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Mills KB, Maciag JJ, Wang C, Crawford JA, Enroth TJ, Keim KC, Dufrêne YF, Robinson DA, Fey PD, Herr AB, Horswill AR. Staphylococcus aureus skin colonization is mediated by SasG lectin variation. Cell Rep 2024; 43:114022. [PMID: 38568806 DOI: 10.1016/j.celrep.2024.114022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/23/2024] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
Staphylococcus aureus causes the majority of skin and soft tissue infections, but this pathogen only transiently colonizes healthy skin. However, this transient skin exposure enables S. aureus to transition to infection. The initial adhesion of S. aureus to skin corneocytes is mediated by surface protein G (SasG). Here, phylogenetic analyses reveal the presence of two major divergent SasG alleles in S. aureus: SasG-I and SasG-II. Structural analyses of SasG-II identify a nonaromatic arginine in the binding pocket of the lectin subdomain that mediates adhesion to corneocytes. Atomic force microscopy and corneocyte adhesion assays indicate that SasG-II can bind to a broader variety of ligands than SasG-I. Glycosidase treatment results in different binding profiles between SasG-I and SasG-II on skin cells. In addition, SasG-mediated adhesion is recapitulated using differentiated N/TERT keratinocytes. Our findings indicate that SasG-II has evolved to adhere to multiple ligands, conferring a distinct advantage to S. aureus during skin colonization.
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Affiliation(s)
- Krista B Mills
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Joseph J Maciag
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Can Wang
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - John A Crawford
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Timothy J Enroth
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Klara C Keim
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - D Ashley Robinson
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA; Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS, USA
| | - Paul D Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Andrew B Herr
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Alexander R Horswill
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Veterans Affairs, VA Eastern Colorado Healthcare System, Aurora, CO, USA.
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2
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Mills KB, Maciag JJ, Wang C, Crawford JA, Enroth TJ, Keim KC, Dufrêne YF, Robinson DA, Fey PD, Herr AB, Horswill AR. Staphylococcus aureus skin colonization is mediated by SasG lectin variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567970. [PMID: 38045275 PMCID: PMC10690190 DOI: 10.1101/2023.11.20.567970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Staphylococcus aureus causes the majority of skin and soft tissue infections, but this pathogen only transiently colonizes healthy skin. However, this transient skin exposure enables S. aureus to transition to infection. Initial adhesion of S. aureus to skin corneocytes is mediated by surface protein G (SasG). Here, phylogenetic analyses reveal the presence of two major divergent SasG alleles in S. aureus, SasG-I and SasG-II. Structural analyses of SasG-II identified a unique non-aromatic arginine in the binding pocket of the lectin subdomain that mediates adhesion to corneocytes. Atomic force microscopy and corneocyte adhesion assays indicated SasG-II can bind to a broader variety of ligands than SasG-I. Glycosidase treatment resulted in different binding profiles between SasG-I and SasG-II on skin cells. Additionally, SasG-mediated adhesion was recapitulated using differentiated N/TERT keratinocytes. Our findings indicate that SasG-II has evolved to adhere to multiple ligands, conferring a distinct advantage to S. aureus during skin colonization.
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Affiliation(s)
- Krista B. Mills
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Joseph J. Maciag
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Can Wang
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - John A. Crawford
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Timothy J. Enroth
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Klara C. Keim
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yves F. Dufrêne
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - D. Ashley Robinson
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS, USA
| | - Paul D. Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Andrew B. Herr
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Alexander R. Horswill
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Veterans Affairs, VA Eastern Colorado Healthcare System, Aurora, CO, USA
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3
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Huang G, Wu W, Chen Y, Zhi X, Zou P, Ning Z, Fan Q, Liu Y, Deng S, Zeng K, Zhou R. Balancing selection on an MYB transcription factor maintains the twig trichome color variation in Melastoma normale. BMC Biol 2023; 21:122. [PMID: 37226197 DOI: 10.1186/s12915-023-01611-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 05/03/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND The factors that maintain phenotypic and genetic variation within a population have received long-term attention in evolutionary biology. Here the genetic basis and evolution of the geographically widespread variation in twig trichome color (from red to white) in a shrub Melastoma normale was investigated using Pool-seq and evolutionary analyses. RESULTS The results show that the twig trichome coloration is under selection in different light environments and that a 6-kb region containing an R2R3 MYB transcription factor gene is the major region of divergence between the extreme red and white morphs. This gene has two highly divergent groups of alleles, one of which likely originated from introgression from another species in this genus and has risen to high frequency (> 0.6) within each of the three populations under investigation. In contrast, polymorphisms in other regions of the genome show no sign of differentiation between the two morphs, suggesting that genomic patterns of diversity have been shaped by homogenizing gene flow. Population genetics analysis reveals signals of balancing selection acting on this gene, and it is suggested that spatially varying selection is the most likely mechanism of balancing selection in this case. CONCLUSIONS This study demonstrate that polymorphisms on a single transcription factor gene largely confer the twig trichome color variation in M. normale, while also explaining how adaptive divergence can occur and be maintained in the face of gene flow.
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Affiliation(s)
- Guilian Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Wei Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yongmei Chen
- College of Chemical Engineering, Sichuan University of Science & Engineering, Zigong, Sichuan, 643000, China
| | - Xueke Zhi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Peishan Zou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zulin Ning
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Shulin Deng
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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4
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Fluctuating selection and the determinants of genetic variation. Trends Genet 2023; 39:491-504. [PMID: 36890036 DOI: 10.1016/j.tig.2023.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 03/08/2023]
Abstract
Recent studies of cosmopolitan Drosophila populations have found hundreds to thousands of genetic loci with seasonally fluctuating allele frequencies, bringing temporally fluctuating selection to the forefront of the historical debate surrounding the maintenance of genetic variation in natural populations. Numerous mechanisms have been explored in this longstanding area of research, but these exciting empirical findings have prompted several recent theoretical and experimental studies that seek to better understand the drivers, dynamics, and genome-wide influence of fluctuating selection. In this review, we evaluate the latest evidence for multilocus fluctuating selection in Drosophila and other taxa, highlighting the role of potential genetic and ecological mechanisms in maintaining these loci and their impacts on neutral genetic variation.
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5
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Ebert D, Fields PD. Host-parasite co-evolution and its genomic signature. Nat Rev Genet 2020; 21:754-768. [PMID: 32860017 DOI: 10.1038/s41576-020-0269-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2020] [Indexed: 01/14/2023]
Abstract
Studies in diverse biological systems have indicated that host-parasite co-evolution is responsible for the extraordinary genetic diversity seen in some genomic regions, such as major histocompatibility (MHC) genes in jawed vertebrates and resistance genes in plants. This diversity is believed to evolve under balancing selection on hosts by parasites. However, the mechanisms that link the genomic signatures in these regions to the underlying co-evolutionary process are only slowly emerging. We still lack a clear picture of the co-evolutionary concepts and of the genetic basis of the co-evolving phenotypic traits in the interacting antagonists. Emerging genomic tools that provide new options for identifying underlying genes will contribute to a fuller understanding of the co-evolutionary process.
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Affiliation(s)
- Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland. .,Wissenschaftskolleg zu Berlin, Berlin, Germany.
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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6
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Castillo JA, Agathos SN. A genome-wide scan for genes under balancing selection in the plant pathogen Ralstonia solanacearum. BMC Evol Biol 2019; 19:123. [PMID: 31208326 PMCID: PMC6580516 DOI: 10.1186/s12862-019-1456-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 06/10/2019] [Indexed: 02/07/2023] Open
Abstract
Background Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to evading plant defenses. In order to acquire long-term fitness, plant bacterial pathogens are usually forced to maintain advantageous genetic diversity in populations. This strategy ensures that different alleles in the pathogen’s gene pool are maintained in a population at frequencies larger than expected under neutral evolution. This selective process, known as balancing selection, is the subject of this work in the context of a common bacterial phytopathogen. We performed a genome-wide scan of Ralstonia solanacearum species complex, an aggressive plant bacterial pathogen that shows broad host range and causes a devastating disease called ‘bacterial wilt’. Results Using a sliding window approach, we analyzed 57 genomes from three phylotypes of the R. solanacearum species complex to detect signatures of balancing selection. A total of 161 windows showed extreme values in three summary statistics of population genetics: Tajima’s D, θw and Fu & Li’s D*. We discarded any confounding effects due to demographic events by means of coalescent simulations of genetic data. The prospective windows correspond to 78 genes with known function that map in any of the two main replicons (1.7% of total number of genes). The candidate genes under balancing selection are related to primary metabolism and other basal activities (51.3%) or directly associated to virulence (48.7%), the latter being involved in key functions targeted to dismantle plant defenses or to participate in critical stages in the pathogenic process. Conclusions We identified various genes under balancing selection that play a significant role in basic metabolism as well as in virulence of the R. solanacearum species complex. These genes are useful to understand and monitor the evolution of bacterial pathogen populations and emerge as potential candidates for future treatments to induce specific plant immune responses. Electronic supplementary material The online version of this article (10.1186/s12862-019-1456-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José A Castillo
- School of Biological Sciences and Engineering, Yachay Tech University, Hacienda San Jose s/n and Proyecto Yachay, Urcuquí, Ecuador.
| | - Spiros N Agathos
- School of Biological Sciences and Engineering, Yachay Tech University, Hacienda San Jose s/n and Proyecto Yachay, Urcuquí, Ecuador
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7
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Buckley J, Holub EB, Koch MA, Vergeer P, Mable BK. Restriction associated DNA-genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen-mediated selection. BMC Genomics 2018; 19:496. [PMID: 29945543 PMCID: PMC6020377 DOI: 10.1186/s12864-018-4806-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 05/18/2018] [Indexed: 11/22/2022] Open
Abstract
Background Genome scans based on outlier analyses have revolutionized detection of genes involved in adaptive processes, but reports of some forms of selection, such as balancing selection, are still limited. It is unclear whether high throughput genotyping approaches for identification of single nucleotide polymorphisms have sufficient power to detect modes of selection expected to result in reduced genetic differentiation among populations. In this study, we used Arabidopsis lyrata to investigate whether signatures of balancing selection can be detected based on genomic smoothing of Restriction Associated DNA sequencing (RAD-seq) data. We compared how different sampling approaches (both within and between subspecies) and different background levels of polymorphism (inbreeding or outcrossing populations) affected the ability to detect genomic regions showing key signatures of balancing selection, specifically elevated polymorphism, reduced differentiation and shifts towards intermediate allele frequencies. We then tested whether candidate genes associated with disease resistance (R-gene analogs) were detected more frequently in these regions compared to other regions of the genome. Results We found that genomic regions showing elevated polymorphism contained a significantly higher density of R-gene analogs predicted to be under pathogen-mediated selection than regions of non-elevated polymorphism, and that many of these also showed evidence for an intermediate site-frequency spectrum based on Tajima’s D. However, we found few genomic regions that showed both elevated polymorphism and reduced FST among populations, despite strong background levels of genetic differentiation among populations. This suggests either insufficient power to detect the reduced population structure predicted for genes under balancing selection using sparsely distributed RAD markers, or that other forms of diversifying selection are more common for the R-gene analogs tested. Conclusions Genome scans based on a small number of individuals sampled from a wide range of populations were sufficient to confirm the relative scarcity of signatures of balancing selection across the genome, but also identified new potential disease resistance candidates within genomic regions showing signatures of balancing selection that would be strong candidates for further sequencing efforts. Electronic supplementary material The online version of this article (10.1186/s12864-018-4806-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- James Buckley
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK. .,Adaptation to a Changing Environment, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.
| | - Eric B Holub
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Wellesbourne, CV35 9EF, UK
| | - Marcus A Koch
- Centre for Organismal Studies (COS) Heidelberg, Biodiversity and Plant Systematics, Heidelberg University, D69120, Heidelberg, Germany
| | - Philippine Vergeer
- Plant Ecology and Nature Conservation Group, Wageningen University, P.O.Box 47, 6700, AA, Wageningen, The Netherlands
| | - Barbara K Mable
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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8
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Suligoy CM, Lattar SM, Noto Llana M, González CD, Alvarez LP, Robinson DA, Gómez MI, Buzzola FR, Sordelli DO. Mutation of Agr Is Associated with the Adaptation of Staphylococcus aureus to the Host during Chronic Osteomyelitis. Front Cell Infect Microbiol 2018; 8:18. [PMID: 29456969 PMCID: PMC5801681 DOI: 10.3389/fcimb.2018.00018] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 01/12/2018] [Indexed: 11/13/2022] Open
Abstract
Selection pressures exerted on Staphylococcus aureus by host factors may lead to the emergence of mutants better adapted to the evolving conditions at the infection site. This study was aimed at identifying the changes that occur in S. aureus exposed to the host defense mechanisms during chronic osteomyelitis and evaluating whether these changes affect the virulence of the organism. Genome assessment of two S. aureus isolates collected 13 months apart (HU-85a and HU-85c) from a host with chronic osteomyelitis was made by whole genome sequencing. Agr functionality was assessed by qRT-PCR. Isolates were tested in a rat model of osteomyelitis and the bacterial load (CFU/tibia) and the morphometric osteomyelitic index (OI) were determined. The ability of the isolates to trigger the release of proinflammatory cytokines was determined on macrophages in culture. Persistence of S. aureus within the host resulted in an agrC frameshift mutation that likely led to the observed phenotype. The capacity to cause bone tissue damage and trigger proinflammatory cytokines by macrophages of the agr-deficient, unencapsulated derivative (HU-85c) was decreased when compared with those of the isogenic CP8-capsulated parental strain (HU-85a). By comparison, no significant differences were found in the bacterial load or the OI from rats challenged with isogenic Reynolds strains [CP5, CP8, and non-typeable (NT)], indicating that lack of CP expression alone was not likely responsible for the reduced capacity to cause tissue damage in HU-85c compared with HU-85a. The production of biofilm was significantly increased in the isogenic derivative HU-85c. Lack of agr-dependent factors makes S. aureus less virulent during chronic osteomyelitis and alteration of the agr functionality seems to permit better adaptation of S. aureus to the chronically infected host.
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Affiliation(s)
- Carlos M Suligoy
- Instituto de Investigaciones en Microbiología y Parasitología Médica, University of Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Santiago M Lattar
- Instituto de Investigaciones en Microbiología y Parasitología Médica, University of Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Mariángeles Noto Llana
- Instituto de Investigaciones en Microbiología y Parasitología Médica, University of Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Cintia D González
- Instituto de Investigaciones en Microbiología y Parasitología Médica, University of Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Lucía P Alvarez
- Instituto de Investigaciones en Microbiología y Parasitología Médica, University of Buenos Aires - CONICET, Buenos Aires, Argentina
| | - D Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, United States
| | - Marisa I Gómez
- Instituto de Investigaciones en Microbiología y Parasitología Médica, University of Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Fernanda R Buzzola
- Instituto de Investigaciones en Microbiología y Parasitología Médica, University of Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Daniel O Sordelli
- Instituto de Investigaciones en Microbiología y Parasitología Médica, University of Buenos Aires - CONICET, Buenos Aires, Argentina
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9
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Ancient balancing selection on heterocyst function in a cosmopolitan cyanobacterium. Nat Ecol Evol 2018; 2:510-519. [DOI: 10.1038/s41559-017-0435-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 11/29/2017] [Indexed: 11/08/2022]
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10
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Pickering H, Teng A, Faal N, Joof H, Makalo P, Cassama E, Nabicassa M, Last AR, Burr SE, Rowland-Jones SL, Thomson NR, Roberts CH, Mabey DCW, Bailey RL, Hayward RD, de la Maza LM, Holland MJ. Genome-wide profiling of humoral immunity and pathogen genes under selection identifies immune evasion tactics of Chlamydia trachomatis during ocular infection. Sci Rep 2017; 7:9634. [PMID: 28851925 PMCID: PMC5575166 DOI: 10.1038/s41598-017-09193-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/24/2017] [Indexed: 11/09/2022] Open
Abstract
The frequency and duration of Chlamydia trachomatis (Ct) ocular infections decrease with age, suggesting development of partial immunity. However, there is a lack of clear correlates of immunity to Ct infection in humans. We screened sera from a cohort of Gambian children followed for six-months against a Ct-proteome microarray. At genome sequence level, we detected signatures of selection from a population of ocular Ct isolates from Guinea-Bissau. Together these approaches allowed us to highlight the focus of humoral responses and hypothesise new modes of pathogen immune evasion. Children who were susceptible to frequent and/or prolonged Ct infection had a less focussed antibody response, including preferential recognition of forty-two antigens. There was evidence of positive and purifying selection across the genome, but little balancing selection. In contrast, most antigens that were associated with susceptibility were under neutral selection. These data suggest an evasion strategy in which Ct presents a large panel of irrelevant antigens to the immune system to block or misdirect protective responses. Development of a focused immune response, possibly induced through vaccination, may be an effective strategy to promote protection to Ct infection.
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Affiliation(s)
- Harry Pickering
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom.
| | - Andy Teng
- ImmPORT Therapeutics, Inc./Antigen Discovery Inc., 1 Technology Dr., Suite E309, Irvine, CA, 92618, United States
| | - Nkoyo Faal
- Disease Control and Elimination Theme, Medical Research Council The Gambia Unit, Fajara, Banjul, The Gambia
| | - Hassan Joof
- Disease Control and Elimination Theme, Medical Research Council The Gambia Unit, Fajara, Banjul, The Gambia
| | - Pateh Makalo
- Disease Control and Elimination Theme, Medical Research Council The Gambia Unit, Fajara, Banjul, The Gambia
| | - Eunice Cassama
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea-Bissau
| | - Meno Nabicassa
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea-Bissau
| | - Anna R Last
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
| | - Sarah E Burr
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom.,Disease Control and Elimination Theme, Medical Research Council The Gambia Unit, Fajara, Banjul, The Gambia
| | - Sarah L Rowland-Jones
- Disease Control and Elimination Theme, Medical Research Council The Gambia Unit, Fajara, Banjul, The Gambia
| | - Nicholas R Thomson
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom.,Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Chrissy H Roberts
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
| | - David C W Mabey
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
| | - Robin L Bailey
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
| | - Richard D Hayward
- Institute of Structural and Molecular Biology, Birkbeck & University College London, Malet Street, London, WC1E 7HX, United Kingdom
| | - Luis M de la Maza
- Department of Pathology and Laboratory Medicine, Medical Sciences I, Room D440, University of California, Irvine, CA, 92697-4800, United States
| | - Martin J Holland
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom.,Disease Control and Elimination Theme, Medical Research Council The Gambia Unit, Fajara, Banjul, The Gambia
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11
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Vanhove M, Beale MA, Rhodes J, Chanda D, Lakhi S, Kwenda G, Molloy S, Karunaharan N, Stone N, Harrison TS, Bicanic T, Fisher MC. Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort. Mol Ecol 2017; 26:1991-2005. [PMID: 27862555 PMCID: PMC5412878 DOI: 10.1111/mec.13891] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 10/15/2016] [Accepted: 10/17/2016] [Indexed: 12/21/2022]
Abstract
Emerging infections caused by fungi have become a widely recognized global phenomenon and are causing an increasing burden of disease. Genomic techniques are providing new insights into the structure of fungal populations, revealing hitherto undescribed fine-scale adaptations to environments and hosts that govern their emergence as infections. Cryptococcal meningitis is a neglected tropical disease that is responsible for a large proportion of AIDS-related deaths across Africa; however, the ecological determinants that underlie a patient's risk of infection remain largely unexplored. Here, we use genome sequencing and ecological genomics to decipher the evolutionary ecology of the aetiological agents of cryptococcal meningitis, Cryptococcus neoformans and Cryptococcus gattii, across the central African country of Zambia. We show that the occurrence of these two pathogens is differentially associated with biotic (macroecological) and abiotic (physical) factors across two key African ecoregions, Central Miombo woodlands and Zambezi Mopane woodlands. We show that speciation of Cryptococcus has resulted in adaptation to occupy different ecological niches, with C. neoformans found to occupy Zambezi Mopane woodlands and C. gattii primarily recovered from Central Miombo woodlands. Genome sequencing shows that C. neoformans causes 95% of human infections in this region, of which over three-quarters belonged to the globalized lineage VNI. We show that VNI infections are largely associated with urbanized populations in Zambia. Conversely, the majority of C. neoformans isolates recovered in the environment belong to the genetically diverse African-endemic lineage VNB, and we show hitherto unmapped levels of genomic diversity within this lineage. Our results reveal the complex evolutionary ecology that underpins the reservoirs of infection for this, and likely other, deadly pathogenic fungi.
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MESH Headings
- Adaptation, Physiological/genetics
- Cryptococcus gattii/genetics
- Cryptococcus neoformans/genetics
- DNA Barcoding, Taxonomic
- DNA, Fungal/genetics
- DNA, Ribosomal Spacer/genetics
- Forests
- Genetics, Population
- Genome, Fungal
- Genomics
- Humans
- Meningitis, Cryptococcal/epidemiology
- Meningitis, Cryptococcal/microbiology
- Models, Biological
- Phylogeny
- Plant Bark/microbiology
- Polymorphism, Single Nucleotide
- Soil Microbiology
- Trees/microbiology
- Zambia
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Affiliation(s)
- Mathieu Vanhove
- Department of Infectious Disease Epidemiology, St Mary's Hospital, Imperial College London, London, W2 1PG, UK
| | - Mathew A Beale
- Department of Infectious Disease Epidemiology, St Mary's Hospital, Imperial College London, London, W2 1PG, UK
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
- Division of Infection & Immunity, University College London, Gower St, London WC1E 6BT, UK
| | - Johanna Rhodes
- Department of Infectious Disease Epidemiology, St Mary's Hospital, Imperial College London, London, W2 1PG, UK
| | - Duncan Chanda
- School of Medicine, University of Zambia, Nationalist Road, PO Box 50110, Lusaka, Zambia
| | - Shabir Lakhi
- School of Medicine, University of Zambia, Nationalist Road, PO Box 50110, Lusaka, Zambia
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Sile Molloy
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
| | - Natasha Karunaharan
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
| | - Neil Stone
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
| | - Thomas S Harrison
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
| | - Tihana Bicanic
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
| | - Matthew C Fisher
- Department of Infectious Disease Epidemiology, St Mary's Hospital, Imperial College London, London, W2 1PG, UK
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12
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Croze M, Wollstein A, Božičević V, Živković D, Stephan W, Hutter S. A genome-wide scan for genes under balancing selection in Drosophila melanogaster. BMC Evol Biol 2017; 17:15. [PMID: 28086750 PMCID: PMC5237213 DOI: 10.1186/s12862-016-0857-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 12/17/2016] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND In the history of population genetics balancing selection has been considered as an important evolutionary force, yet until today little is known about its abundance and its effect on patterns of genetic diversity. Several well-known examples of balancing selection have been reported from humans, mice, plants, and parasites. However, only very few systematic studies have been carried out to detect genes under balancing selection. We performed a genome scan in Drosophila melanogaster to find signatures of balancing selection in a derived (European) and an ancestral (African) population. We screened a total of 34 genomes searching for regions of high genetic diversity and an excess of SNPs with intermediate frequency. RESULTS In total, we found 183 candidate genes: 141 in the European population and 45 in the African one, with only three genes shared between both populations. Most differences between both populations were observed on the X chromosome, though this might be partly due to false positives. Functionally, we find an overrepresentation of genes involved in neuronal development and circadian rhythm. Furthermore, some of the top genes we identified are involved in innate immunity. CONCLUSION Our results revealed evidence of genes under balancing selection in European and African populations. More candidate genes have been found in the European population. They are involved in several different functions.
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Affiliation(s)
- Myriam Croze
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
| | - Andreas Wollstein
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Vedran Božičević
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Daniel Živković
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.,Center of Food and Life Sciences Weihenstephan, Technische Universität München, 85354, Freising, Germany
| | - Wolfgang Stephan
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.,Natural History Museum Berlin, 10115, Berlin, Germany
| | - Stephan Hutter
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
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13
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Kim K, Omori R, Ueno K, Iida S, Ito K. Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review. PLoS One 2016; 11:e0147021. [PMID: 26760775 PMCID: PMC4720117 DOI: 10.1371/journal.pone.0147021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/28/2015] [Indexed: 11/18/2022] Open
Abstract
Understanding the evolutionary dynamics of influenza viruses is essential to control both avian and human influenza. Here, we analyze host-specific and segment-specific Tajima's D trends of influenza A virus through a systematic review using viral sequences registered in the National Center for Biotechnology Information. To avoid bias from viral population subdivision, viral sequences were stratified according to their sampling locations and sampling years. As a result, we obtained a total of 580 datasets each of which consists of nucleotide sequences of influenza A viruses isolated from a single population of hosts at a single sampling site within a single year. By analyzing nucleotide sequences in the datasets, we found that Tajima's D values of viral sequences were different depending on hosts and gene segments. Tajima's D values of viruses isolated from chicken and human samples showed negative, suggesting purifying selection or a rapid population growth of the viruses. The negative Tajima's D values in rapidly growing viral population were also observed in computer simulations. Tajima's D values of PB2, PB1, PA, NP, and M genes of the viruses circulating in wild mallards were close to zero, suggesting that these genes have undergone neutral selection in constant-sized population. On the other hand, Tajima's D values of HA and NA genes of these viruses were positive, indicating HA and NA have undergone balancing selection in wild mallards. Taken together, these results indicated the existence of unknown factors that maintain viral subtypes in wild mallards.
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Affiliation(s)
- Kiyeon Kim
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ryosuke Omori
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, Japan
| | - Keisuke Ueno
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Sayaka Iida
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kimihito Ito
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- * E-mail:
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14
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Haasl RJ, Payseur BA. Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication. Mol Ecol 2015. [PMID: 26224644 DOI: 10.1111/mec.13339] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genomewide scans for natural selection (GWSS) have become increasingly common over the last 15 years due to increased availability of genome-scale genetic data. Here, we report a representative survey of GWSS from 1999 to present and find that (i) between 1999 and 2009, 35 of 49 (71%) GWSS focused on human, while from 2010 to present, only 38 of 83 (46%) of GWSS focused on human, indicating increased focus on nonmodel organisms; (ii) the large majority of GWSS incorporate interpopulation or interspecific comparisons using, for example F(ST), cross-population extended haplotype homozygosity or the ratio of nonsynonymous to synonymous substitutions; (iii) most GWSS focus on detection of directional selection rather than other modes such as balancing selection; and (iv) in human GWSS, there is a clear shift after 2004 from microsatellite markers to dense SNP data. A survey of GWSS meant to identify loci positively selected in response to severe hypoxic conditions support an approach to GWSS in which a list of a priori candidate genes based on potential selective pressures are used to filter the list of significant hits a posteriori. We also discuss four frequently ignored determinants of genomic heterogeneity that complicate GWSS: mutation, recombination, selection and the genetic architecture of adaptive traits. We recommend that GWSS methodology should better incorporate aspects of genomewide heterogeneity using empirical estimates of relevant parameters and/or realistic, whole-chromosome simulations to improve interpretation of GWSS results. Finally, we argue that knowledge of potential selective agents improves interpretation of GWSS results and that new methods focused on correlations between environmental variables and genetic variation can help automate this approach.
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Affiliation(s)
- Ryan J Haasl
- Department of Biology, University of Wisconsin-Platteville, 1 University Plaza, Platteville, WI, 53818, USA
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA
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15
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Fijarczyk A, Babik W. Detecting balancing selection in genomes: limits and prospects. Mol Ecol 2015; 24:3529-45. [DOI: 10.1111/mec.13226] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - Wiesław Babik
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
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16
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Hua ZG, Lin Y, Yuan YZ, Yang DC, Wei W, Guo FB. ZCURVE 3.0: identify prokaryotic genes with higher accuracy as well as automatically and accurately select essential genes. Nucleic Acids Res 2015; 43:W85-90. [PMID: 25977299 PMCID: PMC4489317 DOI: 10.1093/nar/gkv491] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/02/2015] [Indexed: 01/09/2023] Open
Abstract
In 2003, we developed an ab initio program, ZCURVE 1.0, to find genes in bacterial and archaeal genomes. In this work, we present the updated version (i.e. ZCURVE 3.0). Using 422 prokaryotic genomes, the average accuracy was 93.7% with the updated version, compared with 88.7% with the original version. Such results also demonstrate that ZCURVE 3.0 is comparable with Glimmer 3.02 and may provide complementary predictions to it. In fact, the joint application of the two programs generated better results by correctly finding more annotated genes while also containing fewer false-positive predictions. As the exclusive function, ZCURVE 3.0 contains one post-processing program that can identify essential genes with high accuracy (generally >90%). We hope ZCURVE 3.0 will receive wide use with the web-based running mode. The updated ZCURVE can be freely accessed from http://cefg.uestc.edu.cn/zcurve/ or http://tubic.tju.edu.cn/zcurveb/ without any restrictions.
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Affiliation(s)
- Zhi-Gang Hua
- Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yan Lin
- Department of Physics, Tianjin University, Tianjin 300072, China Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin 300072, China Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Ya-Zhou Yuan
- Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - De-Chang Yang
- Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wen Wei
- Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Feng-Biao Guo
- Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
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17
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Continental-scale footprint of balancing and positive selection in a small rodent (Microtus arvalis). PLoS One 2014; 9:e112332. [PMID: 25383542 PMCID: PMC4226552 DOI: 10.1371/journal.pone.0112332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/06/2014] [Indexed: 01/01/2023] Open
Abstract
Genetic adaptation to different environmental conditions is expected to lead to large differences between populations at selected loci, thus providing a signature of positive selection. Whereas balancing selection can maintain polymorphisms over long evolutionary periods and even geographic scale, thus leads to low levels of divergence between populations at selected loci. However, little is known about the relative importance of these two selective forces in shaping genomic diversity, partly due to difficulties in recognizing balancing selection in species showing low levels of differentiation. Here we address this problem by studying genomic diversity in the European common vole (Microtus arvalis) presenting high levels of differentiation between populations (average FST = 0.31). We studied 3,839 Amplified Fragment Length Polymorphism (AFLP) markers genotyped in 444 individuals from 21 populations distributed across the European continent and hence over different environmental conditions. Our statistical approach to detect markers under selection is based on a Bayesian method specifically developed for AFLP markers, which treats AFLPs as a nearly codominant marker system, and therefore has increased power to detect selection. The high number of screened populations allowed us to detect the signature of balancing selection across a large geographic area. We detected 33 markers potentially under balancing selection, hence strong evidence of stabilizing selection in 21 populations across Europe. However, our analyses identified four-times more markers (138) being under positive selection, and geographical patterns suggest that some of these markers are probably associated with alpine regions, which seem to have environmental conditions that favour adaptation. We conclude that despite favourable conditions in this study for the detection of balancing selection, this evolutionary force seems to play a relatively minor role in shaping the genomic diversity of the common vole, which is more influenced by positive selection and neutral processes like drift and demographic history.
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18
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-Biao Guo F, Lin Y, -Ling Chen L. Recognition of Protein-coding Genes Based on Z-curve Algorithms. Curr Genomics 2014; 15:95-103. [PMID: 24822027 PMCID: PMC4009845 DOI: 10.2174/1389202915999140328162724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 01/18/2023] Open
Abstract
Recognition of protein-coding genes, a classical bioinformatics issue, is an absolutely needed step for annotating newly sequenced genomes. The Z-curve algorithm, as one of the most effective methods on this issue, has been successfully applied in annotating or re-annotating many genomes, including those of bacteria, archaea and viruses. Two Z-curve based ab initio gene-finding programs have been developed: ZCURVE (for bacteria and archaea) and ZCURVE_V (for viruses and phages). ZCURVE_C (for 57 bacteria) and Zfisher (for any bacterium) are web servers for re-annotation of bacterial and archaeal genomes. The above four tools can be used for genome annotation or re-annotation, either independently or combined with the other gene-finding programs. In addition to recognizing protein-coding genes and exons, Z-curve algorithms are also effective in recognizing promoters and translation start sites. Here, we summarize the applications of Z-curve algorithms in gene finding and genome annotation.
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Affiliation(s)
- Feng -Biao Guo
- Center of Bioinformatics and Key Laboratory for NeuroInformation of the Ministry of Education, University of Elec-tronic Science and Technology of China, Chengdu, 610054, China
| | - Yan Lin
- Department of Physics, Tianjin University, Tianjin 300072, China
| | - Ling -Ling Chen
- cCollege of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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MHC II DRB variation and trans-species polymorphism in the golden snub-nosed monkey (Rhinopithecus roxellana). CHINESE SCIENCE BULLETIN-CHINESE 2013. [DOI: 10.1007/s11434-013-5713-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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Zhang L, Thomas JC, Didelot X, Robinson DA. Molecular signatures identify a candidate target of balancing selection in an arcD-like gene of Staphylococcus epidermidis. J Mol Evol 2012; 75:43-54. [PMID: 23053194 DOI: 10.1007/s00239-012-9520-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 09/24/2012] [Indexed: 01/19/2023]
Abstract
A comparative population genetics study revealed high levels of nucleotide polymorphism and intermediate-frequency alleles in an arcC gene of Staphylococcus epidermidis, but not in a homologous gene of the more aggressive human pathogen, Staphylococcus aureus. Further investigation showed that the arcC genes used in the multilocus sequence typing schemes of these two species were paralogs. Phylogenetic analyses of arcC-containing loci, including the arginine catabolic mobile element, from both species, suggested that these loci had an eventful history involving gene duplications, rearrangements, deletions, and horizontal transfers. The peak signatures in the polymorphic S. epidermidis locus were traced to an arcD-like gene adjacent to arcC; these signatures consisted of unusually elevated Tajima's D and π/K ratios, which were robust to assumptions about recombination and species divergence time and among the most elevated in the S. epidermidis genome. Amino acid polymorphisms, including one that differed in polarity and hydropathy, were located in the peak signatures and defined two allelic lineages. Recombination events were detected between these allelic lineages and potential donors and recipients of S. epidermidis were identified in each case. By comparison, the orthologous gene of S. aureus showed no unusual signatures. The ArcD-like protein belonged to the unknown ion transporter 3 family and appeared to be unrelated to ArcD from the arginine deiminase pathway. These studies report the first comparative population genetics results for staphylococci and the first statistical evidence for a candidate target of balancing selection in S. epidermidis.
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Affiliation(s)
- Liangfen Zhang
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
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21
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Draft genome sequences of Staphylococcus aureus sequence type 34 (ST34) and ST42 hybrids. J Bacteriol 2012; 194:2740-1. [PMID: 22535928 DOI: 10.1128/jb.00248-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a major cause of antimicrobial-resistant infections of humans. Hybrids of S. aureus, which originate from large-scale chromosomal recombinations between parents of distinct genetic backgrounds, are of interest from clinical and evolutionary perspectives. We present draft genome sequences of two S. aureus hybrids of sequence type 34 (ST34) and ST42.
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Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus. Proc Natl Acad Sci U S A 2012; 109:9107-12. [PMID: 22586109 DOI: 10.1073/pnas.1202869109] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hospital-associated infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a global health burden dominated by a small number of bacterial clones. The pandemic EMRSA-16 clone (ST36-II) has been widespread in UK hospitals for 20 y, but its evolutionary origin and the molecular basis for its hospital association are unclear. We carried out a Bayesian phylogenetic reconstruction on the basis of the genome sequences of 87 S. aureus isolates including 60 EMRSA-16 and 27 additional clonal complex 30 (CC30) isolates, collected from patients in three continents over a 53-y period. The three major pandemic clones to originate from the CC30 lineage, including phage type 80/81, Southwest Pacific, and EMRSA-16, shared a most recent common ancestor that existed over 100 y ago, whereas the hospital-associated EMRSA-16 clone is estimated to have emerged about 35 y ago. Our CC30 genome-wide analysis revealed striking molecular correlates of hospital- or community-associated pandemics represented by mobile genetic elements and nonsynonymous mutations affecting antibiotic resistance and virulence. Importantly, phylogeographic analysis indicates that EMRSA-16 spread within the United Kingdom by transmission from hospitals in large population centers in London and Glasgow to regional health-care settings, implicating patient referrals as an important cause of nationwide transmission. Taken together, the high-resolution phylogenomic approach used resulted in a unique understanding of the emergence and transmission of a major MRSA clone and provided molecular correlates of its hospital adaptation. Similar approaches for hospital-associated clones of other bacterial pathogens may inform appropriate measures for controlling their intra- and interhospital spread.
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