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. 2006 Apr 4;103(14):5332-7.
doi: 10.1073/pnas.0600828103. Epub 2006 Mar 27.

Insights into transcriptional regulation and sigma competition from an equilibrium model of RNA polymerase binding to DNA

Irina L Grigorova  1 , Naum J Phleger, Vivek K Mutalik, Carol A Gross
Affiliations

Insights into transcriptional regulation and sigma competition from an equilibrium model of RNA polymerase binding to DNA

Irina L Grigorova et al. Proc Natl Acad Sci U S A. .

Abstract

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.

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Conflict of interest statement

Conflict of interest statement: No conflicts declared.

Figures

Fig. 1.
Fig. 1.
Equilibrium model reaction channels. E can bind to either of two σ factors, σ70 and σA, to form Eσ70 or EσA, each having the same disassociation constant Kσ. Eσ70 can specifically bind to σ70 promoters, whereas EσA can specifically bind to σA promoters with the same disassociation constant KS. E, Eσ70, and EσA can bind to DNA nonspecifically with a disassociation constant KNS.
Fig. 2.
Fig. 2.
Free RNAP and promoter saturation vs. KS and KNS. Data were calculated according to the equilibrium model. See Materials and Methods and Supporting Text for a complete discussion of the binding constants and approximations used in the models. The number of total σA = 0; ET = 12,000 molecules per cell (the number of total RNAP that is not involved in elongation); total σ70 = 17,000 molecules per cell; σ70 promoters = 10,500; DNA binding sites = 11 × 106 (see Table 4, column 3). (A) Free RNAP as a function of KS and KNS. Solid lines are sets of KS (the dissociation constant for Eσ70 binding to promoters) and KNS (the dissociation constant of nonspecific binding between E or Eσ70 and the random DNA) for which free RNAP (free E plus free Eσ70) is 5%, 1%, or 0.1% of ET. Hatched area is the space of KS and KNS where free RNAP is <1%. The dashed line indicates where KS = KNS; everything to the right of this line is considered nonphysiological. (B) Fraction of σ70 promoters occupied by Eσ70 plotted vs. KS as a function of KNS.
Fig. 3.
Fig. 3.
Decrease in Eσ70 promoter occupancy induced by σ competition. Calculated according to the equilibrium model. See Materials and Methods and Supporting Text for a complete discussion of the binding constants and approximations used in the model. ET, the number of RNAP not included in elongation = 12,000 molecules per cell; σ70 promoters = 10,500; DNA binding sites = 11 × 106 (see Table 4, column 3). The concentration of free RNAP = free E + free Eσ70 is set at 1%. (A) Decrease in Eσ70 promoter occupancy calculated for various numbers of σ70 molecules per cell. Eσ70 promoter occupancy at σA = 0 is 48%. Dashed line: σ70 = 8,000 molecules per cell (KS = 1.19 × 10−7 M, KNS = 4.01 × 10−4 M). Competition starts when σT = σ70 +σA > ET = 12,000 molecules. Solid line: σ70 = 17,000 molecules per cell (KS = 2.76 × 10−7 M, KNS = 4.01 × 10−4 M). An arbitrary line of perfect competition is calculated for σ70 = 17,000 molecules per cell for a “symmetrical” case when EσA has the same number of specific binding sites and the same KS as Eσ70. (B) Decrease in Eσ70 promoter occupancy calculated for promoters with various binding affinities to Eσ70. σ70 is set at 17,000 molecules per cell. The occupancy of σ70 promoters with Eσ70 (at σA = 0) is set at 99% for “strong” promoters (KS = 2.07 × 10−9 M, KNS = 1.88 × 10−3 M), 48% for “intermediate” promoters (KS = 2.76 × 10−7 M, KNS = 4.01 × 10−4 M), and 5% for “weak” promoters (KS = 5.01 × 10−6 M, KNS = 2.42 × 10−4 M).
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References

    1. Gross C. A., Chan C., Dombroski A., Gruber T., Sharp M., Tupy J., Young B. Cold Spring Harbor Symp. Quant. Biol. 1998;63:141–155. - PubMed
    1. deHaseth P. L., Zupancic M. L., Record M. T., Jr. J. Bacteriol. 1998;180:3019–3025. - PMC - PubMed
    1. McClure W. R. Annu. Rev. Biochem. 1985;54:171–204. - PubMed
    1. Buc H., McClure W. R. Biochemistry. 1985;24:2712–2723. - PubMed
    1. Saecker R. M., Tsodikov O. V., McQuade K. L., Schlax P. E., Jr., Capp M. W., Record M. T., Jr. J. Mol. Biol. 2002;319:649–671. - PubMed

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