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

Autor: Patrick Tailliez, Robert Zumbihl, Alain Givaudan, Alexandra Calteau, Sophie Gaudriault, Jean-Claude Ogier, Steve Forst, Heidi Goodrich-Blair, Garret Suen, David Roche, Claudine Médigue, Zoé Rouy
Přispěvatelé: Diversité, Génomes et Interactions Microorganismes-Insectes, Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Biological Sciences, The Open University [Milton Keynes] (OU), Department of Bacteriology, Veterinary Laboratories Agency, University of Wisconsin-Madison, Ecologie microbienne des insectes et interactions hôte-pathogène (EMIP)
Jazyk: francouzština
Rok vydání: 2011
Předmět:
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences
Time Factors
Biodiversité et Ecologie
GENOMIQUE
INSECTE
RGPs
RGPFinder
xenorhabdus
Xenorhabdus
Genome
RNA
Ribosomal
16S
Genomic island
invertébré
Phylogeny
ComputingMilieux_MISCELLANEOUS
Sequence Deletion
nématode
Gene Rearrangement
bactérie
Genetics
0303 health sciences
biology
Chromosome Mapping
Genomics
Chromosomes
Bacterial
Host-Pathogen Interactions
Female
bactérie pathogène
Photorhabdus
Research Article
Biotechnology
lcsh:QH426-470
lcsh:Biotechnology
Bacterial genome size
Synteny
Bacterial genetics
Evolution
Molecular
Biodiversity and Ecology
photorhabdus
03 medical and health sciences
Phylogenetics
lcsh:TP248.13-248.65
Animals
Humans
030304 developmental biology
Comparative genomics
030306 microbiology
génome
plasticité
Genetic Variation
biology.organism_classification
Invertebrates
lcsh:Genetics
Genes
Bacterial
Genetic Loci
Evolutionary biology
[SDE.BE]Environmental Sciences/Biodiversity and Ecology
Genome
Bacterial
Zdroj: 4. Congress of the FEMS
4. Congress of the FEMS, Jun 2011, Geneva, Suisse. 2011
4. Congress of the FEMS, Jun 2011, Geneva, Suisse., 2011
BMC Genomics
BMC Genomics, BioMed Central, 2010, 11, ⟨10.1186/1471-2164-11-568⟩
BMC Genomics (11), . (2010)
BMC Genomics, Vol 11, Iss 1, p 568 (2010)
BMC Genomics, 2010, 11, ⟨10.1186/1471-2164-11-568⟩
ISSN: 1471-2164
Popis: Background Flexible 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). Results RGPs 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. Conclusions This 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.
Databáze: OpenAIRE
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