of two Sylvilagus species members (47% divergence). However, and unexpectedly, the PRYSPRY domain of Lepus species exhibited a great conservation. Our results show a high level of variation in the PRYSPRY domain of Lagomorpha species that belong to the same genus. This suggests that, throughout evolution, the Lagomorpha TRIM5 should have been influenced by constant selective pressures, likely as a result of multiple different retroviral infections.
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Affiliation(s)
- Ana Águeda-Pinto
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto,Porto, Portugal
| | - Ana Lemos de Matos
- Center for Immunotherapy, Vaccines, and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Ana Pinheiro
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto,Porto, Portugal
| | - Fabiana Neves
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Patrícia de Sousa-Pereira
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto,Porto, Portugal
| | - Pedro J. Esteves
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto,Porto, Portugal
- CITS—Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU,Gandra, Portugal
- * E-mail:
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22
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Pinheiro A, Águeda-Pinto A, Melo-Ferreira J, Neves F, Abrantes J, Esteves PJ. Analysis of substitution rates showed that TLR5 is evolving at different rates among mammalian groups. BMC Evol Biol 2019; 19:221. [PMID: 31791244 PMCID: PMC6889247 DOI: 10.1186/s12862-019-1547-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/25/2019] [Indexed: 01/12/2023] Open
Abstract
Background Toll-like receptors (TLRs) are the most widely studied innate immunity receptors responsible for recognition of invading pathogens. Among the TLR family, TLR5 is the only that senses and recognizes flagellin, the major protein of bacterial flagella. TLR5 has been reported to be under overall purifying selection in mammals, with a small proportion of codons under positive selection. However, the variation of substitution rates among major mammalian groups has been neglected. Here, we studied the evolution of TLR5 in mammals, comparing the substitution rates among groups. Results In this study we analysed the TLR5 substitution rates in Euungulata, Carnivora, Chiroptera, Primata, Rodentia and Lagomorpha, groups. For that, Tajima’s relative rate test, Bayesian inference of evolutionary rates and genetic distances were estimated with CODEML’s branch model and RELAX. The combined results showed that in the Lagomorpha, Rodentia, Carnivora and Chiroptera lineages TLR5 is evolving at a higher substitution rate. The RELAX analysis further suggested a significant relaxation of selective pressures for the Lagomorpha (K = 0.22, p < 0.01), Rodentia (K = 0.58, p < 0.01) and Chiroptera (K = 0.65, p < 0.01) lineages and for the Carnivora ancestral branches (K = 0.13, p < 0.01). Conclusions Our results show that the TLR5 substitution rate is not uniform among mammals. In fact, among the different mammal groups studied, the Lagomorpha, Rodentia, Carnivora and Chiroptera are evolving faster. This evolutionary pattern could be explained by 1) the acquisition of new functions of TLR5 in the groups with higher substitution rate, i.e. TLR5 neofunctionalization, 2) by the beginning of a TLR5 pseudogenization in these groups due to some redundancy between the TLRs genes, or 3) an arms race between TLR5 and species-specific parasites.
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Affiliation(s)
- Ana Pinheiro
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
| | - Ana Águeda-Pinto
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.,Center for Immunotherapy, Vaccines, and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - José Melo-Ferreira
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
| | - Fabiana Neves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Joana Abrantes
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
| | - Pedro J Esteves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.,CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, 4585-116, Gandra, Portugal
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23
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Esteves PJ, Abrantes J, Baldauf HM, BenMohamed L, Chen Y, Christensen N, González-Gallego J, Giacani L, Hu J, Kaplan G, Keppler OT, Knight KL, Kong XP, Lanning DK, Le Pendu J, de Matos AL, Liu J, Liu S, Lopes AM, Lu S, Lukehart S, Manabe YC, Neves F, McFadden G, Pan R, Peng X, de Sousa-Pereira P, Pinheiro A, Rahman M, Ruvoën-Clouet N, Subbian S, Tuñón MJ, van der Loo W, Vaine M, Via LE, Wang S, Mage R. Author Correction: The wide utility of rabbits as models of human diseases. Exp Mol Med 2019; 51:1. [PMID: 31270317 PMCID: PMC6802666 DOI: 10.1038/s12276-019-0252-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
This article was originally published under a CC BY-NC-SA License, but has now been made available under a CC BY 4.0 License.
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Affiliation(s)
- Pedro J Esteves
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal. .,Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal.
| | - Joana Abrantes
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, 81377, Munich, Germany
| | - Lbachir BenMohamed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California, Irvine, School of Medicine, Irvine, CA, 92697, USA.,Department of Molecular Biology and Biochemistry, University of California, Irvine School of Medicine, Irvine, CA, 92697, USA.,Institute for Immunology, University of California, Irvine School of Irvine, School of Medicine, Irvine, CA, 92697, USA
| | - Yuxing Chen
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Neil Christensen
- Departments of Pathology, Microbiology and Immunology, and Comparative Medicine, Penn State University, Hershey, PA, USA
| | - Javier González-Gallego
- Institute of Biomedicine (IBIOMED) and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), University of León, 24071, León, Spain
| | - Lorenzo Giacani
- Departments of Medicine and Global Health, University of Washington, Seattle, USA
| | - Jiafen Hu
- Departments of Pathology, Microbiology and Immunology, and Comparative Medicine, Penn State University, Hershey, PA, USA
| | - Gilla Kaplan
- Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, 81377, Munich, Germany
| | - Katherine L Knight
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY10016, USA
| | - Dennis K Lanning
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Jacques Le Pendu
- CRCINA, Inserm, Université d'Angers, Université de Nantes, Nantes, France
| | - Ana Lemos de Matos
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ, 85287-5401, USA
| | - Jia Liu
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR, 72205, USA
| | - Shuying Liu
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Ana M Lopes
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Department of Anatomy and Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Shan Lu
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Sheila Lukehart
- Departments of Medicine and Global Health, University of Washington, Seattle, USA
| | - Yukari C Manabe
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fabiana Neves
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Grant McFadden
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ, 85287-5401, USA
| | - Ruimin Pan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY10016, USA
| | - Xuwen Peng
- Departments of Pathology, Microbiology and Immunology, and Comparative Medicine, Penn State University, Hershey, PA, USA
| | - Patricia de Sousa-Pereira
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.,Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, 81377, Munich, Germany
| | - Ana Pinheiro
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Masmudur Rahman
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ, 85287-5401, USA
| | | | - Selvakumar Subbian
- The Public Health Research Institute (PHRI) at New Jersey Medical School, Rutgers Biomedical and Health Sciences (RBHS), Rutgers University, Newark, NJ, USA
| | - Maria Jesús Tuñón
- Institute of Biomedicine (IBIOMED) and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), University of León, 24071, León, Spain
| | - Wessel van der Loo
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Michael Vaine
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Laura E Via
- Tubercolosis Research Section, Laboratory of Clinical Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Institute of Infectious Disease and Molecular Medicine, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Shixia Wang
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Rose Mage
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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24
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Pinheiro A, de Sousa-Pereira P, Almeida T, Ferreira CC, Otis JA, Boudreau MR, Seguin JL, Lanning DK, Esteves PJ. Sequencing of VDJ genes in Lepus americanus confirms a correlation between VHn expression and the leporid species continent of origin. Mol Immunol 2019; 112:182-187. [PMID: 31174011 DOI: 10.1016/j.molimm.2019.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/12/2019] [Accepted: 05/27/2019] [Indexed: 10/26/2022]
Abstract
Leporid VH genes used in the generation of their primary antibody repertoire exhibit highly divergent lineages. For the European rabbit (Oryctolagus cuniculus) four VHa lineages have been described, the a1, a2, a3 and a4. Hares (Lepus spp.) and cottontail (Sylvilagus floridanus) express one VHa lineage each, the a2L and the a5, respectively, along with a more ancient lineage, the Lepus spp. sL and S. floridanus sS. Both the European rabbit and the Lepus europaeus use a third lineage, VHn, in a low proportion of their VDJ rearrangements. The VHn genes are a conserved ancestral polymorphism that is being maintained in the leporid genome.Their usage in a low proportion of VDJ rearrangements by both European rabbit and L. europaeus but not S. floridanus has been argued to be a remnant of an ancient European leporid immunologic response to pathogens. To address this hypothesis, in this study we sequenced VDJ rearranged genes for another North American leporid, L. americanus. Our results show that L. americanus expressed these genes less frequently and in a highly modified fashion compared to the European Lepus species. Our results suggest that the American leporid species use a different VH repertoire than the European species which may be related with an immune adaptation to different environmental conditions, such as different pathogenic agents.
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Affiliation(s)
- Ana Pinheiro
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - Patricia de Sousa-Pereira
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal; Max von Pettenkofer-Institute for Virology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Tereza Almeida
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
| | - Catarina C Ferreira
- Department of Biology, Trent University, Peterborough, Ontario, Canada; UFZ - Helmholtz Centre for Environmental Research, Department of Conservation Biology, Leipzig, Germany
| | - Josée-Anne Otis
- Department of Biology, Trent University, Peterborough, Ontario, Canada
| | | | - Jacob L Seguin
- Department of Biology, Trent University, Peterborough, Ontario, Canada
| | - Dennis K Lanning
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States
| | - Pedro J Esteves
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal; Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, 4585-116, Gandra, Portugal
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25
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Águeda-Pinto A, Lemos de Matos A, Abrantes M, Kraberger S, Risalde MA, Gortázar C, McFadden G, Varsani A, Esteves PJ. Genetic Characterization of a Recombinant Myxoma Virus in the Iberian Hare ( Lepus granatensis). Viruses 2019; 11:v11060530. [PMID: 31181645 PMCID: PMC6631704 DOI: 10.3390/v11060530] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/30/2019] [Accepted: 06/06/2019] [Indexed: 01/15/2023] Open
Abstract
Myxomatosis is a lethal disease in wild European and domestic rabbits (Oryctolagus cuniculus), which is caused by a Myxoma virus (MYXV) infection-a leporipoxvirus that is found naturally in some Sylvilagus rabbit species in South America and California. The introduction of MYXV into feral European rabbit populations of Australia and Europe, in the early 1950s, demonstrated the best-documented field example of host-virus coevolution, following a cross-species transmission. Recently, a new cross-species jump of MYXV has been suggested in both Great Britain and Spain, where European brown hares (Lepus europaeus) and Iberian hares (Lepus granatensis) were found dead with lesions consistent with those observed in myxomatosis. To investigate the possibility of a new cross-species transmission event by MYXV, tissue samples collected from a wild Iberian hare found dead in Spain (Toledo region) were analyzed and deep sequenced. Our results reported a new MYXV isolate (MYXV Toledo) in the tissues of this species. The genome of this new virus was found to encode three disruptive genes (M009L, M036L, and M152R) and a novel ~2.8 kb recombinant region, which resulted from an insertion of four novel poxviral genes towards the 3' end of the negative strand of its genome. From the open reading frames inserted into the MYXV Toledo virus, a new orthologue of a poxvirus host range gene family member was identified, which was related to the MYXV gene M064R. Overall, we confirmed the identity of a new MYXV isolate in Iberian hares, which, we hypothesized, was able to more effectively counteract the host defenses in hares and start an infectious process in this new host.
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Affiliation(s)
- Ana Águeda-Pinto
- CIBIO/InBio-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
- Center for Immunotherapy, Vaccines, and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Ana Lemos de Matos
- Center for Immunotherapy, Vaccines, and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Mário Abrantes
- Center for Immunotherapy, Vaccines, and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Maria A Risalde
- Dpto. de Anatomía y Anatomía Patológica Comparadas, Universidad de Córdoba, Agrifood Excellence International Campus (ceiA3), 14071 Córdoba, Spain.
| | - Christian Gortázar
- Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo, 28005 Ciudad Real, Spain.
| | - Grant McFadden
- Center for Immunotherapy, Vaccines, and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life sciences, Arizona State University, Tempe, AZ 85287, USA.
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7701, South Africa.
| | - Pedro J Esteves
- CIBIO/InBio-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
- CITS-Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, 4585-116 Gandra, Portugal.
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Santos N, Jambas J, Monteiro A, Amaral J, Martins N, Garcia J, Fernández AM, Tyler KM, Almeida T, Abrantes J, Esteves PJ. Trichomonas Infection in a Community of Free-Ranging Domestic and Wild Columbiformes and Bonelli's Eagle ( Aquila fasciata). Front Vet Sci 2019; 6:148. [PMID: 31192234 PMCID: PMC6549518 DOI: 10.3389/fvets.2019.00148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/29/2019] [Indexed: 11/13/2022] Open
Abstract
Trichomonas gallinae is a pathogen of conservation relevance, whose main maintenance hosts are Columbiformes, but spillover to avian predators has been described. The goal of this study was to characterize the epidemiology of Trichomonas spp. in a community of free-ranging domestic and wild Columbiformes and an endangered predator, Bonelli's eagle Aquila fasciata. We surveyed 253 live-captured Rock doves, 16 nestling Bonelli's eagles and 41 hunted Columbiformes. Oro-esophageal swabs were incubated in culture media and Trichomonas spp. isolated from Bonelli's eagle (6.3%, CI95 1.1-28.3), Turtle dove Streptopelia turtur (56.3%, CI95 39.3-71.8), Wood pigeon Columba palumbus (83.3%, CI95 43.7-97.0) and Rock dove Columba livia (68.4%, CI95 62.4-73.8). Infected Rock doves showed significantly poorer body condition than uninfected ones (p = 0.022). From a subset of 32 isolates, 18S and ITS1/5.8S/ITS2 rRNA genes were sequenced and Maximum-Likelihood trees inferred. Four ribotypes of Trichomonas spp. were identified. In this study area Trichomonas spp. seem to persist in a multi-host system involving several species of Columbiformes. Conservation actions aimed at increasing the availability of trophic resources for Bonelli's eagles through Rock dove restocking should consider the risk of pathogen transmission and of introduction of alien strains.
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Affiliation(s)
- Nuno Santos
- CIBIO/InBio-Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Vairão, Portugal
| | - José Jambas
- Oriolus Ambiente Ecoturismo Lda, Atenor, Portugal
| | - António Monteiro
- Parque Natural do Douro Internacional, Instituto de Conservação da Natureza e Florestas I.P., Mogadouro, Portugal
| | - Jorge Amaral
- Parque Natural do Douro Internacional, Instituto de Conservação da Natureza e Florestas I.P., Mogadouro, Portugal
| | - Nuno Martins
- Palombar-Associação para a Conservação da Natureza e do Património Rural, Uva, Portugal
| | - Javier Garcia
- Department of Biodiversity and Environmental Management, University of León, León, Spain
| | | | - Kevin Morris Tyler
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Tereza Almeida
- CIBIO/InBio-Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Joana Abrantes
- CIBIO/InBio-Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Vairão, Portugal
| | - Pedro J Esteves
- CIBIO/InBio-Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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Abstract
BACKGROUND The S100A7 gene, also called psoriasin, was first described as an upregulated protein in psoriatic skin. For the past years, the importance of this protein as a key effector of innate immunity has been clearly established, not only due to its importance protecting against bacteria skin insult in humans, but also because of its important role in amplifying inflammatory processes. Given the importance of S100A7 in host defense, S100A7 genes have been mostly studied in humans. Here we provide a detailed analysis of the evolution of the gene family encoding for the S100A7 protein in mammals. RESULTS Examination of several mammalian genomes revealed an unexpected variation in the copy number of S100A7. Among the most representative mammalian groups, we report that multiple events of duplication, gene loss and high mutation rates are shaping the evolution of this gene family. An unexpected result comes from Myotis species (order Chiroptera), where we found an outstanding S100A7 gene radiation, resulting in more than 10 copies in M. lucifugus and 5 copies in M. brandtii. These findings suggest a unique adaptive road in these species and are suggestive of special role of this protein in their immune system. CONCLUSIONS We found different evolutionary histories among different mammalian groups. Overall, our results suggest that this gene family is evolving under the birth-and-death model of evolution. To our knowledge, this work represents the first detailed analysis of phylogenetic relationships of S100A7 within mammals and therefore will pave the way to further clarify their unique function in the immune system.
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Affiliation(s)
- Ana Águeda-Pinto
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos genéticos, Universidade do Porto, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal
| | - L. Filipe C. Castro
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Av. general Norton de Matos S/N, 4450-208 Matosinhos, Portugal
| | - Pedro J. Esteves
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos genéticos, Universidade do Porto, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal
- CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Rua Central de Gandra 1317, 4585-116 Gandra, Portugal
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Rocha RG, Magalhães V, López-Bao JV, van der Loo W, Llaneza L, Alvares F, Esteves PJ, Godinho R. Alternated selection mechanisms maintain adaptive diversity in different demographic scenarios of a large carnivore. BMC Evol Biol 2019; 19:90. [PMID: 30975084 PMCID: PMC6460805 DOI: 10.1186/s12862-019-1420-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/04/2019] [Indexed: 01/26/2023] Open
Abstract
Background Different population trajectories are expected to impact the signature of neutral and adaptive processes at multiple levels, challenging the assessment of the relative roles of different microevolutionary forces. Here, we integrate adaptive and neutral variability patterns to disentangle how adaptive diversity is driven under different demographic scenarios within the Iberian wolf (Canis lupus) range. We studied the persistent, the expanding and a small, isolated group within the Iberian wolf population, using 3 MHC class II genes (DRB1, DQA1, and DQB1), which diversity was compared with 39 microsatellite loci. Results Both the persistent and the expanding groups show evidence of balancing selection, revealed by a significant departure from neutrality at MHC loci, significant higher observed and expected heterozygosity and lower differentiation at MHC than at neutral loci, and signs of positive selection. However, despite exhibiting a significantly higher genetic diversity than the isolated group, the persistent group did not show significant excess of MHC heterozygotes. The expanding group, while showing a similar level of genetic diversity than the persistent group, displays by contrast a significant excess of MHC heterozygotes, which is compatible with the heterozygote advantage mechanism. Results are not clear regarding the role of drift and selection in the isolated group due to the small size of this population. Although diversity indices of MHC loci correspond to neutral expectations in the isolated group, accelerated MHC divergence, revealed by a higher differentiation at MHC than neutral loci, may indicate diversifying selection. Conclusion Different selective pressures were observed in the three different demographic scenarios, which are possibly driven by different selection mechanisms to maintain adaptive diversity. Electronic supplementary material The online version of this article (10.1186/s12862-019-1420-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rita G Rocha
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Vanessa Magalhães
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - José V López-Bao
- Research Unit of Biodiversity (UO/CSIC/PA), University of Oviedo, 33600, Mieres, Spain
| | - Wessel van der Loo
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Luis Llaneza
- A.RE.NA, S.L. Asesores en Recursos Naturales S.L., 27003, Lugo, Spain
| | - Francisco Alvares
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Pedro J Esteves
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
| | - Raquel Godinho
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.
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Neves F, Águeda-Pinto A, Pinheiro A, Abrantes J, Esteves PJ. Strong selection of the TLR2 coding region among the Lagomorpha suggests an evolutionary history that differs from other mammals. Immunogenetics 2019; 71:437-443. [PMID: 30874861 DOI: 10.1007/s00251-019-01110-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022]
Abstract
Toll-like receptors (TLRs) are one of the first lines of defense against pathogens and are crucial for triggering an appropriate immune response. Among TLRs, TLR2 is functional in all vertebrates and has high ability in detecting bacterial and viral pathogen ligands. The mammals' phylogenetic tree of TLR2 showed longer branches for the Lagomorpha clade, raising the hypothesis that lagomorphs experienced an acceleration of the mutation rate. This hypothesis was confirmed by (i) Tajima's test of neutrality that revealed different evolutionary rates between lagomorphs and the remaining mammals with lagomorphs presenting higher nucleotide diversity; (ii) genetic distances were similar among lagomorphs and between lagomorphs and other mammals; and (iii) branch models reinforced the existence of an acceleration of the mutation rate in lagomorphs. These results suggest that the lagomorph TLR2 has been strongly involved in pathogen recognition, which probably caused a host-pathogen arms race that led to the observed acceleration of the mutation rate.
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Affiliation(s)
- Fabiana Neves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr.7, 4485-661, Vairão, Portugal
| | - Ana Águeda-Pinto
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr.7, 4485-661, Vairão, Portugal
| | - Ana Pinheiro
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr.7, 4485-661, Vairão, Portugal
| | - Joana Abrantes
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr.7, 4485-661, Vairão, Portugal
| | - Pedro J Esteves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr.7, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal. .,CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal.
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30
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Mage RG, Esteves PJ, Rader C. Rabbit models of human diseases for diagnostics and therapeutics development. Dev Comp Immunol 2019; 92:99-104. [PMID: 30339876 PMCID: PMC6364550 DOI: 10.1016/j.dci.2018.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/07/2018] [Accepted: 10/11/2018] [Indexed: 05/03/2023]
Abstract
This review presents some examples of studies using the European rabbit (Oryctolagus cuniculus) that have led to, and continue to, contribute to advancement of understanding of human diseases as well as therapeutics development. In addition, we tabulate FDA-approved rabbit polyclonal and rabbit monoclonal antibodies (mAbs) that are used for diagnostic applications, as well as an overview of some "humanized" or otherwise altered rabbit mAbs that are in initial phase I, II, or advanced to phase III clinical trials. Information about endogenous retriviruses learned from studies of rabbits and other members of the order Lagomorpha are summarized as this knowledge now applies to new therapeutics being developed for several human diseases including Multiple Sclerosis, Type 1 Diabetes and Cancer.
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Affiliation(s)
- Rose G Mage
- Laboratory of Immune System Biology, NIAID, NIH, Bldg 10 11N311, 10 Center Drive, Bethesda, MD, 20892-1892, USA.
| | - Pedro J Esteves
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal; Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, 33458, USA
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31
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Neves F, Abrantes J, Lopes AM, Fusinatto LA, Magalhães MJ, van der Loo W, Esteves PJ. Evolution of CCL16 in Glires (Rodentia and Lagomorpha) shows an unusual random pseudogenization pattern. BMC Evol Biol 2019; 19:59. [PMID: 30786851 PMCID: PMC6383237 DOI: 10.1186/s12862-019-1390-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 02/13/2019] [Indexed: 12/16/2022] Open
Abstract
Background The C-C motif chemokine ligand 16 (CCL16) is a potent pro-inflammatory chemokine and a chemoattractant for monocytes and lymphocytes. In normal plasma, it is present at high concentrations and elicits its effects on cells by interacting with cell surface chemokine receptors. In the European rabbit and in rodents such as mouse, rat and guinea pig, CCL16 was identified as a pseudogene, while in the thirteen-lined ground squirrel it appears to be potentially functional. To gain insight into the evolution of this gene in the superorder Glires (rodents and lagomorphs), we amplified the CCL16 gene from eleven Leporidae and seven Ochotonidae species. Results We compared our sequences with CCL16 sequences of twelve rodent species retrieved from public databases. The data show that for all leporid species studied CCL16 is a pseudogene. This is primarily due to mutations at the canonical Cys Cys motif, creating either premature stop codons, or disrupting amino acid replacements. In the Mexican cottontail, CCL16 is pseudogenized due to a frameshift deletion. Additionally, in the exon 1 (signal peptide), there are frameshift deletions present in all leporids studied. In contrast, in Ochotona species, CCL16 is potentially functional, except for an allele in Hoffmann’s pika. In rodents, CCL16 is functional in a number of species, but patterns of pseudogenization similar to those observed in lagomorphs also exist. Conclusions Our results suggest that while functional in the Glires ancestor, CCL16 underwent pseudogenization in some species. This process occurred stochastically or in specific lineages at different moments in the evolution of Glires. These observations suggest that the CCL16 had different evolutionary constrains in the Glires group that could be associated with the CCL16 biological function. Electronic supplementary material The online version of this article (10.1186/s12862-019-1390-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fabiana Neves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,UMIB/UP - Unidade Multidisciplinar de Investigação Biomédica/Universidade do Porto, Porto, Portugal
| | - Joana Abrantes
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Ana M Lopes
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,UMIB/UP - Unidade Multidisciplinar de Investigação Biomédica/Universidade do Porto, Porto, Portugal
| | - Luciana A Fusinatto
- Departamento de Ecologia, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), R. São Francisco Xavier 524, Rio de Janeiro, RJ, CEP 20550-013, Brazil
| | - Maria J Magalhães
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Wessel van der Loo
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Pedro J Esteves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal. .,CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal.
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32
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Alves JM, Carneiro M, Cheng JY, Lemos de Matos A, Rahman MM, Loog L, Campos PF, Wales N, Eriksson A, Manica A, Strive T, Graham SC, Afonso S, Bell DJ, Belmont L, Day JP, Fuller SJ, Marchandeau S, Palmer WJ, Queney G, Surridge AK, Vieira FG, McFadden G, Nielsen R, Gilbert MTP, Esteves PJ, Ferrand N, Jiggins FM. Parallel adaptation of rabbit populations to myxoma virus. Science 2019; 363:1319-1326. [PMID: 30765607 DOI: 10.1126/science.aau7285] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 12/10/2018] [Accepted: 02/01/2019] [Indexed: 12/18/2022]
Abstract
In the 1950s the myxoma virus was released into European rabbit populations in Australia and Europe, decimating populations and resulting in the rapid evolution of resistance. We investigated the genetic basis of resistance by comparing the exomes of rabbits collected before and after the pandemic. We found a strong pattern of parallel evolution, with selection on standing genetic variation favoring the same alleles in Australia, France, and the United Kingdom. Many of these changes occurred in immunity-related genes, supporting a polygenic basis of resistance. We experimentally validated the role of several genes in viral replication and showed that selection acting on an interferon protein has increased the protein's antiviral effect.
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Affiliation(s)
- Joel M Alves
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK. .,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal.,Palaeogenomics and Bio-Archaeology Research Network Research Laboratory for Archaeology and History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Jade Y Cheng
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA 94720, USA.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Ana Lemos de Matos
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ 85287-5401, USA
| | - Masmudur M Rahman
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ 85287-5401, USA
| | - Liisa Loog
- Palaeogenomics and Bio-Archaeology Research Network Research Laboratory for Archaeology and History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK.,Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester M1 7DN, UK
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark.,CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark.,Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA.,Department of Archaeology, University of York, King's Manor, York YO1 7EP, UK
| | - Anders Eriksson
- Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Tanja Strive
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia.,Centre for Invasive Species Solutions, University of Canberra, Bruce, ACT 2601, Australia
| | - Stephen C Graham
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Diana J Bell
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Laura Belmont
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ 85287-5401, USA
| | - Jonathan P Day
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Susan J Fuller
- School of Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Brisbane, Australia
| | | | - William J Palmer
- The Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Guillaume Queney
- ANTAGENE, Wildlife Genetics Laboratory, La Tour de Salvagny (Lyon), France
| | - Alison K Surridge
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Grant McFadden
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ 85287-5401, USA
| | - Rasmus Nielsen
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA 94720, USA.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark.,Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
| | - Pedro J Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal.,Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal
| | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park 2006, South Africa
| | - Francis M Jiggins
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
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Neimanis AS, Ahola H, Larsson Pettersson U, Lopes AM, Abrantes J, Zohari S, Esteves PJ, Gavier-Widén D. Overcoming species barriers: an outbreak of Lagovirus europaeus GI.2/RHDV2 in an isolated population of mountain hares (Lepus timidus). BMC Vet Res 2018; 14:367. [PMID: 30477499 PMCID: PMC6258167 DOI: 10.1186/s12917-018-1694-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 11/12/2018] [Indexed: 12/19/2022] Open
Abstract
Background Prior to 2010, the lagoviruses that cause rabbit hemorrhagic disease (RHD) in European rabbits (Oryctolagus cuniculus) and European brown hare syndrome (EBHS) in hares (Lepus spp.) were generally genus-specific. However, in 2010, rabbit hemorrhagic disease virus 2 (RHDV2), also known as Lagovirus europaeus GI.2, emerged and had the distinguishing ability to cause disease in both rabbits and certain hare species. The mountain hare (Lepus timidus) is native to Sweden and is susceptible to European brown hare syndrome virus (EBHSV), also called Lagovirus europaeus GII.1. While most mountain hare populations are found on the mainland, isolated populations also exist on islands. Here we investigate a mortality event in mountain hares on the small island of Hallands Väderö where other leporid species, including rabbits, are absent. Results Post-mortem and microscopic examination of three mountain hare carcasses collected from early November 2016 to mid-March 2017 revealed acute hepatic necrosis consistent with pathogenic lagovirus infection. Using immunohistochemistry, lagoviral capsid antigen was visualized within lesions, both in hepatocytes and macrophages. Genotyping and immunotyping of the virus independently confirmed infection with L. europaeus GI.2, not GII.1. Phylogenetic analyses of the vp60 gene grouped mountain hare strains together with a rabbit strain from an outbreak of GI.2 in July 2016, collected approximately 50 km away on the mainland. Conclusions This is the first documented infection of GI.2 in mountain hares and further expands the host range of GI.2. Lesions and tissue distribution mimic those of GII.1 in mountain hares. The virus was most likely initially introduced from a concurrent, large-scale GI.2 outbreak in rabbits on the adjacent mainland, providing another example of how readily this virus can spread. The mortality event in mountain hares lasted for at least 4.5 months in the absence of rabbits, which would have required virus circulation among mountain hares, environmental persistence and/or multiple introductions. This marks the fourth Lepus species that can succumb to GI.2 infection, suggesting that susceptibility to GI.2 may be common in Lepus species. Measures to minimize the spread of GI.2 to vulnerable Lepus populations therefore are prudent. Electronic supplementary material The online version of this article (10.1186/s12917-018-1694-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aleksija S Neimanis
- Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), 751 89, Uppsala, Sweden. .,Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Box 7028, 750 07, Uppsala, Sweden.
| | - Harri Ahola
- Department of Microbiology, National Veterinary Institute (SVA), 751 89, Uppsala, Sweden
| | - Ulrika Larsson Pettersson
- Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), 751 89, Uppsala, Sweden
| | - Ana M Lopes
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Department of Anatomy and Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Joana Abrantes
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Siamak Zohari
- Department of Microbiology, National Veterinary Institute (SVA), 751 89, Uppsala, Sweden
| | - Pedro J Esteves
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, R. Campo Alegre s/n, 4169-007, Porto, Portugal.,Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal
| | - Dolores Gavier-Widén
- Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), 751 89, Uppsala, Sweden.,Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Box 7028, 750 07, Uppsala, Sweden
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34
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Lopes AM, Rouco C, Esteves PJ, Abrantes J. GI.1b/GI.1b/GI.2 recombinant rabbit hemorrhagic disease virus 2 (Lagovirus europaeus/GI.2) in Morocco, Africa. Arch Virol 2018; 164:279-283. [PMID: 30284631 DOI: 10.1007/s00705-018-4052-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/17/2018] [Indexed: 12/01/2022]
Abstract
Rabbit hemorrhagic disease virus (RHDV) is highly lethal to the European rabbit (Oryctolagus cuniculus). It was first reported in 1984 in China, but in 2010, a new variant of the virus was detected (GI.2) in France. Several recombination events with pathogenic and non-pathogenic strains have been described. Here, we report the first sequences of RHDV in Africa, isolated from Moroccan rabbits, and these resemble GI.1b/GI.1b/GI.2 recombinants found in the Iberian Peninsula. Monitoring and characterization of strains from future outbreaks are advised to guarantee the success of current programs on small-rabbit production for poverty alleviation in African countries.
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Affiliation(s)
- Ana M Lopes
- CIBIO/InBio-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS)/Unidade Multidisciplinar de Investigação Biomédica (UMIB), Universidade do Porto, Porto, Portugal
| | - Carlos Rouco
- Departamento de Zoología, Facultad de Ciencias de la Universidad de Córdoba, Córdoba, Spain
| | - Pedro J Esteves
- CIBIO/InBio-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Joana Abrantes
- CIBIO/InBio-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.
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35
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Pinheiro A, de Sousa-Pereira P, Strive T, Knight KL, Woof JM, Esteves PJ, Abrantes J. Identification of a new European rabbit IgA with a serine-rich hinge region. PLoS One 2018; 13:e0201567. [PMID: 30089177 PMCID: PMC6082545 DOI: 10.1371/journal.pone.0201567] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/17/2018] [Indexed: 12/20/2022] Open
Abstract
In mammals, the most striking IgA system belongs to Lagomorpha. Indeed, 14 IgA subclasses have been identified in European rabbits, 11 of which are expressed. In contrast, most other mammals have only one IgA, or in the case of hominoids, two IgA subclasses. Characteristic features of the mammalian IgA subclasses are the length and amino acid sequence of their hinge regions, which are often rich in Pro, Ser and Thr residues and may also carry Cys residues. Here, we describe a new IgA that was expressed in New Zealand White domestic rabbits of IGHVa1 allotype. This IgA has an extended hinge region containing an intriguing stretch of nine consecutive Ser residues and no Pro or Thr residues, a motif exclusive to this new rabbit IgA. Considering the amino acid properties, this hinge motif may present some advantage over the common IgA hinge by affording novel functional capabilities. We also sequenced for the first time the IgA14 CH2 and CH3 domains and showed that IgA14 and IgA3 are expressed.
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Affiliation(s)
- Ana Pinheiro
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- * E-mail:
| | - Patricia de Sousa-Pereira
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Max von Pettenkofer-Institute for Virology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Tanja Strive
- Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - Katherine L. Knight
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Jenny M. Woof
- Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Pedro J. Esteves
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra, Portugal
| | - Joana Abrantes
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
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Esteves PJ, Abrantes J, Baldauf HM, BenMohamed L, Chen Y, Christensen N, González-Gallego J, Giacani L, Hu J, Kaplan G, Keppler OT, Knight KL, Kong XP, Lanning DK, Le Pendu J, de Matos AL, Liu J, Liu S, Lopes AM, Lu S, Lukehart S, Manabe YC, Neves F, McFadden G, Pan R, Peng X, de Sousa-Pereira P, Pinheiro A, Rahman M, Ruvoën-Clouet N, Subbian S, Tuñón MJ, van der Loo W, Vaine M, Via LE, Wang S, Mage R. The wide utility of rabbits as models of human diseases. Exp Mol Med 2018; 50:1-10. [PMID: 29789565 PMCID: PMC5964082 DOI: 10.1038/s12276-018-0094-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/21/2018] [Accepted: 02/27/2018] [Indexed: 12/11/2022] Open
Abstract
Studies using the European rabbit Oryctolagus cuniculus contributed to elucidating numerous fundamental aspects of antibody structure and diversification mechanisms and continue to be valuable for the development and testing of therapeutic humanized polyclonal and monoclonal antibodies. Additionally, during the last two decades, the use of the European rabbit as an animal model has been increasingly extended to many human diseases. This review documents the continuing wide utility of the rabbit as a reliable disease model for development of therapeutics and vaccines and studies of the cellular and molecular mechanisms underlying many human diseases. Examples include syphilis, tuberculosis, HIV-AIDS, acute hepatic failure and diseases caused by noroviruses, ocular herpes, and papillomaviruses. The use of rabbits for vaccine development studies, which began with Louis Pasteur’s rabies vaccine in 1881, continues today with targets that include the potentially blinding HSV-1 virus infection and HIV-AIDS. Additionally, two highly fatal viral diseases, rabbit hemorrhagic disease and myxomatosis, affect the European rabbit and provide unique models to understand co-evolution between a vertebrate host and viral pathogens. Rabbits offer a powerful complement to rodents as a model for studying human immunology, disease pathology, and responses to infectious disease. A review from Pedro Esteves at the University of Porto, Portugal, Rose Mage of the National Institute of Allergy and Infectious Disease, Bethesda, USA and colleagues highlights some of the areas of research where rabbits offer an edge over rats and mice. Rabbits have a particularly sophisticated adaptive immune system, which could provide useful insights into human biology and produce valuable research and clinical reagents. They are also excellent models for studying - infectious diseases such as syphilis and tuberculosis, which produce pathology that closely resembles that of human patients. Rabbit-specific infections such as myxomatosis are giving researchers insights into how pathogens and hosts can shape each other’s evolution.
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Affiliation(s)
- Pedro J Esteves
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal. .,Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal.
| | - Joana Abrantes
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, 81377, Munich, Germany
| | - Lbachir BenMohamed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California, Irvine, School of Medicine, Irvine, CA, 92697, USA.,Department of Molecular Biology and Biochemistry, University of California, Irvine School of Medicine, Irvine, CA, 92697, USA.,Institute for Immunology, University of California, Irvine School of Irvine, School of Medicine, Irvine, CA, 92697, USA
| | - Yuxing Chen
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Neil Christensen
- Departments of Pathology, Microbiology and Immunology, and Comparative Medicine, Penn State University, Hershey, PA, USA
| | - Javier González-Gallego
- Institute of Biomedicine (IBIOMED) and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), University of León, 24071, León, Spain
| | - Lorenzo Giacani
- Departments of Medicine and Global Health, University of Washington, Seattle, USA
| | - Jiafen Hu
- Departments of Pathology, Microbiology and Immunology, and Comparative Medicine, Penn State University, Hershey, PA, USA
| | - Gilla Kaplan
- Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, 81377, Munich, Germany
| | - Katherine L Knight
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY10016, USA
| | - Dennis K Lanning
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Jacques Le Pendu
- CRCINA, Inserm, Université d'Angers, Université de Nantes, Nantes, France
| | - Ana Lemos de Matos
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ, 85287-5401, USA
| | - Jia Liu
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR, 72205, USA
| | - Shuying Liu
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Ana M Lopes
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Department of Anatomy and Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Shan Lu
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Sheila Lukehart
- Departments of Medicine and Global Health, University of Washington, Seattle, USA
| | - Yukari C Manabe
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fabiana Neves
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Grant McFadden
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ, 85287-5401, USA
| | - Ruimin Pan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY10016, USA
| | - Xuwen Peng
- Departments of Pathology, Microbiology and Immunology, and Comparative Medicine, Penn State University, Hershey, PA, USA
| | - Patricia de Sousa-Pereira
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.,Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, 81377, Munich, Germany
| | - Ana Pinheiro
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Masmudur Rahman
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ, 85287-5401, USA
| | | | - Selvakumar Subbian
- The Public Health Research Institute (PHRI) at New Jersey Medical School, Rutgers Biomedical and Health Sciences (RBHS), Rutgers University, Newark, NJ, USA
| | - Maria Jesús Tuñón
- Institute of Biomedicine (IBIOMED) and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), University of León, 24071, León, Spain
| | - Wessel van der Loo
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Michael Vaine
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Laura E Via
- Tubercolosis Research Section, Laboratory of Clinical Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Institute of Infectious Disease and Molecular Medicine, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Shixia Wang
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Rose Mage
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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Lopes AM, Blanco-Aguiar J, Martín-Alonso A, Leitão M, Foronda P, Mendes M, Gonçalves D, Abrantes J, Esteves PJ. Full genome sequences are key to disclose RHDV2 emergence in the Macaronesian islands. Virus Genes 2017; 54:1-4. [PMID: 29151222 DOI: 10.1007/s11262-017-1523-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/15/2017] [Indexed: 11/27/2022]
Abstract
A recent publication by Carvalho et al. in "Virus Genes" (June 2017) reported the presence of the new variant of rabbit hemorrhagic disease virus (RHDV2) in the two larger islands of the archipelago of Madeira. Based on the capsid protein sequence, the authors suggested that the high sequence identity, along with the short time spanning between outbreaks, points to dissemination from Porto Santo to Madeira. By including information of the full RHDV2 genome of strains from Azores, Madeira, and the Canary Islands, we confirm the results obtained by Carvalho et al., but further show that several subtypes of RHDV2 circulate in these islands: non-recombinant RHDV2 in the Canary Islands, G1/RHDV2 in Azores, Porto Santo and Madeira, and NP/RHDV2 also in Madeira. Here we conclude that RHDV2 has been independently introduced in these archipelagos, and that in Madeira at least two independent introductions must have occurred. We provide additional information on the dynamics of RHDV2 in the Macaronesian archipelagos of Azores, Madeira, and the Canary Islands and highlight the importance of analyzing RHDV2 complete genome.
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Affiliation(s)
- Ana M Lopes
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
- Department of Anatomy and Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Jose Blanco-Aguiar
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
- Instituto de Investigación en Recursos Cinegéticos (IREC) (CSIC-UCLM-JCCM), Ronda de Toledo, s/n, 13071, Ciudad Real, Spain
| | - Aaron Martín-Alonso
- Institute of Tropical Diseases and Public Health of the Canary Islands, Universidad de La Laguna, Avda. Fco. Sanchez s/n, 38203, Tenerife, Canary Islands, Spain
| | - Manuel Leitão
- Direção Regional dos Recursos Florestais, Rua do Contador 23, 9500-050, Ponta Delgada, Açores, Portugal
| | - Pilar Foronda
- Institute of Tropical Diseases and Public Health of the Canary Islands, Universidad de La Laguna, Avda. Fco. Sanchez s/n, 38203, Tenerife, Canary Islands, Spain
| | - Marco Mendes
- Quinta Vila Passos, Instituto das Florestas e Conservação da Natureza, Rua Alferes Veiga Pestana, 15, 9054-505, Funchal, Madeira, Portugal
| | - David Gonçalves
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Joana Abrantes
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Pedro J Esteves
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.
- Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal.
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38
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Lopes AM, Silvério D, Magalhães MJ, Areal H, Alves PC, Esteves PJ, Abrantes J. Characterization of old RHDV strains by complete genome sequencing identifies a novel genetic group. Sci Rep 2017; 7:13599. [PMID: 29051566 PMCID: PMC5648873 DOI: 10.1038/s41598-017-13902-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 04/04/2017] [Indexed: 11/11/2022] Open
Abstract
Rabbit hemorrhagic disease (RHD) is a veterinary disease that affects the European rabbit and has a significant economic and ecological negative impact. In Portugal, rabbit hemorrhagic disease virus (RHDV) was reported in 1989 and still causes enzootic outbreaks. Several recombination events have been detected in RHDV strains, including in the first reported outbreak. Here we describe the occurrence of recombination in RHDV strains recovered from rabbit and Iberian hare samples collected in the mid-1990s in Portugal. Characterization of full genomic sequences revealed the existence of a single recombination breakpoint at the boundary of the non-structural and the structural encoding regions, further supporting the importance of this region as a recombination hotspot in lagoviruses. Phylogenetic analysis showed that in the structural region, the recombinant strains were similar to pathogenic G1 strains, but in the non-structural region they formed a new group that diverged ~13% from known strains. No further reports of such group exist, but this recombination event was also detected in an Iberian hare that was associated with the earliest species jump in RHDV. Our results highlight the importance of the characterization of full genomes to disclose RHDV evolution and show that lagoviruses’ diversity has been significantly undersampled.
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Affiliation(s)
- Ana M Lopes
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Diogo Silvério
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Maria J Magalhães
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Helena Areal
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Paulo C Alves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.,Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, 59812, Montana, USA
| | - Pedro J Esteves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.,Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal
| | - Joana Abrantes
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.
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Abstract
Although IgD first appeared, along with IgM, in the cartilaginous fishes and has been retained throughout subsequent vertebrate evolution, it has been lost in a diverse group of vertebrate species. We previously showed that, unlike vertebrates that express IgD, the rabbit lacks an IgD (Cδ) gene within 13.5 kb downstream of the IgM gene. We report here that, by conducting BLAST searches of rabbit Ig heavy chain genomic DNA with known mammalian IgD exons, we identified the remnant of the rabbit Cδ gene approximately 21 kb downstream of the IgM gene. The remnant Cδ locus lacks the δCH1 and hinge exons, but contains truncated δCH2 and δCH3 exons, as well as largely intact, but non-functional, secretory and transmembrane exons. In addition, we report that the Cδ gene probably became non-functional in leporids at least prior to the divergence of rabbits and hares ~12 million years ago.
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Affiliation(s)
- Dennis K. Lanning
- Department of Microbiology and Immunology, Center for Translational Research and Education, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
- * E-mail:
| | - Pedro J. Esteves
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Campus de Vairão, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal
| | - Katherine L. Knight
- Department of Microbiology and Immunology, Center for Translational Research and Education, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
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40
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Lopes AM, Magalhães MJ, Alves PC, Esteves PJ, Abrantes J. An update on the rabbit hemorrhagic disease virus (RHDV) strains circulating in Portugal in the 1990s: earliest detection of G3-G5 and G6. Arch Virol 2017; 162:2061-2065. [PMID: 28299483 DOI: 10.1007/s00705-017-3318-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/22/2017] [Indexed: 01/23/2023]
Abstract
Rabbit hemorrhagic disease virus (RHDV) causes devastating effects on European rabbit (Oryctolagus cuniculus) populations in the Iberian Peninsula. According to the information available, only genogroup 1 strains were circulating in Iberian wild rabbits until 2011; the antigenic variant G6 has been sporadically detected in rabbitries since 2007. Here, we show for the first time that G3-G5 strains were already present in mainland Portugal in 1998 and that G6 has been circulating since at least 1999. Moreover, we report a G3-G5 strain from the Azores collected in 1998, which is the likely ancestor of Azorean G3-G5like strains. These observations improve the current knowledge on RHDV epidemiology in the Iberian Peninsula and the Azores.
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Affiliation(s)
- Ana M Lopes
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.
| | - Maria J Magalhães
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Paulo C Alves
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.,Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Pedro J Esteves
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.,Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal
| | - Joana Abrantes
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
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41
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Monterroso P, Garrote G, Serronha A, Santos E, Delibes-Mateos M, Abrantes J, Perez de Ayala R, Silvestre F, Carvalho J, Vasco I, Lopes AM, Maio E, Magalhães MJ, Mills LS, Esteves PJ, Simón MÁ, Alves PC. Disease-mediated bottom-up regulation: An emergent virus affects a keystone prey, and alters the dynamics of trophic webs. Sci Rep 2016; 6:36072. [PMID: 27796353 PMCID: PMC5086860 DOI: 10.1038/srep36072] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/10/2016] [Indexed: 11/19/2022] Open
Abstract
Emergent diseases may alter the structure and functioning of ecosystems by creating new biotic interactions and modifying existing ones, producing cascading processes along trophic webs. Recently, a new variant of the rabbit haemorrhagic disease virus (RHDV2 or RHDVb) arguably caused widespread declines in a keystone prey in Mediterranean ecosystems - the European rabbit (Oryctolagus cuniculus). We quantitatively assess the impact of RHDV2 on natural rabbit populations and in two endangered apex predator populations: the Iberian lynx (Lynx pardinus) and the Spanish Imperial eagle (Aquila adalberti). We found 60–70% declines in rabbit populations, followed by decreases of 65.7% in Iberian lynx and 45.5% in Spanish Imperial eagle fecundities. A revision of the web of trophic interactions among rabbits and their dependent predators suggests that RHDV2 acts as a keystone species, and may steer Mediterranean ecosystems to management-dependent alternative states, dominated by simplified mesopredator communities. This model system stresses the importance of diseases as functional players in the dynamics of trophic webs.
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Affiliation(s)
- Pedro Monterroso
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Germán Garrote
- Agencia de Medio Ambiente y Agua de Andalucía, C/Johan G. Gutenberg. 1, 41092, Seville, Spain
| | - Ana Serronha
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Emídio Santos
- Instituto da Conservação da Natureza e das Florestas, Av. da República, 161050-191, Lisbon, Portugal
| | - Miguel Delibes-Mateos
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,IESA-CSIC, Instituto de Estudios Sociales Avanzados, Plz Campo Santo de los Mártires. 7, 14004 Córdoba, Spain
| | - Joana Abrantes
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | | | - Fernando Silvestre
- Fundación CBD-Habitat, C/ Gustavo Fernández Balbuena 2, Entreplanta, Oficina A, 28002, Madrid, Spain
| | - João Carvalho
- ANPC, Associação Nacional Proprietários Rurais, Gestão Cinegética e Biodiversidade, R. Mestre Lima de Freitas, 1-5°, 1549-012, Lisbon, Portugal
| | - Inês Vasco
- Instituto da Conservação da Natureza e das Florestas, Av. da República, 161050-191, Lisbon, Portugal
| | - Ana M Lopes
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, R. Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Elisa Maio
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Maria J Magalhães
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - L Scott Mills
- Wildlife Biology Program, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Pedro J Esteves
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, R. Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Miguel Ángel Simón
- Consejería de Medio Ambiente de la Junta de Andalucía, C/ Doctor Eduardo García-Triviño López 15, 23071 Jaén, Spain
| | - Paulo C Alves
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, R. Campo Alegre s/n, 4169-007, Porto, Portugal.,Wildlife Biology Program, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
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Zurnic I, Hütter S, Lehmann U, Stanke N, Reh J, Kern T, Lindel F, Gerresheim G, Hamann M, Müllers E, Lesbats P, Cherepanov P, Serrao E, Engelman A, Lindemann D, Da Silva Santos C, Tartour K, Cimarelli A, Burdick R, Chen J, Sastri J, Hu WS, Pathak V, Keppler OT, Pradeau K, Eiler S, Levy N, Lennon S, Cianferani S, Emiliani S, Ruff M, Parissi V, Rato S, Rausell A, Munoz M, Telenti A, Ciuffi A, Zhyvoloup A, Melamed A, Anderson I, Planas D, Kriston-Vizi J, Ketteler R, Lee CH, Merritt A, Ancuta P, Bangham C, Fassati A, Rodari A, Van Driessche B, Galais M, Delacourt N, Fauquenoy S, Vanhulle C, Kula A, Burny A, Rohr O, Van Lint C, van Montfort T, van der Sluis R, Speijer D, Berkhout B, Meng B, Rutkowski A, Berry N, Dölken L, Lever A, Schuster T, Asbach B, Wagner R, Gross C, Wiesmann V, Kalmer M, Wittenberg T, Gettemans J, Thoma-Kress AK, Li M, Freed EO, Liu SL, Müller J, Münch J, Sewald X, Uchil P, Ladinsky M, Beloor J, Pi R, Herrmann C, Motamedi N, Murooka T, Brehm M, Greiner D, Mempel T, Bjorkman P, Kumar P, Mothes W, Joas S, Parrish E, Gnanadurai CW, Lump E, Stürzel CM, Parrish NF, Sauermann U, Töpfer K, Schultheiss T, Bosinger S, Silvestri G, Apetrei C, Huot N, Müller-Trutwin M, Sauter D, Hahn BH, Stahl-Hennig C, Kirchhoff F, Schumann G, Jung-Klawitter S, Fuchs NV, Upton KR, Muñoz-Lopez M, Shukla R, Wang J, Garcia-Canadas M, Lopez-Ruiz C, Gerhardt DJ, Sebe A, Grabundzija I, Gerdes P, Merkert S, Pulgarin A, Bock A, Held U, Witthuhn A, Haase A, Wolvetang EJ, Martin U, Ivics Z, Izsvák Z, Garcia-Perez J, Faulkner GJ, Hurst T, Katzourakis A, Magiorkinis G, Schott K, Derua R, Seifried J, Reuter A, Schmitz H, Tondera C, Brandariz-Nuñez A, Diaz-Griffero F, Janssens V, König R, Baldauf HM, Stegmann L, Schwarz SM, Trotard M, Martin M, Lenzi G, Burggraf M, Pan X, Fregoso OI, Lim ES, Abraham L, Erikson E, Nguyen L, Ambiel I, Rutsch F, Kim B, Emerman M, Fackler OT, Wittmann S, Behrendt R, Volkmann B, Eissmann K, Gramberg T, Bolduan S, Koppensteiner H, Regensburg S, Brack-Werner R, Draenert R, Schindler M, Ducroux A, Xu S, Ponnurangam A, Franz S, Malassa A, Ewald E, Goffinet C, Fung SY, Chan CP, Yuen CK, Kok KH, Chan CP, Jin DY, Dittmer U, Kmiec D, Iyer S, Stürzel C, Hahn B, Ariumi Y, Yasuda-Inoue M, Kawano K, Tateishi S, Turelli P, Compton A, Roy N, Porrot F, Billet A, Casartelli N, Yount J, Liang C, Schwartz O, Magnus C, Reh L, Moore P, Uhr T, Weber J, Morris L, Trkola A, Grindberg RV, Schlaepfer E, Schreiber G, Simon V, Speck RF, Debyser Z, Vranckx L, Demeulemeester J, Saleh S, Verdin E, Cereseto A, Christ F, Gijsbers R, Wang G, Zhao N, Das AT, Köstler J, Perdiguero B, Esteban M, Jacobs BL, Montefiori DC, LaBranche CC, Yates NL, Tomaras GD, Ferrari G, Foulds KE, Roederer M, Landucci G, Forthal DN, Seaman MS, Hawkins N, Self SG, Phogat S, Tartaglia J, Barnett SW, Burke B, Cristillo AD, Ding S, Heeney JL, Pantaleo G, Stab V, Ensser A, Tippler B, Burton D, Tenbusch M, Überla K, Alter G, Lofano G, Dugast AS, Kulkarni V, Suscovich T, Opazo T, Barraza F, Herrera D, Garces A, Schwenke T, Tapia D, Cancino J, Arriagada G, Haußner C, Damm D, Rohrhofer A, Schmidt B, Eichler J, Midgley R, Wheeldon J, Piguet V, Khopkar P, Rohamare M, Kulkarni S, Godinho-Santos A, Hance A, Goncalves J, Mammano F, Gasser R, Hamoudi M, Pellicciotta M, Zhou Z, Visdeloup C, Colin P, Braibant M, Lagane B, Negroni M, Wamara J, Bannert N, Mesplede T, Osman N, Anstett K, Liang JC, Pham HT, Wainberg M, Shao W, Shan J, Kearney M, Wu X, Maldarelli F, Mellors J, Luke B, Coffin J, Hughes S, Fricke T, Opp S, Shepard C, Ivanov D, Valle-Casuso J, Kanja M, Cappy P, Negroni M, Lener D, Knyazhanskaya E, Anisenko A, Zatsepin T, Gottikh M, Komkov A, Minervina A, Nugmanov G, Nazarov V, Khodosevich K, Mamedov I, Lebedev Y, Colomer-Lluch M, Serra-Moreno R, Sarracino A, Gharu L, Pasternak A, Marcello A, McCartin AM, Kulkarni A, Le Douce V, Gautier V, Baeyens A, Naessens E, Van Nuffel A, Weening K, Reilly AM, Claeys E, Trypsteen W, Vandekerckhove L, Eyckerman S, Gevaert K, Verhasselt B, Mok HP, Norton N, Fun A, Hirst J, Wills M, Miklik D, Senigl F, Hejnar J, Sakuragi JI, Sakuragi S, Yokoyama M, Shioda T, Sato H, Bodem J, Moschall R, Denk S, Erkelenz S, Schenk C, Schaal H, Donhauser N, Socher E, Millen S, Sticht H, Gross C, Mann M, Wei G, Betts MJ, Liu Y, Kehl T, Russell RB, Löchelt M, Hohn O, Mostafa S, Hanke K, Norley S, Chen CY, Shingai M, Borrego P, Taveira N, Strebel K, Hellmund C, Meng B, Friedrich M, Hahn F, Setz C, Rauch P, Fraedrich K, Matthaei A, Henklein P, Traxdorf M, Fossen T, Schubert U, Khwaja A, Galilee M, Alian A, Schwalbe B, Hauser H, Schreiber M, Scherpenisse M, Cho YK, Kim J, Jeong D, Trejbalova K, Benesova M, Kucerova D, Vernerova Z, Amouroux R, Hajkova P, Elleder D, Hron T, Farkasova H, Padhi A, Paces J, Zhu H, Gifford R, Murcia P, Carrozza ML, Niewiadomska AM, Mazzei M, Abi-Said M, Hughes J, Hué S, Gifford R, Obasa A, Jacobs G, Engelbrecht S, Mack K, Starz K, Geyer M, Bibollet-Ruche F, Stürzel C, Leoz M, Plantier JC, Argaw-Denboba A, Balestrieri E, Serafino A, Bucci I, Cipriani C, Spadafora C, Sinibaldi-Vallebona P, Matteucci C, Jayashree SN, Neogi U, Chhangani AK, Rathore SS, Mathur BRJ, Abati A, Koç BT, Oğuzoğlu TÇ, Shimauchi T, Caucheteux S, Turpin J, Finsterbusch K, Tokura Y, Souriant S, Balboa L, Pingris K, Kviatcowsky D, Raynaud-Messina B, Cougoule C, Mercier I, Kuroda M, González-Montaner P, Inwentarz S, Moraña EJ, del Carmen Sasiain M, Neyrolles O, Maridonneau-Parini I, Lugo-Villarino G, Vérollet C, Herrmann A, Thomas D, Bouzas NF, Lahaye X, Bhargava A, Satoh T, Gentili M, Cerboni S, Silvin A, Conrad C, Ahmed-Belkacem H, Rodriguez EC, Guichou JF, Bosquet N, Piel M, Le Grand R, King M, Pawlotsky JM, Manel N, Hofmann H, Vanwalscappel B, Bloch N, Landau N, Indik S, Hagen B, Valle-Casuso JC, Allouch A, David A, Barré-Sinoussi F, Benkirane M, Pancino G, Saez-Cirion A, Lee WY, Sloan R, Schulte B, Opp S, Blomberg J, Vargiu L, Rodriguez-Tomé P, Tramontano E, Sperber G, Kumari N, Ammosova T, Diaz S, Oneal P, Nekhai S, Fahrny A, Gers-Huber G, Audigé A, Jayaprakash A, Sachidanandam R, Hernandez M, Dillon-White M, Souriant S, Pingris K, Raynaud-Messina B, Cougoule C, Mercier I, Neyrolles O, Maridonneau-Parini I, Lugo-Villarino G, Maze E, Ham C, Almond N, Towers G, Belshaw R, de Sousa-Pereira P, Abrantes J, Pizzato M, Esteves PJ, Kahle T, Schmitt S, Merkel L, Reuter N, Stamminger T, Rosa ID, Bishop K, Spinazzola A, Groom H, Vieyres G, Müsken M, Zillinger T, Hornung V, Barchet W, Häussler S, Pietschmann T, Javed A, Leuchte N, Salinas G, Opitz L, Sopper S, Mummert C, Hofmann C, Hückelhoven AG, Bergmann S, Müller-Schmucker SM, Harrer EG, Dörrie J, Schaft N, Harrer T, Cardinaux L, Zahno ML, Vogt HR, Zanoni R, Bertoni G, Muenchhoff M, Goulder P, Keppler O, Rebensburg S, Helfer M, Zhang Y, Chen H, Bernier A, Gosselin A, Routy JP, Wöhrl B, Schneider A, Corona A, Spöring I, Jordan M, Buchholz B, Maccioni E, Di Santo R, Schweimer K, Schölz C, Weinert B, Wagner S, Beli P, Miyake Y, Qi J, Jensen L, Streicher W, McCarthy A, Westwood N, Lain S, Cox J, Matthias P, Mann M, Bradner J, Choudhary C, Stern M, Valletta E, Frezza C, Marino-Merlo F, Grelli S, Serafino AL, Mastino A, Macchi B, Kaulfuß M, Windmann S, Bayer W, Mikasi S, Jacobs G, Heß R, Bonsmann MSG, Kirschning C, Lepenies B, Kolenbrander A, Temchura V, Iijima K, Kobayashi J, Ishizaka Y. Proceedings of the Frontiers of Retrovirology Conference 2016. Retrovirology 2016. [PMCID: PMC5046194 DOI: 10.1186/s12977-016-0294-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Oral presentations Session 1: Entry & uncoating O1 Host cell polo-like kinases (PLKs) promote early prototype foamy virus (PFV) replication Irena Zurnic, Sylvia Hütter, Ute Lehmann, Nicole Stanke, Juliane Reh, Tobias Kern, Fabian Lindel, Gesche Gerresheim, Martin Hamann, Erik Müllers, Paul Lesbats, Peter Cherepanov, Erik Serrao, Alan Engelman, Dirk Lindemann O2 A novel entry/uncoating assay reveals the presence of at least two species of viral capsids during synchronized HIV-1 infection Claire Da Silva Santos, Kevin Tartour, Andrea Cimarelli O3 Dynamics of nuclear envelope association and nuclear import of HIV-1 complexes Rya Burdick, Jianbo Chen, Jaya Sastri, Wei-Shau Hu, Vinay Pathak O4 Human papillomavirus protein E4 potently enhances the susceptibility to HIV infection Oliver T. Keppler Session 2: Reverse transcription & integration O5 Structure and function of HIV-1 integrase post translational modifications Karine Pradeau, Sylvia Eiler, Nicolas Levy, Sarah Lennon, Sarah Cianferani, Stéphane Emiliani, Marc Ruff O6 Regulation of retroviral integration by RNA polymerase II associated factors and chromatin structure Vincent Parissi Session 3: Transcription and latency O7 A novel single-cell analysis pipeline to identify specific biomarkers of HIV permissiveness Sylvie Rato, Antonio Rausell, Miguel Munoz, Amalio Telenti, Angela Ciuffi O8 A capsid-dependent integration program linking T cell activation to HIV-1 gene expression Alexander Zhyvoloup, Anat Melamed, Ian Anderson, Delphine Planas, Janos Kriston-Vizi, Robin Ketteler, Chen-Hsuin Lee, Andy Merritt, Petronela Ancuta, Charles Bangham, Ariberto Fassati O9 Characterisation of new RNA polymerase III and RNA polymerase II transcriptional promoters in the Bovine Leukemia Virus genome Anthony Rodari, Benoit Van Driessche, Mathilde Galais, Nadége Delacourt, Sylvain Fauquenoy, Caroline Vanhulle, Anna Kula, Arsène Burny, Olivier Rohr, Carine Van Lint O10 Tissue-specific dendritic cells differentially modulate latent HIV-1 reservoirs Thijs van Montfort, Renee van der Sluis, Dave Speijer, Ben Berkhout Session 4: RNA trafficking & packaging O11 A novel cis-acting element affecting HIV replication Bo Meng, Andrzej Rutkowski, Neil Berry, Lars Dölken, Andrew Lever O12 Tolerance of HIV’s late gene expression towards stepwise codon adaptation Thomas Schuster, Benedikt Asbach, Ralf Wagner Session 5: Assembly & release O13 Importance of the tax-inducible actin-bundling protein fascin for transmission of human T cell leukemia virus Type 1 (HTLV-1) Christine Gross, Veit Wiesmann, Martina Kalmer, Thomas Wittenberg, Jan Gettemans, Andrea K. Thoma-Kress O14 Lentiviral nef proteins antagonize TIM-mediated inhibition of viral release Minghua Li, Eric O. Freed, Shan-Lu Liu Session 6: Pathogenesis & evolution O15 SEVI and semen prolong the half-life of HIV-1 Janis Müller, Jan Münch O16 CD169+ macrophages mediate retrovirus trans-infection of permissive lymphocytes to establish infection in vivo Xaver Sewald, Pradeep Uchil, Mark Ladinsky, Jagadish Beloor, Ruoxi Pi, Christin Herrmann, Nasim Motamedi, Thomas Murooka, Michael Brehm, Dale Greiner, Thorsten Mempel, Pamela Bjorkman, Priti Kumar, Walther Mothes O17 Efficient replication of a vpu containing SIVagm construct in African Green Monkeys requires an HIV-1 nef gene Simone Joas, Erica Parrish, Clement Wesley Gnanadurai, Edina Lump, Christina M. Stürzel, Nicholas F. Parrish, Ulrike Sauermann, Katharina Töpfer, Tina Schultheiss, Steven Bosinger, Guido Silvestri, Cristian Apetrei, Nicholas Huot, Michaela Müller-Trutwin, Daniel Sauter, Beatrice H. Hahn, Christiane Stahl-Hennig, Frank Kirchhoff O18 Reprogramming initiates mobilization of endogenous mutagenic LINE-1, Alu and SVA retrotransposons in human induced pluripotent stem cells with consequences for host gene expression Gerald Schumann, Sabine Jung-Klawitter, Nina V. Fuchs, Kyle R. Upton, Martin Muñoz-Lopez, Ruchi Shukla, Jichang Wang, Marta Garcia-Canadas, Cesar Lopez-Ruiz, Daniel J. Gerhardt, Attila Sebe, Ivana Grabundzija, Patricia Gerdes, Sylvia Merkert, Andres Pulgarin, Anja Bock, Ulrike Held, Anett Witthuhn, Alexandra Haase, Ernst J. Wolvetang, Ulrich Martin, Zoltán Ivics, Zsuzsanna Izsvák, J. Garcia-Perez, Geoffrey J. Faulkner O19 NF-κB activation induces expression of human endogenous retrovirus and particle production Tara Hurst, Aris Katzourakis, Gkikas Magiorkinis Session 7a and b: Innate sensing & intrinsic immunity O20 Identification of the phosphatase acting on T592 in SAMHD1 during M/G1 transition Kerstin Schott, Rita Derua, Janna Seifried, Andreas Reuter, Heike Schmitz, Christiane Tondera, Alberto Brandariz-Nuñez, Felipe Diaz-Griffero, Veerle Janssens, Renate König O21 Vpx overcomes a SAMHD1-independent block to HIV reverse transcription that is specific to resting CD4 T cells Hanna-Mari Baldauf, Lena Stegmann, Sarah-Marie Schwarz, Maud Trotard, Margarethe Martin, Gina Lenzi, Manja Burggraf, Xiaoyu Pan, Oliver I. Fregoso, Efrem S. Lim, Libin Abraham, Elina Erikson, Laura Nguyen, Ina Ambiel, Frank Rutsch, Renate König, Baek Kim, Michael Emerman, Oliver T. Fackler, Oliver T. Keppler O22 The role of SAMHD1 in antiviral restriction and immune sensing in the mouse Sabine Wittmann, Rayk Behrendt, Bianca Volkmann, Kristin Eissmann, Thomas Gramberg O23 T cells expressing reduced restriction factors are preferentially infected in therapy naïve HIV-1 patients Sebastian Bolduan, Herwig Koppensteiner, Stefanie Regensburg, Ruth Brack-Werner, Rika Draenert, Michael Schindler O24 cGAS-mediated innate immunity spreads through HIV-1 env-induced membrane fusion sites from infected to uninfected primary HIV-1 target cells Aurélie Ducroux, Shuting Xu, Aparna Ponnurangam, Sergej Franz, Angelina Malassa, Ellen Ewald, Christine Goffinet O25 Perturbation of innate RNA and DNA sensing by human T cell leukemia virus type 1 oncoproteins Sin-Yee Fung, Ching-Ping Chan, Chun-Kit Yuen, Kin-Hang Kok, Chin-Ping Chan, Dong-Yan Jin O26 Induction and anti-viral activity of Interferon α subtypes in HIV-1 infection Ulf Dittmer O27 Vpu-mediated counteraction of tetherin is a major determinant of HIV-1 interferon resistance Dorota Kmiec, Shilpa Iyer, Christina Stürzel, Daniel Sauter, Beatrice Hahn, Frank Kirchhoff O28 DNA repair protein Rad18 restricts HIV-1 and LINE-1 life cycle Yasuo Ariumi, Mariko Yasuda-Inoue, Koudai Kawano, Satoshi Tateishi, Priscilla Turelli O29 Natural mutations in IFITM3 allow escape from post-translational regulation and toggle antiviral specificity Alex Compton, Nicolas Roy, Françoise Porrot, Anne Billet, Nicoletta Casartelli, Jacob Yount, Chen Liang, Oliver Schwartz Session 8: Adaptive immunity & immune evasion O30 Observing evolution in HIV-1 infection: phylogenetics and mutant selection windows to infer the influence of the autologous antibody response on the viral quasispecies Carsten Magnus, Lucia Reh, Penny Moore, Therese Uhr, Jacqueline Weber, Lynn Morris, Alexandra Trkola O31 Dose and subtype specific analyses of the anti-HIV effects of IFN-alpha family members Rashel V. Grindberg, Erika Schlaepfer, Gideon Schreiber, Viviana Simon, Roberto F. Speck Session 9: Novel antiviral strategies O32 LEDGIN-mediated inhibition of the integrase-LEDGF/p75 interaction reduces reactivation of residual latent HIV Zeger Debyser, Lenard Vranckx, Jonas Demeulemeester, Suha Saleh, Eric Verdin, Anna Cereseto, Frauke Christ, Rik Gijsbers O33 NKG2D-mediated clearance of reactivated viral reservoirs by natural killer cells O34 Inhibition of HIV reactivation in brain cells by AAV-mediated delivery of CRISPR/Cas9 O35 CRISPR-Cas9 as antiviral: potent HIV-1 inhibition, but rapid virus escape and the subsequent design of escape-proof antiviral strategies Ben Berkhout, Gang Wang, Na Zhao, Atze T. Das Session 10: Recent advances in HIV vaccine development O36 Priming with a potent HIV-1 DNA vaccine frames the quality of T cell and antibody responses prior to a poxvirus and protein boost Benedikt Asbach, Josef Köstler, Beatriz Perdiguero, Mariano Esteban, Bertram L. Jacobs, David C. Montefiori, Celia C. LaBranche, Nicole L. Yates, Georgia D. Tomaras, Guido Ferrari, Kathryn E. Foulds, Mario Roederer, Gary Landucci, Donald N. Forthal, Michael S. Seaman, Natalie Hawkins, Steven G. Self, Sanjay Phogat, James Tartaglia, Susan W. Barnett, Brian Burke, Anthony D. Cristillo, Song Ding, Jonathan L. Heeney, Giuseppe Pantaleo, Ralf Wagner O37 Passive immunisation with a neutralising antibody against HIV-1 Env prevents infection of the first cells in a mucosal challenge rhesus monkey model Christiane Stahl-Hennig, Viktoria Stab, Armin Ensser, Ulrike Sauermann, Bettina Tippler, Dennis Burton, Matthias Tenbusch, Klaus Überla O38 HIV antibody Fc-glycoforms drive B cell affinity maturation Galit Alter, Giuseppe Lofano, Anne-Sophie Dugast, Viraj Kulkarni, Todd Suscovich Poster presentations Topic 1: Entry & uncoating P1 Dynein light chain is required for murine leukemia virus infection Tatiana Opazo, Felipe Barraza, Diego Herrera, Andrea Garces, Tomas Schwenke, Diego Tapia, Jorge Cancino, Gloria Arriagada P2 Peptide paratope mimics of the broadly neutralising HIV-1 antibody b12 Christina Haußner, Dominik Damm, Anette Rohrhofer, Barbara Schmidt, Jutta Eichler P3 Investigating cellular pathways involved in the transmission of HIV-1 between dendritic cells and T cells using RNAi screening techniques Rebecca Midgley, James Wheeldon, Vincent Piguet P4 Co-receptor tropism in HIV-1, HIV-2 monotypic and dual infections Priyanka Khopkar, Megha Rohamare, Smita Kulkarni P5 Characterisation of the role of CIB1 and CIB2 as HIV-1 helper factors Ana Godinho-Santos, Allan Hance, Joao Goncalves, Fabrizio Mammano P6 Buffering deleterious polymorphisms in the highly constrained C2 region of HIV-1 envelope by the flexible V3 domain Romain Gasser, Meriem Hamoudi, Martina Pellicciotta, Zhicheng Zhou, Clara Visdeloup, Philippe Colin, Martine Braibant, Bernard Lagane, Matteo Negroni P7 Entry inhibition of HERV-K(HML-2) by an Env-IgG fusion protein Jula Wamara, Norbert Bannert Topic 2: Reverse transcription & integration P8 The R263K/H51Y resistance substitutions in HIV integrase decreases levels of integrated HIV DNA over time Thibault Mesplede, Nathan Osman, Kaitlin Anstett, Jiaming Calvin Liang, Hanh Thi Pham, Mark Wainberg P9 The Retrovirus Integration Database (RID) Wei Shao, Jigui Shan, Mary Kearney, Xiaolin Wu, Frank Maldarelli, John Mellors, Brian Luke, John Coffin, Stephen Hughes P10 The small molecule 3G11 inhibits HIV-1 reverse transcription Thomas Fricke, Silvana Opp, Caitlin Shepard, Dmitri Ivanov, Baek Kim, Jose Valle-Casuso, Felipe Diaz-Griffero P11 Dual and opposite regulation of HIV-1 integration by hRAD51: impact on therapeutical approaches using homologous DNA repair modulators Vincent Parissi P12 A flexible motif essential for integration by HIV-1 integrase Marine Kanja, Pierre Cappy, Matteo Negroni, Daniela Lener P13 Interaction between HIV-1 integrase and the host protein Ku70: identification of the binding site and study of the influence on integrase-proteasome interplay Ekaterina Knyazhanskaya, Andrey Anisenko, Timofey Zatsepin, Marina Gottikh P14 Normalisation based method for deep sequencing of somatic retroelement integrations in human genome Alexander Komkov, Anastasia Minervina, Gaiaz Nugmanov, Vadim Nazarov, Konstantin Khodosevich, Ilgar Mamedov, Yuri Lebedev Topic 3: Transcription and latency P15 BCA2/RABRING7 restricts HIV-1 transcription by preventing the nuclear translocation of NF-κB Marta Colomer-Lluch, Ruth Serra-Moreno P16 MATR3 post-transcriptional regulation of HIV-1 transcription during latency Ambra Sarracino, Anna Kula, Lavina Gharu, Alexander Pasternak, Carine Van Lint, Alessandro Marcello P17 HIV-1 tat intersects the SUMO pathway to regulate HIV-1 promoter activity Ann Marie McCartin, Anurag Kulkarni, Valentin Le Douce, Virginie Gautier P18 Conservation in HIV-1 Vpr guides tertiary gRNA folding and alternative splicing Ann Baeyens, Evelien Naessens, Anouk Van Nuffel, Karin Weening, Anne-Marie Reilly, Eva Claeys, Wim Trypsteen, Linos Vandekerckhove, Sven Eyckerman, Kris Gevaert, Bruno Verhasselt P19 The majority of reactivatable latent HIV are genetically distinct Hoi Ping Mok, Nicholas Norton, Axel Fun, Jack Hirst, Mark Wills, Andrew Lever P20 Do mutations in the tat exonic splice enhancer contribute to HIV-1 latency? Nicholas Norton, Hoi Ping Mok, Jack Hirst, Andrew Lever P21 Culture-to-Ct: A fast and direct RT-qPCR HIV gene reactivation screening method using primary T cell culture Valentin Le Douce, Ann Marie McCartin, Virginie Gautier P22 A novel approach to define populations of early silenced proviruses Dalibor Miklik, Filip Senigl, Jiri Hejnar Topic 4: RNA trafficking & packaging P23 Functional analysis of the structure and conformation of HIV-1 genome RNA DIS Jun-ichi Sakuragi, Sayuri Sakuragi, Masaru Yokoyama, Tatsuo Shioda, Hironori Sato P24 Regulation of foamy viral env splicing controls gag and pol expression Jochen Bodem, Rebecca Moschall, Sarah Denk, Steffen Erkelenz, Christian Schenk, Heiner Schaal Topic 5: Assembly & release P25 Transfer of HTLV-1 p8 to target T cells depends on VASP: a novel interaction partner of p8 Norbert Donhauser, Ellen Socher, Sebastian Millen, Heinrich Sticht, Andrea K. Thoma-Kress P26 COL4A1 and COL4A2 are novel HTLV-1 tax targets with a putative role in virus transmission Christine Gross, Sebastian Millen, Melanie Mann, Klaus Überla, Andrea K. Thoma-Kress P27 The C terminus of foamy virus gag protein is required for particle formation, and virus budding: starting assembly at the C terminus? Guochao Wei, Matthew J. Betts, Yang Liu, Timo Kehl, Robert B. Russell, Martin Löchelt P28 Generation of an antigen-capture ELISA and analysis of Rec and Staufen-1 effects on HERV-K(HML-2) virus particle production Oliver Hohn, Saeed Mostafa, Kirsten Hanke, Stephen Norley, Norbert Bannert P29 Antagonism of BST-2/tetherin is a conserved function of primary HIV-2 Env glycoproteins Chia-Yen Chen, Masashi Shingai, Pedro Borrego, Nuno Taveira, Klaus Strebel P30 Mutations in the packaging signal region of the HIV-1 genome cause a late domain mutant phenotype Chris Hellmund, Bo Meng, Andrew Lever P31 p6 regulates membrane association of HIV-1 gag Melanie Friedrich, Friedrich Hahn, Christian Setz, Pia Rauch, Kirsten Fraedrich, Alina Matthaei, Petra Henklein, Maximilian Traxdorf, Torgils Fossen, Ulrich Schubert Topic 6: Pathogenesis & evolution P32 Molecular and structural basis of protein evolution during viral adaptation Aya Khwaja, Meytal Galilee, Akram Alian P33 HIV-1 enhancement and neutralisation by soluble gp120 and its role for the selection of the R5-tropic “best fit” Birco Schwalbe, Heiko Hauser, Michael Schreiber P34 An insertion of seven amino acids in the Env cytoplasmic tail of Human Immunodeficiency Virus type 2 (HIV-2) selected during disease progression enhances viral replication François Dufrasne, Mara Lucchetti, Patrick Goubau, Jean Ruelle P35 Cell-associated HIV-1 unspliced to multiply spliced RNA ratio at 12 weeks ART correlates with markers of immune activation and apoptosis and predicts the CD4 T-cell count at 96 weeks ART Mirte Scherpenisse, Ben Berkhout, Alexander Pasternak P36 Faster progression in non-B subtype HIV-1-infected patients than Korean subclade of subtype B is accompanied by higher variation and no induction of gross deletion in non-B nef gene by Korean red ginseng treatment Young-Keol Cho, Jungeun Kim, Daeun Jeong P37 Aberrant expression of ERVWE1 endogenous retrovirus and overexpression of TET dioxygenases are characteristic features of seminoma Katerina Trejbalova, Martina Benesova, Dana Kucerova, Zdenka Vernerova, Rachel Amouroux, Petra Hajkova, Jiri Hejnar P38 Life history of the oldest lentivirus: characterisation of ELVgv integrations and the TRIM5 selection pattern in dermoptera Daniel Elleder, Tomas Hron, Helena Farkasova, Abinash Padhi, Jan Paces P39 Characterisation of a highly divergent endogenous retrovirus in the equine germ line Henan Zhu, Robert Gifford, Pablo Murcia P40 The emergence of pandemic retroviral infection in small ruminants Maria Luisa Carrozza, Anna-Maria Niewiadomska, Maurizio Mazzei, Mounir Abi-Said, Joseph Hughes, Stéphane Hué, Robert Gifford P41 Near full-length genome (NFLG) Characterisation of HIV-1 subtype B identified in South Africa Adetayo Obasa, Graeme Jacobs, Susan Engelbrecht P42 Acquisition of Vpu-mediated tetherin antagonism by an HIV-1 group O strain Katharina Mack, Kathrin Starz, Daniel Sauter, Matthias Geyer, Frederic Bibollet-Ruche, Christina Stürzel, Marie Leoz, Jean Christophe Plantier, Beatrice H. Hahn, Frank Kirchhoff P43 The human endogenous retrovirus type K is involved in cancer stem cell markers expression and in human melanoma malignancy Ayele Argaw-Denboba, Emanuela Balestrieri, Annalucia Serafino, Ilaria Bucci, Chiara Cipriani, Corrado Spadafora, Paolo Sinibaldi-Vallebona, Claudia Matteucci P44 Natural infection of Indian non-human primates by unique lentiviruses S. Nandi Jayashree, Ujjwal Neogi, Anil K. Chhangani, Shravan Sing Rathore, Bajrang R. J. Mathur P45 Free cervical cancer screening among HIV-positive women receiving antiretroviral treatment in Nigeria Adeyemi Abati P46 Molecular evolutionary status of feline immunodeficiency virus in Turkey B. Taylan Koç, Tuba Çiğdem Oğuzoğlu Topic 7: Innate sensing & intrinsic immunity P47 Cell-to-cell contact with HTLV-1-infected T cells reduces dendritic cell immune functions and contributes to infection in trans. Takatoshi Shimauchi, Stephan Caucheteux, Jocelyn Turpin, Katja Finsterbusch, Charles Bangham, Yoshiki Tokura, Vincent Piguet P48 Deciphering the mechanisms of HIV-1 exacerbation induced by Mycobacterium tuberculosis in monocytes/macrophages Shanti Souriant, Luciana Balboa, Karine Pingris, Denise Kviatcowsky, Brigitte Raynaud-Messina, Céline Cougoule, Ingrid Mercier, Marcelo Kuroda, Pablo González-Montaner, Sandra Inwentarz, Eduardo Jose Moraña, Maria del Carmen Sasiain, Olivier Neyrolles, Isabelle Maridonneau-Parini, Geanncarlo Lugo-Villarino, Christel Vérollet P49 The SAMHD1-mediated inhibition of LINE-1 retroelements is regulated by phosphorylation Alexandra Herrmann, Sabine Wittmann, Caitlin Shepard, Dominique Thomas, Nerea Ferreirós Bouzas, Baek Kim, Thomas Gramberg P50 Activities of nuclear envelope protein SUN2 in HIV infection Xavier Lahaye, Anvita Bhargava, Takeshi Satoh, Matteo Gentili, Silvia Cerboni, Aymeric Silvin, Cécile Conrad, Hakim Ahmed-Belkacem, Elisa C. Rodriguez, Jean-François Guichou, Nathalie Bosquet, Matthieu Piel, Roger Le Grand, Megan King, Jean-Michel Pawlotsky, Nicolas Manel P51 Activation of TLR7/8 with a small molecule agonist induces a novel restriction to HIV-1 infection of monocytes Henning Hofmann, Benedicte Vanwalscappel, Nicolin Bloch, Nathaniel Landau P52 Steady state between the DNA polymerase and Rnase H domain activities of reverse transcriptases determines the sensitivity of retroviruses to inhibition by APOBEC3 proteins Stanislav Indik, Benedikt Hagen P53 HIV restriction in mature dendritic cells is related to p21 induction and p21-mediated control of the dNTP pool and SAMHD1 activity. José Carlos Valle-Casuso, Awatef Allouch, Annie David, Françoise Barré-Sinoussi, Michaela Müller-Trutwin, Monsef Benkirane, Gianfranco Pancino, Asier Saez-Cirion P54 IFITM protens restrict HIV-1 protein synthesis Wing-Yiu Lee, Chen Liang, Richard Sloan P55 Characterisation and functional analysis of the novel restriction factor Serinc5 Bianca Schulte, Silvana Opp, Felipe Diaz-Griffero P56 piRNA sequences are common in Human Endogenous Retroviral Sequences (HERVs): An antiretroviral restriction mechanism? Jonas Blomberg, Luana Vargiu, Patricia Rodriguez-Tomé, Enzo Tramontano, Göran Sperber P57 Ferroportin restricts HIV-1 infection in sickle cell disease Namita Kumari, Tatiana Ammosova, Sharmeen Diaz, Patricia Oneal, Sergei Nekhai P58 APOBEC3G modulates the response to antiretroviral drugs in humanized mice Audrey Fahrny, Gustavo Gers-Huber, Annette Audigé, Roberto F. Speck, Anitha Jayaprakash, Ravi Sachidanandam, Matt Hernandez, Marsha Dillon-White, Viviana Simon P59 High-throughput epigenetic analysis of evolutionarily young endogenous retrovirus presents in the mule deer (Odocoileus hemionus) genome Tomas Hron, Helena Farkasova, Daniel Elleder P60 Characterisation of the expression of novel endogenous retroviruses and immune interactions in a macaque model Neil Berry, Emmanuel Maze, Claire Ham, Neil Almond, Greg Towers, Robert Belshaw P61 HIV-1 restriction by orthologs of SERINC3 and SERINC5 Patrícia de Sousa-Pereira, Joana Abrantes, Massimo Pizzato, Pedro J. Esteves, Oliver T. Fackler, Oliver T. Keppler, Hanna-Mari Baldauf P62 TRIM19/PML restricts HIV infection in a cell type-dependent manner Bianca Volkmann, Tanja Kahle, Kristin Eissmann, Alexandra Herrmann, Sven Schmitt, Sabine Wittmann, Laura Merkel, Nina Reuter, Thomas Stamminger, Thomas Gramberg P63 Recent invasion of the mule deer genome by a retrovirus Helena Farkasova, Tomas Hron, Daniel Elleder P64 Does the antiviral protein SAMHD1 influence mitochondrial function? Ilaria Dalla Rosa, Kate Bishop, Antonella Spinazzola, Harriet Groom P65 cGAMP transfers intercellularly via HIV-1 Env-mediated cell–cell fusion sites and triggers an innate immune response in primary target cells Shuting Xu, Aurélie Ducroux, Aparna Ponnurangam, Sergej Franz, Gabrielle Vieyres, Mathias Müsken, Thomas Zillinger, Angelina Malassa, Ellen Ewald, Veit Hornung, Winfried Barchet, Susanne Häussler, Thomas Pietschmann, Christine Goffinet P66 Pre-infection transcript levels of FAM26F in PBMCS inform about overall plasma viral load in acute and postacute phase after SIV-infection Ulrike Sauermann, Aneela Javed, Nicole Leuchte, Gabriela Salinas, Lennart Opitz, Christiane Stahl-Hennig, Sieghart Sopper P67 Sequence-function analysis of three T cell receptors targeting the HIV-1 p17 epitope SLYNTVATL Christiane Mummert, Christian Hofmann, Angela G. Hückelhoven, Silke Bergmann, Sandra M. Müller-Schmucker, Ellen G. Harrer, Jan Dörrie, Niels Schaft, Thomas Harrer P68 An immunodominant region of the envelope glycoprotein of small ruminant lentiviruses may function as decoy antigen Laure Cardinaux, M.-L. Zahno, H.-R. Vogt, R. Zanoni, G. Bertoni P69 Impact of immune activation, immune exhaustion, broadly neutralising antibodies and viral reservoirs on disease progression in HIV-infected children Maximilian Muenchhoff, Philip Goulder, Oliver Keppler Topic 9: Novel antiviral strategies P70 Identification of natural compounds as new antiviral products by bioassay-guided fractionation Alexandra Herrmann, Stephanie Rebensburg, Markus Helfer, Michael Schindler, Ruth Brack-Werner P71 The PPARG antagonism disconnects the HIV replication and effector functions in Th17 cells Yuwei Zhang, Huicheng Chen, Delphine Planas, Annie Bernier, Annie Gosselin, Jean-Pierre Routy, Petronela Ancuta P72 Characterisation of a multiresistant subtype AG reverse transcriptase: AZT resistance, sensitivity to RNase H inhibitors and inhibitor binding Birgitta Wöhrl, Anna Schneider, Angela Corona, Imke Spöring, Mareike Jordan, Bernd Buchholz, Elias Maccioni, Roberto Di Santo, Jochen Bodem, Enzo Tramontano, Kristian Schweimer P73 Insigths into the acetylation pattern of HDAC inhibitors and their potential role in HIV therapy Christian Schölz, Brian Weinert, Sebastian Wagner, Petra Beli, Yasuyuki Miyake, Jun Qi, Lars Jensen, Werner Streicher, Anna McCarthy, Nicholas Westwood, Sonia Lain, Jürgen Cox, Patrick Matthias, Matthias Mann, James Bradner, Chunaram Choudhary P74 HPV-derived and seminal amyloid peptides enhance HIV-1 infection and impair the efficacy of broadly neutralising antibodies and antiretroviral drugs Marcel Stern, Oliver T. Keppler P75 D(−)lentiginosine inhibits both proliferation and virus expression in cells infected by HTLV-1 in vitro Elena Valletta, Caterina Frezza, Claudia Matteucci, Francesca Marino-Merlo, Sandro Grelli, Anna Lucia Serafino, Antonio Mastino, Beatrice Macchi P76 HIV-1 resistance analyses of the Cape Winelands districts, South Africa Sello Mikasi, Graeme Jacobs, Susan Engelbrecht Topic 10: Recent advances in HIV vaccine development P77 Induction of complex retrovirus antigen-specific immune responses by adenovirus-based vectors depends on the order of vector administration Meike Kaulfuß, Sonja Windmann, Wibke Bayer P78 Direct impact of structural properties of HIV-1 Env on the regulation of the humoral immune response Rebecca Heß, Michael Storcksdieck gen. Bonsmann, Viktoria Stab, Carsten Kirschning, Bernd Lepenies, Matthias Tenbusch, Klaus Überla P79 Lentiviral virus-like particles mediate gerenration of T-follicular helper cells in vitro Anne Kolenbrander, Klaus Überla, Vladimir Temchura P80 Recruitment of HIV-1 Vpr to DNA damage sites and protection of proviral DNA from nuclease activity Kenta Iijima, Junya Kobayashi, Yukihito Ishizaka
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Neves F, Abrantes J, Esteves PJ. Evolution of CCL11: genetic characterization in lagomorphs and evidence of positive and purifying selection in mammals. Innate Immun 2016; 22:336-43. [PMID: 27189425 DOI: 10.1177/1753425916647471] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/06/2016] [Indexed: 12/27/2022] Open
Abstract
The interactions between chemokines and their receptors are crucial for differentiation and activation of inflammatory cells. CC chemokine ligand 11 (CCL11) binds to CCR3 and to CCR5 that in leporids underwent gene conversion with CCR2. Here, we genetically characterized CCL11 in lagomorphs (leporids and pikas). All lagomorphs have a potentially functional CCL11, and the Pygmy rabbit has a mutation in the stop codon that leads to a longer protein. Other mammals also have mutations at the stop codon that result in proteins with different lengths. By employing maximum likelihood methods, we observed that, in mammals, CCL11 exhibits both signatures of purifying and positive selection. Signatures of purifying selection were detected in sites important for receptor binding and activation. Of the three sites detected as under positive selection, two were located close to the stop codon. Our results suggest that CCL11 is functional in all lagomorphs, and that the signatures of purifying and positive selection in mammalian CCL11 probably reflect the protein's biological roles.
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Affiliation(s)
- Fabiana Neves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Vairão, Portugal UMIB/UP - Unidade Multidisciplinar de Investigação Biomédica/Universidade do Porto, Porto, Portugal
| | - Joana Abrantes
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - Pedro J Esteves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Vairão, Portugal Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal
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Alves JM, Carneiro M, Afonso S, Lopes S, Garreau H, Boucher S, Allain D, Queney G, Esteves PJ, Bolet G, Ferrand N. Levels and Patterns of Genetic Diversity and Population Structure in Domestic Rabbits. PLoS One 2015; 10:e0144687. [PMID: 26689909 PMCID: PMC4686922 DOI: 10.1371/journal.pone.0144687] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 11/23/2015] [Indexed: 11/23/2022] Open
Abstract
Over thousands of years humans changed the genetic and phenotypic composition of several organisms and in the process transformed wild species into domesticated forms. From this close association, domestic animals emerged as important models in biomedical and fundamental research, in addition to their intrinsic economical and cultural value. The domestic rabbit is no exception but few studies have investigated the impact of domestication on its genetic variability. In order to study patterns of genetic structure in domestic rabbits and to quantify the genetic diversity lost with the domestication process, we genotyped 45 microsatellites for 471 individuals belonging to 16 breeds and 13 wild localities. We found that both the initial domestication and the subsequent process of breed formation, when averaged across breeds, culminated in losses of ~20% of genetic diversity present in the ancestral wild population and domestic rabbits as a whole, respectively. Despite the short time elapsed since breed diversification we uncovered a well-defined structure in domestic rabbits where the FST between breeds was 22%. However, we failed to detect deeper levels of structure, probably consequence of a recent and single geographic origin of domestication together with a non-bifurcating process of breed formation, which were often derived from crosses between two or more breeds. Finally, we found evidence for intrabreed stratification that is associated with demographic and selective causes such as formation of strains, colour morphs within the same breed, or country/breeder of origin. These additional layers of population structure within breeds should be taken into account in future mapping studies.
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Affiliation(s)
- Joel M. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- * E-mail:
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
| | - Susana Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
| | - Hervé Garreau
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
| | | | - Daniel Allain
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
| | | | - Pedro J. Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra, Portugal
| | - Gerard Bolet
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
| | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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Neves F, Abrantes J, Almeida T, de Matos AL, Costa PP, Esteves PJ. Genetic characterization of interleukins (IL-1α, IL-1β, IL-2, IL-4, IL-8, IL-10, IL-12A, IL-12B, IL-15 and IL-18) with relevant biological roles in lagomorphs. Innate Immun 2015; 21:787-801. [PMID: 26395994 PMCID: PMC4609935 DOI: 10.1177/1753425915606209] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/17/2015] [Indexed: 12/11/2022] Open
Abstract
ILs, as essential innate immune modulators, are involved in an array of biological processes. In the European rabbit (Oryctolagus cuniculus) IL-1α, IL-1β, IL-2, IL-4, IL-8, IL-10, IL-12A, IL-12B, IL-15 and IL-18 have been implicated in inflammatory processes and in the immune response against rabbit hemorrhagic disease virus and myxoma virus infections. In this study we characterized these ILs in six Lagomorpha species (European rabbit, pygmy rabbit, two cottontail rabbit species, European brown hare and American pika). Overall, these ILs are conserved between lagomorphs, including in their exon/intron structure. Most differences were observed between leporids and American pika. Indeed, when comparing both, some relevant differences were observed in American pika, such as the location of the stop codon in IL-1α and IL-2, the existence of a different transcript in IL8 and the number of cysteine residues in IL-1β. Changes at N-glycosylation motifs were also detected in IL-1, IL-10, IL-12B and IL-15. IL-1α is the protein that presents the highest evolutionary distances, which is in contrast to IL-12A where the distances between lagomorphs are the lowest. For all these ILs, sequences of human and European rabbit are more closely related than between human and mouse or European rabbit and mouse.
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Affiliation(s)
- Fabiana Neves
- CIBIO, InBIO-Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Vairão, Portugal UMIB/UP-Unidade Multidisciplinar de Investigação Biomédica/Universidade do Porto, Porto, Portugal
| | - Joana Abrantes
- CIBIO, InBIO-Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - Tereza Almeida
- CIBIO, InBIO-Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - Ana Lemos de Matos
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Paulo P Costa
- UMIB/UP-Unidade Multidisciplinar de Investigação Biomédica/Universidade do Porto, Porto, Portugal Departmento Genética, CSPGF, Instituto Nacional de Saúde Dr. Ricardo Jorge, Porto, Portugal
| | - Pedro J Esteves
- CIBIO, InBIO-Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Vairão, Portugal Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal CITS-Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal
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Magalhães V, Abrantes J, Munõz-Pajares AJ, Esteves PJ. Genetic diversity comparison of the DQA gene in European rabbit (Oryctolagus cuniculus) populations. Immunogenetics 2015; 67:579-90. [PMID: 26307416 DOI: 10.1007/s00251-015-0866-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/13/2015] [Indexed: 10/23/2022]
Abstract
The European rabbit (Oryctolagus cuniculus) natural populations within the species native region, the Iberian Peninsula, are considered a reservoir of genetic diversity. Indeed, the Iberia was a Pleistocene refuge to the species and currently two subspecies are found in the peninsula (Oryctolagus cuniculus cuniculus and Oryctolagus cuniculus algirus). The genes of the major histocompatibility complex (MHC) have been substantially studied in wild populations due to their exceptional variability, believed to be pathogen driven. They play an important function as part of the adaptive immune system affecting the individual fitness and population viability. In this study, the MHC variability was assessed by analysing the exon 2 of the DQA gene in several European rabbit populations from Portugal, Spain and France and in domestic breeds. Twenty-eight DQA alleles were detected, among which 18 are described for the first time. The Iberian rabbit populations are well differentiated from the French population and domestic breeds. The Iberian populations retained the higher allelic diversity with the domestic breeds harbouring the lowest; in contrast, the DQA nucleotide diversity was higher in the French population. Signatures of positive selection were detected in four codons which are putative peptide-binding sites and have been previously detected in other mammals. The evolutionary relationships showed instances of trans-species polymorphism. Overall, our results suggest that the DQA in European rabbits is evolving under selection and genetic drift.
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Affiliation(s)
- Vanessa Magalhães
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Joana Abrantes
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Antonio Jesús Munõz-Pajares
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Pedro J Esteves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal. .,Centro de Investigação em Tecnologias da Saúde (CITS), ISPN, CESPU, Gandra, Portugal.
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Almeida T, Lopes AM, Magalhães MJ, Neves F, Pinheiro A, Gonçalves D, Leitão M, Esteves PJ, Abrantes J. Tracking the evolution of the G1/RHDVb recombinant strains introduced from the Iberian Peninsula to the Azores islands, Portugal. Infection, Genetics and Evolution 2015; 34:307-13. [DOI: 10.1016/j.meegid.2015.07.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 07/06/2015] [Accepted: 07/08/2015] [Indexed: 11/25/2022]
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Lemos de Matos A, de Sousa-Pereira P, Lissovsky AA, van der Loo W, Melo-Ferreira J, Cui J, Esteves PJ. Endogenization of mouse mammary tumor virus (MMTV)-like elements in genomes of pikas (Ochotona sp.). Virus Res 2015; 210:22-6. [PMID: 26151606 DOI: 10.1016/j.virusres.2015.06.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 06/24/2015] [Accepted: 06/25/2015] [Indexed: 11/29/2022]
Abstract
Despite the finding in European rabbit and other leporid genomes of the first ever described endogenous lentivirus and of a European rabbit exclusive endogenous gammaretrovirus, until now no exogenous retroviruses have been isolated in Lagomorpha species. Nevertheless, looking for the presence of endogenous retroviruses (ERVs) in the species genomes could lead to the discovery of retroviral lineages yet to be found in Lagomorpha. Different mammalian genomes harbor endogenous viral sequences phylogenetically close to the betaretrovirus mouse mammary tumor virus (MMTV), propelling us to look for such retroviral "fossil" in American pika (Ochotona princeps) and European rabbit (Oryctolagus cuniculus) genomes. By performing genomic mining using MMTV gag and LTR as query sequences, we found that such viral elements were absent from the European rabbit genome. Oppositely, significant matches were found in American pika, and more importantly, a nearly complete MMTV-like virus (Pika-BERV) was identified. Using Pika-BERV gag and LTR as templates, we found similar sequences endogenized in different pika (Ochotona sp.) species. The orthology of the LTR flanking region between some pika species supported shared ancestry of specific endogenous betaretroviruses, while in other pika species similar sequences, but not orthologous, should have resulted from independent insertions. Our study supports the possible existence of infecting exogenous betaretroviruses for a long term, after the divergence of Ochotonidae from Leporidae, but yet to be identified.
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Affiliation(s)
- Ana Lemos de Matos
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
| | - Patrícia de Sousa-Pereira
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Andrey A Lissovsky
- Zoological Museum, Moscow State Lomonosov University, 125009, B. Nikitskaya 6, Moscow, Russia
| | - Wessel van der Loo
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - José Melo-Ferreira
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
| | - Jie Cui
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Pedro J Esteves
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; CITS - Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, 4585-116 Gandra, Portugal.
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Pinheiro A, Woof JM, Almeida T, Abrantes J, Alves PC, Gortázar C, Esteves PJ. Leporid immunoglobulin G shows evidence of strong selective pressure on the hinge and CH3 domains. Open Biol 2015; 4:140088. [PMID: 25185680 PMCID: PMC4185434 DOI: 10.1098/rsob.140088] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Immunoglobulin G (IgG) is the predominant serum immunoglobulin and has the longest serum half-life of all the antibody classes. The European rabbit IgG has been of significant importance in immunological research, and is therefore well characterized. However, the IgG of other leporids has been disregarded. To evaluate the evolution of this gene in leporids, we sequenced the complete IGHG for six other genera: Bunolagus, Brachylagus, Lepus, Pentalagus, Romerolagus and Sylvilagus. The newly sequenced leporid IGHG gene has an organization and structure similar to that of the European rabbit IgG. A gradient in leporid IgG constant domain diversity was observed, with the CH1 being the most conserved and the CH3 the most variable domain. Positive selection was found to be acting on all constant domains, but with a greater incidence in the CH3 domain, where a cluster of three positively selected sites was identified. In the hinge region, only three polymorphic positions were observed. The same hinge length was observed for all leporids. Unlike the variation observed for the European rabbit, all 11 Lepus species studied share exactly the same hinge motif, suggesting its maintenance as a result of an advantageous structure or conformation.
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Affiliation(s)
- Ana Pinheiro
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal SaBio IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real 13071, Spain
| | - Jenny M Woof
- Division of Cancer Research, Medical Research Institute, University of Dundee Medical School, Ninewells Hospital, Dundee DD1 9SY, UK
| | - Tereza Almeida
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Joana Abrantes
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Paulo C Alves
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT 59812, USA
| | - Christian Gortázar
- SaBio IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real 13071, Spain
| | - Pedro J Esteves
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra PRD, Portugal
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50
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de Sousa-Pereira P, Cova M, Abrantes J, Ferreira R, Trindade F, Barros A, Gomes P, Colaço B, Amado F, Esteves PJ, Vitorino R. Cross-species comparison of mammalian saliva using an LC-MALDI based proteomic approach. Proteomics 2015; 15:1598-607. [PMID: 25641928 DOI: 10.1002/pmic.201400083] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 12/01/2014] [Accepted: 01/13/2015] [Indexed: 01/31/2023]
Abstract
Despite the importance of saliva in the regulation of oral cavity homeostasis, few studies have been conducted to quantitatively compare the saliva of different mammal species. Aiming to define a proteome signature of mammals' saliva, an in-depth SDS-PAGE-LC coupled to MS/MS (GeLC-MS/MS) approach was used to characterize the saliva from primates (human), carnivores (dog), glires (rat and rabbit), and ungulates (sheep, cattle, horse). Despite the high variability in the number of distinct proteins identified per species, most protein families were shared by the mammals studied with the exception of cattle and horse. Alpha-amylase is an example that seems to reflect the natural selection related to digestion efficacy and food recognition. Casein protein family was identified in all species but human, suggesting an alternative to statherin in the protection of hard tissues. Overall, data suggest that different proteins might assure a similar role in the regulation of oral cavity homeostasis, potentially explaining the specific mammals' salivary proteome signature. Moreover, some protein families were identified for the first time in the saliva of some species, the presence of proline-rich proteins in rabbit's saliva being a good example.
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Affiliation(s)
- Patrícia de Sousa-Pereira
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Vairão, Portugal
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