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Arenas M, Bastolla U. ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13341] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology University of Vigo Vigo Spain
- Biomedical Research Center (CINBIO) University of Vigo Vigo Spain
| | - Ugo Bastolla
- Bioinformatics Unit Centre for Molecular Biology Severo Ochoa (CSIC) Madrid Spain
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2
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Blin C, Passet V, Touchon M, Rocha EPC, Brisse S. Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae. Environ Microbiol 2017; 19:1881-1898. [PMID: 28181409 DOI: 10.1111/1462-2920.13689] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/01/2017] [Accepted: 02/01/2017] [Indexed: 11/30/2022]
Abstract
Multidrug resistant and hypervirulent clones of Klebsiella pneumoniae are emerging pathogens. To understand the association between genotypic and phenotypic diversity in this process, we combined genomic, phylogenomic and phenotypic analysis of a diverse set of K. pneumoniae and closely related species. These species were able to use an unusually large panel of metabolic substrates for growth, many of which were shared between all strains. We analysed the substrates used by only a fraction of the strains, identified some of their genetic basis, and found that many could not be explained by the phylogeny of the strains. Puzzlingly, few traits were associated with the ecological origin of the strains. One noticeable exception was the ability to use D-arabinose, which was much more frequent in hypervirulent strains. The broad carbon and nitrogen core metabolism of K. pneumoniae might contribute to its ability to thrive in diverse environments. Accordingly, even the hypervirulent and multidrug resistant clones have the metabolic signature of ubiquitous bacteria. The apparent few metabolic differences between hypervirulent, multi-resistant and environmental strains may favour the emergence of dual-risk strains that combine resistance and hypervirulence.
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Affiliation(s)
- Camille Blin
- UPMC Univ Paris06, IFD, 4 Place Jussieu, Sorbonne Universités, 75252 PARIS cedex 05, France.,Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.,UMR3525, Paris, CNRS, France
| | - Virginie Passet
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.,UMR3525, Paris, CNRS, France
| | - Marie Touchon
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.,UMR3525, Paris, CNRS, France
| | - Eduardo P C Rocha
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.,UMR3525, Paris, CNRS, France
| | - Sylvain Brisse
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.,UMR3525, Paris, CNRS, France.,Institut Pasteur, Molecular Prevention and Therapy of Human Diseases, Paris, France
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Weber CC, Nabholz B, Romiguier J, Ellegren H. Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection. Genome Biol 2015; 15:542. [PMID: 25607475 PMCID: PMC4264323 DOI: 10.1186/s13059-014-0542-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 11/13/2014] [Indexed: 02/02/2023] Open
Abstract
Background The ratio of the rates of non-synonymous and synonymous substitution (dN/dS) is commonly used to estimate selection in coding sequences. It is often suggested that, all else being equal, dN/dS should be lower in populations with large effective size (Ne) due to increased efficacy of purifying selection. As Ne is difficult to measure directly, life history traits such as body mass, which is typically negatively associated with population size, have commonly been used as proxies in empirical tests of this hypothesis. However, evidence of whether the expected positive correlation between body mass and dN/dS is consistently observed is conflicting. Results Employing whole genome sequence data from 48 avian species, we assess the relationship between rates of molecular evolution and life history in birds. We find a negative correlation between dN/dS and body mass, contrary to nearly neutral expectation. This raises the question whether the correlation might be a method artefact. We therefore in turn consider non-stationary base composition, divergence time and saturation as possible explanations, but find no clear patterns. However, in striking contrast to dN/dS, the ratio of radical to conservative amino acid substitutions (Kr/Kc) correlates positively with body mass. Conclusions Our results in principle accord with the notion that non-synonymous substitutions causing radical amino acid changes are more efficiently removed by selection in large populations, consistent with nearly neutral theory. These findings have implications for the use of dN/dS and suggest that caution is warranted when drawing conclusions about lineage-specific modes of protein evolution using this metric. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0542-8) contains supplementary material, which is available to authorized users.
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4
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Fares M. Identifying Natural Selection with Molecular Data. NATURAL SELECTION 2014:48-82. [DOI: 10.1201/b17795-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Boon E, Meehan CJ, Whidden C, Wong DHJ, Langille MGI, Beiko RG. Interactions in the microbiome: communities of organisms and communities of genes. FEMS Microbiol Rev 2014; 38:90-118. [PMID: 23909933 PMCID: PMC4298764 DOI: 10.1111/1574-6976.12035] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/02/2013] [Accepted: 07/10/2013] [Indexed: 12/17/2022] Open
Abstract
A central challenge in microbial community ecology is the delineation of appropriate units of biodiversity, which can be taxonomic, phylogenetic, or functional in nature. The term 'community' is applied ambiguously; in some cases, the term refers simply to a set of observed entities, while in other cases, it requires that these entities interact with one another. Microorganisms can rapidly gain and lose genes, potentially decoupling community roles from taxonomic and phylogenetic groupings. Trait-based approaches offer a useful alternative, but many traits can be defined based on gene functions, metabolic modules, and genomic properties, and the optimal set of traits to choose is often not obvious. An analysis that considers taxon assignment and traits in concert may be ideal, with the strengths of each approach offsetting the weaknesses of the other. Individual genes also merit consideration as entities in an ecological analysis, with characteristics such as diversity, turnover, and interactions modeled using genes rather than organisms as entities. We identify some promising avenues of research that are likely to yield a deeper understanding of microbial communities that shift from observation-based questions of 'Who is there?' and 'What are they doing?' to the mechanistically driven question of 'How will they respond?'
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Affiliation(s)
- Eva Boon
- Department of Biology, Dalhousie University, Halifax, NS, Canada
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Akashi H, Osada N, Ohta T. Weak selection and protein evolution. Genetics 2012; 192:15-31. [PMID: 22964835 PMCID: PMC3430532 DOI: 10.1534/genetics.112.140178] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 06/11/2012] [Indexed: 01/23/2023] Open
Abstract
The "nearly neutral" theory of molecular evolution proposes that many features of genomes arise from the interaction of three weak evolutionary forces: mutation, genetic drift, and natural selection acting at its limit of efficacy. Such forces generally have little impact on allele frequencies within populations from generation to generation but can have substantial effects on long-term evolution. The evolutionary dynamics of weakly selected mutations are highly sensitive to population size, and near neutrality was initially proposed as an adjustment to the neutral theory to account for general patterns in available protein and DNA variation data. Here, we review the motivation for the nearly neutral theory, discuss the structure of the model and its predictions, and evaluate current empirical support for interactions among weak evolutionary forces in protein evolution. Near neutrality may be a prevalent mode of evolution across a range of functional categories of mutations and taxa. However, multiple evolutionary mechanisms (including adaptive evolution, linked selection, changes in fitness-effect distributions, and weak selection) can often explain the same patterns of genome variation. Strong parameter sensitivity remains a limitation of the nearly neutral model, and we discuss concave fitness functions as a plausible underlying basis for weak selection.
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Affiliation(s)
- Hiroshi Akashi
- Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
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7
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Namouchi A, Didelot X, Schöck U, Gicquel B, Rocha EPC. After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection. Genome Res 2012; 22:721-34. [PMID: 22377718 DOI: 10.1101/gr.129544.111] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Many of the most virulent bacterial pathogens show low genetic diversity and sexual isolation. Accordingly, Mycobacterium tuberculosis, the deadliest human pathogen, is thought to be clonal and evolve by genetic drift. Yet, its genome shows few of the concomitant signs of genome degradation. We analyzed 24 genomes and found an excess of genetic diversity in regions encoding key adaptive functions including the type VII secretion system and the ancient horizontally transferred virulence-related regions. Four different approaches showed evident signs of recombination in M. tuberculosis. Recombination tracts add a high density of polymorphisms, and many are thus predicted to arise from outside the clade. Some of these tracts match Mycobacterium canettii sequences. Recombination introduced an excess of non-synonymous diversity in general and even more in genes expected to be under positive or diversifying selection, e.g., cell wall component genes. Mutations leading to non-synonymous SNPs are effectively purged in MTBC, which shows dominance of purifying selection. MTBC mutation bias toward AT nucleotides is not compensated by biased gene conversion, suggesting the action of natural selection also on synonymous changes. Together, all of these observations point to a strong imprint of recombination and selection in the genome affecting both non-synonymous and synonymous positions. Hence, contrary to some other pathogens and previous proposals concerning M. tuberculosis, this lineage may have come out of its ancestral bottleneck as a very successful pathogen that is rapidly diversifying by the action of mutation, recombination, and natural selection.
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Affiliation(s)
- Amine Namouchi
- Unité de Génétique Mycobactérienne, Institut Pasteur, 75015 Paris, France.
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Gama JA, Abby SS, Vieira-Silva S, Dionisio F, Rocha EPC. Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens. PLoS Pathog 2012; 8:e1002503. [PMID: 22319444 PMCID: PMC3271079 DOI: 10.1371/journal.ppat.1002503] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 12/09/2011] [Indexed: 12/22/2022] Open
Abstract
Many studies have been devoted to understand the mechanisms used by pathogenic bacteria to exploit human hosts. These mechanisms are very diverse in the detail, but share commonalities whose quantification should enlighten the evolution of virulence from both a molecular and an ecological perspective. We mined the literature for experimental data on infectious dose of bacterial pathogens in humans (ID50) and also for traits with which ID50 might be associated. These compilations were checked and complemented with genome analyses. We observed that ID50 varies in a continuous way by over 10 orders of magnitude. Low ID50 values are very strongly associated with the capacity of the bacteria to kill professional phagocytes or to survive in the intracellular milieu of these cells. Inversely, high ID50 values are associated with motile and fast-growing bacteria that use quorum-sensing based regulation of virulence factors expression. Infectious dose is not associated with genome size and shows insignificant phylogenetic inertia, in line with frequent virulence shifts associated with the horizontal gene transfer of a small number of virulence factors. Contrary to previous proposals, infectious dose shows little dependence on contact-dependent secretion systems and on the natural route of exposure. When all variables are combined, immune subversion and quorum-sensing are sufficient to explain two thirds of the variance in infectious dose. Our results show the key role of immune subversion in effective human infection by small bacterial populations. They also suggest that cooperative processes might be important for successful infection by bacteria with high ID50. Our results suggest that trade-offs between selection for population growth-related traits and selection for the ability to subvert the immune system shape bacterial infectiousness. Understanding these trade-offs provides guidelines to study the evolution of virulence and in particular the micro-evolutionary paths of emerging pathogens. Every pathogen is unique and uses distinctive combinations of specific mechanisms to exploit the human host. Yet, several common themes in the ways pathogens use these mechanisms can be found among distantly related bacteria. The understanding of these common themes provides useful concepts and uncovers important principles in pathogenesis. Here, we have made a cross-species analysis of traits thought to be relevant for virulence of bacterial pathogens. We have found that the infectious dose of pathogens is much lower when they are able to kill professional phagocytes of the immune system or to survive in the intracellular milieu of these cells. On the other hand, bacteria requiring higher infectious dose are more likely to be motile, fast-growing and regulate the expression of virulence factors when the population quorum is high enough to be effective in starting an infection. This suggests that infectious dose results from a trade-off between selection for fast coordinated growth and the ability to subvert the immune system. This trade-off may underlie other traits such as the ability of a pathogen to live outside the association from a host. Understanding the patterns shaping infectious dose will facilitate the prediction of evolutionary paths of emerging pathogens.
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Affiliation(s)
- João Alves Gama
- Centro de Biologia Ambiental and Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Sophie S. Abby
- Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France
- CNRS, URA2171, Paris, France
| | - Sara Vieira-Silva
- Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France
- CNRS, URA2171, Paris, France
| | - Francisco Dionisio
- Centro de Biologia Ambiental and Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Eduardo P. C. Rocha
- Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France
- CNRS, URA2171, Paris, France
- * E-mail:
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9
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Wernegreen JJ. Reduced selective constraint in endosymbionts: elevation in radical amino acid replacements occurs genome-wide. PLoS One 2011; 6:e28905. [PMID: 22194947 PMCID: PMC3237559 DOI: 10.1371/journal.pone.0028905] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 11/16/2011] [Indexed: 11/18/2022] Open
Abstract
As predicted by the nearly neutral model of evolution, numerous studies have shown that reduced N(e) accelerates the accumulation of slightly deleterious changes under genetic drift. While such studies have mostly focused on eukaryotes, bacteria also offer excellent models to explore the effects of N(e). Most notably, the genomes of host-dependent bacteria with small N(e) show signatures of genetic drift, including elevated K(a)/K(s). Here, I explore the utility of an alternative measure of selective constraint: the per-site rate of radical and conservative amino acid substitutions (D(r)/D(c)). I test the hypothesis that purifying selection against radical amino acid changes is less effective in two insect endosymbiont groups (Blochmannia of ants and Buchnera of aphids), compared to related gamma-Proteobacteria. Genome comparisons demonstrate a significant elevation in D(r)/D(c) in endosymbionts that affects the majority (66-79%) of shared orthologs examined. The elevation of D(r)/D(c) in endosymbionts affects all functional categories examined. Simulations indicate that D(r)/D(c) estimates are sensitive to codon frequencies and mutational parameters; however, estimation biases occur in the opposite direction as the patterns observed in genome comparisons, thereby making the inference of elevated D(r)/D(c) more conservative. Increased D(r)/D(c) and other signatures of genome degradation in endosymbionts are consistent with strong effects of genetic drift in their small populations, as well as linkage to selected sites in these asexual bacteria. While relaxed selection against radical substitutions may contribute, genome-wide processes such as genetic drift and linkage best explain the pervasive elevation in D(r)/D(c) across diverse functional categories that include basic cellular processes. Although the current study focuses on a few bacterial lineages, it suggests D(r)/D(c) is a useful gauge of selective constraint and may provide a valuable alternative to K(a)/K(s) when high sequence divergences preclude estimates of K(s). Broader application of D(r)/D(c) will benefit from approaches less prone to estimation biases.
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Affiliation(s)
- Jennifer J Wernegreen
- Nicholas School of the Environment, Duke University, Durham, North Carolina, United States of America.
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Lynch M, Bobay LM, Catania F, Gout JF, Rho M. The repatterning of eukaryotic genomes by random genetic drift. Annu Rev Genomics Hum Genet 2011; 12:347-66. [PMID: 21756106 DOI: 10.1146/annurev-genom-082410-101412] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent observations on rates of mutation, recombination, and random genetic drift highlight the dramatic ways in which fundamental evolutionary processes vary across the divide between unicellular microbes and multicellular eukaryotes. Moreover, population-genetic theory suggests that the range of variation in these parameters is sufficient to explain the evolutionary diversification of many aspects of genome size and gene structure found among phylogenetic lineages. Most notably, large eukaryotic organisms that experience elevated magnitudes of random genetic drift are susceptible to the passive accumulation of mutationally hazardous DNA that would otherwise be eliminated by efficient selection. Substantial evidence also suggests that variation in the population-genetic environment influences patterns of protein evolution, with the emergence of certain kinds of amino-acid substitutions and protein-protein complexes only being possible in populations with relatively small effective sizes. These observations imply that the ultimate origins of many of the major genomic and proteomic disparities between prokaryotes and eukaryotes and among eukaryotic lineages have been molded as much by intrinsic variation in the genetic and cellular features of species as by external ecological forces.
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Affiliation(s)
- Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47408, USA.
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