Abstract
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.
Highlights
Flexible genomes facilitate bacterial evolution and are classically organized into polymorphic strainspecific segments called regions of genomic plasticity (RGPs)
We investigated the plasticity of the flexible genome, by addressing three questions: what are the respective roles of mobile genetic elements (MGEs) and hypervariable segments within the flexible genome? Are all RGPs, like MGEs, composed of modules? Do all modules undergo accretion? We addressed these questions by studying the flexible genomes of Photorhabdus and Xenorhabdus
Identification of regions of genomic plasticity (RGPs) The size of the flexible genome depends on the methodology used, the depth of phylogenetic comparison and the number of genomes compared [3]
Summary
Flexible genomes facilitate bacterial evolution and are classically organized into polymorphic strainspecific segments called regions of genomic plasticity (RGPs). The flexible genome is organized principally into polymorphic strain-specific DNA segments that are missing in at least one of the genomes analyzed. These segments are named regions of genomic plasticity (RGPs) without any assumption about the evolutionary origin or genetic basis of these variable chromosomal segments [5]. This terminology covers two classes: hypervariable segments that are likely to be the result of deletions of particular DNA regions in one or more strains, and the mobile genetic elements (MGEs). Some MGEs may undergo horizontal genetic transfer (HGT) by natural transformation, transduction or well developed and efficient conjugation mechanisms (intercellular mobility) [4]
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