title: Reconciling molecular regulatory mechanisms with noise patterns of bacterial metabolic promoters in induced and repressed states.
abstract: Assessing gene expression noise in order to obtain mechanistic insights requires accurate quantification of gene expression on many individual cells over a large dynamic range. We used a unique method based on 2-photon fluorescence fluctuation microscopy to measure directly, at the single cell level and with single-molecule sensitivity, the absolute concentration of fluorescent proteins produced from the two Bacillus subtilis promoters that control the switch between glycolysis and gluconeogenesis. We quantified cell-to-cell variations in GFP concentrations in reporter strains grown on glucose or malate, including very weakly transcribed genes under strong catabolite repression. Results revealed strong transcriptional bursting, particularly for the glycolytic promoter. Noise pattern parameters of the two antagonistic promoters controlling the nutrient switch were differentially affected on glycolytic and gluconeogenic carbon sources, discriminating between the different mechanisms that control their activity. Our stochastic model for the transcription events reproduced the observed noise patterns and identified the critical parameters responsible for the differences in expression profiles of the promoters. The model also resolved apparent contradictions between in vitro operator affinity and in vivo repressor activity at these promoters. Finally, our results demonstrate that negative feedback is not noise-reducing in the case of strong transcriptional bursting.
authors.affiliation: Centre de Biochimie Structurale, Institut National pour la Santé et la Recherche Médicale U554, Centre National pour la Recherche Scientifique Unité Mixte de Recherche 5048, Université Montpellier 1 and 2, F-34090 Montpellier, France.
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Ferguson
authors.forename: Dominique
authors.initials: D
authors.lastname: Le Coq
authors.forename: Matthieu
authors.initials: M
authors.lastname: Jules
authors.forename: Stéphane
authors.initials: S
authors.lastname: Aymerich
authors.forename: Ovidiu
authors.initials: O
authors.lastname: Radulescu
authors.forename: Nathalie
authors.initials: N
authors.lastname: Declerck
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Royer
mesh_terms: D001412:Bacillus subtilis / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism*; D001426:Bacterial Proteins / Q000378:metabolism; D002244:Carbon / Q000378:metabolism / Q000494:pharmacology; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D012097:Repressor Proteins / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D012097:Repressor Proteins; D002244:Carbon