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Melepat B, Li T, Vinkler M. Natural selection directing molecular evolution in vertebrate viral sensors. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 154:105147. [PMID: 38325501 DOI: 10.1016/j.dci.2024.105147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 12/30/2023] [Accepted: 02/03/2024] [Indexed: 02/09/2024]
Abstract
Diseases caused by pathogens contribute to molecular adaptations in host immunity. Variety of viral pathogens challenging animal immunity can drive positive selection diversifying receptors recognising the infections. However, whether distinct virus sensing systems differ across animals in their evolutionary modes remains unclear. Our review provides a comparative overview of natural selection shaping molecular evolution in vertebrate viral-binding pattern recognition receptors (PRRs). Despite prevailing negative selection arising from the functional constraints, multiple lines of evidence now suggest diversifying selection in the Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-I-like receptors (RLRs) and oligoadenylate synthetases (OASs). In several cases, location of the positively selected sites in the ligand-binding regions suggests effects on viral detection although experimental support is lacking. Unfortunately, in most other PRR families including the AIM2-like receptor family, C-type lectin receptors (CLRs), and cyclic GMP-AMP synthetase studies characterising their molecular evolution are rare, preventing comparative insight. We indicate shared characteristics of the viral sensor evolution and highlight priorities for future research.
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Affiliation(s)
- Balraj Melepat
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, EU, Czech Republic
| | - Tao Li
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, EU, Czech Republic
| | - Michal Vinkler
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, EU, Czech Republic.
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Stejskalova K, Janova E, Splichalova P, Futas J, Oppelt J, Vodicka R, Horin P. Twelve toll-like receptor (TLR) genes in the family Equidae - comparative genomics, selection and evolution. Vet Res Commun 2024; 48:725-741. [PMID: 37874499 PMCID: PMC10998774 DOI: 10.1007/s11259-023-10245-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/18/2023] [Indexed: 10/25/2023]
Abstract
Toll-like receptors (TLRs) represent an important part of the innate immune system. While human and murine TLRs have been intensively studied, little is known about TLRs in non-model species. The order Perissodactyla comprises a variety of free-living and domesticated species exposed to different pathogens in different habitats and is therefore suitable for analyzing the diversity and evolution of immunity-related genes. We analyzed TLR genes in the order Perissodactyla with a focus on the family Equidae. Twelve TLRs were identified by bioinformatic analyses of online genomic resources; their sequences were confirmed in equids by genomic DNA re-sequencing of a panel of nine species. The expression of TLR11 and TLR12 was confirmed in the domestic horse by cDNA sequencing. Phylogenetic reconstruction of the TLR gene family in Perissodactyla identified six sub-families. TLR4 clustered together with TLR5; the TLR1-6-10 subfamily showed a high degree of sequence identity. The average estimated evolutionary divergence of all twelve TLRs studied was 0.3% among the Equidae; the most divergent CDS were those of Equus caballus and Equus hemionus kulan (1.34%) in the TLR3, and Equus africanus somaliensis and Equus quagga antiquorum (2.1%) in the TLR1 protein. In each TLR gene, there were haplotypes shared between equid species, most extensively in TLR3 and TLR9 CDS, and TLR6 amino acid sequence. All twelve TLR genes were under strong negative overall selection. Signatures of diversifying selection in specific codon sites were detected in all TLRs except TLR8. Differences in the selection patterns between virus-sensing and non-viral TLRs were observed.
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Affiliation(s)
- K Stejskalova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
| | - E Janova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - P Splichalova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
| | - J Futas
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - J Oppelt
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
| | | | - P Horin
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic.
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic.
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Pinto-Pinho P, Soares J, Esteves P, Pinto-Leite R, Fardilha M, Colaço B. Comparative Bioinformatic Analysis of the Proteomes of Rabbit and Human Sex Chromosomes. Animals (Basel) 2024; 14:217. [PMID: 38254386 PMCID: PMC10812427 DOI: 10.3390/ani14020217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/18/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Studying proteins associated with sex chromosomes can provide insights into sex-specific proteins. Membrane proteins accessible through the cell surface may serve as excellent targets for diagnostic, therapeutic, or even technological purposes, such as sperm sexing technologies. In this context, proteins encoded by sex chromosomes have the potential to become targets for X- or Y-chromosome-bearing spermatozoa. Due to the limited availability of proteomic studies on rabbit spermatozoa and poorly annotated databases for rabbits compared to humans, a bioinformatic analysis of the available rabbit X chromosome proteome (RX), as well as the human X (HX) and Y (HY) chromosomes proteome, was conducted to identify potential targets that could be accessible from the cell surface and predict which of the potential targets identified in humans might also exist in rabbits. We identified 100, 211, and 3 proteins associated with the plasma membrane or cell surface for RX, HX, and HY, respectively, of which 61, 132, and 3 proteins exhibit potential as targets as they were predicted to be accessible from the cell surface. Cross-referencing the potential HX targets with the rabbit proteome revealed an additional 60 proteins with the potential to be RX targets, resulting in a total of 121 potential RX targets. In addition, at least 53 possible common HX and RX targets have been previously identified in human spermatozoa, emphasizing their potential as targets of X-chromosome-bearing spermatozoa. Further proteomic studies on rabbit sperm will be essential to identify and validate the usefulness of these proteins for application in rabbit sperm sorting techniques as targets of X-chromosome-bearing spermatozoa.
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Affiliation(s)
- Patrícia Pinto-Pinho
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal;
- Laboratory of Signal Transduction, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal;
- Laboratory of Genetics and Andrology, Hospital Center of Trás-os-Montes and Alto Douro, E.P.E., 5000-508 Vila Real, Portugal;
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center, Portuguese Institute of Oncology of Porto Francisco Gentil, E.P.E., 4200-072 Porto, Portugal
| | - João Soares
- Department of Computer Science, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal; (J.S.); (P.E.)
- Center for Research in Advanced Computing Systems, Institute for Systems and Computer Engineering, Technology and Science (CRACS—INESC TEC), 4150-179 Porto, Portugal
| | - Pedro Esteves
- Department of Computer Science, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal; (J.S.); (P.E.)
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
- CIBIO—Research Centre in Biodiversity and Genetic Resources, InBIO Associate Laboratory, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Research Centre in Biodiversity and Genetic Resources, 4485-661 Vairão, Portugal
| | - Rosário Pinto-Leite
- Laboratory of Genetics and Andrology, Hospital Center of Trás-os-Montes and Alto Douro, E.P.E., 5000-508 Vila Real, Portugal;
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center, Portuguese Institute of Oncology of Porto Francisco Gentil, E.P.E., 4200-072 Porto, Portugal
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Bruno Colaço
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal;
- Animal and Veterinary Research Centre, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal
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Pinto-Pinho P, Ferreira AF, Pinto-Leite R, Fardilha M, Colaço B. The History and Prospects of Rabbit Sperm Sexing. Vet Sci 2023; 10:509. [PMID: 37624296 PMCID: PMC10459625 DOI: 10.3390/vetsci10080509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Sperm sex selection is a longstanding challenge in the field of animal reproduction. The cuniculture industry, in particular producers of males or females for breeding purposes, would greatly benefit from the pre-selection of the offspring's sex. This review article overviews the current and future developments in rabbit sperm sexing technologies, as well as the implications of implementing these methodologies in cuniculture. The first attempts of sperm sexing were performed in rabbits; however, a both efficient and cost-effective methodology was not yet developed for this species. Those included sperm sexing according to differences in sperm density, surface electric charge, pH susceptibility, antisera reaction, and flow cytometry. Separation by flow cytometry has proven to be efficient in rabbits, yielding fractions with approximately 81% and 86% purity for X- and Y-sperm, respectively. However, it is not cost-effective for cuniculture and decreases sperm quality. The advantages, limitations, and practical considerations of each method are presented, highlighting their applicability and efficiency. Furthermore, herein we explore the potential of immunological-based techniques that overcome some of the limitations of earlier methods, as well as recent advancements in sperm sexing technologies in other animal models, which could be applied to rabbits. Finally, the challenges associated with the development and widespread implementation of rabbit sperm sexing technologies are addressed. By understanding the advantages and limitations of existing and emerging methods, researchers can direct their efforts towards the most promising directions, ultimately contributing to a more efficient, profitable, and sustainable cuniculture.
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Affiliation(s)
- Patrícia Pinto-Pinho
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal;
- Laboratory of Signal Transduction, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal;
- Laboratory of Genetics and Andrology, Hospital Center of Trás-os-Montes and Alto Douro, E.P.E, 5000-508 Vila Real, Portugal;
- Experimental Pathology and Terapeutics Group, IPO Porto Research Center, Portuguese Institute of Oncology of Porto Francisco Gentil, E.P.E., 4200-072 Porto, Portugal
| | - Ana F. Ferreira
- Animal and Veterinary Research Centre, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal;
| | - Rosário Pinto-Leite
- Laboratory of Genetics and Andrology, Hospital Center of Trás-os-Montes and Alto Douro, E.P.E, 5000-508 Vila Real, Portugal;
- Experimental Pathology and Terapeutics Group, IPO Porto Research Center, Portuguese Institute of Oncology of Porto Francisco Gentil, E.P.E., 4200-072 Porto, Portugal
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Bruno Colaço
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal;
- Animal and Veterinary Research Centre, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, 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: 0.3] [Reference Citation Analysis] [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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