Insights into transcriptional regulation and sigma competition from an equilibrium model of RNA polymerase binding to DNA.
To explore scenarios that permit transcription regulation by activator recruitment of RNA polymerase and sigma competition in vivo, we used an equilibrium model of RNA polymerase binding to DNA constrained by the values of total RNA polymerase (E) and sigma(70) per cell measured in this work. Our numbers of E and sigma(70) per cell, which are consistent with most of the primary data in the literature, suggest that in vivo (i) only a minor fraction of RNA polymerase (<20%) is involved in elongation and (ii) sigma(70) is in excess of total E. Modeling the partitioning of RNA polymerase between promoters, nonspecific DNA binding sites, and the cytoplasm suggested that even weak promoters will be saturated with Esigma(70) in vivo unless nonspecific DNA binding by Esigma(70) is rather significant. In addition, the model predicted that sigmas compete for binding to E only when their total number exceeds the total amount of RNA polymerase (excluding that involved in elongation) and that weak promoters will be preferentially subjected to sigma competition.
Grigorova
Irina L
IL
Graduate Group in Biophysics and Department of Microbiology, University of California-San Francisco, 600 16th Street, Genentech Hall, Box 2200, San Francisco, CA 94143, USA.
Phleger
Naum J
NJ
Mutalik
Vivek K
VK
Gross
Carol A
CA
D015153:Blotting, Western; D002460:Cell Line; D004247:DNA / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D005786:Gene Expression Regulation; D008954:Models, Biological; D011485:Protein Binding; D012808:Sigma Factor / Q000378:metabolism*; D014158:Transcription, Genetic
D012808:Sigma Factor; D004247:DNA; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases