Extensive Cotransformation of Natural Variation into Chromosomes of Naturally Competent Haemophilus influenzae

Abstract

Naturally competent bacterial species actively take up environmental DNA and can incorporate it into their chromosomes by homologous recombination. This can bring genetic variation from environmental DNA to recipient chromosomes, often in multiple long “donor” segments. Here, we report the results of genome sequencing 96 colonies of a laboratory Haemophilus influenzae strain, which had been experimentally transformed by DNA from a diverged clinical isolate. Donor segments averaged 6.9 kb (spanning several genes) and were clustered into recombination tracts of ~19.5 kb. Individual colonies had replaced from 0.1 to 3.2% of their chromosomes, and ~1/3 of all donor-specific single-nucleotide variants were present in at least one recombinant. We found that nucleotide divergence did not obviously limit the locations of recombination tracts, although there were small but significant reductions in divergence at recombination breakpoints. Although indels occasionally transformed as parts of longer recombination tracts, they were common at breakpoints, suggesting that indels typically block progression of strand exchange. Some colonies had recombination tracts in which variant positions contained mixtures of both donor and recipient alleles. These tracts were clustered around the origin of replication and were interpreted as the result of heteroduplex segregation in the original transformed cell. Finally, a pilot experiment demonstrated the utility of natural transformation for genetically dissecting natural phenotypic variation. We discuss our results in the context of the potential to merge experimental and population genetic approaches, giving a more holistic understanding of bacterial gene transfer.

Adaptive evolution of hybrid bacteria by horizontal gene transfer

“…Transferred segments have an average length of 4200 bp, contain an average of 5.1 genes, and have an approximately exponential length distribution (Fig. 1d), in agreement with previous results in Streptococcus pneumoniae (32) and Haemophilus influenza (33). These statistics show ubiquitous multi-gene transfers with no sharp cutoff on segment length.…”

Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection

“…Researchers studying natural transformation in other bacterial species have reported that 728 donor segments often cluster into complex mosaic patterns, perhaps generated by long 729 stretches of DNA being disrupted after their uptake or as the result of heteroduplex 730 segregation and correction (Mell et al 2014). Our results accord with these previous reports 731 In contrast, the STLE shows that recombination can 743 sometimes act in a manner more analogous to an extremely elevated mutation rate, leading 744 to neutral and even maladaptive changes.…”

Rates of Lateral Gene Transfer in Prokaryotes: High but Why?

“…It could be expected that in times of rapid adaptation, the LGT rate evolves to be higher (or is upregulated) whereas in times of relative ecological stasis, LGT rates evolve to be lower. It has recently been demonstrated that natural variation in transformation is under the control of multiple genes [64]. Multiple loci will form a larger target for mutation and LGT, potentially allowing more efficient fine-tuning of a single optimum gene turnover rate (but note that when the rate of LGT modifier turnover is too high it precludes selection for optimal rates).…”