title: Operator sequence alters gene expression independently of transcription factor occupancy in bacteria.
abstract: A canonical quantitative view of transcriptional regulation holds that the only role of operator sequence is to set the probability of transcription factor binding, with operator occupancy determining the level of gene expression. In this work, we test this idea by characterizing repression in vivo and the binding of RNA polymerase in vitro in experiments where operators of various sequences were placed either upstream or downstream from the promoter in Escherichia coli. Surprisingly, we find that operators with a weaker binding affinity can yield higher repression levels than stronger operators. Repressor bound to upstream operators modulates promoter escape, and the magnitude of this modulation is not correlated with the repressor-operator binding affinity. This suggests that operator sequences may modulate transcription by altering the nature of the interaction of the bound transcription factor with the transcriptional machinery, implying a new layer of sequence dependence that must be confronted in the quantitative understanding of gene expression.
authors: Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA.
authors: Hernan G
authors: HG
authors: Garcia
authors: Alvaro
authors: A
authors: Sanchez
authors: James Q
authors: JQ
authors: Boedicker
authors: Melisa
authors: M
authors: Osborne
authors: Jeff
authors: J
authors: Gelles
authors: Jane
authors: J
authors: Kondev
authors: Rob
authors: R
authors: Phillips
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence / Q000502:physiology; D001665:Binding Sites / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics*; D020868:Gene Silencing / Q000502:physiology; D007763:Lac Operon; D008954:Models, Biological; D009875:Operator Regions, Genetic / Q000235:genetics / Q000502:physiology*; D011485:Protein Binding / Q000502:physiology; D014157:Transcription Factors / Q000378:metabolism* / Q000502:physiology
chemical_list: D029968:Escherichia coli Proteins; D014157:Transcription Factors; D012321:DNA-Directed RNA Polymerases