The rpoS Gene Is Predominantly Inactivated during Laboratory Storage and Undergoes Source-Sink Evolution in Escherichia coli Species

TherpoS gene codes for an alternative RNA polymerase sigma factor, which acts as a general regulator of the stress response. Inactivating alleles ofrpoS in collections of naturalEscherichia coli isolates have been observed at very variable frequencies, from less than 1% to more than 70% of strains.rpoS is easily inactivated in nutrient-deprived environments such as stab storage, which makes it difficult to determine the true frequency ofrpoS inactivation in nature. We studied the evolutionary history ofrpoS and compared it to the phylogenetic history of bacteria in two collections of 82 human commensal and extraintestinalE. coli strains. These strains were representative of the phylogenetic diversity of the species and differed only by their storage conditions. In both collections, the phylogenetic histories ofrpoS and of the strains were congruent, indicating that horizontal gene transfer had not occurred at therpoS locus, andrpoS was under strong purifying selection, with a ratio of the nonsynonymous mutation rate (Ka) to the synonymous substitution rate (Ks) substantially smaller than 1. Stab storage was associated with a high frequency of inactivating alleles, whereas almost no amino acid sequence variation was observed in RpoS in the collection studied directly after isolation of the strains from the host. Furthermore, the accumulation of variations inrpoS was typical of source-sink dynamics. In conclusion,rpoS is rarely inactivated in naturalE. coli isolates within their mammalian hosts, probably because such strains rapidly become evolutionary dead ends. Our data should encourage bacteriologists to freeze isolates immediately and to avoid the use of stab storage.