title: Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates.
abstract: BACKGROUND
  Changes to mRNA lifetime adjust mRNA concentration, facilitating the adaptation of growth rate to changes in growth conditions. However, the mechanisms regulating mRNA lifetime are poorly understood at the genome-wide scale and have not been investigated in bacteria growing at different rates.
  
  
  RESULTS
  We used linear covariance models and the best model selected according to the Akaike information criterion to identify and rank intrinsic and extrinsic general transcript parameters correlated with mRNA lifetime, using mRNA half-life datasets for E. coli, obtained at four growth rates. The principal parameter correlated with mRNA stability was mRNA concentration, the mRNAs most concentrated in the cells being the least stable. However, sequence-related features (codon adaptation index (CAI), ORF length, GC content, polycistronic mRNA), gene function and essentiality also affected mRNA lifetime at all growth rates. We also identified sequence motifs within the 5'UTRs potentially related to mRNA stability. Growth rate-dependent effects were confined to particular functional categories (e.g. carbohydrate and nucleotide metabolism). Finally, mRNA stability was less strongly correlated with the amount of protein produced than mRNA concentration and CAI.
  
  
  CONCLUSIONS
  This study provides the most complete genome-wide analysis to date of the general factors correlated with mRNA lifetime in E. coli. We have generalized for the entire population of transcripts or excluded determinants previously defined as regulators of stability for some particular mRNAs and identified new, unexpected general indicators. These results will pave the way for discussions of the underlying mechanisms and their interaction with the growth physiology of bacteria.
authors.affiliation: Université de Toulouse; ISBP, INSA, UPS, INP; LISBP, 135, avenue de Rangueil, 31077, Toulouse cedex 4, France. thomas_esquerre@hotmail.com.|INRA, UMR792 Ingénierie des systèmes biologiques et des procédés, 31400, Toulouse, France. thomas_esquerre@hotmail.com.|CNRS, UMR5504, 31400, Toulouse, France. thomas_esquerre@hotmail.com.|Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062, Toulouse, France. thomas_esquerre@hotmail.com.
authors.forename: Thomas
authors.initials: T
authors.lastname: Esquerré
authors.affiliation: INRA, UR 875, F-31320, Castanet-Tolosan, France. annick.moisan@toulouse.inra.fr.
authors.forename: Annick
authors.initials: A
authors.lastname: Moisan
authors.affiliation: INRA, UR 875, F-31320, Castanet-Tolosan, France. helene.chiapello@toulouse.inra.fr.
authors.forename: Hélène
authors.initials: H
authors.lastname: Chiapello
authors.affiliation: Competence Center of Food and Fermentation Technologies, Akadeemia tee 15A, 12618, Tallinn, Estonia. liisa@tftak.eu.
authors.forename: Liisa
authors.initials: L
authors.lastname: Arike
authors.affiliation: Competence Center of Food and Fermentation Technologies, Akadeemia tee 15A, 12618, Tallinn, Estonia. raivo@tftak.eu.|Department of Chemistry, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia. raivo@tftak.eu.
authors.forename: Raivo
authors.initials: R
authors.lastname: Vilu
authors.affiliation: INRA, UR 875, F-31320, Castanet-Tolosan, France. cgaspin@toulouse.inra.fr.
authors.forename: Christine
authors.initials: C
authors.lastname: Gaspin
authors.affiliation: Université de Toulouse; ISBP, INSA, UPS, INP; LISBP, 135, avenue de Rangueil, 31077, Toulouse cedex 4, France. cocaign@insa-toulouse.fr.|INRA, UMR792 Ingénierie des systèmes biologiques et des procédés, 31400, Toulouse, France. cocaign@insa-toulouse.fr.|CNRS, UMR5504, 31400, Toulouse, France. cocaign@insa-toulouse.fr.
authors.forename: Muriel
authors.initials: M
authors.lastname: Cocaign-Bousquet
authors.affiliation: Université de Toulouse; ISBP, INSA, UPS, INP; LISBP, 135, avenue de Rangueil, 31077, Toulouse cedex 4, France. girbal@insa-toulouse.fr.|INRA, UMR792 Ingénierie des systèmes biologiques et des procédés, 31400, Toulouse, France. girbal@insa-toulouse.fr.|CNRS, UMR5504, 31400, Toulouse, France. girbal@insa-toulouse.fr.
authors.forename: Laurence
authors.initials: L
authors.lastname: Girbal
mesh_terms: D020121:5' Untranslated Regions; D001482:Base Composition; D001483:Base Sequence; D003062:Codon / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism; D016680:Genome, Bacterial; D006207:Half-Life; D008954:Models, Biological; D016366:Open Reading Frames / Q000235:genetics; D020871:RNA Stability; D012333:RNA, Messenger / Q000378:metabolism*
chemical_list: D020121:5' Untranslated Regions; D003062:Codon; D029968:Escherichia coli Proteins; D012333:RNA, Messenger