TransfoConflict

The key objectives of the TransfoConflict project are to make a large-scale quantification of the frequency of transformation across the genetic diversity of two bacterial species and use this data to characterize, for the first time, the causes and consequences of variation in natural transformation. By interpreting these results in the light of the conflicting interactions between bacteria and their mobile genetic elements (MGEs), TransfoConflict will lead to a much better understanding of the consequences of natural transformation for bacterial evolution. Bacterial genomes evolve very fast by three main mechanisms of horizontal gene transfer (HGT): conjugation, transduction and natural transformation. Both conjugation and transduction involve parasitic MGEs against which bacteria have evolved multiple defense mechanisms. In contrast, natural transformation is a mechanism of HGT under the direct control of the bacteria, which encode in their core-genome the machineries to actively capture, import and recombine exogenous DNA in their chromosome. The observation of large within-species variations in natural transformation rates in several species remained a puzzle for more than a decade. Since natural transformation has an important role in genetic exchanges, it facilitates allelic recombination and the acquisition of novel genes, these variations must affect gene flow across the species. A recent hypothesis proposes that natural transformation is used by bacteria to cure their genomes of MGEs by recombination of DNA imported from uninfected cells. This “chromosome curing” model predicts that MGEs evolved mechanisms to moderate transformation of their host. In agreement, we and others have identified MGEs that inhibit natural transformation. We here hypothesize that (1) the transformation/MGE conflict is a major cause of variation in natural transformation and (2) these variations have important consequences in terms of genome evolution. To test these hypotheses, our foremost objective is to generate the first comprehensive analysis of the variations of natural transformability in two bacterial pathogens populated by distinct MGE families. To do so, we will assemble, sequence and analyze two large collections of isolates uniquely representative of the species’ genetic diversity. We will subject them to a novel high-throughput and quantitative assay for natural transformation. We will use the associated genome sequence to generate an exhaustive list of MGEs in pangenomes and a combination of statistical and conventional genetics to uncover MGEs interfering with natural transformation. This will allow to unravel the molecular mechanisms of transformation-inhibition activity of these MGEs. These will include a novel, already identified transformation-inhibiting MGE of unknown mechanism of action, potentially shedding light on poorly characterized steps of the transformation process (regulation, recombination). Lastly, we will harness the experimentally-determined frequencies of natural transformation to understand the evolution of natural transformability in these bacterial pathogens. We will determine the impact of transformation-modifying MGEs on gene flow in the considered pathogens and more broadly in Proteobacteria. TransfoConflict will bring to the fore the importance of considering the MGEs/transformation interactions to understand genome evolution. MGEs and transformation are also two key drivers of the spread of antibiotic resistance whose effects have so far been considered separately. Beyond its fundamental contribution to understand genome dynamics, TransfoConflict may explain patterns of spread of antibiotic resistance genes across bacterial pathogens and identify intervention strategies.