101
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Abstract
In transcription initiation, all RNA polymerase molecules bound to a promoter have been conventionally supposed to proceed into elongation of transcript. However, for Escherichia coli RNA polymerase, evidence has been accumulated for a view that only its fraction can proceed into elongation and the rest is retained at a promoter in non-productive form: a pathway branching in transcription initiation. Proteins such as GreA and GreB affect these fractions at several promoters in vitro. To reveal the ubiquitous existence of the branched mechanism in E. coli, we searched for candidate genes whose transcription decreased by disruption of greA and greB using a DNA array. Among the arbitrarily selected 11 genes from over 100, the atpC, cspA and rpsA passed the test by Northern blotting. The Gre factors activated transcription initiation from their promoters in vitro, and the results demonstrated that the branched mechanism is exploited in vivo regulation. Consistently, decrease in the level of the GreA in an anaerobic stationary condition accompanied a decrease in the levels of transcripts of these genes.
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Affiliation(s)
- Motoki Susa
- Structural Biology Center, National Institute of Genetics, The Graduate University for Advanced StudiesMishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced StudiesMishima, Shizuoka 411-8540, Japan
| | - Tomoko Kubori
- Structural Biology Center, National Institute of Genetics, The Graduate University for Advanced StudiesMishima, Shizuoka 411-8540, Japan
| | - Nobuo Shimamoto
- Structural Biology Center, National Institute of Genetics, The Graduate University for Advanced StudiesMishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced StudiesMishima, Shizuoka 411-8540, Japan
- *For correspondence. E-mail ; Tel. (+81) 55 981 6843; Fax (+81) 55 981 6844
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102
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Laptenko O, Kim SS, Lee J, Starodubtseva M, Cava F, Berenguer J, Kong XP, Borukhov S. pH-dependent conformational switch activates the inhibitor of transcription elongation. EMBO J 2006; 25:2131-41. [PMID: 16628221 PMCID: PMC1462974 DOI: 10.1038/sj.emboj.7601094] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Accepted: 03/22/2006] [Indexed: 11/08/2022] Open
Abstract
Gfh1, a transcription factor from Thermus thermophilus, inhibits all catalytic activities of RNA polymerase (RNAP). We characterized the Gfh1 structure, function and possible mechanism of action and regulation. Gfh1 inhibits RNAP by competing with NTPs for coordinating the active site Mg2+ ion. This coordination requires at least two aspartates at the tip of the Gfh1 N-terminal coiled-coil domain (NTD). The overall structure of Gfh1 is similar to that of the Escherichia coli transcript cleavage factor GreA, except for the flipped orientation of the C-terminal domain (CTD). We show that depending on pH, Gfh1-CTD exists in two alternative orientations. At pH above 7, it assumes an inactive 'flipped' orientation seen in the structure, which prevents Gfh1 from binding to RNAP. At lower pH, Gfh1-CTD switches to an active 'Gre-like' orientation, which enables Gfh1 to bind to and inhibit RNAP.
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Affiliation(s)
- Oleg Laptenko
- Department of Cell Biology, School of Osteopathic Medicine at Stratford, University of Medicine and Dentistry of New Jersey, Stratford, NJ, USA
| | - Seung-Sup Kim
- Department of Biochemistry, New York University School of Medicine, New York, NY, USA
| | - Jookyung Lee
- Department of Cell Biology, School of Osteopathic Medicine at Stratford, University of Medicine and Dentistry of New Jersey, Stratford, NJ, USA
| | - Marina Starodubtseva
- Department of Cell Biology, School of Osteopathic Medicine at Stratford, University of Medicine and Dentistry of New Jersey, Stratford, NJ, USA
| | - Fellipe Cava
- Centro de Biología Molecular ‘Severo Ochoa' CSIC-UAM, Campus de Cantoblanco, Madrid, Spain
| | - Jose Berenguer
- Centro de Biología Molecular ‘Severo Ochoa' CSIC-UAM, Campus de Cantoblanco, Madrid, Spain
| | - Xiang-Peng Kong
- Department of Biochemistry, New York University School of Medicine, New York, NY, USA
- Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA. Tel.: +1 212 263 7897; Fax: +1 212 263 8951; E-mail:
| | - Sergei Borukhov
- Department of Cell Biology, School of Osteopathic Medicine at Stratford, University of Medicine and Dentistry of New Jersey, Stratford, NJ, USA
- Department of Cell Biology, School of Osteopathic Medicine at Stratford, University of Medicine and Dentistry of New Jersey, 2-Medical Center drive, Rm B108, Stratford, NJ 08084, USA. Tel.:+1 856 566 6271; Fax: +1 856 566 6965; E-mail:
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103
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Potrykus K, Vinella D, Murphy H, Szalewska-Palasz A, D'Ari R, Cashel M. Antagonistic regulation of Escherichia coli ribosomal RNA rrnB P1 promoter activity by GreA and DksA. J Biol Chem 2006; 281:15238-48. [PMID: 16597620 DOI: 10.1074/jbc.m601531200] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli proteins DksA, GreA, and GreB are all structural homologs that bind the secondary channel of RNA polymerase (RNAP) but are thought to act at different levels of transcription. DksA, with its co-factor ppGpp, inhibits rrnB P1 transcription initiation, whereas GreA and GreB activate RNAP to cleave back-tracked RNA during elongational pausing. Here, in vivo and in vitro evidence reveals antagonistic regulation of rrnB P1 transcription initiation by Gre factors (particularly GreA) and DksA; GreA activates and DksA inhibits. DksA inhibition is epistatic to GreA activation. Both modes of regulation are ppGpp-independent in vivo but DksA inhibition requires ppGpp in vitro. Kinetic experiments and studies of rrnB P1-RNA polymerase complexes suggest that GreA mediates conformational changes at an initiation step in the absence of NTP substrates, even before DksA acts. GreA effects on rrnB P1 open complex conformation reveal a new feature of GreA distinct from its general function in elongation. Our findings support the idea that a balance of the interactions between the three secondary channel-binding proteins and RNAP can provide a new mode for regulating transcription.
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MESH Headings
- Base Sequence
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA-Directed RNA Polymerases/chemistry
- DNA-Directed RNA Polymerases/metabolism
- Epistasis, Genetic
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Kinetics
- Models, Biological
- Multiprotein Complexes
- Promoter Regions, Genetic
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
- rRNA Operon
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Affiliation(s)
- Katarzyna Potrykus
- Laboratory of Molecular Genetics, NICHD, National Institutes of Health, Bethesda, Maryland 20892-2785, USA
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104
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Trinh V, Langelier MF, Archambault J, Coulombe B. Structural perspective on mutations affecting the function of multisubunit RNA polymerases. Microbiol Mol Biol Rev 2006; 70:12-36. [PMID: 16524917 PMCID: PMC1393249 DOI: 10.1128/mmbr.70.1.12-36.2006] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
High-resolution crystallographic structures of multisubunit RNA polymerases (RNAPs) have increased our understanding of transcriptional mechanisms. Based on a thorough review of the literature, we have compiled the mutations affecting the function of multisubunit RNA polymerases, many of which having been generated and studied prior to the publication of the first high-resolution structure, and highlighted the positions of the altered amino acids in the structures of both the prokaryotic and eukaryotic enzymes. The observations support many previous hypotheses on the transcriptional process, including the implication of the bridge helix and the trigger loop in the processivity of RNAP, the importance of contacts between the RNAP jaw-lobe module and the downstream DNA in the establishment of a transcription bubble and selection of the transcription start site, the destabilizing effects of ppGpp on the open promoter complex, and the link between RNAP processivity and termination. This study also revealed novel, remarkable features of the RNA polymerase catalytic mechanisms that will require additional investigation, including the putative roles of fork loop 2 in the establishment of a transcription bubble, the trigger loop in start site selection, and the uncharacterized funnel domain in RNAP processivity.
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Affiliation(s)
- Vincent Trinh
- Gene Transcription Laboratory, Institut de Recherches Cliniques de Montréal, 110 Ave. des Pins Ouest, Montréal, Québec, Canada
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105
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Abstract
In bacteria, a fundamental level of gene regulation occurs by competitive association of promoter-specificity factors called sigmas with RNA polymerase (RNAP). This sigma cycle paradigm underpins much of our understanding of all transcriptional regulation. Here, we review recent challenges to the sigma cycle paradigm in the context of its essential features and of the structural basis of sigma interactions with RNAP and elongation complexes. Although sigmas can play dual roles as both initiation and elongation regulators, we suggest that the key postulate of the sigma cycle, that sigmas compete for binding to RNAP after each round of RNA synthesis, remains the central mechanism for programming transcription initiation in bacteria.
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Affiliation(s)
- Rachel Anne Mooney
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
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106
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Sawers RG. Evidence for novel processing of the anaerobically inducible dicistronic focA-pfl mRNA transcript in Escherichia coli. Mol Microbiol 2005; 58:1441-53. [PMID: 16313628 DOI: 10.1111/j.1365-2958.2005.04915.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The anaerobically inducible dicistronic focA-pfl operon is transcribed from three co-ordinately regulated promoters that are located 5' of the operon. Remarkably, the 5' ends of four further highly abundant operon-internal transcripts are located within the focA gene, with a fifth transcript mapping in the intergenic region between focA and pfl. The findings of this study demonstrate that the bulk of these five operon-internal transcripts are the result of processing. Processing was independent of the broad-spectrum endoribonucleases associated with mRNA turnover and still occurred when the upstream regulatory region of the operon was replaced with two different heterologous promoters recognized by Escherichia coli core RNA polymerase, including the tetP promoter. However, when the T7Phi10 promoter was introduced upstream of the focA-pfl operon, mainly full-length transcript and a minor amount of two processing products were observed. T7 RNA polymerase mutants that exhibit reduced elongation speed did not restore the wild-type transcript-processing pattern. Moreover, processing was independent of focA translation. Taken together, these data suggest that processing of the focA-pfl transcripts occurs by a novel mechanism that might require the action of E. coli core RNA polymerase.
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Affiliation(s)
- R Gary Sawers
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK.
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107
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Davies KM, Dedman AJ, van Horck S, Lewis PJ. The NusA:RNA polymerase ratio is increased at sites of rRNA synthesis inBacillus subtilis. Mol Microbiol 2005. [DOI: 10.1111/j.1365-2958.2005.04669.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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