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Miropolskaya N, Esyunina D, Klimasauskas S, Nikiforov V, Artsimovitch I, Kulbachinskiy A. Interplay between the trigger loop and the F loop during RNA polymerase catalysis. Nucleic Acids Res 2013; 42:544-52. [PMID: 24089145 PMCID: PMC3874190 DOI: 10.1093/nar/gkt877] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The trigger loop (TL) in the RNA polymerase (RNAP) active center plays key roles in the reactions of nucleotide addition and RNA cleavage catalyzed by RNAP. The adjacent F loop (FL) was proposed to contribute to RNAP catalysis by modulating structural changes in the TL. Here, we investigate the interplay between these two elements during transcription by bacterial RNAP. Thermodynamic analysis of catalysis by RNAP variants with mutations in the TL and FL suggests that the TL is the key element required for temperature activation in RNAP catalysis, and that the FL promotes TL transitions during nucleotide addition. We reveal characteristic differences in the catalytic parameters between thermophilic Thermus aquaticus and mesophilic Deinococcus radiodurans RNAPs and identify the FL as an adaptable element responsible for the observed differеnces. Mutations in the FL also significantly affect the rate of intrinsic RNA cleavage in a TL-dependent manner. In contrast, much weaker effects of the FL and TL mutations on GreA-assisted RNA cleavage suggest that the FL-dependent TL transitions are not required for this reaction. Thus, functional interplay between the FL and TL is essential for various catalytic activities of RNAP and plays an adaptive role in catalysis by thermophilic and mesophilic enzymes.
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Affiliation(s)
- Nataliya Miropolskaya
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia, Molecular Biology Department, Biological Faculty, Moscow State University, Moscow 119991 Russia, Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius 02241, Lithuania and Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
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2
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Mekler V, Minakhin L, Kuznedelov K, Mukhamedyarov D, Severinov K. RNA polymerase-promoter interactions determining different stability of the Escherichia coli and Thermus aquaticus transcription initiation complexes. Nucleic Acids Res 2012; 40:11352-62. [PMID: 23087380 PMCID: PMC3526302 DOI: 10.1093/nar/gks973] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Transcription initiation complexes formed by bacterial RNA polymerases (RNAPs) exhibit dramatic species-specific differences in stability, leading to different strategies of transcription regulation. The molecular basis for this diversity is unclear. Promoter complexes formed by RNAP from Thermus aquaticus (Taq) are considerably less stable than Escherichia coli RNAP promoter complexes, particularly at temperatures below 37°C. Here, we used a fluorometric RNAP molecular beacon assay to discern partial RNAP-promoter interactions. We quantitatively compared the strength of E. coli and Taq RNAPs partial interactions with the −10, −35 and UP promoter elements; the TG motif of the extended −10 element; the discriminator and the downstream duplex promoter segments. We found that compared with Taq RNAP, E. coli RNAP has much higher affinity only to the UP element and the downstream promoter duplex. This result indicates that the difference in stability between E. coli and Taq promoter complexes is mainly determined by the differential strength of core RNAP–DNA contacts. We suggest that the relative weakness of Taq RNAP interactions with DNA downstream of the transcription start point is the major reason of low stability and temperature sensitivity of promoter complexes formed by this enzyme.
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Affiliation(s)
- Vladimir Mekler
- Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA.
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3
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The anaerobe-specific orange protein complex of Desulfovibrio vulgaris hildenborough is encoded by two divergent operons coregulated by σ54 and a cognate transcriptional regulator. J Bacteriol 2011; 193:3207-19. [PMID: 21531797 DOI: 10.1128/jb.00044-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of sequenced bacterial genomes revealed that the genomes encode more than 30% hypothetical and conserved hypothetical proteins of unknown function. Among proteins of unknown function that are conserved in anaerobes, some might be determinants of the anaerobic way of life. This study focuses on two divergent clusters specifically found in anaerobic microorganisms and mainly composed of genes encoding conserved hypothetical proteins. We show that the two gene clusters DVU2103-DVU2104-DVU2105 (orp2) and DVU2107-DVU2108-DVU2109 (orp1) form two divergent operons transcribed by the σ(54)-RNA polymerase. We further demonstrate that the σ(54)-dependent transcriptional regulator DVU2106, located between orp1 and orp2, collaborates with σ(54)-RNA polymerase to orchestrate the simultaneous expression of the divergent orp operons. DVU2106, whose structural gene is transcribed by the σ(70)-RNA polymerase, negatively retrocontrols its own expression. By using an endogenous pulldown strategy, we identify a physiological complex composed of DVU2103, DVU2104, DVU2105, DVU2108, and DVU2109. Interestingly, inactivation of DVU2106, which is required for orp operon transcription, induces morphological defects that are likely linked to the absence of the ORP complex. A putative role of the ORP proteins in positioning the septum during cell division is discussed.
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4
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Lineage-specific amino acid substitutions in region 2 of the RNA polymerase sigma subunit affect the temperature of promoter opening. J Bacteriol 2008; 190:3088-92. [PMID: 18281402 DOI: 10.1128/jb.00008-08] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Highly conserved amino acid residues in region 2 of the RNA polymerase sigma subunit are known to participate in promoter recognition and opening. We demonstrated that nonconserved residues in this region collectively determine lineage-specific differences in the temperature of promoter opening.
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5
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Berezhnoy AY, Shckorbatov YG. Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence. J Zhejiang Univ Sci B 2006; 6:1063-8. [PMID: 16252339 PMCID: PMC1390652 DOI: 10.1631/jzus.2005.b1063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The energy of interaction between complementary nucleotides in promoter sequences of E. coli was calculated and visualized. The graphic method for presentation of energy properties of promoter sequences was elaborated on. Data obtained indicated that energy distribution through the length of promoter sequence results in picture with minima at -35, -8 and +7 regions corresponding to areas with elevated AT (adenine-thymine) content. The most important difference from the random sequences area is related to -8. Four promoter groups and their energy properties were revealed. The promoters with minimal and maximal energy of interaction between complementary nucleotides have low strengths, the strongest promoters correspond to promoter clusters characterized by intermediate energy values.
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Affiliation(s)
- Andrey Y. Berezhnoy
- National Scientific Center, Kharkov Physical-Technical Institute, Kharkov 61108, Ukraine
| | - Yuriy G. Shckorbatov
- Institute of Biology, Kharkov National University, Kharkov 61077, Ukraine
- †E-mail:
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6
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Schroeder LA, deHaseth PL. Mechanistic differences in promoter DNA melting by Thermus aquaticus and Escherichia coli RNA polymerases. J Biol Chem 2005; 280:17422-9. [PMID: 15731103 DOI: 10.1074/jbc.m501281200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Formation of strand-separated, functional complexes at promoters was compared for RNA polymerases from the mesophile Escherichia coli and the thermophile Thermus aquaticus. The RNA polymerases contained sigma factors that were wild type or bearing homologous alanine substitutions for two aromatic amino acids involved in DNA melting. Substitutions in the sigmaA subunit of T. aquaticus RNA polymerase impair promoter DNA melting equally at temperatures from 25 to 75 degrees C. However, homologous substitutions in sigma70 render E. coli RNA polymerase progressively more melting-defective as the temperature is reduced below 37 degrees C. The effects of the mutations on the mechanism of promoter DNA melting were investigated by studying the interaction of wild type and mutant RNA polymerases with "partial promoters" mimicking promoter DNA where the nucleation of DNA melting had taken place. Because T. aquaticus and E. coli RNA polymerases bound these templates similarly, it was concluded that the different effects of the mutations on the two polymerases are exerted at a step preceding nucleation of DNA melting. A model is presented for how this mechanistic difference between the two RNA polymerase could explain our observations.
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Affiliation(s)
- Lisa A Schroeder
- Center for RNA Molecular Biology and Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106-4973, USA
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7
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Kulbachinskiy A, Bass I, Bogdanova E, Goldfarb A, Nikiforov V. Cold sensitivity of thermophilic and mesophilic RNA polymerases. J Bacteriol 2004; 186:7818-20. [PMID: 15516599 PMCID: PMC524896 DOI: 10.1128/jb.186.22.7818-7820.2004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA polymerase from mesophilic Deinococcus radiodurans displays the same cold sensitivity of promoter opening as RNA polymerase from the closely related thermophilic Thermus aquaticus. This suggests that, contrary to the accepted view, cold sensitivity of promoter opening by thermophilic RNA polymerases may not be a consequence of their thermostability.
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8
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Loziński T, Wierzchowski KL. Inactivation and destruction by KMnO4 of Escherichia coli RNA polymerase open transcription complex: recommendations for footprinting experiments. Anal Biochem 2003; 320:239-51. [PMID: 12927830 DOI: 10.1016/s0003-2697(03)00381-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Potassium permanganate oxidation of pyrimidine residues in single-stranded DNA is commonly used in footprinting studies on formation of open transcription complex (RPo) by RNA polymerases (RNAP) at cognate promoters. Our own experience and literature search led us to conclude that KMnO4 doses often used in such studies might cause multiple-hit oxidation of promoter DNA and oxidative damage to RNAP in RPo and lead to false interpretation of footprints. We have therefore studied as a function of KMnO4 dose (i) transcription activity of RPo formed by Escherichia coli RNAP at a model cognate promoter Pa and (ii) RPo's structural integrity, by gel electrophoresis and footprinting assays. Kinetics of formation of this complex and melting of DNA in the transcription bubble region were thoroughly characterized by us previously. Here we show that (i) RPo becomes completely inactivated at oxidant doses much lower than those needed to cause a detectable footprint of the melted DNA region, (ii) footprinting patterns of the melted promoter region remain practically unaffected by RNAP oxidation within a range of low oxidant doses causing single-hit oxidation of DNA, and (iii) at higher oxidant doses, corresponding to multiple-hit DNA oxidation, the gross structure of RPo changes progressively until its complete collapse and dissociation into constituent components, so that only approximate interpretation of the footprinting data for the melted DNA region is possible. A protocol for accurate RPo footprinting with low single-hit KMnO4 doses and interpretation of the footprinting data in terms of kinetics of oxidation of pyrimidine residues in promoter DNA is recommended.
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Affiliation(s)
- Tomasz Loziński
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warszawa, Poland
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9
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Lim HM, Lee HJ, Roy S, Adhya S. A "master" in base unpairing during isomerization of a promoter upon RNA polymerase binding. Proc Natl Acad Sci U S A 2001; 98:14849-52. [PMID: 11734629 PMCID: PMC64947 DOI: 10.1073/pnas.261517398] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Isomerization of a closed to open complex of a promoter upon RNA polymerase binding involves base unpairing at the -10 region. After potassium permanganate sensitivity of unpaired thymine residues, we studied base unpairing at the -10 region during isomerization upon RNA polymerase binding at the P1 and P3 promoters of the gal operon. Substitution of adenine by 2-amino purine (2-AP) at the invariable A small middle dotT base pair at the -11 position of P1 and P3 prevented unpairing not only at that position but also at the other downstream positions, suggesting a "master" role of the adenine base at -11 of the template strand in overall base unpairing. 2-AP at -11 did not inhibit the formation of RNA polymerase small middle dotpromoter complex and subsequent isomerization of the polymerase. Substitution of adenine by 2-AP at several other positions did not affect thymine unpairing. Changing the position of the amino group from C6 in adenine to C2 in 2-AP is mutational only at the master switch position, -11.
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Affiliation(s)
- H M Lim
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA
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10
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Hethke C, Bergerat A, Hausner W, Forterre P, Thomm M. Cell-free transcription at 95 degrees: thermostability of transcriptional components and DNA topology requirements of Pyrococcus transcription. Genetics 1999; 152:1325-33. [PMID: 10430563 PMCID: PMC1460703 DOI: 10.1093/genetics/152.4.1325] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cell-free transcription of archaeal promoters is mediated by two archaeal transcription factors, aTBP and TFB, which are orthologues of the eukaryotic transcription factors TBP and TFIIB. Using the cell-free transcription system described for the hyperthermophilic Archaeon Pyrococcus furiosus by Hethke et al., the temperature limits and template topology requirements of archaeal transcription were investigated. aTBP activity was not affected after incubation for 1 hr at 100 degrees. In contrast, the half-life of RNA polymerase activity was 23 min and that of TFB activity was 3 min. The half-life of a 328-nt RNA product was 10 min at 100 degrees. Best stability of RNA was observed at pH 6, at 400 mm K-glutamate in the absence of Mg(2+) ions. Physiological concentrations of K-glutamate were found to stabilize protein components in addition, indicating that salt is an important extrinsic factor contributing to thermostability. Both RNA and proteins were stabilized by the osmolyte betaine at a concentration of 1 m. The highest activity for RNA synthesis at 95 degrees was obtained in the presence of 1 m betaine and 400 mm K-glutamate. Positively supercoiled DNA, which was found to exist in Pyrococcus cells, can be transcribed in vitro both at 70 degrees and 90 degrees. However, negatively supercoiled DNA was the preferred template at all temperatures tested. Analyses of transcripts from plasmid topoisomers harboring the glutamate dehydrogenase promoter and of transcription reactions conducted in the presence of reverse gyrase indicate that positive supercoiling of DNA inhibits transcription from this promoter.
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MESH Headings
- Archaeal Proteins/metabolism
- Cell-Free System
- DNA Topoisomerases, Type I
- DNA Topoisomerases, Type II/metabolism
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA-Directed RNA Polymerases/metabolism
- Gene Expression Regulation, Archaeal
- Half-Life
- Hot Temperature
- Nucleic Acid Conformation
- Protein Denaturation
- Pyrococcus furiosus/genetics
- Pyrococcus furiosus/physiology
- RNA, Archaeal/biosynthesis
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- Transcription, Genetic
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Affiliation(s)
- C Hethke
- Institut für Allgemeine Mikrobiologie, Universität Kiel, D-24118 Kiel, Germany
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11
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Coulombe B, Burton ZF. DNA bending and wrapping around RNA polymerase: a "revolutionary" model describing transcriptional mechanisms. Microbiol Mol Biol Rev 1999; 63:457-78. [PMID: 10357858 PMCID: PMC98973 DOI: 10.1128/mmbr.63.2.457-478.1999] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A model is proposed in which bending and wrapping of DNA around RNA polymerase causes untwisting of the DNA helix at the RNA polymerase catalytic center to stimulate strand separation prior to initiation. During elongation, DNA bending through the RNA polymerase active site is proposed to lower the energetic barrier to the advance of the transcription bubble. Recent experiments with mammalian RNA polymerase II along with accumulating evidence from studies of Escherichia coli RNA polymerase indicate the importance of DNA bending and wrapping in transcriptional mechanisms. The DNA-wrapping model describes specific roles for general RNA polymerase II transcription factors (TATA-binding protein [TBP], TFIIB, TFIIF, TFIIE, and TFIIH), provides a plausible explanation for preinitiation complex isomerization, suggests mechanisms underlying the synergy between transcriptional activators, and suggests an unforseen role for TBP-associating factors in transcription.
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Affiliation(s)
- B Coulombe
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada J1K 2R1
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12
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Abstract
The rate-limiting step in transcriptional initiation typically is opening the promoter DNA to expose the template strand. Opening is tightly regulated, but how it occurs is not known. These experiments identify an activity, recognition of specific DNA fork junctions, and suggest that it is critical to bacterial promoter opening. This activity is both sequence and structure specific; it recognizes the bases that constitute the upstream double-stranded/single-stranded boundary of the open complex. Promoter mutations known to reduce opening rates lead to comparable reductions in fork junction binding affinity. The activity acts to establish the upstream boundary of melted DNA and works in conjunction with two single-stranded DNA binding activities that recognize separately the two melted strands. The junction binding activity is contained within the sigma factor component of the holoenzyme. The activity occurs in both a typical prokaryotic transcription system and in a eukaryotic-like bacterial system that responds to enhancers and needs ATP. Thus DNA opening catalyzed by fork junction binding may occur in a variety of systems in which DNA must be opened to be copied.
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Affiliation(s)
- Y Guo
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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13
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Bouthier de la Tour C, Portemer C, Kaltoum H, Duguet M. Reverse gyrase from the hyperthermophilic bacterium Thermotoga maritima: properties and gene structure. J Bacteriol 1998; 180:274-81. [PMID: 9440516 PMCID: PMC106882 DOI: 10.1128/jb.180.2.274-281.1998] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The hyperthermophilic bacterium Thermotoga maritima MSB8 possesses a reverse gyrase whose enzymatic properties are very similar to those of archaeal reverse gyrases. It catalyzes the positive supercoiling of the DNA in an Mg2+- and ATP-dependent process. Its optimal temperature of activity is around 90 degrees C, and it is highly thermostable. We have cloned and DNA sequenced the corresponding gene (T. maritima topR). This is the first report describing the analysis of a gene encoding a reverse gyrase in bacteria. The T. maritima topR gene codes for a protein of 1,104 amino acids with a deduced molecular weight of 128,259, a value in agreement with that estimated from the denaturing gel electrophoresis of the purified enzyme. Like its archaeal homologs, the T. maritima reverse gyrase exhibits helicase and topoisomerase domains, and its sequence matches very well the consensus sequence for six reverse gyrases now available. Phylogenetic analysis shows that all reverse gyrases, including the T. maritima enzyme, form a very homogeneous group, distinct from the type I 5' topoisomerases of the TopA subfamily, for which we have previously isolated a representative gene in T. maritima (topA). The coexistence of these two distinct genes, coding for a reverse gyrase and an omega-like topoisomerase, respectively, together with the recent description of a gyrase in T. maritima (O. Guipaud, E. Marguet, K. M. Noll, C. Bouthier de la Tour, and P. Forterre, Proc. Natl. Acad. Sci. USA 94:10606-10611, 1977) addresses the question of the control of the supercoiling in this organism.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Cloning, Molecular
- DNA Topoisomerases, Type I
- DNA Topoisomerases, Type II/genetics
- DNA Topoisomerases, Type II/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/classification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/enzymology
- Molecular Sequence Data
- Phylogeny
- Sequence Homology, Amino Acid
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Affiliation(s)
- C Bouthier de la Tour
- Laboratoire d'Enzymologie des Acides Nucléiques, Institut de Génétique et Microbiologie, Université Paris-Sud, Orsay, France.
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14
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Severinov K, Darst SA. A mutant RNA polymerase that forms unusual open promoter complexes. Proc Natl Acad Sci U S A 1997; 94:13481-6. [PMID: 9391051 PMCID: PMC28331 DOI: 10.1073/pnas.94.25.13481] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We describe a mutant Escherichia coli RNA polymerase (RNAP) that forms stable open promoter complexes even at -20 degrees C but with a shortened melted region that extends downstream to only position -7. In the presence of initiating transcription substrates, the mutant RNAP undergoes a temperature-dependent isomerization, resulting in a promoter complex that is indistinguishable from the wild-type RNAP-promoter complex, with the melted region extended downstream to position +4. We propose that the open complex formed by the mutant RNAP represents an intermediate on the normal promoter-opening pathway and that our results support earlier findings that initial promoter opening occurs in the upstream region of the -10 promoter consensus element and subsequently extends downstream to encompass the transcription start site.
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Affiliation(s)
- K Severinov
- Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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15
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Chen YF, Helmann JD. DNA-melting at the Bacillus subtilis flagellin promoter nucleates near -10 and expands unidirectionally. J Mol Biol 1997; 267:47-59. [PMID: 9096206 DOI: 10.1006/jmbi.1996.0853] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A central step in promoter activation by RNA polymerase (RNAP) is the localized separation of the DNA strands to form the transcription bubble. We have used potassium permanganate footprinting to monitor DNA strand-separation by the Bacillus subtilis sigmaD RNAP at the strong promoter, Phag, directing transcription of flagellin. The susceptibility of individual thymine bases to permanganate oxidation is influenced by temperature, Mg2+, nucleotides, and the RNAP delta subunit. In the absence of delta, sigmaD RNAP establishes a partially opened complex even at 0 degrees C with permanganate reactivity localized between -11 and -4 (RP(-4)). The region of strand separation expands to near -1 at 20 degrees C (RP(-1)) and to +3 at 40 degrees C (RP(+3)). The delta subunit inhibits the downstream propagation of the transcription bubble and thereby increases the concentration of early intermediates in the melting pathway. Indeed, E delta sigmaD forms a distinct nucleated complex (RPn) at 0 degrees C with a structural distortion localized to an AT base step within the -10 element. We propose a model for promoter melting in which strand separation nucleates within the conserved -10 consensus and subsequently propagates downstream. Mg2+ and nucleoside triphosphates (NTPs) favor the downstream propagation of the transcription bubble and strongly stimulate the RP(-1) to RP(+3) conversion. The NTP effects are apparently mediated by binding of substrate to the initiating NTP site: purines are more effective than pyrimidines and GMP alone can greatly increase the level of DNA-melting. The binding of substrates, but not Mg2+ alone, can effectively overcome the anti-melting effect of delta.
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Affiliation(s)
- Y F Chen
- Section of Microbiology, Cornell University, Ithaca, NY 14853, USA
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16
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Zaychikov E, Denissova L, Meier T, Götte M, Heumann H. Influence of Mg2+ and temperature on formation of the transcription bubble. J Biol Chem 1997; 272:2259-67. [PMID: 8999932 DOI: 10.1074/jbc.272.4.2259] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The transcription bubble formed in the binding complex of T7A1 promoter upon Escherichia coli RNA polymerase was analyzed by chemical probes, namely by single-strand specific reagents, to map the unpaired bases in the bubble, and by FeEDTA, to analyze the accessibility of the DNA backbone. The latter probe could also be used as a local hydroxyl radical probe placed close to the Mg2+-binding site in the active center. The data show that the transcription bubble consists of two parts, an Mg2+-dependent part and an Mg2+-independent part, both having individual transition temperatures. The data further suggest that formation of a transcription active open complex is preceded by a transition state complex having enhanced affinity for those Mg2+ ions presumably participating in the formation of the catalytic site. Our data also suggests that the three catalytically active Mg2+ ions in RNA polymerase are functionally not equivalent. One/two of the three Mg2+ ions are responsible for the polymerization, the other two/one for enlargement of the transcription bubble.
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Affiliation(s)
- E Zaychikov
- Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
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17
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18
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Hethke C, Geerling AC, Hausner W, de Vos WM, Thomm M. A cell-free transcription system for the hyperthermophilic archaeon Pyrococcus furiosus. Nucleic Acids Res 1996; 24:2369-76. [PMID: 8710509 PMCID: PMC145958 DOI: 10.1093/nar/24.12.2369] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We describe here the establishment of a cell-free transcription system for the hyperthermophilic Archaeon Pyrococcus furiosus using the cloned glutamate dehydrogenase (gdh) gene as template. The in vitro system that operated up to a temperature of 85 degrees C initiated transcription 23 bp downstream of a TATA box located 45 bp upstream of the translational start codon of gdh mRNA, at the same site as in Pyrococcus cells. Mutational analyses revealed that this TATA box is essential for in vitro initiation of transcription. Pyrococcus transcriptional components were separated into at least two distinct transcription factor activities and RNA polymerase. One of these transcription factors could be functionally replaced by Methanococcus aTFB and Thermococcus TATA bind- ing protein (TBP). Immunochemical analyses demonstrated a structural relationship between Pyrococcus aTFB and Thermococcus TBP. These findings indicate that a TATA box and a TBP are essential components of the Pyrococcus transcriptional machinery.
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Affiliation(s)
- C Hethke
- Institut für Allgemeine Mikrobiologie, Universität Kiel, Germany
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