Evidence for Diversifying Selection at the Pyoverdine Locus of Pseudomonas aeruginosa

Abstract

Pyoverdine is the primary siderophore of the gram-negative bacterium Pseudomonas aeruginosa. The pyoverdine region was recently identified as the most divergent locus alignable between strains in the P. aeruginosa genome. Here we report the nucleotide sequence and analysis of more than 50 kb in the pyoverdine region from nine strains of P. aeruginosa. There are three divergent sequence types in the pyoverdine region, which correspond to the three structural types of pyoverdine. The pyoverdine outer membrane receptor fpvA may be driving diversity at the locus: it is the most divergent alignable gene in the region, is the only gene that showed substantial intratype variation that did not appear to be generated by recombination, and shows evidence of positive selection. The hypothetical membrane protein PA2403 also shows evidence of positive selection; residues on one side of the membrane after protein folding are under positive selection. R, previously identified as a type IV strain, is clearly derived from a type III strain via a 3.4-kb deletion which removes one amino acid from the pyoverdine side chain peptide. This deletion represents a natural modification of the product of a nonribosomal peptide synthetase enzyme, whose consequences are predictive from the DNA sequence. There is also linkage disequilibrium between the pyoverdine region and pvdY, a pyoverdine gene separated by 30 kb from the pyoverdine region. The pyoverdine region shows evidence of horizontal transfer; we propose that some alleles in the region were introduced from other soil bacteria and have been subsequently maintained by diversifying selection.

The Crystal Structure of the Lipid II-degrading Bacteriocin Syringacin M Suggests Unexpected Evolutionary Relationships between Colicin M-like Bacteriocins

“…Interestingly and perhaps not unexpectedly, considering the data presented here, positive selection has also been detected in the outer membrane receptors of some colicin-like bacteriocins (50,51). The main documented evolutionary pathways of colicinlike bacteriocins are summarized in Fig.…”

Long-term social dynamics drive loss of function in pathogenic bacteria

“…The pyoverdine region is wellcharacterized (25), and the distribution of mutations across the pyoverdine genes in isolates from both collections was not random: two genes accumulated a higher number of mutations than expected by a random distribution. One is the σ-factor affecting pyoverdine biosynthesis, pvdS (pyoverdine sigma factor) [8.6× higher; P(X ≥ 14) ∼ poisson distribution (pois) (X; 1.63) < 0.001] (Fig.…”

“…Whether SNPs were synonymous or nonsynonymous was determined manually in ExPASy translate (web.expasy.org/translate). Reads from all isolates were mapped to four reference regions: the pvdS/pvdG/pvdL region containing the σ-factor controlling the main pyoverdine operon; the main pyoverdine operon containing 17 genes, which is highly diverse with three different variants characterized (25); the pyoverdine chromophore (pvc) region coding the chromophore biosynthesis gene cluster; and the gene for the alternative pyoverdine receptor fpvB (Datasets S3 and S4). For one patient with 18 isolates, the sequencing depth was only of sufficient quality to determine the clone type and not SNPs and indels between isolates.…”

Within-host competitive interactions as a mechanism for the maintenance of parasite diversity

“…Although most of this work has been elucidated in an in vitro setting, multiple competitive phenotypes can be isolated from a host population [78] or a host individual [79]. Moreover, receptors for these molecules demonstrate high levels of diversifying selection [80].…”