Horizontal Gene Transfer Regulation in Bacteria as a “Spandrel” of DNA Repair Mechanisms

Abstract

Horizontal gene transfer (HGT) is recognized as the major force for bacterial genome evolution. Yet, numerous questions remain about the transferred genes, their function, quantity and frequency. The extent to which genetic transformation by exogenous DNA has occurred over evolutionary time was initially addressed by an in silico approach using the complete genome sequence of the Ralstonia solanacearum GMI1000 strain. Methods based on phylogenetic reconstruction of prokaryote homologous genes families detected 151 genes (13.3%) of foreign origin in the R. solanacearum genome and tentatively identified their bacterial origin. These putative transfers were analyzed in comparison to experimental transformation tests involving 18 different genomic DNA positions in the genome as sites for homologous or homeologous recombination. Significant transformation frequency differences were observed among these positions tested regardless of the overall genomic divergence of the R. solanacearum strains tested as recipients. The genomic positions containing the putative exogenous DNA were not systematically transformed at the highest frequencies. The two genomic “hot spots”, which contain recA and mutS genes, exhibited transformation frequencies from 2 to more than 4 orders of magnitude higher than positions associated with other genes depending on the recipient strain. These results support the notion that the bacterial cell is equipped with active mechanisms to modulate acquisition of new DNA in different genomic positions. Bio-informatics study correlated recombination “hot-spots” to the presence of Chi-like signature sequences with which recombination might be preferentially initiated. The fundamental role of HGT is certainly not limited to the critical impact that the very rare foreign genes acquired mainly by chance can have on the bacterial adaptation potential. The frequency to which HGT with homologous and homeologous DNA happens in the environment might have led the bacteria to hijack DNA repair mechanisms in order to generate genetic diversity without losing too much genomic stability.

Contrasting recombination patterns and demographic histories of the plant pathogen Ralstonia solanacearum inferred from MLSA

“…However, some lines of evidence in this study, and several other studies (Bertolla et al, 1999;Fall et al, 2007;Guidot et al, 2009;Coupat-Goutaland et al, 2011), suggest an important contribution of recombination and horizontal gene transfer in the evolutionary dynamics of R. solanacearum.…”

Natural Competence Rates Are Variable Among Xylella fastidiosa Strains and Homologous Recombination Occurs In Vitro Between Subspecies fastidiosa and multiplex

“…Differences in recombination frequencies based on genomic positions was previously reported in Ralstonia solanacearum (Fall et al 2007), with positions containing recombination hot spots (recA and mutS) showing the highest frequency (Fall et al 2007). In this study, higher recombination frequency was observed for pKLN61, a plasmid that recombines in the region of rpfF gene, a diffusible signaling factor involved in cell-to-cell communication of X. fastidiosa (Newman et al 2004), compared with pAX1.Cm, which recombines at a neutral site (Matsumoto et al 2009), and pMOPB-Km and pMSRA-Km, which recombine at regions whose functions are being characterized.…”

Intersubspecific Recombination in Xylella fastidiosa Strains Native to the United States: Infection of Novel Hosts Associated with an Unsuccessful Invasion

“…This is to be expected even if the benefits are large and common. Homologous recombination typically falls off rapidly with genetic distance (19), so a well-established population will usually reflect the mixing of relatively similar alleles. This mixing can be easily detected by the lack of clonality between genes and quantified using evolutionary models (e.g., ClonalFrame) (20); however, detection of recombination breaks within genes is more problematic.…”