tDNA locus polymorphism and ecto-chromosomal DNA insertion hot-spots are related to the phylogenetic group of Escherichia coli strains

Germon, Pierre; Roche, David; Melo, Sandrine; Mignon-Grasteau, Sandrine; Dobrindt, Ulrich; Hacker, Jörg; Schouler, Catherine; Moulin-Schouleur, Maryvonne

doi:10.1099/mic.0.2006/001958-0

Cited by 17 publications

(12 citation statements)

References 47 publications

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“…Likewise, phylogenetic analysis of the collection and assignment of phylogenetic groups to new strains was performed, as described [8]. Briefly, for phylogenetic analysis the sequences of the 7 MLST loci were concatenated and aligned using ClustalW, and phylogenetic trees were constructed using the neighbor-joining algorithm with default parameters and 1000 bootstrap replicates using the MEGA4 (http://www.megasoftware.net/) [61]. The assignment of the phylogenetic groups was performed using STRUCTURE, as described [8].…”

Section: Methodsmentioning

confidence: 99%

Fate of the H-NS–Repressed bgl Operon in Evolution of Escherichia coli

et al. 2009

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In the enterobacterial species Escherichia coli and Salmonella enterica, expression of horizontally acquired genes with a higher than average AT content is repressed by the nucleoid-associated protein H-NS. A classical example of an H-NS–repressed locus is the bgl (aryl-β,D-glucoside) operon of E. coli. This locus is “cryptic,” as no laboratory growth conditions are known to relieve repression of bgl by H-NS in E. coli K12. However, repression can be relieved by spontaneous mutations. Here, we investigated the phylogeny of the bgl operon. Typing of bgl in a representative collection of E. coli demonstrated that it evolved clonally and that it is present in strains of the phylogenetic groups A, B1, and B2, while it is presumably replaced by a cluster of ORFans in the phylogenetic group D. Interestingly, the bgl operon is mutated in 20% of the strains of phylogenetic groups A and B1, suggesting erosion of bgl in these groups. However, bgl is functional in almost all B2 isolates and, in approximately 50% of them, it is weakly expressed at laboratory growth conditions. Homologs of bgl genes exist in Klebsiella, Enterobacter, and Erwinia species and also in low GC-content Gram-positive bacteria, while absent in E. albertii and Salmonella sp. This suggests horizontal transfer of bgl genes to an ancestral Enterobacterium. Conservation and weak expression of bgl in isolates of phylogenetic group B2 may indicate a functional role of bgl in extraintestinal pathogenic E. coli.

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Section: Methodsmentioning

confidence: 99%

Fate of the H-NS–Repressed bgl Operon in Evolution of Escherichia coli

et al. 2009

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“…In order to identify new accessory genes of APEC strains, we previously described tRNA loci in the E. coli genome that could represent potential insertion sites for new genomic islands (18). We had already used this strategy to characterize the AGI-3 region that is involved in the virulence of an avian pathogenic E. coli strain and that confers the ability to grow on fructooligosaccharides (7,43).…”

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confidence: 99%

ICEEc2, a New Integrative and Conjugative Element Belonging to the pKLC102/PAGI-2 Family, Identified inEscherichia coliStrain BEN374

et al. 2010

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The diversity of the Escherichia coli species is in part due to the large number of mobile genetic elements that are exchanged between strains. We report here the identification of a new integrative and conjugative element (ICE) of the pKLC102/PAGI-2 family located downstream of the tRNA gene pheU in the E. coli strain BEN374. Indeed, this new region, which we called ICEEc2, can be transferred by conjugation from strain BEN374 to the E. coli strain C600. We were also able to transfer this region into a Salmonella enterica serovar Typhimurium strain and into a Yersinia pseudotuberculosis strain. This transfer was then followed by the integration of ICEEc2 into the host chromosome downstream of a phe tRNA gene. Our data indicated that this transfer involved a set of three genes encoding DNA mobility enzymes and a type IV pilus encoded by genes present on ICEEc2. Given the wide distribution of members of this family, these mobile genetic elements are likely to play an important role in the diversification of bacteria.

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“…Thus, without any a priori on the data, the most frequently observed STI shapes were with proteins likely to be similar to IntS, indicating a clear tRNA sublocation preference with this integrase subfamily. Several genome analysis studies showed that a vast majority of prophages are inserted in or adjacent to tRNA genes [39]–[41], [52], [53]. Williams revealed that tRNA sequence sites are preferred for prophage integration sites [39].…”

Section: Discussionmentioning

confidence: 99%

“…Our integrase identification procedure, combined with the fact that we were working on >1000 organisms (compared to 302 bacterial genomes analyzed by Fouts [40]) may explain the difference observed (15% vs 33%) of the prophages that used tRNA as target sites. In E. coli and Shigella genomes, comparative genomic analysis also showed that tRNA loci are preferentially used as an insertion site for integrative elements, with the majority of tRNA genes remaining intact after insertion [52], [53]. Finally, Boyd and colleagues' analysis of island-encoded integrases revealed that half of the available tRNA genes were used as integration sites, in particular among members of the γ-Proteobacteria [41].…”

Section: Discussionmentioning

confidence: 99%

Tight Regulation of the intS Gene of the KplE1 Prophage: A New Paradigm for Integrase Gene Regulation

et al. 2010

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Temperate phages have the ability to maintain their genome in their host, a process called lysogeny. For most, passive replication of the phage genome relies on integration into the host's chromosome and becoming a prophage. Prophages remain silent in the absence of stress and replicate passively within their host genome. However, when stressful conditions occur, a prophage excises itself and resumes the viral cycle. Integration and excision of phage genomes are mediated by regulated site-specific recombination catalyzed by tyrosine and serine recombinases. In the KplE1 prophage, site-specific recombination is mediated by the IntS integrase and the TorI recombination directionality factor (RDF). We previously described a sub-family of temperate phages that is characterized by an unusual organization of the recombination module. Consequently, the attL recombination region overlaps with the integrase promoter, and the integrase and RDF genes do not share a common activated promoter upon lytic induction as in the lambda prophage. In this study, we show that the intS gene is tightly regulated by its own product as well as by the TorI RDF protein. In silico analysis revealed that overlap of the attL region with the integrase promoter is widely encountered in prophages present in prokaryotic genomes, suggesting a general occurrence of negatively autoregulated integrase genes. The prediction that these integrase genes are negatively autoregulated was biologically assessed by studying the regulation of several integrase genes from two different Escherichia coli strains. Our results suggest that the majority of tRNA-associated integrase genes in prokaryotic genomes could be autoregulated and that this might be correlated with the recombination efficiency as in KplE1. The consequences of this unprecedented regulation for excisive recombination are discussed.

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tDNA locus polymorphism and ecto-chromosomal DNA insertion hot-spots are related to the phylogenetic group of Escherichia coli strains

Cited by 17 publications

References 47 publications

Fate of the H-NS–Repressed bgl Operon in Evolution of Escherichia coli

Fate of the H-NS–Repressed bgl Operon in Evolution of Escherichia coli

ICEEc2, a New Integrative and Conjugative Element Belonging to the pKLC102/PAGI-2 Family, Identified inEscherichia coliStrain BEN374

Tight Regulation of the intS Gene of the KplE1 Prophage: A New Paradigm for Integrase Gene Regulation

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