Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus. BMC Genomics 2010 Oct 15;11:568
Date
10/19/2010Pubmed ID
20950463Pubmed Central ID
PMC3091717DOI
10.1186/1471-2164-11-568Scopus ID
2-s2.0-77957922333 (requires institutional sign-in at Scopus site) 41 CitationsAbstract
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.
Author List
Ogier JC, Calteau A, Forst S, Goodrich-Blair H, Roche D, Rouy Z, Suen G, Zumbihl R, Givaudan A, Tailliez P, Médigue C, Gaudriault SAuthor
Steven Forst PhD Professor in the Biological Sciences department at University of Wisconsin - MilwaukeeMESH terms used to index this publication - Major topics in bold
AnimalsChromosome Mapping
Chromosomes, Bacterial
Evolution, Molecular
Female
Gene Rearrangement
Genes, Bacterial
Genetic Loci
Genetic Variation
Genome, Bacterial
Genomics
Host-Pathogen Interactions
Humans
Invertebrates
Photorhabdus
Phylogeny
RNA, Ribosomal, 16S
Sequence Deletion
Synteny
Time Factors
Xenorhabdus