51
|
Danson AE, Jovanovic M, Buck M, Zhang X. Mechanisms of σ 54-Dependent Transcription Initiation and Regulation. J Mol Biol 2019; 431:3960-3974. [PMID: 31029702 PMCID: PMC7057263 DOI: 10.1016/j.jmb.2019.04.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 02/02/2023]
Abstract
Cellular RNA polymerase is a multi-subunit macromolecular assembly responsible for gene transcription, a highly regulated process conserved from bacteria to humans. In bacteria, sigma factors are employed to mediate gene-specific expression in response to a variety of environmental conditions. The major variant σ factor, σ54, has a specific role in stress responses. Unlike σ70-dependent transcription, which often can spontaneously proceed to initiation, σ54-dependent transcription requires an additional ATPase protein for activation. As a result, structures of a number of distinct functional states during the dynamic process of transcription initiation have been captured using the σ54 system with both x-ray crystallography and cryo electron microscopy, furthering our understanding of σ54-dependent transcription initiation and DNA opening. Comparisons with σ70 and eukaryotic polymerases reveal unique and common features during transcription initiation.
Collapse
Affiliation(s)
- Amy E Danson
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Milija Jovanovic
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Martin Buck
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK.
| |
Collapse
|
52
|
Lee Y, Lee N, Jeong Y, Hwang S, Kim W, Cho S, Palsson BO, Cho BK. The Transcription Unit Architecture of Streptomyces lividans TK24. Front Microbiol 2019; 10:2074. [PMID: 31555254 PMCID: PMC6742748 DOI: 10.3389/fmicb.2019.02074] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 08/22/2019] [Indexed: 12/15/2022] Open
Abstract
Streptomyces lividans is an attractive host for production of heterologous proteins and secondary metabolites of other Streptomyces species. To fully harness the industrial potential of S. lividans, understanding its metabolism and genetic regulatory elements is essential. This study aimed to determine its transcription unit (TU) architecture and elucidate its diverse regulatory elements, including promoters, ribosome binding sites, 5′-untranslated regions, and transcription terminators. Total 1,978 transcription start sites and 1,640 transcript 3′-end positions were identified, which were integrated to determine 1,300 TUs, consistent with transcriptomic profiles. The conserved promoter sequences were found as 5′-TANNNT and 5′-TGAC, representing the −10 and −35 elements, respectively. Analysis of transcript 3′-end positions revealed the presence of distinctive terminator sequences and the RNA stem structure responsible for the determination of the 3′-boundary of a transcript. Functionally related genes are likely to be regulated simultaneously by using similar promoters and being transcribed as a poly-cistronic TU. Poly-cistronic TUs were further processed or alternatively transcribed into multiple TUs to fine-regulate individual genes in response to environmental conditions. The TU information and regulatory elements identified will serve as invaluable resources for understanding the complex regulatory mechanisms of S. lividans and to elevate its industrial potential.
Collapse
Affiliation(s)
- Yongjae Lee
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Namil Lee
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Yujin Jeong
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Soonkyu Hwang
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Woori Kim
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Suhyung Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Bernhard O Palsson
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Department of Pediatrics, University of California, San Diego, San Diego, CA, United States.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Byung-Kwan Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
| |
Collapse
|
53
|
Chung S, Lerner E, Jin Y, Kim S, Alhadid Y, Grimaud LW, Zhang IX, Knobler CM, Gelbart WM, Weiss S. The effect of macromolecular crowding on single-round transcription by Escherichia coli RNA polymerase. Nucleic Acids Res 2019; 47:1440-1450. [PMID: 30590739 PMCID: PMC6379708 DOI: 10.1093/nar/gky1277] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 12/01/2018] [Accepted: 12/13/2018] [Indexed: 01/09/2023] Open
Abstract
Previous works have reported significant effects of macromolecular crowding on the structure and behavior of biomolecules. The crowded intracellular environment, in contrast to in vitro buffer solutions, likely imparts similar effects on biomolecules. The enzyme serving as the gatekeeper for the genome, RNA polymerase (RNAP), is among the most regulated enzymes. Although it was previously demonstrated that macromolecular crowding affects association of RNAP to DNA, not much is known about how crowding acts on late initiation and promoter clearance steps, which are considered to be the rate-determining steps for many promoters. Here, we demonstrate that macromolecular crowding enhances the rate of late initiation and promoter clearance using in vitro quenching-based single-molecule kinetics assays. Moreover, the enhancement's dependence on crowder size notably deviates from predictions by the scaled-particle theory, commonly used for description of crowding effects. Our findings shed new light on how enzymatic reactions could be affected by crowded conditions in the cellular milieu.
Collapse
Affiliation(s)
- SangYoon Chung
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - Eitan Lerner
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yan Jin
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - Soohong Kim
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yazan Alhadid
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, CA 90095, USA
| | - Logan Wilson Grimaud
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - Irina X Zhang
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Present address: Irina X. Zhang, Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Charles M Knobler
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - William M Gelbart
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute (MBI), University of California Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California Los Angeles, CA 90095, USA
- Correspondence may also be addressed to William M. Gelbart. Tel: +1 310 825 2005; Fax: +1 310 206 4038;
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute (MBI), University of California Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles, CA 90095, USA
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
- To whom correspondence should be addressed. Tel: +1 310 794 0093; Fax: +1 310 267 4672;
| |
Collapse
|
54
|
Duchi D, Gryte K, Robb NC, Morichaud Z, Sheppard C, Brodolin K, Wigneshweraraj S, Kapanidis AN. Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes. Nucleic Acids Res 2019; 46:677-688. [PMID: 29177430 PMCID: PMC5778504 DOI: 10.1093/nar/gkx1146] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 10/31/2017] [Indexed: 12/16/2022] Open
Abstract
Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and an RNAP-promoter open complex; however, the series and sequence of conformational changes, and the factors that influence them are unclear. To address the conformational landscape and transitions in transcription initiation, we applied single-molecule Förster resonance energy transfer (smFRET) on immobilized Escherichia coli transcription open complexes. Our results revealed the existence of two stable states within RNAP–DNA complexes in which the promoter DNA appears to adopt closed and partially open conformations, and we observed large-scale transitions in which the transcription bubble fluctuated between open and closed states; these transitions, which occur roughly on the 0.1 s timescale, are distinct from the millisecond-timescale dynamics previously observed within diffusing open complexes. Mutational studies indicated that the σ70 region 3.2 of the RNAP significantly affected the bubble dynamics. Our results have implications for many steps of transcription initiation, and support a bend-load-open model for the sequence of transitions leading to bubble opening during open complex formation.
Collapse
Affiliation(s)
- Diego Duchi
- Gene Machines Group, Biological Physics Research Unit, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Kristofer Gryte
- Gene Machines Group, Biological Physics Research Unit, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Nicole C Robb
- Gene Machines Group, Biological Physics Research Unit, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Zakia Morichaud
- CNRS UMR 9004, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Carol Sheppard
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Konstantin Brodolin
- CNRS UMR 9004, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | | | - Achillefs N Kapanidis
- Gene Machines Group, Biological Physics Research Unit, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| |
Collapse
|
55
|
Heyduk E, Heyduk T. DNA template sequence control of bacterial RNA polymerase escape from the promoter. Nucleic Acids Res 2019; 46:4469-4486. [PMID: 29546317 PMCID: PMC5961368 DOI: 10.1093/nar/gky172] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 02/28/2018] [Indexed: 01/09/2023] Open
Abstract
Promoter escape involves breaking of the favourable contacts between RNA polymerase (RNAP) and the promoter to allow transition to an elongation complex. The sequence of DNA template that is transcribed during promoter escape (ITS; Initially Transcribed Sequence) can affect promoter escape by mechanisms that are not yet fully understood. We employed a highly parallel strategy utilizing Next Generation Sequencing (NGS) to collect data on escape properties of thousands of ITS variants. We show that ITS controls promoter escape through a combination of position-dependent effects (most prominently, sequence-directed RNAP pausing), and position-independent effects derived from sequence encoded physical properties of the template (for example, RNA/DNA duplex stability). ITS often functions as an independent unit affecting escape in the same manner regardless of the promoter from which transcription initiates. However, in some cases, a strong dependence of ITS effects on promoter context was observed suggesting that promoters may have 'allosteric' abilities to modulate ITS effects. Large effects of ITS on promoter output and the observed interplay between promoter sequence and ITS effects suggests that the definition of bacterial promoter should include ITS sequence.
Collapse
Affiliation(s)
- Ewa Heyduk
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Medical School, 1100 S. Grand Blvd., St. Louis, MO 63104, USA
| | - Tomasz Heyduk
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Medical School, 1100 S. Grand Blvd., St. Louis, MO 63104, USA
| |
Collapse
|
56
|
Pupov D, Petushkov I, Esyunina D, Murakami KS, Kulbachinskiy A. Region 3.2 of the σ factor controls the stability of rRNA promoter complexes and potentiates their repression by DksA. Nucleic Acids Res 2019; 46:11477-11487. [PMID: 30321408 PMCID: PMC6265461 DOI: 10.1093/nar/gky919] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/10/2018] [Indexed: 01/25/2023] Open
Abstract
The σ factor drives promoter recognition by bacterial RNA polymerase (RNAP) and is also essential for later steps of transcription initiation, including RNA priming and promoter escape. Conserved region 3.2 of the primary σ factor (‘σ finger’) directly contacts the template DNA strand in the open promoter complex and facilitates initiating NTP binding in the active center of RNAP. Ribosomal RNA promoters are responsible for most RNA synthesis during exponential growth but should be silenced during the stationary phase to save cell resources. In Escherichia coli, the silencing mainly results from the action of the secondary channel factor DksA, which together with ppGpp binds RNAP and dramatically decreases the stability of intrinsically unstable rRNA promoter complexes. We demonstrate that this switch depends on the σ finger that destabilizes RNAP–promoter interactions. Mutations in the σ finger moderately decrease initiating NTP binding but significantly increase promoter complex stability and reduce DksA affinity to the RNAP–rRNA promoter complex, thus making rRNA transcription less sensitive to DksA/ppGpp both in vitro and in vivo. Thus, destabilization of rRNA promoter complexes by the σ finger makes them a target for robust regulation by the stringent response factors under stress conditions.
Collapse
Affiliation(s)
- Danil Pupov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Ivan Petushkov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| |
Collapse
|
57
|
Abstract
In all living organisms, the flow of genetic information is a two-step process: first DNA is transcribed into RNA, which is subsequently used as template for protein synthesis during translation. In bacteria, archaea and eukaryotes, transcription is carried out by multi-subunit RNA polymerases (RNAPs) sharing a conserved architecture of the RNAP core. RNAPs catalyse the highly accurate polymerisation of RNA from NTP building blocks, utilising DNA as template, being assisted by transcription factors during the initiation, elongation and termination phase of transcription. The complexity of this highly dynamic process is reflected in the intricate network of protein-protein and protein-nucleic acid interactions in transcription complexes and the substantial conformational changes of the RNAP as it progresses through the transcription cycle.In this chapter, we will first briefly describe the early work that led to the discovery of multisubunit RNAPs. We will then discuss the three-dimensional organisation of RNAPs from the bacterial, archaeal and eukaryotic domains of life, highlighting the conserved nature, but also the domain-specific features of the transcriptional apparatus. Another section will focus on transcription factors and their role in regulating the RNA polymerase throughout the different phases of the transcription cycle. This includes a discussion of the molecular mechanisms and dynamic events that govern transcription initiation, elongation and termination.
Collapse
|
58
|
Inniss NL, Prehna G, Morrison DA. The pneumococcal σ X activator, ComW, is a DNA-binding protein critical for natural transformation. J Biol Chem 2019; 294:11101-11118. [PMID: 31160340 DOI: 10.1074/jbc.ra119.007571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/19/2019] [Indexed: 11/06/2022] Open
Abstract
Natural genetic transformation via horizontal gene transfer enables rapid adaptation to dynamic environments and contributes to both antibiotic resistance and vaccine evasion among bacterial populations. In Streptococcus pneumoniae (pneumococcus), transformation occurs when cells enter competence, a transient state in which cells express the competence master regulator, SigX (σΧ), an alternative σ factor (σ), and a competence co-regulator, ComW. Together, ComW and σX facilitate expression of the genes required for DNA uptake and genetic recombination. SigX activity depends on ComW, as ΔcomW cells transcribe late genes and transform at levels 10- and 10,000-fold below that of WT cells, respectively. Previous findings suggest that ComW functions during assembly of the RNA polymerase-σX holoenzyme to help promote transcription from σX-targeted promoters. However, it remains unknown how ComW facilitates holoenzyme assembly. As ComW seems to be unique to Gram-positive cocci and has no sequence similarity with known transcriptional activators, here we used Rosetta to generate an ab initio model of pneumococcal ComW's 3D-structure. Using this model as a basis for further biochemical, biophysical, and genetic investigations into the molecular features important for its function, we report that ComW is a predicted globular protein and that it interacts with DNA, independently of DNA sequence. We also identified conserved motifs in ComW and show that key residues in these motifs contribute to DNA binding. Lastly, we provide evidence that ComW's DNA-binding activity is important for transformation in pneumococcus. Our findings begin to fill the gaps in understanding how ComW regulates σΧ activity during bacterial natural transformation.
Collapse
Affiliation(s)
- Nicole L Inniss
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Gerd Prehna
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Donald A Morrison
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607
| |
Collapse
|
59
|
Belogurov GA, Artsimovitch I. The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase. J Mol Biol 2019; 431:3975-4006. [PMID: 31153902 DOI: 10.1016/j.jmb.2019.05.042] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 11/15/2022]
Abstract
Multi-subunit DNA-dependent RNA polymerases synthesize all classes of cellular RNAs, ranging from short regulatory transcripts to gigantic messenger RNAs. RNA polymerase has to make each RNA product in just one try, even if it takes millions of successive nucleotide addition steps. During each step, RNA polymerase selects a correct substrate, adds it to a growing chain, and moves one nucleotide forward before repeating the cycle. However, RNA synthesis is anything but monotonous: RNA polymerase frequently pauses upon encountering mechanical, chemical and torsional barriers, sometimes stepping back and cleaving off nucleotides from the growing RNA chain. A picture in which these intermittent dynamics enable processive, accurate, and controllable RNA synthesis is emerging from complementary structural, biochemical, computational, and single-molecule studies. Here, we summarize our current understanding of the mechanism and regulation of the on-pathway transcription elongation. We review the details of substrate selection, catalysis, proofreading, and translocation, focusing on rate-limiting steps, structural elements that modulate them, and accessory proteins that appear to control RNA polymerase translocation.
Collapse
Affiliation(s)
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
60
|
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.
Collapse
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.
| |
Collapse
|
61
|
The Role of Pyrophosphorolysis in the Initiation-to-Elongation Transition by E. coli RNA Polymerase. J Mol Biol 2019; 431:2528-2542. [PMID: 31029704 DOI: 10.1016/j.jmb.2019.04.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/13/2019] [Accepted: 04/15/2019] [Indexed: 02/02/2023]
Abstract
RNA polymerase can cleave a phosphodiester bond at the 3' end of a nascent RNA in the presence of pyrophosphate producing NTP. Pyrophosphorolysis has been characterized during elongation steps of transcription where its rate is significantly slower than the forward rate of NMP addition. In contrast, we report here that pyrophosphorolysis can occur in a millisecond time scale during the transition of Escherichia coli RNA polymerase from initiation to elongation at the psbA2 promoter. This rapid pyrophosphorolysis occurs during productive RNA synthesis as opposed to abortive RNA synthesis. Dissociation of σ70 or RNA extension beyond nine nucleotides dramatically reduces the rate of pyrophosphorolysis. We argue that the rapid pyrophosphorolysis allows iterative cycles of cleavage and re-synthesis of the 3' phosphodiester bond by the productive complexes in the early stage of transcription. This iterative process may provide an opportunity for the σ70 to dissociate from the RNA exit channel of the enzyme, enabling RNA to extend through the channel.
Collapse
|
62
|
Henderson KL, Evensen CE, Molzahn CM, Felth LC, Dyke S, Liao G, Shkel IA, Record MT. RNA Polymerase: Step-by-Step Kinetics and Mechanism of Transcription Initiation. Biochemistry 2019; 58:2339-2352. [PMID: 30950601 DOI: 10.1021/acs.biochem.9b00049] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To determine the step-by-step kinetics and mechanism of transcription initiation and escape by E. coli RNA polymerase from the λPR promoter, we quantify the accumulation and decay of transient short RNA intermediates on the pathway to promoter escape and full-length (FL) RNA synthesis over a wide range of NTP concentrations by rapid-quench mixing and phosphorimager analysis of gel separations. Experiments are performed at 19 °C, where almost all short RNAs detected are intermediates in FL-RNA synthesis by productive complexes or end-products in nonproductive (stalled) initiation complexes and not from abortive initiation. Analysis of productive-initiation kinetic data yields composite second-order rate constants for all steps of NTP binding and hybrid extension up to the escape point (11-mer). The largest of these rate constants is for incorporation of UTP into the dinucleotide pppApU in a step which does not involve DNA opening or translocation. Subsequent steps, each of which begins with reversible translocation and DNA opening, are slower with rate constants that vary more than 10-fold, interpreted as effects of translocation stress on the translocation equilibrium constant. Rate constants for synthesis of 4- and 5-mer, 7-mer to 9-mer, and 11-mer are particularly small, indicating that RNAP-promoter interactions are disrupted in these steps. These reductions in rate constants are consistent with the previously determined ∼9 kcal cost of escape from λPR. Structural modeling and previous results indicate that the three groups of small rate constants correspond to sequential disruption of in-cleft, -10, and -35 interactions. Parallels to escape by T7 RNAP are discussed.
Collapse
Affiliation(s)
- Kate L Henderson
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Claire E Evensen
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Cristen M Molzahn
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Lindsey C Felth
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Sarah Dyke
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Guanyu Liao
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Irina A Shkel
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - M Thomas Record
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| |
Collapse
|
63
|
An Introduction to the Structure and Function of the Catalytic Core Enzyme of Escherichia coli RNA Polymerase. EcoSal Plus 2019; 8. [PMID: 30109846 DOI: 10.1128/ecosalplus.esp-0004-2018] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
RNA polymerase (RNAP) is the essential enzyme responsible for transcribing genetic information stored in DNA to RNA. Understanding the structure and function of RNAP is important for those who study basic principles in gene expression, such as the mechanism of transcription and its regulation, as well as translational sciences such as antibiotic development. With over a half-century of investigations, there is a wealth of information available on the structure and function of Escherichia coli RNAP. This review introduces the structural features of E. coli RNAP, organized by subunit, giving information on the function, location, and conservation of these features to early stage investigators who have just started their research of E. coli RNAP.
Collapse
|
64
|
Li L, Fang C, Zhuang N, Wang T, Zhang Y. Structural basis for transcription initiation by bacterial ECF σ factors. Nat Commun 2019; 10:1153. [PMID: 30858373 PMCID: PMC6411747 DOI: 10.1038/s41467-019-09096-y] [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: 10/17/2018] [Accepted: 02/01/2019] [Indexed: 01/07/2023] Open
Abstract
Bacterial RNA polymerase employs extra-cytoplasmic function (ECF) σ factors to regulate context-specific gene expression programs. Despite being the most abundant and divergent σ factor class, the structural basis of ECF σ factor-mediated transcription initiation remains unknown. Here, we determine a crystal structure of Mycobacterium tuberculosis (Mtb) RNAP holoenzyme comprising an RNAP core enzyme and the ECF σ factor σH (σH-RNAP) at 2.7 Å, and solve another crystal structure of a transcription initiation complex of Mtb σH-RNAP (σH-RPo) comprising promoter DNA and an RNA primer at 2.8 Å. The two structures together reveal the interactions between σH and RNAP that are essential for σH-RNAP holoenzyme assembly as well as the interactions between σH-RNAP and promoter DNA responsible for stringent promoter recognition and for promoter unwinding. Our study establishes that ECF σ factors and primary σ factors employ distinct mechanisms for promoter recognition and for promoter unwinding.
Collapse
Affiliation(s)
- Lingting Li
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,0000 0004 1797 8419grid.410726.6University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chengli Fang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,0000 0004 1797 8419grid.410726.6University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ningning Zhuang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Tiantian Wang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,0000 0004 1797 8419grid.410726.6University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yu Zhang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
| |
Collapse
|
65
|
Structural basis of ECF-σ-factor-dependent transcription initiation. Nat Commun 2019; 10:710. [PMID: 30755604 PMCID: PMC6372665 DOI: 10.1038/s41467-019-08443-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/11/2019] [Indexed: 01/24/2023] Open
Abstract
Extracytoplasmic (ECF) σ factors, the largest class of alternative σ factors, are related to primary σ factors, but have simpler structures, comprising only two of six conserved functional modules in primary σ factors: region 2 (σR2) and region 4 (σR4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M. tuberculosis ECF σ factor σL, and promoter DNA. The structures show that σR2 and σR4 of the ECF σ factor occupy the same sites on RNAP as in primary σ factors, show that the connector between σR2 and σR4 of the ECF σ factor–although shorter and unrelated in sequence–follows the same path through RNAP as in primary σ factors, and show that the ECF σ factor uses the same strategy to bind and unwind promoter DNA as primary σ factors. The results define protein-protein and protein-DNA interactions involved in ECF-σ-factor-dependent transcription initiation. No structural data have been available for RNA polymerase holoenzymes or transcription initiation complexes that contain extracytoplasmic σ factors. Here the authors report the crystal structures of transcription initiation complexes comprising Mycobacterium tuberculosis RNA polymerase, extracytoplasmic σ factor σL and promoter DNA.
Collapse
|
66
|
Pupov D, Ignatov A, Agapov A, Kulbachinskiy A. Distinct effects of DNA lesions on RNA synthesis by Escherichia coli RNA polymerase. Biochem Biophys Res Commun 2019; 510:122-127. [PMID: 30665719 DOI: 10.1016/j.bbrc.2019.01.062] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/12/2019] [Indexed: 01/08/2023]
Abstract
DNA lesions can severely compromise genome stability and lead to cell death if unrepaired. RNA polymerase (RNAP) is known to serve as a sensor of DNA damage and to attract DNA repair factors to the damaged template sites. Here, we systematically investigated the ability of Escherichia coli RNAP to transcribe DNA templates containing various types of DNA lesions, and analyzed their effects on transcription fidelity. We showed that transcription is strongly inhibited on templates containing cyclobutane thymine dimers, 1,N6-ethenoadenine and abasic sites, while 8-oxoguanine and thymine glycol have mild effects on transcription efficiency. Similarly to many polymerases, E. coli RNAP follows the "A" rule during nucleotide insertion opposite abasic sites and bulky lesions, and can also incorporate and efficiently extend an adenine nucleotide opposite 8-oxoguanine. Mutations in RNAP regions around the templating nucleotide decrease the efficiency of translesion synthesis, likely by altering the RNAP-template contacts in the active site. Thus, DNA lesions can lead to distinct outcomes in transcription, depending on the severity of the damage and contacts of the damaged template with the active site of RNAP.
Collapse
Affiliation(s)
- Danil Pupov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Artem Ignatov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Aleksei Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
| |
Collapse
|
67
|
Initiating DNA replication: a matter of prime importance. Biochem Soc Trans 2019; 47:351-356. [PMID: 30647143 PMCID: PMC6393858 DOI: 10.1042/bst20180627] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/30/2018] [Accepted: 12/05/2018] [Indexed: 11/17/2022]
Abstract
It has been known for decades that the principal replicative DNA polymerases that effect genome replication are incapable of starting DNA synthesis de novo. Rather, they require a 3′-OH group from which to extend a DNA chain. Cellular DNA replication systems exploit a dedicated, limited processivity RNA polymerase, termed primase, that synthesizes a short oligoribonucleotide primer which is then extended by a DNA polymerase. Thus, primases can initiate synthesis, proceed with primer elongation for a short distance then transfer the primer to a DNA polymerase. Despite these well-established properties, the mechanistic basis of these dynamic behaviours has only recently been established. In the following, the author will describe recent insights from studies of the related eukaryotic and archaeal DNA primases. Significantly, the general conclusions from these studies likely extend to a broad class of extrachromosomal element-associated primases as well as the human primase-related DNA repair enzyme, PrimPol.
Collapse
|
68
|
Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin. Proc Natl Acad Sci U S A 2019; 116:1273-1278. [PMID: 30626643 PMCID: PMC6347699 DOI: 10.1073/pnas.1817352116] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Many bacteria produce antimicrobial peptides for survival under stressful conditions. Some of these antimicrobial peptides are lasso peptides, which have a unique lasso-like topology and have generated great interest as a result of their stability in harsh conditions and amenability to functional engineering. In this study, we determined crystal structures of two lasso peptides, microcin J25 and capistruin, bound to their natural enzymatic target, the bacterial RNA polymerase (RNAP). The structures define peptide inhibitor–RNAP interactions that are important for inhibition and provide detailed insight into how the peptides inhibit RNAP function. This work provides a structural basis to guide the design of more potent lasso peptide antimicrobial approaches. We report crystal structures of the antibacterial lasso peptides microcin J25 (MccJ25) and capistruin (Cap) bound to their natural enzymatic target, the bacterial RNA polymerase (RNAP). Both peptides bind within the RNAP secondary channel, through which NTP substrates enter the RNAP active site, and sterically block trigger-loop folding, which is essential for efficient catalysis by the RNAP. MccJ25 binds deep within the secondary channel in a manner expected to interfere with NTP substrate binding, explaining the partial competitive mechanism of inhibition with respect to NTPs found previously [Mukhopadhyay J, Sineva E, Knight J, Levy RM, Ebright RH (2004) Mol Cell 14:739–751]. The Cap binding determinant on RNAP overlaps, but is not identical to, that of MccJ25. Cap binds further from the RNAP active site and does not sterically interfere with NTP binding, and we show that Cap inhibition is partially noncompetitive with respect to NTPs. This work lays the groundwork for structure determination of other lasso peptides that target the bacterial RNAP and provides a structural foundation to guide lasso peptide antimicrobial engineering approaches.
Collapse
|
69
|
Fouqueau T, Blombach F, Cackett G, Carty AE, Matelska DM, Ofer S, Pilotto S, Phung DK, Werner F. The cutting edge of archaeal transcription. Emerg Top Life Sci 2018; 2:517-533. [PMID: 33525828 PMCID: PMC7289017 DOI: 10.1042/etls20180014] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/01/2018] [Accepted: 10/04/2018] [Indexed: 12/26/2022]
Abstract
The archaeal RNA polymerase (RNAP) is a double-psi β-barrel enzyme closely related to eukaryotic RNAPII in terms of subunit composition and architecture, promoter elements and basal transcription factors required for the initiation and elongation phase of transcription. Understanding archaeal transcription is, therefore, key to delineate the universally conserved fundamental mechanisms of transcription as well as the evolution of the archaeo-eukaryotic transcription machineries. The dynamic interplay between RNAP subunits, transcription factors and nucleic acids dictates the activity of RNAP and ultimately gene expression. This review focusses on recent progress in our understanding of (i) the structure, function and molecular mechanisms of known and less characterized factors including Elf1 (Elongation factor 1), NusA (N-utilization substance A), TFS4, RIP and Eta, and (ii) their evolution and phylogenetic distribution across the expanding tree of Archaea.
Collapse
Affiliation(s)
- Thomas Fouqueau
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Fabian Blombach
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Gwenny Cackett
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Alice E Carty
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Dorota M Matelska
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Sapir Ofer
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Simona Pilotto
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Duy Khanh Phung
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Finn Werner
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| |
Collapse
|
70
|
Esyunina D, Pupov D, Kulbachinskiy A. Dual role of the σ factor in primer RNA synthesis by bacterial RNA polymerase. FEBS Lett 2018; 593:361-368. [PMID: 30536890 DOI: 10.1002/1873-3468.13312] [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: 10/10/2018] [Revised: 11/28/2018] [Accepted: 11/30/2018] [Indexed: 11/08/2022]
Abstract
Bacterial RNA polymerase (RNAP) serves as a primase during replication of single-stranded plasmids and filamentous phages. Primer RNA (prRNA) synthesis from the origin regions of these replicons depends on the σ factor that normally participates in promoter recognition. However, it was proposed that σ may not be required for origin recognition but is rather involved in RNA extension by RNAP. Here, by analyzing the natural replication origin of bacteriophage M13 and synthetic ssDNA templates, we show that interactions of σ with promoter-like motifs stabilize priming complexes and can control prRNA synthesis by trapping RNAP on the template. Thus, the σ factor is involved in both DNA recognition and RNA priming, unifying its functions in transcription initiation from double- and single-stranded templates.
Collapse
Affiliation(s)
- Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Danil Pupov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | | |
Collapse
|
71
|
Turtola M, Mäkinen JJ, Belogurov GA. Active site closure stabilizes the backtracked state of RNA polymerase. Nucleic Acids Res 2018; 46:10870-10887. [PMID: 30256972 PMCID: PMC6237748 DOI: 10.1093/nar/gky883] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/30/2018] [Accepted: 09/19/2018] [Indexed: 01/02/2023] Open
Abstract
All cellular RNA polymerases (RNAP) occasionally backtrack along the template DNA as part of transcriptional proofreading and regulation. Here, we studied the mechanism of RNAP backtracking by one nucleotide using two complementary approaches that allowed us to precisely measure the occupancy and lifetime of the backtracked state. Our data show that the stability of the backtracked state is critically dependent on the closure of the RNAP active site by a mobile domain, the trigger loop (TL). The lifetime and occupancy of the backtracked state measurably decreased by substitutions of the TL residues that interact with the nucleoside triphosphate (NTP) substrate, whereas amino acid substitutions that stabilized the closed active site increased the lifetime and occupancy. These results suggest that the same conformer of the TL closes the active site during catalysis of nucleotide incorporation into the nascent RNA and backtracking by one nucleotide. In support of this hypothesis, we construct a model of the 1-nt backtracked complex with the closed active site and the backtracked nucleotide in the entry pore area known as the E-site. We further propose that 1-nt backtracking mimics the reversal of the NTP substrate loading into the RNAP active site during on-pathway elongation.
Collapse
Affiliation(s)
- Matti Turtola
- University of Turku, Department of Biochemistry, FIN-20014 Turku, Finland
| | - Janne J Mäkinen
- University of Turku, Department of Biochemistry, FIN-20014 Turku, Finland
| | | |
Collapse
|
72
|
Bharanikumar R, Premkumar KAR, Palaniappan A. PromoterPredict: sequence-based modelling of Escherichia coli σ 70 promoter strength yields logarithmic dependence between promoter strength and sequence. PeerJ 2018; 6:e5862. [PMID: 30425888 PMCID: PMC6228582 DOI: 10.7717/peerj.5862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022] Open
Abstract
We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ70 factor of RNA polymerase. σ70 promoters are ubiquitously used in recombinant DNA technology, but characterizing their strength is demanding in terms of both time and money. We parsed a comprehensive database of bacterial promoters for the -35 and -10 hexamer regions of σ70-binding promoters and used these sequences to construct the respective position weight matrices (PWM). Next we used a well-characterized set of promoters to train a multivariate linear regression model and learn the mapping between PWM scores of the -35 and -10 hexamers and the promoter strength. We found that the log of the promoter strength is significantly linearly associated with a weighted sum of the -10 and -35 sequence profile scores. We applied our model to 100 sets of 100 randomly generated promoter sequences to generate a sampling distribution of mean strengths of random promoter sequences and obtained a mean of 6E-4 ± 1E-7. Our model was further validated by cross-validation and on independent datasets of characterized promoters. PromoterPredict accepts -10 and -35 hexamer sequences and returns the predicted promoter strength. It is capable of dynamic learning from user-supplied data to refine the model construction and yield more robust estimates of promoter strength. PromoterPredict is available as both a web service (https://promoterpredict.com) and standalone tool (https://github.com/PromoterPredict). Our work presents an intuitive generalization applicable to modelling the strength of other promoter classes.
Collapse
Affiliation(s)
- Ramit Bharanikumar
- Biotechnology, Sri Venkateswara College of Engineering (Autonomous), Sriperumbudur, Tamil Nadu, India
| | - Keshav Aditya R Premkumar
- Computer Science and Engineering, Sri Venkateswara College of Engineering (Autonomous), Sriperumbudur, Tamil Nadu, India
| | - Ashok Palaniappan
- Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India
| |
Collapse
|
73
|
Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Elisa Donati
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| |
Collapse
|
74
|
Mosaei H, Molodtsov V, Kepplinger B, Harbottle J, Moon CW, Jeeves RE, Ceccaroni L, Shin Y, Morton-Laing S, Marrs ECL, Wills C, Clegg W, Yuzenkova Y, Perry JD, Bacon J, Errington J, Allenby NEE, Hall MJ, Murakami KS, Zenkin N. Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin-Resistant Mycobacterium tuberculosis. Mol Cell 2018; 72:263-274.e5. [PMID: 30244835 PMCID: PMC6202310 DOI: 10.1016/j.molcel.2018.08.028] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/19/2018] [Accepted: 08/17/2018] [Indexed: 01/07/2023]
Abstract
Antibiotic-resistant bacterial pathogens pose an urgent healthcare threat, prompting a demand for new medicines. We report the mode of action of the natural ansamycin antibiotic kanglemycin A (KglA). KglA binds bacterial RNA polymerase at the rifampicin-binding pocket but maintains potency against RNA polymerases containing rifampicin-resistant mutations. KglA has antibiotic activity against rifampicin-resistant Gram-positive bacteria and multidrug-resistant Mycobacterium tuberculosis (MDR-M. tuberculosis). The X-ray crystal structures of KglA with the Escherichia coli RNA polymerase holoenzyme and Thermus thermophilus RNA polymerase-promoter complex reveal an altered-compared with rifampicin-conformation of KglA within the rifampicin-binding pocket. Unique deoxysugar and succinate ansa bridge substituents make additional contacts with a separate, hydrophobic pocket of RNA polymerase and preclude the formation of initial dinucleotides, respectively. Previous ansa-chain modifications in the rifamycin series have proven unsuccessful. Thus, KglA represents a key starting point for the development of a new class of ansa-chain derivatized ansamycins to tackle rifampicin resistance.
Collapse
Affiliation(s)
- Hamed Mosaei
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Vadim Molodtsov
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Bernhard Kepplinger
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK,Demuris Limited, Newcastle Biomedicine Bio-Incubators, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - John Harbottle
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Christopher William Moon
- TB Research Group, National Infection Service, Public Health England, Manor Farm Road, Porton, Salisbury SP4 0JG, UK
| | - Rose Elizabeth Jeeves
- TB Research Group, National Infection Service, Public Health England, Manor Farm Road, Porton, Salisbury SP4 0JG, UK
| | - Lucia Ceccaroni
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Yeonoh Shin
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Stephanie Morton-Laing
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | - Corinne Wills
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - William Clegg
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Yulia Yuzenkova
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - John David Perry
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK
| | - Joanna Bacon
- TB Research Group, National Infection Service, Public Health England, Manor Farm Road, Porton, Salisbury SP4 0JG, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK,Demuris Limited, Newcastle Biomedicine Bio-Incubators, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | | | - Michael John Hall
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Katsuhiko S. Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA,Corresponding author
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK,Corresponding author
| |
Collapse
|
75
|
Peek J, Lilic M, Montiel D, Milshteyn A, Woodworth I, Biggins JB, Ternei MA, Calle PY, Danziger M, Warrier T, Saito K, Braffman N, Fay A, Glickman MS, Darst SA, Campbell EA, Brady SF. Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism. Nat Commun 2018; 9:4147. [PMID: 30297823 PMCID: PMC6175910 DOI: 10.1038/s41467-018-06587-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/29/2018] [Indexed: 11/25/2022] Open
Abstract
Rifamycin antibiotics (Rifs) target bacterial RNA polymerases (RNAPs) and are widely used to treat infections including tuberculosis. The utility of these compounds is threatened by the increasing incidence of resistance (RifR). As resistance mechanisms found in clinical settings may also occur in natural environments, here we postulated that bacteria could have evolved to produce rifamycin congeners active against clinically relevant resistance phenotypes. We survey soil metagenomes and identify a tailoring enzyme-rich family of gene clusters encoding biosynthesis of rifamycin congeners (kanglemycins, Kangs) with potent in vivo and in vitro activity against the most common clinically relevant RifR mutations. Our structural and mechanistic analyses reveal the basis for Kang inhibition of RifR RNAP. Unlike Rifs, Kangs function through a mechanism that includes interfering with 5'-initiating substrate binding. Our results suggest that examining soil microbiomes for new analogues of clinically used antibiotics may uncover metabolites capable of circumventing clinically important resistance mechanisms.
Collapse
Affiliation(s)
- James Peek
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Mirjana Lilic
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Daniel Montiel
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Aleksandr Milshteyn
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Ian Woodworth
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - John B Biggins
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Paula Y Calle
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Michael Danziger
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Thulasi Warrier
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kohta Saito
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Nathaniel Braffman
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Allison Fay
- Immunology Program, Sloan-Kettering Institute, New York, NY, 10065, USA
| | | | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
| |
Collapse
|
76
|
Molodtsov V, Murakami KS. Minimalism and functionality: Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II. J Biol Chem 2018; 293:13616-13625. [PMID: 29991593 PMCID: PMC6120196 DOI: 10.1074/jbc.ra118.003447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/19/2018] [Indexed: 01/07/2023] Open
Abstract
Genomes of phages, mitochondria, and chloroplasts are transcribed by a diverse group of transcriptional machineries with structurally related single-subunit RNA polymerases (RNAPs). Our understanding of transcription mechanisms of these enzymes is predominantly based on biochemical and structural studies of three most-studied members, transcription factor-independent phage T7 RNAP, transcription factor-dependent phage N4 virion-encapsidated RNAP, and transcription factor-dependent mitochondrial RNAPs (mtRNAP). Although these RNAPs employ completely different mechanisms for promoter recognition and transcription termination, these enzymes are relatively large and formed by single polypeptides. Historically being a model enzyme for studying the mechanisms of transcription by T7-like RNAPs, however, T7 RNAP represents only a small group of RNAPs in this family. The vast majority of T7-like RNAPs are transcription factor-dependent, and several of them are heterodimeric enzymes. Here, we report X-ray crystal structures of transcription complexes of the smallest and heterodimeric form of T7-like RNAP, bacteriophage N4 RNAPII, providing insights into the structural organization of a minimum RNAP in this family. We analyze structural and functional aspects of heterodimeric architecture of N4 RNAPII concerning the mechanisms of transcription initiation and transition to processive RNA elongation. Interestingly, N4 RNAPII maintains the same conformation in promoter-bound and elongation transcription complexes, revealing a novel transcription mechanism for single-subunit RNAPs. This work establishes a structural basis for studying mechanistic aspects of transcription by factor-dependent minimum RNAP.
Collapse
Affiliation(s)
- Vadim Molodtsov
- From the Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, To whom correspondence may be addressed. E-mail:
| | - Katsuhiko S. Murakami
- From the Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, To whom correspondence may be addressed. E-mail:
| |
Collapse
|
77
|
Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M, Zhang X. Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation. Mol Cell 2018; 70:1111-1120.e3. [PMID: 29932903 PMCID: PMC6028918 DOI: 10.1016/j.molcel.2018.05.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/25/2018] [Accepted: 05/18/2018] [Indexed: 12/15/2022]
Abstract
Gene transcription is carried out by multi-subunit RNA polymerases (RNAPs). Transcription initiation is a dynamic multi-step process that involves the opening of the double-stranded DNA to form a transcription bubble and delivery of the template strand deep into the RNAP for RNA synthesis. Applying cryoelectron microscopy to a unique transcription system using σ54 (σN), the major bacterial variant sigma factor, we capture a new intermediate state at 4.1 Å where promoter DNA is caught at the entrance of the RNAP cleft. Combining with new structures of the open promoter complex and an initial de novo transcribing complex at 3.4 and 3.7 Å, respectively, our studies reveal the dynamics of DNA loading and mechanism of transcription bubble stabilization that involves coordinated, large-scale conformational changes of the universally conserved features within RNAP and DNA. In addition, our studies reveal a novel mechanism of strand separation by σ54.
Collapse
Affiliation(s)
- Robert Glyde
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Fuzhou Ye
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Milija Jovanovic
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Martin Buck
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK.
| |
Collapse
|
78
|
Dulin D, Bauer DLV, Malinen AM, Bakermans JJW, Kaller M, Morichaud Z, Petushkov I, Depken M, Brodolin K, Kulbachinskiy A, Kapanidis AN. Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria. Nat Commun 2018; 9:1478. [PMID: 29662062 PMCID: PMC5902446 DOI: 10.1038/s41467-018-03902-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 03/20/2018] [Indexed: 01/25/2023] Open
Abstract
Transcription in bacteria is controlled by multiple molecular mechanisms that precisely regulate gene expression. It has been recently shown that initial RNA synthesis by the bacterial RNA polymerase (RNAP) is interrupted by pauses; however, the pausing determinants and the relationship of pausing with productive and abortive RNA synthesis remain poorly understood. Using single-molecule FRET and biochemical analysis, here we show that the pause encountered by RNAP after the synthesis of a 6-nt RNA (ITC6) renders the promoter escape strongly dependent on the NTP concentration. Mechanistically, the paused ITC6 acts as a checkpoint that directs RNAP to one of three competing pathways: productive transcription, abortive RNA release, or a new unscrunching/scrunching pathway. The cyclic unscrunching/scrunching of the promoter generates a long-lived, RNA-bound paused state; the abortive RNA release and DNA unscrunching are thus not as tightly linked as previously thought. Finally, our new model couples the pausing with the abortive and productive outcomes of initial transcription.
Collapse
Affiliation(s)
- David Dulin
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK.
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Hartmannstrasse 14, 91052, Erlangen, Germany.
| | - David L V Bauer
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Anssi M Malinen
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
- Department of Biochemistry, University of Turku, 20014, Turku, Finland
| | - Jacob J W Bakermans
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Martin Kaller
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Zakia Morichaud
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR9004 CNRS-Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, France
| | - Ivan Petushkov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Konstantin Brodolin
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR9004 CNRS-Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, France
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK.
| |
Collapse
|
79
|
Gill EE, Chan LS, Winsor GL, Dobson N, Lo R, Ho Sui SJ, Dhillon BK, Taylor PK, Shrestha R, Spencer C, Hancock REW, Unrau PJ, Brinkman FSL. High-throughput detection of RNA processing in bacteria. BMC Genomics 2018; 19:223. [PMID: 29587634 PMCID: PMC5870498 DOI: 10.1186/s12864-018-4538-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/12/2018] [Indexed: 01/19/2023] Open
Abstract
Background Understanding the RNA processing of an organism’s transcriptome is an essential but challenging step in understanding its biology. Here we investigate with unprecedented detail the transcriptome of Pseudomonas aeruginosa PAO1, a medically important and innately multi-drug resistant bacterium. We systematically mapped RNA cleavage and dephosphorylation sites that result in 5′-monophosphate terminated RNA (pRNA) using monophosphate RNA-Seq (pRNA-Seq). Transcriptional start sites (TSS) were also mapped using differential RNA-Seq (dRNA-Seq) and both datasets were compared to conventional RNA-Seq performed in a variety of growth conditions. Results The pRNA-Seq library revealed known tRNA, rRNA and transfer-messenger RNA (tmRNA) processing sites, together with previously uncharacterized RNA cleavage events that were found disproportionately near the 5′ ends of transcripts associated with basic bacterial functions such as oxidative phosphorylation and purine metabolism. The majority (97%) of the processed mRNAs were cleaved at precise codon positions within defined sequence motifs indicative of distinct endonucleolytic activities. The most abundant of these motifs corresponded closely to an E. coli RNase E site previously established in vitro. Using the dRNA-Seq library, we performed an operon analysis and predicted 3159 potential TSS. A correlation analysis uncovered 105 antiparallel pairs of TSS that were separated by 18 bp from each other and were centered on single palindromic TAT(A/T)ATA motifs (likely − 10 promoter elements), suggesting that, consistent with previous in vitro experimentation, these sites can initiate transcription bi-directionally and may thus provide a novel form of transcriptional regulation. TSS and RNA-Seq analysis allowed us to confirm expression of small non-coding RNAs (ncRNAs), many of which are differentially expressed in swarming and biofilm formation conditions. Conclusions This study uses pRNA-Seq, a method that provides a genome-wide survey of RNA processing, to study the bacterium Pseudomonas aeruginosa and discover extensive transcript processing not previously appreciated. We have also gained novel insight into RNA maturation and turnover as well as a potential novel form of transcription regulation. NOTE: All sequence data has been submitted to the NCBI sequence read archive. Accession numbers are as follows: [NCBI sequence read archive: SRX156386, SRX157659, SRX157660, SRX157661, SRX157683 and SRX158075]. The sequence data is viewable using Jbrowse on www.pseudomonas.com. Electronic supplementary material The online version of this article (10.1186/s12864-018-4538-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Erin E Gill
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Luisa S Chan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Geoffrey L Winsor
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Neil Dobson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Raymond Lo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Shannan J Ho Sui
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Bhavjinder K Dhillon
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Patrick K Taylor
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Raunak Shrestha
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Cory Spencer
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Robert E W Hancock
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
| |
Collapse
|
80
|
Molodtsov V, Sineva E, Zhang L, Huang X, Cashel M, Ades SE, Murakami KS. Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA. Mol Cell 2018; 69:828-839.e5. [PMID: 29478808 DOI: 10.1016/j.molcel.2018.01.035] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/05/2017] [Accepted: 01/25/2018] [Indexed: 02/07/2023]
Abstract
DksA and ppGpp are the central players in the stringent response and mediate a complete reprogramming of the transcriptome. A major component of the response is a reduction in ribosome synthesis, which is accomplished by the synergistic action of DksA and ppGpp bound to RNA polymerase (RNAP) inhibiting transcription of rRNAs. Here, we report the X-ray crystal structures of Escherichia coli RNAP in complex with DksA alone and with ppGpp. The structures show that DksA accesses the template strand at the active site and the downstream DNA binding site of RNAP simultaneously and reveal that binding of the allosteric effector ppGpp reshapes the RNAP-DksA complex. The structural data support a model for transcriptional inhibition in which ppGpp potentiates the destabilization of open complexes by DksA. This work establishes a structural basis for understanding the pleiotropic effects of DksA and ppGpp on transcriptional regulation in proteobacteria.
Collapse
Affiliation(s)
- Vadim Molodtsov
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Elena Sineva
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Michael Cashel
- Intramural Research Program, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah E Ades
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
| |
Collapse
|
81
|
Interplay between σ region 3.2 and secondary channel factors during promoter escape by bacterial RNA polymerase. Biochem J 2017; 474:4053-4064. [DOI: 10.1042/bcj20170436] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 12/29/2022]
Abstract
In bacterial RNA polymerase (RNAP), conserved region 3.2 of the σ subunit was proposed to contribute to promoter escape by interacting with the 5′-end of nascent RNA, thus facilitating σ dissociation. RNAP activity during transcription initiation can also be modulated by protein factors that bind within the secondary channel and reach the enzyme active site. To monitor the kinetics of promoter escape in real time, we used a molecular beacon assay with fluorescently labeled σ70 subunit of Escherichia coli RNAP. We show that substitutions and deletions in σ region 3.2 decrease the rate of promoter escape and lead to accumulation of inactive complexes during transcription initiation. Secondary channel factors differentially regulate this process depending on the promoter and mutations in σ region 3.2. GreA generally increase the rate of promoter escape; DksA also stimulates promoter escape on certain templates, while GreB either stimulates or inhibits this process depending on the template. When observed, the stimulation of promoter escape correlates with the accumulation of stressed transcription complexes with scrunched DNA, while changes in the RNA 5′-end structure modulate promoter clearance. Thus, the initiation-to-elongation transition is controlled by a complex interplay between RNAP-binding protein factors and the growing RNA chain.
Collapse
|
82
|
Barvík I, Rejman D, Panova N, Šanderová H, Krásný L. Non-canonical transcription initiation: the expanding universe of transcription initiating substrates. FEMS Microbiol Rev 2017; 41:131-138. [PMID: 27799279 DOI: 10.1093/femsre/fuw041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2016] [Indexed: 11/13/2022] Open
Abstract
RNA polymerase (RNAP) is the central enzyme of transcription of the genetic information from DNA into RNA. RNAP recognizes four main substrates: ATP, CTP, GTP and UTP. Experimental evidence from the past several years suggests that, besides these four NTPs, other molecules can be used to initiate transcription: (i) ribooligonucleotides (nanoRNAs) and (ii) coenzymes such as NAD+, NADH, dephospho-CoA and FAD. The presence of these molecules at the 5΄ ends of RNAs affects the properties of the RNA. Here, we discuss the expanding portfolio of molecules that can initiate transcription, their mechanism of incorporation, effects on RNA and cellular processes, and we present an outlook toward other possible initiation substrates.
Collapse
Affiliation(s)
- Ivan Barvík
- Division of Biomolecular Physics, Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences v. v. i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Natalya Panova
- Institute of Microbiology, Czech Academy of Sciences v. v. i., Vídenská 1083, 142 20 Prague 4, Czech Republic
| | - Hana Šanderová
- Institute of Microbiology, Czech Academy of Sciences v. v. i., Vídenská 1083, 142 20 Prague 4, Czech Republic
| | - Libor Krásný
- Institute of Microbiology, Czech Academy of Sciences v. v. i., Vídenská 1083, 142 20 Prague 4, Czech Republic
| |
Collapse
|
83
|
Primer synthesis by a eukaryotic-like archaeal primase is independent of its Fe-S cluster. Nat Commun 2017; 8:1718. [PMID: 29167441 PMCID: PMC5700102 DOI: 10.1038/s41467-017-01707-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/09/2017] [Indexed: 01/11/2023] Open
Abstract
DNA replication depends on primase, the specialised polymerase responsible for synthesis of the RNA primers that are elongated by the replicative DNA polymerases. In eukaryotic and archaeal replication, primase is a heterodimer of two subunits, PriS and PriL. Recently, a third primase subunit named PriX was identified in the archaeon Sulfolobus solfataricus. PriX is essential for primer synthesis and is structurally related to the Fe–S cluster domain of eukaryotic PriL. Here we show that PriX contains a nucleotide-binding site required for primer synthesis, and demonstrate equivalence of nucleotide-binding residues in PriX with eukaryotic PriL residues that are known to be important for primer synthesis. A primase chimera, where PriX is fused to a truncated version of PriL lacking the Fe–S cluster domain retains wild-type levels of primer synthesis. Our evidence shows that PriX has replaced PriL as the subunit that endows primase with the unique ability to initiate nucleic acid synthesis. Importantly, our findings reveal that the Fe–S cluster is not required for primer synthesis. Primase is the specialised DNA-dependent RNA polymerase responsible for the initiation of DNA synthesis during DNA replication. Here the authors use a structural biology approach to identify the initiation site in the S. solfataricus PriSLX primase and to demonstrate that its Fe-S cluster is dispensable for primer synthesis.
Collapse
|
84
|
Miropolskaya N, Feklistov A, Nikiforov V, Kulbachinskiy A. Site-specific aptamer inhibitors of Thermus RNA polymerase. Biochem Biophys Res Commun 2017; 495:110-115. [PMID: 29097207 DOI: 10.1016/j.bbrc.2017.10.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 10/28/2017] [Indexed: 11/19/2022]
Abstract
Bacterial RNA polymerase (RNAP) is an RNA-synthesizing molecular machine and a target for antibiotics. In transcription, RNAP can interact with DNA sequence-specifically, during promoter recognition by the σ-containing holoenzyme, or nonspecifically, during productive RNA elongation by the core RNAP. We describe high-affinity single-stranded DNA aptamers that are specifically recognized by the core RNAP from Thermus aquaticus. The aptamers interact with distinct epitopes inside the RNAP main channel, including the rifamycin pocket, and sense the binding of other RNAP ligands such as rifamycin and the σA subunit. The aptamers inhibit RNAP activity and can thus be used for functional studies of transcription and development of novel RNAP inhibitors.
Collapse
Affiliation(s)
- Nataliya Miropolskaya
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia
| | - Andrey Feklistov
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Vadim Nikiforov
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia.
| |
Collapse
|
85
|
Petushkov I, Esyunina D, Kulbachinskiy A. Possible roles of σ-dependent RNA polymerase pausing in transcription regulation. RNA Biol 2017; 14:1678-1682. [PMID: 28816625 DOI: 10.1080/15476286.2017.1356568] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The σ subunit of bacterial RNA polymerase is required for promoter recognition during transcription initiation but may also regulate transcription elongation. The principal σ70 subunit of Escherichia coli was shown to travel with RNA polymerase and induce transcriptional pausing at promoter-like motifs, with potential regulatory output. We recently demonstrated that an alternative σ38 subunit can also induce RNA polymerase pausing. Here, we outline proposed regulatory roles of σ-dependent pausing in bacteria and discuss possible interplay between alternative σ variants and regulatory factors during transcription elongation.
Collapse
Affiliation(s)
- Ivan Petushkov
- a Laboratory of Molecular Genetics of Microorganisms, Institute of Molecular Genetics , Russian Academy of Sciences , Moscow , Russia.,b Molecular Biology Department, Biological Faculty , Moscow State University , Moscow , Russia
| | - Daria Esyunina
- a Laboratory of Molecular Genetics of Microorganisms, Institute of Molecular Genetics , Russian Academy of Sciences , Moscow , Russia
| | - Andrey Kulbachinskiy
- a Laboratory of Molecular Genetics of Microorganisms, Institute of Molecular Genetics , Russian Academy of Sciences , Moscow , Russia.,b Molecular Biology Department, Biological Faculty , Moscow State University , Moscow , Russia
| |
Collapse
|
86
|
Appling FD, Lucius AL, Schneider DA. Quantifying the influence of 5'-RNA modifications on RNA polymerase I activity. Biophys Chem 2017; 230:84-88. [PMID: 28893424 DOI: 10.1016/j.bpc.2017.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 11/19/2022]
Abstract
For ensemble and single-molecule analyses of transcription, the use of synthetic transcription elongation complexes has been a versatile and powerful tool. However, structural analyses demonstrate that short RNA substrates, often employed in these assays, would occupy space within the RNA polymerase. Most commercial RNA oligonucleotides do not carry a 5'-triphosphate as would be present on a natural, de novo synthesized RNA. To examine the effects of 5'-moities on transcription kinetics, we measured nucleotide addition and 3'-dinucleotide cleavage by eukaryotic RNA polymerase I using 5'-hydroxyl and 5'-triphosphate RNA substrates. We found that 5' modifications had no discernable effect on the kinetics of nucleotide addition; however, we observed clear, but modest, effects on the rate of backtracking and/or dinucleotide cleavage. These data suggest that the 5'-end may influence RNA polymerase translocation, consistent with previous prokaryotic studies, and these findings may have implications on kinetic barriers that confront RNA polymerases during the transition from initiation to elongation.
Collapse
Affiliation(s)
- Francis D Appling
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
| |
Collapse
|
87
|
Petushkov I, Esyunina D, Kulbachinskiy A. σ38-dependent promoter-proximal pausing by bacterial RNA polymerase. Nucleic Acids Res 2017; 45:3006-3016. [PMID: 27928053 PMCID: PMC5389655 DOI: 10.1093/nar/gkw1213] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/29/2016] [Indexed: 11/24/2022] Open
Abstract
Transcription initiation by bacterial RNA polymerase (RNAP) requires a variable σ subunit that directs it to promoters for site-specific priming of RNA synthesis. The principal σ subunit responsible for expression of house-keeping genes can bind the transcription elongation complex after initiation and induce RNAP pausing through specific interactions with promoter-like motifs in transcribed DNA. We show that the stationary phase and stress response σ38 subunit can also induce pausing by Escherichia coli RNAP on DNA templates containing promoter-like motifs in the transcribed regions. The pausing depends on σ38 contacts with the DNA template and RNAP core enzyme and results in formation of backtracked transcription elongation complexes, which can be reactivated by Gre factors that induce RNA cleavage by RNAP. Our data suggest that σ38 can bind the transcription elongation complex in trans but likely acts in cis during transcription initiation, by staying bound to RNAP and recognizing promoter-proximal pause signals. Analysis of σ38-dependent promoters reveals that a substantial fraction of them contain potential pause-inducing motifs, suggesting that σ38-depended pausing may be a common phenomenon in bacterial transcription.
Collapse
Affiliation(s)
- Ivan Petushkov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.,Molecular Biology Department, Biological Faculty, Moscow State University, Moscow 119991, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.,Molecular Biology Department, Biological Faculty, Moscow State University, Moscow 119991, Russia
| |
Collapse
|
88
|
Alhadid Y, Chung S, Lerner E, Taatjes DJ, Borukhov S, Weiss S. Studying transcription initiation by RNA polymerase with diffusion-based single-molecule fluorescence. Protein Sci 2017; 26:1278-1290. [PMID: 28370550 PMCID: PMC5477543 DOI: 10.1002/pro.3160] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/11/2017] [Accepted: 03/13/2017] [Indexed: 01/30/2023]
Abstract
Over the past decade, fluorescence-based single-molecule studies significantly contributed to characterizing the mechanism of RNA polymerase at different steps in transcription, especially in transcription initiation. Transcription by bacterial DNA-dependent RNA polymerase is a multistep process that uses genomic DNA to synthesize complementary RNA molecules. Transcription initiation is a highly regulated step in E. coli, but it has been challenging to study its mechanism because of its stochasticity and complexity. In this review, we describe how single-molecule approaches have contributed to our understanding of transcription and have uncovered mechanistic details that were not observed in conventional assays because of ensemble averaging.
Collapse
Affiliation(s)
- Yazan Alhadid
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, California, 90095
| | - SangYoon Chung
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California, 90095
| | - Eitan Lerner
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California, 90095
| | - Dylan J Taatjes
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado, 80303
| | - Sergei Borukhov
- Rowan University School of Osteopathic Medicine, Stratford, New Jersey, 08084
| | - Shimon Weiss
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, California, 90095
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California, 90095
- Molecular Biology Institute (MBI), University of California, Los Angeles, California, 90095
- California NanoSystems Institute, University of California, Los Angeles, California, 90095
- Department of Physiology, University of California, Los Angeles, California, 90095
| |
Collapse
|
89
|
Fouqueau T, Blombach F, Werner F. Evolutionary Origins of Two-Barrel RNA Polymerases and Site-Specific Transcription Initiation. Annu Rev Microbiol 2017; 71:331-348. [PMID: 28657884 DOI: 10.1146/annurev-micro-091014-104145] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Evolution-related multisubunit RNA polymerases (RNAPs) carry out RNA synthesis in all domains life. Although their catalytic cores and fundamental mechanisms of transcription elongation are conserved, the initiation stage of the transcription cycle differs substantially in bacteria, archaea, and eukaryotes in terms of the requirements for accessory factors and details of the molecular mechanisms. This review focuses on recent insights into the evolution of the transcription apparatus with regard to (a) the surprisingly pervasive double-Ψ β-barrel active-site configuration among different nucleic acid polymerase families, (b) the origin and phylogenetic distribution of TBP, TFB, and TFE transcription factors, and
Collapse
Affiliation(s)
- Thomas Fouqueau
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom; ,
| | - Fabian Blombach
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom; ,
| | - Finn Werner
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom; ,
| |
Collapse
|
90
|
X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway. Proc Natl Acad Sci U S A 2017; 114:8211-8216. [PMID: 28652344 DOI: 10.1073/pnas.1702741114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Reiterative transcription is a noncanonical form of RNA synthesis in which a nucleotide specified by a single base in the DNA template is repetitively added to the nascent transcript. Here we determined the crystal structure of an RNA polymerase, the bacterial enzyme from Thermus thermophilus, engaged in reiterative transcription during transcription initiation at a promoter resembling the pyrG promoter of Bacillus subtilis The structure reveals that the reiterative transcript detours from the dedicated RNA exit channel and extends toward the main channel of the enzyme, thereby allowing RNA extension without displacement of the promoter recognition σ-factor. Nascent transcripts containing reiteratively added G residues are eventually extended by nonreiterative transcription, revealing an atypical pathway for the formation of a transcription elongation complex.
Collapse
|
91
|
Abstract
Transcription initiation is highly regulated in bacterial cells, allowing adaptive gene regulation in response to environment cues. One class of promoter specificity factor called sigma54 enables such adaptive gene expression through its ability to lock the RNA polymerase down into a state unable to melt out promoter DNA for transcription initiation. Promoter DNA opening then occurs through the action of specialized transcription control proteins called bacterial enhancer-binding proteins (bEBPs) that remodel the sigma54 factor within the closed promoter complexes. The remodelling of sigma54 occurs through an ATP-binding and hydrolysis reaction carried out by the bEBPs. The regulation of bEBP self-assembly into typically homomeric hexamers allows regulated gene expression since the self-assembly is required for bEBP ATPase activity and its direct engagement with the sigma54 factor during the remodelling reaction. Crystallographic studies have now established that in the closed promoter complex, the sigma54 factor occupies the bacterial RNA polymerase in ways that will physically impede promoter DNA opening and the loading of melted out promoter DNA into the DNA-binding clefts of the RNA polymerase. Large-scale structural re-organizations of sigma54 require contact of the bEBP with an amino-terminal glutamine and leucine-rich sequence of sigma54, and lead to domain movements within the core RNA polymerase necessary for making open promoter complexes and synthesizing the nascent RNA transcript.
Collapse
|
92
|
Marchetti M, Malinowska A, Heller I, Wuite GJL. How to switch the motor on: RNA polymerase initiation steps at the single-molecule level. Protein Sci 2017; 26:1303-1313. [PMID: 28470684 DOI: 10.1002/pro.3183] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/26/2017] [Accepted: 04/26/2017] [Indexed: 11/06/2022]
Abstract
RNA polymerase (RNAP) is the central motor of gene expression since it governs the process of transcription. In prokaryotes, this holoenzyme is formed by the RNAP core and a sigma factor. After approaching and binding the specific promoter site on the DNA, the holoenzyme-promoter complex undergoes several conformational transitions that allow unwinding and opening of the DNA duplex. Once the first DNA basepairs (∼10 bp) are transcribed in an initial transcription process, the enzyme unbinds from the promoter and proceeds downstream along the DNA while continuously opening the helix and polymerizing the ribonucleotides in correspondence with the template DNA sequence. When the gene is transcribed into RNA, the process generally is terminated and RNAP unbinds from the DNA. The first step of transcription-initiation, is considered the rate-limiting step of the entire process. This review focuses on the single-molecule studies that try to reveal the key steps in the initiation phase of bacterial transcription. Such single-molecule studies have, for example, allowed real-time observations of the RNAP target search mechanism, a mechanism still under debate. Moreover, single-molecule studies using Förster Resonance Energy Transfer (FRET) revealed the conformational changes that the enzyme undergoes during initiation. Force-based techniques such as scanning force microscopy and magnetic tweezers allowed quantification of the energy that drives the RNAP translocation along DNA and its dynamics. In addition to these in vitro experiments, single particle tracking in vivo has provided a direct quantification of the relative populations in each phase of transcription and their locations within the cell.
Collapse
Affiliation(s)
- M Marchetti
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - I Heller
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - G J L Wuite
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
93
|
Lerner E, Ingargiola A, Lee JJ, Borukhov S, Michalet X, Weiss S. Different types of pausing modes during transcription initiation. Transcription 2017; 8:242-253. [PMID: 28332923 DOI: 10.1080/21541264.2017.1308853] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
In many cases, initiation is rate limiting to transcription. This due in part to the multiple cycles of abortive transcription that delay promoter escape and the transition from initiation to elongation. Pausing of transcription in initiation can further delay promoter escape. The previously hypothesized pausing in initiation was confirmed by two recent studies from Duchi et al. 1 and from Lerner, Chung et al. 2 In both studies, pausing is attributed to a lack of forward translocation of the nascent transcript during initiation. However, the two works report on different pausing mechanisms. Duchi et al. report on pausing that occurs during initiation predominantly on-pathway of transcript synthesis. Lerner, Chung et al. report on pausing during initiation as a result of RNAP backtracking, which is off-pathway to transcript synthesis. Here, we discuss these studies, together with additional experimental results from single-molecule FRET focusing on a specific distance within the transcription bubble. We show that the results of these studies are complementary to each other and are consistent with a model involving two types of pauses in initiation: a short-lived pause that occurs in the translocation of a 6-mer nascent transcript and a long-lived pause that occurs as a result of 1-2 nucleotide backtracking of a 7-mer transcript.
Collapse
Affiliation(s)
- Eitan Lerner
- a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA
| | - Antonino Ingargiola
- a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA
| | - Jookyung J Lee
- b Rowan University School of Osteopathic Medicine , Stratford , NJ , USA
| | - Sergei Borukhov
- b Rowan University School of Osteopathic Medicine , Stratford , NJ , USA
| | - Xavier Michalet
- a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA
| | - Shimon Weiss
- a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA.,c Molecular Biology Institute , University of California , Los Angeles , CA , USA.,d Department of Physiology , University of California , Los Angeles , CA , USA
| |
Collapse
|
94
|
Smollett K, Blombach F, Reichelt R, Thomm M, Werner F. A global analysis of transcription reveals two modes of Spt4/5 recruitment to archaeal RNA polymerase. Nat Microbiol 2017; 2:17021. [PMID: 28248297 PMCID: PMC7616672 DOI: 10.1038/nmicrobiol.2017.21] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 01/24/2017] [Indexed: 01/21/2023]
Abstract
The archaeal transcription apparatus is closely related to the eukaryotic RNA polymerase (RNAP) II system, while archaeal genomes are more similar to bacteria with densely packed genes organized in operons. This makes understanding transcription in archaea vital, both in terms of molecular mechanisms and evolution. Very little is known about how archaeal cells orchestrate transcription on a systems level. We have characterized the genome-wide occupancy of the Methanocaldococcus jannaschii transcription machinery and its transcriptome. Our data reveal how the TATA and BRE promoter elements facilitate recruitment of the essential initiation factors TATA-binding protein and transcription factor B, respectively, which in turn are responsible for the loading of RNAP into the transcription units. The occupancies of RNAP and Spt4/5 strongly correlate with each other and with RNA levels. Our results show that Spt4/5 is a general elongation factor in archaea as its presence on all genes matches RNAP. Spt4/5 is recruited proximal to the transcription start site on the majority of transcription units, while on a subset of genes, including rRNA and CRISPR loci, Spt4/5 is recruited to the transcription elongation complex during early elongation within 500 base pairs of the transcription start site and akin to its bacterial homologue NusG.
Collapse
Affiliation(s)
- Katherine Smollett
- University College London, Institute for Structural and Molecular Biology, Gower Street, London, WC1E 6BT, UK
| | - Fabian Blombach
- University College London, Institute for Structural and Molecular Biology, Gower Street, London, WC1E 6BT, UK
| | - Robert Reichelt
- Institut of Microbiology and Archaea Center, Universität Regensburg, 93053Regensburg, Germany
| | - Michael Thomm
- Institut of Microbiology and Archaea Center, Universität Regensburg, 93053Regensburg, Germany
| | - Finn Werner
- University College London, Institute for Structural and Molecular Biology, Gower Street, London, WC1E 6BT, UK
| |
Collapse
|
95
|
RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes. Proc Natl Acad Sci U S A 2016; 113:14994-14999. [PMID: 27956639 DOI: 10.1073/pnas.1613673114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Upon RNA polymerase (RNAP) binding to a promoter, the σ factor initiates DNA strand separation and captures the melted nontemplate DNA, whereas the core enzyme establishes interactions with the duplex DNA in front of the active site that stabilize initiation complexes and persist throughout elongation. Among many core RNAP elements that participate in these interactions, the β' clamp domain plays the most prominent role. In this work, we investigate the role of the β gate loop, a conserved and essential structural element that lies across the DNA channel from the clamp, in transcription regulation. The gate loop was proposed to control DNA loading during initiation and to interact with NusG-like proteins to lock RNAP in a closed, processive state during elongation. We show that the removal of the gate loop has large effects on promoter complexes, trapping an unstable intermediate in which the RNAP contacts with the nontemplate strand discriminator region and the downstream duplex DNA are not yet fully established. We find that although RNAP lacking the gate loop displays moderate defects in pausing, transcript cleavage, and termination, it is fully responsive to the transcription elongation factor NusG. Together with the structural data, our results support a model in which the gate loop, acting in concert with initiation or elongation factors, guides the nontemplate DNA in transcription complexes, thereby modulating their regulatory properties.
Collapse
|
96
|
Lee J, Borukhov S. Bacterial RNA Polymerase-DNA Interaction-The Driving Force of Gene Expression and the Target for Drug Action. Front Mol Biosci 2016; 3:73. [PMID: 27882317 PMCID: PMC5101437 DOI: 10.3389/fmolb.2016.00073] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/24/2016] [Indexed: 11/17/2022] Open
Abstract
DNA-dependent multisubunit RNA polymerase (RNAP) is the key enzyme of gene expression and a target of regulation in all kingdoms of life. It is a complex multifunctional molecular machine which, unlike other DNA-binding proteins, engages in extensive and dynamic interactions (both specific and nonspecific) with DNA, and maintains them over a distance. These interactions are controlled by DNA sequences, DNA topology, and a host of regulatory factors. Here, we summarize key recent structural and biochemical studies that elucidate the fine details of RNAP-DNA interactions during initiation. The findings of these studies help unravel the molecular mechanisms of promoter recognition and open complex formation, initiation of transcript synthesis and promoter escape. We also discuss most current advances in the studies of drugs that specifically target RNAP-DNA interactions during transcription initiation and elongation.
Collapse
Affiliation(s)
- Jookyung Lee
- Department of Cell Biology, Rowan University School of Osteopathic Medicine Stratford, NJ, USA
| | - Sergei Borukhov
- Department of Cell Biology, Rowan University School of Osteopathic Medicine Stratford, NJ, USA
| |
Collapse
|
97
|
Regulation of transcription initiation by Gfh factors from Deinococcus radiodurans. Biochem J 2016; 473:4493-4505. [PMID: 27754888 DOI: 10.1042/bcj20160659] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/15/2016] [Accepted: 10/17/2016] [Indexed: 02/06/2023]
Abstract
Transcription factors of the Gre family bind within the secondary channel of bacterial RNA polymerase (RNAP) directly modulating its catalytic activities. Universally conserved Gre factors activate RNA cleavage by RNAP, by chelating catalytic metal ions in the RNAP active site, and facilitate both promoter escape and transcription elongation. Gfh factors are Deinococcus/Thermus-specific homologues of Gre factors whose transcription functions remain poorly understood. Recently, we found that Gfh1 and Gfh2 proteins from Deinococcus radiodurans dramatically stimulate RNAP pausing during transcription elongation in the presence of Mn2+, but not Mg2+, ions. In contrast, we show that Gfh1 and Gfh2 moderately inhibit transcription initiation in the presence of either Mg2+ or Mn2+ ions. By using a molecular beacon assay, we demonstrate that Gfh1 and Gfh2 do not significantly change promoter complex stability or the rate of promoter escape by D. radiodurans RNAP. At the same time, Gfh factors significantly increase the apparent KM value for the 5'-initiating nucleotide, without having major effects on the affinity of metal ions for the RNAP active site. Similar inhibitory effects of Gfh factors are observed for transcription initiation on promoters recognized by the principal and an alternative σ factor. In summary, our data suggest that D. radiodurans Gfh factors impair the binding of initiating substrates independently of the metal ions bound in the RNAP active site, but have only mild overall effects on transcription initiation. Thus the mechanisms of modulation of RNAP activity by these factors are different for various steps of transcription.
Collapse
|
98
|
Duchi D, Bauer DLV, Fernandez L, Evans G, Robb N, Hwang LC, Gryte K, Tomescu A, Zawadzki P, Morichaud Z, Brodolin K, Kapanidis AN. RNA Polymerase Pausing during Initial Transcription. Mol Cell 2016; 63:939-50. [PMID: 27618490 PMCID: PMC5031556 DOI: 10.1016/j.molcel.2016.08.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 04/12/2016] [Accepted: 08/05/2016] [Indexed: 11/11/2022]
Abstract
In bacteria, RNA polymerase (RNAP) initiates transcription by synthesizing short transcripts that are either released or extended to allow RNAP to escape from the promoter. The mechanism of initial transcription is unclear due to the presence of transient intermediates and molecular heterogeneity. Here, we studied initial transcription on a lac promoter using single-molecule fluorescence observations of DNA scrunching on immobilized transcription complexes. Our work revealed a long pause (“initiation pause,” ∼20 s) after synthesis of a 6-mer RNA; such pauses can serve as regulatory checkpoints. Region sigma 3.2, which contains a loop blocking the RNA exit channel, was a major pausing determinant. We also obtained evidence for RNA backtracking during abortive initial transcription and for additional pausing prior to escape. We summarized our work in a model for initial transcription, in which pausing is controlled by a complex set of determinants that modulate the transition from a 6- to a 7-nt RNA. E. coli RNA polymerase pauses during initial transcription at lac promoters Initiation pausing lasts for ∼20 s and occurs at the transition from 6- to 7-nt RNA Region 3.2 of σ70 is the main protein element controlling pausing Pausing is likely to be controlled further by a complex set of determinants
Collapse
Affiliation(s)
- Diego Duchi
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - David L V Bauer
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Laurent Fernandez
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Geraint Evans
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Nicole Robb
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Ling Chin Hwang
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Kristofer Gryte
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Alexandra Tomescu
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Pawel Zawadzki
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Zakia Morichaud
- CNRS FRE 3689, Centre d'études d'agents Pathogénes et Biotechnologies pour la Santé (CPBS), 1919 route de Mende, 34293 Montpellier, France
| | - Konstantin Brodolin
- CNRS FRE 3689, Centre d'études d'agents Pathogénes et Biotechnologies pour la Santé (CPBS), 1919 route de Mende, 34293 Montpellier, France
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK.
| |
Collapse
|
99
|
Wendte JM, Pikaard CS. The RNAs of RNA-directed DNA methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:140-148. [PMID: 27521981 DOI: 10.1016/j.bbagrm.2016.08.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/05/2016] [Accepted: 08/06/2016] [Indexed: 10/21/2022]
Abstract
RNA-directed chromatin modification that includes cytosine methylation silences transposable elements in both plants and mammals, contributing to genome defense and stability. In Arabidopsis thaliana, most RNA-directed DNA methylation (RdDM) is guided by small RNAs derived from double-stranded precursors synthesized at cytosine-methylated loci by nuclear multisubunit RNA Polymerase IV (Pol IV), in close partnership with the RNA-dependent RNA polymerase, RDR2. These small RNAs help keep transposons transcriptionally inactive. However, if transposons escape silencing, and are transcribed by multisubunit RNA polymerase II (Pol II), their mRNAs can be recognized and degraded, generating small RNAs that can also guide initial DNA methylation, thereby enabling subsequent Pol IV-RDR2 recruitment. In both pathways, the small RNAs find their target sites by interacting with longer noncoding RNAs synthesized by multisubunit RNA Polymerase V (Pol V). Despite a decade of progress, numerous questions remain concerning the initiation, synthesis, processing, size and features of the RNAs that drive RdDM. Here, we review recent insights, questions and controversies concerning RNAs produced by Pols IV and V, and their functions in RdDM. We also provide new data concerning Pol V transcript 5' and 3' ends. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
Collapse
Affiliation(s)
- Jered M Wendte
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA
| | - Craig S Pikaard
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA; Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA.
| |
Collapse
|
100
|
Bird JG, Zhang Y, Tian Y, Panova N, Barvík I, Greene L, Liu M, Buckley B, Krásný L, Lee JK, Kaplan CD, Ebright RH, Nickels BE. The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA. Nature 2016; 535:444-7. [PMID: 27383794 PMCID: PMC4961592 DOI: 10.1038/nature18622] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/01/2016] [Indexed: 01/26/2023]
Abstract
The chemical nature of the 5′ end of RNA is a key determinant of RNA stability, processing, localization, translation efficiency1,2, and has been proposed to provide a layer of “epitranscriptomic” gene regulation3. Recently it has been shown that some bacterial RNA species carry a 5′-end structure reminiscent of the 5′ 7-methylguanylate “cap” in eukaryotic RNA. In particular, RNA species containing a 5′-end nicotinamide adenine dinucleotide (NAD+) or 3′-desphospho-coenzyme A (dpCoA) have been identified in both Gram-negative and Gram-positive bacteria3–6. It has been proposed that NAD+, reduced NAD+ (NADH), and dpCoA caps are added to RNA after transcription initiation, in a manner analogous to the addition of 7-methylguanylate caps6–8. Here, we show instead that NAD+, NADH, and dpCoA are incorporated into RNA during transcription initiation, by serving as non-canonical initiating nucleotides (NCINs) for de novo transcription initiation by cellular RNA polymerase (RNAP). We further show that both bacterial RNAP and eukaryotic RNAP II incorporate NCIN caps, that promoter DNA sequences at and upstream of the transcription start site determine the efficiency of NCIN capping, that NCIN capping occurs in vivo, and that NCIN capping has functional consequences. We report crystal structures of transcription initiation complexes containing NCIN-capped RNA products. Our results define the mechanism and structural basis of NCIN capping, and suggest that NCIN-mediated “ab initio capping” may occur in all organisms
Collapse
|