title: The rpoS gene is predominantly inactivated during laboratory storage and undergoes source-sink evolution in Escherichia coli species.
abstract: The rpoS gene codes for an alternative RNA polymerase sigma factor, which acts as a general regulator of the stress response. Inactivating alleles of rpoS in collections of natural Escherichia 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 of rpoS inactivation in nature. 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. 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 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. 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.
authors.affiliation: INSERM, IAME, UMR 1137, Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Bleibtreu
authors.affiliation: INSERM, IAME, UMR 1137, Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Clermont
authors.affiliation: UMR 7206, Eco-anthropologie et ethnobiologie, Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Darlu
authors.affiliation: INSERM, IAME, UMR 1137, Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.
authors.forename: Jérémy
authors.initials: J
authors.lastname: Glodt
authors.affiliation: INSERM, IAME, UMR 1137, Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France APHP, Hôpital Louis Mourier, Service de Microbiologie, Colombes, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Branger
authors.affiliation: INSERM, IAME, UMR 1137, Paris, France Université Paris Nord, IAME, UMR 1137, Sorbonne Paris Cité, Bobigny, France APHP, Hôpitaux Universitaires Paris Seine Saint-Denis, Site Avicenne, Bobigny, France.
authors.forename: Bertrand
authors.initials: B
authors.lastname: Picard
authors.affiliation: INSERM, IAME, UMR 1137, Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France erick.denamur@inserm.fr.
authors.forename: Erick
authors.initials: E
authors.lastname: Denamur
mesh_terms: D000483:Alleles; D001426:Bacterial Proteins / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics*; D019143:Evolution, Molecular; D006801:Humans; D007753:Laboratories; D059645:Mutation Rate; D020125:Mutation, Missense; D010802:Phylogeny; D017354:Point Mutation; D011309:Preservation, Biological; D012808:Sigma Factor / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria