Regulation of genetic flux between bacteria by restriction–modification systems

Abstract

Restriction-modification (R-M) systems are often regarded as bacteria's innate immune systems, protecting cells from infection by mobile genetic elements (MGEs). Their diversification has been recently associated with the emergence of particularly virulent lineages. However, we have previously found more R-M systems in genomes carrying more MGEs. Furthermore, it has been suggested that R-M systems might favor genetic transfer by producing recombinogenic double-stranded DNA ends. To test whether R-M systems favor or disfavor genetic exchanges, we analyzed their frequency with respect to the inferred events of homologous recombination and horizontal gene transfer within 79 bacterial species. Genetic exchanges were more frequent in bacteria with larger genomes and in those encoding more R-M systems. We created a recognition target motif predictor for Type II R-M systems that identifies genomes encoding systems with similar restriction sites. We found more genetic exchanges between these genomes, independently of their evolutionary distance. Our results reconcile previous studies by showing that R-M systems are more abundant in promiscuous species, wherein they establish preferential paths of genetic exchange within and between lineages with cognate R-M systems. Because the repertoire and/or specificity of R-M systems in bacterial lineages vary quickly, the preferential fluxes of genetic transfer within species are expected to constantly change, producing time-dependent networks of gene transfer.homologous recombination | horizontal gene transfer | bacterial evolution

Microdiversity shapes the traits, niche space, and biogeography of microbial taxa

“…Additionally, although the two models operate simultaneously, it is important to note the two models may influence certain taxa at different frequencies. For example, Pseudomonas syringae was found to have a rate of HGT four orders of magnitude higher than that found in Bacillus, Streptococcus, and Corynebacterium isolates (Nowell et al, 2014;Vos et al, 2015), which may be facilitated by the abundance of restriction-modification systems in the genome (Oliveira et al, 2016). Similarly, mutations in the DNA mismatch repair (MMR) system can result in increased mutation rates for specific sub-taxa (Vulic et al, 1999;Schofield and Hsieh, 2003).…”

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

“…Recent extensive genomic analysis has revealed a strong connection between the abundance of RM modules and MGEs in microbial genomes, suggesting that although RM systems are rarely encoded by plasmids or prophages, they nevertheless disseminate with the help of MGEs (123). Conversely, the abundance of RM modules also strongly positively correlates with the estimated rate of horizontal gene transfer (HGT), suggesting a major role of RM in this process (124). These findings indicate that the roles of RM in prokaryotes go beyond defense functions (41).…”

The impact of DNA methylation in Alphaproteobacteria

“…Interestingly, motifs methylated by these two orphan MTases appear as only partially methylated, suggesting the possible existence of methylation patterns or phasevarions controlled by these MTases, although their function remains elusive. So far, the methylomes of ~20 Alphaproteobacteria have been characterized using SMRT sequencing (Kozdon et al, 2013;Blow et al, 2016) and bioinformatics searches indicate that genes encoding putative DNA MTases are frequently found in alphaproteobacterial genomes (Roberts et al, 2015;Oliveira et al, 2016). The function of some of these MTases has now been characterized in more details.…”