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Fryssouli V, Polemis E, Typas MA, Zervakis GI. Revisiting the phylogeny and taxonomy of the genus Sidera (Hymenochaetales, Basidiomycota) with particular emphasis on S.vulgaris. MycoKeys 2024; 105:119-137. [PMID: 38752164 PMCID: PMC11094396 DOI: 10.3897/mycokeys.105.121601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/01/2024] [Indexed: 05/18/2024] Open
Abstract
The genus Sidera (Hymenochaetales, Basidiomycota) comprises white-rot, mono- or dimitic fungi with poroid or hydnoid hymenophore. It has a worldwide distribution albeit with fewer species present in the Southern Hemisphere. Although recent studies revealed the existence of several new Sidera species, there are still taxonomic inconsistencies and obscure phylogenetic relationships amongst certain taxa of the genus. In this work, a large number of Sidera collections were used to obtain an updated phylogeny, based on ITS and 28S rDNA sequences by including new material from Mediterranean Europe. The monophyly of the genus was strongly supported and all species with poroid hymenophore formed a highly-supported lineage with two major subclades. In total, 23 putative species were recognised. Amongst those, five are considered to possibly represent entities new to science, but further work is required since they are represented by single specimens or environmental sequences. Examined collections originally named S.lenis from southern Europe were grouped within S.vulgaris. Similarly, several collections under various names were hereby identified as S.vulgaris, including those of the recently described species S.tibetica. Furthermore, a critical discussion (based on morphoanatomical findings) is made on the key features that could be used to distinguish S.lenis from S.vulgaris.
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Affiliation(s)
- Vassiliki Fryssouli
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, GreeceAgricultural University of AthensAthensGreece
| | - Elias Polemis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, GreeceAgricultural University of AthensAthensGreece
| | - Milton A. Typas
- National and Kapodistrian University of Athens, Department of Genetics and Biotechnology, Faculty of Biology, Panepistemiopolis, Athens 15701, GreeceNational and Kapodistrian University of AthensAthensGreece
| | - Georgios I. Zervakis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, GreeceAgricultural University of AthensAthensGreece
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2
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Walt HK, King JG, Sheele JM, Meyer F, Pietri JE, Hoffmann FG. Do bed bugs transmit human viruses, or do humans spread bed bugs and their viruses? A worldwide survey of the bed bug RNA virosphere. Virus Res 2024; 343:199349. [PMID: 38431055 PMCID: PMC10982078 DOI: 10.1016/j.virusres.2024.199349] [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: 11/07/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
BED BUGS: (Hemiptera: Cimicidae) are a globally distributed hematophagous pest that routinely feed on humans. Unlike many blood-sucking arthropods, they have never been linked to pathogen transmission in a natural setting, and despite increasing interest in their role as disease vectors, little is known about the viruses that bed bugs naturally harbor. Here, we present a global-scale survey of the bed bug RNA virosphere. We sequenced the metatranscriptomes of 22 individual bed bugs (Cimex lectularius and Cimex hemipterus) from 8 locations around the world. We detected sequences from two known bed bug viruses (Shuangao bedbug virus 1 and Shuangao bedbug virus 2) which extends their geographical range. We identified three novel bed bug virus sequences from a tenui-like virus (Bunyavirales), a toti-like virus (Ghabrivirales), and a luteo-like virus (Tolivirales). Interestingly, some of the bed bug viruses branch near to insect-transmitted plant-infecting viruses, opening questions regarding the evolution of plant virus infection. When we analyzed the viral sequences by their host's collection location, we found unexpected patterns of geographical diversity that may reflect humans' role in bed bug dispersal. Additionally, we investigated the effect that Wolbachia, the primary bed bug endosymbiont, may have on viral abundance and found that Wolbachia infection neither promotes nor inhibits viral infection. Finally, our results provide no evidence that bed bugs transmit any known human pathogenic viruses.
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Affiliation(s)
- Hunter K Walt
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Jonas G King
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Johnathan M Sheele
- Department of Emergency Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University, Cleveland, OH, USA
| | - Florencia Meyer
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Jose E Pietri
- Sanford School of Medicine, Division of Basic Biomedical Sciences, University of South Dakota, Vermillion, SD, USA.
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, USA.
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3
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Gerdes K. Diverse genetic contexts of HicA toxin domains propose a role in anti-phage defense. mBio 2024; 15:e0329323. [PMID: 38236063 PMCID: PMC10865869 DOI: 10.1128/mbio.03293-23] [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: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Toxin-antitoxin (TA) modules are prevalent in prokaryotic genomes, often in substantial numbers. For instance, the Mycobacterium tuberculosis genome alone harbors close to 100 TA modules, half of which belong to a singular type. Traditionally ascribed multiple biological roles, recent insights challenge these notions and instead indicate a predominant function in phage defense. TAs are often located within Defense Islands, genomic regions that encode various defense systems. The analysis of genes within Defense Islands has unveiled a wide array of systems, including TAs that serve in anti-phage defense. Prokaryotic cells are equipped with anti-phage Viperins that, analogous to their mammalian counterparts, inhibit viral RNA transcription. Additionally, bacterial Structural Maintenance of Chromosome (SMC) proteins combat plasmid intrusion by recognizing foreign DNA signatures. This study undertakes a comprehensive bioinformatics analysis of genetic elements encoding the HicA double-stranded RNA-binding domain, complemented by protein structure modeling. The HicA toxin domains are found in at least 14 distinct contexts and thus exhibit a remarkable genetic diversity. Traditional bicistronic TA operons represent eight of these contexts, while four are characterized by monocistronic operons encoding fused HicA domains. Two contexts involve hicA adjacent to genes that encode bacterial Viperins. Notably, genes encoding RelE toxins are also adjacent to Viperin genes in some instances. This configuration hints at a synergistic enhancement of Viperin-mediated anti-phage action by HicA and RelE toxins. The discovery of a HicA domain merged with an SMC domain is compelling, prompting further investigation into its potential roles.IMPORTANCEProkaryotic organisms harbor a multitude of toxin-antitoxin (TA) systems, which have long puzzled scientists as "genes in search for a function." Recent scientific advancements have shed light on the primary role of TAs as anti-phage defense mechanisms. To gain an overview of TAs it is important to analyze their genetic contexts that can give hints on function and guide future experimental inquiries. This article describes a thorough bioinformatics examination of genes encoding the HicA toxin domain, revealing its presence in no fewer than 14 unique genetic arrangements. Some configurations notably align with anti-phage activities, underscoring potential roles in microbial immunity. These insights robustly reinforce the hypothesis that HicA toxins are integral components of the prokaryotic anti-phage defense repertoire. The elucidation of these genetic contexts not only advances our understanding of TAs but also contributes to a paradigm shift in how we perceive their functionality within the microbial world.
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Affiliation(s)
- Kenn Gerdes
- Kenn Gerdes is an independent researcher with the residence, Voldmestergade, Copenhagen, Denmark
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Nedvědová Š, De Stefano D, Walker O, Hologne M, Miele AE. Revisiting Schistosoma mansoni Micro-Exon Gene (MEG) Protein Family: A Tour into Conserved Motifs and Annotation. Biomolecules 2023; 13:1275. [PMID: 37759676 PMCID: PMC10526429 DOI: 10.3390/biom13091275] [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: 07/20/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Genome sequencing of the human parasite Schistosoma mansoni revealed an interesting gene superfamily, called micro-exon gene (meg), that encodes secreted MEG proteins. The genes are composed of short exons (3-81 base pairs) regularly interspersed with long introns (up to 5 kbp). This article recollects 35 S. mansoni specific meg genes that are distributed over 7 autosomes and one pair of sex chromosomes and that code for at least 87 verified MEG proteins. We used various bioinformatics tools to produce an optimal alignment and propose a phylogenetic analysis. This work highlighted intriguing conserved patterns/motifs in the sequences of the highly variable MEG proteins. Based on the analyses, we were able to classify the verified MEG proteins into two subfamilies and to hypothesize their duplication and colonization of all the chromosomes. Together with motif identification, we also proposed to revisit MEGs' common names and annotation in order to avoid duplication, to help the reproducibility of research results and to avoid possible misunderstandings.
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Affiliation(s)
- Štěpánka Nedvědová
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
- Department of Chemistry, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 16500 Prague, Czech Republic
- Department of Zoology and Fisheries, Center of Infectious Animal Diseases, Czech University of Life Sciences, 16500 Prague, Czech Republic
| | - Davide De Stefano
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
| | - Olivier Walker
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
| | - Maggy Hologne
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
| | - Adriana Erica Miele
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
- Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy
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Queiroz JPF, Lourenzoni MR, Rocha BAM. Structural evolution of an amphibian-specific globin: A computational evolutionary biochemistry approach. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101055. [PMID: 36566682 DOI: 10.1016/j.cbd.2022.101055] [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: 07/29/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Studies on the globin family are continuously revealing insights into the mechanisms of gene and protein evolution. The rise of a new globin gene type in Pelobatoidea and Neobatrachia (Amphibia:Anura) from an α-globin precursor provides the opportunity to investigate the genetic and physical mechanisms underlying the origin of new protein structural and functional properties. This amphibian-specific globin (globin A/GbA) discovered in the heart of Rana catesbeiana is a monomer. As the ancestral oligomeric state of α-globins is a homodimer, we inferred that the ancestral state was lost somewhere in the GbA lineage. Here, we combined computational molecular evolution with structural bioinformatics to determine the extent to which the loss of the homodimeric state is pervasive in the GbA clade. We also characterized the loci of GbA genes in Bufo bufo. We found two GbA clades in Neobatrachia. One was deleted in Ranidae, but retained and expanded to yield a new globin cluster in Bufonidae species. Loss of the ancestral oligomeric state seems to be pervasive in the GbA clade. However, a taxonomic sampling that includes more Pelobatoidea, as well as early Neobatrachia, lineages would be necessary to determine the oligomeric state of the last common ancestor of all GbA. The evidence presented here points out a possible loss of oligomerization in Pelobatoidea GbA as a result of amino acid substitutions that weaken the homodimeric state. In contrast, the loss of oligomerization in both Neobatrachia GbA clades was linked to independent deletions that disrupted many packing contacts at the homodimer interface.
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Affiliation(s)
- João Pedro Fernandes Queiroz
- Laboratorio de Biocristalografia - LABIC, Departamento de Bioquimica e Biologia Molecular, Universidade Federal do Ceara, Campus do Pici s.n., bloco 907, Av. Mister Hull, Fortaleza, Ceara, 60440-970, Brazil.
| | - Marcos Roberto Lourenzoni
- Protein Engineering and Health Solutions Group - GEPeSS Fundacao Oswaldo Cruz - Ceara, Eusébio, Ceara, 60175-047, Brazil.
| | - Bruno Anderson Matias Rocha
- Laboratorio de Biocristalografia - LABIC, Departamento de Bioquimica e Biologia Molecular, Universidade Federal do Ceara, Campus do Pici s.n., bloco 907, Av. Mister Hull, Fortaleza, Ceara, 60440-970, Brazil.
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6
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Joyce W, Ripley DM, Gillis T, Black AC, Shiels HA, Hoffmann FG. A Revised Perspective on the Evolution of Troponin I and Troponin T Gene Families in Vertebrates. Genome Biol Evol 2022; 15:6904147. [PMID: 36518048 PMCID: PMC9825255 DOI: 10.1093/gbe/evac173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 11/29/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
The troponin (Tn) complex, responsible for the Ca2+ activation of striated muscle, is composed of three interacting protein subunits: TnC, TnI, and TnT, encoded by TNNC, TNNI, and TNNT genes. TNNI and TNNT are sister gene families, and in mammals the three TNNI paralogs (TNNI1, TNNI2, TNNI3), which encode proteins with tissue-specific expression, are each in close genomic proximity with one of the three TNNT paralogs (TNNT2, TNNT3, TNNT1, respectively). It has been widely presumed that all vertebrates broadly possess genes of these same three classes, although earlier work has overlooked jawless fishes (cyclostomes) and cartilaginous fishes (chimeras, rays, and sharks), which are distantly related to other jawed vertebrates. With a new phylogenetic and synteny analysis of a diverse array of vertebrates including these taxonomic groups, we define five distinct TNNI classes (TNNI1-5), with TNNI4 and TNNI5 being only present in non-amniote vertebrates and typically found in tandem, and four classes of TNNT (TNNT1-4). These genes are located in four genomic loci that were generated by the 2R whole-genome duplications. TNNI3, encoding "cardiac TnI" in tetrapods, was independently lost in cartilaginous and ray-finned fishes. Instead, ray-finned fishes predominantly express TNNI1 in the heart. TNNI5 is highly expressed in shark hearts and contains a N-terminal extension similar to that of TNNI3 found in tetrapod hearts. Given that TNNI3 and TNNI5 are distantly related, this supports the hypothesis that the N-terminal extension may be an ancestral feature of vertebrate TNNI and not an innovation unique to TNNI3, as has been commonly believed.
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Affiliation(s)
| | - Daniel M Ripley
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Todd Gillis
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Amanda Coward Black
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, Mississippi 39762, USA
| | - Holly A Shiels
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, United Kingdom
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Petrov PB, Awoniyi LO, Šuštar V, Balci MÖ, Mattila PK. AutoCoEv—A High-Throughput In Silico Pipeline for Predicting Inter-Protein Coevolution. Int J Mol Sci 2022; 23:ijms23063351. [PMID: 35328772 PMCID: PMC8952222 DOI: 10.3390/ijms23063351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022] Open
Abstract
Protein–protein interactions govern cellular processes via complex regulatory networks, which are still far from being understood. Thus, identifying and understanding connections between proteins can significantly facilitate our comprehension of the mechanistic principles of protein functions. Coevolution between proteins is a sign of functional communication and, as such, provides a powerful approach to search for novel direct or indirect molecular partners. However, an evolutionary analysis of large arrays of proteins in silico is a highly time-consuming effort that has limited the usage of this method for protein pairs or small protein groups. Here, we developed AutoCoEv, a user-friendly, open source, computational pipeline for the search of coevolution between a large number of proteins. By driving 15 individual programs, culminating in CAPS2 as the software for detecting coevolution, AutoCoEv achieves a seamless automation and parallelization of the workflow. Importantly, we provide a patch to the CAPS2 source code to strengthen its statistical output, allowing for multiple comparison corrections and an enhanced analysis of the results. We apply the pipeline to inspect coevolution among 324 proteins identified to be located at the vicinity of the lipid rafts of B lymphocytes. We successfully detected multiple coevolutionary relations between the proteins, predicting many novel partners and previously unidentified clusters of functionally related molecules. We conclude that AutoCoEv, can be used to predict functional interactions from large datasets in a time- and cost-efficient manner.
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Affiliation(s)
- Petar B. Petrov
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20014 Turku, Finland; (L.O.A.); (V.Š.); (M.Ö.B.)
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- Correspondence: (P.B.P.); (P.K.M.)
| | - Luqman O. Awoniyi
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20014 Turku, Finland; (L.O.A.); (V.Š.); (M.Ö.B.)
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Vid Šuštar
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20014 Turku, Finland; (L.O.A.); (V.Š.); (M.Ö.B.)
| | - M. Özge Balci
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20014 Turku, Finland; (L.O.A.); (V.Š.); (M.Ö.B.)
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Pieta K. Mattila
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20014 Turku, Finland; (L.O.A.); (V.Š.); (M.Ö.B.)
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- Correspondence: (P.B.P.); (P.K.M.)
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Liu Q, Xu Y, Zhang X, Li K, Li X, Wang F, Xu F, Dong C. Infection Process and Genome Assembly Provide Insights into the Pathogenic Mechanism of Destructive Mycoparasite Calcarisporium cordycipiticola with Host Specificity. J Fungi (Basel) 2021; 7:918. [PMID: 34829206 PMCID: PMC8620734 DOI: 10.3390/jof7110918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 11/21/2022] Open
Abstract
Calcarisporium cordycipiticola is the pathogen in the white mildew disease of Cordyceps militaris, one of the popular mushrooms. This disease frequently occurs and there is no effective method for disease prevention and control. In the present study, C. militaris is found to be the only host of C. cordycipiticola, indicating strict host specificity. The infection process was monitored by fluorescent labeling and scanning and transmission electron microscopes. C. cordycipiticola can invade into the gaps among hyphae of the fruiting bodies of the host and fill them gradually. It can degrade the hyphae of the host by both direct contact and noncontact. The parasitism is initially biotrophic, and then necrotrophic as mycoparasitic interaction progresses. The approximate chromosome-level genome assembly of C. cordycipiticola yielded an N50 length of 5.45 Mbp and a total size of 34.51 Mbp, encoding 10,443 proteins. Phylogenomic analysis revealed that C. cordycipiticola is phylogenetically close to its specific host, C. militaris. A comparative genomic analysis showed that the number of CAZymes of C. cordycipiticola was much less than in other mycoparasites, which might be attributed to its host specificity. Secondary metabolite cluster analysis disclosed the great biosynthetic capabilities and potential mycotoxin production capability. This study provides insights into the potential pathogenesis and interaction between mycoparasite and its host.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyan Xu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
| | - Xiaoling Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
| | - Kuan Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
| | - Xiao Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fen Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
| | - Fangxu Xu
- Experimental Teaching Center, Shenyang Normal University, Shenyang 110034, China;
| | - Caihong Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
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9
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Lei Y, Yang L, Zhou Y, Wang C, Lv W, Li L, He S. Hb adaptation to hypoxia in high-altitude fishes: Fresh evidence from schizothoracinae fishes in the Qinghai-Tibetan Plateau. Int J Biol Macromol 2021; 185:471-484. [PMID: 34214574 DOI: 10.1016/j.ijbiomac.2021.06.186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/27/2021] [Indexed: 10/21/2022]
Abstract
Uncovering the genetic basis of hypoxic adaptation is one of the most active research areas in evolutionary biology. Among air-breathing vertebrates, modifications of hemoglobin (Hb) play a pivotal role in mediating an adaptive response to high-altitude hypoxia. However, the relative contributions in water-breathing organisms are still unclear. Here, we tested the Hb concentration of fish at different altitudes. All species showed species-specific Hb concentration, which has a non-positive correlation with altitude. Moreover, we investigated the expression of Hb genes by the RNA-seq and quantitative real-time PCR (qRT-PCR), and Hb composition by two-dimensional electrophoresis (2-DE). The results showed that the multiple Hb genes and isoforms are co-expressed in schizothoracinae fishes endemic to the Qinghai-Tibetan Plateau (QTP). Phylogenetic analyses of Hb genes indicated that the evolutionary relationships are not easily reconciled with the organismal phylogeny. Furthermore, evidence of positive selection was found in the Hb genes of schizothoracinae fishes through the selection pressure analysis. We demonstrated that positively selected sites likely facilitated the functional divergence of Hb isoforms. Taken together, this study indicated that the long-term maintenance of high Hb concentration may be a disadvantage for physiologically acclimating to high altitude hypoxia. Meanwhile, the genetically based modification of Hb-O2 affinity in schizothoracinae fishes might facilitate the evolutionary adaptation to Tibetan aqueous environments.
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Affiliation(s)
- Yi Lei
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhou
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqi Lv
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Li
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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10
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Yundaeng C, Nawae W, Naktang C, Shearman JR, Sonthirod C, Sangsrakru D, Yoocha T, Jomchai N, Sheedy JR, Mekiyanon S, Tuntaisong M, Pootakham W, Tangphatsornruang S. Chloroplast genome data of Luffa acutangula and Luffa aegyptiaca and their phylogenetic relationships. Data Brief 2020; 33:106470. [PMID: 33195780 PMCID: PMC7644877 DOI: 10.1016/j.dib.2020.106470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 10/26/2022] Open
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The rise and fall of globins in the amphibia. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 37:100759. [PMID: 33202310 DOI: 10.1016/j.cbd.2020.100759] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 10/23/2020] [Accepted: 10/29/2020] [Indexed: 12/28/2022]
Abstract
The globin gene repertoire of gnathostome vertebrates is dictated by differential retention and loss of nine paralogous genes: androglobin, neuroglobin, globin X, cytoglobin, globin Y, myoglobin, globin E, and the α- and β-globins. We report the globin gene repertoire of three orders of modern amphibians: Anura, Caudata, and Gymnophiona. Combining phylogenetic and conserved synteny analysis, we show that myoglobin and globin E were lost only in the Batrachia clade, but retained in Gymnophiona. The major amphibian groups also retained different paralogous copies of globin X. None of the amphibian presented αD-globin gene. Nevertheless, two clades of β-globins are present in all amphibians, indicating that the amphibian ancestor possessed two paralogous proto β-globins. We also show that orthologs of the gene coding for the monomeric hemoglobin found in the heart of Rana catesbeiana are present in Neobatrachia and Pelobatoidea species we analyzed. We suggest that these genes might perform myoglobin- and globin E-related functions. We conclude that the repertoire of globin genes in amphibians is dictated by both retention and loss of the paralogous genes cited above and the rise of a new globin gene through co-option of an α-globin, possibly facilitated by a prior event of transposition.
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Prothmann A, Hoffmann FG, Opazo JC, Herbener P, Storz JF, Burmester T, Hankeln T. The Globin Gene Family in Arthropods: Evolution and Functional Diversity. Front Genet 2020; 11:858. [PMID: 32922435 PMCID: PMC7457136 DOI: 10.3389/fgene.2020.00858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/14/2020] [Indexed: 01/23/2023] Open
Abstract
Globins are small heme-proteins that reversibly bind oxygen. Their most prominent roles in vertebrates are the transport and storage of O2 for oxidative energy metabolism, but recent research has suggested alternative, non-respiratory globin functions. In the species-rich and ecologically highly diverse taxon of arthropods, the copper-containing hemocyanin is considered the main respiratory protein. However, recent studies have suggested the presence of globin genes and their proteins in arthropod taxa, including model species like Drosophila. To systematically assess the taxonomic distribution, evolution and diversity of globins in arthropods, we systematically searched transcriptome and genome sequence data and found a conserved, widespread occurrence of three globin classes in arthropods: hemoglobin-like (HbL), globin X (GbX), and globin X-like (GbXL) protein lineages. These globin types were previously identified in protostome and deuterostome animals including vertebrates, suggesting their early ancestry in Metazoa. The HbL genes show multiple, lineage-specific gene duplications in all major arthropod clades. Some HbL genes (e.g., Glob2 and 3 of Drosophila) display particularly fast substitution rates, possibly indicating the evolution of novel functions, e.g., in spermatogenesis. In contrast, arthropod GbX and GbXL globin genes show high evolutionary stability: GbXL is represented by a single-copy gene in all arthropod groups except Brachycera, and representatives of the GbX clade are present in all examined taxa except holometabolan insects. GbX and GbXL both show a brain-specific expression. Most arthropod GbX and GbXL proteins, but also some HbL variants, include sequence motifs indicative of potential N-terminal acylation (i.e., N-myristoylation, 3C-palmitoylation). All arthropods except for the brachyceran Diptera harbor at least one such potentially acylated globin copy, confirming the hypothesis of an essential, conserved globin function associated with the cell membrane. In contrast to other animals, the fourth ancient globin lineage, represented by neuroglobin, appears to be absent in arthropods, and the putative arthropod orthologs of the fifth metazoan globin lineage, androglobin, lack a recognizable globin domain. Thus, the remarkable evolutionary stability of some globin variants is contrasted by occasional dynamic gene multiplication or even loss of otherwise strongly conserved globin lineages in arthropod phylogeny.
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Affiliation(s)
- Andreas Prothmann
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, University of Mainz, Mainz, Germany
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, MS, United States.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS, United States
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Valdivia, Chile
| | - Peter Herbener
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, University of Mainz, Mainz, Germany
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
| | | | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, University of Mainz, Mainz, Germany
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13
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Fernández R, Gabaldón T. Gene gain and loss across the metazoan tree of life. Nat Ecol Evol 2020; 4:524-533. [PMID: 31988444 PMCID: PMC7124887 DOI: 10.1038/s41559-019-1069-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/21/2019] [Indexed: 12/22/2022]
Abstract
Although recent research has revealed high genomic complexity in the earliest-splitting animals and their ancestors, the macroevolutionary trends orchestrating gene repertoire evolution throughout the animal phyla remain poorly understood. We used a phylogenomic approach to interrogate genome evolution across all animal phyla. Our analysis uncovered a bimodal distribution of recruitment of orthologous genes, with most genes gained very 'early' (that is, at deep nodes) or very 'late', representing lineage-specific acquisitions. The emergence of animals was characterized by high values of gene birth and duplications. Deuterostomes, ecdysozoans and Xenacoelomorpha were characterized by no gene gain but rampant differential gene loss. Genes considered as animal hallmarks, such as Notch/Delta, were convergently duplicated in all phyla and at different evolutionary depths. Genes duplicated in all nodes from Metazoa to phylum-specific levels were enriched in functions related to the neural system, suggesting that this system has been continuously and independently reshaped throughout evolution across animals. Our results indicate that animal genomes evolved by unparalleled gene duplication followed by differential gene loss, and provide an atlas of gene repertoire evolution throughout the animal tree of life to navigate how, when and how often each gene in each genome was gained, duplicated or lost.
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Affiliation(s)
- Rosa Fernández
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Barcelona Supercomputing Centre (BSC-CNS) and Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Barcelona Supercomputing Centre (BSC-CNS) and Institute for Research in Biomedicine (IRB), Barcelona, Spain.
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14
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Jin Y, Zhou T, Li N, Liu S, Xu X, Pan Y, Tan S, Shi H, Yang Y, Yuan Z, Wang W, Luo J, Gao D, Dunham R, Liu Z. JAK and STAT members in channel catfish: Identification, phylogenetic analysis and expression profiling after Edwardsiella ictaluri infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 81:334-341. [PMID: 29274790 DOI: 10.1016/j.dci.2017.12.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/20/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
The Janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling pathway is one of the main pleiotropic cascades used to transmit information from extracellular receptors to the nucleus, which results in DNA transcription and expression of genes involved in immunity, proliferation, differentiation, migration, apoptosis, and cell survival. Members of JAK family and STAT family have been extensively studied in different mammalian species because of their important roles in innate and adaptive immune responses. However, they have not been systematically studied among teleost fish species. In this study, five JAK family members and eight STAT family members were identified and characterized from channel catfish. Phylogenetic analysis was conducted to properly annotate these genes. Syntenic analysis was also conducted to establish orthology, and confirm the results from phylogenetic analysis. Compared to mammals, more members of the JAK and STAT family were identified in channel catfish genome. Expression of JAK and STAT family members was detected in healthy catfish tissues, but was induced in gill, liver, and intestine after bacterial challenge. Notably, the significant upregulation of STAT1b gene in catfish liver, gill and intestine after Edwardsiella ictaluri infection supported the notion that high STAT1 expression are involved in defense against pathogens. Collectively, the increased expression of JAK and STAT members in tested tissues suggested their crucial function in defending the host against pathogen invasion.
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Affiliation(s)
- Yulin Jin
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Ning Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Xiaoyan Xu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Ying Pan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Suxu Tan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Huitong Shi
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Yujia Yang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Zihao Yuan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Wenwen Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Jian Luo
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Dongya Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Rex Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Zhanjiang Liu
- Department of Biology, College of Art and Sciences, Syracuse University, Syracuse, NY 13244, USA.
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15
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Liu X, Liu Y, Huang P, Ma Y, Qing Z, Tang Q, Cao H, Cheng P, Zheng Y, Yuan Z, Zhou Y, Liu J, Tang Z, Zhuo Y, Zhang Y, Yu L, Huang J, Yang P, Peng Q, Zhang J, Jiang W, Zhang Z, Lin K, Ro DK, Chen X, Xiong X, Shang Y, Huang S, Zeng J. The Genome of Medicinal Plant Macleaya cordata Provides New Insights into Benzylisoquinoline Alkaloids Metabolism. MOLECULAR PLANT 2017; 10:975-989. [PMID: 28552780 DOI: 10.1016/j.molp.2017.05.007] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 05/19/2023]
Abstract
The overuse of antibiotics in animal agriculture and medicine has caused a series of potential threats to public health. Macleaya cordata is a medicinal plant species from the Papaveraceae family, providing a safe resource for the manufacture of antimicrobial feed additive for livestock. The active constituents from M. cordata are known to include benzylisoquinoline alkaloids (BIAs) such as sanguinarine (SAN) and chelerythrine (CHE), but their metabolic pathways have yet to be studied in this non-model plant. The active biosynthesis of SAN and CHE in M. cordata was first examined and confirmed by feeding 13C-labeled tyrosine. To gain further insights, we de novo sequenced the whole genome of M. cordata, the first to be sequenced from the Papaveraceae family. The M. cordata genome covering 378 Mb encodes 22,328 predicted protein-coding genes with 43.5% being transposable elements. As a member of basal eudicot, M. cordata genome lacks the paleohexaploidy event that occurred in almost all eudicots. From the genomics data, a complete set of 16 metabolic genes for SAN and CHE biosynthesis was retrieved, and 14 of their biochemical activities were validated. These genomics and metabolic data show the conserved BIA metabolic pathways in M. cordata and provide the knowledge foundation for future productions of SAN and CHE by crop improvement or microbial pathway reconstruction.
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Affiliation(s)
- Xiubin Liu
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha 410128, China; Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Yisong Liu
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha 410128, China; Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; Veterinary Medicine College, Hunan Agricultural University, Changsha 410128, China
| | - Peng Huang
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha 410128, China; Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Yongshuo Ma
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Zhixing Qing
- Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Qi Tang
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha 410128, China; Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Huifen Cao
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Pi Cheng
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha 410128, China; Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Yajie Zheng
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha 410128, China; Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Zejun Yuan
- Micolta Bioresource Inc., Changsha 410016, China
| | - Yuan Zhou
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China
| | - Jinfeng Liu
- Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Zhaoshan Tang
- Herbal Extract Engineering Research Center, Changsha 410331, China
| | - Yixiu Zhuo
- Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Yancong Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Linlan Yu
- Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Jialu Huang
- Veterinary Medicine College, Hunan Agricultural University, Changsha 410128, China
| | - Peng Yang
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Qiong Peng
- Biotechnology Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jinbo Zhang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Zhonghua Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Dae-Kyun Ro
- Department of Biological Sciences, University of Calgary, Calgary T2N1N4, Canada
| | - Xiaoya Chen
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Xingyao Xiong
- Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China.
| | - Yi Shang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
| | - Sanwen Huang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
| | - Jianguo Zeng
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha 410128, China; Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China.
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16
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Tan S, Yao J, Zhou T, Liu S, Yuan Z, Tian C, Li Q, Liu Z. Identification, annotation and expression analysis of 29 Rho GTPase genes from channel catfish (Ictalurus punctatus) after bacterial infections. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 67:445-451. [PMID: 27765605 DOI: 10.1016/j.dci.2016.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/14/2016] [Accepted: 10/14/2016] [Indexed: 06/06/2023]
Abstract
The Rho family GTPases are a group of small monomeric G proteins, which are molecular switches in signaling pathways. They have been known to regulate a diverse range of cellular processes including actin cytoskeleton rearrangement and microtubule dynamics. In particular, their participations in immune responses are also significant. However, little information of the Rho GTPases is available in teleost including channel catfish, an economically important species and one of the best teleost models forimmunological research. In this study, Rho GTPase genes were identified from channel catfish and well annotated by phylogenetic and syntenic analyses. Their expression profiles were determined in channel catfish healthy tissues and infected tissues. Altogether seven Rho GTPase genes were significantly regulated after bacterial infection, with six genes in the gill after Flavobacterium columnare challenge and two genes in the intestine in response to Edwardsiella ictaluri. All the differentially expressed genes were up-regulated soon after bacterial infection. Different expression patterns between the two experiments were observed, which may be attributed to tissue-specific regulation or pathogen-specific regulation. These results suggested that Rho GTPases play important roles in immune responses to bacterial pathogens, setting a foundation for future investigation on Rho GTPases.
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Affiliation(s)
- Suxu Tan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jun Yao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Zihao Yuan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Changxu Tian
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Qi Li
- The Shellfish Genetics and Breeding Laboratory, Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
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17
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Oakley MS, Verma N, Zheng H, Anantharaman V, Takeda K, Gao Y, Myers TG, Pham PT, Mahajan B, Kumar N, Sangweme D, Tripathi AK, Mlambo G, Aravind L, Kumar S. Molecular Markers of Radiation Induced Attenuation in Intrahepatic Plasmodium falciparum Parasites. PLoS One 2016; 11:e0166814. [PMID: 27911910 PMCID: PMC5135057 DOI: 10.1371/journal.pone.0166814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/04/2016] [Indexed: 11/24/2022] Open
Abstract
Experimental immunization with radiation attenuated sporozoites (RAS) and genetically attenuated sporozoites has proved to be a promising approach for malaria vaccine development. However, parasite biomarkers of growth attenuation and enhanced immune protection in response to radiation remain poorly understood. Here, we report on the effect of an attenuating dose of γ-irradiation (15 krad) on the Plasmodium falciparum sporozoite (PfSPZ) ultrastructure by electron microscopy, growth rate of liver stage P. falciparum in liver cell cultures, and genome-wide transcriptional profile of liver stage parasites by microarray. We find that γ-irradiation treated PfSPZ retained a normal cellular structure except that they were vacuous with a partially disrupted plasma membrane and inner membrane complex. A similar infection rate was observed by γ-irradiation-treated and untreated PfSPZ in human HCO-4 liver cells (0.47% versus 0.49%, respectively) on day 3 post-infection. In the microarray studies, cumulatively, 180 liver stage parasite genes were significantly transcriptionally altered on day 3 and/or 6 post-infection. Among the transcriptionally altered biomarkers, we identified a signature of seven candidate parasite genes that associated with functionally diverse pathways that may regulate radiation induced cell cycle arrest of the parasite within the hepatocyte. A repertoire of 14 genes associated with protein translation is transcriptionally overexpressed within the parasite by radiation. Additionally, 37 genes encode proteins expressed on the cell surface or exported into the host cell, 4 encode membrane associated transporters, and 10 encode proteins related to misfolding and stress-related protein processing. These results have significantly increased the repertoire of novel targets for 1) biomarkers of safety to define proper attenuation, 2) generating genetically attenuated parasite vaccine candidates, and 3) subunit candidate vaccines against liver stage malaria.
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Affiliation(s)
- Miranda S. Oakley
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States
| | - Nitin Verma
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States
| | - Hong Zheng
- Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, United States
| | - Kazuyo Takeda
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States
| | - Yamei Gao
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States
| | - Timothy G. Myers
- Genomics Technologies Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, United States
| | - Phuong Thao Pham
- Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States
| | - Babita Mahajan
- Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States
| | - Nirbhay Kumar
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States
| | - Davison Sangweme
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States
| | - Abhai K. Tripathi
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States
| | - Godfree Mlambo
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, United States
| | - Sanjai Kumar
- Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States
- * E-mail:
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18
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Pardo I, Roquet C, Lavergne S, Olesen JM, Gómez D, García MB. Spatial congruence between taxonomic, phylogenetic and functional hotspots: true pattern or methodological artefact? DIVERS DISTRIB 2016. [DOI: 10.1111/ddi.12511] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Iker Pardo
- Instituto Pirenaico de Ecología (IPE-CSIC); Zaragoza-Jaca PO Box 13034 Zaragoza Spain
| | - Cristina Roquet
- Laboratoire d’Écologie Alpine (LECA); CNRS - Université Grenoble Alpes (UMR 5553); F-38000 Grenoble France
| | - Sébastien Lavergne
- Laboratoire d’Écologie Alpine (LECA); CNRS - Université Grenoble Alpes (UMR 5553); F-38000 Grenoble France
| | - Jens M. Olesen
- Department of Bioscience; Aarhus University; Ny Munkegade Building 1540 DK-8000 Aarhus C Denmark
| | - Daniel Gómez
- Instituto Pirenaico de Ecología (IPE-CSIC); Zaragoza-Jaca PO Box 13034 Zaragoza Spain
| | - María B. García
- Instituto Pirenaico de Ecología (IPE-CSIC); Zaragoza-Jaca PO Box 13034 Zaragoza Spain
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19
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Song L, Li C, Xie Y, Liu S, Zhang J, Yao J, Jiang C, Li Y, Liu Z. Genome-wide identification of Hsp70 genes in channel catfish and their regulated expression after bacterial infection. FISH & SHELLFISH IMMUNOLOGY 2016; 49:154-162. [PMID: 26693666 DOI: 10.1016/j.fsi.2015.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 11/12/2015] [Accepted: 12/10/2015] [Indexed: 06/05/2023]
Abstract
Heat shock proteins 70/110 (Hsp70/110) are a family of conserved ubiquitously expressed heat shock proteins which are produced by cells in response to exposure to stressful conditions. Besides the chaperone and housekeeping functions, they are also known to be involved in immune response during infection. In this study, we identified 16 Hsp70/110 geness in channel catfish (Ictalurus punctatus) through in silico analysis using RNA-Seq and genome databases. Among them 12 members of Hsp70 (Hspa) family and 4 members of Hsp110 (Hsph) family were identified. Phylogenetic and syntenic analyses provided strong evidence in supporting the orthologies of these HSPs. In addition, we also determined the expression patterns of Hsp70/110 genes after Flavobacterium columnare and Edwardsiella ictaluri infections by meta-analyses, for the first time in channel catfish. Ten out of sixteen genes were significantly up/down-regulated after bacterial challenges. Specifically, nine genes were found significantly expressed in gill after F. columnare infection. Two genes were found significantly expressed in intestine after E. ictaluri infection. Pathogen-specific pattern and tissue-specific pattern were found in the two infections. The significantly regulated expressions of catfish Hsp70 genes after bacterial infections suggested their involvement in immune response in catfish.
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Affiliation(s)
- Lin Song
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China; Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA
| | - Chao Li
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yangjie Xie
- Fisheries College, Jimei University, Xiamen, 361021, China
| | - Shikai Liu
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA
| | - Jiaren Zhang
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA
| | - Jun Yao
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA
| | - Chen Jiang
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA
| | - Yun Li
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA
| | - Zhanjiang Liu
- Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA.
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Campanini EB, Vandewege MW, Pillai NE, Tay BH, Jones JL, Venkatesh B, Hoffmann FG. Early Evolution of Vertebrate Mybs: An Integrative Perspective Combining Synteny, Phylogenetic, and Gene Expression Analyses. Genome Biol Evol 2015; 7:3009-21. [PMID: 26475318 PMCID: PMC5635590 DOI: 10.1093/gbe/evv197] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The genes in the Myb superfamily encode for three related transcription factors in most vertebrates, A-, B-, and c-Myb, with functionally distinct roles, whereas most invertebrates have a single Myb. B-Myb plays an essential role in cell division and cell cycle progression, c-Myb is involved in hematopoiesis, and A-Myb is involved in spermatogenesis and regulating expression of pachytene PIWI interacting RNAs, a class of small RNAs involved in posttranscriptional gene regulation and the maintenance of reproductive tissues. Comparisons between teleost fish and tetrapods suggest that the emergence and functional divergence of the Myb genes were linked to the two rounds of whole-genome duplication early in vertebrate evolution. We combined phylogenetic, synteny, structural, and gene expression analyses of the Myb paralogs from elephant shark and lampreys with data from 12 bony vertebrates to reconstruct the early evolution of vertebrate Mybs. Phylogenetic and synteny analyses suggest that the elephant shark and Japanese lamprey have copies of the A-, B-, and c-Myb genes, implying their origin could be traced back to the common ancestor of lampreys and gnathostomes. However, structural and gene expression analyses suggest that their functional roles diverged between gnathostomes and cyclostomes. In particular, we did not detect A-Myb expression in testis suggesting that the involvement of A-Myb in the pachytene PIWI interacting RNA pathway is probably a gnathostome-specific innovation. We speculate that the secondary loss of a central domain in lamprey A-Myb underlies the functional differences between the cyclostome and gnathostome A-Myb proteins.
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Affiliation(s)
- Emeline B Campanini
- Departament of Genetics and Evolution, Federal University of São Carlos, Brazil
| | - Michael W Vandewege
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University
| | - Nisha E Pillai
- Institute of Molecular and Cell Biology, Comparative and Medical Genomics Laboratory, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Boon-Hui Tay
- Institute of Molecular and Cell Biology, Comparative and Medical Genomics Laboratory, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Justin L Jones
- Department of Biological & Physical Sciences, Saint Augustine's University
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, Comparative and Medical Genomics Laboratory, Agency for Science, Technology and Research, Biopolis, Singapore Departments of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
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21
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Petrović DM, Kok I, Woortman AJJ, Ćirić J, Loos K. Characterization of oligocellulose synthesized by reverse phosphorolysis using different cellodextrin phosphorylases. Anal Chem 2015; 87:9639-46. [PMID: 26291473 DOI: 10.1021/acs.analchem.5b01098] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Much progress was made in the straightforward and eco-friendly enzymatic synthesis of shorter cellulose chains (oligocellulose). Here, we report the determination of a molar mass distribution of the oligocellulose synthesized from cellobiose (CB) and α-glucose 1-phosphate by reverse phosphorolysis, using enzymes cellodextrin phosphorylase from Clostridium stercorarium or Clostridium thermocellum as catalyst. The oligocellulose molar mass distribution was analyzed using three different methods: (1)H NMR spectroscopy, matrix assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-ToF MS) and size exclusion chromatography (SEC). The molar mass distribution of the synthesized oligocellulose was only dependent on the concentration of cellobiose used in the reaction. Data obtained from MALDI-ToF MS and SEC were almost identical and showed that oligocellulose synthesized using 10 mM CB has an average degree of polymerization (DPn) of ∼7, while a DPn of ∼14 was achieved when 0.2 mM CB was used in the reaction. Because of solvent limitation in SEC analysis, MALDI-ToF MS was shown to be the technique of choice for accurate, easy and fast oligocellulose molar mass distribution determination.
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Affiliation(s)
- Dejan M Petrović
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Inge Kok
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Albert J J Woortman
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Jelena Ćirić
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Katja Loos
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747AG Groningen, The Netherlands
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22
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Xie Y, Song L, Weng Z, Liu S, Liu Z. Hsp90, Hsp60 and sHsp families of heat shock protein genes in channel catfish and their expression after bacterial infections. FISH & SHELLFISH IMMUNOLOGY 2015; 44:642-51. [PMID: 25827625 DOI: 10.1016/j.fsi.2015.03.027] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/25/2015] [Accepted: 03/20/2015] [Indexed: 05/26/2023]
Abstract
Heat shock proteins (Hsps) are a suite of highly conserved proteins whose expressions are generally induced by elevated temperature. However, many Hsps play important roles in both innate and adaptive immunity. On the basis of our previous work on Hsp40 and Hsp70 gene families in channel catfish (Ictalurus punctatus), the objective of this study was to characterize Hsp90, Hsp60, Hsp10, and small Hsp genes, and to investigate their expression profiles after bacterial infections. A total of 20 Hsp genes were identified and annotated in the channel catfish genome, including five Hsp90 genes, one Hsp60 gene, one Hsp10 gene, and 13 sHsp genes. Six Hsp genes were differentially expressed after Edwardsiella ictaluri infection, and 12 were differentially expressed after Flavobacterium columnare infection. Although expression of these genes exhibited both temporal and spatial regulation, the induction of Hsp genes was observed soon after bacterial infection, while the suppression of Hsp genes was observed at later time-points, suggesting their distinct roles in immune responses and disease defenses. A pathogen-specific expression pattern of Hsp90 was observed. After F. columnare infection, all Hsp90 genes were found up-regulated except Hsp90ab1, which was not significantly regulated. However, after E. ictaluri infection, only one Hsp90 gene was found significantly down-regulated. Both pathogen-specific and tissue-specific pattern of expression were observed with small Hsps after E. ictaluri and F. columnare bacterial infections. These results suggested that most of Hsp genes may play important roles in immune response and/or disease defense in channel catfish.
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Affiliation(s)
- Yangjie Xie
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA; Fisheries College, Jimei University, Xiamen 361021, PR China
| | - Lin Song
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Zhaohong Weng
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA; Fisheries College, Jimei University, Xiamen 361021, PR China
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
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23
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Li Y, Liu S, Qin Z, Yao J, Jiang C, Song L, Dunham R, Liu Z. The serpin superfamily in channel catfish: identification, phylogenetic analysis and expression profiling in mucosal tissues after bacterial infections. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 49:267-277. [PMID: 25499033 DOI: 10.1016/j.dci.2014.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/07/2014] [Accepted: 12/08/2014] [Indexed: 06/04/2023]
Abstract
The superfamily of serine protease inhibitors (serpins) are broadly distributed in all kingdoms of life. Serpins play critical roles in an array of fundamental biological processes. In this study, we identified a complete set of 25 serpin genes from channel catfish genome by comprehensive data mining of existing genomic resources. Phylogenetic analysis verified their identities and supported the classification of serpins into six families as in mammals. Extensive comparative genomic analyses suggested that most serpins were conserved among vertebrates, while some were lineage-specific. Analysis of serpin gene expression in mucosal tissues after bacterial infections indicated that serpin genes were regulated in a tissue-specific and time-dependent manner. Distinct expression patterns between infections of the two pathogens were observed, indicating that much more rapid host responses of serpin expression were initiated after ESC infection than after columnaris infection. These studies set the foundation for future studies of host-pathogen interactions.
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Affiliation(s)
- Yun Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA
| | - Zhenkui Qin
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA
| | - Jun Yao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA
| | - Chen Jiang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA
| | - Lin Song
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA
| | - Rex Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA.
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24
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Inducible nitric oxide synthase (iNOS) regulatory region variation in non-human primates. INFECTION GENETICS AND EVOLUTION 2015; 31:236-44. [PMID: 25675838 DOI: 10.1016/j.meegid.2015.01.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/07/2015] [Accepted: 01/19/2015] [Indexed: 01/26/2023]
Abstract
Inducible nitric oxide synthase (iNOS) is an enzyme that plays a key role in intracellular immune response against respiratory infections. Since various species of nonhuman primates exhibit different levels of susceptibility to infectious respiratory diseases, and since variation in regulatory regions of genes is thought to play a key role in expression levels of genes, two candidate regulatory regions of iNOS were mapped, sequenced, and compared across five species of nonhuman primates: African green monkeys (Chlorocebus sabaeus), pig-tailed macaques (Macaca nemestrina), cynomolgus macaques (Macaca fascicularis), Indian rhesus macaques (Macaca mulatta), and Chinese rhesus macaques (M. mulatta). In addition, we conducted an in silico analysis of the transcription factor binding sites associated with genetic variation in these two candidate regulatory regions across species. We found that only one of the two candidate regions showed strong evidence of involvement in iNOS regulation. Specifically, we found evidence of 13 conserved binding site candidates linked to iNOS regulation: AP-1, C/EBPB, CREB, GATA-1, GATA-3, NF-AT, NF-AT5, NF-κB, KLF4, Oct-1, PEA3, SMAD3, and TCF11. Additionally, we found evidence of interspecies variation in binding sites for several regulatory elements linked to iNOS (GATA-3, GATA-4, KLF6, SRF, STAT-1, STAT-3, OLF-1 and HIF-1) across species, especially in African green monkeys relative to other species. Given the key role of iNOS in respiratory immune response, the findings of this study might help guide the direction of future studies aimed to uncover the molecular mechanisms underlying the increased susceptibility of African green monkeys to several viral and bacterial respiratory infections.
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25
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Feng JB, Liu SK, Wang RJ, Zhang JR, Wang XL, Kaltenboeck L, Li JL, Liu ZJ. Molecular characterization, phylogenetic analysis and expression profiling of myoglobin and cytoglobin genes in response to heat stress in channel catfish Ictalurus punctatus. JOURNAL OF FISH BIOLOGY 2015; 86:592-604. [PMID: 25604925 DOI: 10.1111/jfb.12584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/10/2014] [Indexed: 06/04/2023]
Abstract
To understand the function of myoglobin (Mb) and cytoglobin (Cygb) in channel catfish Ictalurus punctatus in response to heat stress, mb and cygb genes were identified and characterized in this study. These genes were widely expressed in all the tested tissues, but strong tissue preferences were observed, with the mb gene being expressed most highly in the heart, cygb1 most highly expressed in the intestine and cygb2 most highly expressed in the brain. After heat-stress challenge, mb and cygb genes were up-regulated in almost all tested tissues. In general, such up-regulation was more dramatic in the tolerant group than in the intolerant group, suggesting that higher expression of mb and cygb genes contributed to greater tolerance of I. punctatus to heat stress.
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Affiliation(s)
- J B Feng
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, U.S.A
- Key Laboratory of Freshwater Fishery Germplasm Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| | - S K Liu
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, U.S.A
| | - R J Wang
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, U.S.A
| | - J R Zhang
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, U.S.A
| | - X L Wang
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, U.S.A
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - L Kaltenboeck
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, U.S.A
| | - J L Li
- Key Laboratory of Freshwater Fishery Germplasm Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| | - Z J Liu
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, U.S.A
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26
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Song L, Zhang J, Li C, Yao J, Jiang C, Li Y, Liu S, Liu Z. Genome-wide identification of hsp40 genes in channel catfish and their regulated expression after bacterial infection. PLoS One 2014; 9:e115752. [PMID: 25542027 PMCID: PMC4277396 DOI: 10.1371/journal.pone.0115752] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 11/27/2014] [Indexed: 11/18/2022] Open
Abstract
Heat shock proteins (HSPs) consist of a large group of chaperones whose expression is induced by high temperature, hypoxia, infection and a number of other stresses. Among all the HSPs, Hsp40 is the largest HSP family, which bind to Hsp70 ATPase domain in assisting protein folding. In this study, we identified 57 hsp40s in channel catfish (Ictalurus punctatus) through in silico analysis using RNA-Seq and genome databases. These genes can be classified into three different types, Type I, II and III, based on their structural similarities. Phylogenetic and syntenic analyses provided strong evidence in supporting the orthologies of these HSPs. Meta-analyses of RNA-Seq datasets were conducted to analyze expression profile of Hsp40s following bacterial infection. Twenty seven hsp40s were found to be significantly up- or down-regulated in the liver after infection with E. ictaluri; 19 hsp40s were found to be significantly regulated in the intestine after infection with E. ictaluri; and 19 hsp40s were found to be significantly regulated in the gill following infection with F. columnare. Altogether, a total of 42 Hsp40 genes were regulated under disease situations involving three tissues and two bacterial infections. The significant regulated expression of Hsp40 genes after bacterial infection suggested their involvement in disease defenses in catfish.
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Affiliation(s)
- Lin Song
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, AL 36849, United States of America
| | - Jiaren Zhang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, AL 36849, United States of America
| | - Chao Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, AL 36849, United States of America
| | - Jun Yao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, AL 36849, United States of America
| | - Chen Jiang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, AL 36849, United States of America
| | - Yun Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, AL 36849, United States of America
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, AL 36849, United States of America
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, AL 36849, United States of America
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27
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Yao J, Li C, Zhang J, Liu S, Feng J, Wang R, Li Y, Jiang C, Song L, Chen A, Liu Z. Expression of nitric oxide synthase (NOS) genes in channel catfish is highly regulated and time dependent after bacterial challenges. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 45:74-86. [PMID: 24560653 DOI: 10.1016/j.dci.2014.02.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 02/08/2014] [Accepted: 02/11/2014] [Indexed: 06/03/2023]
Abstract
Nitric oxide is well known for its roles in immune responses. As such, its synthesizing enzymes have been extensively studied from various species including some teleost fish species. However, the NOS genes have not been characterized in channel catfish (Ictalurus punctatus). In this study, we identified and characterized three NOS genes including one NOS1 and two NOS2 genes in channel catfish. Comparing with the NOS genes from other fish species, the catfish NOS genes are highly conserved in their structural features. Phylogenetic and syntenic analyses allowed determination of NOS1 and NOS2 genes of channel catfish and their orthology relationships. Syntenic analysis, as well as the phylogenetic analysis, indicated that the two NOS2 genes of catfish were lineage-specific duplication. The NOS genes were broadly expressed in most tested tissues, with NOS1 being expressed at the highest levels in the brain, NOS2b1 highly expressed in the skin and gill, and NOS2b2 lowly expressed in most of the tested tissues. The most striking findings of this study was that the expression of the NOS genes are highly regulated after bacterial infection, with time-dependent expression patterns that parallel the migration of macrophages. After Edwardsiella ictaluri challenge, dramatically different responses among the three NOS genes were observed. NOS1 was only significantly in the skin early after infection, while NOS2b1 was rapidly upregulated in gill, but more up-regulated in trunk kidney with the progression of the disease, suggesting such differences in gene expression may be reflective of the migration of macrophages among various tissues of the infected fish. In contrast to NOS1 and NOS2b1, NOS2b2 was normally expressed at very low levels, but it is induced in the brain and liver while significantly down-regulated in most other tissues.
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Affiliation(s)
- Jun Yao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Chao Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jiaren Zhang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jianbin Feng
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ruijia Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Yun Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Chen Jiang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Lin Song
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ailu Chen
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
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28
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Meireles DDA, Alegria TGP, Alves SV, Arantes CRR, Netto LES. A 14.7 kDa protein from Francisella tularensis subsp. novicida (named FTN_1133), involved in the response to oxidative stress induced by organic peroxides, is not endowed with thiol-dependent peroxidase activity. PLoS One 2014; 9:e99492. [PMID: 24959833 PMCID: PMC4069020 DOI: 10.1371/journal.pone.0099492] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 05/15/2014] [Indexed: 01/12/2023] Open
Abstract
Francisella genus comprises Gram-negative facultative intracellular bacteria that are among the most infectious human pathogens. A protein of 14.7 KDa named as FTN_1133 was previously described as a novel hydroperoxide resistance protein in F. tularensis subsp. novicida, implicated in organic peroxide detoxification and virulence. Here, we describe a structural and biochemical characterization of FTN_1133. Contrary to previous assumptions, multiple amino acid sequence alignment analyses revealed that FTN_1133 does not share significant similarity with proteins of the Ohr/OsmC family or any other Cys-based, thiol dependent peroxidase, including conserved motifs around reactive cysteine residues. Circular dichroism analyses were consistent with the in silico prediction of an all-α-helix secondary structure. The pKa of its single cysteine residue, determined by a monobromobimane alkylation method, was shown to be 8.0±0.1, value that is elevated when compared with other Cys-based peroxidases, such as peroxiredoxins and Ohr/OsmC proteins. Attempts to determine a thiol peroxidase activity for FTN_1133 failed, using both dithiols (DTT, thioredoxin and lipoamide) and monothiols (glutathione or 2-mercaptoethanol) as reducing agents. Heterologous expression of FTN_1133 gene in ahpC and oxyR mutants of E. coli showed no complementation. Furthermore, analysis of FTN_1133 protein by non-reducing SDS-PAGE showed that an inter-molecular disulfide bond (not detected in Ohr proteins) can be generated under hydroperoxide treatment, but the observed rates were not comparable to those observed for other thiol-dependent peroxidases. All the biochemical and structural data taken together indicated that FTN_1133 displayed distinct characteristics from other thiol dependent peroxidases and, therefore, suggested that FTN_1133 is not directly involved in hydroperoxide detoxification.
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Affiliation(s)
- Diogo de Abreu Meireles
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Thiago Geronimo Pires Alegria
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Simone Vidigal Alves
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Carla Rani Rocha Arantes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Luis Eduardo Soares Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- * E-mail:
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Castaing JP, Lee S, Anantharaman V, Ravilious GE, Aravind L, Ramamurthi KS. An autoinhibitory conformation of the Bacillus subtilis spore coat protein SpoIVA prevents its premature ATP-independent aggregation. FEMS Microbiol Lett 2014; 358:145-53. [PMID: 24810258 DOI: 10.1111/1574-6968.12452] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 04/28/2014] [Indexed: 12/17/2022] Open
Abstract
Spores of Bacillus subtilis are dormant cell types that are formed when the bacterium encounters starvation conditions. Spores are encased in a shell, termed the coat, which is composed of approximately seventy different proteins and protects the spore's genetic material from environmental insults. The structural component of the basement layer of the coat is an exceptional cytoskeletal protein, termed SpoIVA, which binds and hydrolyzes ATP. ATP hydrolysis is utilized to drive a conformational change in SpoIVA that leads to its irreversible self-assembly into a static polymer in vitro. Here, we characterize the middle domain of SpoIVA, the predicted secondary structure of which resembles the chemotaxis protein CheX but, unlike CheX, does not harbor residues required for phosphatase activity. Disruptions in this domain did not abolish ATP hydrolysis, but resulted in mislocalization of the protein and reduction in sporulation efficiency in vivo. In vitro, disruptions in this domain prevented the ATP hydrolysis-driven conformational change in SpoIVA required for polymerization and led to the aggregation of SpoIVA into particles that did not form filaments. We propose a model in which SpoIVA initially assumes a conformation in which it inhibits its own aggregation into particles, and that ATP hydrolysis remodels the protein so that it assumes a polymerization-competent conformation.
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Affiliation(s)
- Jean-Philippe Castaing
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Pearman PB, Lavergne S, Roquet C, Wüest R, Zimmermann NE, Thuiller W. Phylogenetic patterns of climatic, habitat and trophic niches in a European avian assemblage. GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2014; 23:414-424. [PMID: 24790525 PMCID: PMC4001463 DOI: 10.1111/geb.12127] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
AIM The origins of ecological diversity in continental species assemblages have long intrigued biogeographers. We apply phylogenetic comparative analyses to disentangle the evolutionary patterns of ecological niches in an assemblage of European birds. We compare phylogenetic patterns in trophic, habitat and climatic niche components. LOCATION Europe. METHODS From polygon range maps and handbook data we inferred the realized climatic, habitat and trophic niches of 405 species of breeding birds in Europe. We fitted Pagel's lambda and kappa statistics, and conducted analyses of disparity through time to compare temporal patterns of ecological diversification on all niche axes together. All observed patterns were compared with expectations based on neutral (Brownian) models of niche divergence. RESULTS In this assemblage, patterns of phylogenetic signal (lambda) suggest that related species resemble each other less in regard to their climatic and habitat niches than they do in their trophic niche. Kappa estimates show that ecological divergence does not gradually increase with divergence time, and that this punctualism is stronger in climatic niches than in habitat and trophic niches. Observed niche disparity markedly exceeds levels expected from a Brownian model of ecological diversification, thus providing no evidence for past phylogenetic niche conservatism in these multivariate niches. Levels of multivariate disparity are greatest for the climatic niche, followed by disparity of the habitat and the trophic niches. MAIN CONCLUSIONS Phylogenetic patterns in the three niche components differ within this avian assemblage. Variation in evolutionary rates (degree of gradualism, constancy through the tree) and/or non-random macroecological sampling probably lead here to differences in the phylogenetic structure of niche components. Testing hypotheses on the origin of these patterns requires more complete phylogenetic trees of the birds, and extended ecological data on different niche components for all bird species.
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Affiliation(s)
- Peter B Pearman
- Landscape Dynamics Unit, Swiss Federal Research Institute WSLZürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Sébastien Lavergne
- Laboratoire d'Ecologie Alpine, UMR 5553, Université Grenoble I, CNRSBP 53, F-38041, Grenoble Cedex 9, France
| | - Cristina Roquet
- Laboratoire d'Ecologie Alpine, UMR 5553, Université Grenoble I, CNRSBP 53, F-38041, Grenoble Cedex 9, France
| | - Rafael Wüest
- Landscape Dynamics Unit, Swiss Federal Research Institute WSLZürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Niklaus E Zimmermann
- Landscape Dynamics Unit, Swiss Federal Research Institute WSLZürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Wilfried Thuiller
- Laboratoire d'Ecologie Alpine, UMR 5553, Université Grenoble I, CNRSBP 53, F-38041, Grenoble Cedex 9, France
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31
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Feng J, Liu S, Wang X, Wang R, Zhang J, Jiang Y, Li C, Kaltenboeck L, Li J, Liu Z. Channel catfish hemoglobin genes: Identification, phylogenetic and syntenic analysis, and specific induction in response to heat stress. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2014; 9:11-22. [DOI: 10.1016/j.cbd.2013.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 01/28/2023]
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Hoppe B, Kahl T, Karasch P, Wubet T, Bauhus J, Buscot F, Krüger D. Network analysis reveals ecological links between N-fixing bacteria and wood-decaying fungi. PLoS One 2014; 9:e88141. [PMID: 24505405 PMCID: PMC3914916 DOI: 10.1371/journal.pone.0088141] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 01/06/2014] [Indexed: 11/18/2022] Open
Abstract
Nitrogen availability in dead wood is highly restricted and associations with N-fixing bacteria are thought to enable wood-decaying fungi to meet their nitrogen requirements for vegetative and generative growth. We assessed the diversity of nifH (dinitrogenase reductase) genes in dead wood of the common temperate tree species Fagus sylvatica and Picea abies from differently managed forest plots in Germany using molecular tools. By incorporating these genes into a large compilation of published nifH sequences and subsequent phylogenetic analyses of deduced proteins we verified the presence of diverse pools corresponding to functional nifH, almost all of which are new to science. The distribution of nifH genes strongly correlated with tree species and decay class, but not with forest management, while higher fungal fructification was correlated with decreasing nitrogen content of the dead wood and positively correlated with nifH diversity, especially during the intermediate stage of wood decay. Network analyses based on non-random species co-occurrence patterns revealed interactions among fungi and N-fixing bacteria in the dead wood and strongly indicate the occurrence of at least commensal relationships between these taxa.
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Affiliation(s)
- Björn Hoppe
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- Institute of Silviculture, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg i. Brsg., Germany
- * E-mail: (BH); (DK)
| | - Tiemo Kahl
- Institute of Silviculture, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg i. Brsg., Germany
| | | | - Tesfaye Wubet
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- The German Centre for Integrative Biodiversity Research (iDiv), University Leipzig, Leipzig, Germany
| | - Jürgen Bauhus
- Institute of Silviculture, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg i. Brsg., Germany
| | - François Buscot
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- Institute of Biology I, University of Leipzig, Leipzig, Germany
- The German Centre for Integrative Biodiversity Research (iDiv), University Leipzig, Leipzig, Germany
| | - Dirk Krüger
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- * E-mail: (BH); (DK)
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Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment. Methods Mol Biol 2014; 1079:59-73. [PMID: 24170395 DOI: 10.1007/978-1-62703-646-7_4] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies-based on simulation, consistency, protein structure, and phylogeny-and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application-with a keen awareness of the assumptions underlying each benchmarking strategy.
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Nagar A, Hahsler M. Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment. BMC Bioinformatics 2013; 14 Suppl 11:S2. [PMID: 24564200 PMCID: PMC3846703 DOI: 10.1186/1471-2105-14-s11-s2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. Results In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Conclusion Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to identify conserved regions fast or even interactively using a standard PC. Our method has many potential applications such as finding characteristic signature sequences for families of organisms and studying conserved and variable regions in, for example, 16S rRNA.
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Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Biol Direct 2013; 8:15. [PMID: 23768067 PMCID: PMC3710099 DOI: 10.1186/1745-6150-8-15] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 05/09/2013] [Indexed: 12/20/2022] Open
Abstract
Background The major role of enzymatic toxins that target nucleic acids in biological conflicts at all levels has become increasingly apparent thanks in large part to the advances of comparative genomics. Typically, toxins evolve rapidly hampering the identification of these proteins by sequence analysis. Here we analyze an unexpectedly widespread superfamily of toxin domains most of which possess RNase activity. Results The HEPN superfamily is comprised of all α-helical domains that were first identified as being associated with DNA polymerase β-type nucleotidyltransferases in prokaryotes and animal Sacsin proteins. Using sensitive sequence and structure comparison methods, we vastly extend the HEPN superfamily by identifying numerous novel families and by detecting diverged HEPN domains in several known protein families. The new HEPN families include the RNase LS and LsoA catalytic domains, KEN domains (e.g. RNaseL and Ire1) and the RNase domains of RloC and PrrC. The majority of HEPN domains contain conserved motifs that constitute a metal-independent endoRNase active site. Some HEPN domains lacking this motif probably function as non-catalytic RNA-binding domains, such as in the case of the mannitol repressor MtlR. Our analysis shows that HEPN domains function as toxins that are shared by numerous systems implicated in intra-genomic, inter-genomic and intra-organismal conflicts across the three domains of cellular life. In prokaryotes HEPN domains are essential components of numerous toxin-antitoxin (TA) and abortive infection (Abi) systems and in addition are tightly associated with many restriction-modification (R-M) and CRISPR-Cas systems, and occasionally with other defense systems such as Pgl and Ter. We present evidence of multiple modes of action of HEPN domains in these systems, which include direct attack on viral RNAs (e.g. LsoA and RNase LS) in conjunction with other RNase domains (e.g. a novel RNase H fold domain, NamA), suicidal or dormancy-inducing attack on self RNAs (RM systems and possibly CRISPR-Cas systems), and suicidal attack coupled with direct interaction with phage components (Abi systems). These findings are compatible with the hypothesis on coupling of pathogen-targeting (immunity) and self-directed (programmed cell death and dormancy induction) responses in the evolution of robust antiviral strategies. We propose that altruistic cell suicide mediated by HEPN domains and other functionally similar RNases was essential for the evolution of kin and group selection and cell cooperation. HEPN domains were repeatedly acquired by eukaryotes and incorporated into several core functions such as endonucleolytic processing of the 5.8S-25S/28S rRNA precursor (Las1), a novel ER membrane-associated RNA degradation system (C6orf70), sensing of unprocessed transcripts at the nuclear periphery (Swt1). Multiple lines of evidence suggest that, similar to prokaryotes, HEPN proteins were recruited to antiviral, antitransposon, apoptotic systems or RNA-level response to unfolded proteins (Sacsin and KEN domains) in several groups of eukaryotes. Conclusions Extensive sequence and structure comparisons reveal unexpectedly broad presence of the HEPN domain in an enormous variety of defense and stress response systems across the tree of life. In addition, HEPN domains have been recruited to perform essential functions, in particular in eukaryotic rRNA processing. These findings are expected to stimulate experiments that could shed light on diverse cellular processes across the three domains of life. Reviewers This article was reviewed by Martijn Huynen, Igor Zhulin and Nick Grishin
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Affiliation(s)
- Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Genome-wide identification, characterization and phylogenetic analysis of 50 catfish ATP-binding cassette (ABC) transporter genes. PLoS One 2013; 8:e63895. [PMID: 23696857 PMCID: PMC3655950 DOI: 10.1371/journal.pone.0063895] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 04/09/2013] [Indexed: 12/23/2022] Open
Abstract
Background Although a large set of full-length transcripts was recently assembled in catfish, annotation of large gene families, especially those with duplications, is still a great challenge. Most often, complexities in annotation cause mis-identification and thereby much confusion in the scientific literature. As such, detailed phylogenetic analysis and/or orthology analysis are required for annotation of genes involved in gene families. The ATP-binding cassette (ABC) transporter gene superfamily is a large gene family that encodes membrane proteins that transport a diverse set of substrates across membranes, playing important roles in protecting organisms from diverse environment. Methodology/Principal Findings In this work, we identified a set of 50 ABC transporters in catfish genome. Phylogenetic analysis allowed their identification and annotation into seven subfamilies, including 9 ABCA genes, 12 ABCB genes, 12 ABCC genes, 5 ABCD genes, 2 ABCE genes, 4 ABCF genes and 6 ABCG genes. Most ABC transporters are conserved among vertebrates, though cases of recent gene duplications and gene losses do exist. Gene duplications in catfish were found for ABCA1, ABCB3, ABCB6, ABCC5, ABCD3, ABCE1, ABCF2 and ABCG2. Conclusion/Significance The whole set of catfish ABC transporters provide the essential genomic resources for future biochemical, toxicological and physiological studies of ABC drug efflux transporters. The establishment of orthologies should allow functional inferences with the information from model species, though the function of lineage-specific genes can be distinct because of specific living environment with different selection pressure.
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Pomajbíková K, Oborník M, Horák A, Petrželková KJ, Grim JN, Levecke B, Todd A, Mulama M, Kiyang J, Modrý D. Novel insights into the genetic diversity of Balantidium and Balantidium-like cyst-forming ciliates. PLoS Negl Trop Dis 2013; 7:e2140. [PMID: 23556024 PMCID: PMC3610628 DOI: 10.1371/journal.pntd.0002140] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 02/07/2013] [Indexed: 11/24/2022] Open
Abstract
Balantidiasis is considered a neglected zoonotic disease with pigs serving as reservoir hosts. However, Balantidium coli has been recorded in many other mammalian species, including primates. Here, we evaluated the genetic diversity of B. coli in non-human primates using two gene markers (SSrDNA and ITS1-5.8SDNA-ITS2). We analyzed 49 isolates of ciliates from fecal samples originating from 11 species of captive and wild primates, domestic pigs and wild boar. The phylogenetic trees were computed using Bayesian inference and Maximum likelihood. Balantidium entozoon from edible frog and Buxtonella sulcata from cattle were included in the analyses as the closest relatives of B. coli, as well as reference sequences of vestibuliferids. The SSrDNA tree showed the same phylogenetic diversification of B. coli at genus level as the tree constructed based on the ITS region. Based on the polymorphism of SSrDNA sequences, the type species of the genus, namely B. entozoon, appeared to be phylogenetically distinct from B. coli. Thus, we propose a new genus Neobalantidium for the homeothermic clade. Moreover, several isolates from both captive and wild primates (excluding great apes) clustered with B. sulcata with high support, suggesting the existence of a new species within this genus. The cysts of Buxtonella and Neobalantidium are morphologically indistinguishable and the presence of Buxtonella-like ciliates in primates opens the question about possible occurrence of these pathogens in humans.
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MESH Headings
- Animals
- Animals, Domestic
- Animals, Wild
- Balantidiasis/parasitology
- Balantidiasis/veterinary
- Balantidium/classification
- Balantidium/genetics
- Balantidium/isolation & purification
- Cluster Analysis
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Genes, rRNA
- Genetic Variation
- Molecular Sequence Data
- Phylogeny
- Primate Diseases/parasitology
- Primates
- RNA, Protozoan/genetics
- RNA, Ribosomal, 18S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Kateřina Pomajbíková
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic.
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Lockhart MM, Wirrig EE, Phelps AL, Ghatnekar AV, Barth JL, Norris RA, Wessels A. Mef2c regulates transcription of the extracellular matrix protein cartilage link protein 1 in the developing murine heart. PLoS One 2013; 8:e57073. [PMID: 23468913 PMCID: PMC3582617 DOI: 10.1371/journal.pone.0057073] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 01/16/2013] [Indexed: 11/20/2022] Open
Abstract
Cartilage Link Protein 1 (Crtl1) is an extracellular matrix (ECM) protein that stabilizes the interaction between hyaluronan and versican and is expressed in endocardial and endocardially-derived cells in the developing heart, including cells in the atrioventricular (AV) and outflow tract (OFT) cushions. Previous investigations into the transcriptional regulation of the Crtl1 gene have shown that Sox9 regulates Crtl1 expression in both cartilage and the AV valves. The cardiac transcription factor Mef2c is involved in the regulation of gene expression in cardiac and skeletal muscle cell lineages. In this study we have investigated the potential role of Mef2c in the regulation of ECM production in the endocardial and mesenchymal cell lineages of the developing heart. We demonstrate that the Crtl1 5′ flanking region contains two highly conserved Mef2 binding sites and that Mef2c is able to bind to these sites in vivo during cardiovascular development. Additionally, we show that Crtl1 transcription is dependent on Mef2c expression in fetal mitral valve interstitial cells (VICs). Combined, these findings highlight a new role for Mef2c in cardiac development and the regulation of cardiac extracellular matrix protein expression.
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Affiliation(s)
- Marie M. Lockhart
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Elaine E. Wirrig
- The Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Aimee L. Phelps
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Angela V. Ghatnekar
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Jeremy L. Barth
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Russell A. Norris
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Andy Wessels
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- * E-mail:
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Brindefalk B, Dessailly BH, Yeats C, Orengo C, Werner F, Poole AM. Evolutionary history of the TBP-domain superfamily. Nucleic Acids Res 2013; 41:2832-45. [PMID: 23376926 PMCID: PMC3597702 DOI: 10.1093/nar/gkt045] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The TATA binding protein (TBP) is an essential transcription initiation factor in Archaea and Eucarya. Bacteria lack TBP, and instead use sigma factors for transcription initiation. TBP has a symmetric structure comprising two repeated TBP domains. Using sequence, structural and phylogenetic analyses, we examine the distribution and evolutionary history of the TBP domain, a member of the helix-grip fold family. Our analyses reveal a broader distribution than for TBP, with TBP-domains being present across all three domains of life. In contrast to TBP, all other characterized examples of the TBP domain are present as single copies, primarily within multidomain proteins. The presence of the TBP domain in the ubiquitous DNA glycosylases suggests that this fold traces back to the ancestor of all three domains of life. The TBP domain is also found in RNase HIII, and phylogenetic analyses show that RNase HIII has evolved from bacterial RNase HII via TBP-domain fusion. Finally, our comparative genomic screens confirm and extend earlier reports of proteins consisting of a single TBP domain among some Archaea. These monopartite TBP-domain proteins suggest that this domain is functional in its own right, and that the TBP domain could have first evolved as an independent protein, which was later recruited in different contexts.
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Affiliation(s)
- Björn Brindefalk
- Department of Botany, Stockholm University, 106 91 Stockholm, Sweden
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Roquet C, Thuiller W, Lavergne S. Building megaphylogenies for macroecology: taking up the challenge. ECOGRAPHY 2013; 36:13-26. [PMID: 24790290 PMCID: PMC4001083 DOI: 10.1111/j.1600-0587.2012.07773.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The last decades have seen an upsurge in ecological studies incorporating phylogenetic information with increasing species samples, motivated by the common conjecture that species with common ancestors should share some ecological characteristics due to niche conservatism. This has been carried out using various methods of increasing complexity and reliability: using only taxonomical classification; constructing supertrees that incorporate only topological information from previously published phylogenies; or building supermatrices of molecular data that are used to estimate phylogenies with evolutionary meaningful branch lengths. Although the latter option is more informative than the others, it remains under-used in ecology because ecologists are generally unaware of or unfamiliar with modern molecular phylogenetic methods. However, a solid phylogenetic hypothesis is necessary to conduct reliable ecological analysis integrating evolutive aspects. Our aim here is to clarify the concepts and methodological issues associated with the reconstruction of dated megaphylogenies, and to show that it is nowadays possible to obtain accurate and well sampled megaphylogenies with informative branch-lengths on large species samples. This is possible thanks to improved phylogenetic methods, vast amounts of molecular data available from databases such as Genbank, and consensus knowledge on deep phylogenetic relationships for an increasing number of groups of organisms. Finally, we include a detailed step-by-step workflow pipeline (Supplementary material), from data acquisition to phylogenetic inference, mainly based on the R environment (widely used by ecologists) and the use of free web-servers, that has been applied to the reconstruction of a species-level phylogeny of all breeding birds of Europe.
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Affiliation(s)
- Cristina Roquet
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Univ. Joseph Fourier, Grenoble 1, BP 53, FR-38041 Grenoble Cedex 9, France
| | - Wilfried Thuiller
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Univ. Joseph Fourier, Grenoble 1, BP 53, FR-38041 Grenoble Cedex 9, France
| | - Sébastien Lavergne
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Univ. Joseph Fourier, Grenoble 1, BP 53, FR-38041 Grenoble Cedex 9, France
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Opazo JC, Butts GT, Nery MF, Storz JF, Hoffmann FG. Whole-genome duplication and the functional diversification of teleost fish hemoglobins. Mol Biol Evol 2012; 30:140-53. [PMID: 22949522 PMCID: PMC3525417 DOI: 10.1093/molbev/mss212] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Subsequent to the two rounds of whole-genome duplication that occurred in the common
ancestor of vertebrates, a third genome duplication occurred in the stem lineage of
teleost fishes. This teleost-specific genome duplication (TGD) is thought to have provided
genetic raw materials for the physiological, morphological, and behavioral diversification
of this highly speciose group. The extreme physiological versatility of teleost fish is
manifest in their diversity of blood–gas transport traits, which reflects the myriad
solutions that have evolved to maintain tissue O2 delivery in the face of
changing metabolic demands and environmental O2 availability during different
ontogenetic stages. During the course of development, regulatory changes in
blood–O2 transport are mediated by the expression of multiple,
functionally distinct hemoglobin (Hb) isoforms that meet the particular
O2-transport challenges encountered by the developing embryo or fetus (in
viviparous or oviparous species) and in free-swimming larvae and adults. The main
objective of the present study was to assess the relative contributions of whole-genome
duplication, large-scale segmental duplication, and small-scale gene duplication in
producing the extraordinary functional diversity of teleost Hbs. To accomplish this, we
integrated phylogenetic reconstructions with analyses of conserved synteny to characterize
the genomic organization and evolutionary history of the globin gene clusters of teleosts.
These results were then integrated with available experimental data on functional
properties and developmental patterns of stage-specific gene expression. Our results
indicate that multiple α- and β-globin genes
were present in the common ancestor of gars (order Lepisoteiformes) and teleosts. The
comparative genomic analysis revealed that teleosts possess a dual set of TGD-derived
globin gene clusters, each of which has undergone lineage-specific changes in gene content
via repeated duplication and deletion events. Phylogenetic reconstructions revealed that
paralogous genes convergently evolved similar functional properties in different teleost
lineages. Consistent with other recent studies of globin gene family evolution in
vertebrates, our results revealed evidence for repeated evolutionary transitions in the
developmental regulation of Hb synthesis.
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Affiliation(s)
- Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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Iriarte A, Arbildi P, La-Rocca S, Musto H, Fernández V. Identification of novel glutathione transferases in Echinococcus granulosus. An evolutionary perspective. Acta Trop 2012; 123:208-16. [PMID: 22659461 DOI: 10.1016/j.actatropica.2012.05.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 03/28/2012] [Accepted: 05/18/2012] [Indexed: 11/24/2022]
Abstract
Glutathione transferase enzymes (GSTs) constitute a major detoxification system in helminth parasites and have been related to the modulation of host immune response mechanisms. At least three different GSTs classes have been described in Platyhelminthes: Mu, Sigma and Omega. Mining the genome of Echinococcus multilocularis and the ESTs databases of Taenia solium and E. granulosus identified two new GSTs from the cestode E. granulosus, named EgGST2 and EgGST3. It also revealed that the Omega class of GSTs was absent from the Taenidae family. EgGST2 and EgGST3 are actively expressed in the parasite. In order to know the origin of these new GSTs, in silico analyses were performed. While EgGST2 is classified as belonging to the Sigma class, the data obtained for EgGST3 allowed a less clear interpretation. The study of the evolutionary relatedness based on the C-terminal domain sequence, gene structure conservation and three-dimensional structure predictions, suggests that EgGST3 is derived from the Platyhelminthes' Sigma-class cluster. Interestingly, the N-terminal domain displays some characteristic Omega-class residues, including a Cys residue that is likely to be involved in the catalytic mechanism. We discuss different evolutionary scenarios that could explain the observed patterns.
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Hoffmann FG, Opazo JC, Hoogewijs D, Hankeln T, Ebner B, Vinogradov SN, Bailly X, Storz JF. Evolution of the globin gene family in deuterostomes: lineage-specific patterns of diversification and attrition. Mol Biol Evol 2012; 29:1735-45. [PMID: 22319164 PMCID: PMC3375472 DOI: 10.1093/molbev/mss018] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In the Metazoa, globin proteins display an underlying unity in tertiary structure that belies an extraordinary diversity in primary structures, biochemical properties, and physiological functions. Phylogenetic reconstructions can reveal which of these functions represent novel, lineage-specific innovations, and which represent ancestral functions that are shared with homologous globin proteins in other eukaryotes and even prokaryotes. To date, our understanding of globin diversity in deuterostomes has been hindered by a dearth of genomic sequence data from the Ambulacraria (echinoderms + hemichordates), the sister group of chordates, and the phylum Xenacoelomorpha, which includes xenoturbellids, acoelomorphs, and nemertodermatids. Here, we report the results of a phylogenetic and comparative genomic analysis of the globin gene repertoire of deuterostomes. We first characterized the globin genes of the acorn worm, Saccoglossus kowalevskii, a representative of the phylum Hemichordata. We then integrated genomic sequence data from the acorn worm into a comprehensive analysis of conserved synteny and phylogenetic relationships among globin genes from representatives of the eight lineages that comprise the superphylum Deuterostomia. The primary aims were 1) to unravel the evolutionary history of the globin gene superfamily in deuterostomes and 2) to use the estimated phylogeny to gain insights into the functional evolution of deuterostome globins. Results of our analyses indicate that the deuterostome common ancestor possessed a repertoire of at least four distinct globin paralogs and that different subsets of these ancestral genes have been retained in each of the descendant organismal lineages. In each major deuterostome group, a different subset of ancestral precursor genes underwent lineage-specific expansions of functional diversity through repeated rounds of gene duplication and divergence. By integrating results of the phylogenetic analysis with available functional data, we discovered that circulating oxygen-transport hemoglobins evolved independently in several deuterostome lineages and that intracellular nerve globins evolved independently in chordates and acoelomorph worms.
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Affiliation(s)
- Federico G Hoffmann
- Department of Biochemistry and Molecular Biology, Mississippi State University, USA.
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Stray SJ, Pittman LB. Subtype- and antigenic site-specific differences in biophysical influences on evolution of influenza virus hemagglutinin. Virol J 2012; 9:91. [PMID: 22569196 PMCID: PMC3499391 DOI: 10.1186/1743-422x-9-91] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 04/10/2012] [Indexed: 11/14/2022] Open
Abstract
Background Influenza virus undergoes rapid evolution by both antigenic shift and antigenic drift. Antibodies, particularly those binding near the receptor-binding site of hemagglutinin (HA) or the neuraminidase (NA) active site, are thought to be the primary defense against influenza infection, and mutations in antibody binding sites can reduce or eliminate antibody binding. The binding of antibodies to their cognate antigens is governed by such biophysical properties of the interacting surfaces as shape, non-polar and polar surface area, and charge. Methods To understand forces shaping evolution of influenza virus, we have examined HA sequences of human influenza A and B viruses, assigning each amino acid values reflecting total accessible surface area, non-polar and polar surface area, and net charge due to the side chain. Changes in each of these values between neighboring sequences were calculated for each residue and mapped onto the crystal structures. Results Areas of HA showing the highest frequency of pairwise changes agreed well with previously identified antigenic sites in H3 and H1 HAs, and allowed us to propose more detailed antigenic maps and novel antigenic sites for H1 and influenza B HA. Changes in biophysical properties differed between HAs of different subtypes, and between different antigenic sites of the same HA. For H1, statistically significant differences in several biophysical quantities compared to residues lying outside antigenic sites were seen for some antigenic sites but not others. Influenza B antigenic sites all show statistically significant differences in biophysical quantities for all antigenic sites, whereas no statistically significant differences in biophysical quantities were seen for any antigenic site is seen for H3. In many cases, residues previously shown to be under positive selection at the genetic level also undergo rapid change in biophysical properties. Conclusions The biophysical consequences of amino acid changes introduced by antigenic drift vary from subtype to subtype, and between different antigenic sites. This suggests that the significance of antibody binding in selecting new variants may also be variable for different antigenic sites and influenza subtypes.
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Affiliation(s)
- Stephen J Stray
- Department of Microbiology, University of Mississippi Medical Center, 2500 N State St, Jackson, MS 39216, USA.
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Boucher FC, Thuiller W, Roquet C, Douzet R, Aubert S, Alvarez N, Lavergne S. Reconstructing the origins of high-alpine niches and cushion life form in the genus Androsace S.L. (Primulaceae). Evolution 2012; 66:1255-68. [PMID: 22486702 PMCID: PMC3999638 DOI: 10.1111/j.1558-5646.2011.01483.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Relatively, few species have been able to colonize extremely cold alpine environments. We investigate the role played by the cushion life form in the evolution of climatic niches in the plant genus Androsace s.l., which spreads across the mountain ranges of the Northern Hemisphere. Using robust methods that account for phylogenetic uncertainty, intraspecific variability of climatic requirements and different life-history evolution scenarios, we show that climatic niches of Androsace s.l. exhibit low phylogenetic signal and that they evolved relatively recently and punctually. Models of niche evolution fitted onto phylogenies show that the cushion life form has been a key innovation providing the opportunity to occupy extremely cold environments, thus contributing to rapid climatic niche diversification in the genus Androsace s.l. We then propose a plausible scenario for the adaptation of plants to alpine habitats.
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Hoogewijs D, Dewilde S, Vierstraete A, Moens L, Vinogradov SN. A phylogenetic analysis of the globins in fungi. PLoS One 2012; 7:e31856. [PMID: 22384087 PMCID: PMC3287990 DOI: 10.1371/journal.pone.0031856] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 01/13/2012] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND All globins belong to one of three families: the F (flavohemoglobin) and S (sensor) families that exhibit the canonical 3/3 α-helical fold, and the T (truncated 3/3 fold) globins characterized by a shortened 2/2 α-helical fold. All eukaryote 3/3 hemoglobins are related to the bacterial single domain F globins. It is known that Fungi contain flavohemoglobins and single domain S globins. Our aims are to provide a census of fungal globins and to examine their relationships to bacterial globins. RESULTS Examination of 165 genomes revealed that globins are present in >90% of Ascomycota and ~60% of Basidiomycota genomes. The S globins occur in Blastocladiomycota and Chytridiomycota in addition to the phyla that have FHbs. Unexpectedly, group 1 T globins were found in one Blastocladiomycota and one Chytridiomycota genome. Phylogenetic analyses were carried out on the fungal globins, alone and aligned with representative bacterial globins. The Saccharomycetes and Sordariomycetes with two FHbs form two widely divergent clusters separated by the remaining fungal sequences. One of the Saccharomycete groups represents a new subfamily of FHbs, comprising a previously unknown N-terminal and a FHb missing the C-terminal moiety of its reductase domain. The two Saccharomycete groups also form two clusters in the presence of bacterial FHbs; the surrounding bacterial sequences are dominated by Proteobacteria and Bacilli (Firmicutes). The remaining fungal FHbs cluster with Proteobacteria and Actinobacteria. The Sgbs cluster separately from their bacterial counterparts, except for the intercalation of two Planctomycetes and a Proteobacterium between the Fungi incertae sedis and the Blastocladiomycota and Chytridiomycota. CONCLUSION Our results are compatible with a model of globin evolution put forward earlier, which proposed that eukaryote F, S and T globins originated via horizontal gene transfer of their bacterial counterparts to the eukaryote ancestor, resulting from the endosymbiotic events responsible for the origin of mitochondria and chloroplasts.
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Affiliation(s)
- David Hoogewijs
- Institute of Physiology and Zürich Center for Integrative Human Physiology, University of Zürich, Zürich, Switzerland.
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Cvrčková F, Grunt M, Bezvoda R, Hála M, Kulich I, Rawat A, Žárský V. Evolution of the land plant exocyst complexes. FRONTIERS IN PLANT SCIENCE 2012; 3:159. [PMID: 22826714 PMCID: PMC3399122 DOI: 10.3389/fpls.2012.00159] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 06/29/2012] [Indexed: 05/13/2023]
Abstract
Exocyst is an evolutionarily conserved vesicle tethering complex functioning especially in the last stage of exocytosis. Homologs of its eight canonical subunits - Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70, and Exo84 - were found also in higher plants and confirmed to form complexes in vivo, and to participate in cell growth including polarized expansion of pollen tubes and root hairs. Here we present results of a phylogenetic study of land plant exocyst subunits encoded by a selection of completely sequenced genomes representing a variety of plant, mostly angiosperm, lineages. According to their evolution histories, plant exocyst subunits can be divided into several groups. The core subunits Sec6, Sec8, and Sec10, together with Sec3 and Sec5, underwent few, if any fixed duplications in the tracheophytes (though they did amplify in the moss Physcomitrella patens), while others form larger families, with the number of paralogs ranging typically from two to eight per genome (Sec15, Exo84) to several dozens per genome (Exo70). Most of the diversity, which can be in some cases traced down to the origins of land plants, can be attributed to the peripheral subunits Exo84 and, in particular, Exo70. As predicted previously, early land plants (including possibly also the Rhyniophytes) encoded three ancestral Exo70 paralogs which further diversified in the course of land plant evolution. Our results imply that plants do not have a single "Exocyst complex" - instead, they appear to possess a diversity of exocyst variants unparalleled among other organisms studied so far. This feature might perhaps be directly related to the demands of building and maintenance of the complicated and spatially diverse structures of the endomembranes and cell surfaces in multicellular land plants.
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Affiliation(s)
- Fatima Cvrčková
- Department of Experimental Plant Biology, Faculty of Sciences, Charles UniversityPrague, Czech Republic
- *Correspondence: Fatima Cvrčková, Department of Experimental Plant Biology, Faculty of Sciences, Charles University, Viničná 5, CZ 128 44 Praha 2, Czech Republic. e-mail:
| | - Michal Grunt
- Department of Experimental Plant Biology, Faculty of Sciences, Charles UniversityPrague, Czech Republic
| | - Radek Bezvoda
- Department of Experimental Plant Biology, Faculty of Sciences, Charles UniversityPrague, Czech Republic
| | - Michal Hála
- Department of Experimental Plant Biology, Faculty of Sciences, Charles UniversityPrague, Czech Republic
- Institute of Experimental Botany, Academy of Sciences of the Czech RepublicPrague, Czech Republic
| | - Ivan Kulich
- Department of Experimental Plant Biology, Faculty of Sciences, Charles UniversityPrague, Czech Republic
| | - Anamika Rawat
- Department of Experimental Plant Biology, Faculty of Sciences, Charles UniversityPrague, Czech Republic
| | - Viktor Žárský
- Department of Experimental Plant Biology, Faculty of Sciences, Charles UniversityPrague, Czech Republic
- Institute of Experimental Botany, Academy of Sciences of the Czech RepublicPrague, Czech Republic
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Bacterial classification using genomic fingerprints obtained by virtual hybridization. J Microbiol Methods 2011; 87:286-94. [DOI: 10.1016/j.mimet.2011.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 08/21/2011] [Accepted: 08/24/2011] [Indexed: 11/18/2022]
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Taly JF, Magis C, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Kemena C, Notredame C. Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. Nat Protoc 2011; 6:1669-82. [DOI: 10.1038/nprot.2011.393] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Brindefalk B, Ettema TJG, Viklund J, Thollesson M, Andersson SGE. A phylometagenomic exploration of oceanic alphaproteobacteria reveals mitochondrial relatives unrelated to the SAR11 clade. PLoS One 2011; 6:e24457. [PMID: 21935411 PMCID: PMC3173451 DOI: 10.1371/journal.pone.0024457] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 08/10/2011] [Indexed: 12/03/2022] Open
Abstract
Background According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from an ancestral Alphaproteobacterium. Phylogenetic studies indicate that the mitochondrial ancestor is most closely related to the Rickettsiales. Recently, it was suggested that Candidatus Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the oceans, is a sister taxon to the mitochondrial-Rickettsiales clade. The availability of ocean metagenome data substantially increases the sampling of Alphaproteobacteria inhabiting the oxygen-containing waters of the oceans that likely resemble the originating environment of mitochondria. Methodology/Principal Findings We present a phylogenetic study of the origin of mitochondria that incorporates metagenome data from the Global Ocean Sampling (GOS) expedition. We identify mitochondrially related sequences in the GOS dataset that represent a rare group of Alphaproteobacteria, designated OMAC (Oceanic Mitochondria Affiliated Clade) as the closest free-living relatives to mitochondria in the oceans. In addition, our analyses reject the hypothesis that the mitochondrial system for aerobic respiration is affiliated with that of the SAR11 clade. Conclusions/Significance Our results allude to the existence of an alphaproteobacterial clade in the oxygen-rich surface waters of the oceans that represents the closest free-living relative to mitochondria identified thus far. In addition, our findings underscore the importance of expanding the taxonomic diversity in phylogenetic analyses beyond that represented by cultivated bacteria to study the origin of mitochondria.
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Affiliation(s)
- Björn Brindefalk
- Department of Molecular Evolution, Evolutionary Biology Center, Science for Life Laboratory, Uppsala, Sweden
| | - Thijs J. G. Ettema
- Department of Molecular Evolution, Evolutionary Biology Center, Science for Life Laboratory, Uppsala, Sweden
| | - Johan Viklund
- Department of Molecular Evolution, Evolutionary Biology Center, Science for Life Laboratory, Uppsala, Sweden
| | - Mikael Thollesson
- Department of Molecular Evolution, Evolutionary Biology Center, Science for Life Laboratory, Uppsala, Sweden
| | - Siv G. E. Andersson
- Department of Molecular Evolution, Evolutionary Biology Center, Science for Life Laboratory, Uppsala, Sweden
- * E-mail:
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