Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus

BackgroundFlexible genomes facilitate bacterial evolution and are classically organized into polymorphic strain-specific segments called regions of genomic plasticity (RGPs). Using a new web tool, RGPFinder, we investigated plasticity units in bacterial genomes, by exhaustive description of the RGPs in two Photorhabdus and two Xenorhabdus strains, belonging to the Enterobacteriaceae and interacting with invertebrates (insects and nematodes).ResultsRGPs account for about 60% of the genome in each of the four genomes studied. We classified RGPs into genomic islands (GIs), prophages and two new classes of RGP without the features of classical mobile genetic elements (MGEs) but harboring genes encoding enzymes catalyzing DNA recombination (RGPmob), or with no remarkable feature (RGPnone). These new classes accounted for most of the RGPs and are probably hypervariable regions, ancient MGEs with degraded mobilization machinery or non canonical MGEs for which the mobility mechanism has yet to be described. We provide evidence that not only the GIs and the prophages, but also RGPmob and RGPnone, have a mosaic structure consisting of modules. A module is a block of genes, 0.5 to 60 kb in length, displaying a conserved genomic organization among the different Enterobacteriaceae. Modules are functional units involved in host/environment interactions (22-31%), metabolism (22-27%), intracellular or intercellular DNA mobility (13-30%), drug resistance (4-5%) and antibiotic synthesis (3-6%). Finally, in silico comparisons and PCR multiplex analysis indicated that these modules served as plasticity units within the bacterial genome during genome speciation and as deletion units in clonal variants of Photorhabdus.ConclusionsThis led us to consider the modules, rather than the entire RGP, as the true unit of plasticity in bacterial genomes, during both short-term and long-term genome evolution.

[1]  L. Baxter,et al.  Identification, Typing, and Insecticidal Activity of Xenorhabdus Isolates from Entomopathogenic Nematodes in United Kingdom Soil and Characterization of the xpt Toxin Loci , 2006, Applied and Environmental Microbiology.

[2]  R. ffrench-Constant,et al.  Photorhabdus Virulence Cassettes Confer Injectable Insecticidal Activity against the Wax Moth , 2006, Journal of bacteriology.

[3]  V. Souza,et al.  The elements of the locus of enterocyte effacement in human and wild mammal isolates of Escherichia coli: evolution by assemblage or disruption? , 2001, Microbiology.

[4]  A. Danchin,et al.  Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths , 2009, PLoS genetics.

[5]  R. ffrench-Constant,et al.  Human infection with Photorhabdus asymbiotica: an emerging bacterial pathogen. , 2004, Microbes and infection.

[6]  H. Goodrich-Blair,et al.  Mutualism and pathogenesis in Xenorhabdus and Photorhabdus: two roads to the same destination , 2007, Molecular microbiology.

[7]  F. Kunst,et al.  Whole-Genome Comparison between Photorhabdus Strains To Identify Genomic Regions Involved in the Specificity of Nematode Interaction , 2006, Journal of bacteriology.

[8]  M. Stanhope,et al.  Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition , 2007, Genome Biology.

[9]  J. Parkhill,et al.  Rapid Virulence Annotation (RVA): Identification of virulence factors using a bacterial genome library and multiple invertebrate hosts , 2008, Proceedings of the National Academy of Sciences.

[10]  Graham F Hatfull,et al.  Bacteriophage genomics. , 2008, Current opinion in microbiology.

[11]  V. Souza,et al.  A genomic population genetics analysis of the pathogenic enterocyte effacement island in Escherichia coli: the search for the unit of selection. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Ariane Toussaint,et al.  Mobile elements as a combination of functional modules. , 2002, Plasmid.

[13]  H. Goodrich-Blair,et al.  Masters of conquest and pillage: Xenorhabdus nematophila global regulators control transitions from virulence to nutrient acquisition , 2009, Cellular microbiology.

[14]  S. Lory,et al.  A genomic island in Pseudomonas aeruginosa carries the determinants of flagellin glycosylation , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[15]  B. Birren,et al.  Dynamics of Pseudomonas aeruginosa genome evolution , 2008, Proceedings of the National Academy of Sciences.

[16]  A. Roberts,et al.  Conjugative Transfer of the Integrative Conjugative Elements ICESt1 and ICESt3 from Streptococcus thermophilus , 2009, Journal of bacteriology.

[17]  H. Mobley,et al.  Genomic Islands of Uropathogenic Escherichia coli Contribute to Virulence , 2009, Journal of bacteriology.

[18]  N. Boemare,et al.  Bacteriocinogenesis in cells of Xenorhabdus nematophilus and Photorhabdus luminescens: Enterobacteriaceae associated with entomopathogenic nematodes , 1993 .

[19]  N. Moran,et al.  Genomic changes following host restriction in bacteria. , 2004, Current opinion in genetics & development.

[20]  F. Kunst,et al.  Identification of a P2-related prophage remnant locus of Photorhabdus luminescens encoding an R-type phage tail-like particle. , 2004, FEMS microbiology letters.

[21]  H. Goodrich-Blair,et al.  The Xenorhabdus nematophila nilABC Genes Confer the Ability of Xenorhabdus spp. To Colonize Steinernema carpocapsae Nematodes , 2008, Journal of bacteriology.

[22]  Julian I. Rood,et al.  Revised nomenclature for transposable genetic elements. , 2008, Plasmid.

[23]  Susan E. Brown,et al.  Genome of the Actinomycete Plant Pathogen Clavibacter michiganensis subsp. sepedonicus Suggests Recent Niche Adaptation , 2008, Journal of bacteriology.

[24]  J. Šmarda.  Lysogeny and bacteriocinogeny , 1963, Folia Microbiologica.

[25]  Georgios S. Vernikos,et al.  Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens , 2009, Genome Biology.

[26]  Z. Deng,et al.  Analysis of a genomic island housing genes for DNA S‐modification system in Streptomyces lividans 66 and its counterparts in other distantly related bacteria , 2007, Molecular microbiology.

[27]  Gordon Dougan,et al.  Molecular and Phenotypic Analysis of the CS54 Island of Salmonella enterica Serotype Typhimurium: Identification of Intestinal Colonization and Persistence Determinants , 2003, Infection and Immunity.

[28]  M. Waldor,et al.  Mobile Antibiotic Resistance Encoding Elements Promote Their Own Diversity , 2009, PLoS genetics.

[29]  B. Finlay,et al.  Escherichia Coli of Virulent Verocytotoxin-producing Enterocyte Effacement, and the Evolution Genomic O Island 122, Locus for Supplemental Material , 2008 .

[30]  R. ffrench-Constant,et al.  The tc genes of Photorhabdus: a growing family. , 2001, Trends in microbiology.

[31]  Jia Liu,et al.  The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000 , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[32]  P. Glaser,et al.  Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae , 2008, Proceedings of the National Academy of Sciences.

[33]  R. ffrench-Constant,et al.  Genomic islands in Photorhabdus. , 2002, Trends in microbiology.

[34]  M. Mergeay,et al.  New mobile genetic elements in Cupriavidus metallidurans CH34, their possible roles and occurrence in other bacteria , 2009, Antonie van Leeuwenhoek.

[35]  Georgios S. Vernikos,et al.  Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands , 2006, Bioinform..

[36]  Stephen Lory,et al.  Interstrain transfer of the large pathogenicity island (PAPI-1) of Pseudomonas aeruginosa , 2006, Proceedings of the National Academy of Sciences.

[37]  M. Simmonds,et al.  Genome sequence of Yersinia pestis, the causative agent of plague , 2001, Nature.

[38]  Julian Parkhill,et al.  Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens , 2009, BMC Genomics.

[39]  Ling V. Sun,et al.  Phylogenomics of the Reproductive Parasite Wolbachia pipientis wMel: A Streamlined Genome Overrun by Mobile Genetic Elements , 2004, PLoS biology.

[40]  R. Akhurst,et al.  Xenorhabdus luminescens (DNA hybridization group 5) from human clinical specimens , 1989, Journal of clinical microbiology.

[41]  G. Cornelis,et al.  The type III secretion injectisome , 2006, Nature Reviews Microbiology.

[42]  Guillaume Pavlovic,et al.  Conjugative transposons: the tip of the iceberg , 2002, Molecular microbiology.

[43]  Didier Mazel,et al.  Integrons: agents of bacterial evolution , 2006, Nature Reviews Microbiology.

[44]  G. Poinar,et al.  A new bacterium, Achromobacter nematophilus sp. nov. (Achromobacteriaceae: Eubacteriales) associated with a nematode , 1965 .

[45]  J. Hacker,et al.  Pathogenicity islands and the evolution of microbes. , 2000, Annual review of microbiology.

[46]  F. Taieb,et al.  Cycle Inhibiting Factors (CIFs) Are a Growing Family of Functional Cyclomodulins Present in Invertebrate and Mammal Bacterial Pathogens , 2009, PloS one.

[47]  C. Menck,et al.  Non-gamma-proteobacteria gene islands contribute to the Xanthomonas genome. , 2005, Omics : a journal of integrative biology.

[48]  M. Brehélin,et al.  Lysogeny and bacteriocinogeny in Xenorhabdus nematophilus and other Xenorhabdus spp , 1992, Applied and environmental microbiology.

[49]  Scott Mann,et al.  Bacterial genomic G+C composition-eliciting environmental adaptation. , 2010, Genomics.

[50]  Fiona S. L. Brinkman,et al.  Detecting genomic islands using bioinformatics approaches , 2010, Nature Reviews Microbiology.

[51]  M. Bondi,et al.  Antimicrobial properties and morphological characteristics of two Photorhabdus luminescens strains. , 1999, The new microbiologica.

[52]  H. Engelberg-Kulka,et al.  Addiction modules and programmed cell death and antideath in bacterial cultures. , 1999, Annual review of microbiology.

[53]  E. Rocha.  The organization of the bacterial genome. , 2008, Annual review of genetics.

[54]  E. Martínez-García,et al.  Polymorphism in the yclC-rpoS Region of Enterobacteria , 2003, Current Microbiology.

[55]  Jeffrey E. Barrick,et al.  Genome evolution and adaptation in a long-term experiment with Escherichia coli , 2009, Nature.

[56]  H. Goodrich-Blair,et al.  Expression and activity of a Xenorhabdus nematophila haemolysin required for full virulence towards Manduca sexta insects , 2004, Cellular microbiology.

[57]  D. Ferguson,et al.  Novel Type IV Secretion System Involved in Propagation of Genomic Islands , 2006, Journal of bacteriology.

[58]  S. Andersson,et al.  Strong asymmetric mutation bias in endosymbiont genomes coincide with loss of genes for replication restart pathways. , 2006, Molecular biology and evolution.

[59]  Ulrich Dobrindt,et al.  Genomic islands in pathogenic and environmental microorganisms , 2004, Nature Reviews Microbiology.

[60]  S. Mande,et al.  Identification and Functional Characterization of Gene Components of Type VI Secretion System in Bacterial Genomes , 2008, PloS one.

[61]  C. Schouler,et al.  Genomic subtraction for the identification of putative new virulence factors of an avian pathogenic Escherichia coli strain of O2 serogroup. , 2004, Microbiology.

[62]  C. Ronson,et al.  Plasmid-Located Pathogenicity Determinants of Serratia entomophila, the Causal Agent of Amber Disease of Grass Grub, Show Similarity to the Insecticidal Toxins of Photorhabdus luminescens , 2000, Journal of bacteriology.

[63]  R. Akhurst,et al.  Taxonomy of Australian clinical isolates of the genus Photorhabdus and proposal of Photorhabdus asymbiotica subsp. asymbiotica subsp. nov. and P. asymbiotica subsp. australis subsp. nov. , 2004, International journal of systematic and evolutionary microbiology.

[64]  M. Touchon,et al.  A Module Located at a Chromosomal Integration Hot Spot Is Responsible for the Multidrug Resistance of a Reference Strain from Escherichia coli Clonal Group A , 2009, Antimicrobial Agents and Chemotherapy.

[65]  V. Daubin,et al.  Comparative genomics and the evolution of prokaryotes. , 2007, Trends in microbiology.

[66]  N. Boemare.  Interactions between the partners of the entomopathogenic bacterium nematode complexes, Steinernema-Xenorhabdus and Heterorhabditis-Photorhabdus , 2002 .

[67]  Yan Boucher,et al.  Integrons: mobilizable platforms that promote genetic diversity in bacteria. , 2007, Trends in microbiology.

[68]  A. Givaudan,et al.  Plastic architecture of bacterial genome revealed by comparative genomics of Photorhabdus variants , 2008, Genome Biology.

[69]  J. Shapiro.  Letting Escherichia coli Teach Me About Genome Engineering , 2009, Genetics.

[70]  Vincent Burrus,et al.  Shaping bacterial genomes with integrative and conjugative elements. , 2004, Research in microbiology.

[71]  M. Carlomagno,et al.  Enterobacterial Repetitive Intergenic Consensus Sequence Repeats in Yersiniae: Genomic Organization and Functional Properties , 2005, Journal of bacteriology.

[72]  C. Médigue,et al.  MaGe: a microbial genome annotation system supported by synteny results , 2006, Nucleic acids research.

[73]  E. Stackebrandt,et al.  Xenorhabdus and Photorhabdus spp.: bugs that kill bugs. , 1997, Annual review of microbiology.

[74]  J. Weissenbach,et al.  Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila , 2006, Nature Biotechnology.

[75]  Direk Limmathurotsakul,et al.  Burkholderia pseudomallei genome plasticity associated with genomic island variation , 2008, BMC Genomics.

[76]  Eduardo P C Rocha,et al.  Order and disorder in bacterial genomes. , 2004, Current opinion in microbiology.

[77]  C. Ronson,et al.  Excision and transfer of the Mesorhizobium loti R7A symbiosis island requires an integrase IntS, a novel recombination directionality factor RdfS, and a putative relaxase RlxS , 2006, Molecular microbiology.

[78]  J. Hacker,et al.  Ecological fitness, genomic islands and bacterial pathogenicity , 2001, EMBO reports.

[79]  Georgios S. Vernikos,et al.  Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways. , 2008, Genome research.

[80]  N. Boemare,et al.  Purification and characterization of xenorhabdicin, a phage tail-like bacteriocin, from the lysogenic strain F1 of Xenorhabdus nematophilus , 1995, Applied and environmental microbiology.

[81]  A. Danchin,et al.  The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens , 2003, Nature Biotechnology.

[82]  B. Goldman,et al.  Optical mapping as a routine tool for bacterial genome sequence finishing , 2007, BMC Genomics.

[83]  J. R. van der Meer,et al.  Low-Frequency Horizontal Transfer of an Element Containing the Chlorocatechol Degradation Genes fromPseudomonas sp. Strain B13 to Pseudomonas putidaF1 and to Indigenous Bacteria in Laboratory-Scale Activated-Sludge Microcosms , 1998, Applied and Environmental Microbiology.

[84]  M. Moens,et al.  Steinernema jollieti sp n. (Rhabditida: Steinernematidae), a new entomopathogenic nematode from the American midwest , 2004 .

[85]  Ghislain Fournous,et al.  The impact of prophages on bacterial chromosomes , 2004, Molecular microbiology.

[86]  T. Lilburn,et al.  A Comparative Genomics, Network-Based Approach to Understanding Virulence in Vibrio cholerae , 2009, Journal of bacteriology.

[87]  M. Mulvey,et al.  Secondary Chromosomal Attachment Site and Tandem Integration of the Mobilizable Salmonella Genomic Island 1 , 2008, PloS one.

[88]  A. Billault,et al.  YAPI, a New Yersinia pseudotuberculosis Pathogenicity Island , 2004, Infection and Immunity.

[89]  C. Ubeda,et al.  Role of Staphylococcal Phage and SaPI Integrase in Intra- and Interspecies SaPI Transfer , 2007, Journal of bacteriology.

[90]  Laura S. Frost,et al.  Mobile genetic elements: the agents of open source evolution , 2005, Nature Reviews Microbiology.

[91]  G. Pavlovic,et al.  Evolution of genomic islands by deletion and tandem accretion by site-specific recombination: ICESt1-related elements from Streptococcus thermophilus. , 2004, Microbiology.

[92]  Iman Chouikha,et al.  A selC-Associated Genomic Island of the Extraintestinal Avian Pathogenic Escherichia coli Strain BEN2908 Is Involved in Carbohydrate Uptake and Virulence , 2006, Journal of bacteriology.

[93]  M. Mulvey,et al.  Potential integration sites of the Salmonella genomic island 1 in Proteus mirabilis and other bacteria. , 2007, The Journal of antimicrobial chemotherapy.

[94]  John W. Beaber,et al.  SOS response promotes horizontal dissemination of antibiotic resistance genes , 2004, Nature.

[95]  J. Parkhill,et al.  Variation in the Effectors of the Type III Secretion System among Photorhabdus Species as Revealed by Genomic Analysis , 2004, Journal of bacteriology.

[96]  Sébastien Carrère,et al.  Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. , 2008, Genome research.

[97]  C. Buchrieser,et al.  Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity , 2004, Nature Genetics.

[98]  M. Brehélin,et al.  Site‐specific antiphagocytic function of the Photorhabdus luminescens type III secretion system during insect colonization , 2005, Cellular microbiology.

[99]  Jacques van Helden,et al.  Prophinder: a computational tool for prophage prediction in prokaryotic genomes , 2008, Bioinform..

[100]  Anu Raghunathan,et al.  Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale , 2006, Nature Genetics.

[101]  T. Fuchs,et al.  Comparative analysis of the Photorhabdus luminescens and the Yersinia enterocolitica genomes: uncovering candidate genes involved in insect pathogenicity , 2008, BMC Genomics.