1
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Qian J, Wang B, Artsimovitch I, Dunlap D, Finzi L. Force and the α-C-terminal domains bias RNA polymerase recycling. Nat Commun 2024; 15:7520. [PMID: 39214958 PMCID: PMC11364550 DOI: 10.1038/s41467-024-51603-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
After an RNA polymerase reaches a terminator, instead of dissociating from the template, it may diffuse along the DNA and recommence RNA synthesis from the previous or a different promoter. Magnetic tweezers were used to monitor such secondary transcription and determine the effects of low forces assisting or opposing translocation, protein roadblocks, and transcription factors. Remarkably, up to 50% of Escherichia coli (E. coli) RNA polymerases diffused along the DNA after termination. Force biased the direction of diffusion (sliding) and the velocity increased rapidly with force up to 0.7 pN and much more slowly thereafter. Sigma factor 70 (σ70) likely remained associated with the DNA promoting sliding and enabling re-initiation from promoters in either orientation. However, deletions of the α-C-terminal domains severely limited the ability of RNAP to turn around between successive rounds of transcription. The addition of elongation factor NusG, which competes with σ70 for binding to RNAP, limited additional rounds of transcription. Surprisingly, sliding RNA polymerases blocked by a DNA-bound lac repressor could slowly re-initiate transcription and were not affected by NusG, suggesting a σ-independent pathway. Low forces effectively biased promoter selection suggesting a prominent role for topological entanglements that affect RNA polymerase translocation.
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Affiliation(s)
- Jin Qian
- Physics Department, Emory University, Atlanta, GA, USA
| | - Bing Wang
- The Center for RNA Biology and Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Irina Artsimovitch
- The Center for RNA Biology and Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - David Dunlap
- Department of Physics & Astronomy, Clemson University, Clemson, SC, USA
| | - Laura Finzi
- Department of Physics & Astronomy, Clemson University, Clemson, SC, USA.
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2
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Voedts H, Anoyatis-Pelé C, Langella O, Rusconi F, Hugonnet JE, Arthur M. (p)ppGpp modifies RNAP function to confer β-lactam resistance in a peptidoglycan-independent manner. Nat Microbiol 2024; 9:647-656. [PMID: 38443580 DOI: 10.1038/s41564-024-01609-w] [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: 02/21/2023] [Accepted: 01/16/2024] [Indexed: 03/07/2024]
Abstract
(p)ppGpp is a nucleotide alarmone that controls bacterial response to nutrient deprivation. Since elevated (p)ppGpp levels confer mecillinam resistance and are essential for broad-spectrum β-lactam resistance as mediated by the β-lactam-insensitive transpeptidase YcbB (LdtD), we hypothesized that (p)ppGpp might affect cell wall peptidoglycan metabolism. Here we report that (p)ppGpp-dependent β-lactam resistance does not rely on any modification of peptidoglycan metabolism, as established by analysis of Escherichia coli peptidoglycan structure using high-resolution mass spectrometry. Amino acid substitutions in the β or β' RNA polymerase (RNAP) subunits, alone or in combination with the CRISPR interference-mediated downregulation of three of seven ribosomal RNA operons, were sufficient for resistance, although β-lactams have no known impact on the RNAP or ribosomes. This implies that modifications of RNAP and ribosome functions are critical to prevent downstream effects of the inactivation of peptidoglycan transpeptidases by β-lactams.
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Affiliation(s)
- Henri Voedts
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
| | - Constantin Anoyatis-Pelé
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
| | - Olivier Langella
- GQE-Le Moulon/PAPPSO, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, Gif-sur-Yvette, France
| | - Filippo Rusconi
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
- GQE-Le Moulon/PAPPSO, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, Gif-sur-Yvette, France
| | - Jean-Emmanuel Hugonnet
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France.
| | - Michel Arthur
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France.
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3
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Clamp Interactions with +3/+6 Duplex and Upstream-to-Downstream Allosteric Effects in Late Steps of Forming a Stable RNA Polymerase-Promoter Open Complex. J Mol Biol 2023; 435:167990. [PMID: 36736885 DOI: 10.1016/j.jmb.2023.167990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/04/2023]
Abstract
Stable 37 °C open complexes (OC) of E. coli RNA polymerase (RNAP) at λPR and T7A1 promoters form at similar rates but have very different lifetimes. To understand the downstream interactions responsible for OC lifetime, how promoter sequence directs them and when they form, we report lifetimes of stable OC and unstable late (I2) intermediates for promoters with different combinations of λPR (L) and T7A1 (T) discriminators, core promoters and UP elements. I2 lifetimes are similarly short, while stable OC lifetimes differ greatly, determined largely by the discriminator and modulated by core-promoter and UP elements. The free energy change ΔG3o for I2 → stable OC is approximately -4 kcal more favorable for L-discriminator than for T-discriminator promoters. Downstream-truncation at +6 (DT+6) greatly destabilizes OC at L-discriminator but not T-discriminator promoters, making all ΔG3o values similar (approximately -4 kcal). Urea reduces OC lifetime greatly by affecting ΔG3o. We deduce that urea acts by disfavoring coupled folding of key elements of the β'-clamp, that I2 is an open-clamp OC, and that clamp-closing in I2 → stable OC involves coupled folding. Differences in ΔG3o between downstream-truncated and full-length promoters yield contributions to ΔG3o from interactions with downstream mobile elements (DME) including β-lobe and β'-jaw, more favorable for L-discriminator than for T-discriminator promoters. We deduce how competition between far-downstream DNA and σ70 region 1.1 affects ΔG3o values. We discuss variant-specific ΔG3o contributions in terms of the allosteric network by which differences in discriminator and -10 sequence are sensed and transmitted downstream to affect DME-duplex interactions in I2 → stable OC.
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4
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He D, You L, Wu X, Shi J, Wen A, Yan Z, Mu W, Fang C, Feng Y, Zhang Y. Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding. Nat Commun 2022; 13:4204. [PMID: 35859063 PMCID: PMC9300723 DOI: 10.1038/s41467-022-31871-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 07/07/2022] [Indexed: 12/23/2022] Open
Abstract
Pseudomonas aeruginosa (Pae) SutA adapts bacteria to hypoxia and nutrition-limited environment during chronic infection by increasing transcription activity of an RNA polymerase (RNAP) holoenzyme comprising the stress-responsive σ factor σS (RNAP-σS). SutA shows no homology to previously characterized RNAP-binding proteins. The structure and mode of action of SutA remain unclear. Here we determined cryo-EM structures of Pae RNAP-σS holoenzyme, Pae RNAP-σS holoenzyme complexed with SutA, and Pae RNAP-σS transcription initiation complex comprising SutA. The structures show SutA pinches RNAP-β protrusion and facilitates promoter unwinding by wedging RNAP-β lobe open. Our results demonstrate that SutA clears an energetic barrier to facilitate promoter unwinding of RNAP-σS holoenzyme. SutA is a transcription factor which increases transcription activity of an RNA polymerase (RNAP). Here, authors present cryo-EM structures of SutA-bound RNAP-σS holoenzyme and SutA-bound transcription initiation complex, which reveals SutA wedging the RNAP-β lobe open to aid unwinding.
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Affiliation(s)
- Dingwei He
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Linlin You
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxian Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jing Shi
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Aijia Wen
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhi Yan
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wenhui Mu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Chengli Fang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu Feng
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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5
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Molina JA, Galaz-Davison P, Komives EA, Artsimovitch I, Ramírez-Sarmiento CA. Allosteric couplings upon binding of RfaH to transcription elongation complexes. Nucleic Acids Res 2022; 50:6384-6397. [PMID: 35670666 PMCID: PMC9226497 DOI: 10.1093/nar/gkac453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/07/2022] [Accepted: 05/18/2022] [Indexed: 12/03/2022] Open
Abstract
In every domain of life, NusG-like proteins bind to the elongating RNA polymerase (RNAP) to support processive RNA synthesis and to couple transcription to ongoing cellular processes. Structures of factor-bound transcription elongation complexes (TECs) reveal similar contacts to RNAP, consistent with a shared mechanism of action. However, NusG homologs differ in their regulatory roles, modes of recruitment, and effects on RNA synthesis. Some of these differences could be due to conformational changes in RNAP and NusG-like proteins, which cannot be captured in static structures. Here, we employed hydrogen-deuterium exchange mass spectrometry to investigate changes in local and non-local structural dynamics of Escherichia coli NusG and its paralog RfaH, which have opposite effects on expression of xenogenes, upon binding to TEC. We found that NusG and RfaH regions that bind RNAP became solvent-protected in factor-bound TECs, whereas RNAP regions that interact with both factors showed opposite deuterium uptake changes when bound to NusG or RfaH. Additional changes far from the factor-binding site were observed only with RfaH. Our results provide insights into differences in structural dynamics exerted by NusG and RfaH during binding to TEC, which may explain their different functional outcomes and allosteric regulation of transcriptional pausing by RfaH.
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Affiliation(s)
- José Alejandro Molina
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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6
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Structural origins of Escherichia coli RNA polymerase open promoter complex stability. Proc Natl Acad Sci U S A 2021; 118:2112877118. [PMID: 34599106 DOI: 10.1073/pnas.2112877118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2021] [Indexed: 11/18/2022] Open
Abstract
The first step in gene expression in all organisms requires opening the DNA duplex to expose one strand for templated RNA synthesis. In Escherichia coli, promoter DNA sequence fundamentally determines how fast the RNA polymerase (RNAP) forms "open" complexes (RPo), whether RPo persists for seconds or hours, and how quickly RNAP transitions from initiation to elongation. These rates control promoter strength in vivo, but their structural origins remain largely unknown. Here, we use cryoelectron microscopy to determine the structures of RPo formed de novo at three promoters with widely differing lifetimes at 37 °C: λPR (t1/2 ∼10 h), T7A1 (t1/2 ∼4 min), and a point mutant in λPR (λPR-5C) (t1/2 ∼2 h). Two distinct RPo conformers are populated at λPR, likely representing productive and unproductive forms of RPo observed in solution studies. We find that changes in the sequence and length of DNA in the transcription bubble just upstream of the start site (+1) globally alter the network of DNA-RNAP interactions, base stacking, and strand order in the single-stranded DNA of the transcription bubble; these differences propagate beyond the bubble to upstream and downstream DNA. After expanding the transcription bubble by one base (T7A1), the nontemplate strand "scrunches" inside the active site cleft; the template strand bulges outside the cleft at the upstream edge of the bubble. The structures illustrate how limited sequence changes trigger global alterations in the transcription bubble that modulate the RPo lifetime and affect the subsequent steps of the transcription cycle.
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7
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Shin Y, Qayyum MZ, Pupov D, Esyunina D, Kulbachinskiy A, Murakami KS. Structural basis of ribosomal RNA transcription regulation. Nat Commun 2021; 12:528. [PMID: 33483500 PMCID: PMC7822876 DOI: 10.1038/s41467-020-20776-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 12/14/2020] [Indexed: 01/30/2023] Open
Abstract
Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. Here, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) σ70 holoenzyme during rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element using dimerized α subunit carboxyl-terminal domains and scrunches the template DNA with the σ finger and β' lid to select the transcription start site favorable for rapid promoter escape. Promoter binding induces conformational change of σ domain 2 that opens a gate for DNA loading and ejects σ1.1 from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to σ1.1 ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp.
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Affiliation(s)
- Yeonoh Shin
- grid.29857.310000 0001 2097 4281Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802 USA
| | - M. Zuhaib Qayyum
- grid.29857.310000 0001 2097 4281Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802 USA
| | - Danil Pupov
- grid.4886.20000 0001 2192 9124Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182 Russia
| | - Daria Esyunina
- grid.4886.20000 0001 2192 9124Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182 Russia
| | - Andrey Kulbachinskiy
- grid.4886.20000 0001 2192 9124Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182 Russia
| | - Katsuhiko S. Murakami
- grid.29857.310000 0001 2097 4281Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802 USA
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8
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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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9
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Abstract
In every cell from bacteria to mammals, NusG-like proteins bind transcribing RNA polymerase to modulate the rate of nascent RNA synthesis and to coordinate it with numerous cotranscriptional processes that ultimately determine the transcript fate. Housekeeping NusG factors regulate expression of the bulk of the genome, whereas their highly specialized paralogs control just a few targets. In every cell from bacteria to mammals, NusG-like proteins bind transcribing RNA polymerase to modulate the rate of nascent RNA synthesis and to coordinate it with numerous cotranscriptional processes that ultimately determine the transcript fate. Housekeeping NusG factors regulate expression of the bulk of the genome, whereas their highly specialized paralogs control just a few targets. In Escherichia coli, NusG stimulates silencing of horizontally acquired genes, while its paralog RfaH counters NusG action by activating a subset of these genes. Acting alone or as part of regulatory complexes, NusG factors can promote uninterrupted RNA synthesis, bring about transcription pausing or premature termination, modulate RNA processing, and facilitate translation. Recent structural and mechanistic studies of NusG homologs from all domains of life reveal molecular details of multifaceted interactions that underpin their unexpectedly diverse regulatory roles. NusG proteins share conserved binding sites on RNA polymerase and many effects on the transcription elongation complex but differ in their mechanisms of recruitment, interactions with nucleic acids and secondary partners, and regulatory outcomes. Strikingly, some can alternate between autoinhibited and activated states that possess dramatically different secondary structures to achieve exquisite target specificity.
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10
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Svetlov D, Shi D, Twentyman J, Nedialkov Y, Rosen DA, Abagyan R, Artsimovitch I. In silico discovery of small molecules that inhibit RfaH recruitment to RNA polymerase. Mol Microbiol 2018; 110:128-142. [PMID: 30069925 DOI: 10.1111/mmi.14093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 02/03/2023]
Abstract
RfaH is required for virulence in several Gram-negative pathogens including Escherichia coli and Klebsiella pneumoniae. Through direct interactions with RNA polymerase (RNAP) and ribosome, RfaH activates the expression of capsule, cell wall and pilus biosynthesis operons by reducing transcription termination and activating translation. While E. coli RfaH has been extensively studied using structural and biochemical approaches, limited data are available for other RfaH homologs. Here we set out to identify small molecule inhibitors of E. coli and K. pneumoniae RfaHs. Results of biochemical and functional assays show that these proteins act similarly, with a notable difference between their interactions with the RNAP β subunit gate loop. We focused on high-affinity RfaH interactions with the RNAP β' subunit clamp helices as a shared target for inhibition. Among the top 10 leads identified by in silico docking using ZINC database, 3 ligands were able to inhibit E. coli RfaH recruitment in vitro. The most potent lead was active against both E. coli and K. pneumoniae RfaHs in vitro. Our results demonstrate the feasibility of identifying RfaH inhibitors using in silico docking and pave the way for rational design of antivirulence therapeutics against antibiotic-resistant pathogens.
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Affiliation(s)
- Dmitri Svetlov
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Da Shi
- Department of Chemistry and Biochemistry and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, 92093, USA
| | - Joy Twentyman
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yuri Nedialkov
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - David A Rosen
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ruben Abagyan
- Department of Chemistry and Biochemistry and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, 92093, USA
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
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11
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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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12
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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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13
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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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14
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Zuber PK, Artsimovitch I, NandyMazumdar M, Liu Z, Nedialkov Y, Schweimer K, Rösch P, Knauer SH. The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand. eLife 2018; 7:36349. [PMID: 29741479 PMCID: PMC5995543 DOI: 10.7554/elife.36349] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/05/2018] [Indexed: 12/31/2022] Open
Abstract
RfaH, a transcription regulator of the universally conserved NusG/Spt5 family, utilizes a unique mode of recruitment to elongating RNA polymerase to activate virulence genes. RfaH function depends critically on an ops sequence, an exemplar of a consensus pause, in the non-template DNA strand of the transcription bubble. We used structural and functional analyses to elucidate the role of ops in RfaH recruitment. Our results demonstrate that ops induces pausing to facilitate RfaH binding and establishes direct contacts with RfaH. Strikingly, the non-template DNA forms a hairpin in the RfaH:ops complex structure, flipping out a conserved T residue that is specifically recognized by RfaH. Molecular modeling and genetic evidence support the notion that ops hairpin is required for RfaH recruitment. We argue that both the sequence and the structure of the non-template strand are read out by transcription factors, expanding the repertoire of transcriptional regulators in all domains of life.
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Affiliation(s)
- Philipp K Zuber
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Bayreuth, Germany
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, United States.,The Center for RNA Biology, The Ohio State University, Columbus, United States
| | - Monali NandyMazumdar
- Department of Microbiology, The Ohio State University, Columbus, United States.,The Center for RNA Biology, The Ohio State University, Columbus, United States
| | - Zhaokun Liu
- Department of Microbiology, The Ohio State University, Columbus, United States.,The Center for RNA Biology, The Ohio State University, Columbus, United States
| | - Yuri Nedialkov
- Department of Microbiology, The Ohio State University, Columbus, United States.,The Center for RNA Biology, The Ohio State University, Columbus, United States
| | - Kristian Schweimer
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Bayreuth, Germany
| | - Paul Rösch
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Bayreuth, Germany
| | - Stefan H Knauer
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Bayreuth, Germany
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15
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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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