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Midha T, Mallory JD, Kolomeisky AB, Igoshin OA. Synergy among Pausing, Intrinsic Proofreading, and Accessory Proteins Results in Optimal Transcription Speed and Tolerable Accuracy. J Phys Chem Lett 2023; 14:3422-3429. [PMID: 37010247 DOI: 10.1021/acs.jpclett.3c00345] [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: 06/19/2023]
Abstract
Cleavage of dinucleotides after the misincorporational pauses serves as a proofreading mechanism that increases transcriptional elongation accuracy. The accuracy is further improved by accessory proteins such as GreA and TFIIS. However, it is not clear why RNAP pauses and why cleavage-factor-assisted proofreading is necessary despite transcriptional errors in vitro being of the same order as those in downstream translation. Here, we developed a chemical-kinetic model that incorporates most relevant features of transcriptional proofreading and uncovers how the balance between speed and accuracy is achieved. We found that long pauses are essential for high accuracy, whereas cleavage-factor-stimulated proofreading optimizes speed. Moreover, in comparison to the cleavage of a single nucleotide or three nucleotides, RNAP backtracking and dinucleotide cleavage improve both speed and accuracy. Our results thereby show how the molecular mechanism and the kinetic parameters of the transcriptional process were evolutionarily optimized to achieve maximal speed and tolerable accuracy.
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Affiliation(s)
- Tripti Midha
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Joel D Mallory
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Anatoly B Kolomeisky
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, United States
| | - Oleg A Igoshin
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
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2
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Nakajima RT, Costa PR, Lemke N. Cooperative and sequence-dependent model for RNAP dynamics: Application to ribosomal gene transcription. J Theor Biol 2020; 488:110134. [PMID: 31874133 DOI: 10.1016/j.jtbi.2019.110134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/11/2019] [Accepted: 12/19/2019] [Indexed: 11/29/2022]
Abstract
Escherichia coli ribosomal genes are a well-established experimental model used to investigate the transcription process. These genes are essential to cell physiology and are therefore strongly expressed. Multiple transcription units collaborate in rrn expression. Experiments involving electron microscopy have shown the non-uniform density of the RNA polymerases transcribing these ribosomal operons. Here, we investigate RNAP collaborative transcription in E. coli ribosomal genes using a stochastic sequence-dependent model that included interactions among the RNAPs. We achieved results consistent with experimental data using a model with variable parametrization for genic and intergenic regions, compared with previous attempts that used uniform parameters for genic and intergenic regions. Our model also showed that cooperative behaviour reduced the dwell times in pause sites predicted by the single-round approach but induced a new pausing event at an upstream position. This work may stimulate new experimental research and provide other scenarios to test our model predictions.
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Affiliation(s)
- Rafael Takahiro Nakajima
- Institute of Biosciences, UNESP - Univ Estadual Paulista, Department of Physics and Biophysics, Botucatu, 18618-689, Brazil.
| | - Pedro Rafael Costa
- Institute of Biosciences, UNESP - Univ Estadual Paulista, Department of Physics and Biophysics, Botucatu, 18618-689, Brazil.
| | - Ney Lemke
- Institute of Biosciences, UNESP - Univ Estadual Paulista, Department of Physics and Biophysics, Botucatu, 18618-689, Brazil.
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3
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Long C, E. C, Da LT, Yu J. A Viral T7 RNA Polymerase Ratcheting Along DNA With Fidelity Control. Comput Struct Biotechnol J 2019; 17:638-644. [PMID: 31193497 PMCID: PMC6535458 DOI: 10.1016/j.csbj.2019.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/25/2019] [Accepted: 05/04/2019] [Indexed: 12/02/2022] Open
Abstract
RNA polymerase (RNAP) from bacteriophage T7 is a representative single-subunit viral RNAP that can transcribe with high promoter activities without assistances from transcription factors. We accordingly studied this small transcription machine computationally as a model system to understand underlying mechanisms of mechano-chemical coupling and fidelity control in the RNAP transcription elongation. Here we summarize our computational work from several recent publications to demonstrate first how T7 RNAP translocates via Brownian alike motions along DNA right after the catalytic product release. Then we show how the backward translocation motions are prevented at post-translocation upon successful nucleotide incorporation, which is also subject to stepwise nucleotide selection and acts as a pawl for "selective ratcheting". The structural dynamics and energetics features revealed from our atomistic molecular dynamics (MD) simulations and related analyses on the single-subunit T7 RNAP thus provided detailed and quantitative characterizations on the Brownian-ratchet working scenario of a prototypical transcription machine with sophisticated nucleotide selectivity for fidelity control. The presented mechanisms can be more or less general for structurally similar viral or mitochondrial RNAPs and some of DNA polymerases, or even for the RNAP engine of the more complicated transcription machinery in higher organisms.
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Affiliation(s)
- Chunhong Long
- Beijing Computational Science Research Center, Beijing, 100193, China
| | - Chao E.
- Beijing Computational Science Research Center, Beijing, 100193, China
| | - Lin-Tai Da
- Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, Shanghai 200240, China
| | - Jin Yu
- Beijing Computational Science Research Center, Beijing, 100193, China
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4
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Unarta IC, Zhu L, Tse CKM, Cheung PPH, Yu J, Huang X. Molecular mechanisms of RNA polymerase II transcription elongation elucidated by kinetic network models. Curr Opin Struct Biol 2018; 49:54-62. [PMID: 29414512 DOI: 10.1016/j.sbi.2018.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/22/2017] [Accepted: 01/02/2018] [Indexed: 12/30/2022]
Abstract
Transcription elongation cycle (TEC) of RNA polymerase II (Pol II) is a process of adding a nucleoside triphosphate to the growing messenger RNA chain. Due to the long timescale events in Pol II TEC, an advanced computational technique, such as Markov State Model (MSM), is needed to provide atomistic mechanism and reaction rates. The combination of MSM and experimental results can be used to build a kinetic network model (KNM) of the whole TEC. This review provides a brief protocol to build MSM and KNM of the whole TEC, along with the latest findings of MSM and other computational studies of Pol II TEC. Lastly, we offer a perspective on potentially using a sequence dependent KNM to predict genome-wide transcription error.
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Affiliation(s)
- Ilona Christy Unarta
- Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, Hong Kong
| | - Lizhe Zhu
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, Hong Kong; Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Carmen Ka Man Tse
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, Hong Kong; Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Peter Pak-Hang Cheung
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, Hong Kong
| | - Jin Yu
- Beijing Computational Science Research Center, Beijing 100084, China
| | - Xuhui Huang
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, Hong Kong; Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; HKUST-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.
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5
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Mellenius H, Ehrenberg M. Transcriptional accuracy modeling suggests two-step proofreading by RNA polymerase. Nucleic Acids Res 2017; 45:11582-11593. [PMID: 29036494 PMCID: PMC5714138 DOI: 10.1093/nar/gkx849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/10/2017] [Accepted: 09/22/2017] [Indexed: 01/01/2023] Open
Abstract
We suggest a novel two-step proofreading mechanism with two sequential rounds of proofreading selection in mRNA transcription. It is based on the previous experimental observations that the proofreading RNA polymerase cleaves off transcript fragments of at least 2 nt and that transcript elongation after a nucleotide misincorporation is anomalously slow. Taking these results into account, we extend the description of the accuracy of template guided nucleotide selection beyond previous models of RNA polymerase-dependent DNA transcription. The model derives the accuracy of initial and proofreading base selection from experimentally estimated nearest-neighbor parameters. It is also used to estimate the small accuracy enhancement of polymerase revisiting of previous positions following transcript cleavage.
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Affiliation(s)
- Harriet Mellenius
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 752 37, Sweden
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 752 37, Sweden
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Zhang J, Ieong KW, Mellenius H, Ehrenberg M. Proofreading neutralizes potential error hotspots in genetic code translation by transfer RNAs. RNA (NEW YORK, N.Y.) 2016; 22:896-904. [PMID: 27090284 PMCID: PMC4878615 DOI: 10.1261/rna.055632.115] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/07/2016] [Indexed: 06/05/2023]
Abstract
The ribosome uses initial and proofreading selection of aminoacyl-tRNAs for accurate protein synthesis. Anomalously high initial misreading in vitro of near-cognate codons by tRNA(His) and tRNA(Glu) suggested potential error hotspots in protein synthesis, but in vivo data suggested their partial neutralization. To clarify the role of proofreading in this error reduction, we varied the Mg(2+) ion concentration to calibrate the total accuracy of our cell-free system to that in the living Escherichia coli cell. We found the total accuracy of tRNA selection in our system to vary by five orders of magnitude depending on tRNA identity, type of mismatch, and mismatched codon position. Proofreading and initial selection were positively correlated at high, but uncorrelated at low initial selection, suggesting hyperactivated proofreading as a means to neutralize potentially disastrous initial selection errors.
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Affiliation(s)
- Jingji Zhang
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Ka-Weng Ieong
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Harriet Mellenius
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
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Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome. Proc Natl Acad Sci U S A 2015. [PMID: 26195797 DOI: 10.1073/pnas.1506823112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We used a cell-free system with pure Escherichia coli components to study initial codon selection of aminoacyl-tRNAs in ternary complex with elongation factor Tu and GTP on messenger RNA-programmed ribosomes. We took advantage of the universal rate-accuracy trade-off for all enzymatic selections to determine how the efficiency of initial codon readings decreased linearly toward zero as the accuracy of discrimination against near-cognate and wobble codon readings increased toward the maximal asymptote, the d value. We report data on the rate-accuracy variation for 7 cognate, 7 wobble, and 56 near-cognate codon readings comprising about 15% of the genetic code. Their d values varied about 400-fold in the 200-80,000 range depending on type of mismatch, mismatch position in the codon, and tRNA isoacceptor type. We identified error hot spots (d = 200) for U:G misreading in second and U:U or G:A misreading in third codon position by His-tRNA(His) and, as also seen in vivo, Glu-tRNA(Glu). We suggest that the proofreading mechanism has evolved to attenuate error hot spots in initial selection such as those found here.
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