Comparative Analyses of Selection Operating on Nontranslated Intergenic Regions of Diverse Bacterial Species

Abstract

Nontranslated intergenic regions (IGRs) compose 10-15% of bacterial genomes, and contain many regulatory elements with key functions. Despite this, there are few systematic studies on the strength and direction of selection operating on IGRs in bacteria using whole-genome sequence data sets. Here we exploit representative whole-genome data sets from six diverse bacterial species: ,, ,, , and We compare patterns of selection operating on IGRs using two independent methods: the proportion of singleton mutations and the / ratio, where is the number of intergenic SNPs per intergenic site. We find that the strength of purifying selection operating over all intergenic sites is consistently intermediate between that operating on synonymous and nonsynonymous sites. Ribosome binding sites and noncoding RNAs tend to be under stronger selective constraint than promoters and Rho-independent terminators. Strikingly, a clear signal of purifying selection remains even when all these major categories of regulatory elements are excluded, and this constraint is highest immediately upstream of genes. While a paucity of variation means that the data for are more equivocal than for the other species, we find strong evidence for positive selection within promoters of this species. This points to a key adaptive role for regulatory changes in this important pathogen. Our study underlines the feasibility and utility of gauging the selective forces operating on bacterial IGRs from whole-genome sequence data, and suggests that our current understanding of the functionality of these sequences is far from complete.

Long-term intrahost evolution of methicillin resistant Staphylococcus aureus among cystic fibrosis patients with respiratory carriage

“…Selection has historically been thought to act largely on amino acid changes in coding sequences; however, recently it has been shown that IGRs, which account for ~15% of microbial genomes, may also be acted upon by selection (Thorpe et al, 2017). Further, parallel evolution has also been observed among longitudinal intrahost samples of P. aeruginosa from CF infection (Khademi and Jelsbak, 2017).…”

The Distribution of Bacterial Doubling Times in the Wild

“…This implies, from the rate at which non-synonymous mutations accumulate relative to synonymous mutations, that δ n = 0.6. A recent analysis of intergenic regions in several species of bacteria has concluded that selection is weaker in intergenic regions than at non-synonymous sites, we therefore assume that δ i = 0.8 (30). Using these estimates suggests that selection leads us to an underestimate of the true mutation rate per year in the wild by ~27%; this in turn means we have underestimated the DT by ~27%, a relatively small effect.…”

Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia

“…Due to computational limitations (BEAST analyses), we necessarily took measures to limit our data set to <600 isolates. For countries with large numbers of available genomes, we implemented a subsampling strategy similar one previously described (Thorpe, Bayliss, Hurst, & Feil, ), whereby phylogenetic lineage diversity was captured thus minimizing the overrepresentation of clonal complexes (e.g., outbreaks): phylogenetic inference on all isolates available from a country was performed with Fasttree (Price, Dehal, & Arkin, ) and a random isolate was selected from each clade extending from n branches, where n was the desired number of isolates from the country. Numbers of isolates per country were selected based on the availability of appropriate genome sequence data as well as TB prevalence (Figure ) (World Health Organization, ).…”