1
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Winkler RG. Conformational properties of active polar semiflexible phantom polymers. J Chem Phys 2025; 162:154903. [PMID: 40249039 DOI: 10.1063/5.0260802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2025] [Accepted: 03/31/2025] [Indexed: 04/19/2025] Open
Abstract
The conformational properties of semiflexible active polar linear and ring phantom polymers are analyzed analytically to shed light on their dependence on activity. Special attention is paid to the influence of the implemented bond force for discrete and continuous polymer models. In detail, the Gaussian semiflexible polymer model and a model with a harmonic bond potential with finite bond length are considered. The studies reveal the immanent effects of the particular bond model on the polymer conformations as well as on the discrete or continuous representation. For continuum models, activity implies polymer end effects only, whereas for discrete models, all bonds can contribute to activity-dependent conformational changes. Ring polymers lack end effects; hence, continuous rings exhibit the same conformations as passive polymers. Similarly, the conformations of inextensible continuous polymers (Kratky-Porod worm-like chain) are activity-independent. These findings are in contrast to passive polymers, where a wide spectrum of bond potentials capture their generic features. Hence, this universality is broken by activity, and a model must be carefully selected to capture the characteristics observed in experiments.
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Affiliation(s)
- Roland G Winkler
- Theoretical Physics of Living Matter, Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany and Department of Physics, College of Science and Mathematics, Mindanao State University-Iligan Institute of Technology, Iligan City 9200, Philippines
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2
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Arseniev A, Panfilov M, Pobegalov G, Potyseva A, Pavlinova P, Yakunina M, Lee J, Borukhov S, Severinov K, Khodorkovskii M. Single-molecule studies reveal the off-pathway early paused state intermediates as a target of streptolydigin inhibition of RNA polymerase and its dramatic enhancement by Gre factors. Nucleic Acids Res 2025; 53:gkae1135. [PMID: 39656915 PMCID: PMC11724273 DOI: 10.1093/nar/gkae1135] [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: 07/08/2023] [Revised: 10/21/2024] [Accepted: 11/08/2024] [Indexed: 12/17/2024] Open
Abstract
Antibiotic streptolydigin (Stl) inhibits bacterial transcription by blocking the trigger loop folding in the active center of RNA polymerase (RNAP), which is essential for catalysis. We use acoustic force spectroscopy to characterize the dynamics of transcription elongation in ternary elongation complexes (ECs) of RNAP in the presence of Stl at a single-molecule level. We found that Stl induces long-lived stochastic pauses while the instantaneous velocity of transcription between the pauses is unaffected. Stl enhances the short-lived pauses associated with an off-pathway early paused state intermediates of the RNAP nucleotide addition cycle. Unexpectedly, we found that transcript cleavage factors GreA and GreB, which were thought to be Stl competitors, do not alleviate the Stl-induced pausing; instead, they synergistically increase transcription inhibition by Stl. This is the first known instance of a transcriptional factor enhancing antibiotic activity. We propose a structural model of the EC-Gre-Stl complex that explains the observed Stl activities and provides insight into possible cooperative action of secondary channel factors and other antibiotics binding at the Stl pocket. These results offer a new strategy for high-throughput screening for prospective antibacterial agents.
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Affiliation(s)
- Anatolii Arseniev
- Peter the Great St. Petersburg Polytechnic University, Research Center of Nanobiotechnologies, Polytechnicheskaya, 29 B, Saint Petersburg, 195251,Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq., 2, Moscow, 123182, Russia
| | - Mikhail Panfilov
- Peter the Great St. Petersburg Polytechnic University, Research Center of Nanobiotechnologies, Polytechnicheskaya, 29 B, Saint Petersburg, 195251,Russia
| | - Georgii Pobegalov
- Department of Physics and Astronomy, University College London, Gower street, London, WC1E 6BT, UK
| | - Alina Potyseva
- Peter the Great St. Petersburg Polytechnic University, Research Center of Nanobiotechnologies, Polytechnicheskaya, 29 B, Saint Petersburg, 195251,Russia
| | - Polina Pavlinova
- Peter the Great St. Petersburg Polytechnic University, Research Center of Nanobiotechnologies, Polytechnicheskaya, 29 B, Saint Petersburg, 195251,Russia
| | - Maria Yakunina
- Peter the Great St. Petersburg Polytechnic University, Research Center of Nanobiotechnologies, Polytechnicheskaya, 29 B, Saint Petersburg, 195251,Russia
| | - Jookyung Lee
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, 2 Medical Center Drive, Stratford, NJ 08084-1489, USA
| | - Sergei Borukhov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, 2 Medical Center Drive, Stratford, NJ 08084-1489, USA
| | - Konstantin Severinov
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova Street, Moscow, 119334, Russia
| | - Mikhail Khodorkovskii
- Peter the Great St. Petersburg Polytechnic University, Research Center of Nanobiotechnologies, Polytechnicheskaya, 29 B, Saint Petersburg, 195251,Russia
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3
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McMinn SE, Miller DV, Yur D, Stone K, Xu Y, Vikram A, Murali S, Raffaele J, Holland D, Wang SC, Smith JP. High-Throughput Algorithmic Optimization of In Vitro Transcription for SARS-CoV-2 mRNA Vaccine Production. Biochemistry 2024; 63:2793-2802. [PMID: 39428617 DOI: 10.1021/acs.biochem.4c00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2024]
Abstract
The in vitro transcription (IVT) of messenger ribonucleic acid (mRNA) from the linearized deoxyribonucleic acid (DNA) template of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant (B.1.617.2) was optimized for total mRNA yield and purity (by percent intact mRNA) utilizing machine learning in conjunction with automated, high-throughput liquid handling technology. An iterative Bayesian optimization approach successfully optimized 11 critical process parameters in 42 reactions across 5 experimental rounds. Once the optimized conditions were achieved, an automated, high-throughput screen was conducted to evaluate commercially available T7 RNA polymerases for rate and quality of mRNA production. Final conditions showed a 12% yield improvement and a 50% reduction in reaction time, while simultaneously significantly decreasing (up to 44% reduction) the use of expensive reagents. This novel platform offers a powerful new approach for optimizing IVT reactions for mRNA production.
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Affiliation(s)
- Spencer E McMinn
- Process Research and Development, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Danielle V Miller
- Process Research and Development, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Daniel Yur
- Process Research and Development, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Kevin Stone
- Process Research and Development, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Yuting Xu
- Biometrics Research, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ajit Vikram
- Process Research and Development, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Shashank Murali
- Process Development, Eurofins PSS, West Point, Pennsylvania 19486, United States
| | - Jessica Raffaele
- Analytical Research and Development, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - David Holland
- Analytical Research and Development, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Sheng-Ching Wang
- Process Research and Development, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Joseph P Smith
- Process Research and Development, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
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4
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Nova IC, Craig JM, Mazumder A, Laszlo AH, Derrington IM, Noakes MT, Brinkerhoff H, Yang S, Vahedian-Movahed H, Li L, Zhang Y, Bowman JL, Huang JR, Mount JW, Ebright RH, Gundlach JH. Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase. Proc Natl Acad Sci U S A 2024; 121:e2321017121. [PMID: 38990947 PMCID: PMC11260103 DOI: 10.1073/pnas.2321017121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/23/2024] [Indexed: 07/13/2024] Open
Abstract
RNA polymerases (RNAPs) carry out the first step in the central dogma of molecular biology by transcribing DNA into RNA. Despite their importance, much about how RNAPs work remains unclear, in part because the small (3.4 Angstrom) and fast (~40 ms/nt) steps during transcription were difficult to resolve. Here, we used high-resolution nanopore tweezers to observe the motion of single Escherichia coli RNAP molecules as it transcribes DNA ~1,000 times improved temporal resolution, resolving single-nucleotide and fractional-nucleotide steps of individual RNAPs at saturating nucleoside triphosphate concentrations. We analyzed RNAP during processive transcription elongation and sequence-dependent pausing at the yrbL elemental pause sequence. Each time RNAP encounters the yrbL elemental pause sequence, it rapidly interconverts between five translocational states, residing predominantly in a half-translocated state. The kinetics and force-dependence of this half-translocated state indicate it is a functional intermediate between pre- and post-translocated states. Using structural and kinetics data, we show that, in the half-translocated and post-translocated states, sequence-specific protein-DNA interaction occurs between RNAP and a guanine base at the downstream end of the transcription bubble (core recognition element). Kinetic data show that this interaction stabilizes the half-translocated and post-translocated states relative to the pre-translocated state. We develop a kinetic model for RNAP at the yrbL pause and discuss this in the context of key structural features.
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Affiliation(s)
- Ian C. Nova
- Department of Physics, University of Washington, Seattle, WA98195
| | | | - Abhishek Mazumder
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ08854
| | - Andrew H. Laszlo
- Department of Physics, University of Washington, Seattle, WA98195
| | | | | | | | - Shuya Yang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ08854
| | | | - Lingting Li
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | | | - Jesse R. Huang
- Department of Physics, University of Washington, Seattle, WA98195
| | | | - Richard H. Ebright
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ08854
| | - Jens H. Gundlach
- Department of Physics, University of Washington, Seattle, WA98195
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5
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Tare P, Bhowmick T, Katagi G, China A, Nagaraja V. Comparison of Transcription Elongation Rates of Three RNA Polymerases in Real Time. ACS OMEGA 2023; 8:47510-47519. [PMID: 38144119 PMCID: PMC10733919 DOI: 10.1021/acsomega.3c04754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/11/2023] [Indexed: 12/26/2023]
Abstract
RNA polymerases (RNAPs) across the bacterial kingdom have retained a conserved structure and function. In spite of the remarkable similarity of the enzyme in different bacteria, a wide variation is found in the promoter-polymerase interaction, transcription initiation, and termination. However, the transcription elongation was considered to be a monotonic process, although the rate of elongation could vary in different bacteria. Such variations in RNAP elongation rates could be important to fine-tune the transcription, which in turn would influence cellular metabolism and growth rates. Here, we describe a quantitative study to measure the transcription rates for the RNAPs from three bacteria, namely, Mycobacterium tuberculosis, Mycobacterium smegmatis, and Escherichia coli, which exhibit different growth kinetics. The RNA synthesis rates of the RNAPs were calculated from the real-time elongation kinetic profile using surface plasmon resonance through a computational flux flow model. The computational model revealed the modular process of elongation, with different rate profiles for the three RNAPs. Notably, the transcription elongation rates of these RNAPs followed the trend in the growth rates of these bacteria.
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Affiliation(s)
- Priyanka Tare
- Department
of Microbiology and Cell Biology, Indian
Institute of Science, Bangalore 560012, India
| | - Tuhin Bhowmick
- Department
of Physics, Indian Institute of Science, Bangalore 560012, India
- Centre
for Cellular and Molecular Platforms, NCBS-TIFR, Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Gurunath Katagi
- Centre
for Cellular and Molecular Platforms, NCBS-TIFR, Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Arnab China
- Department
of Microbiology and Cell Biology, Indian
Institute of Science, Bangalore 560012, India
| | - Valakunja Nagaraja
- Department
of Microbiology and Cell Biology, Indian
Institute of Science, Bangalore 560012, India
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6
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Arseniev A, Panfilov M, Pobegalov G, Potyseva A, Pavlinova P, Yakunina M, Lee J, Borukhov S, Severinov K, Khodorkovskii M. Single-molecule studies reveal the off-pathway elemental pause state as a target of streptolydigin inhibition of RNA polymerase and its dramatic enhancement by Gre factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.542125. [PMID: 37333075 PMCID: PMC10274647 DOI: 10.1101/2023.06.05.542125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Antibiotic streptolydigin (Stl) inhibits bacterial transcription by blocking the trigger loop folding in the active center of RNA polymerase (RNAP), which is essential for catalysis. We use acoustic force spectroscopy to characterize the dynamics of transcription elongation in ternary elongation complexes of RNAP (ECs) in the presence of Stl at a single-molecule level. We found that Stl induces long-lived stochastic pauses while the instantaneous velocity of transcription between the pauses is unaffected. Stl enhances the short-lived pauses associated with an off-pathway elemental paused state of the RNAP nucleotide addition cycle. Unexpectedly, we found that transcript cleavage factors GreA and GreB, which were thought to be Stl competitors, do not alleviate the streptolydigin-induced pausing; instead, they synergistically increase transcription inhibition by Stl. This is the first known instance of a transcriptional factor enhancing antibiotic activity. We propose a structural model of the EC-Gre-Stl complex that explains the observed Stl activities and provides insight into possible cooperative action of secondary channel factors and other antibiotics binding at the Stl-pocket. These results offer a new strategy for high-throughput screening for prospective antibacterial agents.
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Affiliation(s)
- Anatolii Arseniev
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Mikhail Panfilov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Georgii Pobegalov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Alina Potyseva
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Polina Pavlinova
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Maria Yakunina
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Jookyung Lee
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084-1489, USA
| | - Sergei Borukhov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084-1489, USA
| | - Konstantin Severinov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
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7
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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: 24] [Impact Index Per Article: 12.0] [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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8
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Philipps CA, Gompper G, Winkler RG. Dynamics of active polar ring polymers. Phys Rev E 2022; 105:L062501. [PMID: 35854564 DOI: 10.1103/physreve.105.l062501] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The conformational and dynamical properties of isolated semiflexible active polar ring polymers are investigated analytically. A ring is modeled as a continuous Gaussian polymer exposed to tangential active forces. The analytical solution of the linear non-Hermitian equation of motion in terms of an eigenfunction expansion shows that ring conformations are independent of activity. In contrast, activity strongly affects the internal ring dynamics and yields characteristic time regimes, which are absent in passive rings. On intermediate timescales, flexible rings show an activity-enhanced diffusive regime, while semiflexible rings exhibit ballistic motion. Moreover, a second active time regime emerges on longer timescales, where rings display a snake-like motion, which is reminiscent to a tank-treading rotational dynamics in shear flow, dominated by the mode with the longest relaxation time.
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Affiliation(s)
- Christian A Philipps
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA, 52425 Jülich, Germany
- Department of Physics, RWTH Aachen University, 52056 Aachen, Germany
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA, 52425 Jülich, Germany
| | - Roland G Winkler
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA, 52425 Jülich, Germany
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9
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Janissen R, Eslami-Mossallam B, Artsimovitch I, Depken M, Dekker NH. High-throughput single-molecule experiments reveal heterogeneity, state switching, and three interconnected pause states in transcription. Cell Rep 2022; 39:110749. [PMID: 35476989 DOI: 10.1016/j.celrep.2022.110749] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 02/17/2022] [Accepted: 04/07/2022] [Indexed: 11/19/2022] Open
Abstract
Pausing by bacterial RNA polymerase (RNAp) is vital in the recruitment of regulatory factors, RNA folding, and coupled translation. While backtracking and intra-structural isomerization have been proposed to trigger pausing, our mechanistic understanding of backtrack-associated pauses and catalytic recovery remains incomplete. Using high-throughput magnetic tweezers, we examine the Escherichia coli RNAp transcription dynamics over a wide range of forces and NTP concentrations. Dwell-time analysis and stochastic modeling identify, in addition to a short-lived elemental pause, two distinct long-lived backtrack pause states differing in recovery rates. We identify two stochastic sources of transcription heterogeneity: alterations in short-pause frequency that underlies elongation-rate switching, and variations in RNA cleavage rates in long-lived backtrack states. Together with effects of force and Gre factors, we demonstrate that recovery from deep backtracks is governed by intrinsic RNA cleavage rather than diffusional Brownian dynamics. We introduce a consensus mechanistic model that unifies our findings with prior models.
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Affiliation(s)
- Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Behrouz Eslami-Mossallam
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Irina Artsimovitch
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA.
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands.
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10
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Eisenstecken T, Winkler RG. Path integral description of semiflexible active Brownian polymers. J Chem Phys 2022; 156:064105. [DOI: 10.1063/5.0081020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Roland G. Winkler
- Institute for Advanced Simulation, Forschungszentrum Jülich, Germany
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11
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Palo MZ, Zhu J, Mishanina TV, Landick R. Conserved Trigger Loop Histidine of RNA Polymerase II Functions as a Positional Catalyst Primarily through Steric Effects. Biochemistry 2021; 60:3323-3336. [PMID: 34705427 DOI: 10.1021/acs.biochem.1c00528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In all domains of life, multisubunit RNA polymerases (RNAPs) catalyze both the extension of mRNA transcripts by nucleotide addition and the hydrolysis of RNA, which enables proofreading by removal of misincorporated nucleotides. A highly conserved catalytic module within RNAPs called the trigger loop (TL) functions as the key controller of these activities. The TL is proposed to act as a positional catalyst of phosphoryl transfer and transcript cleavage via electrostatic and steric contacts with substrates in its folded helical form. The function of a near-universally conserved TL histidine that contacts NTP phosphates is of particular interest. Despite its exceptional conservation, substitutions of the TL His with Gln support efficient catalysis in bacterial and yeast RNAPs. Unlike bacterial TLs, which contain a nearby Arg, the TL His is the only acid-base catalyst candidate in the eukaryotic RNAPII TL. Nonetheless, replacement of the TL His with Leu is reported to support cell growth in yeast, suggesting that even hydrogen bonding and polarity at this position may be dispensable for efficient catalysis by RNAPII. To test how a TL His-to-Leu substitution affects the enzymatic functions of RNAPII, we compared its rates of nucleotide addition, pyrophosphorolysis, and RNA hydrolysis to those of the wild-type RNAPII enzyme. The His-to-Leu substitution slightly reduced rates of phosphoryl transfer with little if any effect on intrinsic transcript cleavage. These findings indicate that the highly conserved TL His is neither an obligate acid-base catalyst nor a polar contact for NTP phosphates but instead functions as a positional catalyst mainly through steric effects.
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Affiliation(s)
- Michael Z Palo
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Junqiao Zhu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Tatiana V Mishanina
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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12
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Affiliation(s)
- Roland G. Winkler
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
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13
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Abstract
During transcription elongation at saturating nucleotide concentrations, RNA polymerase (RNAP) performs ∼50 nucleotide-addition cycles every second. The RNAP active center contains a structural element, termed the trigger loop (TL), that has been suggested, but not previously shown, to open to allow a nucleotide to enter and then to close to hold the nucleotide in each nucleotide-addition cycle. Here, using single-molecule fluorescence spectroscopy to monitor distances between a probe incorporated into the TL and a probe incorporated elsewhere in the transcription elongation complex, we show that TL closing and opening occur in solution, define time scales and functional roles of TL closing and opening, and, most crucially, demonstrate that one cycle of TL closing and opening occurs in each nucleotide-addition cycle. The RNA polymerase (RNAP) trigger loop (TL) is a mobile structural element of the RNAP active center that, based on crystal structures, has been proposed to cycle between an “unfolded”/“open” state that allows an NTP substrate to enter the active center and a “folded”/“closed” state that holds the NTP substrate in the active center. Here, by quantifying single-molecule fluorescence resonance energy transfer between a first fluorescent probe in the TL and a second fluorescent probe elsewhere in RNAP or in DNA, we detect and characterize TL closing and opening in solution. We show that the TL closes and opens on the millisecond timescale; we show that TL closing and opening provides a checkpoint for NTP complementarity, NTP ribo/deoxyribo identity, and NTP tri/di/monophosphate identity, and serves as a target for inhibitors; and we show that one cycle of TL closing and opening typically occurs in each nucleotide addition cycle in transcription elongation.
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14
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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: 1.6] [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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15
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Douglas J, Kingston R, Drummond AJ. Bayesian inference and comparison of stochastic transcription elongation models. PLoS Comput Biol 2020; 16:e1006717. [PMID: 32059006 PMCID: PMC7046298 DOI: 10.1371/journal.pcbi.1006717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/27/2020] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Transcription elongation can be modelled as a three step process, involving polymerase translocation, NTP binding, and nucleotide incorporation into the nascent mRNA. This cycle of events can be simulated at the single-molecule level as a continuous-time Markov process using parameters derived from single-molecule experiments. Previously developed models differ in the way they are parameterised, and in their incorporation of partial equilibrium approximations. We have formulated a hierarchical network comprised of 12 sequence-dependent transcription elongation models. The simplest model has two parameters and assumes that both translocation and NTP binding can be modelled as equilibrium processes. The most complex model has six parameters makes no partial equilibrium assumptions. We systematically compared the ability of these models to explain published force-velocity data, using approximate Bayesian computation. This analysis was performed using data for the RNA polymerase complexes of E. coli, S. cerevisiae and Bacteriophage T7. Our analysis indicates that the polymerases differ significantly in their translocation rates, with the rates in T7 pol being fast compared to E. coli RNAP and S. cerevisiae pol II. Different models are applicable in different cases. We also show that all three RNA polymerases have an energetic preference for the posttranslocated state over the pretranslocated state. A Bayesian inference and model selection framework, like the one presented in this publication, should be routinely applicable to the interrogation of single-molecule datasets. Transcription is a critical biological process which occurs in all living organisms. It involves copying the organism’s genetic material into messenger RNA (mRNA) which directs protein synthesis on the ribosome. Transcription is performed by RNA polymerases which have been extensively studied using both ensemble and single-molecule techniques. Single-molecule data provides unique insights into the molecular behaviour of RNA polymerases. Transcription at the single-molecule level can be computationally simulated as a continuous-time Markov process and the model outputs compared with experimental data. In this study we use Bayesian techniques to perform a systematic comparison of 12 stochastic models of transcriptional elongation. We demonstrate how equilibrium approximations can strengthen or weaken the model, and show how Bayesian techniques can identify necessary or unnecessary model parameters. We describe a framework to a) simulate, b) perform inference on, and c) compare models of transcription elongation.
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Affiliation(s)
- Jordan Douglas
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Centre for Computational Evolution, School of Computer Science, University of Auckland, Auckland, New Zealand
- * E-mail:
| | - Richard Kingston
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Alexei J. Drummond
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Centre for Computational Evolution, School of Computer Science, University of Auckland, Auckland, New Zealand
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16
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Chung S, Lerner E, Jin Y, Kim S, Alhadid Y, Grimaud LW, Zhang IX, Knobler CM, Gelbart WM, Weiss S. The effect of macromolecular crowding on single-round transcription by Escherichia coli RNA polymerase. Nucleic Acids Res 2019; 47:1440-1450. [PMID: 30590739 PMCID: PMC6379708 DOI: 10.1093/nar/gky1277] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 12/01/2018] [Accepted: 12/13/2018] [Indexed: 01/09/2023] Open
Abstract
Previous works have reported significant effects of macromolecular crowding on the structure and behavior of biomolecules. The crowded intracellular environment, in contrast to in vitro buffer solutions, likely imparts similar effects on biomolecules. The enzyme serving as the gatekeeper for the genome, RNA polymerase (RNAP), is among the most regulated enzymes. Although it was previously demonstrated that macromolecular crowding affects association of RNAP to DNA, not much is known about how crowding acts on late initiation and promoter clearance steps, which are considered to be the rate-determining steps for many promoters. Here, we demonstrate that macromolecular crowding enhances the rate of late initiation and promoter clearance using in vitro quenching-based single-molecule kinetics assays. Moreover, the enhancement's dependence on crowder size notably deviates from predictions by the scaled-particle theory, commonly used for description of crowding effects. Our findings shed new light on how enzymatic reactions could be affected by crowded conditions in the cellular milieu.
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Affiliation(s)
- SangYoon Chung
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - Eitan Lerner
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yan Jin
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - Soohong Kim
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yazan Alhadid
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, CA 90095, USA
| | - Logan Wilson Grimaud
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - Irina X Zhang
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Present address: Irina X. Zhang, Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Charles M Knobler
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - William M Gelbart
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute (MBI), University of California Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California Los Angeles, CA 90095, USA
- Correspondence may also be addressed to William M. Gelbart. Tel: +1 310 825 2005; Fax: +1 310 206 4038;
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute (MBI), University of California Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles, CA 90095, USA
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
- To whom correspondence should be addressed. Tel: +1 310 794 0093; Fax: +1 310 267 4672;
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17
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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: 7.2] [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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18
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Belitsky V, Schütz G. RNA Polymerase interactions and elongation rate. J Theor Biol 2019; 462:370-380. [DOI: 10.1016/j.jtbi.2018.11.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/19/2018] [Accepted: 11/26/2018] [Indexed: 11/30/2022]
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19
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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: 51] [Impact Index Per Article: 8.5] [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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20
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Belitsky V, Schütz GM. Stationary RNA polymerase fluctuations during transcription elongation. Phys Rev E 2019; 99:012405. [PMID: 30780341 DOI: 10.1103/physreve.99.012405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Indexed: 06/09/2023]
Abstract
We study fluctuation effects of nonsteric molecular interactions between RNA polymerase (RNAP) motors that move simultaneously on the same DNA track during transcription elongation. Based on a stochastic model that allows for the exact analytical computation of the stationary distribution of RNAPs as a function of their density, interaction strength, nucleoside triphosphate concentration, and rate of pyrophosphate release we predict an almost geometric headway distribution of subsequent RNAP transcribing on the same DNA segment. The localization length which characterizes the decay of the headway distribution depends directly only the average density of RNAP and the interaction strength, but not on specific single-RNAP properties. Density correlations are predicted to decay exponentially with the distance (in units of DNA base pairs), with a correlation length that is significantly shorter than the localization length.
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Affiliation(s)
- V Belitsky
- Instituto de Matemática e Estátistica, Universidade de São Paulo, Rua do Matão, 1010, CEP 05508-090 São Paulo, São Paulo, Brazil
| | - G M Schütz
- Institute of Complex Systems II, Theoretical Soft Matter and Biophysics, Forschungszentrum Jülich, 52425 Jülich, Germany
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21
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Turtola M, Mäkinen JJ, Belogurov GA. Active site closure stabilizes the backtracked state of RNA polymerase. Nucleic Acids Res 2018; 46:10870-10887. [PMID: 30256972 PMCID: PMC6237748 DOI: 10.1093/nar/gky883] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/30/2018] [Accepted: 09/19/2018] [Indexed: 01/02/2023] Open
Abstract
All cellular RNA polymerases (RNAP) occasionally backtrack along the template DNA as part of transcriptional proofreading and regulation. Here, we studied the mechanism of RNAP backtracking by one nucleotide using two complementary approaches that allowed us to precisely measure the occupancy and lifetime of the backtracked state. Our data show that the stability of the backtracked state is critically dependent on the closure of the RNAP active site by a mobile domain, the trigger loop (TL). The lifetime and occupancy of the backtracked state measurably decreased by substitutions of the TL residues that interact with the nucleoside triphosphate (NTP) substrate, whereas amino acid substitutions that stabilized the closed active site increased the lifetime and occupancy. These results suggest that the same conformer of the TL closes the active site during catalysis of nucleotide incorporation into the nascent RNA and backtracking by one nucleotide. In support of this hypothesis, we construct a model of the 1-nt backtracked complex with the closed active site and the backtracked nucleotide in the entry pore area known as the E-site. We further propose that 1-nt backtracking mimics the reversal of the NTP substrate loading into the RNAP active site during on-pathway elongation.
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Affiliation(s)
- Matti Turtola
- University of Turku, Department of Biochemistry, FIN-20014 Turku, Finland
| | - Janne J Mäkinen
- University of Turku, Department of Biochemistry, FIN-20014 Turku, Finland
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22
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Atitey K, Loskot P, Rees P. Determining the Transcription Rates Yielding Steady-State Production of mRNA in the Lac Genetic Switch of Escherichia coli. J Comput Biol 2018; 25:1023-1039. [PMID: 29957031 DOI: 10.1089/cmb.2018.0055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
To elucidate the regulatory dynamics of the gene expression activation and inactivation, an in silico biochemical model of the lac circuit in Escherichia coli was used to evaluate the transcription rates that yield the steady-state mRNA production in active and inactive states of the lac circuit. This result can be used in synthetic biology applications to understand the limits of the genetic synthesis. Since most genetic networks involve many interconnected components with positive and negative feedback control, intuitive understanding of their dynamics is often difficult to obtain. Although the kinetic model of the lac circuit considered involves only a single positive feedback, the developed computational framework can be used to evaluate supported ranges of other reaction rates in genetic circuits with more complex regulatory networks. More specifically, the inducible lac gene switch in E. coli is regulated by unbinding and binding of the inducer-repressor complexes to or from the DNA operator to switch the gene expression on and off. The dependency of mRNA production at steady state on different transcription rates and the repressor complexes has been studied by computer simulations in the Lattice Microbe software. Provided that the lac circuit is in active state, the transcription rate is independent of the inducer-repressor complexes present in the cell. In inactive state, the transcription rate is dependent on the specific inducer-repressor complex bound to the operator that inactivates the gene expression. We found that the repressor complex with the largest affinity to the operator yields the smallest range of the feasible transcription rates to yield the steady state while the lac circuit is in inactive state. In contrast, the steady state in active state can be obtained for any value of the transcription rate.
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Affiliation(s)
- Komlan Atitey
- College of Engineering, Swansea University , Swansea, United Kingdom
| | - Pavel Loskot
- College of Engineering, Swansea University , Swansea, United Kingdom
| | - Paul Rees
- College of Engineering, Swansea University , Swansea, United Kingdom
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23
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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 2018; 46:5764-5775. [PMID: 29771376 PMCID: PMC6009650 DOI: 10.1093/nar/gky393] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/24/2018] [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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24
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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: 1.5] [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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25
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Nedialkov YA, Opron K, Caudill HL, Assaf F, Anderson AJ, Cukier RI, Wei G, Burton ZF. Hinge action versus grip in translocation by RNA polymerase. Transcription 2017; 9:1-16. [PMID: 28853995 PMCID: PMC5791816 DOI: 10.1080/21541264.2017.1330179] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Based on molecular dynamics simulations and functional studies, a conformational mechanism is posited for forward translocation by RNA polymerase (RNAP). In a simulation of a ternary elongation complex, the clamp and downstream cleft were observed to close. Hinges within the bridge helix and trigger loop supported generation of translocation force against the RNA-DNA hybrid resulting in opening of the furthest upstream i-8 RNA-DNA bp, establishing conditions for RNAP sliding. The β flap tip helix and the most N-terminal β' Zn finger engage the RNA, indicating a path of RNA threading out of the exit channel. Because the β flap tip connects to the RNAP active site through the β subunit double-Ψ-β-barrel and the associated sandwich barrel hybrid motif (also called the flap domain), the RNAP active site is coupled to the RNA exit channel and to the translocation of RNA-DNA. Using an exonuclease III assay to monitor translocation of RNAP elongation complexes, we show that K+ and Mg2+ and also an RNA 3'-OH or a 3'-H2 affect RNAP sliding. Because RNAP grip to template suggests a sticky translocation mechanism, and because grip is enhanced by increasing K+ and Mg2+concentration, biochemical assays are consistent with a conformational change that drives forward translocation as observed in simulations. Mutational analysis of the bridge helix indicates that 778-GARKGL-783 (Escherichia coli numbering) is a homeostatic hinge that undergoes multiple bends to compensate for complex conformational dynamics during phosphodiester bond formation and translocation.
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Affiliation(s)
- Yuri A Nedialkov
- a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA.,b Department of Microbiology , The Ohio State University , Columbus , OH , USA
| | - Kristopher Opron
- a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA.,c Department of Mathematics , Michigan State University , E. Lansing , MI , USA.,d Bioinformatics Core , North Campus Research Complex (NCRC) , Ann Arbor , MI , USA
| | - Hailey L Caudill
- a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA
| | - Fadi Assaf
- a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA
| | - Amanda J Anderson
- a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA
| | - Robert I Cukier
- e Department of Chemistry , Michigan State University , E. Lansing , MI , USA
| | - Guowei Wei
- c Department of Mathematics , Michigan State University , E. Lansing , MI , USA
| | - Zachary F Burton
- a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA
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26
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An excited state underlies gene regulation of a transcriptional riboswitch. Nat Chem Biol 2017; 13:968-974. [PMID: 28719589 PMCID: PMC5562522 DOI: 10.1038/nchembio.2427] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/22/2017] [Indexed: 11/08/2022]
Abstract
Riboswitches control gene expression through ligand-dependent structural rearrangements of the sensing aptamer domain. However, we found that the Bacillus cereus fluoride riboswitch aptamer adopts identical tertiary structures in solution with and without ligand. Using chemical-exchange saturation transfer (CEST) NMR spectroscopy, we revealed that the structured ligand-free aptamer transiently accesses a low-populated (∼1%) and short-lived (∼3 ms) excited conformational state that unravels a conserved 'linchpin' base pair to signal transcription termination. Upon fluoride binding, this highly localized, fleeting process is allosterically suppressed, which activates transcription. We demonstrated that this mechanism confers effective fluoride-dependent gene activation over a wide range of transcription rates, which is essential for robust toxicity responses across diverse cellular conditions. These results unveil a novel switching mechanism that employs ligand-dependent suppression of an aptamer excited state to coordinate regulatory conformational transitions rather than adopting distinct aptamer ground-state tertiary architectures, exemplifying a new mode of ligand-dependent RNA regulation.
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27
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Wang B, Sexton RE, Feig M. Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2017; 1860:482-490. [PMID: 28242207 PMCID: PMC5393355 DOI: 10.1016/j.bbagrm.2017.02.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/29/2017] [Accepted: 02/15/2017] [Indexed: 10/20/2022]
Abstract
During transcription, RNA polymerase II elongates RNA by adding nucleotide triphosphates (NTPs) complementary to a DNA template. Structural studies have suggested that NTPs enter and exit the active site via the narrow secondary pore but details have remained unclear. A kinetic model is presented that integrates molecular dynamics simulations with experimental data. Previous simulations of trigger loop dynamics and the dynamics of matched and mismatched NTPs in and near the active site were combined with new simulations describing NTP exit from the active site via the secondary pore. Markov state analysis was applied to identify major states and estimate kinetic rates for transitions between those states. The kinetic model predicts elongation and misincorporation rates in close agreement with experiment and provides mechanistic hypotheses for how NTP entry and exit via the secondary pore is feasible and a key feature for achieving high elongation and low misincorporation rates during RNA elongation.
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Affiliation(s)
- Beibei Wang
- Department of Biochemistry & Molecular Biology, 603 Wilson Rd., Room 218 BCH, Michigan State University, East Lansing, MI 48824, USA.
| | - Rachel E Sexton
- Department of Biochemistry & Molecular Biology, 603 Wilson Rd., Room 218 BCH, Michigan State University, East Lansing, MI 48824, USA.
| | - Michael Feig
- Department of Biochemistry & Molecular Biology, 603 Wilson Rd., Room 218 BCH, Michigan State University, East Lansing, MI 48824, USA.
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High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop. PLoS Genet 2016; 12:e1006321. [PMID: 27898685 PMCID: PMC5127505 DOI: 10.1371/journal.pgen.1006321] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/24/2016] [Indexed: 11/30/2022] Open
Abstract
The active sites of multisubunit RNA polymerases have a “trigger loop” (TL) that multitasks in substrate selection, catalysis, and translocation. To dissect the Saccharomyces cerevisiae RNA polymerase II TL at individual-residue resolution, we quantitatively phenotyped nearly all TL single variants en masse. Three mutant classes, revealed by phenotypes linked to transcription defects or various stresses, have distinct distributions among TL residues. We find that mutations disrupting an intra-TL hydrophobic pocket, proposed to provide a mechanism for substrate-triggered TL folding through destabilization of a catalytically inactive TL state, confer phenotypes consistent with pocket disruption and increased catalysis. Furthermore, allele-specific genetic interactions among TL and TL-proximal domain residues support the contribution of the funnel and bridge helices (BH) to TL dynamics. Our structural genetics approach incorporates structural and phenotypic data for high-resolution dissection of transcription mechanisms and their evolution, and is readily applicable to other essential yeast proteins. Proper regulation of Pol II transcription, the first step of gene expression, is essential for life. Extensive evidence has revealed a widely conserved and dynamic polymerase active site component, termed the Trigger Loop (TL), in balancing transcription rate and fidelity while possibly allowing control of transcription elongation. Coupling high-throughput sequencing with our previously established genetic system, we are able to assess the in vivo phenotypes for almost all possible single substitution Pol II TL mutants in the budding yeast Saccharomyces cerevisiae. We show that mutants in the TL nucleotide interacting and linker regions widely confer dominant and severe growth defects. Clustering of TL mutants’ transcription-related and general stress phenotypes reveals three main classes of TL mutants, including previously identified fast and slow elongating mutants. Comprehensive analyses of the distribution of fast and slow elongation mutants in light of existing Pol II crystal structures reveal critical regions contributing to proper TL dynamics and function. Evidence is presented linking a previously observed hydrophobic pocket to NTP substrate-induced TL closing, the mechanism critical for correct substrates selection and transcription fidelity. Finally, we assess the functional interplay between TL and its proximal domains, and their presumptive roles in the function and evolution of the TL. Utilizing the Pol II TL as a case study, we present a structural genetics approach that reveals insights into a complex, multi-functional, and essential domain in yeast.
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Abstract
During transcription, RNA polymerase moves downstream along the DNA template and maintains a transcription bubble. Several recent structural studies of transcription complexes with a complete transcription bubble provide new insights into how RNAP couples the nucleotide addition reaction to its directional movement.
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Affiliation(s)
- Yuhong Zuo
- a Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , CT , USA
| | - Thomas A Steitz
- a Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , CT , USA.,b Howard Hughes Medical Institute , New Haven , CT , USA.,c Department of Chemistry , Yale University , New Haven , CT , USA
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30
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Liu B, Zuo Y, Steitz TA. Structures of E. coli σS-transcription initiation complexes provide new insights into polymerase mechanism. Proc Natl Acad Sci U S A 2016; 113:4051-6. [PMID: 27035955 PMCID: PMC4839411 DOI: 10.1073/pnas.1520555113] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In bacteria, multiple σ factors compete to associate with the RNA polymerase (RNAP) core enzyme to form a holoenzyme that is required for promoter recognition. During transcription initiation RNAP remains associated with the upstream promoter DNA via sequence-specific interactions between the σ factor and the promoter DNA while moving downstream for RNA synthesis. As RNA polymerase repetitively adds nucleotides to the 3'-end of the RNA, a pyrophosphate ion is generated after each nucleotide incorporation. It is currently unknown how the release of pyrophosphate affects transcription. Here we report the crystal structures of E coli transcription initiation complexes (TICs) containing the stress-responsive σ(S) factor, a de novo synthesized RNA oligonucleotide, and a complete transcription bubble (σ(S)-TIC) at about 3.9-Å resolution. The structures show the 3D topology of the σ(S) factor and how it recognizes the promoter DNA, including likely specific interactions with the template-strand residues of the -10 element. In addition, σ(S)-TIC structures display a highly stressed pretranslocated initiation complex that traps a pyrophosphate at the active site that remains closed. The position of the pyrophosphate and the unusual phosphodiester linkage between the two terminal RNA residues suggest an unfinished nucleotide-addition reaction that is likely at equilibrium between nucleotide addition and pyrophosphorolysis. Although these σ(S)-TIC crystals are enzymatically active, they are slow in nucleotide addition, as suggested by an NTP soaking experiment. Pyrophosphate release completes the nucleotide addition reaction and is associated with extensive conformational changes around the secondary channel but causes neither active site opening nor transcript translocation.
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Affiliation(s)
- Bin Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Yuhong Zuo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520; Department of Chemistry, Yale University, New Haven, CT 06520
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31
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Esyunina D, Turtola M, Pupov D, Bass I, Klimašauskas S, Belogurov G, Kulbachinskiy A. Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases. Nucleic Acids Res 2016; 44:1298-308. [PMID: 26733581 PMCID: PMC4756841 DOI: 10.1093/nar/gkv1521] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 12/20/2015] [Indexed: 02/01/2023] Open
Abstract
RNA cleavage by bacterial RNA polymerase (RNAP) has been implicated in transcriptional proofreading and reactivation of arrested transcription elongation complexes but its molecular mechanism is less understood than the mechanism of nucleotide addition, despite both reactions taking place in the same active site. RNAP from the radioresistant bacterium Deinococcus radiodurans is characterized by highly efficient intrinsic RNA cleavage in comparison with Escherichia coli RNAP. We find that the enhanced RNA cleavage activity largely derives from amino acid substitutions in the trigger loop (TL), a mobile element of the active site involved in various RNAP activities. The differences in RNA cleavage between these RNAPs disappear when the TL is deleted, or in the presence of GreA cleavage factors, which replace the TL in the active site. We propose that the TL substitutions modulate the RNA cleavage activity by altering the TL folding and its contacts with substrate RNA and that the resulting differences in transcriptional proofreading may play a role in bacterial stress adaptation.
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Affiliation(s)
- Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov square 2, Moscow 123182, Russia
| | - Matti Turtola
- Department of Biochemistry, University of Turku, Turku 20014, Finland
| | - Danil Pupov
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov square 2, Moscow 123182, Russia
| | - Irina Bass
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov square 2, Moscow 123182, Russia
| | | | - Georgiy Belogurov
- Department of Biochemistry, University of Turku, Turku 20014, Finland
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov square 2, Moscow 123182, Russia
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32
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Washburn RS, Gottesman ME. Regulation of transcription elongation and termination. Biomolecules 2015; 5:1063-78. [PMID: 26035374 PMCID: PMC4496710 DOI: 10.3390/biom5021063] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 11/16/2022] Open
Abstract
This article will review our current understanding of transcription elongation and termination in E. coli. We discuss why transcription elongation complexes pause at certain template sites and how auxiliary host and phage transcription factors affect elongation and termination. The connection between translation and transcription elongation is described. Finally we present an overview indicating where progress has been made and where it has not.
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Affiliation(s)
- Robert S Washburn
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.
| | - Max E Gottesman
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA.
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