51
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Pearce ME, Alikhan NF, Dallman TJ, Zhou Z, Grant K, Maiden MCJ. Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak. Int J Food Microbiol 2018; 274:1-11. [PMID: 29574242 PMCID: PMC5899760 DOI: 10.1016/j.ijfoodmicro.2018.02.023] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 01/10/2023]
Abstract
Multi-country outbreaks of foodborne bacterial disease present challenges in their detection, tracking, and notification. As food is increasingly distributed across borders, such outbreaks are becoming more common. This increases the need for high-resolution, accessible, and replicable isolate typing schemes. Here we evaluate a core genome multilocus typing (cgMLST) scheme for the high-resolution reproducible typing of Salmonella enterica (S. enterica) isolates, by its application to a large European outbreak of S. enterica serovar Enteritidis. This outbreak had been extensively characterised using single nucleotide polymorphism (SNP)-based approaches. The cgMLST analysis was congruent with the original SNP-based analysis, the epidemiological data, and whole genome MLST (wgMLST) analysis. Combination of the cgMLST and epidemiological data confirmed that the genetic diversity among the isolates predated the outbreak, and was likely present at the infection source. There was consequently no link between country of isolation and genetic diversity, but the cgMLST clusters were congruent with date of isolation. Furthermore, comparison with publicly available Enteritidis isolate data demonstrated that the cgMLST scheme presented is highly scalable, enabling outbreaks to be contextualised within the Salmonella genus. The cgMLST scheme is therefore shown to be a standardised and scalable typing method, which allows Salmonella outbreaks to be analysed and compared across laboratories and jurisdictions. cgMLST is proposed as a universal typing scheme for Salmonella. cgMLST is congruent with SNP analyses and easier to implement across laboratories. Genomic data are consistent with the epidemiology of the outbreak.
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Affiliation(s)
- Madison E Pearce
- Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, United Kingdom; National Institute for Health Research, Health Protection Research Unit, Gastrointestinal Infections, University of Oxford, United Kingdom.
| | - Nabil-Fareed Alikhan
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom.
| | - Timothy J Dallman
- Public Health England, Gastrointestinal Bacteria Reference Unit, 61 Colindale Avenue, London NW9 5EQ, United Kingdom.
| | - Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom.
| | - Kathie Grant
- Public Health England, Gastrointestinal Bacteria Reference Unit, 61 Colindale Avenue, London NW9 5EQ, United Kingdom.
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, United Kingdom; National Institute for Health Research, Health Protection Research Unit, Gastrointestinal Infections, University of Oxford, United Kingdom.
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52
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Lo WS, Huang YY, Kuo CH. Winding paths to simplicity: genome evolution in facultative insect symbionts. FEMS Microbiol Rev 2018; 40:855-874. [PMID: 28204477 PMCID: PMC5091035 DOI: 10.1093/femsre/fuw028] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/28/2016] [Accepted: 07/10/2016] [Indexed: 02/07/2023] Open
Abstract
Symbiosis between organisms is an important driving force in evolution. Among the diverse relationships described, extensive progress has been made in insect–bacteria symbiosis, which improved our understanding of the genome evolution in host-associated bacteria. Particularly, investigations on several obligate mutualists have pushed the limits of what we know about the minimal genomes for sustaining cellular life. To bridge the gap between those obligate symbionts with extremely reduced genomes and their non-host-restricted ancestors, this review focuses on the recent progress in genome characterization of facultative insect symbionts. Notable cases representing various types and stages of host associations, including those from multiple genera in the family Enterobacteriaceae (class Gammaproteobacteria), Wolbachia (Alphaproteobacteria) and Spiroplasma (Mollicutes), are discussed. Although several general patterns of genome reduction associated with the adoption of symbiotic relationships could be identified, extensive variation was found among these facultative symbionts. These findings are incorporated into the established conceptual frameworks to develop a more detailed evolutionary model for the discussion of possible trajectories. In summary, transitions from facultative to obligate symbiosis do not appear to be a universal one-way street; switches between hosts and lifestyles (e.g. commensalism, parasitism or mutualism) occur frequently and could be facilitated by horizontal gene transfer. This review synthesizes the recent progress in genome characterization of insect-symbiotic bacteria, the emphases include (i) patterns of genome organization, (ii) evolutionary models and trajectories, and (iii) comparisons between facultative and obligate symbionts.
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Affiliation(s)
- Wen-Sui Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 11529, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Ya-Yi Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 11529, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
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53
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Kuley R, Kuijt E, Smits MA, Roest HIJ, Smith HE, Bossers A. Genome Plasticity and Polymorphisms in Critical Genes Correlate with Increased Virulence of Dutch Outbreak-Related Coxiella burnetii Strains. Front Microbiol 2017; 8:1526. [PMID: 28848533 PMCID: PMC5554327 DOI: 10.3389/fmicb.2017.01526] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/28/2017] [Indexed: 12/20/2022] Open
Abstract
Coxiella burnetii is an obligate intracellular bacterium and the etiological agent of Q fever. During 2007-2010 the largest Q fever outbreak ever reported occurred in The Netherlands. It is anticipated that strains from this outbreak demonstrated an increased zoonotic potential as more than 40,000 individuals were assumed to be infected. The acquisition of novel genetic factors by these C. burnetii outbreak strains, such as virulence-related genes, has frequently been proposed and discussed, but is not proved yet. In the present study, the whole genome sequence of several Dutch strains (CbNL01 and CbNL12 genotypes), a few additionally selected strains from different geographical locations and publicly available genome sequences were used for a comparative bioinformatics approach. The study focuses on the identification of specific genetic differences in the outbreak related CbNL01 strains compared to other C. burnetii strains. In this approach we investigated the phylogenetic relationship and genomic aspects of virulence and host-specificity. Phylogenetic clustering of whole genome sequences showed a genotype-specific clustering that correlated with the clustering observed using Multiple Locus Variable-number Tandem Repeat Analysis (MLVA). Ortholog analysis on predicted genes and single nucleotide polymorphism (SNP) analysis of complete genome sequences demonstrated the presence of genotype-specific gene contents and SNP variations in C. burnetii strains. It also demonstrated that the currently used MLVA genotyping methods are highly discriminatory for the investigated outbreak strains. In the fully reconstructed genome sequence of the Dutch outbreak NL3262 strain of the CbNL01 genotype, a relatively large number of transposon-linked genes were identified as compared to the other published complete genome sequences of C. burnetii. Additionally, large numbers of SNPs in its membrane proteins and predicted virulence-associated genes were identified in all Dutch outbreak strains compared to the NM reference strain and other strains of the CbNL12 genotype. The presence of large numbers of transposable elements and mutated genes, thereof most likely resulted in high level of genome rearrangements and genotype-specific pathogenicity of outbreak strains. Thus, the epidemic potential of Dutch outbreak strains could be linked to increased genome plasticity and mutations in critical genes involved in virulence and the evasion of the host immune system.
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Affiliation(s)
- Runa Kuley
- Department of Infection Biology, Wageningen Bioveterinary ResearchLelystad, Netherlands
- Host Microbe Interactomics, Wageningen University and Research CentreWageningen, Netherlands
| | - Eric Kuijt
- Department of Infection Biology, Wageningen Bioveterinary ResearchLelystad, Netherlands
| | - Mari A. Smits
- Department of Infection Biology, Wageningen Bioveterinary ResearchLelystad, Netherlands
- Host Microbe Interactomics, Wageningen University and Research CentreWageningen, Netherlands
| | - Hendrik I. J. Roest
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary ResearchLelystad, Netherlands
| | - Hilde E. Smith
- Department of Infection Biology, Wageningen Bioveterinary ResearchLelystad, Netherlands
| | - Alex Bossers
- Department of Infection Biology, Wageningen Bioveterinary ResearchLelystad, Netherlands
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54
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Disentangling the effects of selection and loss bias on gene dynamics. Proc Natl Acad Sci U S A 2017; 114:E5616-E5624. [PMID: 28652353 DOI: 10.1073/pnas.1704925114] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We combine mathematical modeling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most nonparasitic genes is low albeit positive, compatible with observed positive correlation between genome size and effective population size. Free-living microbes evolve under stronger selection for gene retention than parasites. Different classes of MGE show a broad range of fitness effects, from the nearly neutral transposons to prophages, which are actively eliminated by selection. Genes involved in antiparasite defense, on average, incur a fitness cost to the host that is at least as high as the cost of plasmids. This cost is probably due to the adverse effects of autoimmunity and curtailment of horizontal gene transfer caused by the defense systems and selfish behavior of some of these systems, such as toxin-antitoxin and restriction modification modules. Transposons follow a biphasic dynamics, with bursts of gene proliferation followed by decay in the copy number that is quantitatively captured by the model. The horizontal gene transfer to loss ratio, but not duplication to loss ratio, correlates with genome size, potentially explaining increased abundance of neutral and costly elements in larger genomes.
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55
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Snopková K, Sedlář K, Bosák J, Chaloupková E, Sedláček I, Provazník I, Šmajs D. Free-Living Enterobacterium Pragia fontium 24613: Complete Genome Sequence and Metabolic Profiling. Evol Bioinform Online 2017; 13:1176934317700863. [PMID: 28469381 PMCID: PMC5395255 DOI: 10.1177/1176934317700863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/12/2017] [Indexed: 11/23/2022] Open
Abstract
Pragia fontium is one of the few species that belongs to the group of atypical hydrogen sulfide-producing enterobacteria. Unlike other members of this closely related group, P. fontium is not associated with any known host and has been reported as a free-living bacterium. Whole genome sequencing and metabolic fingerprinting confirmed the phylogenetic position of P. fontium inside the group of atypical H2S producers. Genomic data have revealed that P. fontium 24613 has limited pathogenic potential, although there are signs of genome decay. Although the lack of specific virulence factors and no association with a host species suggest a free-living style, the signs of genome decay suggest a process of adaptation to an as-yet-unknown host.
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Affiliation(s)
| | - Karel Sedlář
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Juraj Bosák
- Department of Biology, Masaryk University, Brno, Czech Republic
| | - Eva Chaloupková
- Department of Biology, Masaryk University, Brno, Czech Republic
| | - Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Ivo Provazník
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Masaryk University, Brno, Czech Republic
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56
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Larkin AA, Martiny AC. Microdiversity shapes the traits, niche space, and biogeography of microbial taxa. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:55-70. [PMID: 28185400 DOI: 10.1111/1758-2229.12523] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 06/06/2023]
Abstract
With rapidly improving sequencing technologies, scientists have recently gained the ability to examine diverse microbial communities at high genomic resolution, revealing that both free-living and host-associated microbes partition their environment at fine phylogenetic scales. This 'microdiversity,' or closely related (> 97% similar 16S rRNA gene) but ecologically and physiologically distinct sub-taxonomic groups, appears to be an intrinsic property of microorganisms. However, the functional implications of microdiversity as well as its effects on microbial biogeography are poorly understood. Here, we present two theoretical models outlining the evolutionary mechanisms that drive the formation of microdiverse 'sub-taxa.' Additionally, we review recent literature and reveal that microdiversity influences a wide range of functional traits across diverse ecosystems and microbes. Moving to higher levels of organization, we use laboratory data from marine, soil, and host-associated bacteria to demonstrate that the aggregated trait-based response of microdiverse sub-taxa modifies the fundamental niche of microbes. The correspondence between microdiversity and niche space represents a critical tool for future studies of microbial ecology. By combining growth experiments on diverse isolates with examinations of environmental abundance patterns, researchers can better quantify the fundamental and realized niches of microbes and improve understanding of microbial biogeography and response to future environmental change.
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Affiliation(s)
- Alyse A Larkin
- Department of Earth System Science, University of California, Irvine, CA, 92697, USA
| | - Adam C Martiny
- Department of Earth System Science, University of California, Irvine, CA, 92697, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
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57
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Wigley P. Salmonella enterica serovar Gallinarum: addressing fundamental questions in bacteriology sixty years on from the 9R vaccine. Avian Pathol 2017; 46:119-124. [DOI: 10.1080/03079457.2016.1240866] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Paul Wigley
- Department of Infection Biology, Institute for Infection & Global Health and School of Veterinary Science, University of Liverpool, Neston, UK
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58
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Omer S, Harlow TJ, Gogarten JP. Does Sequence Conservation Provide Evidence for Biological Function? Trends Microbiol 2017; 25:11-18. [DOI: 10.1016/j.tim.2016.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/16/2016] [Accepted: 09/22/2016] [Indexed: 01/14/2023]
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59
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Koonin EV. Splendor and misery of adaptation, or the importance of neutral null for understanding evolution. BMC Biol 2016; 14:114. [PMID: 28010725 PMCID: PMC5180405 DOI: 10.1186/s12915-016-0338-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The study of any biological features, including genomic sequences, typically revolves around the question: what is this for? However, population genetic theory, combined with the data of comparative genomics, clearly indicates that such a "pan-adaptationist" approach is a fallacy. The proper question is: how has this sequence evolved? And the proper null hypothesis posits that it is a result of neutral evolution: that is, it survives by sheer chance provided that it is not deleterious enough to be efficiently purged by purifying selection. To claim adaptation, the neutral null has to be falsified. The adaptationist fallacy can be costly, inducing biologists to relentlessly seek function where there is none.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
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60
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Ortega A, Villagra N, Urrutia I, Valenzuela L, Talamilla-Espinoza A, Hidalgo A, Rodas P, Gil F, Calderón I, Paredes-Sabja D, Mora G, Fuentes J. Lose to win: marT pseudogenization in Salmonella enterica serovar Typhi contributed to the surV -dependent survival to H 2 O 2 , and inside human macrophage-like cells. INFECTION GENETICS AND EVOLUTION 2016; 45:111-121. [DOI: 10.1016/j.meegid.2016.08.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 08/17/2016] [Accepted: 08/22/2016] [Indexed: 02/06/2023]
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61
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Abstract
Almost all cellular life forms are hosts to diverse genetic parasites with various levels of autonomy including plasmids, transposons and viruses. Theoretical modeling of the evolution of primordial replicators indicates that parasites (cheaters) necessarily evolve in such systems and can be kept at bay primarily via compartmentalization. Given the (near) ubiquity, abundance and diversity of genetic parasites, the question becomes pertinent: are such parasites intrinsic to life? At least in prokaryotes, the persistence of parasites is linked to the rate of horizontal gene transfer (HGT). We mathematically derive the threshold value of the minimal transfer rate required for selfish element persistence, depending on the element duplication and loss rates as well as the cost to the host. Estimation of the characteristic gene duplication, loss and transfer rates for transposons, plasmids and virus-related elements in multiple groups of diverse bacteria and archaea indicates that most of these rates are compatible with the long term persistence of parasites. Notably, a small but non-zero rate of HGT is also required for the persistence of non-parasitic genes. We hypothesize that cells cannot tune their horizontal transfer rates to be below the threshold required for parasite persistence without experiencing highly detrimental side-effects. As a lower boundary to the minimum DNA transfer rate that a cell can withstand, we consider the process of genome degradation and mutational meltdown of populations through Muller's ratchet. A numerical assessment of this hypothesis suggests that microbial populations cannot purge parasites while escaping Muller's ratchet. Thus, genetic parasites appear to be virtually inevitable in cellular organisms.
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Affiliation(s)
- Jaime Iranzo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda
| | - Pere Puigbò
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda Present address: Department of Biology, University of Turku, Finland
| | - Alexander E Lobkovsky
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda
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62
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Wheeler NE, Barquist L, Kingsley RA, Gardner PP. A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes. Bioinformatics 2016; 32:3566-3574. [PMID: 27503221 PMCID: PMC5181535 DOI: 10.1093/bioinformatics/btw518] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/17/2016] [Accepted: 08/02/2016] [Indexed: 02/04/2023] Open
Abstract
Motivation: Next generation sequencing technologies have provided us with a wealth of information on genetic variation, but predicting the functional significance of this variation is a difficult task. While many comparative genomics studies have focused on gene flux and large scale changes, relatively little attention has been paid to quantifying the effects of single nucleotide polymorphisms and indels on protein function, particularly in bacterial genomics. Results: We present a hidden Markov model based approach we call delta-bitscore (DBS) for identifying orthologous proteins that have diverged at the amino acid sequence level in a way that is likely to impact biological function. We benchmark this approach with several widely used datasets and apply it to a proof-of-concept study of orthologous proteomes in an investigation of host adaptation in Salmonella enterica. We highlight the value of the method in identifying functional divergence of genes, and suggest that this tool may be a better approach than the commonly used dN/dS metric for identifying functionally significant genetic changes occurring in recently diverged organisms. Availability and Implementation: A program implementing DBS for pairwise genome comparisons is freely available at: https://github.com/UCanCompBio/deltaBS. Contact:nicole.wheeler@pg.canterbury.ac.nz or lars.barquist@uni-wuerzburg.de Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nicole E Wheeler
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Lars Barquist
- Institute for Molecular Infection Biology, University of Wuerzburg, Wuerzburg, Germany
| | - Robert A Kingsley
- Institute of Food Research, Norwich Research Park, Norwich, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | - Paul P Gardner
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.,Bio-protection Research Centre, University of Canterbury, Christchurch, New Zealand
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63
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Price MN, Arkin AP. A Theoretical Lower Bound for Selection on the Expression Levels of Proteins. Genome Biol Evol 2016; 8:1917-28. [PMID: 27289091 PMCID: PMC4943197 DOI: 10.1093/gbe/evw126] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We use simple models of the costs and benefits of microbial gene expression to show that changing a protein's expression away from its optimum by 2-fold should reduce fitness by at least [Formula: see text], where P is the fraction the cell's protein that the gene accounts for. As microbial genes are usually expressed at above 5 parts per million, and effective population sizes are likely to be above 10(6), this implies that 2-fold changes to gene expression levels are under strong selection, as [Formula: see text], where Ne is the effective population size and s is the selection coefficient. Thus, most gene duplications should be selected against. On the other hand, we predict that for most genes, small changes in the expression will be effectively neutral.
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Affiliation(s)
- Morgan N Price
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Lab
| | - Adam P Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Lab
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64
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Shapiro LR, Scully ED, Straub TJ, Park J, Stephenson AG, Beattie GA, Gleason ML, Kolter R, Coelho MC, De Moraes CM, Mescher MC, Zhaxybayeva O. Horizontal Gene Acquisitions, Mobile Element Proliferation, and Genome Decay in the Host-Restricted Plant Pathogen Erwinia Tracheiphila. Genome Biol Evol 2016; 8:649-64. [PMID: 26992913 PMCID: PMC4824170 DOI: 10.1093/gbe/evw016] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2016] [Indexed: 12/18/2022] Open
Abstract
Modern industrial agriculture depends on high-density cultivation of genetically similar crop plants, creating favorable conditions for the emergence of novel pathogens with increased fitness in managed compared with ecologically intact settings. Here, we present the genome sequence of six strains of the cucurbit bacterial wilt pathogen Erwinia tracheiphila (Enterobacteriaceae) isolated from infected squash plants in New York, Pennsylvania, Kentucky, and Michigan. These genomes exhibit a high proportion of recent horizontal gene acquisitions, invasion and remarkable amplification of mobile genetic elements, and pseudogenization of approximately 20% of the coding sequences. These genome attributes indicate that E. tracheiphila recently emerged as a host-restricted pathogen. Furthermore, chromosomal rearrangements associated with phage and transposable element proliferation contribute to substantial differences in gene content and genetic architecture between the six E. tracheiphila strains and other Erwinia species. Together, these data lead us to hypothesize that E. tracheiphila has undergone recent evolution through both genome decay (pseudogenization) and genome expansion (horizontal gene transfer and mobile element amplification). Despite evidence of dramatic genomic changes, the six strains are genetically monomorphic, suggesting a recent population bottleneck and emergence into E. tracheiphila's current ecological niche.
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Affiliation(s)
- Lori R Shapiro
- Department of Organismic and Evolutionary Biology, Harvard University
| | - Erin D Scully
- Grain, Forage, and Bioenergy Research Unit, USDA-ARS, Lincoln, Nebraska and Department of Agronomy and Horticulture, University of Nebraska-Lincoln
| | | | - Jihye Park
- Graduate Program in Bioinformatics and Genomics, Pennsylvania State University Present address: Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Gwyn A Beattie
- Department of Plant Pathology and Microbiology, Iowa State University
| | - Mark L Gleason
- Department of Plant Pathology and Microbiology, Iowa State University
| | - Roberto Kolter
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts
| | - Miguel C Coelho
- Department of Molecular and Cellular Biology, Harvard University
| | | | - Mark C Mescher
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College Department of Computer Science, Dartmouth College
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65
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Liu F, Wang C, Wu Z, Zhang Q, Liu P. A zero-inflated Poisson model for insertion tolerance analysis of genes based on Tn-seq data. Bioinformatics 2016; 32:1701-8. [PMID: 26833344 DOI: 10.1093/bioinformatics/btw061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 01/25/2016] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Transposon insertion sequencing (Tn-seq) is an emerging technology that combines transposon mutagenesis with next-generation sequencing technologies for the identification of genes related to bacterial survival. The resulting data from Tn-seq experiments consist of sequence reads mapped to millions of potential transposon insertion sites and a large portion of insertion sites have zero mapped reads. Novel statistical method for Tn-seq data analysis is needed to infer functions of genes on bacterial growth. RESULTS In this article, we propose a zero-inflated Poisson model for analyzing the Tn-seq data that are high-dimensional and with an excess of zeros. Maximum likelihood estimates of model parameters are obtained using an expectation-maximization (EM) algorithm, and pseudogenes are utilized to construct appropriate statistical tests for the transposon insertion tolerance of normal genes of interest. We propose a multiple testing procedure that categorizes genes into each of the three states, hypo-tolerant, tolerant and hyper-tolerant, while controlling the false discovery rate. We evaluate the proposed method with simulation studies and apply the proposed method to a real Tn-seq data from an experiment that studied the bacterial pathogen, Campylobacter jejuniAvailability and implementation: We provide R code for implementing our proposed method at http://github.com/ffliu/TnSeq A user's guide with example data analysis is also available there. CONTACT pliu@iastate.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Chong Wang
- Department of Statistics, Iowa State University, Department of Veterinary Diagnostic and Production Animal Medicine and
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50010, USA
| | - Qijing Zhang
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50010, USA
| | - Peng Liu
- Department of Statistics, Iowa State University
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66
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Ershova A, Rusinov I, Vasiliev M, Spirin S, Karyagina A. Restriction-Modification systems interplay causes avoidance of GATC site in prokaryotic genomes. J Bioinform Comput Biol 2016; 14:1641003. [PMID: 26972562 DOI: 10.1142/s0219720016410031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Palindromes are frequently underrepresented in prokaryotic genomes. Palindromic 5[Formula: see text]-GATC-3[Formula: see text] site is a recognition site of different Restriction-Modification (R-M) systems, as well as solitary methyltransferase Dam. Classical GATC-specific R-M systems methylate GATC and cleave unmethylated GATC. On the contrary, methyl-directed Type II restriction endonucleases cleave methylated GATC. Methylation of GATC by Dam methyltransferase is involved in the regulation of different cellular processes. The diversity of functions of GATC-recognizing proteins makes GATC sequence a good model for studying the reasons of palindrome avoidance in prokaryotic genomes. In this work, the influence of R-M systems and solitary proteins on the GATC site avoidance is described by a mathematical model. GATC avoidance is strongly associated with the presence of alternate (methyl-directed or classical Type II R-M system) genes in different strains of the same species, as we have shown for Streptococcus pneumoniae, Neisseria meningitidis, Eubacterium rectale, and Moraxella catarrhalis. We hypothesize that GATC avoidance can result from a DNA exchange between strains with different methylation status of GATC site within the process of natural transformation. If this hypothesis is correct, the GATC avoidance is a sign of a DNA exchange between bacteria with different methylation status in a mixed population.
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Affiliation(s)
- Anna Ershova
- * Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.,† Gamaleya Center for Epidemiology and Microbiology, the Ministry of Health of the Russian Federation, Moscow 123098, Russia.,‡ Institute of Agricultural Biotechnology, the Russian Academy of Sciences, Moscow 127550, Russia
| | - Ivan Rusinov
- * Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.,§ Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow 119992, Russia
| | - Mikhail Vasiliev
- ¶ Moscow Institute of Physics and Technology, the Ministry of Education and Science of the Russian Federation, Dolgoprudny, Moscow Region, 141700, Russia
| | - Sergey Spirin
- * Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.,§ Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow 119992, Russia.,∥ Scientific Research Institute for System Studies, the Russian Academy of Science (NIISI RAS), Moscow 117218, Russia
| | - Anna Karyagina
- * Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.,† Gamaleya Center for Epidemiology and Microbiology, the Ministry of Health of the Russian Federation, Moscow 123098, Russia.,‡ Institute of Agricultural Biotechnology, the Russian Academy of Sciences, Moscow 127550, Russia
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Rusinov I, Ershova A, Karyagina A, Spirin S, Alexeevski A. Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes. BMC Genomics 2015; 16:1084. [PMID: 26689194 PMCID: PMC4687349 DOI: 10.1186/s12864-015-2288-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/11/2015] [Indexed: 01/10/2023] Open
Abstract
Background Avoidance of palindromic recognition sites of Type II restriction-modification (R-M) systems was shown for many R-M systems in dozens of prokaryotic genomes. However the phenomenon has not been investigated systematically for all presently available genomes and annotated R-M systems. We have studied all known recognition sites in thousands of prokaryotic genomes and found factors that influence their avoidance. Results Only Type II R-M systems consisting of independently acting endonuclease and methyltransferase (called ‘orthodox’ here) cause avoidance of their sites, both palindromic and asymmetric, in corresponding prokaryotic genomes; the avoidance takes place for ~ 50 % of 1774 studied cases. It is known that prokaryotes can acquire and lose R-M systems. Thus it is possible to talk about the lifespan of an R-M system in a genome. We have shown that the recognition site avoidance correlates with the lifespan of R-M systems. The sites of orthodox R-M systems that are encoded in host genomes for a long time are avoided more often (up to 100 % in certain cohorts) than the sites of recently acquired ones. We also found cases of site avoidance in absence of the corresponding R-M systems in the genome. An analysis of closely related bacteria shows that such avoidance can be a trace of lost R-M systems. Sites of Type I, IIС/G, IIM, III, and IV R-M systems are not avoided in vast majority of cases. Conclusions The avoidance of orthodox Type II R-M system recognition sites in prokaryotic genomes is a widespread phenomenon. Presence of an R-M system without an underrepresentation of its site may indicate that the R-M system was acquired recently. At the same time, a significant underrepresentation of a site may be a sign of presence of the corresponding R-M system in this organism or in its ancestors for a long time. The drastic difference between site avoidance for orthodox Type II R-M systems and R-M systems of other types can be explained by a higher rate of specificity changes or a less self-toxicity of the latter. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2288-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ivan Rusinov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - Anna Ershova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Gamaleya Center of Epidemiology and Microbiology, Moscow, 123098, Russia. .,Institute of Agricultural Biotechnology, the Russian Academy of Sciences, Moscow, 127550, Russia.
| | - Anna Karyagina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Gamaleya Center of Epidemiology and Microbiology, Moscow, 123098, Russia. .,Institute of Agricultural Biotechnology, the Russian Academy of Sciences, Moscow, 127550, Russia.
| | - Sergey Spirin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Scientific Research Institute for System Studies, the Russian Academy of Science (NIISI RAS), Moscow, 117281, Russia.
| | - Andrei Alexeevski
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Scientific Research Institute for System Studies, the Russian Academy of Science (NIISI RAS), Moscow, 117281, Russia.
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Melnyk RA, Coates JD. The Perchlorate Reduction Genomic Island: Mechanisms and Pathways of Evolution by Horizontal Gene Transfer. BMC Genomics 2015; 16:862. [PMID: 26502901 PMCID: PMC4623255 DOI: 10.1186/s12864-015-2011-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 10/03/2015] [Indexed: 12/03/2022] Open
Abstract
Background Perchlorate is a widely distributed anion that is toxic to humans, but serves as a valuable electron acceptor for several lineages of bacteria. The ability to utilize perchlorate is conferred by a horizontally transferred piece of DNA called the perchlorate reduction genomic island (PRI). Methods We compared genomes of perchlorate reducers using phylogenomics, SNP mapping, and differences in genomic architecture to interrogate the evolutionary history of perchlorate respiration. Results Here we report on the PRI of 13 genomes of perchlorate-reducing bacteria from four different classes of Phylum Proteobacteria (the Alpha-, Beta-, Gamma- and Epsilonproteobacteria). Among the different phylogenetic classes, the island varies considerably in genetic content as well as in its putative mechanism and location of integration. However, the islands of the densely sampled genera Azospira and Magnetospirillum have striking nucleotide identity despite divergent genomes, implying horizontal transfer and positive selection within narrow phylogenetic taxa. We also assess the phylogenetic origin of accessory genes in the various incarnations of the island, which can be traced to chromosomal paralogs from phylogenetically similar organisms. Conclusion These observations suggest a complex phylogenetic history where the island is rarely transferred at the class level but undergoes frequent and continuous transfer within narrow phylogenetic groups. This restricted transfer is seen directly by the independent integration of near-identical islands within a genus and indirectly due to the acquisition of lineage-specific accessory genes. The genomic reversibility of perchlorate reduction may present a unique equilibrium for a metabolism that confers a competitive advantage only in the presence of an electron acceptor, which although widely distributed, is generally present at low concentrations in nature. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2011-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ryan A Melnyk
- Department of Plant and Microbial Biology and Energy Biosciences Institute, University of California, Berkeley, CA, 94720, USA. .,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - John D Coates
- Department of Plant and Microbial Biology and Energy Biosciences Institute, University of California, Berkeley, CA, 94720, USA.
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Hershberg R. Mutation--The Engine of Evolution: Studying Mutation and Its Role in the Evolution of Bacteria. Cold Spring Harb Perspect Biol 2015; 7:a018077. [PMID: 26330518 DOI: 10.1101/cshperspect.a018077] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mutation is the engine of evolution in that it generates the genetic variation on which the evolutionary process depends. To understand the evolutionary process we must therefore characterize the rates and patterns of mutation. Starting with the seminal Luria and Delbruck fluctuation experiments in 1943, studies utilizing a variety of approaches have revealed much about mutation rates and patterns and about how these may vary between different bacterial strains and species along the chromosome and between different growth conditions. This work provides a critical overview of the results and conclusions drawn from these studies, of the debate surrounding some of these conclusions, and of the challenges faced when studying mutation and its role in bacterial evolution.
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Affiliation(s)
- Ruth Hershberg
- Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
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Lo WS, Gasparich GE, Kuo CH. Found and Lost: The Fates of Horizontally Acquired Genes in Arthropod-Symbiotic Spiroplasma. Genome Biol Evol 2015; 7:2458-72. [PMID: 26254485 PMCID: PMC4607517 DOI: 10.1093/gbe/evv160] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Horizontal gene transfer (HGT) is an important mechanism that contributed to biological diversity, particularly in bacteria. Through acquisition of novel genes, the recipient cell may change its ecological preference and the process could promote speciation. In this study, we determined the complete genome sequence of two Spiroplasma species for comparative analyses and inferred the putative gene gains and losses. Although most Spiroplasma species are symbionts of terrestrial insects, Spiroplasma eriocheiris has evolved to be a lethal pathogen of freshwater crustaceans. We found that approximately 7% of the genes in this genome may have originated from HGT and these genes expanded the metabolic capacity of this organism. Through comparison with the closely related Spiroplasma atrichopogonis, as well as other more divergent lineages, our results indicated that these HGT events could be traced back to the most recent common ancestor of these two species. However, most of these horizontally acquired genes have been pseudogenized in S. atrichopogonis, suggesting that they did not contribute to the fitness of this lineage that maintained the association with terrestrial insects. Thus, accumulation of small deletions that disrupted these foreign genes was not countered by natural selection. On the other hand, the long-term survival of these horizontally acquired genes in the S. eriocheiris genome hinted that they might play a role in the ecological shift of this species. Finally, the implications of these findings and the conflicts among gene content, 16S rRNA gene sequencing, and serological typing, are discussed in light of defining bacterial species.
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Affiliation(s)
- Wen-Sui Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, NationalChung Hsing University and Academia Sinica, Taipei, Taiwan Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | | | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, NationalChung Hsing University and Academia Sinica, Taipei, Taiwan Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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71
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Black Queen evolution: the role of leakiness in structuring microbial communities. Trends Genet 2015; 31:475-82. [DOI: 10.1016/j.tig.2015.05.004] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 11/21/2022]
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Mechanisms of Evolutionary Innovation Point to Genetic Control Logic as the Key Difference Between Prokaryotes and Eukaryotes. J Mol Evol 2015. [PMID: 26208881 DOI: 10.1007/s00239-015-9688-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The evolution of life from the simplest, original form to complex, intelligent animal life occurred through a number of key innovations. Here we present a new tool to analyze these key innovations by proposing that the process of evolutionary innovation may follow one of three underlying processes, namely a Random Walk, a Critical Path, or a Many Paths process, and in some instances may also constitute a "Pull-up the Ladder" event. Our analysis is based on the occurrence of function in modern biology, rather than specific structure or mechanism. A function in modern biology may be classified in this way either on the basis of its evolution or the basis of its modern mechanism. Characterizing key innovations in this way helps identify the likelihood that an innovation could arise. In this paper, we describe the classification, and methods to classify functional features of modern organisms into these three classes based on the analysis of how a function is implemented in modern biology. We present the application of our categorization to the evolution of eukaryotic gene control. We use this approach to support the argument that there are few, and possibly no basic chemical differences between the functional constituents of the machinery of gene control between eukaryotes, bacteria and archaea. This suggests that the difference between eukaryotes and prokaryotes that allows the former to develop the complex genetic architecture seen in animals and plants is something other than their chemistry. We tentatively identify the difference as a difference in control logic, that prokaryotic genes are by default 'on' and eukaryotic genes are by default 'off.' The Many Paths evolutionary process suggests that, from a 'default off' starting point, the evolution of the genetic complexity of higher eukaryotes is a high probability event.
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Bolotin E, Hershberg R. Gene Loss Dominates As a Source of Genetic Variation within Clonal Pathogenic Bacterial Species. Genome Biol Evol 2015; 7:2173-87. [PMID: 26163675 PMCID: PMC4558853 DOI: 10.1093/gbe/evv135] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Some of the most dangerous pathogens such as Mycobacterium tuberculosis and Yersinia pestis evolve clonally. This means that little or no recombination occurs between strains belonging to these species. Paradoxically, although different members of these species show extreme sequence similarity of orthologous genes, some show considerable intraspecies phenotypic variation, the source of which remains elusive. To examine the possible sources of phenotypic variation within clonal pathogenic bacterial species, we carried out an extensive genomic and pan-genomic analysis of the sources of genetic variation available to a large collection of clonal and nonclonal pathogenic bacterial species. We show that while nonclonal species diversify through a combination of changes to gene sequences, gene loss and gene gain, gene loss completely dominates as a source of genetic variation within clonal species. Indeed, gene loss is so prevalent within clonal species as to lead to levels of gene content variation comparable to those found in some nonclonal species that are much more diverged in their gene sequences and that acquire a substantial number of genes horizontally. Gene loss therefore needs to be taken into account as a potential dominant source of phenotypic variation within clonal bacterial species.
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Affiliation(s)
- Evgeni Bolotin
- Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ruth Hershberg
- Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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Matthews TD, Schmieder R, Silva GGZ, Busch J, Cassman N, Dutilh BE, Green D, Matlock B, Heffernan B, Olsen GJ, Farris Hanna L, Schifferli DM, Maloy S, Dinsdale EA, Edwards RA. Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum. PLoS One 2015; 10:e0126883. [PMID: 26039056 PMCID: PMC4454671 DOI: 10.1371/journal.pone.0126883] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 04/08/2015] [Indexed: 11/18/2022] Open
Abstract
The Salmonella enterica serovars Enteritidis, Dublin, and Gallinarum are closely related but differ in virulence and host range. To identify the genetic elements responsible for these differences and to better understand how these serovars are evolving, we sequenced the genomes of Enteritidis strain LK5 and Dublin strain SARB12 and compared these genomes to the publicly available Enteritidis P125109, Dublin CT 02021853 and Dublin SD3246 genome sequences. We also compared the publicly available Gallinarum genome sequences from biotype Gallinarum 287/91 and Pullorum RKS5078. Using bioinformatic approaches, we identified single nucleotide polymorphisms, insertions, deletions, and differences in prophage and pseudogene content between strains belonging to the same serovar. Through our analysis we also identified several prophage cargo genes and pseudogenes that affect virulence and may contribute to a host-specific, systemic lifestyle. These results strongly argue that the Enteritidis, Dublin and Gallinarum serovars of Salmonella enterica evolve by acquiring new genes through horizontal gene transfer, followed by the formation of pseudogenes. The loss of genes necessary for a gastrointestinal lifestyle ultimately leads to a systemic lifestyle and niche exclusion in the host-specific serovars.
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Affiliation(s)
- T. David Matthews
- Department of Biology, San Diego State University, San Diego, California, 92182, United States of America
| | - Robert Schmieder
- Department of Computer Science, San Diego State University, San Diego, California, 92182, United States of America
| | - Genivaldo G. Z. Silva
- Computational Science Research Center, San Diego State University, San Diego, California, 92182, United States of America
| | - Julia Busch
- Department of Biology, San Diego State University, San Diego, California, 92182, United States of America
| | - Noriko Cassman
- Department of Biology, San Diego State University, San Diego, California, 92182, United States of America
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Dawn Green
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Brian Matlock
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Brian Heffernan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Gary J. Olsen
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Leigh Farris Hanna
- Molecular Sciences Department, University of Tennessee Health Sciences Center, 858 Madison Ave, Memphis, Tennessee, United States of America
| | - Dieter M. Schifferli
- University of Pennsylvania School of Veterinary Medicine, 3800 Spruce St, Philadelphia, Pennsylvania, 19104, United States of America
| | - Stanley Maloy
- Department of Biology, San Diego State University, San Diego, California, 92182, United States of America
| | - Elizabeth A. Dinsdale
- Department of Biology, San Diego State University, San Diego, California, 92182, United States of America
| | - Robert A. Edwards
- Department of Biology, San Diego State University, San Diego, California, 92182, United States of America
- Department of Computer Science, San Diego State University, San Diego, California, 92182, United States of America
- Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Argonne National Laboratory, 9700 S. Cass Ave, Argonne, Illinois, 60349, United States of America
- * E-mail:
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75
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Wernegreen JJ. Endosymbiont evolution: predictions from theory and surprises from genomes. Ann N Y Acad Sci 2015; 1360:16-35. [PMID: 25866055 DOI: 10.1111/nyas.12740] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/27/2015] [Accepted: 02/11/2015] [Indexed: 10/23/2022]
Abstract
Genome data have created new opportunities to untangle evolutionary processes shaping microbial variation. Among bacteria, long-term mutualists of insects represent the smallest and (typically) most AT-rich genomes. Evolutionary theory provides a context to predict how an endosymbiotic lifestyle may alter fundamental evolutionary processes--mutation, selection, genetic drift, and recombination--and thus contribute to extreme genomic outcomes. These predictions can then be explored by comparing evolutionary rates, genome size and stability, and base compositional biases across endosymbiotic and free-living bacteria. Recent surprises from such comparisons include genome reduction among uncultured, free-living species. Some studies suggest that selection generally drives this streamlining, while drift drives genome reduction in endosymbionts; however, this remains an hypothesis requiring additional data. Unexpected evidence of selection acting on endosymbiont GC content hints that even weak selection may be effective in some long-term mutualists. Moving forward, intraspecific analysis offers a promising approach to distinguish underlying mechanisms, by testing the null hypothesis of neutrality and by quantifying mutational spectra. Such analyses may clarify whether endosymbionts and free-living bacteria occupy distinct evolutionary trajectories or, alternatively, represent varied outcomes of similar underlying forces.
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Affiliation(s)
- Jennifer J Wernegreen
- Nicholas School of the Environment and Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
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76
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Sung W, Ackerman MS, Gout JF, Miller SF, Williams E, Foster PL, Lynch M. Asymmetric Context-Dependent Mutation Patterns Revealed through Mutation-Accumulation Experiments. Mol Biol Evol 2015; 32:1672-83. [PMID: 25750180 DOI: 10.1093/molbev/msv055] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Despite the general assumption that site-specific mutation rates are independent of the local sequence context, a growing body of evidence suggests otherwise. To further examine context-dependent patterns of mutation, we amassed 5,645 spontaneous mutations in wild- type (WT) and mismatch-repair deficient (MMR(-)) mutation-accumulation (MA) lines of the gram-positive model organism Bacillus subtilis. We then analyzed>7,500 spontaneous base-substitution mutations across B. subtilis, Escherichia coli, and Mesoplasma florum WT and MMR(-) MA lines, finding a context-dependent mutation pattern that is asymmetric around the origin of replication. Different neighboring nucleotides can alter site-specific mutation rates by as much as 75-fold, with sites neighboring G:C base pairs or dimers involving alternating pyrimidine-purine and purine-pyrimidine nucleotides having significantly elevated mutation rates. The influence of context-dependent mutation on genome architecture is strongest in M. florum, consistent with the reduced efficiency of selection in organisms with low effective population size. If not properly accounted for, the disparities arising from patterns of context-dependent mutation can significantly influence interpretations of positive and purifying selection.
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Affiliation(s)
- Way Sung
- Department of Biology, Indiana University, Bloomington
| | | | | | | | | | | | - Michael Lynch
- Department of Biology, Indiana University, Bloomington
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Raghavan R, Kacharia FR, Millar JA, Sislak CD, Ochman H. Genome rearrangements can make and break small RNA genes. Genome Biol Evol 2015; 7:557-66. [PMID: 25601101 PMCID: PMC4350180 DOI: 10.1093/gbe/evv009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Small RNAs (sRNAs) are short, transcribed regulatory elements that are typically encoded in the intergenic regions (IGRs) of bacterial genomes. Several sRNAs, first recognized in Escherichia coli, are conserved among enteric bacteria, but because of the regulatory roles of sRNAs, differences in sRNA repertoires might be responsible for features that differentiate closely related species. We scanned the E. coli MG1655 and Salmonella enterica Typhimurium genomes for nonsyntenic IGRs as a potential source of uncharacterized, species-specific sRNAs and found that genome rearrangements have reconfigured several IGRs causing the disruption and formation of sRNAs. Within an IGR that is present in E. coli but was disrupted in Salmonella by a translocation event is an sRNA that is associated with the FNR/CRP global regulators and influences E. coli biofilm formation. A Salmonella-specific sRNA evolved de novo through point mutations that generated a σ70 promoter sequence in an IGR that arose through genome rearrangement events. The differences in the sRNA pools among bacterial species have previously been ascribed to duplication, deletion, or horizontal acquisition. Here, we show that genomic rearrangements also contribute to this process by either disrupting sRNA-containing IGRs or creating IGRs in which novel sRNAs may evolve.
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Affiliation(s)
- Rahul Raghavan
- Department of Biology and Center for Life in Extreme Environments, Portland State University
| | - Fenil R Kacharia
- Department of Biology and Center for Life in Extreme Environments, Portland State University
| | - Jess A Millar
- Department of Biology and Center for Life in Extreme Environments, Portland State University
| | - Christine D Sislak
- Department of Biology and Center for Life in Extreme Environments, Portland State University
| | - Howard Ochman
- Department of Integrative Biology, The University of Texas at Austin
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Goodhead I, Darby AC. Taking the pseudo out of pseudogenes. Curr Opin Microbiol 2014; 23:102-9. [PMID: 25461580 DOI: 10.1016/j.mib.2014.11.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/11/2014] [Accepted: 11/12/2014] [Indexed: 12/23/2022]
Abstract
Pseudogenes are defined as fragments of once-functional genes that have been silenced by one or more nonsense, frameshift or missense mutations. Despite continuing increases in the speed of sequencing and annotating bacterial genomes, the identification and categorisation of pseudogenes remains problematic. Even when identified, pseudogenes are considered to be rare and tend to be ignored. On the contrary, pseudogenes are surprisingly prevalent and can persist for long evolutionary time periods, representing a record of once-functional genetic characteristics. Most importantly, pseudogenes provide an insight into prokaryotic evolutionary history as a record of phenotypic traits that have been lost. Focusing on the intracellular and symbiotic bacteria in which pseudogenes predominate, this review discusses the importance of identifying pseudogenes to fully understand the abilities of bacteria, and to understand prokaryotes within their evolutionary context.
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Affiliation(s)
- Ian Goodhead
- Functional and Comparative Genomics, School of Biological Sciences, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
| | - Alistair C Darby
- Functional and Comparative Genomics, School of Biological Sciences, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
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79
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Hansen AK, Degnan PH. Widespread expression of conserved small RNAs in small symbiont genomes. THE ISME JOURNAL 2014; 8:2490-502. [PMID: 25012903 PMCID: PMC4260695 DOI: 10.1038/ismej.2014.121] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 06/02/2014] [Accepted: 06/05/2014] [Indexed: 12/17/2022]
Abstract
Genome architecture of a microbe markedly changes when it transitions from a free-living lifestyle to an obligate symbiotic association within eukaryotic cells. These symbiont genomes experience numerous rearrangements and massive gene loss, which is expected to radically alter gene regulatory networks compared with those of free-living relatives. As such, it remains unclear whether and how these small symbiont genomes regulate gene expression. Here, using a label-free mass-spec quantification approach we found that differential protein regulation occurs in Buchnera, a model symbiont with a reduced genome, when it transitions between two distinct life stages. However, differential mRNA expression could not be detected between Buchnera life stages, despite the presence of a small number of putative transcriptional regulators. Instead a comparative analysis of small RNA expression profiles among five divergent Buchnera lineages, spanning a variety of Buchnera life stages, reveals 140 novel intergenic and antisense small RNAs and 517 untranslated regions that were significantly expressed, some of which have been conserved for ∼65 million years. In addition, the majority of these small RNAs exhibit both sequence covariation and thermodynamic stability, indicators of a potential structural RNA role. Together, these data suggest that gene regulation at the post-transcriptional level may be important in Buchnera. This is the first study to empirically identify Buchnera small RNAs, and we propose that these novel small RNAs may facilitate post-transcriptional regulation through translational inhibition/activation, and/or transcript stability. Ultimately, post-transcriptional regulation may shape metabolic complementation between Buchnera and its aphid host, thus impacting the animal's ecology and evolution.
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Affiliation(s)
- Allison K Hansen
- Department of Entomology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Ecology and Evolutionary Biology, Microbial Diversity Institute, Yale University, New Haven, CT, USA
| | - Patrick H Degnan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Microbial Pathogenesis, Microbial Diversity Institute, Yale University, New Haven, CT, USA
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80
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Touchon M, Bobay LM, Rocha EPC. The chromosomal accommodation and domestication of mobile genetic elements. Curr Opin Microbiol 2014; 22:22-9. [DOI: 10.1016/j.mib.2014.09.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/17/2014] [Indexed: 11/17/2022]
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81
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Chang TH, Lo WS, Ku C, Chen LL, Kuo CH. Molecular evolution of the substrate utilization strategies and putative virulence factors in mosquito-associated Spiroplasma species. Genome Biol Evol 2014; 6:500-9. [PMID: 24534435 PMCID: PMC3971584 DOI: 10.1093/gbe/evu033] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Comparative genomics provides a powerful tool to characterize the genetic differences among species that may be linked to their phenotypic variations. In the case of mosquito-associated Spiroplasma species, such approach is useful for the investigation of their differentiations in substrate utilization strategies and putative virulence factors. Among the four species that have been assessed for pathogenicity by artificial infection experiments, Spiroplasma culicicola and S. taiwanense were found to be pathogenic, whereas S. diminutum and S. sabaudiense were not. Intriguingly, based on the species phylogeny, the association with mosquito hosts and the gain or loss of pathogenicity in these species appears to have evolved independently. Through comparison of their complete genome sequences, we identified the genes and pathways that are shared by all or specific to one of these four species. Notably, we found that a glycerol-3-phosphate oxidase gene (glpO) is present in S. culicicola and S. taiwanense but not in S. diminutum or S. sabaudiense. Because this gene is involved in the production of reactive oxygen species and has been demonstrated as a major virulence factor in Mycoplasma, this distribution pattern suggests that it may be linked to the observed differences in pathogenicity among these species as well. Moreover, through comparative analysis with other Spiroplasma, Mycoplasma, and Mesoplasma species, we found that the absence of glpO in S. diminutum and S. sabaudiense is best explained by independent losses. Finally, our phylogenetic analyses revealed possible recombination of glpO between distantly related lineages and local rearrangements of adjacent genes.
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Affiliation(s)
- Tean-Hsu Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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82
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Feng S, Powell SM, Wilson R, Bowman JP. Extensive gene acquisition in the extremely psychrophilic bacterial species Psychroflexus torquis and the link to sea-ice ecosystem specialism. Genome Biol Evol 2014; 6:133-48. [PMID: 24391155 PMCID: PMC3914696 DOI: 10.1093/gbe/evt209] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Sea ice is a highly dynamic and productive environment that includes a diverse array of psychrophilic prokaryotic and eukaryotic taxa distinct from the underlying water column. Because sea ice has only been extensive on Earth since the mid-Eocene, it has been hypothesized that bacteria highly adapted to inhabit sea ice have traits that have been acquired through horizontal gene transfer (HGT). Here we compared the genomes of the psychrophilic bacterium Psychroflexus torquis ATCC 700755T, associated with both Antarctic and Arctic sea ice, and its closely related nonpsychrophilic sister species, P. gondwanensis ACAM 44T. Results show that HGT has occurred much more extensively in P. torquis in comparison to P. gondwanensis. Genetic features that can be linked to the psychrophilic and sea ice-specific lifestyle of P. torquis include genes for exopolysaccharide (EPS) and polyunsaturated fatty acid (PUFA) biosynthesis, numerous specific modes of nutrient acquisition, and proteins putatively associated with ice-binding, light-sensing (bacteriophytochromes), and programmed cell death (metacaspases). Proteomic analysis showed that several genes associated with these traits are highly translated, especially those involved with EPS and PUFA production. Because most of the genes relating to the ability of P. torquis to dwell in sea-ice ecosystems occur on genomic islands that are absent in closely related P. gondwanensis, its adaptation to the sea-ice environment appears driven mainly by HGT. The genomic islands are rich in pseudogenes, insertional elements, and addiction modules, suggesting that gene acquisition is being followed by a process of genome reduction potentially indicative of evolving ecosystem specialism.
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Affiliation(s)
- Shi Feng
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Australia
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83
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Bachmann NL, Fraser TA, Bertelli C, Jelocnik M, Gillett A, Funnell O, Flanagan C, Myers GSA, Timms P, Polkinghorne A. Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum. BMC Genomics 2014; 15:667. [PMID: 25106440 PMCID: PMC4137089 DOI: 10.1186/1471-2164-15-667] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/31/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of three koala C. pecorum strains, isolated from the urogenital tracts and conjunctiva of diseased koalas. The genome of the C. pecorum VR629 (IPA) strain, isolated from a sheep with polyarthritis, was also sequenced. RESULTS Comparisons of the draft C. pecorum genomes against the complete genomes of livestock C. pecorum isolates revealed that these strains have a conserved gene content and order, sharing a nucleotide sequence similarity > 98%. Single nucleotide polymorphisms (SNPs) appear to be key factors in understanding the adaptive process. Two regions of the chromosome were found to be accumulating a large number of SNPs within the koala strains. These regions include the Chlamydia plasticity zone, which contains two cytotoxin genes (toxA and toxB), and a 77 kbp region that codes for putative type III effector proteins. In one koala strain (MC/MarsBar), the toxB gene was truncated by a premature stop codon but is full-length in IPTaLE and DBDeUG. Another five pseudogenes were also identified, two unique to the urogenital strains C. pecorum MC/MarsBar and C. pecorum DBDeUG, respectively, while three were unique to the koala C. pecorum conjunctival isolate IPTaLE. An examination of the distribution of these pseudogenes in C. pecorum strains from a variety of koala populations, alongside a number of sheep and cattle C. pecorum positive samples from Australian livestock, confirmed the presence of four predicted pseudogenes in koala C. pecorum clinical samples. Consistent with our genomics analyses, none of these pseudogenes were observed in the livestock C. pecorum samples examined. Interestingly, three SNPs resulting in pseudogenes identified in the IPTaLE isolate were not found in any other C. pecorum strain analysed, raising questions over the origin of these point mutations. CONCLUSIONS The genomic data revealed that variation between C. pecorum strains were mainly due to the accumulation of SNPs, some of which cause gene inactivation. The identification of these genetic differences will provide the basis for further studies to understand the biology and evolution of this important animal pathogen.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Adam Polkinghorne
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs 4558, Queensland, Australia.
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84
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Abstract
Integrated phages (prophages) are major contributors to the diversity of bacterial gene repertoires. Domestication of their components is thought to have endowed bacteria with molecular systems involved in secretion, defense, warfare, and gene transfer. However, the rates and mechanisms of domestication remain unknown. We used comparative genomics to study the evolution of prophages within the bacterial genome. We identified over 300 vertically inherited prophages within enterobacterial genomes. Some of these elements are very old and might predate the split between Escherichia coli and Salmonella enterica. The size distribution of prophage elements is bimodal, suggestive of rapid prophage inactivation followed by much slower genetic degradation. Accordingly, we observed a pervasive pattern of systematic counterselection of nonsynonymous mutations in prophage genes. Importantly, such patterns of purifying selection are observed not only on accessory regions but also in core phage genes, such as those encoding structural and lysis components. This suggests that bacterial hosts select for phage-associated functions. Several of these conserved prophages have gene repertoires compatible with described functions of adaptive prophage-derived elements such as bacteriocins, killer particles, gene transfer agents, or satellite prophages. We suggest that bacteria frequently domesticate their prophages. Most such domesticated elements end up deleted from the bacterial genome because they are replaced by analogous functions carried by new prophages. This puts the bacterial genome in a state of continuous flux of acquisition and loss of phage-derived adaptive genes.
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85
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Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever. Proc Natl Acad Sci U S A 2014; 111:12199-204. [PMID: 25092320 DOI: 10.1073/pnas.1411012111] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Multiple epidemic diseases have been designated as emerging or reemerging because the numbers of clinical cases have increased. Emerging diseases are often suspected to be driven by increased virulence or fitness, possibly associated with the gain of novel genes or mutations. However, the time period over which humans have been afflicted by such diseases is only known for very few bacterial pathogens, and the evidence for recently increased virulence or fitness is scanty. Has Darwinian (diversifying) selection at the genomic level recently driven microevolution within bacterial pathogens of humans? Salmonella enterica serovar Paratyphi A is a major cause of enteric fever, with a microbiological history dating to 1898. We identified seven modern lineages among 149 genomes on the basis of 4,584 SNPs in the core genome and estimated that Paratyphi A originated 450 y ago. During that time period, the effective population size has undergone expansion, reduction, and recent expansion. Mutations, some of which inactivate genes, have occurred continuously over the history of Paratyphi A, as has the gain or loss of accessory genes. We also identified 273 mutations that were under Darwinian selection. However, most genetic changes are transient, continuously being removed by purifying selection, and the genome of Paratyphi A has not changed dramatically over centuries. We conclude that Darwinian selection is not responsible for increased frequency of enteric fever and suggest that environmental changes may be more important for the frequency of disease.
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86
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Epstein B, Sadowsky MJ, Tiffin P. Selection on horizontally transferred and duplicated genes in sinorhizobium (ensifer), the root-nodule symbionts of medicago. Genome Biol Evol 2014; 6:1199-209. [PMID: 24803571 PMCID: PMC4040998 DOI: 10.1093/gbe/evu090] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Structural variation, including variation in gene copy number and presence or absence of genes, is a widespread and important source of genomic variation. We used whole-genome DNA sequences from 48 strains of Sinorhizobium (recently renamed Ensifer), including 20 strains of Sinorhizobium meliloti and 12 strains of S. medicae that were the focus of the analyses, to study the fitness effects of new structural variants created by duplication and horizontal gene transfer. We find that derived duplicated and horizontally transferred (HT) genes segregate at lower frequency than synonymous and nonsynonymous nucleotide variants in S. meliloti and S. medicae. Furthermore, the relative frequencies of different types of variants are more similar in S. medicae than in S. meliloti, the species with the larger effective population size. These results are consistent with the hypothesis that most duplications and HT genes have deleterious effects. Diversity of duplications, as measured by segregating duplicated genes per gene, is greater than nucleotide diversity, consistent with a high rate of duplication. Our results suggest that the vast majority of structural variants found among closely related bacterial strains are short-lived and unlikely to be involved in species-wide adaptation.
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Affiliation(s)
- Brendan Epstein
- Department of Plant Biology, University of MinnesotaSchool of Biological Sciences, Washington State University
| | - Michael J Sadowsky
- Department of Soil, Water, and Climate, University of MinnesotaBioTechnology Institute, Saint Paul, MN
| | - Peter Tiffin
- Department of Plant Biology, University of Minnesota
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87
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Abstract
A pseudogene arises when a gene loses the ability to produce a protein, which can be due to mutation or inaccurate duplication. Previous dogma has dictated that because the pseudogene no longer produces a protein it becomes functionless and evolutionarily inert, being neither conserved nor removed. However, recent evidence has forced a re-evaluation of this view. Some pseudogenes, although not translated into protein, are at least transcribed into RNA. In some cases, these pseudogene transcripts are capable of influencing the activity of other genes that code for proteins, thereby altering expression and in turn affecting the phenotype of the organism. In the present chapter, we will define pseudogenes, describe the evidence that they are transcribed into non-coding RNAs and outline the mechanisms by which they are able to influence the machinery of the eukaryotic cell.
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88
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Sesto N, Touchon M, Andrade JM, Kondo J, Rocha EPC, Arraiano CM, Archambaud C, Westhof É, Romby P, Cossart P. A PNPase dependent CRISPR System in Listeria. PLoS Genet 2014; 10:e1004065. [PMID: 24415952 PMCID: PMC3886909 DOI: 10.1371/journal.pgen.1004065] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 11/12/2013] [Indexed: 12/26/2022] Open
Abstract
The human bacterial pathogen Listeria monocytogenes is emerging as a model organism to study RNA-mediated regulation in pathogenic bacteria. A class of non-coding RNAs called CRISPRs (clustered regularly interspaced short palindromic repeats) has been described to confer bacterial resistance against invading bacteriophages and conjugative plasmids. CRISPR function relies on the activity of CRISPR associated (cas) genes that encode a large family of proteins with nuclease or helicase activities and DNA and RNA binding domains. Here, we characterized a CRISPR element (RliB) that is expressed and processed in the L. monocytogenes strain EGD-e, which is completely devoid of cas genes. Structural probing revealed that RliB has an unexpected secondary structure comprising basepair interactions between the repeats and the adjacent spacers in place of canonical hairpins formed by the palindromic repeats. Moreover, in contrast to other CRISPR-Cas systems identified in Listeria, RliB-CRISPR is ubiquitously present among Listeria genomes at the same genomic locus and is never associated with the cas genes. We showed that RliB-CRISPR is a substrate for the endogenously encoded polynucleotide phosphorylase (PNPase) enzyme. The spacers of the different Listeria RliB-CRISPRs share many sequences with temperate and virulent phages. Furthermore, we show that a cas-less RliB-CRISPR lowers the acquisition frequency of a plasmid carrying the matching protospacer, provided that trans encoded cas genes of a second CRISPR-Cas system are present in the genome. Importantly, we show that PNPase is required for RliB-CRISPR mediated DNA interference. Altogether, our data reveal a yet undescribed CRISPR system whose both processing and activity depend on PNPase, highlighting a new and unexpected function for PNPase in “CRISPRology”. CRISPR-Cas systems confer to bacteria and archaea an adaptive immunity that protects them against invading bacteriophages and plasmids. In this study, we characterize a CRISPR (RliB-CRISPR) that is present in all L. monocytogenes strains at the same genomic locus but is never associated with a cas operon. It is an unusual CRISPR that, as we demonstrate, has a secondary structure consisting of basepair interactions between the repeat sequence and the adjacent spacer. We show that the RliB-CRISPR is processed by the endogenously encoded polynucleotide phosphorylase enzyme (PNPase). In addition, we show that the RliB-CRISPR system requires PNPase and presence of trans encoded cas genes of a second CRISPR-Cas system, to mediate DNA interference directed against a plasmid carrying a matching protospacer. Altogether, our data reveal a novel type of CRISPR system in bacteria that requires endogenously encoded PNPase enzyme for its processing and interference activity.
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Affiliation(s)
- Nina Sesto
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France ; INSERM, U604, Paris, France ; INRA, USC2020, Paris, France
| | - Marie Touchon
- Unité de Génomique Evolutive des Microbes, Institut Pasteur, Paris, France ; CNRS, UMR3525, Paris, France
| | - José Marques Andrade
- Control of Gene Expression, Instituto de Tecnologia Química e Biológica, Oeiras, Portugal
| | - Jiro Kondo
- Architecture et Réactivité de l'ARN Université de Strasbourg, CNRS, Strasbourg, France
| | - Eduardo P C Rocha
- Unité de Génomique Evolutive des Microbes, Institut Pasteur, Paris, France ; CNRS, UMR3525, Paris, France
| | - Cecilia Maria Arraiano
- Control of Gene Expression, Instituto de Tecnologia Química e Biológica, Oeiras, Portugal
| | - Cristel Archambaud
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France ; INSERM, U604, Paris, France ; INRA, USC2020, Paris, France
| | - Éric Westhof
- Architecture et Réactivité de l'ARN Université de Strasbourg, CNRS, Strasbourg, France
| | - Pascale Romby
- Architecture et Réactivité de l'ARN Université de Strasbourg, CNRS, Strasbourg, France
| | - Pascale Cossart
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France ; INSERM, U604, Paris, France ; INRA, USC2020, Paris, France
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89
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Nielsen KM, Bøhn T, Townsend JP. Detecting rare gene transfer events in bacterial populations. Front Microbiol 2014; 4:415. [PMID: 24432015 PMCID: PMC3882822 DOI: 10.3389/fmicb.2013.00415] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 12/16/2013] [Indexed: 11/23/2022] Open
Abstract
Horizontal gene transfer (HGT) enables bacteria to access, share, and recombine genetic variation, resulting in genetic diversity that cannot be obtained through mutational processes alone. In most cases, the observation of evolutionary successful HGT events relies on the outcome of initially rare events that lead to novel functions in the new host, and that exhibit a positive effect on host fitness. Conversely, the large majority of HGT events occurring in bacterial populations will go undetected due to lack of replication success of transformants. Moreover, other HGT events that would be highly beneficial to new hosts can fail to ensue due to lack of physical proximity to the donor organism, lack of a suitable gene transfer mechanism, genetic compatibility, and stochasticity in tempo-spatial occurrence. Experimental attempts to detect HGT events in bacterial populations have typically focused on the transformed cells or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to reach relative population sizes that will allow their immediate identification; the exception being the unusually strong positive selection conferred by antibiotics. Most HGT events are not expected to alter the likelihood of host survival to such an extreme extent, and will confer only minor changes in host fitness. Due to the large population sizes of bacteria and the time scales involved, the process and outcome of HGT are often not amenable to experimental investigation. Population genetic modeling of the growth dynamics of bacteria with differing HGT rates and resulting fitness changes is therefore necessary to guide sampling design and predict realistic time frames for detection of HGT, as it occurs in laboratory or natural settings. Here we review the key population genetic parameters, consider their complexity and highlight knowledge gaps for further research.
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Affiliation(s)
- Kaare M Nielsen
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø Tromsø, Norway ; GenØk-Centre for Biosafety, The Science Park Tromsø, Norway
| | - Thomas Bøhn
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø Tromsø, Norway ; GenØk-Centre for Biosafety, The Science Park Tromsø, Norway
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale University New Haven, CT, USA ; Program in Computational Biology and Bioinformatics, Yale University New Haven, CT, USA ; Program in Microbiology, Yale University New Haven, CT, USA
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90
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Lo WS, Ku C, Chen LL, Chang TH, Kuo CH. Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense. Genome Biol Evol 2013; 5:1512-23. [PMID: 23873917 PMCID: PMC3762197 DOI: 10.1093/gbe/evt108] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Mosquitoes are hosts of several Spiroplasma species that belong to different serogroups. To investigate the genetic mechanisms that may be involved in the utilization of similar hosts in these phylogenetically distinct bacteria, we determined the complete genome sequences of Spiroplasma diminutum and S. taiwanense for comparative analysis. The genome alignment indicates that their chromosomal organization is highly conserved, which is in sharp contrast to the elevated genome instabilities observed in other Spiroplasma lineages. Examination of the substrate utilization strategies revealed that S. diminutum can use a wide range of carbohydrates, suggesting that it is well suited to living in the gut (and possibly the circulatory system) of its mosquito hosts. In comparison, S. taiwanense has lost several carbohydrate utilization genes and acquired additional sets of oligopeptide transporter genes through tandem duplications, suggesting that proteins from digested blood meal or lysed host cells may be an important nutrient source. Moreover, one glycerol-3-phosphate oxidase gene (glpO) was found in S. taiwanense but not S. diminutum. This gene is linked to the production of reactive oxygen species and has been shown to be a major virulence factor in Mycoplasma mycoides. This finding may explain the pathogenicity of S. taiwanense observed in previous artificial infection experiments, while no apparent effect was found for S. diminutum. To infer the gene content evolution at deeper divergence levels, we incorporated other Mollicutes genomes for comparative analyses. The results suggest that the losses of biosynthetic pathways are a recurrent theme in these host-associated bacteria.
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Affiliation(s)
- Wen-Sui Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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91
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Katju V, Bergthorsson U. Copy-number changes in evolution: rates, fitness effects and adaptive significance. Front Genet 2013; 4:273. [PMID: 24368910 PMCID: PMC3857721 DOI: 10.3389/fgene.2013.00273] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 11/18/2013] [Indexed: 11/13/2022] Open
Abstract
Gene copy-number differences due to gene duplications and deletions are rampant in natural populations and play a crucial role in the evolution of genome complexity. Per-locus analyses of gene duplication rates in the pre-genomic era revealed that gene duplication rates are much higher than the per nucleotide substitution rate. Analyses of gene duplication and deletion rates in mutation accumulation lines of model organisms have revealed that these high rates of copy-number mutations occur at a genome-wide scale. Furthermore, comparisons of the spontaneous duplication and deletion rates to copy-number polymorphism data and bioinformatic-based estimates of duplication rates from sequenced genomes suggest that the vast majority of gene duplications are detrimental and removed by natural selection. The rate at which new gene copies appear in populations greatly influences their evolutionary dynamics and standing gene copy-number variation in populations. The opportunity for mutations that result in the maintenance of duplicate copies, either through neofunctionalization or subfunctionalization, also depends on the equilibrium frequency of additional gene copies in the population, and hence on the spontaneous gene duplication (and loss) rate. The duplication rate may therefore have profound effects on the role of adaptation in the evolution of duplicated genes as well as important consequences for the evolutionary potential of organisms. We further discuss the broad ramifications of this standing gene copy-number variation on fitness and adaptive potential from a population-genetic and genome-wide perspective.
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Affiliation(s)
- Vaishali Katju
- Department of Biology, University of New Mexico Albuquerque, NM, USA
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92
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Foley SL, Johnson TJ, Ricke SC, Nayak R, Danzeisen J. Salmonella pathogenicity and host adaptation in chicken-associated serovars. Microbiol Mol Biol Rev 2013; 77:582-607. [PMID: 24296573 PMCID: PMC3973385 DOI: 10.1128/mmbr.00015-13] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Enteric pathogens such as Salmonella enterica cause significant morbidity and mortality. S. enterica serovars are a diverse group of pathogens that have evolved to survive in a wide range of environments and across multiple hosts. S. enterica serovars such as S. Typhi, S. Dublin, and S. Gallinarum have a restricted host range, in which they are typically associated with one or a few host species, while S. Enteritidis and S. Typhimurium have broad host ranges. This review examines how S. enterica has evolved through adaptation to different host environments, especially as related to the chicken host, and continues to be an important human pathogen. Several factors impact host range, and these include the acquisition of genes via horizontal gene transfer with plasmids, transposons, and phages, which can potentially expand host range, and the loss of genes or their function, which would reduce the range of hosts that the organism can infect. S. Gallinarum, with a limited host range, has a large number of pseudogenes in its genome compared to broader-host-range serovars. S. enterica serovars such as S. Kentucky and S. Heidelberg also often have plasmids that may help them colonize poultry more efficiently. The ability to colonize different hosts also involves interactions with the host's immune system and commensal organisms that are present. Thus, the factors that impact the ability of Salmonella to colonize a particular host species, such as chickens, are complex and multifactorial, involving the host, the pathogen, and extrinsic pressures. It is the interplay of these factors which leads to the differences in host ranges that we observe today.
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93
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Luo Y, Battistuzzi F, Lin K. Evolutionary dynamics of overlapped genes in Salmonella. PLoS One 2013; 8:e81016. [PMID: 24312259 PMCID: PMC3843671 DOI: 10.1371/journal.pone.0081016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 10/16/2013] [Indexed: 11/19/2022] Open
Abstract
Presence of overlapping genes (OGs) is a common phenomenon in bacterial genomes. Most frequently, overlapping genes share coding regions with as few as one nucleotide to as many as thousands of nucleotides. Overlapping genes are often co-regulated, transcriptionally and translationally. Overlapping genes are also subject to the whims of evolution, as the gene overlap is known to be disrupted in some species/strains and participating genes are sometimes lost in independent lineages. Therefore, a better understanding of evolutionary patterns and rates of the disruption of overlapping genes is an important component of genome structure and evolution of gene function. In this study, we investigate the fate of ancestrally overlapping genes in complete genomes from 15 contemporary strains of Salmonella species. We find that the fates of overlapping genes inside and outside operons are distinctly different. A larger fraction of overlapping genes inside operons conserves their overlap as compared to gene pairs outside of the operons (average 0.89 vs. 0.83 per genome). However, when overlapping genes in the operons separate, one partner is lost more frequently than in those separated genes outside of operons (average 0.02 vs. 0.01 per genome). We also investigate the fate of a pan set of overlapping genes at the present and ancestral nodes over a phylogenetic tree based on genome sequence data, respectively. We propose that co-regulation plays important roles on the fates of genes. Furthermore, a vast majority of disruptions occurred prior to the common ancestor of all 15 Salmonella strains, which enables us to obtain an estimate of disruptions between Salmonella and E. coli.
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Affiliation(s)
- Yingqin Luo
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Fabia Battistuzzi
- Department of Biological Sciences, Oakland University, Rochester, Michigan, United States of America
| | - Kui Lin
- College of Life Sciences, Beijing Normal University, Beijing, China
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94
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Darrasse A, Carrère S, Barbe V, Boureau T, Arrieta-Ortiz ML, Bonneau S, Briand M, Brin C, Cociancich S, Durand K, Fouteau S, Gagnevin L, Guérin F, Guy E, Indiana A, Koebnik R, Lauber E, Munoz A, Noël LD, Pieretti I, Poussier S, Pruvost O, Robène-Soustrade I, Rott P, Royer M, Serres-Giardi L, Szurek B, van Sluys MA, Verdier V, Vernière C, Arlat M, Manceau C, Jacques MA. Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads. BMC Genomics 2013; 14:761. [PMID: 24195767 PMCID: PMC3826837 DOI: 10.1186/1471-2164-14-761] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/26/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences. RESULTS Comparative genomics analyses revealed core characteristics shared between Xff 4834-R and other xanthomonads including chemotaxis elements, two-component systems, TonB-dependent transporters, secretion systems (from T1SS to T6SS) and multiple effectors. For instance a repertoire of 29 Type 3 Effectors (T3Es) with two Transcription Activator-Like Effectors was predicted. Mobile elements were associated with major modifications in the genome structure and gene content in comparison to other Xanthomonas genomes. Notably, a deletion of 33 kbp affects flagellum biosynthesis in Xff 4834-R. The presence of a complete flagellar cluster was assessed in a collection of more than 300 strains representing different species and pathovars of Xanthomonas. Five percent of the tested strains presented a deletion in the flagellar cluster and were non-motile. Moreover, half of the Xff strains isolated from the same epidemic than 4834-R was non-motile and this ratio was conserved in the strains colonizing the next bean seed generations. CONCLUSIONS This work describes the first genome of a Xanthomonas strain pathogenic on bean and reports the existence of non-motile xanthomonads belonging to different species and pathovars. Isolation of such Xff variants from a natural epidemic may suggest that flagellar motility is not a key function for in planta fitness.
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Affiliation(s)
- Armelle Darrasse
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | - Sébastien Carrère
- INRA, LIPM UMR 441, F-31326, Castanet-Tolosan, France
- CNRS, LIPM UMR 2594, F-31326, Castanet-Tolosan, France
| | - Valérie Barbe
- CEA, Genoscope, Centre National de Séquençage, F-91057, Evry Cedex, France
| | - Tristan Boureau
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | - Mario L Arrieta-Ortiz
- Universidad de Los Andes, Laboratorio de Micología y Fitopatología Uniandes, Bogotá, Colombia
- current address: Department of Biology, Center for Genomics and Systems Biology, New York University, 10003, New York, NY, USA
| | - Sophie Bonneau
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | - Martial Briand
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | - Chrystelle Brin
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | | | - Karine Durand
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | - Stéphanie Fouteau
- CEA, Genoscope, Centre National de Séquençage, F-91057, Evry Cedex, France
| | - Lionel Gagnevin
- CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France
- Université de la Réunion, UMR PVBMT, F-97715, Saint-Denis, La Réunion, France
| | - Fabien Guérin
- CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France
- Université de la Réunion, UMR PVBMT, F-97715, Saint-Denis, La Réunion, France
| | - Endrick Guy
- INRA, LIPM UMR 441, F-31326, Castanet-Tolosan, France
- CNRS, LIPM UMR 2594, F-31326, Castanet-Tolosan, France
| | - Arnaud Indiana
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | - Ralf Koebnik
- IRD, UMR RPB, F-34394, Montpellier Cedex 5, France
| | - Emmanuelle Lauber
- INRA, LIPM UMR 441, F-31326, Castanet-Tolosan, France
- CNRS, LIPM UMR 2594, F-31326, Castanet-Tolosan, France
| | - Alejandra Munoz
- Universidad de Los Andes, Laboratorio de Micología y Fitopatología Uniandes, Bogotá, Colombia
| | - Laurent D Noël
- INRA, LIPM UMR 441, F-31326, Castanet-Tolosan, France
- CNRS, LIPM UMR 2594, F-31326, Castanet-Tolosan, France
| | | | - Stéphane Poussier
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
- Université de la Réunion, UMR PVBMT, F-97715, Saint-Denis, La Réunion, France
| | - Olivier Pruvost
- CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France
- Université de la Réunion, UMR PVBMT, F-97715, Saint-Denis, La Réunion, France
| | - Isabelle Robène-Soustrade
- CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France
- Université de la Réunion, UMR PVBMT, F-97715, Saint-Denis, La Réunion, France
| | - Philippe Rott
- CIRAD, UMR BGPI, F-34398, Montpellier Cedex 5, France
| | - Monique Royer
- CIRAD, UMR BGPI, F-34398, Montpellier Cedex 5, France
| | - Laurana Serres-Giardi
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | - Boris Szurek
- IRD, UMR RPB, F-34394, Montpellier Cedex 5, France
| | | | | | - Christian Vernière
- CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France
- Université de la Réunion, UMR PVBMT, F-97715, Saint-Denis, La Réunion, France
| | - Matthieu Arlat
- INRA, LIPM UMR 441, F-31326, Castanet-Tolosan, France
- CNRS, LIPM UMR 2594, F-31326, Castanet-Tolosan, France
- Université de Toulouse, Université Paul Sabatier, UMR LIPM, F-31326, Castanet-Tolosan Cedex, France
| | - Charles Manceau
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
- current address: ANSES, Laboratoire de Santé des végétaux, F-49044, Angers, France
| | - Marie-Agnès Jacques
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
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95
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Sen K, Ghosh TC. Pseudogenes and their composers: delving in the 'debris' of human genome. Brief Funct Genomics 2013; 12:536-47. [PMID: 23900003 DOI: 10.1093/bfgp/elt026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Pseudogenes, the nonfunctional homologs of functional genes and thus exemplified as 'genomic fossils' provide intriguing snapshots of the evolutionary history of human genome. These defunct copies generally arise by retrotransposition or duplication followed by various genetic disablements. In this study, focusing on human pseudogenes and their functional homologues we describe their characteristic features and relevance to protein sequence evolution. We recapitulate that pseudogenes harbor disease-causing degenerative sequence variations in conjunction with the immense disease gene association of their progenitors. Furthermore, we also discuss the issue of functional resurrection and the potentiality observed in some pseudogenes to regulate their functional counterparts.
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Affiliation(s)
- Kamalika Sen
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India. Tel.: +91 33 2355 6626; Fax: +91 33 2355 3886;
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96
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Antonov I, Coakley A, Atkins JF, Baranov PV, Borodovsky M. Identification of the nature of reading frame transitions observed in prokaryotic genomes. Nucleic Acids Res 2013; 41:6514-30. [PMID: 23649834 PMCID: PMC3711429 DOI: 10.1093/nar/gkt274] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Our goal was to identify evolutionary conserved frame transitions in protein coding regions and to uncover an underlying functional role of these structural aberrations. We used the ab initio frameshift prediction program, GeneTack, to detect reading frame transitions in 206 991 genes (fs-genes) from 1106 complete prokaryotic genomes. We grouped 102 731 fs-genes into 19 430 clusters based on sequence similarity between protein products (fs-proteins) as well as conservation of predicted position of the frameshift and its direction. We identified 4010 pseudogene clusters and 146 clusters of fs-genes apparently using recoding (local deviation from using standard genetic code) due to possessing specific sequence motifs near frameshift positions. Particularly interesting was finding of a novel type of organization of the dnaX gene, where recoding is required for synthesis of the longer subunit, τ. We selected 20 clusters of predicted recoding candidates and designed a series of genetic constructs with a reporter gene or affinity tag whose expression would require a frameshift event. Expression of the constructs in Escherichia coli demonstrated enrichment of the set of candidates with sequences that trigger genuine programmed ribosomal frameshifting; we have experimentally confirmed four new families of programmed frameshifts.
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Affiliation(s)
- Ivan Antonov
- School of Computational Science and Engineering at Georgia Tech, Atlanta, GA 30332, USA
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97
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Hoekstra LA, Montooth KL. Inducing extra copies of the Hsp70 gene in Drosophila melanogaster increases energetic demand. BMC Evol Biol 2013; 13:68. [PMID: 23510136 PMCID: PMC3641968 DOI: 10.1186/1471-2148-13-68] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 02/26/2013] [Indexed: 12/17/2022] Open
Abstract
Background Mutations that increase gene expression are predicted to increase energy allocation to transcription, translation and protein function. Despite an appreciation that energetic tradeoffs may constrain adaptation, the energetic costs of increased gene expression are challenging to quantify and thus easily ignored when modeling the evolution of gene expression, particularly for multicellular organisms. Here we use the well-characterized, inducible heat-shock response to test whether expressing additional copies of the Hsp70 gene increases energetic demand in Drosophila melanogaster. Results We measured metabolic rates of larvae with different copy numbers of the Hsp70 gene to quantify energy expenditure before, during, and after exposure to 36°C, a temperature known to induce robust expression of Hsp70. We observed a rise in metabolic rate within the first 30 minutes of 36°C exposure above and beyond the increase in routine metabolic rate at 36°C. The magnitude of this increase in metabolic rate was positively correlated with Hsp70 gene copy number and reflected an increase as great as 35% of the 22°C metabolic rate. Gene copy number also affected Hsp70 mRNA levels as early as 15 minutes after larvae were placed at 36°C, demonstrating that gene copy number affects transcript abundance on the same timescale as the metabolic effects that we observed. Inducing Hsp70 also had lasting physiological costs, as larvae had significantly depressed metabolic rate when returned to 22°C after induction. Conclusions Our results demonstrate both immediate and persistent energetic consequences of gene copy number in a multicellular organism. We discuss these consequences in the context of existing literature on the pleiotropic effects of variation in Hsp70 copy number, and argue that the increased energetic demand of expressing extra copies of Hsp70 may contribute to known tradeoffs in physiological performance of extra-copy larvae. Physiological costs of mutations that greatly increase gene expression, such as these, may constrain their utility for adaptive evolution.
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Affiliation(s)
- Luke A Hoekstra
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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98
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Batista DFA, de Freitas Neto OC, Lopes PD, de Almeida AM, Barrow PA, Berchieri A. Polymerase chain reaction assay based on ratA gene allows differentiation between Salmonella enterica subsp. enterica serovar Gallinarum biovars Gallinarum and Pullorum. J Vet Diagn Invest 2013; 25:259-62. [DOI: 10.1177/1040638713479361] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Salmonella Pullorum and Salmonella Gallinarum are classified as biovars of Salmonella enterica subsp. enterica serovar Gallinarum. These salmonellae are the causative agents of Pullorum disease and fowl typhoid, respectively, and are widely distributed throughout the world. Although many developed countries have eradicated these diseases from commercial poultry, they are still the cause of significant economic loss in developing countries. When serovar Gallinarum is isolated, it is difficult to immediately differentiate between biovars because they are antigenically identical by serotyping. However, they cause distinct diseases with different epidemiology, and therefore it is important to differentiate them. This may be done biochemically but takes 2 to 3 days. In the present study, S. Pullorum and S. Gallinarum whole genomes were compared, and 1 genomic region of difference, which is part of the ratA gene, was chosen as a molecular marker for a polymerase chain reaction assay to differentiate rapidly between these organisms. In all, 26 strains of S. Gallinarum and 17 S. Pullorum strains were tested and successfully differentiated by the assay.
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Affiliation(s)
- Diego Felipe Alves Batista
- Faculty of Agriculture and Veterinary Sciences, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil (Batista, Freitas Neto, Lopes, Almeida, Berchieri Jr)
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK (Barrow)
| | - Oliveiro Caetano de Freitas Neto
- Faculty of Agriculture and Veterinary Sciences, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil (Batista, Freitas Neto, Lopes, Almeida, Berchieri Jr)
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK (Barrow)
| | - Priscila Diniz Lopes
- Faculty of Agriculture and Veterinary Sciences, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil (Batista, Freitas Neto, Lopes, Almeida, Berchieri Jr)
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK (Barrow)
| | - Adriana Maria de Almeida
- Faculty of Agriculture and Veterinary Sciences, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil (Batista, Freitas Neto, Lopes, Almeida, Berchieri Jr)
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK (Barrow)
| | - Paul Andrew Barrow
- Faculty of Agriculture and Veterinary Sciences, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil (Batista, Freitas Neto, Lopes, Almeida, Berchieri Jr)
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK (Barrow)
| | - Angelo Berchieri
- Faculty of Agriculture and Veterinary Sciences, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil (Batista, Freitas Neto, Lopes, Almeida, Berchieri Jr)
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK (Barrow)
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99
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Park JH, Ahn S, Kim S, Lee J, Nam JW, Shin C. Degradome sequencing reveals an endogenous microRNA target inC. elegans. FEBS Lett 2013; 587:964-9. [DOI: 10.1016/j.febslet.2013.02.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/15/2013] [Accepted: 02/15/2013] [Indexed: 11/15/2022]
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100
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Gilmore MS, Lebreton F, van Schaik W. Genomic transition of enterococci from gut commensals to leading causes of multidrug-resistant hospital infection in the antibiotic era. Curr Opin Microbiol 2013; 16:10-6. [PMID: 23395351 DOI: 10.1016/j.mib.2013.01.006] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/11/2012] [Accepted: 01/08/2013] [Indexed: 01/30/2023]
Abstract
The enterococci evolved over eons as highly adapted members of gastrointestinal consortia of a wide variety of hosts, but for reasons that are not entirely clear, emerged in the 1970s as leading causes of multidrug resistant hospital infection. Hospital-adapted pathogenic isolates are characterized by the presence of multiple mobile elements conferring antibiotic resistance, as well as pathogenicity islands, capsule loci and other variable traits. Enterococci may have been primed to emerge among the vanguard of antibiotic resistant strains because of their occurrence in the GI tracts of insects and simple organisms living and feeding on organic matter that is colonized by antibiotic resistant, antibiotic producing micro-organisms. In response to the opportunity to inhabit a new niche--the antibiotic treated hospital patient--the enterococcal genome is evolving in a pattern characteristic of other bacteria that have emerged as pathogens because of opportunities stemming from anthropogenic change.
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Affiliation(s)
- Michael S Gilmore
- Department of Ophthalmology, Harvard Medical School, 243 Charles St., Boston, MA 02114, USA.
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