1
|
Da LT, E C, Shuai Y, Wu S, Su XD, Yu J. T7 RNA polymerase translocation is facilitated by a helix opening on the fingers domain that may also prevent backtracking. Nucleic Acids Res 2017; 45:7909-7921. [PMID: 28575393 PMCID: PMC5737862 DOI: 10.1093/nar/gkx495] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/24/2017] [Indexed: 12/04/2022] Open
Abstract
Here, we studied the complete process of a viral T7 RNA polymerase (RNAP) translocation on DNA during transcription elongation by implementing extensive all-atom molecular dynamics (MD) simulations to construct a Markov state model (MSM). Our studies show that translocation proceeds in a Brownian motion, and the RNAP thermally transits among multiple metastable states. We observed non-synchronized backbone movements of the nucleic acid (NA) chains with the RNA translocation accomplished first, while the template DNA lagged. Notably, both the O-helix and Y-helix on the fingers domain play key roles in facilitating NA translocation through the helix opening. The helix opening allows a key residue Tyr639 to become inserted into the active site, which pushes the RNA–DNA hybrid forward. Another key residue, Phe644, coordinates the downstream template DNA motions by stacking and un-stacking with a transition nucleotide (TN) and its adjacent nucleotide. Moreover, the O-helix opening at pre-translocation (pre-trans) likely resists backtracking. To test this hypothesis, we computationally designed mutants of T7 RNAP by replacing the amino acids on the O-helix with counterpart residues from a mitochondrial RNAP that is capable of backtracking. The current experimental results support the hypothesis.
Collapse
Affiliation(s)
- Lin-Tai Da
- Beijing Computational Science Research Center, Beijing 100193, China.,Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Chao E
- Beijing Computational Science Research Center, Beijing 100193, China
| | - Yao Shuai
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Shaogui Wu
- Beijing Computational Science Research Center, Beijing 100193, China
| | - Xiao-Dong Su
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Jin Yu
- Beijing Computational Science Research Center, Beijing 100193, China
| |
Collapse
|
2
|
Opron K, Xia K, Burton Z, Wei GW. Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis. J Comput Chem 2016; 37:1283-95. [PMID: 26927815 PMCID: PMC5844491 DOI: 10.1002/jcc.24320] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 12/02/2015] [Accepted: 01/17/2016] [Indexed: 12/29/2022]
Abstract
Protein-nucleic acid complexes are important for many cellular processes including the most essential functions such as transcription and translation. For many protein-nucleic acid complexes, flexibility of both macromolecules has been shown to be critical for specificity and/or function. The flexibility-rigidity index (FRI) has been proposed as an accurate and efficient approach for protein flexibility analysis. In this article, we introduce FRI for the flexibility analysis of protein-nucleic acid complexes. We demonstrate that a multiscale strategy, which incorporates multiple kernels to capture various length scales in biomolecular collective motions, is able to significantly improve the state of art in the flexibility analysis of protein-nucleic acid complexes. We take the advantage of the high accuracy and O(N) computational complexity of our multiscale FRI method to investigate the flexibility of ribosomal subunits, which are difficult to analyze by alternative approaches. An anisotropic FRI approach, which involves localized Hessian matrices, is utilized to study the translocation dynamics in an RNA polymerase.
Collapse
Affiliation(s)
- Kristopher Opron
- Department of Biochemistry and Molecular Biology, Michigan State University, MI 48824, USA
| | - Kelin Xia
- Department of Mathematics Michigan State University, MI 48824, USA
| | - Zach Burton
- Department of Biochemistry and Molecular Biology, Michigan State University, MI 48824, USA
| | - Guo-Wei Wei
- Mathematical Biosciences Institute The Ohio State University, Columbus, Ohio 43210, USA
| |
Collapse
|
3
|
Xu L, Wang W, Chong J, Shin JH, Xu J, Wang D. RNA polymerase II transcriptional fidelity control and its functional interplay with DNA modifications. Crit Rev Biochem Mol Biol 2015; 50:503-19. [PMID: 26392149 DOI: 10.3109/10409238.2015.1087960] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Accurate genetic information transfer is essential for life. As a key enzyme involved in the first step of gene expression, RNA polymerase II (Pol II) must maintain high transcriptional fidelity while it reads along DNA template and synthesizes RNA transcript in a stepwise manner during transcription elongation. DNA lesions or modifications may lead to significant changes in transcriptional fidelity or transcription elongation dynamics. In this review, we will summarize recent progress toward understanding the molecular basis of RNA Pol II transcriptional fidelity control and impacts of DNA lesions and modifications on Pol II transcription elongation.
Collapse
Affiliation(s)
- Liang Xu
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Wei Wang
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Jenny Chong
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Ji Hyun Shin
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Jun Xu
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Dong Wang
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| |
Collapse
|
4
|
Wang B, Opron K, Burton ZF, Cukier RI, Feig M. Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details. Nucleic Acids Res 2014; 43:1133-46. [PMID: 25550432 PMCID: PMC4333413 DOI: 10.1093/nar/gku1370] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Transcriptional fidelity, which prevents the misincorporation of incorrect nucleoside monophosphates in RNA, is essential for life. Results from molecular dynamics (MD) simulations of eukaryotic RNA polymerase (RNAP) II and bacterial RNAP with experimental data suggest that fidelity may involve as many as five checkpoints. Using MD simulations, the effects of different active site NTPs in both open and closed trigger loop (TL) structures of RNAPs are compared. Unfavorable initial binding of mismatched substrates in the active site with an open TL is proposed to be the first fidelity checkpoint. The leaving of an incorrect substrate is much easier than a correct one energetically from the umbrella sampling simulations. Then, the closing motion of the TL, required for catalysis, is hindered by the presence of mismatched NTPs. Mismatched NTPs also lead to conformational changes in the active site, which perturb the coordination of magnesium ions and likely affect the ability to proceed with catalysis. This step appears to be the most important checkpoint for deoxy-NTP discrimination. Finally, structural perturbations in the template DNA and the nascent RNA in the presence of mismatches likely hinder nucleotide addition and provide the structural foundation for backtracking followed by removing erroneously incorporated nucleotides during proofreading.
Collapse
Affiliation(s)
- Beibei Wang
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Kristopher Opron
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Zachary F Burton
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert I Cukier
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Michael Feig
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
5
|
Zhang R, Bhattacharjee A, Field MJ, Salahub DR. Multiple proton relay routes in the reaction mechanism of RNAP II: Assessing the effect of structural model. Proteins 2014; 83:268-81. [DOI: 10.1002/prot.24732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 11/05/2014] [Accepted: 11/06/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Rui Zhang
- Department of Chemistry; Centre for Molecular Simulation, Institute for Quantum Science and Technology, University of Calgary; Calgary Canada
| | - Anirban Bhattacharjee
- Department of Chemistry; Centre for Molecular Simulation, Institute for Quantum Science and Technology, University of Calgary; Calgary Canada
| | - Martin J. Field
- DYNAMOP; Institut de Biologie Structurale, Jean-Pierre Ebel; Grenoble France
| | - Dennis R. Salahub
- Department of Chemistry; Centre for Molecular Simulation, Institute for Quantum Science and Technology, University of Calgary; Calgary Canada
| |
Collapse
|
6
|
Yu J, Da LT, Huang X. Constructing kinetic models to elucidate structural dynamics of a complete RNA polymerase II elongation cycle. Phys Biol 2014; 12:016004. [DOI: 10.1088/1478-3975/12/1/016004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
7
|
Xu L, Da L, Plouffe SW, Chong J, Kool E, Wang D. Molecular basis of transcriptional fidelity and DNA lesion-induced transcriptional mutagenesis. DNA Repair (Amst) 2014; 19:71-83. [PMID: 24767259 DOI: 10.1016/j.dnarep.2014.03.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Maintaining high transcriptional fidelity is essential for life. Some DNA lesions lead to significant changes in transcriptional fidelity. In this review, we will summarize recent progress towards understanding the molecular basis of RNA polymerase II (Pol II) transcriptional fidelity and DNA lesion-induced transcriptional mutagenesis. In particular, we will focus on the three key checkpoint steps of controlling Pol II transcriptional fidelity: insertion (specific nucleotide selection and incorporation), extension (differentiation of RNA transcript extension of a matched over mismatched 3'-RNA terminus), and proofreading (preferential removal of misincorporated nucleotides from the 3'-RNA end). We will also discuss some novel insights into the molecular basis and chemical perspectives of controlling Pol II transcriptional fidelity through structural, computational, and chemical biology approaches.
Collapse
Affiliation(s)
- Liang Xu
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA 92093-0625, United States
| | - Linati Da
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA 92093-0625, United States
| | - Steven W Plouffe
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA 92093-0625, United States
| | - Jenny Chong
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA 92093-0625, United States
| | - Eric Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, United States.
| | - Dong Wang
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA 92093-0625, United States.
| |
Collapse
|
8
|
Wang B, Predeus AV, Burton ZF, Feig M. Energetic and structural details of the trigger-loop closing transition in RNA polymerase II. Biophys J 2014; 105:767-75. [PMID: 23931324 DOI: 10.1016/j.bpj.2013.05.060] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 05/26/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022] Open
Abstract
An evolutionarily conserved element in RNA polymerase II, the trigger loop (TL), has been suggested to play an important role in the elongation rate, fidelity of selection of the matched nucleoside triphosphate (NTP), catalysis of transcription elongation, and translocation in both eukaryotes and prokaryotes. In response to NTP binding, the TL undergoes large conformational changes to switch between distinct open and closed states to tighten the active site and avail catalysis. A computational strategy for characterizing the conformational transition pathway is presented to bridge the open and closed states of the TL. Information from a large number of independent all-atom molecular dynamics trajectories from Hamiltonian replica exchange and targeted molecular dynamics simulations is gathered together to assemble a connectivity map of the conformational transition. The results show that with a cognate NTP, TL closing should be a spontaneous process. One major intermediate state is identified along the conformational transition pathway, and the key structural features are characterized. The complete pathway from the open TL to the closed TL provides a clear picture of the TL closing.
Collapse
Affiliation(s)
- Beibei Wang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
| | | | | | | |
Collapse
|
9
|
PARDO-AVILA FÁTIMA, DA LINTAI, WANG YING, HUANG XUHUI. THEORETICAL INVESTIGATIONS ON ELUCIDATING FUNDAMENTAL MECHANISMS OF CATALYSIS AND DYNAMICS INVOLVED IN TRANSCRIPTION BY RNA POLYMERASE. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613410058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
RNA polymerase is the enzyme that synthesizes RNA during the transcription process. To understand its mechanism, structural studies have provided us pictures of the series of steps necessary to add a new nucleotide to the nascent RNA chain, the steps altogether known as the nucleotide addition cycle (NAC). However, these static snapshots do not provide dynamic information of these processes involved in NAC, such as the conformational changes of the protein and the atomistic details of the catalysis. Computational studies have made efforts to fill these knowledge gaps. In this review, we provide examples of different computational approaches that have improved our understanding of the transcription elongation process for RNA polymerase, such as normal mode analysis, molecular dynamic (MD) simulations, Markov state models (MSMs). We also point out some unsolved questions that could be addressed using computational tools in the future.
Collapse
Affiliation(s)
- FÁTIMA PARDO-AVILA
- Department of Chemistry, Center of Systems Biology and Human Health, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Clear Water Bay Road, Kowloon, Hong Kong
| | - LIN-TAI DA
- Department of Chemistry, Center of Systems Biology and Human Health, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Clear Water Bay Road, Kowloon, Hong Kong
| | - YING WANG
- Department of Chemistry, Center of Systems Biology and Human Health, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Clear Water Bay Road, Kowloon, Hong Kong
| | - XUHUI HUANG
- Department of Chemistry, Center of Systems Biology and Human Health, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Clear Water Bay Road, Kowloon, Hong Kong
- Division of Biomedical Engineering, Center of Systems Biology and Human Health, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Clear Water Bay Road, Kowloon, Hong Kong
| |
Collapse
|
10
|
Wang B, Feig M, Cukier RI, Burton ZF. Computational simulation strategies for analysis of multisubunit RNA polymerases. Chem Rev 2013; 113:8546-66. [PMID: 23987500 PMCID: PMC3829680 DOI: 10.1021/cr400046x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Indexed: 12/13/2022]
Affiliation(s)
- Beibei Wang
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824-1319, United States
| | - Michael Feig
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824-1319, United States
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Robert I. Cukier
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Zachary F. Burton
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824-1319, United States
| |
Collapse
|
11
|
Seo S, Jang Y, Qian P, Liu WK, Choi JB, Lim BS, Kim MK. Efficient prediction of protein conformational pathways based on the hybrid elastic network model. J Mol Graph Model 2013; 47:25-36. [PMID: 24296313 DOI: 10.1016/j.jmgm.2013.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Revised: 10/19/2013] [Accepted: 10/22/2013] [Indexed: 11/18/2022]
Abstract
Various computational models have gained immense attention by analyzing the dynamic characteristics of proteins. Several models have achieved recognition by fulfilling either theoretical or experimental predictions. Nonetheless, each method possesses limitations, mostly in computational outlay and physical reality. These limitations remind us that a new model or paradigm should advance theoretical principles to elucidate more precisely the biological functions of a protein and should increase computational efficiency. With these critical caveats, we have developed a new computational tool that satisfies both physical reality and computational efficiency. In the proposed hybrid elastic network model (HENM), a protein structure is represented as a mixture of rigid clusters and point masses that are connected with linear springs. Harmonic analyses based on the HENM have been performed to generate normal modes and conformational pathways. The results of the hybrid normal mode analyses give new physical insight to the 70S ribosome. The feasibility of the conformational pathways of hybrid elastic network interpolation (HENI) was quantitatively evaluated by comparing three different overlap values proposed in this paper. A remarkable observation is that the obtained mode shapes and conformational pathways are consistent with each other. Our timing results show that HENM has some advantage in computational efficiency over a coarse-grained model, especially for large proteins, even though it takes longer to construct the HENM. Consequently, the proposed HENM will be one of the best alternatives to the conventional coarse-grained ENMs and all-atom based methods (such as molecular dynamics) without loss of physical reality.
Collapse
Affiliation(s)
- Sangjae Seo
- SKKU Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Yunho Jang
- Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, MA 01003, USA
| | - Pengfei Qian
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Wing Kam Liu
- Department of Mechanical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Jae-Boong Choi
- SKKU Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon 440-746, Republic of Korea; School of Mechanical Engineering, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Byeong Soo Lim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Moon Ki Kim
- SKKU Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon 440-746, Republic of Korea; School of Mechanical Engineering, Sungkyunkwan University, Suwon 440-746, Republic of Korea.
| |
Collapse
|
12
|
Affiliation(s)
- Finn Werner
- RNAP Laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London , Darwin Building, Gower Street, London WC1E 6BT, U.K
| |
Collapse
|
13
|
Da LT, Pardo Avila F, Wang D, Huang X. A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase. PLoS Comput Biol 2013; 9:e1003020. [PMID: 23592966 PMCID: PMC3617016 DOI: 10.1371/journal.pcbi.1003020] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 02/19/2013] [Indexed: 01/10/2023] Open
Abstract
The dynamics of the PPi release during the transcription elongation of bacterial RNA polymerase and its effects on the Trigger Loop (TL) opening motion are still elusive. Here, we built a Markov State Model (MSM) from extensive all-atom molecular dynamics (MD) simulations to investigate the mechanism of the PPi release. Our MSM has identified a simple two-state mechanism for the PPi release instead of a more complex four-state mechanism observed in RNA polymerase II (Pol II). We observed that the PPi release in bacterial RNA polymerase occurs at sub-microsecond timescale, which is ∼3-fold faster than that in Pol II. After escaping from the active site, the (Mg-PPi)(2-) group passes through a single elongated metastable region where several positively charged residues on the secondary channel provide favorable interactions. Surprisingly, we found that the PPi release is not coupled with the TL unfolding but correlates tightly with the side-chain rotation of the TL residue R1239. Our work sheds light on the dynamics underlying the transcription elongation of the bacterial RNA polymerase.
Collapse
Affiliation(s)
- Lin-Tai Da
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Fátima Pardo Avila
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Dong Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Center of Systems Biology and Human Health, Institute for Advance Study and School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- * E-mail:
| |
Collapse
|
14
|
Nedialkov YA, Opron K, Assaf F, Artsimovitch I, Kireeva ML, Kashlev M, Cukier RI, Nudler E, Burton ZF. The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1829:187-98. [PMID: 23202476 PMCID: PMC3619131 DOI: 10.1016/j.bbagrm.2012.11.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/14/2012] [Accepted: 11/17/2012] [Indexed: 01/22/2023]
Abstract
The bridge α-helix in the β' subunit of RNA polymerase (RNAP) borders the active site and may have roles in catalysis and translocation. In Escherichia coli RNAP, a bulky hydrophobic segment near the N-terminal end of the bridge helix is identified (β' 772-YFI-774; the YFI motif). YFI is located at a distance from the active center and adjacent to a glycine hinge (β' 778-GARKG-782) involved in dynamic bending of the bridge helix. Remarkably, amino acid substitutions in YFI significantly alter intrinsic termination, pausing, fidelity and translocation of RNAP. F773V RNAP largely ignores the λ tR2 terminator at 200μM NTPs and is strongly reduced in λ tR2 recognition at 1μM NTPs. F773V alters RNAP pausing and backtracking and favors misincorporation. By contrast, the adjacent Y772A substitution increases fidelity and exhibits other transcriptional defects generally opposite to those of F773V. All atom molecular dynamics simulation revealed two separate functional connections emanating from YFI explaining the distinct effects of substitutions: Y772 communicates with the active site through the link domain in the β subunit, whereas F773 communicates through the fork domain in the β subunit. I774 interacts with the F-loop, which also contacts the glycine hinge of the bridge helix. These results identified negative and positive circuits coupled at YFI and employed for regulation of catalysis, elongation, termination and translocation.
Collapse
Affiliation(s)
- Yuri A. Nedialkov
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI 48824-1319, USA
- Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
| | - Kristopher Opron
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI 48824-1319, USA
| | - Fadi Assaf
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI 48824-1319, USA
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, Ohio USA
| | - Maria L. Kireeva
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Mikhail Kashlev
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Robert I. Cukier
- Department of Chemistry, Michigan State University, E. Lansing, MI 48824-1319, USA
| | - Evgeny Nudler
- Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
| | - Zachary F. Burton
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI 48824-1319, USA
| |
Collapse
|
15
|
Kaplan CD. Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:39-54. [PMID: 23022618 DOI: 10.1016/j.bbagrm.2012.09.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 09/18/2012] [Accepted: 09/20/2012] [Indexed: 01/12/2023]
Abstract
Transcription by RNA polymerase II (Pol II), and all RNA polymerases for that matter, may be understood as comprising two cycles. The first cycle relates to the basic mechanism of the transcription process wherein Pol II must select the appropriate nucleoside triphosphate (NTP) substrate complementary to the DNA template, catalyze phosphodiester bond formation, and translocate to the next position on the DNA template. Performing this cycle in an iterative fashion allows the synthesis of RNA chains that can be over one million nucleotides in length in some larger eukaryotes. Overlaid upon this enzymatic cycle, transcription may be divided into another cycle of three phases: initiation, elongation, and termination. Each of these phases has a large number of associated transcription factors that function to promote or regulate the gene expression process. Complicating matters, each phase of the latter transcription cycle are coincident with cotranscriptional RNA processing events. Additionally, transcription takes place within a highly dynamic and regulated chromatin environment. This chromatin environment is radically impacted by active transcription and associated chromatin modifications and remodeling, while also functioning as a major platform for Pol II regulation. This review will focus on our basic knowledge of the Pol II transcription mechanism, and how altered Pol II activity impacts gene expression in vivo in the model eukaryote Saccharomyces cerevisiae. This article is part of a Special Issue entitled: RNA Polymerase II Transcript Elongation.
Collapse
Affiliation(s)
- Craig D Kaplan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
| |
Collapse
|
16
|
Kireeva ML, Opron K, Seibold SA, Domecq C, Cukier RI, Coulombe B, Kashlev M, Burton ZF. Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase. BMC BIOPHYSICS 2012; 5:11. [PMID: 22676913 PMCID: PMC3533926 DOI: 10.1186/2046-1682-5-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 06/07/2012] [Indexed: 11/10/2022]
Abstract
UNLABELLED BACKGROUND During elongation, multi-subunit RNA polymerases (RNAPs) cycle between phosphodiester bond formation and nucleic acid translocation. In the conformation associated with catalysis, the mobile "trigger loop" of the catalytic subunit closes on the nucleoside triphosphate (NTP) substrate. Closing of the trigger loop is expected to exclude water from the active site, and dehydration may contribute to catalysis and fidelity. In the absence of a NTP substrate in the active site, the trigger loop opens, which may enable translocation. Another notable structural element of the RNAP catalytic center is the "bridge helix" that separates the active site from downstream DNA. The bridge helix may participate in translocation by bending against the RNA/DNA hybrid to induce RNAP forward movement and to vacate the active site for the next NTP loading. The transition between catalytic and translocation conformations of RNAP is not evident from static crystallographic snapshots in which macromolecular motions may be restrained by crystal packing. RESULTS All atom molecular dynamics simulations of Thermus thermophilus (Tt) RNAP reveal flexible hinges, located within the two helices at the base of the trigger loop, and two glycine hinges clustered near the N-terminal end of the bridge helix. As simulation progresses, these hinges adopt distinct conformations in the closed and open trigger loop structures. A number of residues (described as "switch" residues) trade atomic contacts (ion pairs or hydrogen bonds) in response to changes in hinge orientation. In vivo phenotypes and in vitro activities rendered by mutations in the hinge and switch residues in Saccharomyces cerevisiae (Sc) RNAP II support the importance of conformational changes predicted from simulations in catalysis and translocation. During simulation, the elongation complex with an open trigger loop spontaneously translocates forward relative to the elongation complex with a closed trigger loop. CONCLUSIONS Switching between catalytic and translocating RNAP forms involves closing and opening of the trigger loop and long-range conformational changes in the atomic contacts of amino acid side chains, some located at a considerable distance from the trigger loop and active site. Trigger loop closing appears to support chemistry and the fidelity of RNA synthesis. Trigger loop opening and limited bridge helix bending appears to promote forward nucleic acid translocation.
Collapse
Affiliation(s)
- Maria L Kireeva
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Kristopher Opron
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI, 48824-1319, USA
| | - Steve A Seibold
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI, 48824-1319, USA
- Department of Chemistry, Michigan State University, E. Lansing, MI, 48824, USA
- Department of Chemistry, University of Saint Mary, Leavenworth, KS, 66048, USA
| | - Céline Domecq
- Gene Transcription and Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), 110, Avenue des Pins Ouest, Montréal, Québec, H2W 1R7, CANADA
| | - Robert I Cukier
- Department of Chemistry, Michigan State University, E. Lansing, MI, 48824, USA
| | - Benoit Coulombe
- Gene Transcription and Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), 110, Avenue des Pins Ouest, Montréal, Québec, H2W 1R7, CANADA
- Department of Biochemistry, Université de Montréal, Montréal, Québec, H3C 3J7, CANADA
| | - Mikhail Kashlev
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Zachary F Burton
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI, 48824-1319, USA
| |
Collapse
|
17
|
Malinen AM, Turtola M, Parthiban M, Vainonen L, Johnson MS, Belogurov GA. Active site opening and closure control translocation of multisubunit RNA polymerase. Nucleic Acids Res 2012; 40:7442-51. [PMID: 22570421 PMCID: PMC3424550 DOI: 10.1093/nar/gks383] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multisubunit RNA polymerase (RNAP) is the central information-processing enzyme in all cellular life forms, yet its mechanism of translocation along the DNA molecule remains conjectural. Here, we report direct monitoring of bacterial RNAP translocation following the addition of a single nucleotide. Time-resolved measurements demonstrated that translocation is delayed relative to nucleotide incorporation and occurs shortly after or concurrently with pyrophosphate release. An investigation of translocation equilibrium suggested that the strength of interactions between RNA 3′ nucleotide and nucleophilic and substrate sites determines the translocation state of transcription elongation complexes, whereas active site opening and closure modulate the affinity of the substrate site, thereby favoring the post- and pre-translocated states, respectively. The RNAP translocation mechanism is exploited by the antibiotic tagetitoxin, which mimics pyrophosphate and induces backward translocation by closing the active site.
Collapse
Affiliation(s)
- Anssi M Malinen
- Department of Biochemistry and Food Chemistry, University of Turku, 20014, Turku, Finland
| | | | | | | | | | | |
Collapse
|
18
|
Larson MH, Zhou J, Kaplan CD, Palangat M, Kornberg RD, Landick R, Block SM. Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II. Proc Natl Acad Sci U S A 2012; 109:6555-60. [PMID: 22493230 PMCID: PMC3340090 DOI: 10.1073/pnas.1200939109] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During transcription, RNA polymerase II (RNAPII) must select the correct nucleotide, catalyze its addition to the growing RNA transcript, and move stepwise along the DNA until a gene is fully transcribed. In all kingdoms of life, transcription must be finely tuned to ensure an appropriate balance between fidelity and speed. Here, we used an optical-trapping assay with high spatiotemporal resolution to probe directly the motion of individual RNAPII molecules as they pass through each of the enzymatic steps of transcript elongation. We report direct evidence that the RNAPII trigger loop, an evolutionarily conserved protein subdomain, serves as a master regulator of transcription, affecting each of the three main phases of elongation, namely: substrate selection, translocation, and catalysis. Global fits to the force-velocity relationships of RNAPII and its trigger loop mutants support a Brownian ratchet model for elongation, where the incoming NTP is able to bind in either the pre- or posttranslocated state, and movement between these two states is governed by the trigger loop. Comparison of the kinetics of pausing by WT and mutant RNAPII under conditions that promote base misincorporation indicate that the trigger loop governs fidelity in substrate selection and mismatch recognition, and thereby controls aspects of both transcriptional accuracy and rate.
Collapse
Affiliation(s)
| | | | - Craig D. Kaplan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843; and
| | - Murali Palangat
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | | | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Steven M. Block
- Biophysics Program
- Department of Applied Physics
- Department of Biology, Stanford University, Stanford, CA 94305
| |
Collapse
|
19
|
Lopéz-Blanco JR, Garzón JI, Chacón P. iMod: multipurpose normal mode analysis in internal coordinates. ACTA ACUST UNITED AC 2011; 27:2843-50. [PMID: 21873636 DOI: 10.1093/bioinformatics/btr497] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION Dynamic simulations of systems with biologically relevant sizes and time scales are critical for understanding macromolecular functioning. Coarse-grained representations combined with normal mode analysis (NMA) have been established as an alternative to atomistic simulations. The versatility and efficiency of current approaches normally based on Cartesian coordinates can be greatly enhanced with internal coordinates (IC). RESULTS Here, we present a new versatile tool chest to explore conformational flexibility of both protein and nucleic acid structures using NMA in IC. Consideration of dihedral angles as variables reduces the computational cost and non-physical distortions of classical Cartesian NMA methods. Our proposed framework operates at different coarse-grained levels and offers an efficient framework to conduct NMA-based conformational studies, including standard vibrational analysis, Monte-Carlo simulations or pathway exploration. Examples of these approaches are shown to demonstrate its applicability, robustness and efficiency. CONTACT pablo@chaconlab.org SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- José Ramón Lopéz-Blanco
- Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute, CSIC, Serrano 119, Madrid 28006, Spain
| | | | | |
Collapse
|
20
|
Feig M, Burton ZF. RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation. Biophys J 2011; 99:2577-86. [PMID: 20959099 DOI: 10.1016/j.bpj.2010.08.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 07/28/2010] [Accepted: 08/10/2010] [Indexed: 10/18/2022] Open
Abstract
RNA polymerase II is the central eukaryotic enzyme in transcription from DNA to RNA. The dynamics of RNA polymerase II is described from molecular-dynamics simulations started from two crystal structures with open and closed trigger loop (TL) forms. Dynamic transitions between neutral and forward translocated states were observed, especially for the downstream DNA duplex. Dynamic rearrangements were also seen in the active site environment, including conformations in which the active site nucleotide assumed a possibly precatalytic conformation in close proximity to the terminal 3'-hydroxyl of the nascent RNA. Because nucleic acid translocation was observed primarily in the simulations with an open TL structure, whereas close approach of the active site nucleotide to the terminal RNA ribose predominantly occurred in the closed TL structure, a modified Brownian ratchet mechanism is proposed whereby thermally driven translocation is only possible with an open TL, and fidelity control and catalysis require TL closing.
Collapse
Affiliation(s)
- Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA.
| | | |
Collapse
|
21
|
Weinzierl ROJ. The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain. BMC Biol 2010; 8:134. [PMID: 21034443 PMCID: PMC2988716 DOI: 10.1186/1741-7007-8-134] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 10/29/2010] [Indexed: 01/24/2023] Open
Abstract
Background Cellular RNA polymerases (RNAPs) are complex molecular machines that combine catalysis with concerted conformational changes in the active center. Previous work showed that kinking of a hinge region near the C-terminus of the Bridge Helix (BH-HC) plays a critical role in controlling the catalytic rate. Results Here, new evidence for the existence of an additional hinge region in the amino-terminal portion of the Bridge Helix domain (BH-HN) is presented. The nanomechanical properties of BH-HN emerge as a direct consequence of the highly conserved primary amino acid sequence. Mutations that are predicted to influence its flexibility cause corresponding changes in the rate of the nucleotide addition cycle (NAC). BH-HN displays functional properties that are distinct from BH-HC, suggesting that conformational changes in the Bridge Helix control the NAC via two independent mechanisms. Conclusions The properties of two distinct molecular hinges in the Bridge Helix of RNAP determine the functional contribution of this domain to key stages of the NAC by coordinating conformational changes in surrounding domains.
Collapse
|
22
|
Seibold SA, Singh BN, Zhang C, Kireeva M, Domecq C, Bouchard A, Nazione AM, Feig M, Cukier RI, Coulombe B, Kashlev M, Hampsey M, Burton ZF. Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:575-87. [PMID: 20478425 DOI: 10.1016/j.bbagrm.2010.05.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 04/21/2010] [Accepted: 05/07/2010] [Indexed: 01/22/2023]
Abstract
Molecular dynamics simulation of Thermus thermophilus (Tt) RNA polymerase (RNAP) in a catalytic conformation demonstrates that the active site dNMP-NTP base pair must be substantially dehydrated to support full active site closing and optimum conditions for phosphodiester bond synthesis. In silico mutant beta R428A RNAP, which was designed based on substitutions at the homologous position (Rpb2 R512) of Saccharomyces cerevisiae (Sc) RNAP II, was used as a reference structure to compare to Tt RNAP in simulations. Long range conformational coupling linking a dynamic segment of the bridge alpha-helix, the extended fork loop, the active site, and the trigger loop-trigger helix is apparent and adversely affected in beta R428A RNAP. Furthermore, bridge helix bending is detected in the catalytic structure, indicating that bridge helix dynamics may regulate phosphodiester bond synthesis as well as translocation. An active site "latch" assembly that includes a key trigger helix residue Tt beta' H1242 and highly conserved active site residues beta E445 and R557 appears to help regulate active site hydration/dehydration. The potential relevance of these observations in understanding RNAP and DNAP induced fit and fidelity is discussed.
Collapse
Affiliation(s)
- Steve A Seibold
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI 48824-1319, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|