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Ross W, Gourse RL. Analysis of RNA polymerase-promoter complex formation. Methods 2008; 47:13-24. [PMID: 18952176 DOI: 10.1016/j.ymeth.2008.10.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2008] [Revised: 10/16/2008] [Accepted: 10/17/2008] [Indexed: 12/01/2022] Open
Abstract
Bacterial promoter identification and characterization is not as straightforward as one might presume. Promoters vary widely in their similarity to the consensus recognition element sequences, in their activities, and in their utilization of transcription factors, and multiple approaches often must be used to provide a framework for understanding promoter regulation. Characterization of RNA polymerase-promoter complex formation in the absence of additional regulatory factors (basal promoter function) can provide a basis for understanding the steps in transcription initiation that are ultimately targeted by nutritional or environmental factors. Promoters can be localized using genetic approaches in vivo, but the detailed properties of the RNAP-promoter complex are studied most productively in vitro. We first describe approaches for identification of bacterial promoters and transcription start sites in vivo, including promoter-reporter fusions and primer-extension. We then describe a number of methods for characterization of RNAP-promoter complexes in vitro, including in vitro transcription, gel mobility shift assays, footprinting, and filter binding. Utilization of these methods can result in determination of not only basal promoter strength but also the rates of transcription initiation complex formation and decay.
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Affiliation(s)
- Wilma Ross
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr., Madison, WI 53706, USA.
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2
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Abstract
Over the last two decades, a large amount of data on initiation of transcription by bacterial RNA polymerase (RNAP) has been obtained. However, a question of how the open complex is formed still remains open, and several qualitative hypotheses for opening of DNA by RNAP have been proposed. To provide a theoretical framework needed to analyze the assembled experimental data, we here develop the first quantitative model of the open complex formation by bacterial RNAP. We first show that a simple hypothesis (which might follow from recent bioinformatic and experimental results), by which promoter DNA is melted in one step through thermal fluctuations, is inconsistent with experimental data. We next consider a more complex two-step view of the open complex formation. According to this hypothesis, the transcription bubble is formed in the -10 region, and consequently extends to the transcription start site. We derive how the open complex formation rate depends on DNA duplex melting energy and on interaction energies of RNAP with promoter DNA in the closed and open complex. This relationship provides an explicit connection between transcription initiation rate and physical properties of the promoter sequence and promoter-RNAP interactions. We compare our model with both biochemical measurements and genomics data and report a very good agreement with the experiments, with no free parameters used in model testing. This agreement therefore strongly supports both the quantitative model that we propose and the qualitative hypothesis on which the model is based. From a practical point, our results allow efficient estimation of promoter kinetic parameters, as well as engineering of promoter sequences with the desired kinetic properties.
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Revyakin A, Ebright RH, Strick TR. Promoter unwinding and promoter clearance by RNA polymerase: detection by single-molecule DNA nanomanipulation. Proc Natl Acad Sci U S A 2004; 101:4776-80. [PMID: 15037753 PMCID: PMC387324 DOI: 10.1073/pnas.0307241101] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
By monitoring the end-to-end extension of a mechanically stretched, supercoiled, single DNA molecule, we have been able directly to observe the change in extension associated with unwinding of approximately one turn of promoter DNA by RNA polymerase (RNAP). By performing parallel experiments with negatively and positively supercoiled DNA, we have been able to deconvolute the change in extension caused by RNAP-dependent DNA unwinding (with approximately 1-bp resolution) and the change in extension caused by RNAP-dependent DNA compaction (with approximately 5-nm resolution). We have used this approach to quantify the extent of unwinding and compaction, the kinetics of unwinding and compaction, and effects of supercoiling, sequence, ppGpp, and nucleotides. We also have used this approach to detect promoter clearance and promoter recycling by successive RNAP molecules. We find that the rate of formation and the stability of the unwound complex depend profoundly on supercoiling and that supercoiling exerts its effects mechanically (through torque), and not structurally (through the number and position of supercoils). The approach should permit analysis of other nucleic-acid-processing factors that cause changes in DNA twist and/or DNA compaction.
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Affiliation(s)
- Andrey Revyakin
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry, Rutgers, The State University of New Jersey, Piscataway NJ 08854, USA
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Bordes P, Conter A, Morales V, Bouvier J, Kolb A, Gutierrez C. DNA supercoiling contributes to disconnect sigmaS accumulation from sigmaS-dependent transcription in Escherichia coli. Mol Microbiol 2003; 48:561-71. [PMID: 12675812 DOI: 10.1046/j.1365-2958.2003.03461.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The sigmaS subunit of RNA polymerase is a key regulator of Escherichia coli transcription in stress conditions. sigmaS accumulates in cells subjected to stresses such as an osmotic upshift or the entry into stationary phase. We show here that, at elevated osmolarity, sigmaS accumulates long before the beginning of the sigmaS-dependent induction of osmEp, one of its target promoters. A combination of in vivo and in vitro evidence indicates that a high level of DNA negative supercoiling inhibits transcription by EsigmaS. The variations in superhelical densities occurring as a function of growth conditions can modulate transcription of a subset of sigmaS targets and thereby contribute to the temporal disconnection between the accumulation of sigmaS and sigmaS-driven transcription. We propose that, in stress conditions leading to the accumulation of sigmaS without lowering the growth rate, the level of DNA supercoiling acts as a checkpoint that delays the shift from the major (Esigma70) to the general stress (EsigmaS) transcriptional machinery, retarding the induction of a subset of the sigmaS regulon until the conditions become unfavourable enough to cause entry into stationary phase.
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Affiliation(s)
- Patricia Bordes
- Laboratoire de Microbiologie et Génétique Moléculaire, UMR 5100 CNRS - Université Toulouse III, France
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Bumann D. In vivo visualization of bacterial colonization, antigen expression, and specific T-cell induction following oral administration of live recombinant Salmonella enterica serovar Typhimurium. Infect Immun 2001; 69:4618-26. [PMID: 11402006 PMCID: PMC98539 DOI: 10.1128/iai.69.7.4618-4626.2001] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Live attenuated Salmonella strains that express a foreign antigen are promising oral vaccine candidates. Numerous genetic modifications have been empirically tested, but their effects on immunogenicity are difficult to interpret since important in vivo properties of recombinant Salmonella strains such as antigen expression and localization are incompletely characterized and the crucial early inductive events of an immune response to the foreign antigen are not fully understood. Here, methods were developed to directly localize and quantitate the in situ expression of an ovalbumin model antigen in recombinant Salmonella enterica serovar Typhimurium using two-color flow cytometry and confocal microscopy. In parallel, the in vivo activation, blast formation, and division of ovalbumin-specific CD4(+) T cells were followed using a well-characterized transgenic T-cell receptor mouse model. This combined approach revealed a biphasic induction of ovalbumin-specific T cells in the Peyer's patches that followed the local ovalbumin expression of orally administered recombinant Salmonella cells in a dose- and time-dependent manner. Interestingly, intact Salmonella cells and cognate T cells seemed to remain in separate tissue compartments throughout induction, suggesting a transport of killed Salmonella cells from the colonized subepithelial dome area to the interfollicular inductive sites. The findings of this study will help to rationally optimize recombinant Salmonella strains as efficacious live antigen carriers for oral vaccination.
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Affiliation(s)
- D Bumann
- Abteilung Molekulare Biologie, Max-Planck-Institut für Infektionsbiologie, D-10117 Berlin, Germany.
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McKane M, Gussin GN. Changes in the 17 bp spacer in the P(R) promoter of bacteriophage lambda affect steps in open complex formation that precede DNA strand separation. J Mol Biol 2000; 299:337-49. [PMID: 10860742 DOI: 10.1006/jmbi.2000.3757] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tau plots and temperature-shift experiments were used to determine which step in the formation of transcriptionally-competent open complexes is affected by changing the length of the 17 bp spacer separating the -10 and -35 consensus regions of the P(R) promoter of bacteriophage lambda. Abortive initiation assays at 37 degrees C indicate that the primary effect of insertion of a base-pair, thereby increasing spacer length to 18 bp, is a decrease in k(f), the rate constant for conversion from closed (RP(c)) to open (RP(o)) complexes, by approximately a factor of 4. The mutation did not significantly affect K(B), the equilibrium constant for formation of closed complexes, and decreased K(B)k(f) by a factor of 3. Deletion of a bp to create a 16 bp spacer had a much greater effect, decreasing the measured value of k(f) by a factor of about 25 to 30, and K(B)k(f) by a factor of 7 to 8. When the values of the parameters for the deletion mutant were corrected for incomplete occupancy of RP(o) at equilibrium, the effects of the deletion were even greater. In particular, the corrected value of K(B)k(f) was about 15 times lower than the corresponding value for two promoters with wild-type spacing. Based on temperature shift experiments, the changes in spacer length did not affect the equilibrium at 20 degrees C between RP(i), a stable intermediate in which DNA strands are not separated, and RP(o). Although differential sensitivity of single-stranded bases to KMnO(4) indicated that in about 20% of the open complexes at 20 degrees C the DNA strands are not fully separated (RP(o1)), the distribution between these complexes and RP(o2) (DNA strands fully separated) was also not affected significantly by changes in spacer length. Thus, changes in spacer length primarily affect k(2), the rate constant for conversion of RP(c) to RP(i), which corresponds to a nucleation of DNA strand-separation. Application of published data and/or algorithms for determining effects of nucleotide sequence on twist angle or rise at individual bp steps does not provide a simple explanation of the difference in promoter strength between P(R) derivatives with 16 bp spacing and those with 18 bp spacing.
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MESH Headings
- Algorithms
- Bacteriophage lambda/genetics
- Base Pairing/genetics
- Base Sequence
- DNA Footprinting
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- DNA, Viral/chemistry
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Genes, Viral/genetics
- Heparin/pharmacology
- Isomerism
- Kinetics
- Models, Genetic
- Mutagenesis, Insertional/genetics
- Nucleic Acid Denaturation/genetics
- Potassium Permanganate/metabolism
- Promoter Regions, Genetic/genetics
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- Reproducibility of Results
- Sequence Deletion/genetics
- Temperature
- Templates, Genetic
- Thermodynamics
- Transcription, Genetic/drug effects
- Transcription, Genetic/genetics
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Affiliation(s)
- M McKane
- Department of Biological Sciences, University of Iowa, Iowa City, IA, 52246, USA
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Kahn JD. Topological effects of the TATA box binding protein on minicircle DNA and a possible thermodynamic linkage to chromatin remodeling. Biochemistry 2000; 39:3520-4. [PMID: 10736150 DOI: 10.1021/bi992263f] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA ring closure experiments on short restriction fragments ( approximately 160 bp) bound by the TATA box binding protein (TBP) have demonstrated the formation of negative topoisomers, consistent with crystallographically observed TBP-induced DNA untwisting but in contrast to most previous results on topological effects in plasmid DNA. The difference may be due to the high free energy cost of substantial writhe in minicircles. A speculative mechanism for the loss of TBP-induced writhe suggests that TBP is capable of inducing DeltaTw between 0 and -0.3 in minicircles, via loss of out-of-plane bending upon retraction of intercalating Phe stirrups, and that TBP can thus act as a "supercoil shock absorber". The proposed biological relevance of these observations is that they may model the behavior of DNA in constrained chromatin environments. Irrespective of the detailed mechanism of TBP-induced supercoiling, its existence suggests that chromatin remodeling and enhanced TBP binding are thermodynamically linked. Remodeling ATPases or histone acetylases release some of the negative supercoiling previously restrained by the nucleosome. When TBP takes up the supercoiling, its binding should be enhanced transiently until the unrestrained supercoiling is removed by diffusion or topoisomerases. The effect is predicted to be independent of local remodeling-induced changes in TATA box accessibility.
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Affiliation(s)
- J D Kahn
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742-2021, USA.
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deHaseth PL, Zupancic ML, Record MT. RNA polymerase-promoter interactions: the comings and goings of RNA polymerase. J Bacteriol 1998; 180:3019-25. [PMID: 9620948 PMCID: PMC107799 DOI: 10.1128/jb.180.12.3019-3025.1998] [Citation(s) in RCA: 234] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- P L deHaseth
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106-4935, USA.
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Dai X, Greizerstein MB, Nadas-Chinni K, Rothman-Denes LB. Supercoil-induced extrusion of a regulatory DNA hairpin. Proc Natl Acad Sci U S A 1997; 94:2174-9. [PMID: 9122167 PMCID: PMC20060 DOI: 10.1073/pnas.94.6.2174] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Bacteriophage N4 virion RNA polymerase (N4 vRNAP) promoters contain inverted repeats, which form a 5- to 7-base-pair stem, 3-base loop hairpin that is required for vRNAP recognition. We show that, contrary to certain theoretical predictions, hairpin extrusion can occur at physiological superhelical densities in a Mg2+-dependent manner. Specific sequences on the template strand are required for hairpin extrusion. These sequences define stable DNA hairpins that are relatively unreactive to single strand-specific probes. In addition, a specific stable hairpin-inducing sequence can regulate transcription in vivo. Thus, a DNA structure, in its natural environment, is involved in transcriptional regulation.
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Affiliation(s)
- X Dai
- Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637, USA
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deHaseth PL, Helmann JD. Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA. Mol Microbiol 1995; 16:817-24. [PMID: 7476180 DOI: 10.1111/j.1365-2958.1995.tb02309.x] [Citation(s) in RCA: 135] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Escherichia coli RNA polymerase is able to site-specifically melt 12 bp of promoter DNA at temperatures far below those normally associated with DNA melting. Here we consider several models to explain how RNA polymerase destabilizes duplex DNA. One popular model proposes that upon binding to the promoter, RNA polymerase untwists the spacer DNA between the -10 and -35 regions, which results in a destabilization of the -10 region at a TA base step where melting initiates. Promoter untwisting may result, in part, from extensive wrapping of the DNA around RNA polymerase. Formation of the strand-separated open complex appears to be facilitated by specific protein-DNA interactions which occur predominantly on the non-template strand. Recent evidence suggests that these include important contacts with sigma factor region 2.3, which we propose binds the displaced single strand of DNA.
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Affiliation(s)
- P L deHaseth
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106-4935, USA
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