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Deb S, Wild MA, LeClair T, Shah DH. Discovery of novel treponemes associated with pododermatitis in elk ( Cervus canadensis). Appl Environ Microbiol 2024; 90:e0010524. [PMID: 38742897 PMCID: PMC11218636 DOI: 10.1128/aem.00105-24] [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: 01/17/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
Pododermatitis, also known as treponeme-associated hoof disease (TAHD), presents a significant challenge to elk (Cervus canadensis) populations in the northwestern USA, with Treponema spp. consistently implicated in the lesion development. However, identifying species-specific Treponema strains from these lesions is hindered by its culture recalcitrance and limited genomic information. This study utilized shotgun sequencing, in silico genome reconstruction, and comparative genomics as a culture-independent approach to identify metagenome-assembled Treponema genomes (MATGs) from skin scraping samples collected from captive elk experimentally challenged with TAHD. The genomic analysis revealed 10 new MATGs, with 6 representing novel genomospecies associated with pododermatitis in elk and 4 corresponding to previously identified species-Treponema pedis and Treponema phagedenis. Importantly, genomic signatures of novel genomospecies identified in this study were consistently detected in biopsy samples of free-ranging elk diagnosed with TAHD, indicating a potential etiologic association. Comparative metabolic profiling of the MATGs against other Treponema genomes showed a distinct metabolic profile, suggesting potential host adaptation or geographic uniqueness of these newly identified genomospecies. The discovery of novel Treponema genomospecies enhances our understanding of the pathogenesis of pododermatitis and lays the foundation for the development of improved molecular surveillance tools to monitor and manage the disease in free-ranging elk.IMPORTANCETreponema spp. play an important role in the development of pododermatitis in free-ranging elk; however, the species-specific detection of Treponema from pododermatitis lesions is challenging due to culture recalcitrance and limited genomic information. The study utilized shotgun sequencing and in silico genome reconstruction to identify novel Treponema genomospecies from elk with pododermatitis. The discovery of the novel Treponema species opens new avenues to develop molecular diagnostic and epidemiologic tools for the surveillance of pododermatitis in elk. These findings significantly enhance our understanding of the genomic landscape of the Treponemataceae consortium while offering valuable insights into the etiology and pathogenesis of emerging pododermatitis in elk populations.
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Affiliation(s)
- Sushanta Deb
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Margaret A. Wild
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Thomas LeClair
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Devendra H. Shah
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
- School of Veterinary Medicine, Texas Tech University, Amarillo, Texas, USA
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2
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Amundsen SK, Smith GR. RecBCD enzyme: mechanistic insights from mutants of a complex helicase-nuclease. Microbiol Mol Biol Rev 2023; 87:e0004123. [PMID: 38047637 PMCID: PMC10732027 DOI: 10.1128/mmbr.00041-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
SUMMARYRecBCD enzyme is a multi-functional protein that initiates the major pathway of homologous genetic recombination and DNA double-strand break repair in Escherichia coli. It is also required for high cell viability and aids proper DNA replication. This 330-kDa, three-subunit enzyme is one of the fastest, most processive helicases known and contains a potent nuclease controlled by Chi sites, hotspots of recombination, in DNA. RecBCD undergoes major changes in activity and conformation when, during DNA unwinding, it encounters Chi (5'-GCTGGTGG-3') and nicks DNA nearby. Here, we discuss the multitude of mutations in each subunit that affect one or another activity of RecBCD and its control by Chi. These mutants have given deep insights into how the multiple activities of this complex enzyme are coordinated and how it acts in living cells. Similar studies could help reveal how other complex enzymes are controlled by inter-subunit interactions and conformational changes.
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Affiliation(s)
| | - Gerald R. Smith
- Fred Hutchinson Cancer Center Seattle, Seattle, Washington, USA
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3
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Shekhar C, Maeda T. A simple approach for random genomic insertion-deletions using ambiguous sequences in Escherichia coli. J Basic Microbiol 2022; 62:948-962. [PMID: 35739617 DOI: 10.1002/jobm.202100636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/20/2022] [Accepted: 06/11/2022] [Indexed: 11/07/2022]
Abstract
Escherichia coli K-12, being one of the best understood and thoroughly analyzed organisms, is the preferred platform for genetic and biochemical research. Among all genetic engineering approaches applied on E. coli, the homologous recombination approach is versatile and precise, which allows engineering genes or large segments of the chromosome directly by using polymerase chain reaction (PCR) products or synthetic oligonucleotides. The previously explained approaches for random insertion and deletions were reported as technically not easy and laborious. This study, first, finds the minimum length of homology extension that is efficient and accurate for homologous recombination, as 30 nt. Second, proposes an approach utilizing PCR products flanking ambiguous NNN-sequence (30-nt) extensions, which facilitate the homologous recombination to recombine them at multiple regions on the genome and generate insertion-deletion mutations. Further analysis found that these mutations were varying in number, that is, multiple genomic regions were deleted. Moreover, evaluation of the phenotype of all the multiple random insertion-deletion mutants demonstrated no significant changes in the normal metabolism of bacteria. This study not only presents the efficiency of ambiguous sequences in making random deletion mutations, but also demonstrates their further applicability in genomics.
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Affiliation(s)
- Chandra Shekhar
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
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4
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Foster-Nyarko E, Pallen MJ. The microbial ecology of Escherichia coli in the vertebrate gut. FEMS Microbiol Rev 2022; 46:fuac008. [PMID: 35134909 PMCID: PMC9075585 DOI: 10.1093/femsre/fuac008] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli has a rich history as biology's 'rock star', driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance-including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.
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Affiliation(s)
- Ebenezer Foster-Nyarko
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, United Kingdom
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5
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Yu D, Banting G, Neumann NF. A review of the taxonomy, genetics, and biology of the genus Escherichia and the type species Escherichia coli. Can J Microbiol 2021; 67:553-571. [PMID: 33789061 DOI: 10.1139/cjm-2020-0508] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Historically, bacteriologists have relied heavily on biochemical and structural phenotypes for bacterial taxonomic classification. However, advances in comparative genomics have led to greater insights into the remarkable genetic diversity within the microbial world, and even within well-accepted species such as Escherichia coli. The extraordinary genetic diversity in E. coli recapitulates the evolutionary radiation of this species in exploiting a wide range of niches (i.e., ecotypes), including the gastrointestinal system of diverse vertebrate hosts as well as non-host natural environments (soil, natural waters, wastewater), which drives the adaptation, natural selection, and evolution of intragenotypic conspecific specialism as a strategy for survival. Over the last few years, there has been increasing evidence that many E. coli strains are very host (or niche)-specific. While biochemical and phylogenetic evidence support the classification of E. coli as a distinct species, the vast genomic (diverse pan-genome and intragenotypic variability), phenotypic (e.g., metabolic pathways), and ecotypic (host-/niche-specificity) diversity, comparable to the diversity observed in known species complexes, suggest that E. coli is better represented as a complex. Herein we review the taxonomic classification of the genus Escherichia and discuss how phenotype, genotype, and ecotype recapitulate our understanding of the biology of this remarkable bacterium.
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Affiliation(s)
- Daniel Yu
- School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada.,School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada
| | - Graham Banting
- School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada.,School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada
| | - Norman F Neumann
- School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada.,School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada
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6
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Stott CM, Bobay LM. Impact of homologous recombination on core genome phylogenies. BMC Genomics 2020; 21:829. [PMID: 33238876 PMCID: PMC7691112 DOI: 10.1186/s12864-020-07262-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/19/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains. However, there is growing evidence that bacterial strains exchange DNA through homologous recombination at rates that vary widely across prokaryote species, indicating that core genome phylogenies might not be able to reconstruct true phylogenies when recombination rate is high. Few attempts have been made to evaluate the robustness of core genome phylogenies to recombination, but some analyses suggest that reconstructed trees are not always accurate. RESULTS In this study, we tested the robustness of core genome phylogenies to various levels of recombination rates. By analyzing simulated and empirical data, we observed that core genome phylogenies are relatively robust to recombination rates; nevertheless, our results suggest that many reconstructed trees are not completely accurate even when bootstrap supports are high. We found that some core genome phylogenies are highly robust to recombination whereas others are strongly impacted by it, and we identified that the robustness of core genome phylogenies to recombination is highly linked to the levels of selective pressures acting on a species. Stronger selective pressures lead to less accurate tree reconstructions, presumably because selective pressures more strongly bias the routes of DNA transfers, thereby causing phylogenetic artifacts. CONCLUSIONS Overall, these results have important implications for the application of core genome phylogenies in prokaryotes.
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Affiliation(s)
- Caroline M Stott
- Department of Biology, University of North Carolina Greensboro, 321 McIver Street, PO Box 26170, Greensboro, NC, 27402, USA
| | - Louis-Marie Bobay
- Department of Biology, University of North Carolina Greensboro, 321 McIver Street, PO Box 26170, Greensboro, NC, 27402, USA.
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7
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Abstract
Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times during E. coli evolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.
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8
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DeSalle R, Riley M. Should Networks Supplant Tree Building? Microorganisms 2020; 8:E1179. [PMID: 32756444 PMCID: PMC7466111 DOI: 10.3390/microorganisms8081179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/21/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022] Open
Abstract
Recent studies suggested that network methods should supplant tree building as the basis of genealogical analysis. This proposition is based upon two arguments. First is the observation that bacterial and archaeal lineages experience processes oppositional to bifurcation and hence the representation of the evolutionary process in a tree like structure is illogical. Second is the argument tree building approaches are circular-you ask for a tree and you get one, which pins a verificationist label on tree building that, if correct, should be the end of phylogenetic analysis as we currently know it. In this review, we examine these questions and suggest that rumors of the death of the bacterial tree of life are exaggerated at best.
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Affiliation(s)
- Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA;
| | - Margaret Riley
- Department of Biology, University of Massachusetts Amherst, 116 North Pleasant Street, Amherst, MA 01003, USA
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9
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Gonzalez-Alba JM, Baquero F, Cantón R, Galán JC. Stratified reconstruction of ancestral Escherichia coli diversification. BMC Genomics 2019; 20:936. [PMID: 31805853 PMCID: PMC6896753 DOI: 10.1186/s12864-019-6346-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/28/2019] [Indexed: 12/15/2022] Open
Abstract
Background Phylogenetic analyses of the bacterial genomes based on the simple classification in core- genes and accessory genes pools could offer an incomplete view of the evolutionary processes, of which some are still unresolved. A combined strategy based on stratified phylogeny and ancient molecular polymorphisms is proposed to infer detailed evolutionary reconstructions by using a large number of whole genomes. This strategy, based on the highest number of genomes available in public databases, was evaluated for improving knowledge of the ancient diversification of E. coli. This staggered evolutionary scenario was also used to investigate whether the diversification of the ancient E. coli lineages could be associated with particular lifestyles and adaptive strategies. Results Phylogenetic reconstructions, exploiting 6220 available genomes in Genbank, established the E. coli core genome in 1023 genes, representing about 20% of the complete genome. The combined strategy using stratified phylogeny plus molecular polymorphisms inferred three ancient lineages (D, EB1A and FGB2). Lineage D was the closest to E. coli root. A staggered diversification could also be proposed in EB1A and FGB2 lineages and the phylogroups into these lineages. Several molecular markers suggest that each lineage had different adaptive trajectories. The analysis of gained and lost genes in the main lineages showed that functions of carbohydrates utilization (uptake of and metabolism) were gained principally in EB1A lineage, whereas loss of environmental-adaptive functions in FGB2 lineage were observed, but this lineage showed higher accumulated mutations and ancient recombination events. The population structure of E. coli was re-evaluated including up to 7561 new sequenced genomes, showing a more complex population structure of E. coli, as a new phylogroup, phylogroup I, was proposed. Conclusions A staggered reconstruction of E. coli phylogeny is proposed, indicating evolution from three ancestral lineages to reach all main known phylogroups. New phylogroups were confirmed, suggesting an increasingly complex population structure of E. coli. However these new phylogroups represent < 1% of the global E. coli population. A few key evolutionary forces have driven the diversification of the two main E. coli lineages, metabolic flexibility in one of them and colonization-virulence in the other.
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Affiliation(s)
- José Maria Gonzalez-Alba
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana, Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Juan Carlos Galán
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain. .,CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain. .,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana, Madrid, Spain.
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10
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Abstract
Microbial populations exchange genetic material through a process called homologous recombination. Although this process has been studied in particular organisms, we lack an understanding of its differential impact over the genome and across microbes with different life-styles. We used a common analytical framework to assess this process in a representative set of microorganisms. Our results uncovered important trends. First, microbes with different lifestyles are differentially impacted, with endosymbionts and obligate pathogens being those less prone to undergo this process. Second, certain genetic elements such as restriction-modification systems seem to be associated with higher rates of recombination. Most importantly, recombined genomes show the footprints of natural selection in which recombined regions preferentially contain genes that can be related to specific ecological adaptations. Taken together, our results clarify the relative contributions of factors modulating homologous recombination and show evidence for a clear a role of this process in shaping microbial genomes and driving ecological adaptations. Homologous recombination (HR) enables the exchange of genetic material between and within species. Recent studies suggest that this process plays a major role in the microevolution of microbial genomes, contributing to core genome homogenization and to the maintenance of cohesive population structures. However, we still have a very poor understanding of the possible adaptive roles of intraspecific HR and of the factors that determine its differential impact across clades and lifestyles. Here we used a unified methodological framework to assess HR in 338 complete genomes from 54 phylogenetically diverse and representative prokaryotic species, encompassing different lifestyles and a broad phylogenetic distribution. Our results indicate that lifestyle and presence of restriction-modification (RM) machineries are among the main factors shaping HR patterns, with symbionts and intracellular pathogens having the lowest HR levels. Similarly, the size of exchanged genomic fragments correlated with the presence of RM and competence machineries. Finally, genes exchanged by HR showed functional enrichments which could be related to adaptations to different environments and ecological strategies. Taken together, our results clarify the factors underlying HR impact and suggest important adaptive roles of genes exchanged through this mechanism. Our results also revealed that the extent of genetic exchange correlated with lifestyle and some genomic features. Moreover, the genes in exchanged regions were enriched for functions that reflected specific adaptations, supporting identification of HR as one of the main evolutionary mechanisms shaping prokaryotic core genomes.
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11
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Nesbø CL, Charchuk R, Pollo SMJ, Budwill K, Kublanov IV, Haverkamp THA, Foght J. Genomic analysis of the mesophilic Thermotogae genusMesotogareveals phylogeographic structure and genomic determinants of its distinct metabolism. Environ Microbiol 2018; 21:456-470. [DOI: 10.1111/1462-2920.14477] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/15/2018] [Accepted: 11/06/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Camilla L. Nesbø
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
- BioZone, Department of Chemical Engineering and Applied Chemistry; Wallberg Building, University of Toronto; Toronto ON Canada
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences; University of Oslo; Blindern, Oslo Norway
| | - Rhianna Charchuk
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
| | - Stephen M. J. Pollo
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
| | | | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology; Russian Academy of Sciences; Moscow Russia
| | - Thomas H. A. Haverkamp
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences; University of Oslo; Blindern, Oslo Norway
- Norwegian Veterinary Institute; Oslo Norway
| | - Julia Foght
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
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12
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Torregrosa-Crespo J, González-Torres P, Bautista V, Esclapez JM, Pire C, Camacho M, Bonete MJ, Richardson DJ, Watmough NJ, Martínez-Espinosa RM. Analysis of multiple haloarchaeal genomes suggests that the quinone-dependent respiratory nitric oxide reductase is an important source of nitrous oxide in hypersaline environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:788-796. [PMID: 28925557 DOI: 10.1111/1758-2229.12596] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Microorganisms, including Bacteria and Archaea, play a key role in denitrification, which is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. While the enzymology of denitrification is well understood in Bacteria, the details of the last two reactions in this pathway, which catalyse the reduction of nitric oxide (NO) via nitrous oxide (N2 O) to nitrogen (N2 ), are little studied in Archaea, and hardly at all in haloarchaea. This work describes an extensive interspecies analysis of both complete and draft haloarchaeal genomes aimed at identifying the genes that encode respiratory nitric oxide reductases (Nors). The study revealed that the only nor gene found in haloarchaea is one that encodes a single subunit quinone dependent Nor homologous to the qNor found in bacteria. This surprising discovery is considered in terms of our emerging understanding of haloarchaeal bioenergetics and NO management.
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Affiliation(s)
- Javier Torregrosa-Crespo
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Pedro González-Torres
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88. 08003 Barcelona, Spain
| | - Vanesa Bautista
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Julia M Esclapez
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Carmen Pire
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Mónica Camacho
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - María José Bonete
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - David J Richardson
- Centre for Molecular Structure and Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Nicholas J Watmough
- Centre for Molecular Structure and Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Rosa María Martínez-Espinosa
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
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13
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Abstract
Bacteria reproduce asexually and pass on a single genome copied from the parent, a reproductive mode that assures the clonal descent of progeny; however, a truly clonal bacterial species is extremely rare. The signal of clonality can be interrupted by gene uptake and exchange, initiating homologous recombination that results in the unique sequence of one clone being incorporated into another. Because recombination occurs sporadically and on local scales, these events are often difficult to recognize, even when considering large samples of completely sequenced genomes. Moreover, several processes can produce the appearance of clonality in populations that undergo frequent recombination. The rates and consequences of recombination have been studied in Escherichia coli for over 40 y, and, during this time, there have been several shifting views of its clonal status, population structure, and rates of gene exchange. We reexamine the studies and retrace the evolution of the methods that have assessed the extent of DNA flux, largely focusing on its impact on the E. coli genome.
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14
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Abstract
An approximation to the ∼4-Mbp basic genome shared by 32 strains of Escherichia coli representing six evolutionary groups has been derived and analyzed computationally. A multiple alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ∼90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single base-pair mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome pairs have one or two recombinant transfers of length ∼40-115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4-1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kilobase pairs. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. Most recombinant transfers seem likely to be due to generalized transduction by coevolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.
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15
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Leushkin EV, Logacheva MD, Penin AA, Sutormin RA, Gerasimov ES, Kochkina GA, Ivanushkina NE, Vasilenko OV, Kondrashov AS, Ozerskaya SM. Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages. BMC Genomics 2015; 16:400. [PMID: 25994131 PMCID: PMC4438637 DOI: 10.1186/s12864-015-1570-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/23/2015] [Indexed: 01/17/2023] Open
Abstract
Background Pseudogymnoascus spp. is a wide group of fungi lineages in the family Pseudorotiaceae including an aggressive pathogen of bats P. destructans. Although several lineages of P. spp. were shown to produce ascospores in culture, the vast majority of P. spp. demonstrates no evidence of sexual reproduction. P. spp. can tolerate a wide range of different temperatures and salinities and can survive even in permafrost layer. Adaptability of P. spp. to different environments is accompanied by extremely variable morphology and physiology. Results We sequenced genotypes of 14 strains of P. spp., 5 of which were extracted from permafrost, 1 from a cryopeg, a layer of unfrozen ground in permafrost, and 8 from temperate surface environments. All sequenced genotypes are haploid. Nucleotide diversity among these genomes is very high, with a typical evolutionary distance at synonymous sites dS ≈ 0.5, suggesting that the last common ancestor of these strains lived >50Mya. The strains extracted from permafrost do not form a separate clade. Instead, each permafrost strain has close relatives from temperate environments. We observed a strictly clonal population structure with no conflicting topologies for ~99% of genome sequences. However, there is a number of short (~100–10,000 nt) genomic segments with the total length of 67.6 Kb which possess phylogenetic patterns strikingly different from the rest of the genome. The most remarkable case is a MAT-locus, which has 2 distinct alleles interspersed along the whole-genome phylogenetic tree. Conclusions Predominantly clonal structure of genome sequences is consistent with the observations that sexual reproduction is rare in P. spp. Small number of regions with noncanonical phylogenies seem to arise due to some recombination events between derived lineages of P. spp., with MAT-locus being transferred on multiple occasions. All sequenced strains have heterothallic configuration of MAT-locus. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1570-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evgeny V Leushkin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. .,Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127994, Russia.
| | - Maria D Logacheva
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. .,Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127994, Russia. .,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Aleksey A Penin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. .,Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127994, Russia. .,Department of Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - Roman A Sutormin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. .,Lawrence Berkeley National Laboratory, Berkeley, 94710, CA, USA.
| | - Evgeny S Gerasimov
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. .,Department of Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - Galina A Kochkina
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, 142290, Russia.
| | - Natalia E Ivanushkina
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, 142290, Russia.
| | - Oleg V Vasilenko
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, 142290, Russia.
| | - Alexey S Kondrashov
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. .,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Svetlana M Ozerskaya
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, 142290, Russia.
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Abstract
Horizontal or Lateral Gene Transfer (HGT or LGT) is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate the investigations of evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages. Computational identification of HGT events relies upon the investigation of sequence composition or evolutionary history of genes. Sequence composition-based ("parametric") methods search for deviations from the genomic average, whereas evolutionary history-based ("phylogenetic") approaches identify genes whose evolutionary history significantly differs from that of the host species. The evaluation and benchmarking of HGT inference methods typically rely upon simulated genomes, for which the true history is known. On real data, different methods tend to infer different HGT events, and as a result it can be difficult to ascertain all but simple and clear-cut HGT events.
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Affiliation(s)
| | - Nives Škunca
- ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| | | | - Christophe Dessimoz
- University College London, London, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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17
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Turrientes MC, González-Alba JM, del Campo R, Baquero MR, Cantón R, Baquero F, Galán JC. Recombination blurs phylogenetic groups routine assignment in Escherichia coli: setting the record straight. PLoS One 2014; 9:e105395. [PMID: 25137251 PMCID: PMC4138120 DOI: 10.1371/journal.pone.0105395] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 07/24/2014] [Indexed: 01/24/2023] Open
Abstract
The characterization of population structures plays a main role for understanding outbreaks and the dynamics of bacterial spreading. In Escherichia coli, the widely used combination of multiplex-PCR scheme together with goeBURST has some limitations. The purpose of this study is to show that the combination of different phylogenetic approaches based on concatenated sequences of MLST genes results in a more precise assignment of E. coli phylogenetic groups, complete understanding of population structure and reconstruction of ancestral clones. A collection of 80 Escherichia coli strains of different origins was analyzed following the Clermont and Doumith's multiplex-PCR schemes. Doumith's multiplex-PCR showed only 1.7% of misassignment, whereas Clermont's-2000 protocol reached 14.0%, although the discrepancies reached 30% and 38.7% respectively when recombinant C, F and E phylogroups were considered. Therefore, correct phylogroup attribution is highly variable and depends on the clonal composition of the sample. As far as population structure of these E. coli strains, including 48 E. coli genomes from GenBank, goeBURST provides a quite dispersed population structure; whereas NeighborNet approach reveals a complex population structure. MLST-based eBURST can infer different founder genotypes, for instance ST23/ST88 could be detected as the founder genotypes for STC23; however, phylogenetic reconstructions might suggest ST410 as the ancestor clone and several evolutionary trajectories with different founders. To improve our routine understanding of E. coli molecular epidemiology, we propose a strategy based on three successive steps; first, to discriminate three main groups A/B1/C, D/F/E and B2 following Doumith's protocol; second, visualization of population structure based on MLST genes according to goeBURST, using NeighborNet to establish more complex relationships among STs; and third, to perform, a cost-free characterization of evolutionary trajectories in variants emerging along the clonal expansion using parsimony methods of phylogenetic analysis.
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Affiliation(s)
- María-Carmen Turrientes
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - José-María González-Alba
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Rosa del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Red Española para la Investigación en Enfermedades Infecciosas (REIPI), Madrid, Spain
| | | | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Red Española para la Investigación en Enfermedades Infecciosas (REIPI), Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- * E-mail: (FB); (JCG)
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- * E-mail: (FB); (JCG)
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18
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Nunney L, Schuenzel EL, Scally M, Bromley RE, Stouthamer R. Large-scale intersubspecific recombination in the plant-pathogenic bacterium Xylella fastidiosa is associated with the host shift to mulberry. Appl Environ Microbiol 2014; 80:3025-33. [PMID: 24610840 PMCID: PMC4018926 DOI: 10.1128/aem.04112-13] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 02/27/2014] [Indexed: 11/20/2022] Open
Abstract
Homologous recombination plays an important role in the structuring of genetic variation of many bacteria; however, its importance in adaptive evolution is not well established. We investigated the association of intersubspecific homologous recombination (IHR) with the shift to a novel host (mulberry) by the plant-pathogenic bacterium Xylella fastidiosa. Mulberry leaf scorch was identified about 25 years ago in native red mulberry in the eastern United States and has spread to introduced white mulberry in California. Comparing a sequence of 8 genes (4,706 bp) from 21 mulberry-type isolates to published data (352 isolates representing all subspecies), we confirmed previous indications that the mulberry isolates define a group distinct from the 4 subspecies, and we propose naming the taxon X. fastidiosa subsp. morus. The ancestry of its gene sequences was mixed, with 4 derived from X. fastidiosa subsp. fastidiosa (introduced from Central America), 3 from X. fastidiosa subsp. multiplex (considered native to the United States), and 1 chimeric, demonstrating that this group originated by large-scale IHR. The very low within-type genetic variation (0.08% site polymorphism), plus the apparent inability of native X. fastidiosa subsp. multiplex to infect mulberry, suggests that this host shift was achieved after strong selection acted on genetic variants created by IHR. Sequence data indicate that a single ancestral IHR event gave rise not only to X. fastidiosa subsp. morus but also to the X. fastidiosa subsp. multiplex recombinant group which infects several hosts but is the only type naturally infecting blueberry, thus implicating this IHR in the invasion of at least two novel native hosts, mulberry and blueberry.
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Affiliation(s)
- Leonard Nunney
- Department of Biology, University of California, Riverside, California, USA
| | - Erin L. Schuenzel
- Department of Biology, University of Texas—Pan American, Edinburg, Texas, USA
| | - Mark Scally
- Department of Biology, University of Texas—Pan American, Edinburg, Texas, USA
| | - Robin E. Bromley
- Department of Entomology, University of California, Riverside, California, USA
| | - Richard Stouthamer
- Department of Entomology, University of California, Riverside, California, USA
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19
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Signatures of Natural Selection and Ecological Differentiation in Microbial Genomes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 781:339-59. [DOI: 10.1007/978-94-007-7347-9_17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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20
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Detection of homologous recombination events in bacterial genomes. PLoS One 2013; 8:e75230. [PMID: 24116030 PMCID: PMC3792089 DOI: 10.1371/journal.pone.0075230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 08/13/2013] [Indexed: 11/19/2022] Open
Abstract
We study the detection of mutations, sequencing errors, and homologous recombination events (HREs) in a set of closely related microbial genomes. We base the model on single nucleotide polymorphisms (SNPs) and break the genomes into blocks to handle the rearrangement problem. Then we apply a dynamic programming algorithm to model whether changes within each block are likely a result of mutations, sequencing errors, or HREs. Results from simulation experiments show that we can detect 31%–61% of HREs and the precision of our detection is about 48%–90% depending on the rates of mutation and missing data. The HREfinder software for predicting HREs in a set of whole genomes is available as open source (http://sourceforge.net/projects/hrefinder/).
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21
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Leimbach A, Hacker J, Dobrindt U. E. coli as an All-Rounder: The Thin Line Between Commensalism and Pathogenicity. Curr Top Microbiol Immunol 2013; 358:3-32. [PMID: 23340801 DOI: 10.1007/82_2012_303] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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22
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Nunney L, Yuan X, Bromley RE, Stouthamer R. Detecting genetic introgression: high levels of intersubspecific recombination found in Xylella fastidiosa in Brazil. Appl Environ Microbiol 2012; 78:4702-14. [PMID: 22544234 PMCID: PMC3370496 DOI: 10.1128/aem.01126-12] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 04/09/2012] [Indexed: 11/20/2022] Open
Abstract
Documenting the role of novel mutation versus homologous recombination in bacterial evolution, and especially in the invasion of new hosts, is central to understanding the long-term dynamics of pathogenic bacteria. We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS). All 55 citrus isolates typed (plus one coffee isolate) defined three similar sequence types (STs) dominated by ST11 (85%), while the remaining 22 coffee isolates defined two STs, mainly ST16 (74%). This low level of variation masked unusually large allelic differences (>1% divergence with no intermediates) at five loci (leuA, petC, malF, cysG, and holC). We developed an introgression test to detect whether these large differences were due to introgression via homologous recombination from another X. fastidiosa subspecies. Using additional sequencing around these loci, we established that the seven randomly chosen MLST targets contained seven regions of introgression totaling 2,172 bp of 4,161 bp (52%), only 409 bp (10%) of which were detected by other recombination tests. This high level of introgression suggests the hypothesis that X. fastidiosa subsp. pauca became pathogenic on citrus and coffee (crops cultivated in Brazil for several hundred years) only recently after it gained genetic variation via intersubspecific recombination, facilitating a switch from native hosts. A candidate donor is the subspecies infecting plum in the region since 1935 (possibly X. fastidiosa subsp. multiplex). This hypothesis predicts that nonrecombinant native X. fastidiosa subsp. pauca (not yet isolated) does not cause disease in citrus or coffee.
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Affiliation(s)
- Leonard Nunney
- Department of Biology, University of California, Riverside, USA.
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23
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Yahara K, Kawai M, Furuta Y, Takahashi N, Handa N, Tsuru T, Oshima K, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I. Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species. Genome Biol Evol 2012; 4:628-40. [PMID: 22534164 PMCID: PMC3381677 DOI: 10.1093/gbe/evs043] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2012] [Indexed: 12/11/2022] Open
Abstract
The nature of a species remains a fundamental and controversial question. The era of genome/metagenome sequencing has intensified the debate in prokaryotes because of extensive horizontal gene transfer. In this study, we conducted a genome-wide survey of outcrossing homologous recombination in the highly sexual bacterial species Helicobacter pylori. We conducted multiple genome alignment and analyzed the entire data set of one-to-one orthologous genes for its global strains. We detected mosaic structures due to repeated recombination events and discordant phylogenies throughout the genomes of this species. Most of these genes including the "core" set of genes and horizontally transferred genes showed at least one recombination event. Taking into account the relationship between the nucleotide diversity and the minimum number of recombination events per nucleotide, we evaluated the recombination rate in every gene. The rate appears constant across the genome, but genes with a particularly high or low recombination rate were detected. Interestingly, genes with high recombination included those for DNA transformation and for basic cellular functions, such as biosynthesis and metabolism. Several highly divergent genes with a high recombination rate included those for host interaction, such as outer membrane proteins and lipopolysaccharide synthesis. These results provide a global picture of genome-wide distribution of outcrossing homologous recombination in a bacterial species for the first time, to our knowledge, and illustrate how a species can be shaped by mutual homologous recombination.
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Affiliation(s)
- Koji Yahara
- Division of Biostatistics, Graduate School of Medicine, Kurume University, Fukuoka, Japan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Japan
| | - Mikihiko Kawai
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Japan
- Laboratory of Genome Informatics, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Yoshikazu Furuta
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Japan
| | - Noriko Takahashi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Japan
| | - Naofumi Handa
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Japan
| | - Takeshi Tsuru
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Japan
| | - Kenshiro Oshima
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Masaru Yoshida
- Department of Gastroenterology, Graduate School of Medicine, Kobe University, Chuo-ku, Hyogo, Japan
| | - Takeshi Azuma
- Department of Gastroenterology, Graduate School of Medicine, Kobe University, Chuo-ku, Hyogo, Japan
| | - Masahira Hattori
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Ikuo Uchiyama
- Laboratory of Genome Informatics, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Ichizo Kobayashi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Japan
- Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan
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24
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Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, Polz MF, Alm EJ. Population genomics of early events in the ecological differentiation of bacteria. Science 2012; 336:48-51. [PMID: 22491847 PMCID: PMC3337212 DOI: 10.1126/science.1218198] [Citation(s) in RCA: 342] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here, we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations. These findings reconcile previous, seemingly contradictory empirical observations of the genetic structure of bacterial populations and point to a more unified process of differentiation in bacteria and sexual eukaryotes than previously thought.
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Affiliation(s)
- B. Jesse Shapiro
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute, Cambridge, MA 02142, USA
| | - Jonathan Friedman
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Otto X. Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sarah P. Preheim
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sonia C. Timberlake
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gitta Szabó
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Martin F. Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eric J. Alm
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute, Cambridge, MA 02142, USA
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25
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Chaudhuri RR, Henderson IR. The evolution of the Escherichia coli phylogeny. INFECTION GENETICS AND EVOLUTION 2012; 12:214-26. [DOI: 10.1016/j.meegid.2012.01.005] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 01/04/2012] [Accepted: 01/05/2012] [Indexed: 10/14/2022]
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26
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Baumler DJ, Banta LM, Hung KF, Schwarz JA, Cabot EL, Glasner JD, Perna NT. Using comparative genomics for inquiry-based learning to dissect virulence of Escherichia coli O157:H7 and Yersinia pestis. CBE LIFE SCIENCES EDUCATION 2012; 11:81-93. [PMID: 22383620 PMCID: PMC3292067 DOI: 10.1187/cbe.10-04-0057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis of Genomes database. In the second module, students use an alignment of five Yersinia pestis genomes to analyze single-nucleotide polymorphisms of three genes to classify strains into biovar groups. Students are then given sequences of bacterial DNA amplified from the teeth of corpses from the first and second pandemics of the bubonic plague and asked to classify these new samples. Learning-assessment results reveal student improvement in self-efficacy and content knowledge, as well as students' ability to use BLAST to identify genomic islands and conduct analyses of virulence factors from E. coli O157:H7 or Y. pestis. Each of these educational modules offers educators new ready-to-implement resources for integrating comparative genomic topics into their curricula.
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Affiliation(s)
- David J Baumler
- BACTER Institute, University of Wisconsin, Madison, WI 53706, USA.
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27
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Leopold SR, Sawyer SA, Whittam TS, Tarr PI. Obscured phylogeny and possible recombinational dormancy in Escherichia coli. BMC Evol Biol 2011; 11:183. [PMID: 21708031 PMCID: PMC3152902 DOI: 10.1186/1471-2148-11-183] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 06/27/2011] [Indexed: 12/02/2022] Open
Abstract
Background Escherichia coli is one of the best studied organisms in all of biology, but its phylogenetic structure has been difficult to resolve with current data and analytical techniques. We analyzed single nucleotide polymorphisms in chromosomes of representative strains to reconstruct the topology of its emergence. Results The phylogeny of E. coli varies according to the segment of chromosome analyzed. Recombination between extant E. coli groups is largely limited to only three intergroup pairings. Conclusions Segment-dependent phylogenies most likely are legacies of a complex recombination history. However, E. coli are now in an epoch in which they no longer broadly share DNA. Using the definition of species as organisms that freely exchange genetic material, this recombinational dormancy could reflect either the end of E. coli as a species, or herald the coalescence of E. coli groups into new species.
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Affiliation(s)
- Shana R Leopold
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, USA
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28
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Fernández-Romero N, Romero-Gómez MP, Gómez-Gil MR, Mingorance J. Epidemic population structure of extraintestinal pathogenic Escherichia coli determined by single nucleotide polymorphism pyrosequencing. INFECTION GENETICS AND EVOLUTION 2011; 11:1655-63. [PMID: 21723423 DOI: 10.1016/j.meegid.2011.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 06/10/2011] [Accepted: 06/16/2011] [Indexed: 12/01/2022]
Abstract
We have developed an MLST-based scheme for typing Escherichia coli isolates using pyrosequencing of single nucleotide polymorphic positions (SNP). The SNP sequences are converted into allelic patterns and analyzed using the same approach used for MLST analyses. We have tested the method in two unselected collections of clinical isolates of E. coli obtained from blood and urine cultures. The two collections had a similar structure, 25% of the profiles (representing 68% of the isolates) were common to both, and 62% of the profiles (nearly 20% of the isolates) were unique. The four major profiles accounted for 44% of the isolates, and among these the most frequent one was related to the pandemic ST131 clone. The method is easy to implement and might be useful for typing large microbial collections.
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Affiliation(s)
- Natalia Fernández-Romero
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana, Madrid, Spain
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29
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Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T. Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res 2011; 21:599-609. [PMID: 21270172 DOI: 10.1101/gr.115592.110] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Lateral gene transfer (LGT) plays a major role in prokaryote evolution with only a few genes that are resistant to it; yet the nature and magnitude of barriers to lateral transfer are still debated. Here, we implement directed networks to investigate donor-recipient events of recent lateral gene transfer among 657 sequenced prokaryote genomes. For 2,129,548 genes investigated, we detected 446,854 recent lateral gene transfer events through nucleotide pattern analysis. Among these, donor-recipient relationships could be specified through phylogenetic reconstruction for 7% of the pairs, yielding 32,028 polarized recent gene acquisition events, which constitute the edges of our directed networks. We find that the frequency of recent LGT is linearly correlated both with genome sequence similarity and with proteome similarity of donor-recipient pairs. Genome sequence similarity accounts for 25% of the variation in gene-transfer frequency, with proteome similarity adding only 1% to the variability explained. The range of donor-recipient GC content similarity within the network is extremely narrow, with 86% of the LGTs occurring between donor-recipient pairs having ≤5% difference in GC content. Hence, genome sequence similarity and GC content similarity are strong barriers to LGT in prokaryotes. But they are not insurmountable, as we detected 1530 recent transfers between distantly related genomes. The directed network revealed that recipient genomes of distant transfers encode proteins of nonhomologous end-joining (NHEJ; a DNA repair mechanism) far more frequently than the recipient lacking that mechanism. This implicates NHEJ in genes spread across distantly related prokaryotes through bypassing the donor-recipient sequence similarity barrier.
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Affiliation(s)
- Ovidiu Popa
- Institute of Botany III, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
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30
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Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. Proc Natl Acad Sci U S A 2010; 107:21576-81. [PMID: 21115831 DOI: 10.1073/pnas.1016295107] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The best known outcome of horizontal gene transfer (HGT) is the introduction of novel genes, but other outcomes have been described. When a transferred gene has a homolog in the recipient genome, the native gene may be functionally replaced (and subsequently lost) or partially overwritten by gene conversion with transiently present foreign DNA. Here we report the discovery, in two lineages of plant mitochondrial genes, of novel gene combinations that arose by conversion between coresident native and foreign homologs. These lineages have undergone intricate conversion between native and foreign copies, with conversion occurring repeatedly and differentially over the course of speciation, leading to radiations of mosaic genes involved in respiration and intron splicing. Based on these findings, we develop a model--the duplicative HGT and differential gene conversion model--that integrates HGT and ongoing gene conversion in the context of speciation. Finally, we show that one of these HGT-driven gene-conversional radiations followed two additional types of conversional chimerism, namely, intramitochondrial retroprocessing and interorganellar gene conversion across the 2 billion year divide between mitochondria and chloroplasts. These findings expand our appreciation of HGT and gene conversion as creative evolutionary forces, establish plant mitochondria as a premiere system for studying the evolutionary dynamics of HGT and its genetic reverberations, and recommend careful examination of bacterial and other genomes for similar, likely overlooked phenomena.
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progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010; 5:e11147. [PMID: 20593022 PMCID: PMC2892488 DOI: 10.1371/journal.pone.0011147] [Citation(s) in RCA: 2875] [Impact Index Per Article: 205.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 05/24/2010] [Indexed: 11/21/2022] Open
Abstract
Background Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. Methodology/Principal Findings We describe a new method to align two or more genomes that have undergone rearrangements due to recombination and substantial amounts of segmental gain and loss (flux). We demonstrate that the new method can accurately align regions conserved in some, but not all, of the genomes, an important case not handled by our previous work. The method uses a novel alignment objective score called a sum-of-pairs breakpoint score, which facilitates accurate detection of rearrangement breakpoints when genomes have unequal gene content. We also apply a probabilistic alignment filtering method to remove erroneous alignments of unrelated sequences, which are commonly observed in other genome alignment methods. We describe new metrics for quantifying genome alignment accuracy which measure the quality of rearrangement breakpoint predictions and indel predictions. The new genome alignment algorithm demonstrates high accuracy in situations where genomes have undergone biologically feasible amounts of genome rearrangement, segmental gain and loss. We apply the new algorithm to a set of 23 genomes from the genera Escherichia, Shigella, and Salmonella. Analysis of whole-genome multiple alignments allows us to extend the previously defined concepts of core- and pan-genomes to include not only annotated genes, but also non-coding regions with potential regulatory roles. The 23 enterobacteria have an estimated core-genome of 2.46Mbp conserved among all taxa and a pan-genome of 15.2Mbp. We document substantial population-level variability among these organisms driven by segmental gain and loss. Interestingly, much variability lies in intergenic regions, suggesting that the Enterobacteriacae may exhibit regulatory divergence. Conclusions The multiple genome alignments generated by our software provide a platform for comparative genomic and population genomic studies. Free, open-source software implementing the described genome alignment approach is available from http://gel.ahabs.wisc.edu/mauve.
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Touzain F, Denamur E, Médigue C, Barbe V, El Karoui M, Petit MA. Small variable segments constitute a major type of diversity of bacterial genomes at the species level. Genome Biol 2010; 11:R45. [PMID: 20433696 PMCID: PMC2884548 DOI: 10.1186/gb-2010-11-4-r45] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 03/15/2010] [Accepted: 04/30/2010] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Analysis of large scale diversity in bacterial genomes has mainly focused on elements such as pathogenicity islands, or more generally, genomic islands. These comprise numerous genes and confer important phenotypes, which are present or absent depending on strains. We report that despite this widely accepted notion, most diversity at the species level is composed of much smaller DNA segments, 20 to 500 bp in size, which we call microdiversity. RESULTS We performed a systematic analysis of the variable segments detected by multiple whole genome alignments at the DNA level on three species for which the greatest number of genomes have been sequenced: Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes. Among the numerous sites of variability, 62 to 73% were loci of microdiversity, many of which were located within genes. They contribute to phenotypic variations, as 3 to 6% of all genes harbor microdiversity, and 1 to 9% of total genes are located downstream from a microdiversity locus. Microdiversity loci are particularly abundant in genes encoding membrane proteins. In-depth analysis of the E. coli alignments shows that most of the diversity does not correspond to known mobile or repeated elements, and it is likely that they were generated by illegitimate recombination. An intriguing class of microdiversity includes small blocks of highly diverged sequences, whose origin is discussed. CONCLUSIONS This analysis uncovers the importance of this small-sized genome diversity, which we expect to be present in a wide range of bacteria, and possibly also in many eukaryotic genomes.
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Affiliation(s)
- Fabrice Touzain
- INRA, UMR1319, Micalis, Bat 222, Jouy en Josas, 78350, France
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Cohen O, Pupko T. Inference and characterization of horizontally transferred gene families using stochastic mapping. Mol Biol Evol 2009; 27:703-13. [PMID: 19808865 PMCID: PMC2822287 DOI: 10.1093/molbev/msp240] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Macrogenomic events, in which genes are gained and lost, play a pivotal evolutionary role in microbial evolution. Nevertheless, probabilistic-evolutionary models describing such events and methods for their robust inference are considerably less developed than existing methodologies for analyzing site-specific sequence evolution. Here, we present a novel method for the inference of gains and losses of gene families. First, we develop probabilistic-evolutionary models describing the dynamics of gene-family content, which are more biologically realistic than previously suggested models. In our likelihood-based models, gains and losses are represented by transitions between presence and absence, given an underlying phylogeny. We employ a mixture-model approach in which we allow both the gain rate and the loss rate to vary among gene families. Second, we use these models together with the analytic implementation of stochastic mapping to infer branch-specific events. Our novel methodology allows us to infer and quantify horizontal gene transfer (HGT) events. This enables us to rank various gene families and lineages according to their propensity to undergo gains and losses. Applying our methodology to 4,873 gene families shows that: 1) the novel mixture models describe the observed variability in gene-family content among microbes significantly better than previous models; 2) The stochastic mapping approach enables accurate inference of gain and loss events based on simulations; 3) At least 34% of the gene families analyzed are inferred to have experienced HGT at least once during their evolution; and 4) Gene families that were inferred to experience HGT are both enriched and depleted with respect to specific functional categories.
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Affiliation(s)
- Ofir Cohen
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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Ragan MA, Beiko RG. Lateral genetic transfer: open issues. Philos Trans R Soc Lond B Biol Sci 2009; 364:2241-51. [PMID: 19571244 DOI: 10.1098/rstb.2009.0031] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Lateral genetic transfer (LGT) is an important adaptive force in evolution, contributing to metabolic, physiological and ecological innovation in most prokaryotes and some eukaryotes. Genomic sequences and other data have begun to illuminate the processes, mechanisms, quantitative extent and impact of LGT in diverse organisms, populations, taxa and environments; deep questions are being posed, and the provisional answers sometimes challenge existing paradigms. At the same time, there is an enhanced appreciation of the imperfections, biases and blind spots in the data and in analytical approaches. Here we identify and consider significant open questions concerning the role of LGT in genome evolution.
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Affiliation(s)
- Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
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Abstract
The notion that all prokaryotes belong to genomically and phenomically cohesive clusters that we might legitimately call "species" is a contentious one. At issue are (1) whether such clusters actually exist; (2) what species definition might most reliably identify them, if they do; and (3) what species concept -- by which is meant a genetic and ecological theory of speciation -- might best explain species existence and rationalize a species definition, if we could agree on one. We review existing theories and some relevant data. We conclude that microbiologists now understand in some detail the various genetic, population, and ecological processes that effect the evolution of prokaryotes. There will be on occasion circumstances under which these, working together, will form groups of related organisms sufficiently like each other that we might all agree to call them "species," but there is no reason that this must always be so. Thus, there is no principled way in which questions about prokaryotic species, such as how many there are, how large their populations are, or how globally they are distributed, can be answered. These questions can, however, be reformulated so that metagenomic methods and thinking will meaningfully address the biological patterns and processes whose understanding is our ultimate target.
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Dunn KA, Bielawski JP, Ward TJ, Urquhart C, Gu H. Reconciling ecological and genomic divergence among lineages of listeria under an "extended mosaic genome concept". Mol Biol Evol 2009; 26:2605-15. [PMID: 19666992 DOI: 10.1093/molbev/msp176] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
There is growing evidence for a discontinuity between genomic and ecological divergence in several groups of bacteria. This evidence is difficult to reconcile with the traditional concept that ecologically divergent species maintain a cohesive gene pool isolated from other gene pools by barriers to homologous recombination (HR). There have been several innovative models of bacterial divergence that permit such discontinuity; we refer to these, collectively, as "mosaic genome concepts" (MGCs). These concepts remain a point of contention. Here, we undertake an investigation among ecologically divergent lineages of genus Listeria, and report our assessment of both niche-specific selection pressure and HR in their core genome. We find evidence of a mosaic Listeria core genome. Some core genes appear to have been free to recombine across ecologically divergent lineages or across named species. In contrast, other core genes have histories consistent with the expected organism relationships and have evolved under niche-specific selective pressures. The products of some of those genes can even be linked to metabolic phenotypes with ecological significance. This finding indicates a potentially strong connection between ecological divergence and core-genome evolution, even among lineages that also experience frequent recombination. Based on these findings, we propose an expanded role for natural selection in core-genome evolution under the MGC.
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Affiliation(s)
- Katherine A Dunn
- Department of Biology, Dalhousie University, Halifax Nova Scotia, Canada.
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Evidence of extensive homologous recombination in the core genome of rickettsia. Comp Funct Genomics 2009:510270. [PMID: 19478958 PMCID: PMC2685993 DOI: 10.1155/2009/510270] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Accepted: 04/11/2009] [Indexed: 01/23/2023] Open
Abstract
The important role of homologous recombination has been extensively demonstrated to be fundamental for genetic variation in bacterial genomes. In contrast to extracellular or facultative intracellular bacteria, obligate intracellular bacteria are considered to be less prone to recombination, especially for their core genomes. In Rickettsia, only antigen-related genes were identified to have experienced homologous recombination. In this study, we employed evolutionary genomic approaches to investigate the impact of recombination on the core genome of Rickettsia. Phylogenetic network and phylogenetic compatibility matrix analyses are clearly consistent with the hypothesis that recombination has occurred frequently during Rickettsia evolution. 28% of Rickettsia core genes (194 out of 690) are found to present the evidence of recombination under four independent statistical methods. Further functional classification shows that these recombination events occur across all functional categories, with a significant overrepresentation in the cell wall/membrane/envelope biogenesis, which may provide a molecular basis for the parasite adaptation to host immunity. This evolutionary genomic analysis provides insight into the substantial role of recombination in the evolution of the intracellular pathogenic bacteria Rickettsia.
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Vos M. Why do bacteria engage in homologous recombination? Trends Microbiol 2009; 17:226-32. [PMID: 19464181 DOI: 10.1016/j.tim.2009.03.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 03/15/2009] [Accepted: 03/20/2009] [Indexed: 11/27/2022]
Abstract
Microbiologists have long recognized that the uptake and incorporation of homologous DNA from outside the cell is a common feature of bacteria, with important implications for their evolution. However, the exact reasons why bacteria engage in homologous recombination remain elusive. This Opinion article aims to reinvigorate the debate by examining the costs and benefits that homologous recombination could engender in natural populations of bacteria. It specifically focuses on the hypothesis that homologous recombination is selectively maintained because the genetic variation it generates improves the response of bacterial populations to natural selection, analogous to sex in eukaryotes.
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Affiliation(s)
- Michiel Vos
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
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Abstract
This chapter discusses the pros and cons of the existing computational methods for the detection of horizontal (or lateral) gene transfer and highlights the genome-wide studies utilizing these methods. The impact of horizontal gene transfer (HGT) on prokaryote genome evolution is discussed.
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Shapiro BJ, David LA, Friedman J, Alm EJ. Looking for Darwin's footprints in the microbial world. Trends Microbiol 2009; 17:196-204. [PMID: 19375326 DOI: 10.1016/j.tim.2009.02.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Revised: 01/26/2009] [Accepted: 02/09/2009] [Indexed: 10/20/2022]
Abstract
As we observe the 200th anniversary of Charles Darwin's birth, microbiologists interested in the application of Darwin's ideas to the microscopic world have a lot to celebrate: an emerging picture of the (mostly microbial) Tree of Life at ever-increasing resolution, an understanding of horizontal gene transfer as a driving force in the evolution of microbes, and thousands of complete genome sequences to help formulate and refine our theories. At the same time, quantitative models of the microevolutionary processes shaping microbial populations remain just out of reach, a point that is perhaps most dramatically illustrated by the lack of consensus on how (or even whether) to define bacterial species. Here, we summarize progress and prospects in bacterial population genetics, with an emphasis on detecting the footprint of positive Darwinian selection in microbial genomes.
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Affiliation(s)
- B Jesse Shapiro
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Abstract
Background In prokaryotes and some eukaryotes, genetic material can be transferred laterally among unrelated lineages and recombined into new host genomes, providing metabolic and physiological novelty. Although the process is usually framed in terms of gene sharing (e.g. lateral gene transfer, LGT), there is little reason to imagine that the units of transfer and recombination correspond to entire, intact genes. Proteins often consist of one or more spatially compact structural regions (domains) which may fold autonomously and which, singly or in combination, confer the protein's specific functions. As LGT is frequent in strongly selective environments and natural selection is based on function, we hypothesized that domains might also serve as modules of genetic transfer, i.e. that regions of DNA that are transferred and recombined between lineages might encode intact structural domains of proteins. Methodology/Principal Findings We selected 1,462 orthologous gene sets representing 144 prokaryotic genomes, and applied a rigorous two-stage approach to identify recombination breakpoints within these sequences. Recombination breakpoints are very significantly over-represented in gene sets within which protein domain-encoding regions have been annotated. Within these gene sets, breakpoints significantly avoid the domain-encoding regions (domons), except where these regions constitute most of the sequence length. Recombination breakpoints that fall within longer domons are distributed uniformly at random, but those that fall within shorter domons may show a slight tendency to avoid the domon midpoint. As we find no evidence for differential selection against nucleotide substitutions following the recombination event, any bias against disruption of domains must be a consequence of the recombination event per se. Conclusions/Significance This is the first systematic study relating the units of LGT to structural features at the protein level. Many genes have been interrupted by recombination following inter-lineage genetic transfer, during which the regions within these genes that encode protein domains have not been preferentially preserved intact. Protein domains are units of function, but domons are not modules of transfer and recombination. Our results demonstrate that LGT can remodel even the most functionally conservative modules within genomes.
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Abstract
In recent years, the importance of horizontal gene transfer (HGT) in bacterial evolution has been elevated to such a degree that many bacteriologists now question the very existence of bacterial species. If gene transfer is as rampant as comparative genomic studies have suggested, how could bacterial species survive such genomic fluidity? And yet, most bacteriologists recognize, and name, as species, clusters of bacterial isolates that share complex phenotypic properties. The Core Genome Hypothesis (CGH) has been proposed to explain this apparent paradox of fluid bacterial genomes associated with stable phenotypic clusters. It posits that there is a core of genes responsible for maintaining the species-specific phenotypic clusters observed throughout bacterial diversity and argues that, even in the face of substantial genomic fluidity, bacterial species can be rationally identified and named.
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Affiliation(s)
- Margaret A Riley
- Department of Biology, University of Massachusetts, Amherst, MA, USA
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Simmons SL, DiBartolo G, Denef VJ, Goltsman DSA, Thelen MP, Banfield JF. Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol 2008; 6:e177. [PMID: 18651792 PMCID: PMC2475542 DOI: 10.1371/journal.pbio.0060177] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Accepted: 06/12/2008] [Indexed: 12/20/2022] Open
Abstract
Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth ∼20×). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types (∼94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination. Communities of microbes in nature consist of a large number of distinct individuals. The variation in DNA sequence between these individuals contains a record of the evolutionary processes that have shaped each community. In most environments, however, the high number of distinct species makes obtaining information about the nature of this variation difficult or impossible. We obtained large amounts of sequence data for a natural community in an acid mine drainage system consisting of only a few species. This enabled us to reconstruct the genome of the dominant bacterium (Leptospirillum group II) and obtain detailed information about sequence variation between individuals, including differences in both gene content and gene sequence. Our analysis shows extensive recombination between closely related populations, as well as fewer instances of recombination between more distantly related individuals. Additionally, viruses and plasmids account for high variability in gene content between individuals. We conclude that sequence-level variation in this population is maintained through neutral processes (migration, recombination, and genetic drift) rather than natural selection. This suggests that closely related strains of the Leptospirillum group II population may not be ecologically distinct. Deep sequencing of a low-complexity microbial community revealed extensive recombination as well as polymorphic and gene content variation between individuals of the dominant organism. We show that strains defined by linked polymorphisms are not maintained by positive selection; instead, they are predominantly maintained by the forces of migration and drift.
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Affiliation(s)
- Sheri L Simmons
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
| | - Genevieve DiBartolo
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
| | - Vincent J Denef
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
| | - Daniela S. Aliaga Goltsman
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
| | - Michael P Thelen
- Chemistry Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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Novichkov PS, Ratnere I, Wolf YI, Koonin EV, Dubchak I. ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. Nucleic Acids Res 2008; 37:D448-54. [PMID: 18845571 PMCID: PMC2686458 DOI: 10.1093/nar/gkn684] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.gov
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Affiliation(s)
- Pavel S Novichkov
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
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46
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Vos M, Didelot X. A comparison of homologous recombination rates in bacteria and archaea. ISME JOURNAL 2008; 3:199-208. [PMID: 18830278 DOI: 10.1038/ismej.2008.93] [Citation(s) in RCA: 387] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
It is a standard practice to test for the signature of homologous recombination in studies examining the genetic diversity of bacterial populations. Although it has emerged that homologous recombination rates can vary widely between species, comparing the results from different studies is made difficult by the diversity of estimation methods used. Here, Multi Locus Sequence Typing (MLST) datasets from a wide variety of bacteria and archaea are analyzed using the ClonalFrame method. This enables a direct comparison between species and allows for a first exploration of the question whether phylogeny or ecology is the primary determinant of homologous recombination rate.
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Affiliation(s)
- Michiel Vos
- Department of Zoology, University of Oxford, Oxford, UK.
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47
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Denef VJ, VerBerkmoes NC, Shah MB, Abraham P, Lefsrud M, Hettich RL, Banfield JF. Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environ Microbiol 2008; 11:313-25. [PMID: 18826438 DOI: 10.1111/j.1462-2920.2008.01769.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Analyses of ecological and evolutionary processes that shape microbial consortia are facilitated by comprehensive studies of ecosystems with low species richness. In the current study we evaluated the role of recombination in altering the fitness of chemoautotrophic bacteria in their natural environment. Proteomics-inferred genome typing (PIGT) was used to genotype the dominant Leptospirillum group II populations in 27 biofilms sampled from six locations in the Richmond Mine acid mine drainage system (Iron Mountain, CA) over a 4-year period. We observed six distinct genotypes that are recombinants comprised of segments from two 'parental' genotypes. Community genomic analyses revealed additional low abundance recombinant variants. The dominance of some genotypes despite a larger available genome pool, and patterns of spatiotemporal distribution within the ecosystem, indicate selection for distinct recombinants. Genes involved in motility, signal transduction and transport were over-represented in the tens to hundreds of kilobase recombinant blocks, whereas core metabolic functions were significantly under-represented. Our findings demonstrate the power of PIGT and reveal that recombination is a mechanism for fine-scale adaptation in this system.
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Darling AE, Miklós I, Ragan MA. Dynamics of genome rearrangement in bacterial populations. PLoS Genet 2008; 4:e1000128. [PMID: 18650965 PMCID: PMC2483231 DOI: 10.1371/journal.pgen.1000128] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2007] [Accepted: 06/16/2008] [Indexed: 11/24/2022] Open
Abstract
Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability of several Yersinia genomes offers an unprecedented opportunity to study the evolution of genome structure and arrangement. We introduce a set of statistical methods to study patterns of rearrangement in circular chromosomes and apply them to the Yersinia. We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. Based on the alignment, we applied Bayesian statistical methods to infer the phylogenetic inversion history of Yersinia. The sampling of genome arrangement reconstructions contains seven parsimonious tree topologies, each having different histories of 79 inversions. Topologies with a greater number of inversions also exist, but were sampled less frequently. The inversion phylogenies agree with results suggested by SNP patterns. We then analyzed reconstructed inversion histories to identify patterns of rearrangement. We confirm an over-representation of "symmetric inversions"-inversions with endpoints that are equally distant from the origin of chromosomal replication. Ancestral genome arrangements demonstrate moderate preference for replichore balance in Yersinia. We found that all inversions are shorter than expected under a neutral model, whereas inversions acting within a single replichore are much shorter than expected. We also found evidence for a canonical configuration of the origin and terminus of replication. Finally, breakpoint reuse analysis reveals that inversions with endpoints proximal to the origin of DNA replication are nearly three times more frequent. Our findings represent the first characterization of genome arrangement evolution in a bacterial population evolving outside laboratory conditions. Insight into the process of genomic rearrangement may further the understanding of pathogen population dynamics and selection on the architecture of circular bacterial chromosomes.
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Affiliation(s)
- Aaron E Darling
- ARC Center of Excellence in Bioinformatics, The University of Queensland, St. Lucia, Queensland, Australia.
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Shapiro BJ, Alm EJ. Comparing patterns of natural selection across species using selective signatures. PLoS Genet 2008; 4:e23. [PMID: 18266472 PMCID: PMC2233676 DOI: 10.1371/journal.pgen.0040023] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Accepted: 12/18/2007] [Indexed: 12/04/2022] Open
Abstract
Comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments. In the same way, comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys. Toward this end, we show how variation in protein evolutionary rates, after correcting for genome-wide effects such as mutation rate and demographic factors, can be used to estimate the level and types of natural selection acting on genes across different species. We identify unusually rapidly and slowly evolving genes, relative to empirically derived genome-wide and gene family-specific background rates for 744 core protein families in 30 γ-proteobacterial species. We describe the pattern of fast or slow evolution across species as the “selective signature” of a gene. Selective signatures represent a profile of selection across species that is predictive of gene function: pairs of genes with correlated selective signatures are more likely to share the same cellular function, and genes in the same pathway can evolve in concert. For example, glycolysis and phenylalanine metabolism genes evolve rapidly in Idiomarina loihiensis, mirroring an ecological shift in carbon source from sugars to amino acids. In a broader context, our results suggest that the genomic landscape is organized into functional modules even at the level of natural selection, and thus it may be easier than expected to understand the complex evolutionary pressures on a cell. Natural selection promotes the survival of the fittest individuals within a species. Over many generations, this may result in the maintenance of ancestral traits (conservation through purifying selection), or the emergence of newly beneficial traits (adaptation through positive selection). At the genetic level, long-term purifying or positive selection can cause genes to evolve more slowly, or more rapidly, providing a way to identify these evolutionary forces. While some genes are subject to consistent purifying or positive selection in most species, other genes show unexpected levels of selection in a particular species or group of species—a pattern we refer to as the “selective signature” of the gene. In this work, we demonstrate that these patterns of natural selection can be mined for information about gene function and species ecology. In the future, this method could be applied to any set of related species with fully sequenced genomes to better understand the genetic basis of ecological divergence.
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Affiliation(s)
- B. Jesse Shapiro
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Eric J Alm
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- The Virtual institute of Microbial Stress and Survival, Berkeley, California, United States of America
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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Vergin KL, Tripp HJ, Wilhelm LJ, Denver DR, Rappé MS, Giovannoni SJ. High intraspecific recombination rate in a native population of Candidatus pelagibacter ubique (SAR11). Environ Microbiol 2008; 9:2430-40. [PMID: 17803769 DOI: 10.1111/j.1462-2920.2007.01361.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recombination is an important process in microbial evolution. Rates of recombination with extracellular DNA matter because models of microbial population structure are profoundly influenced by the degree to which recombination is occurring within the population. Low rates of recombination may be sufficient to ensure the lateral propagation of genes that have a high selective advantage without disrupting the clonal pattern of inheritance for other genes. High rates of recombination potentially can obscure clonal patterns, leading to linkage equilibrium, and give microbial populations a population genetic structure more akin to sexually interbreeding eukaryotic populations. We examined eight loci from nine strains of candidatus Pelagibacter ubique (SAR11), isolated from a single 2L niskin sample of natural seawater, for evidence of genetic recombination between strains. The Shimodaira-Hasegawa test revealed significant phylogenetic incongruence in seven of the genes, indicating that frequent recombination obscures phylogenetic signals from the linear inheritance of genes in this population. Statistical evidence for intragenic recombination was found for six loci. An informative sites matrix showed extensive evidence for a widespread breakdown of linkage disequilibrium. Although the mechanisms of genetic transfer in native SAR11 populations are unknown, we measured recombination rates, rho, that are much higher than point mutation rates, theta, as a source of genetic diversity in this clade. The eukaryotic model of species sharing a common pool of alleles is more apt for this SAR11 population than a strictly clonal model of inheritance in which allelic diversity is controlled by periodic selection.
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Affiliation(s)
- Kevin L Vergin
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
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