Simple sequence repeats together with mismatch repair deficiency can bias mutagenic pathways in Pseudomonas aeruginosa during chronic lung infection.

ABSTRACT

Pseudomonas aeruginosa is an opportunistic pathogen that chronically infects the airways of cystic fibrosis (CF) patients and undergoes a process of genetic adaptation based on mutagenesis. We evaluated the role of mononucleotide GC and AT simple sequence repeats (SSRs) in this adaptive process. An in silico survey of the genome sequences of 7 P. aeruginosa strains showed that mononucleotide GC SSRs but not AT SSRs were greatly under-represented in coding regions, suggesting a strong counterselection process for GC SSRs with lengths >5 bp but not for AT SSRs. A meta-analysis of published whole genome sequence data for a P. aeruginosa strain from a CF patient with chronic airway infection showed that GC SSRs but not AT SSRs were frequently mutated during the infection process through the insertion or deletion of one or more SSR subunits. The mutation tendency of GC SSRs was length-dependent and increased exponentially as a function of SSR length. When this strain naturally became a stable Mismatch Repair System (MRS)-deficient mutator, the degree of increase of GC SSRs mutations (5-fold) was much higher than that of other types of mutation (2.2-fold or less). Sequence analysis of several mutated genes reported for two different collections, both containing mutator and non-mutator strains of P. aeruginosa from CF chronic infections, showed that the proportion of GC SSR mutations was significantly higher in mutators than in non-mutators, whereas no such difference was observed for AT SSR mutations. Our findings, taken together, provide genome-scale evidences that under a MRS-deficient background, long GC SSRs are able to stochastically bias mutagenic pathways by making the genes in which they are harbored more prone to mutation. The combination of MRS deficiency and virulence-related genes that contain long GC SSRs is therefore a matter of concern in P. aeruginosa CF chronic infection.