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Structural and Phylogenetic Analysis of CXCR4 Protein Reveals New Insights into Its Role in Emerging and Re-Emerging Diseases in Mammals. Vaccines (Basel) 2023; 11:vaccines11030671. [PMID: 36992255 DOI: 10.3390/vaccines11030671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
Chemokine receptor type 4 (CXCR4) is a G protein-coupled receptor that plays an essential role in immune system function and disease processes. Our study aims to conduct a comparative structural and phylogenetic analysis of the CXCR4 protein to gain insights into its role in emerging and re-emerging diseases that impact the health of mammals. In this study, we analyzed the evolution of CXCR4 genes across a wide range of mammalian species. The phylogenetic study showed species-specific evolutionary patterns. Our analysis revealed novel insights into the evolutionary history of CXCR4, including genetic changes that may have led to functional differences in the protein. This study revealed that the structural homologous human proteins and mammalian CXCR4 shared many characteristics. We also examined the three-dimensional structure of CXCR4 and its interactions with other molecules in the cell. Our findings provide new insights into the genomic landscape of CXCR4 in the context of emerging and re-emerging diseases, which could inform the development of more effective treatments or prevention strategies. Overall, our study sheds light on the vital role of CXCR4 in mammalian health and disease, highlighting its potential as a therapeutic target for various diseases impacting human and animal health. These findings provided insight into the study of human immunological disorders by indicating that Chemokines may have activities identical to or similar to those in humans and several mammalian species.
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Wilson RE, Sonsthagen SA, Smé N, Gharrett AJ, Majewski AR, Wedemeyer K, Nelson RJ, Talbot SL. Mitochondrial genome diversity and population mitogenomics of polar cod (Boreogadus saida) and Arctic dwelling gadoids. Polar Biol 2020. [DOI: 10.1007/s00300-020-02703-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Lee-Yaw JA, Grassa CJ, Joly S, Andrew RL, Rieseberg LH. An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus). THE NEW PHYTOLOGIST 2019; 221:515-526. [PMID: 30136727 DOI: 10.1111/nph.15386] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 07/05/2018] [Indexed: 05/03/2023]
Abstract
Cytonuclear discordance is commonly observed in phylogenetic studies, yet few studies have tested whether these patterns reflect incomplete lineage sorting or organellar introgression. Here, we used whole-chloroplast sequence data in combination with over 1000 nuclear single-nucleotide polymorphisms to clarify the extent of cytonuclear discordance in wild annual sunflowers (Helianthus), and to test alternative explanations for such discordance. Our phylogenetic analyses indicate that cytonuclear discordance is widespread within this group, both in terms of the relationships among species and among individuals within species. Simulations of chloroplast evolution show that incomplete lineage sorting cannot explain these patterns in most cases. Instead, most of the observed discordance is better explained by cytoplasmic introgression. Molecular tests of evolution further indicate that selection may have played a role in driving patterns of plastid variation - although additional experimental work is needed to fully evaluate the importance of selection on organellar variants in different parts of the geographic range. Overall, this study represents one of the most comprehensive tests of the drivers of cytonuclear discordance and highlights the potential for gene flow to lead to extensive organellar introgression in hybridizing taxa.
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Affiliation(s)
- Julie A Lee-Yaw
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Christopher J Grassa
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Harvard University Herbaria, Cambridge, MA, 02138, USA
| | - Simon Joly
- Institut Recherche en Biologie Végétale, QC, H1X 2B2, Canada
- Jardin botanique de Montréal, Department Sciences Biologiques, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Rose L Andrew
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Diaz F, Allan CW, Matzkin LM. Positive selection at sites of chemosensory genes is associated with the recent divergence and local ecological adaptation in cactophilic Drosophila. BMC Evol Biol 2018; 18:144. [PMID: 30236055 PMCID: PMC6148956 DOI: 10.1186/s12862-018-1250-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/20/2018] [Indexed: 11/25/2022] Open
Abstract
Background Adaptation to new hosts in phytophagous insects often involves mechanisms of host recognition by genes of sensory pathways. Most often the molecular evolution of sensory genes has been explained in the context of the birth-and-death model. The role of positive selection is less understood, especially associated with host adaptation and specialization. Here we aim to contribute evidence for this latter hypothesis by considering the case of Drosophila mojavensis, a species with an evolutionary history shaped by multiple host shifts in a relatively short time scale, and its generalist sister species, D. arizonae. Results We used a phylogenetic and population genetic analysis framework to test for positive selection in a subset of four chemoreceptor genes, one gustatory receptor (Gr) and three odorant receptors (Or), for which their expression has been previously associated with host shifts. We found strong evidence of positive selection at several amino acid sites in all genes investigated, most of which exhibited changes predicted to cause functional effects in these transmembrane proteins. A significant portion of the sites identified as evolving positively were largely found in the cytoplasmic region, although a few were also present in the extracellular domains. Conclusions The pattern of substitution observed suggests that some of these changes likely had an effect on signal transduction as well as odorant recognition and protein-protein interactions. These findings support the role of positive selection in shaping the pattern of variation at chemosensory receptors, both during the specialization onto one or a few related hosts, but as well as during the evolution and adaptation of generalist species into utilizing several hosts. Electronic supplementary material The online version of this article (10.1186/s12862-018-1250-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fernando Diaz
- Department of Entomology, University of Arizona, Tucson, AZ, 85721, USA
| | - Carson W Allan
- Department of Entomology, University of Arizona, Tucson, AZ, 85721, USA
| | - Luciano M Matzkin
- Department of Entomology, University of Arizona, Tucson, AZ, 85721, USA. .,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA. .,BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA.
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Velová H, Gutowska-Ding MW, Burt DW, Vinkler M. Toll-Like Receptor Evolution in Birds: Gene Duplication, Pseudogenization, and Diversifying Selection. Mol Biol Evol 2018; 35:2170-2184. [PMID: 29893911 PMCID: PMC6107061 DOI: 10.1093/molbev/msy119] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Toll-like receptors (TLRs) are key sensor molecules in vertebrates triggering initial phases of immune responses to pathogens. The avian TLR family typically consists of ten receptors, each adapted to distinct ligands. To understand the complex evolutionary history of each avian TLR, we analyzed all members of the TLR family in the whole genome assemblies and target sequence data of 63 bird species covering all major avian clades. Our results indicate that gene duplication events most probably occurred in TLR1 before synapsids diversified from sauropsids. Unlike mammals, ssRNA-recognizing TLR7 has duplicated independently in several avian taxa, while flagellin-sensing TLR5 has pseudogenized multiple times in bird phylogeny. Our analysis revealed stronger positive, diversifying selection acting in TLR5 and the three-domain TLRs (TLR10 [TLR1A], TLR1 [TLR1B], TLR2A, TLR2B, TLR4) that face the extracellular space and bind complex ligands than in single-domain TLR15 and endosomal TLRs (TLR3, TLR7, TLR21). In total, 84 out of 306 positively selected sites were predicted to harbor substitutions dramatically changing the amino acid physicochemical properties. Furthermore, 105 positively selected sites were located in the known functionally relevant TLR regions. We found evidence for convergent evolution acting between birds and mammals at 54 of these sites. Our comparative study provides a comprehensive insight into the evolution of avian TLR genetic variability. Besides describing the history of avian TLR gene gain and gene loss, we also identified candidate positions in the receptors that have been likely shaped by direct molecular host-pathogen coevolutionary interactions and most probably play key functional roles in birds.
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Affiliation(s)
- Hana Velová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Maria W Gutowska-Ding
- Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The Roslin Institute Building, University of Edinburgh, Midlothian, United Kingdom
| | - David W Burt
- Office of DVC (Research), University of Queensland, St. Lucia, QLD, Australia
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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Shepherd FK, Murtaugh MP, Chen F, Culhane MR, Marthaler DG. Longitudinal Surveillance of Porcine Rotavirus B Strains from the United States and Canada and In Silico Identification of Antigenically Important Sites. Pathogens 2017; 6:pathogens6040064. [PMID: 29207506 PMCID: PMC5750588 DOI: 10.3390/pathogens6040064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 11/29/2017] [Accepted: 11/30/2017] [Indexed: 12/20/2022] Open
Abstract
Rotavirus B (RVB) is an important swine pathogen, but control and prevention strategies are limited without an available vaccine. To develop a subunit RVB vaccine with maximal effect, we characterized the amino acid sequence variability and predicted antigenicity of RVB viral protein 7 (VP7), a major neutralizing antibody target, from clinically infected pigs in the United States and Canada. We identified genotype-specific antigenic sites that may be antibody neutralization targets. While some antigenic sites had high amino acid functional group diversity, nine antigenic sites were completely conserved. Analysis of nucleotide substitution rates at amino acid sites (dN/dS) suggested that negative selection appeared to be playing a larger role in the evolution of the identified antigenic sites when compared to positive selection, and was identified in six of the nine conserved antigenic sites. These results identified important characteristics of RVB VP7 variability and evolution and suggest antigenic residues on RVB VP7 that are negatively selected and highly conserved may be good candidate regions to include in a subunit vaccine design due to their tendency to remain stable.
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Affiliation(s)
- Frances K Shepherd
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA.
| | - Michael P Murtaugh
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA.
| | - Fangzhou Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
| | - Marie R Culhane
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1365 Gortner Avenue, St. Paul, MN 55108, USA.
| | - Douglas G Marthaler
- Veterinary Diagnostic Laboratory, Kansas State University, 1800 Denison Ave, Manhattan, KS 66506, USA.
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Abstract
Evidence is mounting that the major histocompatibility complex (MHC) molecule HLA-F (human leukocyte antigen F) regulates the immune system in pregnancy, infection, and autoimmunity by signaling through NK cell receptors (NKRs). We present structural, biochemical, and evolutionary analyses demonstrating that HLA-F presents peptides of unconventional length dictated by a newly arisen mutation (R62W) that has produced an open-ended groove accommodating particularly long peptides. Compared to empty HLA-F open conformers (OCs), HLA-F tetramers bound with human-derived peptides differentially stained leukocytes, suggesting peptide-dependent engagement. Our in vitro studies confirm that NKRs differentiate between peptide-bound and peptide-free HLA-F. The complex structure of peptide-loaded β2m-HLA-F bound to the inhibitory LIR1 revealed similarities to high-affinity recognition of the viral MHC-I mimic UL18 and a docking strategy that relies on contacts with HLA-F as well as β2m, thus precluding binding to HLA-F OCs. These findings provide a biochemical framework to understand how HLA-F could regulate immunity via interactions with NKRs.
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Campanini EB, de Brito RA. Molecular evolution of Odorant-binding proteins gene family in two closely related Anastrepha fruit flies. BMC Evol Biol 2016; 16:198. [PMID: 27716035 PMCID: PMC5054612 DOI: 10.1186/s12862-016-0775-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 09/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Odorant-binding proteins (OBPs) are of great importance for survival and reproduction since they participate in initial steps of the olfactory signal transduction cascade, solubilizing and transporting chemical signals to the olfactory receptors. A comparative analysis of OBPs between closely related species may help explain how these genes evolve and are maintained under natural selection and how differences in these proteins can affect olfactory responses. We studied OBP genes in the closely related species Anastrepha fraterculus and A. obliqua, which have different host preferences, using data from RNA-seq cDNA libraries of head and reproductive tissues from male and female adults, aiming to understand the speciation process occurred between them. RESULTS We identified 23 different OBP sequences from Anastrepha fraterculus and 24 from A. obliqua, which correspond to 20 Drosophila melanogaster OBP genes. Phylogenetic analysis separated Anastrepha OBPs sequences in four branches that represent four subfamilies: classic, minus-C, plus-C and dimer. Both species showed five plus-C members, which is the biggest number found in tephritids until now. We found evidence of positive selection in four genes and at least one duplication event that preceded the speciation of these two species. Inferences on tertiary structures of putative proteins from these genes revealed that at least one positively selected change involves the binding cavity (the odorant binding region) in the plus-C OBP50a. CONCLUSIONS A. fraterculus and A. obliqua have a bigger OBP repertoire than the other tephritids studied, though the total number of Anastrepha OBPs may be larger, since we studied only a limited number of tissues. The contrast of these closely related species reveals that there are several amino acid changes between the homologous genes, which might be related to their host preferences. The plus-C OBP that has one amino acid under positive selection located in the binding cavity may be under a selection pressure to recognize and bind a new odorant. The other positively selected sites found may be involved in important structural and functional changes, especially ones in which site-specific changes would radically change amino acid properties.
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Affiliation(s)
- Emeline Boni Campanini
- Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washington Luís km235, 13565-905 São Carlos, São Paulo Brasil
| | - Reinaldo Alves de Brito
- Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washington Luís km235, 13565-905 São Carlos, São Paulo Brasil
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Huang BH, Chen YW, Huang CL, Gao J, Liao PC. Diversifying selection of the anthocyanin biosynthetic downstream gene UFGT accelerates floral diversity of island Scutellaria species. BMC Evol Biol 2016; 16:191. [PMID: 27639694 PMCID: PMC5027097 DOI: 10.1186/s12862-016-0759-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/05/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Adaptive divergence, which usually explains rapid diversification within island species, might involve the positive selection of genes. Anthocyanin biosynthetic pathway (ABP) genes are important for floral diversity, and are related to stress resistance and pollination, which could be responsible for species diversification. Previous studies have shown that upstream genes of ABP are subject to selective constraints and have a slow evolutionary rate, while the constraints on downstream genes are lower. RESULTS In this study, we confirmed these earlier observations of heterogeneous evolutionary rate in upstream gene CHS and the downstream gene UFGT, both of which were expressed in Scutellaria sp. inflorescence buds. We found a higher evolutionary rate and positive selection for UFGT. The codons under positive selection corresponded to the diversified regions, and the presence or absence of an α-helix might produce conformation changes in the Rossmann-like fold structure. The significantly high evolutionary rates for UFGT genes in Taiwanese lineages suggested rapid accumulation of amino acid mutations in island species. The results showed positive selection in closely related species and explained the high diversification of floral patterns in these recently diverged species. In contrast, non-synonymous mutation rate decreases in long-term divergent species could reduce mutational load and prevent the accumulation of deleterious mutations. CONCLUSIONS Together with the positive selection of transcription factors for ABP genes described in a previous study, these results confirmed that positive selection takes place at a translational level and suggested that the high divergence of ABP genes is related to the floral diversity in island Scutellaria species.
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Affiliation(s)
- Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, No. 88, Ting-Chow Rd, Sec 4, Taipei, Taiwan 11677 Republic of China
| | - Yi-Wen Chen
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Pingtung, Taiwan 91201 Republic of China
| | - Chia-Lung Huang
- Department of Life Science, National Taiwan Normal University, No. 88, Ting-Chow Rd, Sec 4, Taipei, Taiwan 11677 Republic of China
| | - Jian Gao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, No.35, Tsinghua East Road, Beijing, 100083 China
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, No. 88, Ting-Chow Rd, Sec 4, Taipei, Taiwan 11677 Republic of China
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10
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Simões BF, Sampaio FL, Douglas RH, Kodandaramaiah U, Casewell NR, Harrison RA, Hart NS, Partridge JC, Hunt DM, Gower DJ. Visual Pigments, Ocular Filters and the Evolution of Snake Vision. Mol Biol Evol 2016; 33:2483-95. [DOI: 10.1093/molbev/msw148] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Zehender G, Sorrentino C, Veo C, Fiaschi L, Gioffrè S, Ebranati E, Tanzi E, Ciccozzi M, Lai A, Galli M. Distribution of Marburg virus in Africa: An evolutionary approach. INFECTION GENETICS AND EVOLUTION 2016; 44:8-16. [PMID: 27282469 DOI: 10.1016/j.meegid.2016.06.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/01/2016] [Accepted: 06/04/2016] [Indexed: 10/21/2022]
Abstract
The aim of this study was to investigate the origin and geographical dispersion of Marburg virus, the first member of the Filoviridae family to be discovered. Seventy-three complete genome sequences of Marburg virus isolated from animals and humans were retrieved from public databases and analysed using a Bayesian phylogeographical framework. The phylogenetic tree of the Marburg virus data set showed two significant evolutionary lineages: Ravn virus (RAVV) and Marburg virus (MARV). MARV divided into two main clades; clade A included isolates from Uganda (five from the European epidemic in 1967), Kenya (1980) and Angola (from the epidemic of 2004-2005); clade B included most of the isolates obtained during the 1999-2000 epidemic in the Democratic Republic of the Congo (DRC) and a group of Ugandan isolates obtained in 2007-2009. The estimated mean evolutionary rate of the whole genome was 3.3×10(-4) substitutions/site/year (credibility interval 2.0-4.8). The MARV strain had a mean root time of the most recent common ancestor of 177.9years ago (YA) (95% highest posterior density 87-284), thus indicating that it probably originated in the mid-XIX century, whereas the RAVV strain had a later origin dating back to a mean 33.8 YA. The most probable location of the MARV ancestor was Uganda (state posterior probability, spp=0.41), whereas that of the RAVV ancestor was Kenya (spp=0.71). There were significant migration rates from Uganda to the DRC (Bayes Factor, BF=42.0) and in the opposite direction (BF=5.7). Our data suggest that Uganda may have been the cradle of Marburg virus in Africa.
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Affiliation(s)
- Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy.
| | - Chiara Sorrentino
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Carla Veo
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Lisa Fiaschi
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Sonia Gioffrè
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Erika Ebranati
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Elisabetta Tanzi
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Massimo Ciccozzi
- Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
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Almeida D, Maldonado E, Khan I, Silva L, Gilbert MTP, Zhang G, Jarvis ED, O'Brien SJ, Johnson WE, Antunes A. Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds. Genome Biol Evol 2016; 8:1115-31. [PMID: 26979796 PMCID: PMC4860681 DOI: 10.1093/gbe/evw041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2016] [Indexed: 12/19/2022] Open
Abstract
The cytochrome P450 (CYP) superfamily defends organisms from endogenous and noxious environmental compounds, and thus is crucial for survival. However, beyond mammals the molecular evolution of CYP2 subfamilies is poorly understood. Here, we characterized the CYP2 family across 48 avian whole genomes representing all major extant bird clades. Overall, 12 CYP2 subfamilies were identified, including the first description of the CYP2F, CYP2G, and several CYP2AF genes in avian genomes. Some of the CYP2 genes previously described as being lineage-specific, such as CYP2K and CYP2W, are ubiquitous to all avian groups. Furthermore, we identified a large number of CYP2J copies, which have been associated previously with water reabsorption. We detected positive selection in the avian CYP2C, CYP2D, CYP2H, CYP2J, CYP2K, and CYP2AC subfamilies. Moreover, we identified new substrate recognition sites (SRS0, SRS2_SRS3, and SRS3.1) and heme binding areas that influence CYP2 structure and function of functional importance as under significant positive selection. Some of the positively selected sites in avian CYP2D are located within the same SRS1 region that was previously linked with the metabolism of plant toxins. Additionally, we find that selective constraint variations in some avian CYP2 subfamilies are consistently associated with different feeding habits (CYP2H and CYP2J), habitats (CYP2D, CYP2H, CYP2J, and CYP2K), and migratory behaviors (CYP2D, CYP2H, and CYP2J). Overall, our findings indicate that there has been active enzyme site selection on CYP2 subfamilies and differential selection associated with different life history traits among birds.
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Affiliation(s)
- Daniela Almeida
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - Emanuel Maldonado
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal
| | - Imran Khan
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - Liliana Silva
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzen, China Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Erich D Jarvis
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia Oceanographic Center, Nova Southeastern University, Ft Lauderdale
| | - Warren E Johnson
- National Zoological Park, Smithsonian Conservation Biology Institute, Washington DC
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Portugal
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Bataille A, Cashins SD, Grogan L, Skerratt LF, Hunter D, McFadden M, Scheele B, Brannelly LA, Macris A, Harlow PS, Bell S, Berger L, Waldman B. Susceptibility of amphibians to chytridiomycosis is associated with MHC class II conformation. Proc Biol Sci 2015; 282:rspb.2014.3127. [PMID: 25808889 PMCID: PMC4389617 DOI: 10.1098/rspb.2014.3127] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The pathogenic chytrid fungus Batrachochytrium dendrobatidis (Bd) can cause precipitous population declines in its amphibian hosts. Responses of individuals to infection vary greatly with the capacity of their immune system to respond to the pathogen. We used a combination of comparative and experimental approaches to identify major histocompatibility complex class II (MHC-II) alleles encoding molecules that foster the survival of Bd-infected amphibians. We found that Bd-resistant amphibians across four continents share common amino acids in three binding pockets of the MHC-II antigen-binding groove. Moreover, strong signals of selection acting on these specific sites were evident among all species co-existing with the pathogen. In the laboratory, we experimentally inoculated Australian tree frogs with Bd to test how each binding pocket conformation influences disease resistance. Only the conformation of MHC-II pocket 9 of surviving subjects matched those of Bd-resistant species. This MHC-II conformation thus may determine amphibian resistance to Bd, although other MHC-II binding pockets also may contribute to resistance. Rescuing amphibian biodiversity will depend on our understanding of amphibian immune defence mechanisms against Bd. The identification of adaptive genetic markers for Bd resistance represents an important step forward towards that goal.
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Affiliation(s)
- Arnaud Bataille
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea
| | - Scott D Cashins
- School of Public Health, Tropical Medicine and Rehabilitation Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Laura Grogan
- School of Public Health, Tropical Medicine and Rehabilitation Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Lee F Skerratt
- School of Public Health, Tropical Medicine and Rehabilitation Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - David Hunter
- New South Wales Office of Environment and Heritage, Biodiversity Conservation Section, Queanbeyan, New South Wales 2620, Australia
| | - Michael McFadden
- Taronga Conservation Society Australia, Herpetofauna Division, Mosman, New South Wales 2088, Australia
| | - Benjamin Scheele
- Fenner School of Environment and Society, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Laura A Brannelly
- School of Public Health, Tropical Medicine and Rehabilitation Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Amy Macris
- Fenner School of Environment and Society, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Peter S Harlow
- Taronga Conservation Society Australia, Herpetofauna Division, Mosman, New South Wales 2088, Australia
| | - Sara Bell
- School of Public Health, Tropical Medicine and Rehabilitation Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Lee Berger
- School of Public Health, Tropical Medicine and Rehabilitation Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Bruce Waldman
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea
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Scienski K, Fay JC, Conant GC. Patterns of Gene Conversion in Duplicated Yeast Histones Suggest Strong Selection on a Coadapted Macromolecular Complex. Genome Biol Evol 2015; 7:3249-58. [PMID: 26560339 PMCID: PMC4700949 DOI: 10.1093/gbe/evv216] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We find evidence for interlocus gene conversion in five duplicated histone genes from six yeast species. The sequences of these duplicated genes, surviving from the ancient genome duplication, show phylogenetic patterns inconsistent with the well-resolved orthology relationships inferred from a likelihood model of gene loss after the genome duplication. Instead, these paralogous genes are more closely related to each other than any is to its nearest ortholog. In addition to simulations supporting gene conversion, we also present evidence for elevated rates of radical amino acid substitutions along the branches implicated in the conversion events. As these patterns are similar to those seen in ribosomal proteins that have undergone gene conversion, we speculate that in cases where duplicated genes code for proteins that are a part of tightly interacting complexes, selection may favor the fixation of gene conversion events in order to maintain high protein identities between duplicated copies.
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Affiliation(s)
- Kathy Scienski
- Division of Animal Sciences, University of Missouri, Columbia Present address: Genetics Graduate Program, Texas A&M University, College Station, TX
| | - Justin C Fay
- Department of Genetics, Washington University Center for Genome Sciences and Systems Biology, Washington University
| | - Gavin C Conant
- Division of Animal Sciences, University of Missouri, Columbia Informatics Institute, University of Missouri, Columbia
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15
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Oellermann M, Strugnell JM, Lieb B, Mark FC. Positive selection in octopus haemocyanin indicates functional links to temperature adaptation. BMC Evol Biol 2015; 15:133. [PMID: 26142723 PMCID: PMC4491423 DOI: 10.1186/s12862-015-0411-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 06/04/2015] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Octopods have successfully colonised the world's oceans from the tropics to the poles. Yet, successful persistence in these habitats has required adaptations of their advanced physiological apparatus to compensate impaired oxygen supply. Their oxygen transporter haemocyanin plays a major role in cold tolerance and accordingly has undergone functional modifications to sustain oxygen release at sub-zero temperatures. However, it remains unknown how molecular properties evolved to explain the observed functional adaptations. We thus aimed to assess whether natural selection affected molecular and structural properties of haemocyanin that explains temperature adaptation in octopods. RESULTS Analysis of 239 partial sequences of the haemocyanin functional units (FU) f and g of 28 octopod species of polar, temperate, subtropical and tropical origin revealed natural selection was acting primarily on charge properties of surface residues. Polar octopods contained haemocyanins with higher net surface charge due to decreased glutamic acid content and higher numbers of basic amino acids. Within the analysed partial sequences, positive selection was present at site 2545, positioned between the active copper binding centre and the FU g surface. At this site, methionine was the dominant amino acid in polar octopods and leucine was dominant in tropical octopods. Sites directly involved in oxygen binding or quaternary interactions were highly conserved within the analysed sequence. CONCLUSIONS This study has provided the first insight into molecular and structural mechanisms that have enabled octopods to sustain oxygen supply from polar to tropical conditions. Our findings imply modulation of oxygen binding via charge-charge interaction at the protein surface, which stabilize quaternary interactions among functional units to reduce detrimental effects of high pH on venous oxygen release. Of the observed partial haemocyanin sequence, residue 2545 formed a close link between the FU g surface and the active centre, suggesting a role as allosteric binding site. The prevalence of methionine at this site in polar octopods, implies regulation of oxygen affinity via increased sensitivity to allosteric metal binding. High sequence conservation of sites directly involved in oxygen binding indicates that functional modifications of octopod haemocyanin rather occur via more subtle mechanisms, as observed in this study.
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Affiliation(s)
- Michael Oellermann
- Integrative Ecophysiology, Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany.
| | - Jan M Strugnell
- Department of Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia.
| | - Bernhard Lieb
- Institute of Zoology, Johannes Gutenberg-Universität, Müllerweg 6, 55099, Mainz, Germany.
| | - Felix C Mark
- Integrative Ecophysiology, Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany.
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16
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Dueholm B, Krieger C, Drew D, Olry A, Kamo T, Taboureau O, Weitzel C, Bourgaud F, Hehn A, Simonsen HT. Evolution of substrate recognition sites (SRSs) in cytochromes P450 from Apiaceae exemplified by the CYP71AJ subfamily. BMC Evol Biol 2015; 15:122. [PMID: 26111527 PMCID: PMC4482195 DOI: 10.1186/s12862-015-0396-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 05/29/2015] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Large proliferations of cytochrome P450 encoding genes resulting from gene duplications can be termed as 'blooms', providing genetic material for the genesis and evolution of biosynthetic pathways. Furanocoumarins are allelochemicals produced by many of the species in Apiaceaous plants belonging to the Apioideae subfamily of Apiaceae and have been described as being involved in the defence reaction against phytophageous insects. RESULTS A bloom in the cytochromes P450 CYP71AJ subfamily has been identified, showing at least 2 clades and 6 subclades within the CYP71AJ subfamily. Two of the subclades were functionally assigned to the biosynthesis of furanocoumarins. Six substrate recognition sites (SRS1-6) important for the enzymatic conversion were investigated in the described cytochromes P450 and display significant variability within the CYP71AJ subfamily. Homology models underline a significant modification of the accession to the iron atom, which might explain the difference of the substrate specificity between the cytochromes P450 restricted to furanocoumarins as substrates and the orphan CYP71AJ. CONCLUSION Two subclades functionally assigned to the biosynthesis of furanocoumarins and four other subclades were identified and shown to be part of two distinct clades within the CYP71AJ subfamily. The subclades show significant variability within their substrate recognition sites between the clades, suggesting different biochemical functions and providing insights into the evolution of cytochrome P450 'blooms' in response to environmental pressures.
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Affiliation(s)
- Bjørn Dueholm
- University of Copenhagen, Department of Plant and Environmental Science, Copenhagen Plant Science Centre, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
- University of South Australia, School of Pharmacy and Medical Sciences, Adelaide, South Australia.
| | - Célia Krieger
- UMR1121 Université de Lorraine, 2 Avenue de la Forêt de Haye, 54518, Vandoeuvre-les-Nancy, France.
- UMR1121 INRA, 2 Avenue de la Forêt de Haye, 54518, Vandoeuvre-les-Nancy, France.
| | - Damian Drew
- University of Copenhagen, Department of Plant and Environmental Science, Copenhagen Plant Science Centre, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
| | - Alexandre Olry
- UMR1121 Université de Lorraine, 2 Avenue de la Forêt de Haye, 54518, Vandoeuvre-les-Nancy, France.
- UMR1121 INRA, 2 Avenue de la Forêt de Haye, 54518, Vandoeuvre-les-Nancy, France.
| | - Tsunashi Kamo
- UMR1121 Université de Lorraine, 2 Avenue de la Forêt de Haye, 54518, Vandoeuvre-les-Nancy, France.
- UMR1121 INRA, 2 Avenue de la Forêt de Haye, 54518, Vandoeuvre-les-Nancy, France.
- National Institute for Agro-Environmental Sciences, 3-1-3 Kan-nondai, Tsukuba, 305-8604, Ibaraki, Japan.
| | - Olivier Taboureau
- Technical University of Denmark, Centre for Biological and Sequence Analysis (CBS), Anker Engelunds Vej 1, 2800, Kgs. Lyngby, Denmark.
- Molécules Thérapeutiques in silice (MTi), Inserm UMR-S 973 - Université Paris Diderot, Bat Lamarck A, 35 Rue Hélène Brion, 75205, Paris, France.
| | - Corinna Weitzel
- University of Copenhagen, Department of Plant and Environmental Science, Copenhagen Plant Science Centre, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
- UMR1121 Université de Lorraine, 2 Avenue de la Forêt de Haye, 54518, Vandoeuvre-les-Nancy, France.
- UMR1121 INRA, 2 Avenue de la Forêt de Haye, 54518, Vandoeuvre-les-Nancy, France.
| | - Frédéric Bourgaud
- UMR1121 Université de Lorraine, 2 Avenue de la Forêt de Haye, 54518, Vandoeuvre-les-Nancy, France.
- UMR1121 INRA, 2 Avenue de la Forêt de Haye, 54518, Vandoeuvre-les-Nancy, France.
| | - Alain Hehn
- UMR1121 Université de Lorraine, 2 Avenue de la Forêt de Haye, 54518, Vandoeuvre-les-Nancy, France.
- UMR1121 INRA, 2 Avenue de la Forêt de Haye, 54518, Vandoeuvre-les-Nancy, France.
| | - Henrik Toft Simonsen
- University of Copenhagen, Department of Plant and Environmental Science, Copenhagen Plant Science Centre, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
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Edlefsen PT, Rolland M, Hertz T, Tovanabutra S, Gartland AJ, deCamp AC, Magaret CA, Ahmed H, Gottardo R, Juraska M, McCoy C, Larsen BB, Sanders-Buell E, Carrico C, Menis S, Bose M, Arroyo MA, O’Connell RJ, Nitayaphan S, Pitisuttithum P, Kaewkungwal J, Rerks-Ngarm S, Robb ML, Kirys T, Georgiev IS, Kwong PD, Scheffler K, Pond SLK, Carlson JM, Michael NL, Schief WR, Mullins JI, Kim JH, Gilbert PB. Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial. PLoS Comput Biol 2015; 11:e1003973. [PMID: 25646817 PMCID: PMC4315437 DOI: 10.1371/journal.pcbi.1003973] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/08/2014] [Indexed: 01/25/2023] Open
Abstract
The RV144 clinical trial showed the partial efficacy of a vaccine regimen with an estimated vaccine efficacy (VE) of 31% for protecting low-risk Thai volunteers against acquisition of HIV-1. The impact of vaccine-induced immune responses can be investigated through sieve analysis of HIV-1 breakthrough infections (infected vaccine and placebo recipients). A V1/V2-targeted comparison of the genomes of HIV-1 breakthrough viruses identified two V2 amino acid sites that differed between the vaccine and placebo groups. Here we extended the V1/V2 analysis to the entire HIV-1 genome using an array of methods based on individual sites, k-mers and genes/proteins. We identified 56 amino acid sites or "signatures" and 119 k-mers that differed between the vaccine and placebo groups. Of those, 19 sites and 38 k-mers were located in the regions comprising the RV144 vaccine (Env-gp120, Gag, and Pro). The nine signature sites in Env-gp120 were significantly enriched for known antibody-associated sites (p = 0.0021). In particular, site 317 in the third variable loop (V3) overlapped with a hotspot of antibody recognition, and sites 369 and 424 were linked to CD4 binding site neutralization. The identified signature sites significantly covaried with other sites across the genome (mean = 32.1) more than did non-signature sites (mean = 0.9) (p < 0.0001), suggesting functional and/or structural relevance of the signature sites. Since signature sites were not preferentially restricted to the vaccine immunogens and because most of the associations were insignificant following correction for multiple testing, we predict that few of the genetic differences are strongly linked to the RV144 vaccine-induced immune pressure. In addition to presenting results of the first complete-genome analysis of the breakthrough infections in the RV144 trial, this work describes a set of statistical methods and tools applicable to analysis of breakthrough infection genomes in general vaccine efficacy trials for diverse pathogens.
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Affiliation(s)
- Paul T. Edlefsen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Morgane Rolland
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Tomer Hertz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- The Shraga Segal Dept. of Microbiology, Immunology and Genetics, Faculty of Health Sciences, and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Sodsai Tovanabutra
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Andrew J. Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Allan C. deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Craig A. Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Hasan Ahmed
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michal Juraska
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Connor McCoy
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Brendan B. Larsen
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Eric Sanders-Buell
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Chris Carrico
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California, United States of America
| | - Sergey Menis
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California, United States of America
| | - Meera Bose
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | | | | | | | | | | | | | | | - Merlin L. Robb
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Tatsiana Kirys
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Ivelin S. Georgiev
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Peter D. Kwong
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Konrad Scheffler
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Sergei L. Kosakovsky Pond
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Jonathan M. Carlson
- eSience Research Group, Microsoft Research, Redmond, Washington, United States of America
| | - Nelson L. Michael
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - William R. Schief
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Jerome H. Kim
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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18
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Filipi K, Marková S, Searle JB, Kotlík P. Mitogenomic phylogenetics of the bank vole Clethrionomys glareolus, a model system for studying end-glacial colonization of Europe. Mol Phylogenet Evol 2014; 82 Pt A:245-57. [PMID: 25450101 DOI: 10.1016/j.ympev.2014.10.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/17/2014] [Accepted: 10/22/2014] [Indexed: 10/24/2022]
Abstract
We have revisited the mtDNA phylogeny of the bank vole Clethrionomys glareolus based on Sanger and next-generation Illumina sequencing of 32 complete mitochondrial genomes. The bank vole is a key study species for understanding the response of European fauna to the climate change following the Last Glacial Maximum (LGM) and one of the most convincing examples of a woodland mammal surviving in cryptic northern glacial refugia in Europe. The genomes sequenced included multiple representatives of each of the eight bank vole clades previously described based on cytochrome b (cob) sequences. All clades with the exception of the Basque - likely a misidentified pseudogene clade - were highly supported in all phylogenetic analyses and the relationships between the clades were resolved with high confidence. Our data extend the distribution of the Carpathian clade, the marker of a northern glacial refugium in the Carpathian Mountains, to include Britain and Fennoscandia (but not adjacent areas of continental Europe). The Carpathian sub-clade that colonized Britain and Fennoscandia had a somewhat different history from the sub-clade currently found in or close to the Carpathians and may have derived from a more north-westerly refugial area. The two bank vole populations that colonized Britain at the end of the last glaciation are for the first time linked with particular continental clades, the first colonists with the Carpathian clade and the second colonists with the western clade originating in a more southerly refugium in the vicinity of the Alps. We however found no evidence that a functional divergence of proteins encoded in the mitochondrial genome promoted the partial genetic replacement of the first colonists by the second colonists detected previously in southern Britain. We did identify one codon site that changed more often and more radically in the tree than expected and where the observed amino acid change may affect the reductase activity of the cytochrome bc1 complex, but the change was not specific to a particular clade. We also found an excess of radical changes to the primary protein structure for geographically restricted clades from southern Italy and Norway, respectively, possibly related to stronger selective pressure at the latitudinal extremes of the bank vole distribution. However, overall, we find little evidence of pervasive effects of deviation from neutrality on bank vole mtDNA phylogeography.
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Affiliation(s)
- Karolína Filipi
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 27721 Liběchov, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 12844 Prague 2, Czech Republic
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 27721 Liběchov, Czech Republic
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 27721 Liběchov, Czech Republic.
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Molecular evolutionary history of Sugarcane yellow leaf virus based on sequence analysis of RNA-dependent RNA polymerase and putative aphid transmission factor-coding genes. J Mol Evol 2014; 78:349-65. [PMID: 24952671 DOI: 10.1007/s00239-014-9630-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 06/12/2014] [Indexed: 10/25/2022]
Abstract
RNA-dependent RNA polymerase (RdRp) encoded by ORF2 and putative aphid transmission factor (PATF) encoded by ORF5 of Sugarcane yellow leaf virus (SCYLV) were detected in six sugarcane cultivars affected by yellow leaf using RT-PCR and real-time RT-PCR assays. Expression of both genes varied among infected plants, but overall expression of RdRp was higher than expression of PATF. Cultivar H87-4094 from Hawaii yielded the highest transcript levels of RdRp, whereas cultivar C1051-73 from Cuba exhibited the lowest levels. Sequence comparisons among 25 SCYLV isolates from various geographical locations revealed an amino acid similarity of 72.1-99.4 and 84.7-99.8 % for the RdRp and PATF genes, respectively. The 25 SCYLV isolates were separated into three (RdRp) and two (PATF) phylogenetic groups using the MEGA6 program that does not account for genetic recombination. However, the SCYLV genome contained potential recombination signals in the RdRp and PATF coding genes based on the GARD genetic algorithm. Use of this later program resulted in the reconstruction of phylogenies on the left as well as on the right sides of the putative recombination breaking points, and the 25 SCYLV isolates were distributed into three distinct phylogenetic groups based on either RdRp or PATF sequences. As a result, recombination reshuffled the affiliation of the accessions to the different clusters. Analysis of selection pressures exerted on RdRp and PATF encoded proteins revealed that ORF 2 and ORF 5 underwent predominantly purifying selection. However, a few sites were also under positive selection as assessed by various models such as FEL, IFEL, REL, FUBAR, MEME, GA-Branch, and PRIME.
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20
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Melo-Ferreira J, Vilela J, Fonseca MM, da Fonseca RR, Boursot P, Alves PC. The elusive nature of adaptive mitochondrial DNA evolution of an arctic lineage prone to frequent introgression. Genome Biol Evol 2014; 6:886-96. [PMID: 24696399 PMCID: PMC4007550 DOI: 10.1093/gbe/evu059] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2014] [Indexed: 12/21/2022] Open
Abstract
Mitochondria play a fundamental role in cellular metabolism, being responsible for most of the energy production of the cell in the oxidative phosphorylation (OXPHOS) pathway. Mitochondrial DNA (mtDNA) encodes for key components of this process, but its direct role in adaptation remains far from understood. Hares (Lepus spp.) are privileged models to study the impact of natural selection on mitogenomic evolution because 1) species are adapted to contrasting environments, including arctic, with different metabolic pressures, and 2) mtDNA introgression from arctic into temperate species is widespread. Here, we analyzed the sequences of 11 complete mitogenomes (ten newly obtained) of hares of temperate and arctic origins (including two of arctic origin introgressed into temperate species). The analysis of patterns of codon substitutions along the reconstructed phylogeny showed evidence for positive selection in several codons in genes of the OXPHOS complexes, most notably affecting the arctic lineage. However, using theoretical models, no predictable effect of these differences was found on the structure and physicochemical properties of the encoded proteins, suggesting that the focus of selection may lie on complex interactions with nuclear encoded peptides. Also, a cloverleaf structure was detected in the control region only from the arctic mtDNA lineage, which may influence mtDNA replication and transcription. These results suggest that adaptation impacted the evolution of hare mtDNA and may have influenced the occurrence and consequences of the many reported cases of massive mtDNA introgression. However, the origin of adaptation remains elusive.
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Affiliation(s)
- José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
| | - Joana Vilela
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
- Departamento de Biologia da Faculdade de Ciências da Universidade do Porto, Portugal
| | - Miguel M. Fonseca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Spain
| | - Rute R. da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Portugal
| | - Pierre Boursot
- Institut des Sciences de l’Evolution, Université Montpellier 2, CNRS, IRD, France
| | - Paulo C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
- Departamento de Biologia da Faculdade de Ciências da Universidade do Porto, Portugal
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula
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21
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Zimmerman SW, Yi YJ, Sutovsky M, van Leeuwen FW, Conant G, Sutovsky P. Identification and characterization of RING-finger ubiquitin ligase UBR7 in mammalian spermatozoa. Cell Tissue Res 2014; 356:261-78. [PMID: 24664117 DOI: 10.1007/s00441-014-1808-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 01/13/2014] [Indexed: 01/03/2023]
Abstract
The ubiquitin-proteasome system (UPS) controls intracellular protein turnover in a substrate-specific manner via E3-type ubiquitin ligases. Mammalian fertilization and particularly sperm penetration through the oocyte vitelline coat, the zona pellucida (ZP), is regulated by UPS. We use an extrinsic substrate of the proteasome-dependent ubiquitin-fusion degradation pathway, the mutant ubiquitin UBB(+1), to provide evidence that an E3-type ligase activity exists in sperm-acrosomal fractions. Protein electrophoresis gels from such de novo ubiquitination experiments contained a unique protein band identified by tandem mass spectrometry as being similar to ubiquitin ligase UBR7 (alternative name: C14ORF130). Corresponding mRNA was amplified from boar testis and several variants of the UBR7 protein were detected in boar, mouse and human sperm extracts by Western blotting. Genomic analysis indicated a high degree of evolutionary conservation, remarkably constant purifying selection and conserved testis expression of the UBR7 gene. By immunofluorescence, UBR7 was localized to the spermatid acrosomal cap and sperm acrosome, in addition to hotspots of proteasomal activity in spermatids, such as the cytoplasmic lobe, caudal manchette, nucleus and centrosome. During fertilization, UBR7 remained with the ZP-bound acrosomal shroud following acrosomal exocytosis. Thus, UBR7 is present in the acrosomal cap of round spermatids and within the acrosomal matrix of mature boar spermatozoa. These data provide the first evidence of ubiquitin ligase activity in mammalian spermatozoa and indicate UBR7 involvement in spermiogenesis.
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Affiliation(s)
- Shawn W Zimmerman
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211-5300, USA
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22
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Scherrer MP, Meyer AG, Wilke CO. Modeling coding-sequence evolution within the context of residue solvent accessibility. BMC Evol Biol 2012; 12:179. [PMID: 22967129 PMCID: PMC3527230 DOI: 10.1186/1471-2148-12-179] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 09/03/2012] [Indexed: 11/30/2022] Open
Abstract
Background Protein structure mediates site-specific patterns of sequence divergence. In particular, residues in the core of a protein (solvent-inaccessible residues) tend to be more evolutionarily conserved than residues on the surface (solvent-accessible residues). Results Here, we present a model of sequence evolution that explicitly accounts for the relative solvent accessibility of each residue in a protein. Our model is a variant of the Goldman-Yang 1994 (GY94) model in which all model parameters can be functions of the relative solvent accessibility (RSA) of a residue. We apply this model to a data set comprised of nearly 600 yeast genes, and find that an evolutionary-rate ratio ω that varies linearly with RSA provides a better model fit than an RSA-independent ω or an ω that is estimated separately in individual RSA bins. We further show that the branch length t and the transition-transverion ratio κ also vary with RSA. The RSA-dependent GY94 model performs better than an RSA-dependent Muse-Gaut 1994 (MG94) model in which the synonymous and non-synonymous rates individually are linear functions of RSA. Finally, protein core size affects the slope of the linear relationship between ω and RSA, and gene expression level affects both the intercept and the slope. Conclusions Structure-aware models of sequence evolution provide a significantly better fit than traditional models that neglect structure. The linear relationship between ω and RSA implies that genes are better characterized by their ω slope and intercept than by just their mean ω.
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Affiliation(s)
- Michael P Scherrer
- Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, and Section of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
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Aledo JC, Valverde H, Ruíz-Camacho M. Thermodynamic stability explains the differential evolutionary dynamics of cytochrome b and COX I in mammals. J Mol Evol 2012; 74:69-80. [PMID: 22362464 DOI: 10.1007/s00239-012-9489-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 02/02/2012] [Indexed: 12/29/2022]
Abstract
By using a combination of evolutionary and structural data from 231 species, we have addressed the relationship between evolution and structural features of cytochrome b and COX I, two mtDNA-encoded proteins. The interior of cytochrome b, in contrast to that of COX I, exhibits a remarkable tolerance to changes. The higher evolvability of cytochrome b contrasts with the lower rate of synonymous substitutions of its gene when compared to that of COX I, suggesting that the latter is subjected to a stronger purifying selection. We present evidences that the stability effect of mutations (ΔΔG) may be behind these differential behaviour.
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Affiliation(s)
- Juan Carlos Aledo
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, 29071, Málaga, Spain.
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24
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Pentony MM, Winters P, Penfold-Brown D, Drew K, Narechania A, DeSalle R, Bonneau R, Purugganan MD. The plant proteome folding project: structure and positive selection in plant protein families. Genome Biol Evol 2012; 4:360-71. [PMID: 22345424 PMCID: PMC3318447 DOI: 10.1093/gbe/evs015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Despite its importance, relatively little is known about the relationship between the structure, function, and evolution of proteins, particularly in land plant species. We have developed a database with predicted protein domains for five plant proteomes (http://pfp.bio.nyu.edu) and used both protein structural fold recognition and de novo Rosetta-based protein structure prediction to predict protein structure for Arabidopsis and rice proteins. Based on sequence similarity, we have identified ∼15,000 orthologous/paralogous protein family clusters among these species and used codon-based models to predict positive selection in protein evolution within 175 of these sequence clusters. Our results show that codons that display positive selection appear to be less frequent in helical and strand regions and are overrepresented in amino acid residues that are associated with a change in protein secondary structure. Like in other organisms, disordered protein regions also appear to have more selected sites. Structural information provides new functional insights into specific plant proteins and allows us to map positively selected amino acid sites onto protein structures and view these sites in a structural and functional context.
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Affiliation(s)
- M M Pentony
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
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25
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Hudson CM, Puckett EE, Bekaert M, Pires JC, Conant GC. Selection for higher gene copy number after different types of plant gene duplications. Genome Biol Evol 2011; 3:1369-80. [PMID: 22056313 PMCID: PMC3240960 DOI: 10.1093/gbe/evr115] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2011] [Indexed: 01/03/2023] Open
Abstract
The evolutionary origins of the multitude of duplicate genes in the plant genomes are still incompletely understood. To gain an appreciation of the potential selective forces acting on these duplicates, we phylogenetically inferred the set of metabolic gene families from 10 flowering plant (angiosperm) genomes. We then compared the metabolic fluxes for these families, predicted using the Arabidopsis thaliana and Sorghum bicolor metabolic networks, with the families' duplication propensities. For duplications produced by both small scale (small-scale duplications) and genome duplication (whole-genome duplications), there is a significant association between the flux and the tendency to duplicate. Following this global analysis, we made a more fine-scale study of the selective constraints observed on plant sodium and phosphate transporters. We find that the different duplication mechanisms give rise to differing selective constraints. However, the exact nature of this pattern varies between the gene families, and we argue that the duplication mechanism alone does not define a duplicated gene's subsequent evolutionary trajectory. Collectively, our results argue for the interplay of history, function, and selection in shaping the duplicate gene evolution in plants.
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26
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Selective constraints on amino acids estimated by a mechanistic codon substitution model with multiple nucleotide changes. PLoS One 2011; 6:e17244. [PMID: 21445250 PMCID: PMC3060808 DOI: 10.1371/journal.pone.0017244] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 01/24/2011] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code, and the strength of selective constraints against amino acid replacements can be tailored to a given gene. First, selective constraints averaged over proteins are estimated by maximizing the likelihood of each 1-PAM matrix of empirical amino acid (JTT, WAG, and LG) and codon (KHG) substitution matrices. Then, selective constraints specific to given proteins are approximated as a linear function of those estimated from the empirical substitution matrices. RESULTS Akaike information criterion (AIC) values indicate that a model allowing multiple nucleotide changes fits the empirical substitution matrices significantly better. Also, the ML estimates of transition-transversion bias obtained from these empirical matrices are not so large as previously estimated. The selective constraints are characteristic of proteins rather than species. However, their relative strengths among amino acid pairs can be approximated not to depend very much on protein families but amino acid pairs, because the present model, in which selective constraints are approximated to be a linear function of those estimated from the JTT/WAG/LG/KHG matrices, can provide a good fit to other empirical substitution matrices including cpREV for chloroplast proteins and mtREV for vertebrate mitochondrial proteins. CONCLUSIONS/SIGNIFICANCE The present codon-based model with the ML estimates of selective constraints and with adjustable mutation rates of nucleotide would be useful as a simple substitution model in ML and Bayesian inferences of molecular phylogenetic trees, and enables us to obtain biologically meaningful information at both nucleotide and amino acid levels from codon and protein sequences.
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27
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Delport W, Scheffler K, Botha G, Gravenor MB, Muse SV, Kosakovsky Pond SL. CodonTest: modeling amino acid substitution preferences in coding sequences. PLoS Comput Biol 2010; 6. [PMID: 20808876 PMCID: PMC2924240 DOI: 10.1371/journal.pcbi.1000885] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2010] [Accepted: 07/14/2010] [Indexed: 12/21/2022] Open
Abstract
Codon models of evolution have facilitated the interpretation of selective forces operating on genomes. These models, however, assume a single rate of non-synonymous substitution irrespective of the nature of amino acids being exchanged. Recent developments have shown that models which allow for amino acid pairs to have independent rates of substitution offer improved fit over single rate models. However, these approaches have been limited by the necessity for large alignments in their estimation. An alternative approach is to assume that substitution rates between amino acid pairs can be subdivided into rate classes, dependent on the information content of the alignment. However, given the combinatorially large number of such models, an efficient model search strategy is needed. Here we develop a Genetic Algorithm (GA) method for the estimation of such models. A GA is used to assign amino acid substitution pairs to a series of rate classes, where is estimated from the alignment. Other parameters of the phylogenetic Markov model, including substitution rates, character frequencies and branch lengths are estimated using standard maximum likelihood optimization procedures. We apply the GA to empirical alignments and show improved model fit over existing models of codon evolution. Our results suggest that current models are poor approximations of protein evolution and thus gene and organism specific multi-rate models that incorporate amino acid substitution biases are preferred. We further anticipate that the clustering of amino acid substitution rates into classes will be biologically informative, such that genes with similar functions exhibit similar clustering, and hence this clustering will be useful for the evolutionary fingerprinting of genes. Evolution in protein-coding DNA sequences can be modeled at three levels: nucleotides, amino acids or codons that encode the amino acids. Codon models incorporate nucleotide and amino acid information, and allow the estimation of the rate at which amino acids are replaced () versus the rate at which they are preserved (). The ratio has been used in thousands of studies to detect molecular footprints of natural selection. A serious limitation of most codon models is the unrealistic assumption that all non-synonymous substitutions occur at the same rate. Indeed, amino acid models have consistently demonstrated that different residues are exchanged more or less frequently, depending on incompletely understood factors. We derive and validate a computational approach for inferring codon models which combine the power to investigate natural selection with data-driven amino acid substitution biases from alignments. The addition of amino acid properties can lead to more powerful and accurate methods for studying natural selection and the evolutionary history of protein-coding sequences. The pattern of amino acid substitutions specific to a given alignment can be used to compare and contrast the evolutionary properties of different genes, providing an evolutionary analog to protein family comparisons.
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Affiliation(s)
- Wayne Delport
- Department of Pathology, University of California, San Diego, La Jolla, California, United States of America
| | - Konrad Scheffler
- Computer Science Division, Department of Mathematical Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Gordon Botha
- Computer Science Division, Department of Mathematical Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Mike B. Gravenor
- School of Medicine, University of Swansea, Swansea, United Kingdom
| | - Spencer V. Muse
- Department of Statistics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Sergei L. Kosakovsky Pond
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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28
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Studer RA, Robinson-Rechavi M. Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution. Mol Biol Evol 2010; 27:2618-27. [PMID: 20551039 PMCID: PMC2955734 DOI: 10.1093/molbev/msq149] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Functional divergence between homologous proteins is expected to affect amino acid sequences in two main ways, which can be considered as proxies of biochemical divergence: a “covarion-like” pattern of correlated changes in evolutionary rates, and switches in conserved residues (“conserved but different”). Although these patterns have been used in case studies, a large-scale analysis is needed to estimate their frequency and distribution. We use a phylogenomic framework of animal genes to answer three questions: 1) What is the prevalence of such patterns? 2) Can we link such patterns at the amino acid level with selection inferred at the codon level? 3) Are patterns different between paralogs and orthologs? We find that covarion-like patterns are more frequently detected than “constant but different,” but that only the latter are correlated with signal for positive selection. Finally, there is no obvious difference in patterns between orthologs and paralogs.
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Affiliation(s)
- Romain A Studer
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
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29
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How confident can we be that orthologs are similar, but paralogs differ? Trends Genet 2009; 25:210-6. [PMID: 19368988 DOI: 10.1016/j.tig.2009.03.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Revised: 03/15/2009] [Accepted: 03/16/2009] [Indexed: 11/24/2022]
Abstract
Homologous genes are classified into orthologs and paralogs, depending on whether they arose by speciation or duplication. It is widely assumed that orthologs share similar functions, whereas paralogs are expected to diverge more from each other. But does this assumption hold up on further examination? We present evidence that orthologs and paralogs are not so different in either their evolutionary rates or their mechanisms of divergence. We emphasize the importance of appropriately designed studies to test models of gene evolution between orthologs and between paralogs. Thus, functional change between orthologs might be as common as between paralogs, and future studies should be designed to test the impact of duplication against this alternative model.
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30
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Conant GC, Stadler PF. Solvent exposure imparts similar selective pressures across a range of yeast proteins. Mol Biol Evol 2009; 26:1155-61. [PMID: 19233963 DOI: 10.1093/molbev/msp031] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study how an amino acid residue's solvent exposure influences its propensity for substitution by analyzing multiple alignments of 61 yeast genes for which the crystal structure is known. We find that the selective constraint on the interior residues is on average 10 times that of residues on the surface. Surprisingly, there is no correlation between the overall selective constraint observed for a protein alignment and the ratio of constraints on interior and surface residues. By modeling the selective constraint on several amino acid properties, we show that although residue volume and hydropathy are strongly conserved across most alignments, there is little variation in interior versus surface conservation for these two properties. By contrast, residue charge (isoelectric point) is less generally conserved when considering the protein as a whole but shows a strong constraint against the introduction of charged residues into the protein interior.
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Affiliation(s)
- Gavin C Conant
- Division of Animal Sciences and Informatics Institute, University of Missouri-Columbia, USA.
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31
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Studer RA, Penel S, Duret L, Robinson-Rechavi M. Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res 2008; 18:1393-402. [PMID: 18562677 DOI: 10.1101/gr.076992.108] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A stringent branch-site codon model was used to detect positive selection in vertebrate evolution. We show that the test is robust to the large evolutionary distances involved. Positive selection was detected in 77% of 884 genes studied. Most positive selection concerns a few sites on a single branch of the phylogenetic tree: Between 0.9% and 4.7% of sites are affected by positive selection depending on the branches. No functional category was overrepresented among genes under positive selection. Surprisingly, whole genome duplication had no effect on the prevalence of positive selection, whether the fish-specific genome duplication or the two rounds at the origin of vertebrates. Thus positive selection has not been limited to a few gene classes, or to specific evolutionary events such as duplication, but has been pervasive during vertebrate evolution.
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Affiliation(s)
- Romain A Studer
- Department of Ecology and Evolution, Biophore, Lausanne University, CH-1015 Lausanne, Switzerland
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32
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Kosakovsky Pond SL, Poon AFY, Leigh Brown AJ, Frost SDW. A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus. Mol Biol Evol 2008; 25:1809-24. [PMID: 18511426 DOI: 10.1093/molbev/msn123] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We develop a model-based phylogenetic maximum likelihood test for evidence of preferential substitution toward a given residue at individual positions of a protein alignment--directional evolution of protein sequences (DEPS). DEPS can identify both the target residue and sites evolving toward it, help detect selective sweeps and frequency-dependent selection--scenarios that confound most existing tests for selection, and achieve good power and accuracy on simulated data. We applied DEPS to alignments representing different genomic regions of influenza A virus (IAV), sampled from avian hosts (H5N1 serotype) and human hosts (H3N2 serotype), and identified multiple directionally evolving sites in 5/8 genomic segments of H5N1 and H3N2 IAV. We propose a simple descriptive classification of directionally evolving sites into 5 groups based on the temporal distribution of residue frequencies and document known functional correlates, such as immune escape or host adaptation.
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33
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Scannell DR, Wolfe KH. A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast. Genes Dev 2008; 18:137-47. [PMID: 18025270 PMCID: PMC2134778 DOI: 10.1101/gr.6341207] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2007] [Accepted: 09/23/2007] [Indexed: 11/24/2022]
Abstract
It is widely accepted that newly arisen duplicate gene pairs experience an altered selective regime that is often manifested as an increase in the rate of protein sequence evolution. Many details about the nature of the rate acceleration remain unknown, however, including its typical magnitude and duration, and whether it applies to both gene copies or just one. We provide initial answers to these questions by comparing the rate of protein sequence evolution among eight yeast species, between a large set of duplicate gene pairs that were created by a whole-genome duplication (WGD) and a set of genes that were returned to single-copy after this event. Importantly, we use a new method that takes into account the tendency for slowly evolving genes to be retained preferentially in duplicate. We show that, on average, proteins encoded by duplicate gene pairs evolved at least three times faster immediately after the WGD than single-copy genes to which they behave identically in non-WGD lineages. Although the high rate in duplicated genes subsequently declined rapidly, it has not yet returned to the typical rate for single-copy genes. In addition, we show that although duplicate gene pairs often have highly asymmetric rates of evolution, even the slower members of pairs show evidence of a burst of protein sequence evolution immediately after duplication. We discuss the contribution of neofunctionalization to duplicate gene preservation and propose that a form of subfunctionalization mediated by coding region activity-reducing mutations is likely to have played an important role.
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Affiliation(s)
- Devin R Scannell
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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