Marsin S, Mathieu A, Kortulewski T, Guérois R, Radicella JP. Unveiling novel RecO distant orthologues involved in homologous recombination.
PLoS Genet 2008;
4:e1000146. [PMID:
18670631 PMCID:
PMC2475510 DOI:
10.1371/journal.pgen.1000146]
[Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Accepted: 06/30/2008] [Indexed: 01/19/2023] Open
Abstract
The generation of a RecA filament on single-stranded DNA is a critical step in homologous recombination. Two main pathways leading to the formation of the nucleofilament have been identified in bacteria, based on the protein complexes mediating RecA loading: RecBCD (AddAB) and RecFOR. Many bacterial species seem to lack some of the components involved in these complexes. The current annotation of the Helicobacter pylori genome suggests that this highly diverse bacterial pathogen has a reduced set of recombination mediator proteins. While it is now clear that homologous recombination plays a critical role in generating H. pylori diversity by allowing genomic DNA rearrangements and integration through transformation of exogenous DNA into the chromosome, no complete mediator complex is deduced from the sequence of its genome. Here we show by bioinformatics analysis the presence of a RecO remote orthologue that allowed the identification of a new set of RecO proteins present in all bacterial species where a RecR but not RecO was previously identified. HpRecO shares less than 15% identity with previously characterized homologues. Genetic dissection of recombination pathways shows that this novel RecO and the remote RecB homologue present in H. pylori are functional in repair and in RecA-dependent intrachromosomal recombination, defining two initiation pathways with little overlap. We found, however, that neither RecOR nor RecB contributes to transformation, suggesting the presence of a third, specialized, RecA-dependent pathway responsible for the integration of transforming DNA into the chromosome of this naturally competent bacteria. These results provide insight into the mechanisms that this successful pathogen uses to generate genetic diversity and adapt to changing environments and new hosts.
Homologous recombination plays an essential role in maintaining genomic integrity and in allowing genetic diversity within a population. In the case of bacteria, two main pathways for the initiation of recombination have been described. These pathways are defined by the protein complexes, present in the model systems Escherichia coli and Bacillus subtilis, that allow the loading of RecA onto single-stranded DNA to engage it in the annealing process. Depending on the DNA substrate, either RecFOR or RecBCD (AddAB) act as mediators for RecA filament formation. However, analysis of the completed bacterial genome sequences shows that in many species, not all of the components seem to be present. One such example is the human pathogen Helicobacter pylori, where homologous recombination is known to play a critical role in its high genetic diversity by facilitating intrachromosomal rearrangements and allowing integration of exogenous DNA into its genome. In this species, classical sequence comparisons have only identified RecR and RecB mediator genes. Here we show that H. pylori possesses a RecO functional orthologue. This finding allowed the identification of remote homologues of RecO in all those bacterial species where RecR but no RecO was previously found.
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