1
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Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA. Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. Nat Struct Mol Biol 2024:10.1038/s41594-024-01349-9. [PMID: 38951624 DOI: 10.1038/s41594-024-01349-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 06/06/2024] [Indexed: 07/03/2024]
Abstract
During formation of the transcription-competent open complex (RPo) by bacterial RNA polymerases (RNAPs), transient intermediates pile up before overcoming a rate-limiting step. Structural descriptions of these interconversions in real time are unavailable. To address this gap, here we use time-resolved cryogenic electron microscopy (cryo-EM) to capture four intermediates populated 120 ms or 500 ms after mixing Escherichia coli σ70-RNAP and the λPR promoter. Cryo-EM snapshots revealed that the upstream edge of the transcription bubble unpairs rapidly, followed by stepwise insertion of two conserved nontemplate strand (nt-strand) bases into RNAP pockets. As the nt-strand 'read-out' extends, the RNAP clamp closes, expelling an inhibitory σ70 domain from the active-site cleft. The template strand is fully unpaired by 120 ms but remains dynamic, indicating that yet unknown conformational changes complete RPo formation in subsequent steps. Given that these events likely describe DNA opening at many bacterial promoters, this study provides insights into how DNA sequence regulates steps of RPo formation.
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Affiliation(s)
- Ruth M Saecker
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Andreas U Mueller
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Brandon Malone
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
- Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY, USA
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - William C Budell
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Venkata P Dandey
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Kashyap Maruthi
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Joshua H Mendez
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Nina Molina
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Edward T Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Laura Y Yen
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Clinton S Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Chan Zuckerberg Imaging Institute, San Francisco, CA, USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Chan Zuckerberg Imaging Institute, San Francisco, CA, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA.
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Tarău D, Grünberger F, Pilsl M, Reichelt R, Heiß F, König S, Urlaub H, Hausner W, Engel C, Grohmann D. Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment. Nucleic Acids Res 2024; 52:6017-6035. [PMID: 38709902 PMCID: PMC11162788 DOI: 10.1093/nar/gkae282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 05/08/2024] Open
Abstract
Archaeal transcription is carried out by a multi-subunit RNA polymerase (RNAP) that is highly homologous in structure and function to eukaryotic RNAP II. Among the set of basal transcription factors, only Spt5 is found in all domains of life, but Spt5 has been shaped during evolution, which is also reflected in the heterodimerization of Spt5 with Spt4 in Archaea and Eukaryotes. To unravel the mechanistic basis of Spt4/5 function in Archaea, we performed structure-function analyses using the archaeal transcriptional machinery of Pyrococcus furiosus (Pfu). We report single-particle cryo-electron microscopy reconstructions of apo RNAP and the archaeal elongation complex (EC) in the absence and presence of Spt4/5. Surprisingly, Pfu Spt4/5 also binds the RNAP in the absence of nucleic acids in a distinct super-contracted conformation. We show that the RNAP clamp/stalk module exhibits conformational flexibility in the apo state of RNAP and that the enzyme contracts upon EC formation or Spt4/5 engagement. We furthermore identified a contact of the Spt5-NGN domain with the DNA duplex that stabilizes the upstream boundary of the transcription bubble and impacts Spt4/5 activity in vitro. This study, therefore, provides the structural basis for Spt4/5 function in archaeal transcription and reveals a potential role beyond the well-described support of elongation.
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Affiliation(s)
- Daniela Tarău
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Felix Grünberger
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Michael Pilsl
- Regensburg Center for Biochemistry (RCB), Structural Biochemistry Group, University of Regensburg, Regensburg, Germany
| | - Robert Reichelt
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Florian Heiß
- Regensburg Center for Biochemistry (RCB), Structural Biochemistry Group, University of Regensburg, Regensburg, Germany
| | - Sabine König
- Bioanalytic Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytic Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Winfried Hausner
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry (RCB), Structural Biochemistry Group, University of Regensburg, Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
- Regensburg Center for Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
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3
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Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA. Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584744. [PMID: 38559232 PMCID: PMC10979975 DOI: 10.1101/2024.03.13.584744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
During formation of the transcription-competent open complex (RPo) by bacterial RNA polymerases (RNAP), transient intermediates pile up before overcoming a rate-limiting step. Structural descriptions of these interconversions in real time are unavailable. To address this gap, time-resolved cryo-electron microscopy (cryo-EM) was used to capture four intermediates populated 120 or 500 milliseconds (ms) after mixing Escherichia coli σ70-RNAP and the λPR promoter. Cryo-EM snapshots revealed the upstream edge of the transcription bubble unpairs rapidly, followed by stepwise insertion of two conserved nontemplate strand (nt-strand) bases into RNAP pockets. As nt-strand "read-out" extends, the RNAP clamp closes, expelling an inhibitory σ70 domain from the active-site cleft. The template strand is fully unpaired by 120 ms but remains dynamic, indicating yet unknown conformational changes load it in subsequent steps. Because these events likely describe DNA opening at many bacterial promoters, this study provides needed insights into how DNA sequence regulates steps of RPo formation.
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Affiliation(s)
- Ruth M. Saecker
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - Andreas U. Mueller
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - Brandon Malone
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - William C. Budell
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Venkata P. Dandey
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Kashyap Maruthi
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Joshua H. Mendez
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Nina Molina
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - Edward T. Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Laura Y. Yen
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Clinton S. Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY USA
| | - Seth A. Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
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Porubiaková O, Havlík J, Indu, Šedý M, Přepechalová V, Bartas M, Bidula S, Šťastný J, Fojta M, Brázda V. Variability of Inverted Repeats in All Available Genomes of Bacteria. Microbiol Spectr 2023; 11:e0164823. [PMID: 37358458 PMCID: PMC10434271 DOI: 10.1128/spectrum.01648-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/03/2023] [Indexed: 06/27/2023] Open
Abstract
Noncanonical secondary structures in nucleic acids have been studied intensively in recent years. Important biological roles of cruciform structures formed by inverted repeats (IRs) have been demonstrated in diverse organisms, including humans. Using Palindrome analyser, we analyzed IRs in all accessible bacterial genome sequences to determine their frequencies, lengths, and localizations. IR sequences were identified in all species, but their frequencies differed significantly across various evolutionary groups. We detected 242,373,717 IRs in all 1,565 bacterial genomes. The highest mean IR frequency was detected in the Tenericutes (61.89 IRs/kbp) and the lowest mean frequency was found in the Alphaproteobacteria (27.08 IRs/kbp). IRs were abundant near genes and around regulatory, tRNA, transfer-messenger RNA (tmRNA), and rRNA regions, pointing to the importance of IRs in such basic cellular processes as genome maintenance, DNA replication, and transcription. Moreover, we found that organisms with high IR frequencies were more likely to be endosymbiotic, antibiotic producing, or pathogenic. On the other hand, those with low IR frequencies were far more likely to be thermophilic. This first comprehensive analysis of IRs in all available bacterial genomes demonstrates their genomic ubiquity, nonrandom distribution, and enrichment in genomic regulatory regions. IMPORTANCE Our manuscript reports for the first time a complete analysis of inverted repeats in all fully sequenced bacterial genomes. Thanks to the availability of unique computational resources, we were able to statistically evaluate the presence and localization of these important regulatory sequences in bacterial genomes. This work revealed a strong abundance of these sequences in regulatory regions and provides researchers with a valuable tool for their manipulation.
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Affiliation(s)
- Otília Porubiaková
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jan Havlík
- Mendel University in Brno, Brno, Czech Republic
| | - Indu
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michal Šedý
- Brno University of Technology, Faculty of Chemistry, Brno, Czech Republic
| | - Veronika Přepechalová
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Brno University of Technology, Faculty of Chemistry, Brno, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Stefan Bidula
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jiří Šťastný
- Mendel University in Brno, Brno, Czech Republic
- Brno University of Technology, Faculty of Mechanical Engineering, Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Brno University of Technology, Faculty of Chemistry, Brno, Czech Republic
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5
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Wee LM, Tong AB, Florez Ariza AJ, Cañari-Chumpitaz C, Grob P, Nogales E, Bustamante CJ. A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery. Cell 2023; 186:1244-1262.e34. [PMID: 36931247 PMCID: PMC10135430 DOI: 10.1016/j.cell.2023.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 03/18/2023]
Abstract
In prokaryotes, translation can occur on mRNA that is being transcribed in a process called coupling. How the ribosome affects the RNA polymerase (RNAP) during coupling is not well understood. Here, we reconstituted the E. coli coupling system and demonstrated that the ribosome can prevent pausing and termination of RNAP and double the overall transcription rate at the expense of fidelity. Moreover, we monitored single RNAPs coupled to ribosomes and show that coupling increases the pause-free velocity of the polymerase and that a mechanical assisting force is sufficient to explain the majority of the effects of coupling. Also, by cryo-EM, we observed that RNAPs with a terminal mismatch adopt a backtracked conformation, while a coupled ribosome allosterically induces these polymerases toward a catalytically active anti-swiveled state. Finally, we demonstrate that prolonged RNAP pausing is detrimental to cell viability, which could be prevented by polymerase reactivation through a coupled ribosome.
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Affiliation(s)
- Liang Meng Wee
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alexander B Tong
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Alfredo Jose Florez Ariza
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Cristhian Cañari-Chumpitaz
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Patricia Grob
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Eva Nogales
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Carlos J Bustamante
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Department of Physics, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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6
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Cheng A, Wan D, Ghatak A, Wang C, Feng D, Fondell JD, Ebright RH, Fan H. Identification and Structural Modeling of the RNA Polymerase Omega Subunits in Chlamydiae and Other Obligate Intracellular Bacteria. mBio 2023; 14:e0349922. [PMID: 36719197 PMCID: PMC9973325 DOI: 10.1128/mbio.03499-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 01/04/2023] [Indexed: 02/01/2023] Open
Abstract
Gene transcription in bacteria is carried out by the multisubunit RNA polymerase (RNAP), which is composed of a catalytic core enzyme and a promoter-recognizing σ factor. The core enzyme comprises two α subunits, one β subunit, one β' subunit, and one ω subunit. The ω subunit plays critical roles in the assembly of the core enzyme and other cellular functions, including the regulation of bacterial growth, the stress response, and biofilm formation. However, the identity of an ω subunit for the obligate intracellular bacterium Chlamydia has not previously been determined. Here, we report the identification of the hypothetical protein CTL0286 as the probable chlamydial ω subunit based on sequence, synteny, and AlphaFold and AlphaFold-Multimer three-dimensional-structure predictions. Our findings indicate that CTL0286 functions as the missing ω subunit of chlamydial RNAP. Our extended analysis also indicates that all obligate intracellular bacteria have ω orthologs. IMPORTANCE Chlamydiae are obligate intracellular bacteria that replicate only inside eukaryotic cells. Previously, it has not been possible to identify a candidate gene encoding the chlamydial RNA polymerase ω subunit, and it has been hypothesized that the chlamydial RNA polymerase ω subunit was lost in the evolutionary process through which Chlamydiae reduced their genome size and proteome sizes to adapt to an obligate intracellular lifestyle. Here, we report the identification of the chlamydial RNA polymerase ω subunit, based on conserved sequence, conserved synteny, AlphaFold-predicted conserved three-dimensional structure, and AlfaFold-Multimer-predicted conserved interactions. Our identification of the previously elusive chlamydial RNA polymerase ω subunit sets the stage for investigation of its roles in regulation of gene expression during chlamydial growth, development, and stress responses, and sets the stage for preparation and study of the intact chlamydial RNA polymerase and its interactions with inhibitors.
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Affiliation(s)
- Andrew Cheng
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Danny Wan
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
- Graduate Program in Physiology and Integrative Biology, Rutgers School of Graduate Studies, Piscataway, New Jersey, USA
| | - Arkaprabha Ghatak
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Chengyuan Wang
- Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Deyu Feng
- Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Joseph D. Fondell
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Richard H. Ebright
- Waksman Institute, Rutgers University, Piscataway, New Jersey, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Huizhou Fan
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
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7
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Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase. Proc Natl Acad Sci U S A 2023; 120:e2218516120. [PMID: 36745813 PMCID: PMC9963633 DOI: 10.1073/pnas.2218516120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
NusG is a transcription elongation factor that stimulates transcription pausing in Gram+ bacteria including B. subtilis by sequence-specific interaction with a conserved pause-inducing -11TTNTTT-6 motif found in the non-template DNA (ntDNA) strand within the transcription bubble. To reveal the structural basis of NusG-dependent pausing, we determined a cryo-EM structure of a paused transcription complex (PTC) containing RNA polymerase (RNAP), NusG, and the TTNTTT motif in the ntDNA strand. The interaction of NusG with the ntDNA strand rearranges the transcription bubble by positioning three consecutive T residues in a cleft between NusG and the β-lobe domain of RNAP. We revealed that the RNAP swivel module rotation (swiveling), which widens (swiveled state) and narrows (non-swiveled state) a cleft between NusG and the β-lobe, is an intrinsic motion of RNAP and is directly linked to trigger loop (TL) folding, an essential conformational change of all cellular RNAPs for the RNA synthesis reaction. We also determined cryo-EM structures of RNAP escaping from the paused transcription state. These structures revealed the NusG-dependent pausing mechanism by which NusG-ntDNA interaction inhibits the transition from swiveled to non-swiveled states, thereby preventing TL folding and RNA synthesis allosterically. This motion is also reduced by the formation of an RNA hairpin within the RNA exit channel. Thus, the pause half-life can be modulated by the strength of the NusG-ntDNA interaction and/or the stability of the RNA hairpin. NusG residues that interact with the TTNTTT motif are widely conserved in bacteria, suggesting that NusG-dependent pausing is widespread.
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8
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Li R, Wang M, Gong P. Crystal structure of a pre-chemistry viral RNA-dependent RNA polymerase suggests participation of two basic residues in catalysis. Nucleic Acids Res 2022; 50:12389-12399. [PMID: 36477355 PMCID: PMC9757066 DOI: 10.1093/nar/gkac1133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 10/19/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022] Open
Abstract
The nucleic acid polymerase-catalyzed nucleotidyl transfer reaction associated with polymerase active site closure is a key step in the nucleotide addition cycle (NAC). Two proton transfer events can occur in such a nucleotidyl transfer: deprotonation of the priming nucleotide 3'-hydroxyl nucleophile and protonation of the pyrophosphate (PPi) leaving group. In viral RNA-dependent RNA polymerases (RdRPs), whether and how active site residues participate in this two-proton transfer reaction remained to be clarified. Here we report a 2.5 Å resolution crystal structure of enterovirus 71 (EV71) RdRP in a catalytically closed pre-chemistry conformation, with a proposed proton donor candidate K360 in close contact with the NTP γ-phosphate. Enzymology data reveal that K360 mutations not only reduce RdRP catalytic efficiency but also alter pH dependency profiles in both elongation and pre-elongation synthesis modes. Interestingly, mutations at R174, an RdRP-invariant residue in motif F, had similar effects with additional impact on the Michaelis constant of NTP (KM,NTP). However, direct participation in protonation was not evident for K360 or R174. Our data suggest that both K360 and R174 participate in nucleotidyl transfer, while their possible roles in acid-base or positional catalysis are discussed in comparison with other classes of nucleic acid polymerases.
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Affiliation(s)
| | | | - Peng Gong
- To whom correspondence should be addressed.
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9
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Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-André C, Weixlbaumer A. Structural insights into RNA-mediated transcription regulation in bacteria. Mol Cell 2022; 82:3885-3900.e10. [DOI: 10.1016/j.molcel.2022.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/07/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
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10
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Failure of Translation Initiation of the Next Gene Decouples Transcription at Intercistronic Sites and the Resultant mRNA Generation. mBio 2022; 13:e0128722. [PMID: 35695461 PMCID: PMC9239205 DOI: 10.1128/mbio.01287-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Escherichia coli, transcription is coupled with translation. The polar gal operon is transcribed galE-galT-galK-galM; however, about 10% of transcription terminates at the end of galE because of Rho-dependent termination (RDT). When galE translation is complete, galT translation should begin immediately. It is unclear whether RDT at the end of galE is due to decoupling of translation termination and transcription at the cistron junction. In this study, we show that RDT at the galE/galT cistron junction is linked to the failure of translation initiation at the start of galT, rather than translation termination at the end of galE. We also show that transcription pauses 130 nucleotides downstream from the site of galE translation termination, and this pause is required for RDT. IMPORTANCE Transcription of operons is initiated at the promoter of the first gene in the operon, continues through cistron junctions, and terminates at the end of the operon, generating a full-length mRNA. Here, we show that Rho-dependent termination of transcription occurs stochastically at a cistron junction, generating a stable mRNA that is shorter than the full-length mRNA. We further show that stochastic failure in translation initiation of the next gene, rather than the failure of translation termination of the preceding gene, causes the Rho-dependent termination. Thus, stochastic failure in translation initiation at the cistron junction causes the promoter-proximal gene to be transcribed more than promoter-distal genes within the operon.
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11
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Pilotto S, Fouqueau T, Lukoyanova N, Sheppard C, Lucas-Staat S, Díaz-Santín LM, Matelska D, Prangishvili D, Cheung ACM, Werner F. Structural basis of RNA polymerase inhibition by viral and host factors. Nat Commun 2021; 12:5523. [PMID: 34535646 PMCID: PMC8448823 DOI: 10.1038/s41467-021-25666-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/19/2021] [Indexed: 12/26/2022] Open
Abstract
RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution structures of two such RNAP-inhibitor complexes that provide the structural bases underlying RNAP inhibition in archaea. The Acidianus two-tailed virus encodes the RIP factor that binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. Infection with the Sulfolobus Turreted Icosahedral Virus induces the expression of the host factor TFS4, which binds in the RNAP funnel similarly to eukaryotic transcript cleavage factors. However, TFS4 allosterically induces a widening of the DNA-binding channel which disrupts trigger loop and bridge helix motifs. Importantly, the conformational changes induced by TFS4 are closely related to inactivated states of RNAP in other domains of life indicating a deep evolutionary conservation of allosteric RNAP inhibition.
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Affiliation(s)
- Simona Pilotto
- RNAP Laboratory, Institute for Structural and Molecular Biology, University College London, London, UK
| | - Thomas Fouqueau
- RNAP Laboratory, Institute for Structural and Molecular Biology, University College London, London, UK
| | - Natalya Lukoyanova
- Institute for Structural and Molecular Biology, Birkbeck College, London, UK
| | - Carol Sheppard
- Section of Virology, Department of Infectious disease, Imperial College London, London, UK
| | | | | | - Dorota Matelska
- RNAP Laboratory, Institute for Structural and Molecular Biology, University College London, London, UK
| | | | | | - Finn Werner
- RNAP Laboratory, Institute for Structural and Molecular Biology, University College London, London, UK.
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12
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Gupta S, Pal D. Clusters of hairpins induce intrinsic transcription termination in bacteria. Sci Rep 2021; 11:16194. [PMID: 34376740 PMCID: PMC8355165 DOI: 10.1038/s41598-021-95435-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 07/20/2021] [Indexed: 01/13/2023] Open
Abstract
Intrinsic transcription termination (ITT) sites are currently identified by locating single and double-adjacent RNA hairpins downstream of the stop codon. ITTs for a limited number of genes/operons in only a few bacterial genomes are currently known. This lack of coverage is a lacuna in the existing ITT inference methods. We have studied the inter-operon regions of 13 genomes covering all major phyla in bacteria, for which good quality public RNA-seq data exist. We identify ITT sites in 87% of cases by predicting hairpin(s) and validate against 81% of cases for which the RNA-seq derived sites could be calculated. We identify 72% of these sites correctly, with 98% of them located ≤ 80 bases downstream of the stop codon. The predicted hairpins form a cluster (when present < 15 bases) in two-thirds of the cases, the remaining being single hairpins. The largest number of clusters is formed by two hairpins, and the occurrence decreases exponentially with an increasing number of hairpins in the cluster. Our study reveals that hairpins form an effective ITT unit when they act in concert in a cluster. Their pervasiveness along with single hairpin terminators corroborates a wider utilization of ITT mechanisms for transcription control across bacteria.
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Affiliation(s)
- Swati Gupta
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka, 560012, India.
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13
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Abstract
Cellular life depends on transcription of DNA by RNA polymerase to express genetic information. RNA polymerase has evolved not just to read information from DNA and write it to RNA but also to sense and process information from the cellular and extracellular environments. Much of this information processing occurs during transcript elongation, when transcriptional pausing enables regulatory decisions. Transcriptional pauses halt RNA polymerase in response to DNA and RNA sequences and structures at locations and times that help coordinate interactions with small molecules and transcription factors important for regulation. Four classes of transcriptional pause signals are now evident after decades of study: elemental pauses, backtrack pauses, hairpin-stabilized pauses, and regulator-stabilized pauses. In this review, I describe current understanding of the molecular mechanisms of these four classes of pause signals, remaining questions about how RNA polymerase responds to pause signals, and the many exciting directions now open to understand pausing and the regulation of transcript elongation on a genome-wide scale. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Robert Landick
- Department of Biochemistry and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
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14
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A comprehensive mechanism for 5-carboxylcytosine-induced transcriptional pausing revealed by Markov state models. J Biol Chem 2021; 296:100735. [PMID: 33991521 PMCID: PMC8191312 DOI: 10.1016/j.jbc.2021.100735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 11/23/2022] Open
Abstract
RNA polymerase II (Pol II) surveils the genome, pausing as it encounters DNA lesions and base modifications and initiating signals for DNA repair among other important regulatory events. Recent work suggests that Pol II pauses at 5-carboxycytosine (5caC), an epigenetic modification of cytosine, because of a specific hydrogen bond between the carboxyl group of 5caC and a specific residue in fork loop 3 of Pol II. This hydrogen bond compromises productive NTP binding and slows down elongation. Apart from this specific interaction, the carboxyl group of 5caC can potentially interact with numerous charged residues in the cleft of Pol II. However, it is not clear how other interactions between Pol II and 5caC contribute to pausing. In this study, we use Markov state models (a type of kinetic network models) built from extensive molecular dynamics simulations to comprehensively study the impact of 5caC on Pol II translocation. We describe two translocation intermediates with specific interactions that prevent the template base from loading into the Pol II active site. In addition to the previously observed state with 5caC constrained by fork loop 3, we discovered a new intermediate state with a hydrogen bond between 5caC and fork loop 2. Surprisingly, we find that 5caC may curb translocation by suppressing kinking of the helix bordering the active site (the bridge helix) because its high flexibility is critical to translocation. Our work provides new insights into how epigenetic modifications of genomic DNA can modulate Pol II translocation, inducing pauses in transcription.
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15
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Mazumder A, Wang A, Uhm H, Ebright RH, Kapanidis AN. RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding. Nucleic Acids Res 2021; 49:2790-2802. [PMID: 33589919 PMCID: PMC7969002 DOI: 10.1093/nar/gkab074] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 01/23/2021] [Accepted: 01/28/2021] [Indexed: 02/04/2023] Open
Abstract
The RNA polymerase (RNAP) clamp, a mobile structural element conserved in RNAP from all domains of life, has been proposed to play critical roles at different stages of transcription. In previous work, we demonstrated using single-molecule Förster resonance energy transfer (smFRET) that RNAP clamp interconvert between three short-lived conformational states (lifetimes ∼ 0.3–0.6 s), that the clamp can be locked into any one of these states by small molecules, and that the clamp stays closed during initial transcription and elongation. Here, we extend these studies to obtain a comprehensive understanding of clamp dynamics under conditions RNAP may encounter in living cells. We find that the RNAP clamp can populate long-lived conformational states (lifetimes > 1.0 s) and can switch between these long-lived states and the previously observed short-lived states. In addition, we find that clamp motions are increased in the presence of molecular crowding, are unchanged in the presence of elevated monovalent-cation concentrations, and are reduced in the presence of elevated divalent-cation concentrations. Finally, we find that RNAP bound to non-specific DNA predominantly exhibits a closed clamp conformation. Our results raise the possibility of additional regulatory checkpoints that could affect clamp dynamics and consequently could affect transcription and transcriptional regulation.
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Affiliation(s)
- Abhishek Mazumder
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Anna Wang
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Heesoo Uhm
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
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16
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Kilic Z, Sgouralis I, Pressé S. Residence time analysis of RNA polymerase transcription dynamics: A Bayesian sticky HMM approach. Biophys J 2021; 120:1665-1679. [PMID: 33705761 DOI: 10.1016/j.bpj.2021.02.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 01/09/2023] Open
Abstract
The time spent by a single RNA polymerase (RNAP) at specific locations along the DNA, termed "residence time," reports on the initiation, elongation, and termination stages of transcription. At the single-molecule level, this information can be obtained from dual ultrastable optical trapping experiments, revealing a transcriptional elongation of RNAP interspersed with residence times of variable duration. Successfully discriminating between long and short residence times was used by previous approaches to learn about RNAP's transcription elongation dynamics. Here, we propose an approach based on the Bayesian sticky hidden Markov model that treats all residence times for an Escherichia coli RNAP on an equal footing without a priori discriminating between long and short residence times. Furthermore, our method has two additional advantages: we provide full distributions around key point statistics and directly treat the sequence dependence of RNAP's elongation rate. By applying our approach to experimental data, we find assigned relative probabilities on long versus short residence times, force-dependent average residence time transcription elongation dynamics, ∼10% drop in the average backtracking durations in the presence of GreB, and ∼20% drop in the average residence time as a function of applied force in the presence of RNaseA.
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Affiliation(s)
- Zeliha Kilic
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona
| | - Ioannis Sgouralis
- Department of Mathematics, University of Tennessee, Knoxville, Tennessee
| | - Steve Pressé
- Center for Biological Physics, Department of Physics and School of Molecular Sciences, Arizona State University, Tempe, Arizona. spresse@%20asu.edu
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17
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Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria. Nat Commun 2021; 12:906. [PMID: 33568644 PMCID: PMC7876045 DOI: 10.1038/s41467-021-21150-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 01/14/2021] [Indexed: 01/29/2023] Open
Abstract
Promoter-proximal pausing regulates eukaryotic gene expression and serves as checkpoints to assemble elongation/splicing machinery. Little is known how broadly this type of pausing regulates transcription in bacteria. We apply nascent elongating transcript sequencing combined with RNase I footprinting for genome-wide analysis of σ70-dependent transcription pauses in Escherichia coli. Retention of σ70 induces strong backtracked pauses at a 10−20-bp distance from many promoters. The pauses in the 10−15-bp register of the promoter are dictated by the canonical −10 element, 6−7 nt spacer and “YR+1Y” motif centered at the transcription start site. The promoters for the pauses in the 16−20-bp register contain an additional −10-like sequence recognized by σ70. Our in vitro analysis reveals that DNA scrunching is involved in these pauses relieved by Gre cleavage factors. The genes coding for transcription factors are enriched in these pauses, suggesting that σ70 and Gre proteins regulate transcription in response to changing environmental cues. Transcription by bacterial RNA polymerase is interrupted by pausing events that play diverse regulatory roles. Here, the authors find that a large number of E. coli sigma70-dependent pauses, clustered at a 10−20-bp distance from promoters, are regulated by Gre cleavage factors constituting a mechanism for rapid response to changing environmental cues.
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18
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Qian J, Dunlap D, Finzi L. Basic mechanisms and kinetics of pause-interspersed transcript elongation. Nucleic Acids Res 2021; 49:15-24. [PMID: 33330935 PMCID: PMC7797061 DOI: 10.1093/nar/gkaa1182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 11/13/2022] Open
Abstract
RNA polymerase pausing during elongation is an important mechanism in the regulation of gene expression. Pausing along DNA templates is thought to be induced by distinct signals encoded in the nucleic acid sequence and halt elongation complexes to allow time for necessary co-transcriptional events. Pausing signals have been classified as those producing short-lived elemental, long-lived backtracked, or hairpin-stabilized pauses. In recent years, structural microbiology and single-molecule studies have significantly advanced our understanding of the paused states, but the dynamics of these states are still uncertain, although several models have been proposed to explain the experimentally observed pausing behaviors. This review summarizes present knowledge about the paused states, discusses key discrepancies among the kinetic models and their basic assumptions, and highlights the importance and challenges in constructing theoretical models that may further our biochemical understanding of transcriptional pausing.
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Affiliation(s)
- Jin Qian
- Physics, Emory University, Atlanta, GA 30307, USA
| | - David Dunlap
- Physics, Emory University, Atlanta, GA 30307, USA
| | - Laura Finzi
- Physics, Emory University, Atlanta, GA 30307, USA
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19
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Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA. Structural basis for transcription complex disruption by the Mfd translocase. eLife 2021; 10:62117. [PMID: 33480355 PMCID: PMC7864632 DOI: 10.7554/elife.62117] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/21/2021] [Indexed: 12/30/2022] Open
Abstract
Transcription-coupled repair (TCR) is a sub-pathway of nucleotide excision repair (NER) that preferentially removes lesions from the template-strand (t-strand) that stall RNA polymerase (RNAP) elongation complexes (ECs). Mfd mediates TCR in bacteria by removing the stalled RNAP concealing the lesion and recruiting Uvr(A)BC. We used cryo-electron microscopy to visualize Mfd engaging with a stalled EC and attempting to dislodge the RNAP. We visualized seven distinct Mfd-EC complexes in both ATP and ADP-bound states. The structures explain how Mfd is remodeled from its repressed conformation, how the UvrA-interacting surface of Mfd is hidden during most of the remodeling process to prevent premature engagement with the NER pathway, how Mfd alters the RNAP conformation to facilitate disassembly, and how Mfd forms a processive translocation complex after dislodging the RNAP. Our results reveal an elaborate mechanism for how Mfd kinetically discriminates paused from stalled ECs and disassembles stalled ECs to initiate TCR.
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Affiliation(s)
- Jin Young Kang
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
| | - Eliza Llewellyn
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Joshua Brewer
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
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20
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Brodolin K, Morichaud Z. Region 4 of the RNA polymerase σ subunit counteracts pausing during initial transcription. J Biol Chem 2021; 296:100253. [PMID: 33380428 PMCID: PMC7948647 DOI: 10.1074/jbc.ra120.016299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/22/2020] [Accepted: 12/30/2020] [Indexed: 01/24/2023] Open
Abstract
All cellular genetic information is transcribed into RNA by multisubunit RNA polymerases (RNAPs). The basal transcription initiation factors of cellular RNAPs stimulate the initial RNA synthesis via poorly understood mechanisms. Here, we explored the mechanism employed by the bacterial factor σ in promoter-independent initial transcription. We found that the RNAP holoenzyme lacking the promoter-binding domain σ4 is ineffective in de novo transcription initiation and displays high propensity to pausing upon extension of RNAs 3 to 7 nucleotides in length. The nucleotide at the RNA 3' end determines the pause lifetime. The σ4 domain stabilizes short RNA:DNA hybrids and suppresses pausing by stimulating RNAP active-center translocation. The antipausing activity of σ4 is modulated by its interaction with the β subunit flap domain and by the σ remodeling factors AsiA and RbpA. Our results suggest that the presence of σ4 within the RNA exit channel compensates for the intrinsic instability of short RNA:DNA hybrids by increasing RNAP processivity, thus favoring productive transcription initiation. This "RNAP boosting" activity of the initiation factor is shaped by the thermodynamics of RNA:DNA interactions and thus, should be relevant for any factor-dependent RNAP.
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Affiliation(s)
- Konstantin Brodolin
- Institut de Recherche en Infectiologie de Montpellier, Centre national de la recherche scientifique, Univ Montpellier, Montpellier, France; Institut national de la santé et de la recherche médicale, Institut de Recherche en Infectiologie de Montpellier, Montpellier, France.
| | - Zakia Morichaud
- Institut de Recherche en Infectiologie de Montpellier, Centre national de la recherche scientifique, Univ Montpellier, Montpellier, France
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21
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Said N, Hilal T, Sunday ND, Khatri A, Bürger J, Mielke T, Belogurov GA, Loll B, Sen R, Artsimovitch I, Wahl MC. Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase ρ. Science 2021; 371:eabd1673. [PMID: 33243850 PMCID: PMC7864586 DOI: 10.1126/science.abd1673] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/26/2020] [Indexed: 12/31/2022]
Abstract
Factor-dependent transcription termination mechanisms are poorly understood. We determined a series of cryo-electron microscopy structures portraying the hexameric adenosine triphosphatase (ATPase) ρ on a pathway to terminating NusA/NusG-modified elongation complexes. An open ρ ring contacts NusA, NusG, and multiple regions of RNA polymerase, trapping and locally unwinding proximal upstream DNA. NusA wedges into the ρ ring, initially sequestering RNA. Upon deflection of distal upstream DNA over the RNA polymerase zinc-binding domain, NusA rotates underneath one capping ρ subunit, which subsequently captures RNA. After detachment of NusG and clamp opening, RNA polymerase loses its grip on the RNA:DNA hybrid and is inactivated. Our structural and functional analyses suggest that ρ, and other termination factors across life, may use analogous strategies to allosterically trap transcription complexes in a moribund state.
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Affiliation(s)
- Nelly Said
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Tarek Hilal
- Research Center of Electron Microscopy and Core Facility BioSupraMol, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Nicholas D Sunday
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Ajay Khatri
- Laboratory of Transcription, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate Studies, Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Jörg Bürger
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
- Institute of Medical Physics und Biophysics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
| | | | - Bernhard Loll
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Ranjan Sen
- Laboratory of Transcription, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Irina Artsimovitch
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany
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22
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Abstract
Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.
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Affiliation(s)
- Sara Osman
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
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23
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Stringent control of the RNA-dependent RNA polymerase translocation revealed by multiple intermediate structures. Nat Commun 2020; 11:2605. [PMID: 32451382 PMCID: PMC7248106 DOI: 10.1038/s41467-020-16234-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/21/2020] [Indexed: 01/07/2023] Open
Abstract
Each polymerase nucleotide addition cycle is associated with two primary conformational changes of the catalytic complex: the pre-chemistry active site closure and post-chemistry translocation. While active site closure is well interpreted by numerous crystallographic snapshots, translocation intermediates are rarely captured. Here we report three types of intermediate structures in an RNA-dependent RNA polymerase (RdRP). The first two types, captured in forward and reverse translocation events, both highlight the role of RdRP-unique motif G in restricting the RNA template movement, corresponding to the rate-limiting step in translocation. By mutating two critical residues in motif G, we obtain the third type of intermediates that may mimic the transition state of this rate-limiting step, demonstrating a previously unidentified movement of the template strand. We propose that a similar strategy may be utilized by other classes of nucleic acid polymerases to ensure templating nucleotide positioning for efficient catalysis through restricting interactions with template RNA.
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24
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Riaz-Bradley A, James K, Yuzenkova Y. High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors. Nucleic Acids Res 2020; 48:1341-1352. [PMID: 31840183 PMCID: PMC7026648 DOI: 10.1093/nar/gkz1130] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/05/2019] [Accepted: 11/18/2019] [Indexed: 12/14/2022] Open
Abstract
The vast majority of organisms possess transcription elongation factors, the functionally similar bacterial Gre and eukaryotic/archaeal TFIIS/TFS. Their main cellular functions are to proofread errors of transcription and to restart elongation via stimulation of RNA hydrolysis by the active centre of RNA polymerase (RNAP). However, a number of taxons lack these factors, including one of the largest and most ubiquitous groups of bacteria, cyanobacteria. Using cyanobacterial RNAP as a model, we investigated alternative mechanisms for maintaining a high fidelity of transcription and for RNAP arrest prevention. We found that this RNAP has very high intrinsic proofreading activity, resulting in nearly as low a level of in vivo mistakes in RNA as Escherichia coli. Features of the cyanobacterial RNAP hydrolysis are reminiscent of the Gre-assisted reaction—the energetic barrier is similarly low, and the reaction involves water activation by a general base. This RNAP is resistant to ubiquitous and most regulatory pausing signals, decreasing the probability to go off-pathway and thus fall into arrest. We suggest that cyanobacterial RNAP has a specific Trigger Loop domain conformation, and isomerises easier into a hydrolytically proficient state, possibly aided by the RNA 3′-end. Cyanobacteria likely passed these features of transcription to their evolutionary descendants, chloroplasts.
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Affiliation(s)
- Amber Riaz-Bradley
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Katherine James
- Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.,Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Yulia Yuzenkova
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
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25
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Chen J, Gopalkrishnan S, Chiu C, Chen AY, Campbell EA, Gourse RL, Ross W, Darst SA. E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation. eLife 2019; 8:e49375. [PMID: 31841111 PMCID: PMC6970531 DOI: 10.7554/elife.49375] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 12/13/2019] [Indexed: 12/21/2022] Open
Abstract
TraR and its homolog DksA are bacterial proteins that regulate transcription initiation by binding directly to RNA polymerase (RNAP) rather than to promoter DNA. Effects of TraR mimic the combined effects of DksA and its cofactor ppGpp, but the structural basis for regulation by these factors remains unclear. Here, we use cryo-electron microscopy to determine structures of Escherichia coli RNAP, with or without TraR, and of an RNAP-promoter complex. TraR binding induced RNAP conformational changes not seen in previous crystallographic analyses, and a quantitative analysis revealed TraR-induced changes in RNAP conformational heterogeneity. These changes involve mobile regions of RNAP affecting promoter DNA interactions, including the βlobe, the clamp, the bridge helix, and several lineage-specific insertions. Using mutational approaches, we show that these structural changes, as well as effects on σ70 region 1.1, are critical for transcription activation or inhibition, depending on the kinetic features of regulated promoters.
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Affiliation(s)
- James Chen
- The Rockefeller UniversityNew YorkUnited States
| | | | | | - Albert Y Chen
- Department of BacteriologyUniversity of Wisconsin-MadisonMadisonUnited States
| | | | - Richard L Gourse
- Department of BacteriologyUniversity of Wisconsin-MadisonMadisonUnited States
| | - Wilma Ross
- Department of BacteriologyUniversity of Wisconsin-MadisonMadisonUnited States
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26
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KIreeva M, Trang C, Matevosyan G, Turek-Herman J, Chasov V, Lubkowska L, Kashlev M. RNA-DNA and DNA-DNA base-pairing at the upstream edge of the transcription bubble regulate translocation of RNA polymerase and transcription rate. Nucleic Acids Res 2019; 46:5764-5775. [PMID: 29771376 PMCID: PMC6009650 DOI: 10.1093/nar/gky393] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/30/2018] [Indexed: 12/19/2022] Open
Abstract
Translocation of RNA polymerase (RNAP) along DNA may be rate-limiting for transcription elongation. The Brownian ratchet model posits that RNAP rapidly translocates back and forth until the post-translocated state is stabilized by NTP binding. An alternative model suggests that RNAP translocation is slow and poorly reversible. To distinguish between these two models, we take advantage of an observation that pyrophosphorolysis rates directly correlate with the abundance of the pre-translocated fraction. Pyrophosphorolysis by RNAP stabilized in the pre-translocated state by bacteriophage HK022 protein Nun was used as a reference point to determine the pre-translocated fraction in the absence of Nun. The stalled RNAP preferentially occupies the post-translocated state. The forward translocation rate depends, among other factors, on melting of the RNA–DNA base pair at the upstream edge of the transcription bubble. DNA–DNA base pairing immediately upstream from the RNA–DNA hybrid stabilizes the post-translocated state. This mechanism is conserved between E. coli RNAP and S. cerevisiae RNA polymerase II and is partially dependent on the lid domain of the catalytic subunit. Thus, the RNA–DNA hybrid and DNA reannealing at the upstream edge of the transcription bubble emerge as targets for regulation of the transcription elongation rate.
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Affiliation(s)
- Maria KIreeva
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Cyndi Trang
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Gayane Matevosyan
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Joshua Turek-Herman
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Vitaly Chasov
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Lucyna Lubkowska
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Mikhail Kashlev
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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Kang JY, Mishanina TV, Landick R, Darst SA. Mechanisms of Transcriptional Pausing in Bacteria. J Mol Biol 2019; 431:4007-4029. [PMID: 31310765 DOI: 10.1016/j.jmb.2019.07.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 12/21/2022]
Abstract
Pausing by RNA polymerase (RNAP) during transcription regulates gene expression in all domains of life. In this review, we recap the history of transcriptional pausing discovery, summarize advances in our understanding of the underlying causes of pausing since then, and describe new insights into the pausing mechanisms and pause modulation by transcription factors gained from structural and biochemical experiments. The accumulated evidence to date suggests that upon encountering a pause signal in the nucleic-acid sequence being transcribed, RNAP rearranges into an elemental, catalytically inactive conformer unable to load NTP substrate. The conformation, and as a consequence lifetime, of an elemental paused RNAP is modulated by backtracking, nascent RNA structure, binding of transcription regulators, or a combination of these mechanisms. We conclude the review by outlining open questions and directions for future research in the field of transcriptional pausing.
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Affiliation(s)
- Jin Young Kang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejon 34141, Republic of Korea.
| | - Tatiana V Mishanina
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Seth A Darst
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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28
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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.
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Affiliation(s)
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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29
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Abstract
In this review, Core et al. discuss the recent advances in our understanding of the early steps in Pol II transcription, highlighting the events and factors involved in the establishment and release of paused Pol II. They also discuss a number of unanswered questions about the regulation and function of Pol II pausing. Precise spatio–temporal control of gene activity is essential for organismal development, growth, and survival in a changing environment. Decisive steps in gene regulation involve the pausing of RNA polymerase II (Pol II) in early elongation, and the controlled release of paused polymerase into productive RNA synthesis. Here we describe the factors that enable pausing and the events that trigger Pol II release into the gene. We also discuss open questions in the field concerning the stability of paused Pol II, nucleosomes as obstacles to elongation, and potential roles of pausing in defining the precision and dynamics of gene expression.
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Affiliation(s)
- Leighton Core
- Department of Molecular and Cell Biology, Institute of Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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30
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Roberts JW. Mechanisms of Bacterial Transcription Termination. J Mol Biol 2019; 431:4030-4039. [PMID: 30978344 DOI: 10.1016/j.jmb.2019.04.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 01/28/2023]
Abstract
Bacterial transcription termination, described mostly for Escherichia coli, occurs in three recognized ways: intrinsic termination, an activity only of the core RNAP enzyme and transcript sequences that encode an RNA hairpin and terminal uridine-rich segment; termination by the enzyme Rho, an ATP-dependent RNA translocase that releases RNA by forcing uncharacterized structural changes in the elongating complex; and Mfd-dependent termination, the activity of an ATP-dependent DNA translocase that is thought to dissociate the elongation complex by exerting torque on a stalled RNAP. Intrinsic termination can be described in terms of the nucleic acid movements in the process, whereas the enzymatic mechanisms have been illuminated importantly by definitive structural and biochemical analysis of their activity.
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Affiliation(s)
- Jeffrey W Roberts
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA.
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31
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Sanders TJ, Lammers M, Marshall CJ, Walker JE, Lynch ER, Santangelo TJ. TFS and Spt4/5 accelerate transcription through archaeal histone-based chromatin. Mol Microbiol 2019; 111:784-797. [PMID: 30592095 PMCID: PMC6417941 DOI: 10.1111/mmi.14191] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2018] [Indexed: 12/25/2022]
Abstract
RNA polymerase must surmount translocation barriers for continued transcription. In Eukarya and most Archaea, DNA-bound histone proteins represent the most common and troublesome barrier to transcription elongation. Eukaryotes encode a plethora of chromatin-remodeling complexes, histone-modification enzymes and transcription elongation factors to aid transcription through nucleosomes, while archaea seemingly lack machinery to remodel/modify histone-based chromatin and thus must rely on elongation factors to accelerate transcription through chromatin-barriers. TFS (TFIIS in Eukarya) and the Spt4-Spt5 complex are universally encoded in archaeal genomes, and here we demonstrate that both elongation factors, via different mechanisms, can accelerate transcription through archaeal histone-based chromatin. Histone proteins in Thermococcus kodakarensis are sufficiently abundant to completely wrap all genomic DNA, resulting in a consistent protein barrier to transcription elongation. TFS-enhanced cleavage of RNAs in backtracked transcription complexes reactivates stalled RNAPs and dramatically accelerates transcription through histone-barriers, while Spt4-Spt5 changes to clamp-domain dynamics play a lesser-role in stabilizing transcription. Repeated attempts to delete TFS, Spt4 and Spt5 from the T. kodakarensis genome were not successful, and the essentiality of both conserved transcription elongation factors suggests that both conserved elongation factors play important roles in transcription regulation in vivo, including mechanisms to accelerate transcription through downstream protein barriers.
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Affiliation(s)
- Travis J. Sanders
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Marshall Lammers
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Craig J. Marshall
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Julie E. Walker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
- Current address: Renewable and Sustainable Energy Institute, University of Colorado, Boulder, Colorado, 80303, USA
| | - Erin R. Lynch
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Thomas J. Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
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32
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Bellecourt MJ, Ray-Soni A, Harwig A, Mooney RA, Landick R. RNA Polymerase Clamp Movement Aids Dissociation from DNA but Is Not Required for RNA Release at Intrinsic Terminators. J Mol Biol 2019; 431:696-713. [PMID: 30630008 DOI: 10.1016/j.jmb.2019.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 10/27/2022]
Abstract
In bacteria, disassembly of elongating transcription complexes (ECs) can occur at intrinsic terminators in a 2- to 3-nucleotide window after transcription of multiple kilobase pairs of DNA. Intrinsic terminators trigger pausing on weak RNA-DNA hybrids followed by formation of a strong, GC-rich stem-loop in the RNA exit channel of RNA polymerase (RNAP), inactivating nucleotide addition and inducing dissociation of RNA and RNAP from DNA. Although the movements of RNA and DNA during intrinsic termination have been studied extensively leading to multiple models, the effects of RNAP conformational changes remain less well defined. RNAP contains a clamp domain that closes around the nucleic acid scaffold during transcription initiation and can be displaced by either swiveling or opening motions. Clamp opening is proposed to promote termination by releasing RNAP-nucleic acid contacts. We developed a cysteine crosslinking assay to constrain clamp movements and study effects on intrinsic termination. We found that biasing the clamp into different conformations perturbed termination efficiency, but that perturbations were due primarily to changes in elongation rate, not the competing rate at which ECs commit to termination. After commitment, however, inhibiting clamp movements slowed release of DNA but not of RNA from the EC. We also found that restricting trigger-loop movements with the RNAP inhibitor microcin J25 prior to commitment inhibits termination, in agreement with a recently proposed multistate-multipath model of intrinsic termination. Together our results support views that termination commitment and DNA release are separate steps and that RNAP may remain associated with DNA after termination.
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Affiliation(s)
- Michael J Bellecourt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ananya Ray-Soni
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alex Harwig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Rachel Anne Mooney
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Saba J, Chua XY, Mishanina TV, Nayak D, Windgassen TA, Mooney RA, Landick R. The elemental mechanism of transcriptional pausing. eLife 2019; 8:e40981. [PMID: 30618376 PMCID: PMC6336406 DOI: 10.7554/elife.40981] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/19/2018] [Indexed: 12/20/2022] Open
Abstract
Transcriptional pausing underlies regulation of cellular RNA biogenesis. A consensus pause sequence that acts on RNA polymerases (RNAPs) from bacteria to mammals halts RNAP in an elemental paused state from which longer-lived pauses can arise. Although the structural foundations of pauses prolonged by backtracking or nascent RNA hairpins are recognized, the fundamental mechanism of the elemental pause is less well-defined. Here we report a mechanistic dissection that establishes the elemental pause signal (i) is multipartite; (ii) causes a modest conformational shift that puts γ-proteobacterial RNAP in an off-pathway state in which template base loading but not RNA translocation is inhibited; and (iii) allows RNAP to enter pretranslocated and one-base-pair backtracked states easily even though the half-translocated state observed in paused cryo-EM structures rate-limits pause escape. Our findings provide a mechanistic basis for the elemental pause and a framework to understand how pausing is modulated by sequence, cellular conditions, and regulators.
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Affiliation(s)
- Jason Saba
- Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUnited States
| | - Xien Yu Chua
- Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUnited States
| | - Tatiana V Mishanina
- Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUnited States
| | - Dhananjaya Nayak
- Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUnited States
| | - Tricia A Windgassen
- Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUnited States
| | - Rachel Anne Mooney
- Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUnited States
| | - Robert Landick
- Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUnited States
- Department of BacteriologyUniversity of Wisconsin-MadisonMadisonUnited States
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34
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Kang JY, Mishanina TV, Bellecourt MJ, Mooney RA, Darst SA, Landick R. RNA Polymerase Accommodates a Pause RNA Hairpin by Global Conformational Rearrangements that Prolong Pausing. Mol Cell 2019; 69:802-815.e5. [PMID: 29499135 DOI: 10.1016/j.molcel.2018.01.018] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/27/2017] [Accepted: 01/12/2018] [Indexed: 01/10/2023]
Abstract
Sequence-specific pausing by RNA polymerase (RNAP) during transcription plays crucial and diverse roles in gene expression. In bacteria, RNA structures are thought to fold within the RNA exit channel of the RNAP and can increase pause lifetimes significantly. The biophysical mechanism of pausing is uncertain. We used single-particle cryo-EM to determine structures of paused complexes, including a 3.8-Å structure of an RNA hairpin-stabilized, paused RNAP that coordinates RNA folding in the his operon attenuation control region of E. coli. The structures revealed a half-translocated pause state (RNA post-translocated, DNA pre-translocated) that can explain transcriptional pausing and a global conformational change of RNAP that allosterically inhibits trigger loop folding and can explain pause hairpin action. Pause hairpin interactions with the RNAP RNA exit channel suggest how RNAP guides the formation of nascent RNA structures.
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Affiliation(s)
- Jin Young Kang
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Tatiana V Mishanina
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael J Bellecourt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Rachel Anne Mooney
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Seth A Darst
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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35
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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.
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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
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36
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Gene expression and protein synthesis of esterase from Streptococcus mutans are affected by biodegradation by-product from methacrylate resin composites and adhesives. Acta Biomater 2018; 81:158-168. [PMID: 30268915 DOI: 10.1016/j.actbio.2018.09.050] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 09/14/2018] [Accepted: 09/26/2018] [Indexed: 11/22/2022]
Abstract
An esterase from S. mutans UA159, SMU_118c, was shown to hydrolyze methacrylate resin-based dental monomers. OBJECTIVE To investigate the association of SMU_118c to the whole cellular hydrolytic activity of S. mutans toward polymerized resin composites, and to examine how the bacterium adapts its hydrolytic activity in response to environmental stresses triggered by the presence of a resin composites and adhesives biodegradation by-product (BBP). MATERIALS AND METHODS Biofilms of S. mutans UA159 parent wild strain, SMU_118c knockout strain (ΔSMU_118c), and SMU_118c complemented strain (ΔSMU_118cC) were incubated with photo-polymerized resin composite. High performance liquid chromatography was used to quantify the amount of a universal 2,2-Bis[4-(2-hydroxy-3-methacryloxypropoxy)phenyl]propane (bisGMA)-derived BBP, bishydroxy-propoxy-phenyl-propane (bisHPPP) in the media. Fluorescence in situ hybridization (FISH) and quantitative proteomic analysis were used to measure SMU_118c gene expression and production of SMU_118c protein, respectively, from biofilms of S. mutans UA159 wild strain that were cultured with bisHPPP. RESULTS The levels of bisHPPP released from composite were similar for ΔSMU_118c and media control, and these were significantly lower compared to the parent wild-strain UA159 and complemented strain (ΔSMU_118cC) (p < 0.05). Gene expression of SMU_118c and productions of SMU_118c protein were higher for bisHPPP incubated biofilms (p < 0.05). SIGNIFICANCE This study suggests that SMU_118c is a dominant esterase in S. mutans and capable of catalyzing the hydrolysis of the resinous matrix of polymerized composites and adhesives. In turn, the bacterial response to BBP was to increase the expression of the esterase gene and enhance esterase production, potentially accelerating the biodegradation of the restoration, adhesive and restoration-tooth interface, ultimately contributing to premature restoration failure. STATEMENT OF SIGNIFICANCE We recently reported (Huang et al., 2018) on the isolation and initial characterization of a specific esterase (SMU_118c) from S. mutans that show degradative activity toward the hydrolysis of dental monomers. The current study further characterize this enzyme and shows that SMU_118c is a dominant degradative esterase activity in the cariogenic bacterium S. mutans and is capable of catalyzing the hydrolysis of the resinous matrix of polymerized composites and adhesives. In turn, the bacterial response to biodegradation by-products from composites and adhesives was to increase the expression of the esterase gene and enhance esterase production, accelerating the biodegradation of the restoration, adhesive and the restoration-tooth interface, potentially contributing to the pathogenesis of recurrent caries around resin composite restorations.
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37
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Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H. Structural basis of the nucleosome transition during RNA polymerase II passage. Science 2018; 362:595-598. [PMID: 30287617 DOI: 10.1126/science.aau9904] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/19/2018] [Indexed: 12/28/2022]
Abstract
Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo-electron microscopy structures of RNAPII-nucleosome complexes in which RNAPII pauses at the superhelical locations SHL(-6), SHL(-5), SHL(-2), and SHL(-1) of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, in which RNAPII gradually tears DNA from the histone surface while preserving the histone octamer. The nucleosomes in the SHL(-1) complexes are bound to a "foreign" DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation.
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Affiliation(s)
- Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Haruhiko Ehara
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuka Fujino
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Mikako Shirouzu
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shun-Ichi Sekine
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. .,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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38
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Portman JR, Strick TR. Transcription-Coupled Repair and Complex Biology. J Mol Biol 2018; 430:4496-4512. [DOI: 10.1016/j.jmb.2018.04.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 10/24/2022]
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39
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Abstract
Transcription is a discontinuous process, where each nucleotide incorporation cycle offers a decision between elongation, pausing, halting, or termination. Many cis-acting regulatory RNAs, such as riboswitches, exert their influence over transcription elongation. Through such mechanisms, certain RNA elements can couple physiological or environmental signals to transcription attenuation, a process where cis-acting regulatory RNAs directly influence formation of transcription termination signals. However, through another regulatory mechanism called processive antitermination (PA), RNA polymerase can bypass termination sites over much greater distances than transcription attenuation. PA mechanisms are widespread in bacteria, although only a few classes have been discovered overall. Also, although traditional, signal-responsive riboswitches have not yet been discovered to promote PA, it is increasingly clear that small RNA elements are still oftentimes required. In some instances, small RNA elements serve as loading sites for cellular factors that promote PA. In other instances, larger, more complicated RNA elements participate in PA in unknown ways, perhaps even acting alone to trigger PA activity. These discoveries suggest that what is now needed is a systematic exploration of PA in bacteria, to determine how broadly these transcription elongation mechanisms are utilized, to reveal the diversity in their molecular mechanisms, and to understand the general logic behind their cellular applications. This review covers the known examples of PA regulatory mechanisms and speculates that they may be broadly important to bacteria.
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Affiliation(s)
- Jonathan R. Goodson
- The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD 20742
| | - Wade C. Winkler
- The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD 20742
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40
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Nedialkov Y, Svetlov D, Belogurov GA, Artsimovitch I. Locking the nontemplate DNA to control transcription. Mol Microbiol 2018; 109:445-457. [PMID: 29758107 PMCID: PMC6173972 DOI: 10.1111/mmi.13983] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2018] [Indexed: 12/31/2022]
Abstract
Universally conserved NusG/Spt5 factors reduce RNA polymerase pausing and arrest. In a widely accepted model, these proteins bridge the RNA polymerase clamp and lobe domains across the DNA channel, inhibiting the clamp opening to promote pause-free RNA synthesis. However, recent structures of paused transcription elongation complexes show that the clamp does not open and suggest alternative mechanisms of antipausing. Among these mechanisms, direct contacts of NusG/Spt5 proteins with the nontemplate DNA in the transcription bubble have been proposed to prevent unproductive DNA conformations and thus inhibit arrest. We used Escherichia coli RfaH, whose interactions with DNA are best characterized, to test this idea. We report that RfaH stabilizes the upstream edge of the transcription bubble, favoring forward translocation, and protects the upstream duplex DNA from exonuclease cleavage. Modeling suggests that RfaH loops the nontemplate DNA around its surface and restricts the upstream DNA duplex mobility. Strikingly, we show that RfaH-induced DNA protection and antipausing activity can be mimicked by shortening the nontemplate strand in elongation complexes assembled on synthetic scaffolds. We propose that remodeling of the nontemplate DNA controls recruitment of regulatory factors and R-loop formation during transcription elongation across all life.
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Affiliation(s)
- Yuri Nedialkov
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210
| | - Dmitri Svetlov
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | | | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210
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41
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Svetlov V, Nudler E. Reading of the non-template DNA by transcription elongation factors. Mol Microbiol 2018; 109:417-421. [PMID: 29757477 PMCID: PMC6173973 DOI: 10.1111/mmi.13984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2018] [Indexed: 02/02/2023]
Abstract
Unlike transcription initiation and termination, which have easily discernable signals, such as promoters and terminators, elongation is regulated through a dynamic network involving RNA/DNA pause signals and states-rather than sequence-specific protein interactions. A report by Nedialkov et al. () provides experimental evidence for sequence-specific recruitment of elongation factor RfaH to transcribing RNA polymerase (RNAP) and outlines the mechanism of gene expression regulation by restraint ('locking') of the DNA non-template strand. According to this model, the elongation complex pauses at the so called 'operon polarity sequence' (found in some long bacterial operons coding for virulence genes), when the usually flexible non-template DNA strand adopts a distinct hairpin-loop conformation on the surface of transcribing RNAP. Sequence-specific binding of RfaH to this DNA segment facilitates conversion of RfaH from its inactive closed to its active open conformation. The interaction network formed between RfaH, non-template DNA and RNAP locks DNA in a conformation that renders RNAP resistant to pausing and termination. The effects of such locking on elongation can be mimicked by restraint of the non-template strand due to its shortening. This work advances our understanding of transcription regulation and has important implications for the action of general elongation factors, such as NusG, which lack apparent sequence-specificity, as well as for the mechanisms of other linked processes, such as transcription-coupled DNA repair.
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Affiliation(s)
- Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016
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42
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Gabizon R, Lee A, Vahedian-Movahed H, Ebright RH, Bustamante CJ. Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates. Nat Commun 2018; 9:2930. [PMID: 30050038 PMCID: PMC6062546 DOI: 10.1038/s41467-018-05344-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/21/2018] [Indexed: 11/25/2022] Open
Abstract
Transcription by RNA polymerase (RNAP) is interspersed with sequence-dependent pausing. The processes through which paused states are accessed and stabilized occur at spatiotemporal scales beyond the resolution of previous methods, and are poorly understood. Here, we combine high-resolution optical trapping with improved data analysis methods to investigate the formation of paused states at enhanced temporal resolution. We find that pause sites reduce the forward transcription rate of nearly all RNAP molecules, rather than just affecting the subset of molecules that enter long-lived pauses. We propose that the reduced rates at pause sites allow time for the elongation complex to undergo conformational changes required to enter long-lived pauses. We also find that backtracking occurs stepwise, with states backtracked by at most one base pair forming quickly, and further backtracking occurring slowly. Finally, we find that nascent RNA structures act as modulators that either enhance or attenuate pausing, depending on the sequence context.
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Affiliation(s)
- Ronen Gabizon
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA, 94720, USA
| | - Antony Lee
- Department of Physics, University of California, Berkeley, CA, 94720, USA
| | - Hanif Vahedian-Movahed
- Department of Chemistry and Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Richard H Ebright
- Department of Chemistry and Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA
| | - Carlos J Bustamante
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA, 94720, USA.
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
- Department of Molecular and Cell Biology, and Kavli Energy Nanoscience Institute, University of California, Berkeley, CA, 94720, USA.
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43
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Kang JY, Mooney RA, Nedialkov Y, Saba J, Mishanina TV, Artsimovitch I, Landick R, Darst SA. Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators. Cell 2018; 173:1650-1662.e14. [PMID: 29887376 PMCID: PMC6003885 DOI: 10.1016/j.cell.2018.05.017] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/09/2018] [Accepted: 05/08/2018] [Indexed: 10/14/2022]
Abstract
NusG/RfaH/Spt5 transcription elongation factors are the only transcription regulators conserved across all life. Bacterial NusG regulates RNA polymerase (RNAP) elongation complexes (ECs) across most genes, enhancing elongation by suppressing RNAP backtracking and coordinating ρ-dependent termination and translation. The NusG paralog RfaH engages the EC only at operon polarity suppressor (ops) sites and suppresses both backtrack and hairpin-stabilized pausing. We used single-particle cryoelectron microscopy (cryo-EM) to determine structures of ECs at ops with NusG or RfaH. Both factors chaperone base-pairing of the upstream duplex DNA to suppress backtracking, explaining stimulation of elongation genome-wide. The RfaH-opsEC structure reveals how RfaH confers operon specificity through specific recognition of an ops hairpin in the single-stranded nontemplate DNA and tighter binding to the EC to exclude NusG. Tight EC binding by RfaH sterically blocks the swiveled RNAP conformation necessary for hairpin-stabilized pausing. The universal conservation of NusG/RfaH/Spt5 suggests that the molecular mechanisms uncovered here are widespread.
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Affiliation(s)
- Jin Young Kang
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Rachel Anne Mooney
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yuri Nedialkov
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Jason Saba
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tatiana V Mishanina
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Seth A Darst
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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44
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Lin W, Das K, Degen D, Mazumder A, Duchi D, Wang D, Ebright YW, Ebright RY, Sineva E, Gigliotti M, Srivastava A, Mandal S, Jiang Y, Liu Y, Yin R, Zhang Z, Eng ET, Thomas D, Donadio S, Zhang H, Zhang C, Kapanidis AN, Ebright RH. Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3). Mol Cell 2018; 70:60-71.e15. [PMID: 29606590 PMCID: PMC6205224 DOI: 10.1016/j.molcel.2018.02.026] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/14/2018] [Accepted: 02/23/2018] [Indexed: 12/16/2022]
Abstract
Fidaxomicin is an antibacterial drug in clinical use for treatment of Clostridium difficile diarrhea. The active ingredient of fidaxomicin, lipiarmycin A3 (Lpm), functions by inhibiting bacterial RNA polymerase (RNAP). Here we report a cryo-EM structure of Mycobacterium tuberculosis RNAP holoenzyme in complex with Lpm at 3.5-Å resolution. The structure shows that Lpm binds at the base of the RNAP "clamp." The structure exhibits an open conformation of the RNAP clamp, suggesting that Lpm traps an open-clamp state. Single-molecule fluorescence resonance energy transfer experiments confirm that Lpm traps an open-clamp state and define effects of Lpm on clamp dynamics. We suggest that Lpm inhibits transcription by trapping an open-clamp state, preventing simultaneous interaction with promoter -10 and -35 elements. The results account for the absence of cross-resistance between Lpm and other RNAP inhibitors, account for structure-activity relationships of Lpm derivatives, and enable structure-based design of improved Lpm derivatives.
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Affiliation(s)
- Wei Lin
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Kalyan Das
- Rega Institute and Department of Microbiology and Immunology, KU Leuven, 3000 Leuven, Belgium.
| | - David Degen
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Abhishek Mazumder
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Diego Duchi
- Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Dongye Wang
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Yon W Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Richard Y Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Elena Sineva
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Matthew Gigliotti
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Aashish Srivastava
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Sukhendu Mandal
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Yi Jiang
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Liu
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Ruiheng Yin
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Zhening Zhang
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York NY 10027, USA
| | - Edward T Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York NY 10027, USA
| | - Dennis Thomas
- Center for Integrative Proteomics, Rutgers University, Piscataway, NJ 08854, USA
| | | | - Haibo Zhang
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Changsheng Zhang
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | | | - Richard H Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA.
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45
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Guo X, Myasnikov AG, Chen J, Crucifix C, Papai G, Takacs M, Schultz P, Weixlbaumer A. Structural Basis for NusA Stabilized Transcriptional Pausing. Mol Cell 2018; 69:816-827.e4. [PMID: 29499136 PMCID: PMC5842316 DOI: 10.1016/j.molcel.2018.02.008] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/22/2018] [Accepted: 02/02/2018] [Indexed: 12/12/2022]
Abstract
Transcriptional pausing by RNA polymerases (RNAPs) is a key mechanism to regulate gene expression in all kingdoms of life and is a prerequisite for transcription termination. The essential bacterial transcription factor NusA stimulates both pausing and termination of transcription, thus playing a central role. Here, we report single-particle electron cryo-microscopy reconstructions of NusA bound to paused E. coli RNAP elongation complexes with and without a pause-enhancing hairpin in the RNA exit channel. The structures reveal four interactions between NusA and RNAP that suggest how NusA stimulates RNA folding, pausing, and termination. An asymmetric translocation intermediate of RNA and DNA converts the active site of the enzyme into an inactive state, providing a structural explanation for the inhibition of catalysis. Comparing RNAP at different stages of pausing provides insights on the dynamic nature of the process and the role of NusA as a regulatory factor.
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Affiliation(s)
- Xieyang Guo
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France; Université de Strasbourg, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale (Inserm), U964, 67404 Illkirch Cedex, France
| | - Alexander G Myasnikov
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France; Université de Strasbourg, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale (Inserm), U964, 67404 Illkirch Cedex, France
| | - James Chen
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Corinne Crucifix
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France; Université de Strasbourg, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale (Inserm), U964, 67404 Illkirch Cedex, France
| | - Gabor Papai
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France; Université de Strasbourg, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale (Inserm), U964, 67404 Illkirch Cedex, France
| | - Maria Takacs
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France; Université de Strasbourg, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale (Inserm), U964, 67404 Illkirch Cedex, France
| | - Patrick Schultz
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France; Université de Strasbourg, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale (Inserm), U964, 67404 Illkirch Cedex, France
| | - Albert Weixlbaumer
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France; Université de Strasbourg, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale (Inserm), U964, 67404 Illkirch Cedex, France.
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46
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Abascal-Palacios G, Ramsay EP, Beuron F, Morris E, Vannini A. Structural basis of RNA polymerase III transcription initiation. Nature 2018; 553:301-306. [PMID: 29345637 DOI: 10.1038/nature25441] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/08/2017] [Indexed: 12/14/2022]
Abstract
RNA polymerase (Pol) III transcribes essential non-coding RNAs, including the entire pool of transfer RNAs, the 5S ribosomal RNA and the U6 spliceosomal RNA, and is often deregulated in cancer cells. The initiation of gene transcription by Pol III requires the activity of the transcription factor TFIIIB to form a transcriptionally active Pol III preinitiation complex (PIC). Here we present electron microscopy reconstructions of Pol III PICs at 3.4-4.0 Å and a reconstruction of unbound apo-Pol III at 3.1 Å. TFIIIB fully encircles the DNA and restructures Pol III. In particular, binding of the TFIIIB subunit Bdp1 rearranges the Pol III-specific subunits C37 and C34, thereby promoting DNA opening. The unwound DNA directly contacts both sides of the Pol III cleft. Topologically, the Pol III PIC resembles the Pol II PIC, whereas the Pol I PIC is more divergent. The structures presented unravel the molecular mechanisms underlying the first steps of Pol III transcription and also the general conserved mechanisms of gene transcription initiation.
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Affiliation(s)
| | | | | | - Edward Morris
- The Institute of Cancer Research, London SW7 3RP, UK
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47
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Trigger loop dynamics can explain stimulation of intrinsic termination by bacterial RNA polymerase without terminator hairpin contact. Proc Natl Acad Sci U S A 2017; 114:E9233-E9242. [PMID: 29078293 DOI: 10.1073/pnas.1706247114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In bacteria, intrinsic termination signals cause disassembly of the highly stable elongating transcription complex (EC) over windows of two to three nucleotides after kilobases of RNA synthesis. Intrinsic termination is caused by the formation of a nascent RNA hairpin adjacent to a weak RNA-DNA hybrid within RNA polymerase (RNAP). Although the contributions of RNA and DNA sequences to termination are largely understood, the roles of conformational changes in RNAP are less well described. The polymorphous trigger loop (TL), which folds into the trigger helices to promote nucleotide addition, also is proposed to drive termination by folding into the trigger helices and contacting the terminator hairpin after invasion of the hairpin in the RNAP main cleft [Epshtein V, Cardinale CJ, Ruckenstein AE, Borukhov S, Nudler E (2007) Mol Cell 28:991-1001]. To investigate the contribution of the TL to intrinsic termination, we developed a kinetic assay that distinguishes effects of TL alterations on the rate at which ECs terminate from effects of the TL on the nucleotide addition rate that indirectly affect termination efficiency by altering the time window in which termination can occur. We confirmed that the TL stimulates termination rate, but found that stabilizing either the folded or unfolded TL conformation decreased termination rate. We propose that conformational fluctuations of the TL (TL dynamics), not TL-hairpin contact, aid termination by increasing EC conformational diversity and thus access to favorable termination pathways. We also report that the TL and the TL sequence insertion (SI3) increase overall termination efficiency by stimulating pausing, which increases the flux of ECs into the termination pathway.
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48
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Han Z, Porrua O. Helicases as transcription termination factors: Different solutions for a common problem. Transcription 2017; 9:152-158. [PMID: 28886303 DOI: 10.1080/21541264.2017.1361503] [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] [Indexed: 10/18/2022] Open
Abstract
Helicases are enzymes that remodel nucleic acids or protein-nucleic acid complexes in an ATP-dependent manner. They are ubiquitous and can play many diverse functions related to the metabolism of nucleic acids. A few helicases from both the prokaryotic and the eukaryotic worlds have the ability to induce transcription termination. Here we discuss how the same biological function is achieved by different helicases with quite divergent structures and mechanisms of action.
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Affiliation(s)
- Zhong Han
- a Institut Jacques Monod, Centre Nationale pour la Recherche Scientifique (CNRS), UMR 7592, Université Paris Diderot, Sorbonne Paris Cité , Paris , France.,b Université Paris-Saclay , Gif sur Yvette , France
| | - Odil Porrua
- a Institut Jacques Monod, Centre Nationale pour la Recherche Scientifique (CNRS), UMR 7592, Université Paris Diderot, Sorbonne Paris Cité , Paris , France
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49
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Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. Nat Struct Mol Biol 2017; 24:809-815. [PMID: 28892040 DOI: 10.1038/nsmb.3465] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 08/14/2017] [Indexed: 12/25/2022]
Abstract
During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA processing. We combined cryo-EM and X-ray crystallography to determine the structure of the mammalian Pol II-DSIF elongation complex at a nominal resolution of 3.4 Å. Human DSIF has a modular structure with two domains forming a DNA clamp, two domains forming an RNA clamp, and one domain buttressing the RNA clamp. The clamps maintain the transcription bubble, position upstream DNA, and retain the RNA transcript in the exit tunnel. The mobile C-terminal region of DSIF is located near exiting RNA, where it can recruit factors for RNA processing. The structure provides insight into the roles of DSIF during mRNA synthesis.
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50
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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.
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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
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