The large majority of intergenic sites in bacteria are selectively constrained, even when known regulatory elements are excluded

Abstract

There are currently no broad estimates of the overall strength and direction of selection operating on intergenic variation in bacteria. Here we address this using large whole genome sequence datasets representing six diverse bacterial species; Escherichia coli , Staphylococcus aureus, Salmonella enterica , Streptococcus pneumoniae , Klebsiella pneumoniae , and Mycobacterium tuberculosis . Excluding M. tuberculosis , we find that a high proportion (62%79%; mean 70%) of intergenic sites are selectively constrained, relative to synonymous sites. Noncoding RNAs tend to be under stronger selective constraint than promoters, which in turn are typically more constrained than rhoindependent terminators. Even when these regulatory elements are excluded, the mean proportion of constrained intergenic sites only falls to 69%; thus our current understanding of the functionality of intergenic regions (IGRs) in bacteria is severely limited. Consistent with a role for positive as well as negative selection on intergenic sites, we present evidence for strong positive selection in Mycobacterium tuberculosis promoters, underlining the key role of regulatory changes as an adaptive mechanism in this highly monomorphic pathogen.

Discovering Complete Quasispecies in Bacterial Genomes

“…This is presumably because a REPIN insertion into a gene would immediately destroy the open reading frame of the gene, which would have detrimental fitness effects for the host. To estimate the proportion of the genome that is permissive of REPIN insertion, we can rely on recent estimates of neutrally evolving sites in the extragenic space of a bacterial genome ( Thorpe et al 2016 ). If these estimates are similar among bacteria and also hold for REPIN insertions, then it is safe for REPINs to transpose into ∼4% of the genome.…”

Analysis of the association between polymorphisms in intergenic regions of Staphylococcus aureus genes involved in biofilm formation and periprosthetic joint infections

“…Studies in Salmonella Typhimurium, Pseudomonas aeruginosa, S. aureus, and Mycobacterium tuberculosis, have demonstrated that some genetic variations in IGRs are not neutral and mutations in IGRs may have an adaptative and evolutionary significant role in connection to bacterial pathogenesis, making its study necessary (Khademi et al, 2019;Osborne et al, 2009;Thorpe et al, 2016Thorpe et al, , 2017.…”

“…However, again, these epidemiological approaches do not consider the changes that take place in the IGRs as possible sources of variation that make some strains more likely to cause PJI. In this regard, recent studies have shown that changes in IGRs are not necessarily silent (Thorpe et al, 2016(Thorpe et al, , 2017. Ma et al observed an accumulation of SNPs in IGRs adjacent to genes encoding surface adhesins during the PJI outcome (Ma et al, 2021).…”