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Evolution and Diversity of Clonal Bacteria: The Paradigm of Mycobacterium tuberculosis

BACKGROUND: Mycobacterium tuberculosis complex species display relatively static genomes and 99.9% nucleotide sequence identity. Studying the evolutionary history of such monomorphic bacteria is a difficult and challenging task. PRINCIPAL FINDINGS: We found that single-nucleotide polymorphism (SNP)...

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Autores principales: Dos Vultos, Tiago, Mestre, Olga, Rauzier, Jean, Golec, Marcin, Rastogi, Nalin, Rasolofo, Voahangy, Tonjum, Tone, Sola, Christophe, Matic, Ivan, Gicquel, Brigitte
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2211405/
https://www.ncbi.nlm.nih.gov/pubmed/18253486
http://dx.doi.org/10.1371/journal.pone.0001538
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author Dos Vultos, Tiago
Mestre, Olga
Rauzier, Jean
Golec, Marcin
Rastogi, Nalin
Rasolofo, Voahangy
Tonjum, Tone
Sola, Christophe
Matic, Ivan
Gicquel, Brigitte
author_facet Dos Vultos, Tiago
Mestre, Olga
Rauzier, Jean
Golec, Marcin
Rastogi, Nalin
Rasolofo, Voahangy
Tonjum, Tone
Sola, Christophe
Matic, Ivan
Gicquel, Brigitte
author_sort Dos Vultos, Tiago
collection PubMed
description BACKGROUND: Mycobacterium tuberculosis complex species display relatively static genomes and 99.9% nucleotide sequence identity. Studying the evolutionary history of such monomorphic bacteria is a difficult and challenging task. PRINCIPAL FINDINGS: We found that single-nucleotide polymorphism (SNP) analysis of DNA repair, recombination and replication (3R) genes in a comprehensive selection of M. tuberculosis complex strains from across the world, yielded surprisingly high levels of polymorphisms as compared to house-keeping genes, making it possible to distinguish between 80% of clinical isolates analyzed in this study. Bioinformatics analysis suggests that a large number of these polymorphisms are potentially deleterious. Site frequency spectrum comparison of synonymous and non-synonymous variants and Ka/Ks ratio analysis suggest a general negative/purifying selection acting on these sets of genes that may lead to suboptimal 3R system activity. In turn, the relaxed fidelity of 3R genes may allow the occurrence of adaptive variants, some of which will survive. Furthermore, 3R-based phylogenetic trees are a new tool for distinguishing between M. tuberculosis complex strains. CONCLUSIONS/SIGNIFICANCE: This situation, and the consequent lack of fidelity in genome maintenance, may serve as a starting point for the evolution of antibiotic resistance, fitness for survival and pathogenicity, possibly conferring a selective advantage in certain stressful situations. These findings suggest that 3R genes may play an important role in the evolution of highly clonal bacteria, such as M. tuberculosis. They also facilitate further epidemiological studies of these bacteria, through the development of high-resolution tools. With many more microbial genomes being sequenced, our results open the door to 3R gene-based studies of adaptation and evolution of other, highly clonal bacteria.
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spelling pubmed-22114052008-02-06 Evolution and Diversity of Clonal Bacteria: The Paradigm of Mycobacterium tuberculosis Dos Vultos, Tiago Mestre, Olga Rauzier, Jean Golec, Marcin Rastogi, Nalin Rasolofo, Voahangy Tonjum, Tone Sola, Christophe Matic, Ivan Gicquel, Brigitte PLoS One Research Article BACKGROUND: Mycobacterium tuberculosis complex species display relatively static genomes and 99.9% nucleotide sequence identity. Studying the evolutionary history of such monomorphic bacteria is a difficult and challenging task. PRINCIPAL FINDINGS: We found that single-nucleotide polymorphism (SNP) analysis of DNA repair, recombination and replication (3R) genes in a comprehensive selection of M. tuberculosis complex strains from across the world, yielded surprisingly high levels of polymorphisms as compared to house-keeping genes, making it possible to distinguish between 80% of clinical isolates analyzed in this study. Bioinformatics analysis suggests that a large number of these polymorphisms are potentially deleterious. Site frequency spectrum comparison of synonymous and non-synonymous variants and Ka/Ks ratio analysis suggest a general negative/purifying selection acting on these sets of genes that may lead to suboptimal 3R system activity. In turn, the relaxed fidelity of 3R genes may allow the occurrence of adaptive variants, some of which will survive. Furthermore, 3R-based phylogenetic trees are a new tool for distinguishing between M. tuberculosis complex strains. CONCLUSIONS/SIGNIFICANCE: This situation, and the consequent lack of fidelity in genome maintenance, may serve as a starting point for the evolution of antibiotic resistance, fitness for survival and pathogenicity, possibly conferring a selective advantage in certain stressful situations. These findings suggest that 3R genes may play an important role in the evolution of highly clonal bacteria, such as M. tuberculosis. They also facilitate further epidemiological studies of these bacteria, through the development of high-resolution tools. With many more microbial genomes being sequenced, our results open the door to 3R gene-based studies of adaptation and evolution of other, highly clonal bacteria. Public Library of Science 2008-02-06 /pmc/articles/PMC2211405/ /pubmed/18253486 http://dx.doi.org/10.1371/journal.pone.0001538 Text en Dos Vultos et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Dos Vultos, Tiago
Mestre, Olga
Rauzier, Jean
Golec, Marcin
Rastogi, Nalin
Rasolofo, Voahangy
Tonjum, Tone
Sola, Christophe
Matic, Ivan
Gicquel, Brigitte
Evolution and Diversity of Clonal Bacteria: The Paradigm of Mycobacterium tuberculosis
title Evolution and Diversity of Clonal Bacteria: The Paradigm of Mycobacterium tuberculosis
title_full Evolution and Diversity of Clonal Bacteria: The Paradigm of Mycobacterium tuberculosis
title_fullStr Evolution and Diversity of Clonal Bacteria: The Paradigm of Mycobacterium tuberculosis
title_full_unstemmed Evolution and Diversity of Clonal Bacteria: The Paradigm of Mycobacterium tuberculosis
title_short Evolution and Diversity of Clonal Bacteria: The Paradigm of Mycobacterium tuberculosis
title_sort evolution and diversity of clonal bacteria: the paradigm of mycobacterium tuberculosis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2211405/
https://www.ncbi.nlm.nih.gov/pubmed/18253486
http://dx.doi.org/10.1371/journal.pone.0001538
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