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Evolution of CCR5 and CCR2 Genes in Bats Showed Multiple Independent Gene Conversion Events. Viruses 2022; 14:v14020169. [PMID: 35215768 PMCID: PMC8877049 DOI: 10.3390/v14020169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 11/16/2022] Open
Abstract
Chemokine receptors are an important determinant for the infectiousness of different pathogens, which are able to target the host cells by binding to the extracellular domains of these proteins. This is the mechanism of infection of HIV-1, among other concerning human diseases. Over the past years, it has been shown that two chemokine receptors, CCR2 and CCR5, have been shaped by events of gene conversion in different mammalian lineages, which has been linked to a possible selective advantage against pathogens. Here, by taking advantage of available bat genomes, we present the first insight of CCR2 and CCR5 evolution within the Chiroptera order. In total, four independent events of recombination between CCR2 and CCR5 were detected: two in a single species, Miniopterus natalensis; one in two species from the Rhinolophoidea superfamily; and one in four species from the Pteropodidae family. The regions affected by the gene conversions were generally extensive and always encompassed extracellular domains. Overall, we demonstrate that CCR2 and CCR5 have been subject to extensive gene conversion in multiple species of bats. Considering that bats are known to be large reservoirs of virus in nature, these results might indicate that chimeric CCR2-CCR5 genes might grant some bat species a selective advantage against viruses that rely in the extracellular portions of either CCR2 or CCR5 as gateways into the cell.
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Geng S, Xu T, Sun Y. Genome-wide identification and analysis of chemokine receptor superfamily in miiuy croaker, Miichthys miiuy. FISH & SHELLFISH IMMUNOLOGY 2021; 118:343-353. [PMID: 34555531 DOI: 10.1016/j.fsi.2021.09.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
The chemokine receptor (ChemR) superfamily, which is divided into 4 subfamilies (CXCR, CCR, XCR, and CX3CR), is the main receptors of chemokines in innate immune responses. In the current study, we have identified 27 ChemRs in miiuy croaker: 13 CCR genes, 11 CXCR genes, and 3 XCR genes. Multiple characteristics of these genes, including phylogeny, gene structures, conserved motifs, chromosome locations, evolutionary mechanism, and expression levels upon the bacterial challenge were analyzed. Gene structure and location analysis showed that all ChemR genes contain fewer introns (≤4) and they are unevenly distributed on the 12 chromosomes. And the XCR subfamily of miiuy croaker don't have the DRY motif of ChemR. Phylogenetic and synteny analysis showed that these genes experienced tandem and segmental duplication event in several species, and tandem duplication might be the main expansion way in miiuy croaker. The major ChemRs of each orthologous group in vertebrates were selected for molecular evolution analysis, the results of which indicated that compared with vertebrates, ChemRs of teleost fishes may have a relatively high evolutionary dynamic. In addition, a total of 21 positively selected codons were detected in vertebrate ChemRs under Model 8. RNA-Seq analysis and qRT-PCR verification demonstrated that CXCR3.2, CXCR5, and XCR1 genes were up-regulated significantly upon the Vibrio harveyi infection. These results provide valuable information for investigating the evolutionary relationships of chemokine receptor superfamily in miiuy croaker and laid the basis for further functional analysis.
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Affiliation(s)
- Shang Geng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, China
| | - Yuena Sun
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, China.
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3
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Gangele K, Jamsandekar M, Mishra A, Poluri KM. Unraveling the evolutionary origin of ELR motif using fish CXC chemokine CXCL8. FISH & SHELLFISH IMMUNOLOGY 2019; 93:17-27. [PMID: 31310848 DOI: 10.1016/j.fsi.2019.07.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 05/19/2023]
Abstract
Chemokines are chemotactic proteins involved in host defense through the migration of immune-regulatory cells to the site of infection. Interleukin-8 (CXCL8/IL8) is the most studied "ELR-CXC chemokine/neutrophil activating chemokine (NAC) that regulate neutrophil trafficking during infections and inflammation by binding to its cognate G-protein coupled receptors CXCR1/CXCR2. The "ELR" motif of NAC chemokines is essential for the CXCR1/CXCR2 receptor activation. In order to understand the evolutionary origin of "ELR" motif in the CXC chemokines, a thorough evolutionary study of CXCL8 gene from various fishes and primates was performed. Phylogenetic analysis revealed that the CXCL8 gene can be classified into four distinct lineages (CXCL8-L1a, CXCL8-L1b, CXCL8-L2, and CXCL8-L3), where CXCL8-L1a is the fastest evolving lineage and CXCL8-L3 is the slowest. Selection analysis suggested that The "ELR/DLR" motif containing branches (gadoid and coelacanth) are positively selected. The probable evolutionary trend of "ELR" motif suggested that this motif in ancestor CXCL8 is evolved from the GGR of Lamprey (Agnatha), followed by duplication giving rise to two main motifs in CXCL8 "NXH" in L3 lineage and "ELR/DLR" in L1a/L1b lineages. Although, structural analysis suggested that the overall topology of the CXCL8 proteins is similar, differences do exist at the individual structural elements among the members of different lineages. Functional distance analysis suggested that the CXCL8-L3 lineage is more distant compared to the CXCL8-L1a and L1b lineages from the inferred ancestor. Functional divergence analysis between different lineages suggested that most of the selected residues are important for receptor or glycosaminoglycan binding. Such a functional diversification can be attributed to the novel set of functions adopted by CXCL8 in various species.
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Affiliation(s)
- Krishnakant Gangele
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Minal Jamsandekar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, 342011, Rajasthan, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
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4
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Vázquez N, Vieira CP, Amorim BSR, Torres A, López-Fernández H, Fdez-Riverola F, Sousa JLR, Reboiro-Jato M, Vieira J. Large Scale Analyses and Visualization of Adaptive Amino Acid Changes Projects. Interdiscip Sci 2018; 10:24-32. [PMID: 29383564 PMCID: PMC5838210 DOI: 10.1007/s12539-018-0282-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 01/09/2018] [Accepted: 01/17/2018] [Indexed: 11/02/2022]
Abstract
When changes at few amino acid sites are the target of selection, adaptive amino acid changes in protein sequences can be identified using maximum-likelihood methods based on models of codon substitution (such as codeml). Although such methods have been employed numerous times using a variety of different organisms, the time needed to collect the data and prepare the input files means that tens or hundreds of coding regions are usually analyzed. Nevertheless, the recent availability of flexible and easy to use computer applications that collect relevant data (such as BDBM) and infer positively selected amino acid sites (such as ADOPS), means that the entire process is easier and quicker than before. However, the lack of a batch option in ADOPS, here reported, still precludes the analysis of hundreds or thousands of sequence files. Given the interest and possibility of running such large-scale projects, we have also developed a database where ADOPS projects can be stored. Therefore, this study also presents the B+ database, which is both a data repository and a convenient interface that looks at the information contained in ADOPS projects without the need to download and unzip the corresponding ADOPS project file. The ADOPS projects available at B+ can also be downloaded, unzipped, and opened using the ADOPS graphical interface. The availability of such a database ensures results repeatability, promotes data reuse with significant savings on the time needed for preparing datasets, and effortlessly allows further exploration of the data contained in ADOPS projects.
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Affiliation(s)
- Noé Vázquez
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Universidade de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain
- CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain
| | - Cristina P Vieira
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Bárbara S R Amorim
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto Nacional de Engenharia Biomédica (INEB), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - André Torres
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Hugo López-Fernández
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Universidade de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain
- CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Florentino Fdez-Riverola
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Universidade de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain
- CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain
| | - José L R Sousa
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Miguel Reboiro-Jato
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Universidade de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain
- CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain
| | - Jorge Vieira
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
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Ishengoma E, Agaba M. Evolution of toll-like receptors in the context of terrestrial ungulates and cetaceans diversification. BMC Evol Biol 2017; 17:54. [PMID: 28209121 PMCID: PMC5314619 DOI: 10.1186/s12862-017-0901-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 02/02/2017] [Indexed: 11/17/2022] Open
Abstract
Background Toll-like receptors (TLRs) are the frontline actors in the innate immune response to various pathogens and are expected to be targets of natural selection in species adapted to habitats with contrasting pathogen burdens. The recent publication of genome sequences of giraffe and okapi together afforded the opportunity to examine the evolution of selected TLRs in broad range of terrestrial ungulates and cetaceans during their complex habitat diversification. Through direct sequence comparisons and standard evolutionary approaches, the extent of nucleotide and protein sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5, TLR7, TLR9 and TLR10) between giraffe and closely related species was determined. In addition, comparison of the patterning of key TLR motifs and domains between giraffe and related species was performed. The quantification of selection pressure and divergence on TLRs among terrestrial ungulates and cetaceans was also performed. Results Sequence analysis shows that giraffe has 94–99% nucleotide identity with okapi and cattle for all TLRs analyzed. Variations in the number of Leucine-rich repeats were observed in some of TLRs between giraffe, okapi and cattle. Patterning of key TLR domains did not reveal any significant differences in the domain architecture among giraffe, okapi and cattle. Molecular evolutionary analysis for selection pressure identifies positive selection on key sites for all TLRs examined suggesting that pervasive evolutionary pressure has taken place during the evolution of terrestrial ungulates and cetaceans. Analysis of positively selected sites showed some site to be part of Leucine-rich motifs suggesting functional relevance in species-specific recognition of pathogen associated molecular patterns. Notably, clade analysis reveals significant selection divergence between terrestrial ungulates and cetaceans in viral sensing TLR3. Mapping of giraffe TLR3 key substitutions to the structure of the receptor indicates that at least one of giraffe altered sites coincides with TLR3 residue known to play a critical role in receptor signaling activity. Conclusion There is overall structural conservation in TLRs among giraffe, okapi and cattle indicating that the mechanism for innate immune response utilizing TLR pathways may not have changed very much during the evolution of these species. However, a broader phylogenetic analysis revealed signatures of adaptive evolution among terrestrial ungulates and cetaceans, including the observed selection divergence in TLR3. This suggests that long term ecological dynamics has led to species-specific innovation and functional variation in the mechanisms mediating innate immunity in terrestrial ungulates and cetaceans. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0901-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Edson Ishengoma
- School of Life Science and Biongineering, The Nelson Mandela African Institution of Sciences and Technology, P.O. Box 447, Arusha, Tanzania. .,Mkwawa University College of Education, University of Dar es Salaam, P.O. Box 2513, Iringa, Tanzania.
| | - Morris Agaba
- School of Life Science and Biongineering, The Nelson Mandela African Institution of Sciences and Technology, P.O. Box 447, Arusha, Tanzania.,Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, GPO00100, Kenya
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6
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Fijarczyk A, Dudek K, Babik W. Selective Landscapes in newt Immune Genes Inferred from Patterns of Nucleotide Variation. Genome Biol Evol 2016; 8:3417-3432. [PMID: 27702815 PMCID: PMC5203778 DOI: 10.1093/gbe/evw236] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Host–pathogen interactions may result in either directional selection or in pressure for the maintenance of polymorphism at the molecular level. Hence signatures of both positive and balancing selection are expected in immune genes. Because both overall selective pressure and specific targets may differ between species, large-scale population genomic studies are useful in detecting functionally important immune genes and comparing selective landscapes between taxa. Such studies are of particular interest in amphibians, a group threatened worldwide by emerging infectious diseases. Here, we present an analysis of polymorphism and divergence of 634 immune genes in two lineages of Lissotriton newts: L. montandoni and L. vulgaris graecus. Variation in newt immune genes has been shaped predominantly by widespread purifying selection and strong evolutionary constraint, implying long-term importance of these genes for functioning of the immune system. The two evolutionary lineages differ in the overall strength of purifying selection which can partially be explained by demographic history but may also signal differences in long-term pathogen pressure. The prevalent constraint notwithstanding, 23 putative targets of positive selection and 11 putative targets of balancing selection were identified. The latter were detected by composite tests involving the demographic model and further validated in independent population samples. Putative targets of balancing selection encode proteins which may interact closely with pathogens but include also regulators of immune response. The identified candidates will be useful for testing whether genes affected by balancing selection are more prone to interspecific introgression than other genes in the genome.
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Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Wieslaw Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
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7
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Swift DG, Dunning LT, Igea J, Brooks EJ, Jones CS, Noble LR, Ciezarek A, Humble E, Savolainen V. Evidence of positive selection associated with placental loss in tiger sharks. BMC Evol Biol 2016; 16:126. [PMID: 27296413 PMCID: PMC4906603 DOI: 10.1186/s12862-016-0696-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/02/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND All vertebrates initially feed their offspring using yolk reserves. In some live-bearing species these yolk reserves may be supplemented with extra nutrition via a placenta. Sharks belonging to the Carcharhinidae family are all live-bearing, and with the exception of the tiger shark (Galeocerdo cuvier), develop placental connections after exhausting yolk reserves. Phylogenetic relationships suggest the lack of placenta in tiger sharks is due to secondary loss. This represents a dramatic shift in reproductive strategy, and is likely to have left a molecular footprint of positive selection within the genome. RESULTS We sequenced the transcriptome of the tiger shark and eight other live-bearing shark species. From this data we constructed a time-calibrated phylogenetic tree estimating the tiger shark lineage diverged from the placental carcharhinids approximately 94 million years ago. Along the tiger shark lineage, we identified five genes exhibiting a signature of positive selection. Four of these genes have functions likely associated with brain development (YWHAE and ARL6IP5) and sexual reproduction (VAMP4 and TCTEX1D2). CONCLUSIONS Our results indicate the loss of placenta in tiger sharks may be associated with subsequent adaptive changes in brain development and sperm production.
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Affiliation(s)
- Dominic G Swift
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Berkshire, SL5 7PY, UK.
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Javier Igea
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EQ, UK
| | - Edward J Brooks
- Shark Research & Conservation Program, Cape Eleuthera Institute, PO Box EL - 26029, Eleuthera, the Bahamas
| | - Catherine S Jones
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland, UK
| | - Leslie R Noble
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland, UK
| | - Adam Ciezarek
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Berkshire, SL5 7PY, UK
| | - Emily Humble
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501, Bielefeld, Germany
| | - Vincent Savolainen
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Berkshire, SL5 7PY, UK.
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Neves F, Abrantes J, Esteves PJ. Evolution of CCL11: genetic characterization in lagomorphs and evidence of positive and purifying selection in mammals. Innate Immun 2016; 22:336-43. [PMID: 27189425 DOI: 10.1177/1753425916647471] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/06/2016] [Indexed: 12/27/2022] Open
Abstract
The interactions between chemokines and their receptors are crucial for differentiation and activation of inflammatory cells. CC chemokine ligand 11 (CCL11) binds to CCR3 and to CCR5 that in leporids underwent gene conversion with CCR2. Here, we genetically characterized CCL11 in lagomorphs (leporids and pikas). All lagomorphs have a potentially functional CCL11, and the Pygmy rabbit has a mutation in the stop codon that leads to a longer protein. Other mammals also have mutations at the stop codon that result in proteins with different lengths. By employing maximum likelihood methods, we observed that, in mammals, CCL11 exhibits both signatures of purifying and positive selection. Signatures of purifying selection were detected in sites important for receptor binding and activation. Of the three sites detected as under positive selection, two were located close to the stop codon. Our results suggest that CCL11 is functional in all lagomorphs, and that the signatures of purifying and positive selection in mammalian CCL11 probably reflect the protein's biological roles.
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Affiliation(s)
- Fabiana Neves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Vairão, Portugal UMIB/UP - Unidade Multidisciplinar de Investigação Biomédica/Universidade do Porto, Porto, Portugal
| | - Joana Abrantes
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - Pedro J Esteves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Vairão, Portugal Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal
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Liu X, Weidle K, Schröck K, Tönjes A, Schleinitz D, Breitfeld J, Stumvoll M, Böttcher Y, Schöneberg T, Kovacs P. Signatures of natural selection at the FTO (fat mass and obesity associated) locus in human populations. PLoS One 2015; 10:e0117093. [PMID: 25647475 PMCID: PMC4315420 DOI: 10.1371/journal.pone.0117093] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 12/18/2014] [Indexed: 11/19/2022] Open
Abstract
Background and aims Polymorphisms in the first intron of FTO have been robustly replicated for associations with obesity. In the Sorbs, a Slavic population resident in Germany, the strongest effect on body mass index (BMI) was found for a variant in the third intron of FTO (rs17818902). Since this may indicate population specific effects of FTO variants, we initiated studies testing FTO for signatures of selection in vertebrate species and human populations. Methods First, we analyzed the coding region of 35 vertebrate FTO orthologs with Phylogenetic Analysis by Maximum Likelihood (PAML, ω = dN/dS) to screen for signatures of selection among species. Second, we investigated human population (Europeans/CEU, Yoruba/YRI, Chinese/CHB, Japanese/JPT, Sorbs) SNP data for footprints of selection using DnaSP version 4.5 and the Haplotter/PhaseII. Finally, using ConSite we compared transcription factor (TF) binding sites at sequences harbouring FTO SNPs in intron three. Results PAML analyses revealed strong conservation in coding region of FTO (ω<1). Sliding-window results from population genetic analyses provided highly significant (p<0.001) signatures for balancing selection specifically in the third intron (e.g. Tajima’s D in Sorbs = 2.77). We observed several alterations in TF binding sites, e.g. TCF3 binding site introduced by the rs17818902 minor allele. Conclusion Population genetic analysis revealed signatures of balancing selection at the FTO locus with a prominent signal in intron three, a genomic region with strong association with BMI in the Sorbs. Our data support the hypothesis that genes associated with obesity may have been under evolutionary selective pressure.
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Affiliation(s)
- Xuanshi Liu
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Kerstin Weidle
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Kristin Schröck
- Institute of Biochemistry, Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | | | - Jana Breitfeld
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Yvonne Böttcher
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - Torsten Schöneberg
- Institute of Biochemistry, Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Peter Kovacs
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- * E-mail:
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10
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Brinkworth JF, Barreiro LB. The contribution of natural selection to present-day susceptibility to chronic inflammatory and autoimmune disease. Curr Opin Immunol 2014; 31:66-78. [PMID: 25458997 DOI: 10.1016/j.coi.2014.09.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/08/2014] [Accepted: 09/29/2014] [Indexed: 12/20/2022]
Abstract
Chronic inflammatory and autoimmune diseases have been the focus of many genome-wide association studies (GWAS) because they represent a significant cause of illness and morbidity, and many are heritable. Almost a decade of GWAS studies suggests that the pathological inflammation associated with these diseases is controlled by a limited number of networked immune system genes. Chronic inflammatory and autoimmune diseases are enigmatic from an evolutionary perspective because they exert a negative affect on reproductive fitness. The persistence of these conditions may be partially explained by the important roles the implicated immune genes play in pathogen defense and other functions thought to be under strong natural selection in humans. The evolutionary reasons for chronic inflammatory and autoimmune disease persistence and uneven distribution across populations are the focus of this review.
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Affiliation(s)
- Jessica F Brinkworth
- Sainte-Justine Hospital Research Centre, Montréal, Quebec H3T 1C5, Canada; Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec H3T 1J4, Canada
| | - Luis B Barreiro
- Sainte-Justine Hospital Research Centre, Montréal, Quebec H3T 1C5, Canada; Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec H3T 1J4, Canada.
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Huang BH, Liao PC. Tracing evolutionary relicts of positive selection on eight malaria-related immune genes in mammals. Innate Immun 2014; 21:463-76. [PMID: 25201904 DOI: 10.1177/1753425914547744] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 07/24/2014] [Indexed: 11/17/2022] Open
Abstract
Plasmodium-induced malaria widely infects primates and other mammals. Multiple past studies have revealed that positive selection could be the main evolutionary force triggering the genetic diversity of anti-malaria resistance-associated genes in human or primates. However, researchers focused most of their attention on the infra-generic and intra-specific genome evolution rather than analyzing the complete evolutionary history of mammals. Here we extend previous research by testing the evolutionary link of natural selection on eight candidate genes associated with malaria resistance in mammals. Three of the eight genes were detected to be affected by recombination, including TNF-α, iNOS and DARC. Positive selection was detected in the rest five immunogenes multiple times in different ancestral lineages of extant species throughout the mammalian evolution. Signals of positive selection were exposed in four malaria-related immunogenes in primates: CCL2, IL-10, HO1 and CD36. However, selection signals of G6PD have only been detected in non-primate eutherians. Significantly higher evolutionary rates and more radical amino acid replacement were also detected in primate CD36, suggesting its functional divergence from other eutherians. Prevalent positive selection throughout the evolutionary trajectory of mammalian malaria-related genes supports the arms race evolutionary hypothesis of host genetic response of mammalian immunogenes to infectious pathogens.
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Affiliation(s)
- Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan, Republic of China
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan, Republic of China
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12
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Arenas M, Posada D. Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories. Mol Biol Evol 2014; 31:1295-301. [PMID: 24557445 PMCID: PMC3995339 DOI: 10.1093/molbev/msu078] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Genomic evolution can be highly heterogeneous. Here, we introduce a new framework to simulate genome-wide sequence evolution under a variety of substitution models that may change along the genome and the phylogeny, following complex multispecies coalescent histories that can include recombination, demographics, longitudinal sampling, population subdivision/species history, and migration. A key aspect of our simulation strategy is that the heterogeneity of the whole evolutionary process can be parameterized according to statistical prior distributions specified by the user. We used this framework to carry out a study of the impact of variable codon frequencies across genomic regions on the estimation of the genome-wide nonsynonymous/synonymous ratio. We found that both variable codon frequencies across genes and rate variation among sites and regions can lead to severe underestimation of the global dN/dS values. The program SGWE—Simulation of Genome-Wide Evolution—is freely available from http://code.google.com/p/sgwe-project/, including extensive documentation and detailed examples.
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Affiliation(s)
- Miguel Arenas
- Centre for Molecular Biology "Severo Ochoa," Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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13
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Zhu Z, Wang R, Ren L, Xu T. Characterization of the CCR3 and CCR9 genes in miiuy croaker and different selection pressures imposed on different domains between mammals and teleosts. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 41:631-643. [PMID: 23817141 DOI: 10.1016/j.dci.2013.06.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Revised: 06/22/2013] [Accepted: 06/24/2013] [Indexed: 06/02/2023]
Abstract
The innate immune system can recognize non-self through pattern recognition receptors and provides a first line of antimicrobial host defense. Thus innate immunity plays a very important role in resistance against major bacterial disease in vertebrates. In the innate immune responses, the chemokine receptors act as the main receptors of chemokines which are released at the sites of infection, inflammation and injury. In this study, the Miichthys miiuy CCR3 and CCR9 genes were cloned and characterized, showing that MIMI-CCR3 possesses a highly conserved DRYLA motif similar to that of other fishes. MIMI-CCR3 and CCR9 were ubiquitously expressed in all tested tissues and the expressions were significantly up-regulated after infection with Vibrio anguillarum except that of CCR9 in spleen. Evolutionary analysis showed that all the ancestral lineages of CCR3 and CCR9 in mammals and teleosts underwent positive selection, indicating that the ancestor of terrestrial animals further evolved to adapt to terrestrial environments and the continuous intrusion of microbes stimulated the evolution of CCR genes in the ancestor of teleost. Multiple ML methods were used to detect the robust candidates for sites under positive selection. In total, 11 and 8 positively selected sites were found in the subsets of current mammal and teleost CCR3 genes, and 3 and 2 sites were detected in the subsets of current mammals and teleosts in CCR9. Interestingly, for mammal CCR3 and CCR9 genes, the robust candidates of positively selected sites were mainly located in the extracellular domains which were the ligand binding and pathogen interaction regions. For teleost CCR3 and CCR9 genes, the positively selected sites were not only located in the extracellular domains but also in the C-terminal and intracellular domains, indicating mammals and teleosts experienced different selection pressures upon their N-terminus, C-terminus and intracellular loops of CCRs.
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Affiliation(s)
- Zhihuang Zhu
- Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, PR China
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14
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Abstract
Background Molecular evolution is a very active field of research, with several complementary approaches, including dN/dS, HON90, MM01, and others. Each has documented strengths and weaknesses, and no one approach provides a clear picture of how natural selection works at the molecular level. The purpose of this work is to present a simple new method that uses quantitative amino acid properties to identify and characterize directional selection in proteins. Methods Inferred amino acid replacements are viewed through the prism of a single physicochemical property to determine the amount and direction of change caused by each replacement. This allows the calculation of the probability that the mean change in the single property associated with the amino acid replacements is equal to zero (H0: μ = 0; i.e., no net change) using a simple two-tailed t-test. Results Example data from calanoid and cyclopoid copepod cytochrome oxidase subunit I sequence pairs are presented to demonstrate how directional selection may be linked to major shifts in adaptive zones, and that convergent evolution at the whole organism level may be the result of convergent protein adaptations. Conclusions Rather than replace previous methods, this new method further complements existing methods to provide a holistic glimpse of how natural selection shapes protein structure and function over evolutionary time.
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Abstract
All multicellular organisms protect themselves against pathogens using sophisticated immune defenses. Functionally interconnected humoral and cellular facilities maintain immune homeostasis in the absence of overt infection and regulate the initiation and termination of immune responses directed against pathogens. Immune responses of invertebrates, such as flies, are innate and usually stereotyped; those of vertebrates, encompassing species as diverse as jawless fish and humans, are additionally adaptive, enabling more rapid and efficient immune reactivity upon repeated encounters with a pathogen. Many of the attributes historically defining innate and adaptive immunity are in fact common to both, blurring their functional distinction and emphasizing shared ancestry and co-evolution. These findings provide indications of the evolutionary forces underlying the origin of somatic diversification of antigen receptors and contribute to our understanding of the complex phenotypes of human immune disorders. Moreover, informed by phylogenetic considerations and inspired by improved knowledge of functional networks, new avenues emerge for innovative therapeutic strategies.
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Dass JFP, Sudandiradoss C. The function and structural influence of selective relaxed constraint at functional intracellular loop3 of 5-HT1A serotonin-1 receptor family. Gene 2012; 508:211-20. [DOI: 10.1016/j.gene.2012.07.066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 07/30/2012] [Indexed: 10/28/2022]
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Species-specific chitin-binding module 18 expansion in the amphibian pathogen Batrachochytrium dendrobatidis. mBio 2012; 3:e00150-12. [PMID: 22718849 PMCID: PMC3569864 DOI: 10.1128/mbio.00150-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Batrachochytrium dendrobatidis is the causative agent of chytridiomycosis, which is considered one of the driving forces behind the worldwide decline in populations of amphibians. As a member of the phylum Chytridiomycota, B. dendrobatidis has diverged significantly to emerge as the only pathogen of adult vertebrates. Such shifts in lifestyle are generally accompanied by various degrees of genomic modifications, yet neither its mode of pathogenicity nor any factors associated with it have ever been identified. Presented here is the identification and characterization of a unique expansion of the carbohydrate-binding module family 18 (CBM18), specific to B. dendrobatidis. CBM (chitin-binding module) expansions have been likened to the evolution of pathogenicity in a variety of fungus species, making this expanded group a prime candidate for the identification of potential pathogenicity factors. Furthermore, the CBM18 expansions are confined to three categories of genes, each having been previously implicated in host-pathogen interactions. These correlations highlight this specific domain expansion as a potential key player in the mode of pathogenicity in this unique fungus. The expansion of CBM18 in B. dendrobatidis is exceptional in its size and diversity compared to other pathogenic species of fungi, making this genomic feature unique in an evolutionary context as well as in pathogenicity. Amphibian populations are declining worldwide at an unprecedented rate. Although various factors are thought to contribute to this phenomenon, chytridiomycosis has been identified as one of the leading causes. This deadly fungal disease is cause by Batrachochytrium dendrobatidis, a chytrid fungus species unique in its pathogenicity and, furthermore, its specificity to amphibians. Despite more than two decades of research, the biology of this fungus species and its deadly interaction with amphibians had been notoriously difficult to unravel. Due to the alarming rate of worldwide spread and associated decline in amphibian populations, it is imperative to incorporate novel genomic and genetic techniques into the study of this species. In this study, we present the first reported potential pathogenicity factors in B. dendrobatidis. In silico studies such as this allow us to identify putative targets for more specific molecular analyses, furthering our hope for the control of this pathogen.
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Dass JFP, Sudandiradoss C. Insight into pattern of codon biasness and nucleotide base usage in serotonin receptor gene family from different mammalian species. Gene 2012; 503:92-100. [PMID: 22480817 DOI: 10.1016/j.gene.2012.03.057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 03/14/2012] [Accepted: 03/17/2012] [Indexed: 11/16/2022]
Abstract
5-HT (5-Hydroxy-tryptamine) or serotonin receptors are found both in central and peripheral nervous system as well as in non-neuronal tissues. In the animal and human nervous system, serotonin produces various functional effects through a variety of membrane bound receptors. In this study, we focus on 5-HT receptor family from different mammals and examined the factors that account for codon and nucleotide usage variation. A total of 110 homologous coding sequences from 11 different mammalian species were analyzed using relative synonymous codon usage (RSCU), correspondence analysis (COA) and hierarchical cluster analysis together with nucleotide base usage frequency of chemically similar amino acid codons. The mean effective number of codon (ENc) value of 37.06 for 5-HT(6) shows very high codon bias within the family and may be due to high selective translational efficiency. The COA and Spearman's rank correlation reveals that the nucleotide compositional mutation bias as the major factors influencing the codon usage in serotonin receptor genes. The hierarchical cluster analysis suggests that gene function is another dominant factor that affects the codon usage bias, while species is a minor factor. Nucleotide base usage was reported using Goldman, Engelman, Stietz (GES) scale reveals the presence of high uracil (>45%) content at functionally important hydrophobic regions. Our in silico approach will certainly help for further investigations on critical inference on evolution, structure, function and gene expression aspects of 5-HT receptors family which are potential antipsychotic drug targets.
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Affiliation(s)
- J Febin Prabhu Dass
- School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu State, India
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19
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Gong X, Padhi A. Evidence for positive selection in the extracellular domain of human cytomegalovirus encoded G protein-coupled receptor US28. J Med Virol 2011; 83:1255-61. [PMID: 21520142 DOI: 10.1002/jmv.22098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2011] [Indexed: 11/09/2022]
Abstract
The human cytomegalovirus (HCMV)-encoded chemokine receptor US28 is also a seven-transmembrane G-protein coupled receptor, whose signaling pathway is known for its involvement in host immune system evasion. HCMV infection can result in serious disease in immunocompromised individuals and is also linked to atherosclerosis and cardiovascular disease. Identifying amino acid residues that play a crucial role in successful viral adaptation in response to the host's immune defense is critical for effective drug design. In this study maximum likelihood-based codon substitution analyses were carried out to determine whether any codon of US28 has evolved adaptively. If the rate of nonsynonymous (dn) to the rate of synonymous (ds) nucleotide substitutions (ω = dn/ds) is greater than one, the codon is said to be under positive selection, indicating adaptive evolution. Although the overall ω for US28 gene was 0.154, indicating that most codon sites were subject to strong purifying selection, five codon sites are under strong positive selection. Three (E18D/L, D19A/E/G, and R267K/Q) of these positively selected sites are located in extracellular domains, the domains that play a crucial role for successful viral adaptation in response to the host's immune defense. The C-terminal (R329Q/W) and the fifth transmembrane domain (V190I), each have one positively selected site. These results suggest that relative to the extracellular domains, amino acid residues present in intracellular domains are more selectively constrained. A few amino acid residues in extracellular domains of US28 evolved more rapidly, presumably due to positive selection pressure resulting from ligand-binding and pathogen interactions of extracellular domains.
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Affiliation(s)
- Xiaoyan Gong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, China
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