Official websites use. Share sensitive information only on official, secure websites. Address correspondence to Erick Denamur, erick. The rpoS gene codes for an alternative RNA polymerase sigma factor, which acts as a general regulator of the stress response. We studied the evolutionary history of rpoS and compared it to the phylogenetic history of bacteria in two collections of 82 human commensal and extraintestinal E.
These strains were representative of the phylogenetic diversity of the species and differed only by their storage conditions. In both collections, the phylogenetic histories of rpoS and of the strains were congruent, indicating that horizontal gene transfer had not occurred at the rpoS locus, and rpoS 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 in rpoS was typical of source-sink dynamics.
In conclusion, rpoS is rarely inactivated in natural E. Our data should encourage bacteriologists to freeze isolates immediately and to avoid the use of stab storage. The rates of recombination and mutation in a genome are critical issues because the diversity generated by these mechanisms is the substrate for selection. Some regions of bacterial chromosomes are more prone to mutation 1 — 4 or recombination 5 than other regions, due to physical or physiological constraints.
Then, selection can favor diversification, for example, that of cell surface proteins such as beta barrel porins 6 , and recombination events, which can restore particular functions, as in the case of the mismatch repair MR genes 7 , 8. There is growing evidence that selection also acts on central regulators to allow adaptation by rewiring of networks. In vitro experimental models of Escherichia coli evolution have shown that adaptation occurs through modifications of global regulatory networks, which are often interconnected 9 — These networks control DNA superhelicity 12 , the stringent response 12 , and the general stress response, via RpoS 9 , 10 , A particular case of in vitro evolution is the inactivation of crl which modulates the balance between different sigma factors in the RNA polymerase holoenzyme, particularly RpoS [ 16 — 18 ] or rpoS 19 — 21 , during stab storage of E.
