1
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Clamp Interactions with +3/+6 Duplex and Upstream-to-Downstream Allosteric Effects in Late Steps of Forming a Stable RNA Polymerase-Promoter Open Complex. J Mol Biol 2023; 435:167990. [PMID: 36736885 DOI: 10.1016/j.jmb.2023.167990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/04/2023]
Abstract
Stable 37 °C open complexes (OC) of E. coli RNA polymerase (RNAP) at λPR and T7A1 promoters form at similar rates but have very different lifetimes. To understand the downstream interactions responsible for OC lifetime, how promoter sequence directs them and when they form, we report lifetimes of stable OC and unstable late (I2) intermediates for promoters with different combinations of λPR (L) and T7A1 (T) discriminators, core promoters and UP elements. I2 lifetimes are similarly short, while stable OC lifetimes differ greatly, determined largely by the discriminator and modulated by core-promoter and UP elements. The free energy change ΔG3o for I2 → stable OC is approximately -4 kcal more favorable for L-discriminator than for T-discriminator promoters. Downstream-truncation at +6 (DT+6) greatly destabilizes OC at L-discriminator but not T-discriminator promoters, making all ΔG3o values similar (approximately -4 kcal). Urea reduces OC lifetime greatly by affecting ΔG3o. We deduce that urea acts by disfavoring coupled folding of key elements of the β'-clamp, that I2 is an open-clamp OC, and that clamp-closing in I2 → stable OC involves coupled folding. Differences in ΔG3o between downstream-truncated and full-length promoters yield contributions to ΔG3o from interactions with downstream mobile elements (DME) including β-lobe and β'-jaw, more favorable for L-discriminator than for T-discriminator promoters. We deduce how competition between far-downstream DNA and σ70 region 1.1 affects ΔG3o values. We discuss variant-specific ΔG3o contributions in terms of the allosteric network by which differences in discriminator and -10 sequence are sensed and transmitted downstream to affect DME-duplex interactions in I2 → stable OC.
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2
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Structural origins of Escherichia coli RNA polymerase open promoter complex stability. Proc Natl Acad Sci U S A 2021; 118:2112877118. [PMID: 34599106 DOI: 10.1073/pnas.2112877118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2021] [Indexed: 11/18/2022] Open
Abstract
The first step in gene expression in all organisms requires opening the DNA duplex to expose one strand for templated RNA synthesis. In Escherichia coli, promoter DNA sequence fundamentally determines how fast the RNA polymerase (RNAP) forms "open" complexes (RPo), whether RPo persists for seconds or hours, and how quickly RNAP transitions from initiation to elongation. These rates control promoter strength in vivo, but their structural origins remain largely unknown. Here, we use cryoelectron microscopy to determine the structures of RPo formed de novo at three promoters with widely differing lifetimes at 37 °C: λPR (t1/2 ∼10 h), T7A1 (t1/2 ∼4 min), and a point mutant in λPR (λPR-5C) (t1/2 ∼2 h). Two distinct RPo conformers are populated at λPR, likely representing productive and unproductive forms of RPo observed in solution studies. We find that changes in the sequence and length of DNA in the transcription bubble just upstream of the start site (+1) globally alter the network of DNA-RNAP interactions, base stacking, and strand order in the single-stranded DNA of the transcription bubble; these differences propagate beyond the bubble to upstream and downstream DNA. After expanding the transcription bubble by one base (T7A1), the nontemplate strand "scrunches" inside the active site cleft; the template strand bulges outside the cleft at the upstream edge of the bubble. The structures illustrate how limited sequence changes trigger global alterations in the transcription bubble that modulate the RPo lifetime and affect the subsequent steps of the transcription cycle.
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3
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The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation. J Bacteriol 2021; 203:JB.00512-20. [PMID: 33139481 DOI: 10.1128/jb.00512-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The fitness of an individual bacterial cell is highly dependent upon the temporal tuning of gene expression levels when subjected to different environmental cues. Kinetic regulation of transcription initiation is a key step in modulating the levels of transcribed genes to promote bacterial survival. The initiation phase encompasses the binding of RNA polymerase (RNAP) to promoter DNA and a series of coupled protein-DNA conformational changes prior to entry into processive elongation. The time required to complete the initiation phase can vary by orders of magnitude and is ultimately dictated by the DNA sequence of the promoter. In this review, we aim to provide the required background to understand how promoter sequence motifs may affect initiation kinetics during promoter recognition and binding, subsequent conformational changes which lead to DNA opening around the transcription start site, and promoter escape. By calculating the steady-state flux of RNA production as a function of these effects, we illustrate that the presence/absence of a consensus promoter motif cannot be used in isolation to make conclusions regarding promoter strength. Instead, the entire series of linked, sequence-dependent structural transitions must be considered holistically. Finally, we describe how individual transcription factors take advantage of the broad distribution of sequence-dependent basal kinetics to either increase or decrease RNA flux.
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4
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Mazumder A, Kapanidis AN. Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms. J Mol Biol 2019; 431:3947-3959. [PMID: 31082441 PMCID: PMC7057261 DOI: 10.1016/j.jmb.2019.04.046] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/26/2019] [Accepted: 04/29/2019] [Indexed: 11/23/2022]
Abstract
Prokaryotic transcription is one of the most studied biological systems, with relevance to many fields including the development and use of antibiotics, the construction of synthetic gene networks, and the development of many cutting-edge methodologies. Here, we discuss recent structural, biochemical, and single-molecule biophysical studies targeting the mechanisms of transcription initiation in bacteria, including the formation of the open complex, the reaction of initial transcription, and the promoter escape step that leads to elongation. We specifically focus on the mechanisms employed by the RNA polymerase holoenzyme with the housekeeping sigma factor σ70. The recent progress provides answers to long-held questions, identifies intriguing new behaviours, and opens up fresh questions for the field of transcription.
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Affiliation(s)
- Abhishek Mazumder
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.
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5
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Real-time observation of polymerase-promoter contact remodeling during transcription initiation. Nat Commun 2017; 8:1178. [PMID: 29079833 PMCID: PMC5660091 DOI: 10.1038/s41467-017-01041-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/11/2017] [Indexed: 01/22/2023] Open
Abstract
Critical contacts made between the RNA polymerase (RNAP) holoenzyme and promoter DNA modulate not only the strength of promoter binding, but also the frequency and timing of promoter escape during transcription. Here, we describe a single-molecule optical-trapping assay to study transcription initiation in real time, and use it to map contacts formed between σ70 RNAP holoenzyme from E. coli and the T7A1 promoter, as well as to observe the remodeling of those contacts during the transition to the elongation phase. The strong binding contacts identified in certain well-known promoter regions, such as the −35 and −10 elements, do not necessarily coincide with the most highly conserved portions of these sequences. Strong contacts formed within the spacer region (−10 to −35) and with the −10 element are essential for initiation and promoter escape, respectively, and the holoenzyme releases contacts with promoter elements in a non-sequential fashion during escape. Contacts between RNA polymerase and promoter DNA modulate the strength of binding and the frequency of promoter escape during transcription. Here, the authors describe a single molecule optical-trapping assay to study transcription initiation and observe the dynamic remodeling of enzyme contacts in real time.
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6
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TraR directly regulates transcription initiation by mimicking the combined effects of the global regulators DksA and ppGpp. Proc Natl Acad Sci U S A 2017; 114:E5539-E5548. [PMID: 28652326 PMCID: PMC5514744 DOI: 10.1073/pnas.1704105114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Escherichia coli F element-encoded protein TraR is a distant homolog of the chromosome-encoded transcription factor DksA. Here we address the mechanism by which TraR acts as a global regulator, inhibiting some promoters and activating others. We show that TraR regulates transcription directly in vitro by binding to the secondary channel of RNA polymerase (RNAP) using interactions similar, but not identical, to those of DksA. Even though it binds to RNAP with only slightly higher affinity than DksA and is only half the size of DksA, TraR by itself inhibits transcription as strongly as DksA and ppGpp combined and much more than DksA alone. Furthermore, unlike DksA, TraR activates transcription even in the absence of ppGpp. TraR lacks the residues that interact with ppGpp in DksA, and TraR binding to RNAP uses the residues in the β' rim helices that contribute to the ppGpp binding site in the DksA-ppGpp-RNAP complex. Thus, unlike DksA, TraR does not bind ppGpp. We propose a model in which TraR mimics the effects of DksA and ppGpp together by binding directly to the region of the RNAP secondary channel that otherwise binds ppGpp, and its N-terminal region, like the coiled-coil tip of DksA, engages the active-site region of the enzyme and affects transcription allosterically. These data provide insights into the function not only of TraR but also of an evolutionarily widespread and diverse family of TraR-like proteins encoded by bacteria, as well as bacteriophages and other extrachromosomal elements.
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7
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Abstract
Background Transcription initiation is in bacteria exhibited by different σ factors, most of which fall within σ70 family. This family is diverse, ranging from the housekeeping Group I (RpoDs), to Group IV (ECF) σ factors, that transcribe smaller regulons under more stringent conditions. RpoDs employ a kinetic mix-and-match mechanism, where promoter elements complement each other binding strengths in achieving sufficient transcription activity. On the other hand, it is assumed that ECF σs, which are the most distant from the housekeeping σ factors, cannot exhibit mix-and-matching. However, mix-and-matching for ECF σ factors was not quantitatively checked before, and recent results show a much larger flexibility in the promoter recognition by the members of this group. Results To this end, we quantitatively investigate mix-and-matching in two canonical ECF σ family members (σE and σW), for which we use a biophysics based model of transcription initiation. For σE, we perform a separate analysis for in-vitro active and in-vitro inactive promoters, which allows us investigating how mix-and-matching depends on the external factors that may control transcription activity in the in-vitro inactive set. We show that the promoter elements of canonical ECF σs significantly complement each other strengths, where such mix-and-matching is in the in-vitro active set even stronger compared to the correlations observed for the housekeeping σs. This complementation however significantly decreases for the in-vitro inactive set, which we propose is due to mix-and-matching with regulatory sequences outside of the canonical promoter elements. In line with this proposition, we show that a conserved spacer element, which appears in the in-vitro inactive promoter set, significantly increases the promoter element complementation. While RpoD promoter elements mix-and-match to achieve sufficient total transcription activity, for σE they complement each other to achieve sufficiently strong total binding affinity, which we relate to differences in physiological responses between the two groups of σ factors. Conclusion Despite a common notion that smaller σ factor specificity leads to a larger mix-and-matching, we here obtain a larger promoter element complementation for σE compared to RpoDs. Finally, to explain this finding, we propose a simple model which relates the size of σ factor regulon with the extent of mix-and-matching, based on an assumption of a selection pressure on promoters that are near the non-specific binding boundary to remain functional. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0865-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jelena Guzina
- Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia.,Multidisciplinary PhD program in Biophysics, University of Belgrade, Belgrade, Serbia
| | - Marko Djordjevic
- Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia.
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8
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Ross W, Sanchez-Vazquez P, Chen AY, Lee JH, Burgos HL, Gourse RL. ppGpp Binding to a Site at the RNAP-DksA Interface Accounts for Its Dramatic Effects on Transcription Initiation during the Stringent Response. Mol Cell 2016; 62:811-823. [PMID: 27237053 DOI: 10.1016/j.molcel.2016.04.029] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/06/2016] [Accepted: 04/22/2016] [Indexed: 11/30/2022]
Abstract
Throughout the bacterial domain, the alarmone ppGpp dramatically reprograms transcription following nutrient limitation. This "stringent response" is critical for survival and antibiotic tolerance and is a model for transcriptional regulation by small ligands. We report that ppGpp binds to two distinct sites 60 Å apart on E. coli RNA polymerase (RNAP), one characterized previously (site 1) and a second identified here at an interface of RNAP and the transcription factor DksA (site 2). The location and unusual tripartite nature of site 2 account for the DksA-ppGpp synergism and suggest mechanisms for ppGpp enhancement of DksA's effects on RNAP. Site 2 binding results in the majority of ppGpp's effects on transcription initiation in vitro and in vivo, and strains lacking site 2 are severely impaired for growth following nutritional shifts. Filling of the two sites at different ppGpp concentrations would expand the dynamic range of cellular responses to changes in ppGpp levels.
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Affiliation(s)
- Wilma Ross
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Patricia Sanchez-Vazquez
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Albert Y Chen
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Jeong-Hyun Lee
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Hector L Burgos
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Richard L Gourse
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA.
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9
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Sreenivasan R, Heitkamp S, Chhabra M, Saecker R, Lingeman E, Poulos M, McCaslin D, Capp MW, Artsimovitch I, Record MT. Fluorescence Resonance Energy Transfer Characterization of DNA Wrapping in Closed and Open Escherichia coli RNA Polymerase-λP(R) Promoter Complexes. Biochemistry 2016; 55:2174-86. [PMID: 26998673 DOI: 10.1021/acs.biochem.6b00125] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Initial recognition of promoter DNA by RNA polymerase (RNAP) is proposed to trigger a series of conformational changes beginning with bending and wrapping of the 40-50 bp of DNA immediately upstream of the -35 region. Kinetic studies demonstrated that the presence of upstream DNA facilitates bending and entry of the downstream duplex (to +20) into the active site cleft to form an advanced closed complex (CC), prior to melting of ∼13 bp (-11 to +2), including the transcription start site (+1). Atomic force microscopy and footprinting revealed that the stable open complex (OC) is also highly wrapped (-60 to +20). To test the proposed bent-wrapped model of duplex DNA in an advanced RNAP-λP(R) CC and compare wrapping in the CC and OC, we use fluorescence resonance energy transfer (FRET) between cyanine dyes at far-upstream (-100) and downstream (+14) positions of promoter DNA. Similarly large intrinsic FRET efficiencies are observed for the CC (0.30 ± 0.07) and the OC (0.32 ± 0.11) for both probe orientations. Fluorescence enhancements at +14 are observed in the single-dye-labeled CC and OC. These results demonstrate that upstream DNA is extensively wrapped and the start site region is bent into the cleft in the advanced CC, reducing the distance between positions -100 and +14 on promoter DNA from >300 to <100 Å. The proximity of upstream DNA to the downstream cleft in the advanced CC is consistent with the proposed mechanism for facilitation of OC formation by upstream DNA.
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Affiliation(s)
- Raashi Sreenivasan
- Biophysics Program, ‡Department of Biochemistry, and §Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Microbiology and ⊥Center for RNA Biology, The Ohio State University , Columbus, Ohio 43210, United States
| | - Sara Heitkamp
- Biophysics Program, ‡Department of Biochemistry, and §Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Microbiology and ⊥Center for RNA Biology, The Ohio State University , Columbus, Ohio 43210, United States
| | - Munish Chhabra
- Biophysics Program, ‡Department of Biochemistry, and §Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Microbiology and ⊥Center for RNA Biology, The Ohio State University , Columbus, Ohio 43210, United States
| | - Ruth Saecker
- Biophysics Program, ‡Department of Biochemistry, and §Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Microbiology and ⊥Center for RNA Biology, The Ohio State University , Columbus, Ohio 43210, United States
| | - Emily Lingeman
- Biophysics Program, ‡Department of Biochemistry, and §Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Microbiology and ⊥Center for RNA Biology, The Ohio State University , Columbus, Ohio 43210, United States
| | - Mikaela Poulos
- Biophysics Program, ‡Department of Biochemistry, and §Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Microbiology and ⊥Center for RNA Biology, The Ohio State University , Columbus, Ohio 43210, United States
| | - Darrell McCaslin
- Biophysics Program, ‡Department of Biochemistry, and §Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Microbiology and ⊥Center for RNA Biology, The Ohio State University , Columbus, Ohio 43210, United States
| | - Michael W Capp
- Biophysics Program, ‡Department of Biochemistry, and §Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Microbiology and ⊥Center for RNA Biology, The Ohio State University , Columbus, Ohio 43210, United States
| | - Irina Artsimovitch
- Biophysics Program, ‡Department of Biochemistry, and §Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Microbiology and ⊥Center for RNA Biology, The Ohio State University , Columbus, Ohio 43210, United States
| | - M Thomas Record
- Biophysics Program, ‡Department of Biochemistry, and §Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Microbiology and ⊥Center for RNA Biology, The Ohio State University , Columbus, Ohio 43210, United States
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10
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E. coli RNA Polymerase Determinants of Open Complex Lifetime and Structure. J Mol Biol 2015; 427:2435-2450. [PMID: 26055538 DOI: 10.1016/j.jmb.2015.05.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/29/2015] [Accepted: 05/29/2015] [Indexed: 11/24/2022]
Abstract
In transcription initiation by Escherichia coli RNA polymerase (RNAP), initial binding to promoter DNA triggers large conformational changes, bending downstream duplex DNA into the RNAP cleft and opening 13bp to form a short-lived open intermediate (I2). Subsequent conformational changes increase lifetimes of λPR and T7A1 open complexes (OCs) by >10(5)-fold and >10(2)-fold, respectively. OC lifetime is a target for regulation. To characterize late conformational changes, we determine effects on OC dissociation kinetics of deletions in RNAP mobile elements σ(70) region 1.1 (σ1.1), β' jaw and β' sequence insertion 3 (SI3). In very stable OC formed by the wild type WT RNAP with λPR (RPO) and by Δσ1.1 RNAP with λPR or T7A1, we conclude that downstream duplex DNA is bound to the jaw in an assembly with SI3, and bases -4 to +2 of the nontemplate strand discriminator region are stably bound in a positively charged track in the cleft. We deduce that polyanionic σ1.1 destabilizes OC by competing for binding sites in the cleft and on the jaw with the polyanionic discriminator strand and downstream duplex, respectively. Examples of σ1.1-destabilized OC are the final T7A1 OC and the λPR I3 intermediate OC. Deleting σ1.1 and either β' jaw or SI3 equalizes OC lifetimes for λPR and T7A1. DNA closing rates are similar for both promoters and all RNAP variants. We conclude that late conformational changes that stabilize OC, like early ones that bend the duplex into the cleft, are primary targets of regulation, while the intrinsic DNA opening/closing step is not.
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11
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Abstract
Transcription initiation is a highly regulated step of gene expression. Here, we discuss the series of large conformational changes set in motion by initial specific binding of bacterial RNA polymerase (RNAP) to promoter DNA and their relevance for regulation. Bending and wrapping of the upstream duplex facilitates bending of the downstream duplex into the active site cleft, nucleating opening of 13 bp in the cleft. The rate-determining opening step, driven by binding free energy, forms an unstable open complex, probably with the template strand in the active site. At some promoters, this initial open complex is greatly stabilized by rearrangements of the discriminator region between the -10 element and +1 base of the nontemplate strand and of mobile in-cleft and downstream elements of RNAP. The rate of open complex formation is regulated by effects on the rapidly-reversible steps preceding DNA opening, while open complex lifetime is regulated by effects on the stabilization of the initial open complex. Intrinsic DNA opening-closing appears less regulated. This noncovalent mechanism and its regulation exhibit many analogies to mechanisms of enzyme catalysis.
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12
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Kästle B, Geiger T, Gratani FL, Reisinger R, Goerke C, Borisova M, Mayer C, Wolz C. rRNA regulation during growth and under stringent conditions in Staphylococcus aureus. Environ Microbiol 2015; 17:4394-405. [PMID: 25845735 DOI: 10.1111/1462-2920.12867] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 03/31/2015] [Indexed: 12/01/2022]
Abstract
The control of rRNA synthesis and, thereby, translation is vital for adapting to changing environmental conditions. The decrease of rRNA is a common feature of the stringent response, which is elicited by the rapid synthesis of (p)ppGpp. Here we analysed the properties and regulation of one representative rRNA operon of Staphylococcus aureus under stringent conditions and during growth. The promoters, P1 and P2, are severely downregulated at low intracellular guanosine triphosphate (GTP) concentrations either imposed by stringent conditions or in a guanine auxotroph guaBA mutant. In a (p)ppGpp(0) strain, the GTP level increased under stringent conditions, and rRNA transcription was upregulated. The correlation of the intracellular GTP levels and rRNA promoter activity could be linked to GTP nucleotides in the initiation region of both promoters at positions between +1 and +4. This indicates that not only transcriptional initiation, but also the first steps of elongation, requires high concentrations of free nucleotides. However, the severe downregulation of rRNA in post-exponential growth phase is independent of (p)ppGpp, the composition of the initiation region and the intracellular nucleotide pool. In summary, rRNA transcription in S. aureus is only partially and presumably indirectly controlled by (p)ppGpp.
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Affiliation(s)
- Benjamin Kästle
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Elfriede-Aulhorn-Strasse 6, Tübingen, 72076, Germany
| | - Tobias Geiger
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Elfriede-Aulhorn-Strasse 6, Tübingen, 72076, Germany
| | - Fabio Lino Gratani
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Elfriede-Aulhorn-Strasse 6, Tübingen, 72076, Germany
| | - Rudolf Reisinger
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Elfriede-Aulhorn-Strasse 6, Tübingen, 72076, Germany
| | - Christiane Goerke
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Elfriede-Aulhorn-Strasse 6, Tübingen, 72076, Germany
| | - Marina Borisova
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Elfriede-Aulhorn-Strasse 6, Tübingen, 72076, Germany
| | - Christoph Mayer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Elfriede-Aulhorn-Strasse 6, Tübingen, 72076, Germany
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Elfriede-Aulhorn-Strasse 6, Tübingen, 72076, Germany
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13
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Mekler V, Severinov K. RNA polymerase molecular beacon as tool for studies of RNA polymerase-promoter interactions. Methods 2015; 86:19-26. [PMID: 25956222 DOI: 10.1016/j.ymeth.2015.04.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 10/23/2022] Open
Abstract
The molecular details of formation of transcription initiation complex upon the interaction of bacterial RNA polymerase (RNAP) with promoters are not completely understood. One way to address this problem is to understand how RNAP interacts with different parts of promoter DNA. A recently developed fluorometric RNAP molecular beacon assay allows one to monitor the RNAP interactions with various unlabeled DNA probes and quantitatively characterize partial RNAP-promoter interactions. This paper focuses on methodological aspects of application of this powerful assay to study the mechanism of transcription initiation complex formation by Escherichia coli RNA polymerase σ(70) holoenzyme and its regulation by bacterial and phage encoded factors.
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Affiliation(s)
- Vladimir Mekler
- Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA; Skolkovo Institute of Science and Technology, 143025 Skolkovo, Russia; Institutes of Gene Biology and Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia.
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