1
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Watanabe S, Nsofor CA, Thitiananpakorn K, Tan XE, Aiba Y, Takenouchi R, Kiga K, Sasahara T, Miyanaga K, Veeranarayanan S, Shimamori Y, Lian AYS, Nguyen TM, Nguyen HM, Alessa O, Kumwenda GP, Jayathilake S, Revilleza JEC, Baranwal P, Nishikawa Y, Li FY, Kawaguchi T, Sankaranarayanan S, Arbaah M, Zhang Y, Maniruzzaman, Liu Y, Sarah H, Li J, Sugano T, Ho TMD, Batbold A, Nayanjin T, Cui L. Metabolic remodeling by RNA polymerase gene mutations is associated with reduced β-lactam susceptibility in oxacillin-susceptible MRSA. mBio 2024; 15:e0033924. [PMID: 38988221 PMCID: PMC11237739 DOI: 10.1128/mbio.00339-24] [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: 02/01/2024] [Accepted: 03/27/2024] [Indexed: 07/12/2024] Open
Abstract
The emergence of oxacillin-susceptible methicillin-resistant Staphylococcus aureus (OS-MRSA) has imposed further challenges to the clinical management of MRSA infections. When exposed to β-lactam antibiotics, these strains can easily acquire reduced β-lactam susceptibility through chromosomal mutations, including those in RNA polymerase (RNAP) genes such as rpoBC, which may then lead to treatment failure. Despite the increasing prevalence of such strains and the apparent challenges they pose for diagnosis and treatment, there is limited information available on the actual mechanisms underlying such chromosomal mutation-related transitions to reduced β-lactam susceptibility, as it does not directly associate with the expression of mecA. This study investigated the cellular physiology and metabolism of six missense mutants with reduced oxacillin susceptibility, each carrying respective mutations on RpoBH929P, RpoBQ645H, RpoCG950R, RpoCG498D, RpiAA64E, and FruBA211E, using capillary electrophoresis-mass spectrometry-based metabolomics analysis. Our results showed that rpoBC mutations caused RNAP transcription dysfunction, leading to an intracellular accumulation of ribonucleotides. These mutations also led to the accumulation of UDP-Glc/Gal and UDP-GlcNAc, which are precursors of UTP-associated peptidoglycan and wall teichoic acid. Excessive amounts of building blocks then contributed to the cell wall thickening of mutant strains, as observed in transmission electron microscopy, and ultimately resulted in decreased susceptibility to β-lactam in OS-MRSA. IMPORTANCE The emergence of oxacillin-susceptible methicillin-resistant Staphylococcus aureus (OS-MRSA) strains has created new challenges for treating MRSA infections. These strains can become resistant to β-lactam antibiotics through chromosomal mutations, including those in the RNA polymerase (RNAP) genes such as rpoBC, leading to treatment failure. This study investigated the mechanisms underlying reduced β-lactam susceptibility in four rpoBC mutants of OS-MRSA. The results showed that rpoBC mutations caused RNAP transcription dysfunction, leading to an intracellular accumulation of ribonucleotides and precursors of peptidoglycan as well as wall teichoic acid. This, in turn, caused thickening of the cell wall and ultimately resulted in decreased susceptibility to β-lactam in OS-MRSA. These findings provide insights into the mechanisms of antibiotic resistance in OS-MRSA and highlight the importance of continued research in developing effective treatments to combat antibiotic resistance.
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Affiliation(s)
- Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Chijioke A Nsofor
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
- Department of Biotechnology, School of Biological Sciences, Federal University of Technology Owerri Nigeria, Owerri, Nigeria
| | - Kanate Thitiananpakorn
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Yoshifumi Aiba
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Remi Takenouchi
- School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Kotaro Kiga
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Teppei Sasahara
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Kazuhiko Miyanaga
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Srivani Veeranarayanan
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Yuzuki Shimamori
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Adeline Yeo Syin Lian
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Thuy Minh Nguyen
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Huong Minh Nguyen
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Ola Alessa
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | | | - Sarangi Jayathilake
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | | | - Priyanka Baranwal
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Yutaro Nishikawa
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Feng-Yu Li
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Tomofumi Kawaguchi
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Sowmiya Sankaranarayanan
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Mahmoud Arbaah
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Yuancheng Zhang
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Maniruzzaman
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Yi Liu
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Hossain Sarah
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Junjie Li
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Takashi Sugano
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Thi My Duyen Ho
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Anujin Batbold
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Tergel Nayanjin
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
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2
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Szekely O, Rangadurai AK, Gu S, Manghrani A, Guseva S, Al-Hashimi HM. NMR measurements of transient low-populated tautomeric and anionic Watson-Crick-like G·T/U in RNA:DNA hybrids: implications for the fidelity of transcription and CRISPR/Cas9 gene editing. Nucleic Acids Res 2024; 52:2672-2685. [PMID: 38281263 PMCID: PMC10954477 DOI: 10.1093/nar/gkae027] [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: 08/24/2023] [Revised: 01/02/2024] [Accepted: 01/17/2024] [Indexed: 01/30/2024] Open
Abstract
Many biochemical processes use the Watson-Crick geometry to distinguish correct from incorrect base pairing. However, on rare occasions, mismatches such as G·T/U can transiently adopt Watson-Crick-like conformations through tautomerization or ionization of the bases, giving rise to replicative and translational errors. The propensities to form Watson-Crick-like mismatches in RNA:DNA hybrids remain unknown, making it unclear whether they can also contribute to errors during processes such as transcription and CRISPR/Cas editing. Here, using NMR R1ρ experiments, we show that dG·rU and dT·rG mismatches in two RNA:DNA hybrids transiently form tautomeric (Genol·T/U $ \mathbin{\lower.3ex\hbox{$\buildrel\textstyle\rightarrow\over {\smash{\leftarrow}\vphantom{_{\vbox to.5ex{\vss}}}}$}}$ G·Tenol/Uenol) and anionic (G·T-/U-) Watson-Crick-like conformations. The tautomerization dynamics were like those measured in A-RNA and B-DNA duplexes. However, anionic dG·rU- formed with a ten-fold higher propensity relative to dT-·rG and dG·dT- and this could be attributed to the lower pKa (ΔpKa ∼0.4-0.9) of U versus T. Our findings suggest plausible roles for Watson-Crick-like G·T/U mismatches in transcriptional errors and CRISPR/Cas9 off-target gene editing, uncover a crucial difference between the chemical dynamics of G·U versus G·T, and indicate that anionic Watson-Crick-like G·U- could play a significant role evading Watson-Crick fidelity checkpoints in RNA:DNA hybrids and RNA duplexes.
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Affiliation(s)
- Or Szekely
- Department of Biology, Duke University, Durham, NC 27710, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27710, USA
| | | | - Stephanie Gu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, NY, NY 10032, USA
| | - Akanksha Manghrani
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, NY, NY 10032, USA
| | - Serafima Guseva
- Department of Biochemistry and Molecular Biophysics, Columbia University, NY, NY 10032, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, NY, NY 10032, USA
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3
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Bose D, Singh RK, Robertson ES. KSHV-encoded LANA bypasses transcriptional block through the stabilization of RNA Pol II in hypoxia. mBio 2024; 15:e0277423. [PMID: 38095447 PMCID: PMC10790784 DOI: 10.1128/mbio.02774-23] [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: 10/13/2023] [Accepted: 11/07/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Hypoxia can induce the reactivation of Kaposi sarcoma-associated virus (KSHV), which necessitates the synthesis of critical structural proteins. Despite the unfavorable energetic conditions of hypoxia, KSHV utilizes mechanisms to prevent the degradation of essential cellular machinery required for successful reactivation. Our study provides new insights on strategies employed by KSHV-infected cells to maintain steady-state transcription by overcoming hypoxia-mediated metabolic stress to enable successful reactivation. Our discovery that the interaction of latency-associated nuclear antigen with HIF1α and NEDD4 inhibits its polyubiquitination activity, which blocks the degradation of RNA Pol II during hypoxia, is a significant contribution to our understanding of KSHV biology. This newfound knowledge provides new leads in the development of novel therapies for KSHV-associated diseases.
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Affiliation(s)
- Dipayan Bose
- Tumor Virology Program, Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rajnish Kumar Singh
- Tumor Virology Program, Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Erle S. Robertson
- Tumor Virology Program, Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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4
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Betancurt-Anzola L, Martínez-Carranza M, Delarue M, Zatopek KM, Gardner AF, Sauguet L. Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases. Nat Commun 2023; 14:8306. [PMID: 38097591 PMCID: PMC10721889 DOI: 10.1038/s41467-023-44125-x] [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: 08/09/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Replicative DNA polymerases duplicate entire genomes at high fidelity. This feature is shared among the three domains of life and is facilitated by their dual polymerase and exonuclease activities. Family D replicative DNA polymerases (PolD), found exclusively in Archaea, contain an unusual RNA polymerase-like catalytic core, and a unique Mre11-like proofreading active site. Here, we present cryo-EM structures of PolD trapped in a proofreading mode, revealing an unanticipated correction mechanism that extends the repertoire of protein domains known to be involved in DNA proofreading. Based on our experimental structures, mutants of PolD were designed and their contribution to mismatch bypass and exonuclease kinetics was determined. This study sheds light on the convergent evolution of structurally distinct families of DNA polymerases, and the domain acquisition and exchange mechanism that occurred during the evolution of the replisome in the three domains of life.
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Affiliation(s)
- Leonardo Betancurt-Anzola
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA
- New England Biolabs France, 5 Rue Henri Auguste Desbruères, 91000, Évry-Courcouronnes, France
- Sorbonne Université, Collège Doctoral, ED 515, Paris, France
| | - Markel Martínez-Carranza
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Marc Delarue
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Kelly M Zatopek
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA.
| | - Andrew F Gardner
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA.
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France.
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5
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Szekely O, Rangadurai AK, Gu S, Manghrani A, Guseva S, Al-Hashimi HM. NMR measurements of transient low-populated tautomeric and anionic Watson-Crick-like G·T/U in RNA:DNA hybrids: Implications for the fidelity of transcription and CRISPR/Cas9 gene editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554670. [PMID: 37662220 PMCID: PMC10473728 DOI: 10.1101/2023.08.24.554670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Many biochemical processes use the Watson-Crick geometry to distinguish correct from incorrect base pairing. However, on rare occasions, mismatches such as G•T/U can transiently adopt Watson-Crick-like conformations through tautomerization or ionization of the bases, giving rise to replicative and translational errors. The propensities to form Watson-Crick-like mismatches in RNA:DNA hybrids remain unknown, making it unclear whether they can also contribute to errors during processes such as transcription and CRISPR/Cas editing. Here, using NMR R 1ρ experiments, we show that dG•rU and dT•rG mismatches in two RNA:DNA hybrids transiently form tautomeric (G enol •T/U ⇄G•T enol /U enol ) and anionic (G•T - /U - ) Watson-Crick-like conformations. The tautomerization dynamics were like those measured in A-RNA and B-DNA duplexes. However, anionic dG•rU - formed with a ten-fold higher propensity relative to dT - •rG and dG•dT - and this could be attributed to the lower pK a (Δ pK a ∼0.4-0.9) of U versus T. Our findings suggest plausible roles for Watson-Crick-like G•T/U mismatches in transcriptional errors and CRISPR/Cas9 off-target gene editing, uncover a crucial difference between the chemical dynamics of G•U versus G•T, and indicate that anionic Watson-Crick-like G•U - could play a significant role evading Watson-Crick fidelity checkpoints in RNA:DNA hybrids and RNA duplexes.
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6
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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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7
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Chung C, Verheijen BM, Navapanich Z, McGann EG, Shemtov S, Lai GJ, Arora P, Towheed A, Haroon S, Holczbauer A, Chang S, Manojlovic Z, Simpson S, Thomas KW, Kaplan C, van Hasselt P, Timmers M, Erie D, Chen L, Gout JF, Vermulst M. Evolutionary conservation of the fidelity of transcription. Nat Commun 2023; 14:1547. [PMID: 36941254 PMCID: PMC10027832 DOI: 10.1038/s41467-023-36525-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/03/2023] [Indexed: 03/23/2023] Open
Abstract
Accurate transcription is required for the faithful expression of genetic information. However, relatively little is known about the molecular mechanisms that control the fidelity of transcription, or the conservation of these mechanisms across the tree of life. To address these issues, we measured the error rate of transcription in five organisms of increasing complexity and found that the error rate of RNA polymerase II ranges from 2.9 × 10-6 ± 1.9 × 10-7/bp in yeast to 4.0 × 10-6 ± 5.2 × 10-7/bp in worms, 5.69 × 10-6 ± 8.2 × 10-7/bp in flies, 4.9 × 10-6 ± 3.6 × 10-7/bp in mouse cells and 4.7 × 10-6 ± 9.9 × 10-8/bp in human cells. These error rates were modified by various factors including aging, mutagen treatment and gene modifications. For example, the deletion or modification of several related genes increased the error rate substantially in both yeast and human cells. This research highlights the evolutionary conservation of factors that control the fidelity of transcription. Additionally, these experiments provide a reasonable estimate of the error rate of transcription in human cells and identify disease alleles in a subunit of RNA polymerase II that display error-prone transcription. Finally, we provide evidence suggesting that the error rate and spectrum of transcription co-evolved with our genetic code.
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Affiliation(s)
- Claire Chung
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Bert M Verheijen
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Zoe Navapanich
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Eric G McGann
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Sarah Shemtov
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Guan-Ju Lai
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Payal Arora
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Atif Towheed
- Children's hospital of Philadelphia, Center for Mitochondrial and Epigenomic Medicine, Philadelphia, PA, USA
| | - Suraiya Haroon
- Children's hospital of Philadelphia, Center for Mitochondrial and Epigenomic Medicine, Philadelphia, PA, USA
| | - Agnes Holczbauer
- Children's hospital of Philadelphia, Center for Mitochondrial and Epigenomic Medicine, Philadelphia, PA, USA
| | - Sharon Chang
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zarko Manojlovic
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephen Simpson
- College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH, USA
| | - Kelley W Thomas
- College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH, USA
| | - Craig Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter van Hasselt
- Department of Metabolic Disease, University of Utrecht, Utrecht, the Netherlands
| | - Marc Timmers
- Department of Urology, Medical Center - University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dorothy Erie
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Lin Chen
- Department of Molecular and Cellular Biology, University of Southern California, Los Angeles, CA, USA
| | - Jean-Franćois Gout
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Marc Vermulst
- School of Gerontology, University of Southern California, Los Angeles, CA, USA.
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8
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Wee LM, Tong AB, Florez Ariza AJ, Cañari-Chumpitaz C, Grob P, Nogales E, Bustamante CJ. A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery. Cell 2023; 186:1244-1262.e34. [PMID: 36931247 PMCID: PMC10135430 DOI: 10.1016/j.cell.2023.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 03/18/2023]
Abstract
In prokaryotes, translation can occur on mRNA that is being transcribed in a process called coupling. How the ribosome affects the RNA polymerase (RNAP) during coupling is not well understood. Here, we reconstituted the E. coli coupling system and demonstrated that the ribosome can prevent pausing and termination of RNAP and double the overall transcription rate at the expense of fidelity. Moreover, we monitored single RNAPs coupled to ribosomes and show that coupling increases the pause-free velocity of the polymerase and that a mechanical assisting force is sufficient to explain the majority of the effects of coupling. Also, by cryo-EM, we observed that RNAPs with a terminal mismatch adopt a backtracked conformation, while a coupled ribosome allosterically induces these polymerases toward a catalytically active anti-swiveled state. Finally, we demonstrate that prolonged RNAP pausing is detrimental to cell viability, which could be prevented by polymerase reactivation through a coupled ribosome.
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Affiliation(s)
- Liang Meng Wee
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alexander B Tong
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Alfredo Jose Florez Ariza
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Cristhian Cañari-Chumpitaz
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Patricia Grob
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Eva Nogales
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Carlos J Bustamante
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Department of Physics, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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9
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Li X, Chou T. Stochastic dynamics and ribosome-RNAP interactions in transcription-translation coupling. Biophys J 2023; 122:254-266. [PMID: 36199250 PMCID: PMC9822797 DOI: 10.1016/j.bpj.2022.09.041] [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: 06/23/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 01/11/2023] Open
Abstract
Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such transcription-translation coupling (TTC) has been evoked as a mechanism that speeds up the overall process, provides protection against premature termination, and/or regulates the timing of transcript and protein formation. What molecular mechanisms underlie ribosome-RNAP coupling and how they can perform these functions have not been explicitly modeled. We develop and analyze a continuous-time stochastic model that incorporates ribosome and RNAP elongation rates, initiation and termination rates, RNAP pausing, and direct ribosome and RNAP interactions (exclusion and binding). Our model predicts how distributions of delay times depend on these molecular features of transcription and translation. We also propose additional measures for TTC: a direct ribosome-RNAP binding probability and the fraction of time the translation-transcription process is "protected" from attack by transcription-terminating proteins. These metrics quantify different aspects of TTC and differentially depend on parameters of known molecular processes. We use our metrics to reveal how and when our model can exhibit either acceleration or deceleration of transcription, as well as protection from termination. Our detailed mechanistic model provides a basis for designing new experimental assays that can better elucidate the mechanisms of TTC.
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Affiliation(s)
- Xiangting Li
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California
| | - Tom Chou
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California; Department of Mathematics, University of California, Los Angeles, Los Angeles, California.
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10
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Luo X, Wang X, Yao Y, Gao X, Zhang L. Unveiling the "Template-Dependent" Inhibition on the Viral Transcription of SARS-CoV-2. J Phys Chem Lett 2022; 13:7197-7205. [PMID: 35912566 PMCID: PMC9363016 DOI: 10.1021/acs.jpclett.2c01314] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Remdesivir is one nucleotide analogue prodrug capable to terminate RNA synthesis in SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) by two distinct mechanisms. Although the "delayed chain termination" mechanism has been extensively investigated, the "template-dependent" inhibitory mechanism remains elusive. In this study, we have demonstrated that remdesivir embedded in the template strand seldom directly disrupted the complementary NTP incorporation at the active site. Instead, the translocation of remdesivir from the +2 to the +1 site was hindered due to the steric clash with V557. Moreover, we have elucidated the molecular mechanism characterizing the drug resistance upon V557L mutation. Overall, our studies have provided valuable insight into the "template-dependent" inhibitory mechanism exerted by remdesivir on SARS-CoV-2 RdRp and paved venues for an alternative antiviral strategy for the COVID-19 pandemic. As the "template-dependent" inhibition occurs across diverse viral RdRps, our findings may also shed light on a common acting mechanism of inhibitors.
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Affiliation(s)
- Xueying Luo
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, 350002 Fuzhou, Fujian, China
- University
of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xiaowei Wang
- Department
of Chemical and Biological Engineering, Department of Mathematics, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Yuan Yao
- Department
of Mathematics, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Xin Gao
- Computer
Science Program, Computer, Electrical and Mathematical Sciences and
Engineering (CEMSE) Division, King Abdullah
University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- KAUST
Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Lu Zhang
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, 350002 Fuzhou, Fujian, China
- University
of Chinese Academy of Sciences, 100049 Beijing, China
- Fujian Provincial
Key Laboratory of Theoretical and Computational Chemistry, 361005 Fujian, China
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11
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Vatandaslar H. A Systematic Study on the Optimal Nucleotide Analogue Concentration and Rate Limiting Nucleotide of the SARS-CoV-2 RNA-Dependent RNA Polymerase. Int J Mol Sci 2022; 23:ijms23158302. [PMID: 35955442 PMCID: PMC9369030 DOI: 10.3390/ijms23158302] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/23/2022] [Accepted: 07/24/2022] [Indexed: 02/01/2023] Open
Abstract
The current COVID-19 pandemic has highlighted the necessity of more efficient antiviral compounds. The antiviral efficacy of adenosine-based analogs, the main repurposed drugs for SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) inhibition, is mainly assessed through in vitro or cell-free polymerization assays, under arbitrary conditions that do not reflect the physiological environment. We show that SARS-CoV-2 RdRp inhibition efficiency of remdesivir and cordycepin, two common adenosine analogs, is influenced by endogenous adenosine level, and that the current clinically approved concentrations for COVID-19 treatment are suboptimal for effective RdRp inhibition. Furthermore, we identified GTP as the rate-limiting nucleotide of SARS-CoV-2 replication. Our results demonstrate that nucleotide sensitivity of the RdRp complex and competition of nucleoside analog drugs against endogenous concentrations of nucleotides are crucial elements to be considered when designing new SARS-CoV-2 antiviral compounds.
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Affiliation(s)
- Hasan Vatandaslar
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
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12
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Miropolskaya N, Petushkov I, Esyunina D, Kulbachinskiy A. Suppressor mutations in Escherichia coli RNA polymerase alter transcription initiation but do not affect translesion RNA synthesis in vitro. J Biol Chem 2022; 298:102099. [PMID: 35667439 PMCID: PMC9254596 DOI: 10.1016/j.jbc.2022.102099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/19/2022] Open
Abstract
Bacterial RNA polymerase (RNAP) coordinates transcription with DNA repair and replication. Many RNAP mutations have pleiotropic phenotypes with profound effects on transcription-coupled processes. One class of RNAP mutations (rpo*) has been shown to suppress mutations in regulatory factors responsible for changes in gene expression during stationary phase or starvation, as well as in factors involved in the restoration of replication forks after DNA damage. These mutations were suggested to affect the ability of RNAP to transcribe damaged DNA and to decrease the stability of transcription complexes, thus facilitating their dislodging during DNA replication and repair, although this was not explicitly demonstrated. Here, we obtained nine mutations of this class located around the DNA/RNA binding cleft of E. coli RNAP and analyzed their transcription properties in vitro. We found that these mutations decreased promoter complex stability to varying degrees and all decreased the activity of rRNA promoters. However, they did not have strong effects on elongation complex stability. Some mutations were shown to stimulate transcriptional pauses or decrease intrinsic RNA cleavage by RNAP, but none altered the ability of RNAP to transcribe DNA templates containing damaged nucleotides. Thus, we conclude that the suppressor phenotypes of the mutations are unlikely to result from direct effects on DNA lesion recognition by RNAP but may be primarily explained by changes in transcription initiation. Further analysis of the effects of these mutations on the genomic distribution of RNAP and its interactions with regulatory factors will be essential for understanding their diverse phenotypes in vivo.
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Affiliation(s)
- Nataliya Miropolskaya
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Ivan Petushkov
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia.
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia.
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13
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Abstract
Biochemistry and molecular biology rely on the recognition of structural complementarity between molecules. Molecular interactions must be both quickly reversible, i.e., tenuous, and specific. How the cell reconciles these conflicting demands is the subject of this article. The problem and its theoretical solution are discussed within the wider theoretical context of the thermodynamics of stochastic processes (stochastic thermodynamics). The solution-an irreversible reaction cycle that decreases internal error at the expense of entropy export into the environment-is shown to be widely employed by biological processes that transmit genetic and regulatory information. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Hinrich Boeger
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California;
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14
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RNA polymerase I (Pol I) lobe-binding subunit Rpa12.2 promotes RNA cleavage and proofreading. J Biol Chem 2022; 298:101862. [PMID: 35341765 PMCID: PMC9108883 DOI: 10.1016/j.jbc.2022.101862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/13/2022] [Accepted: 03/17/2022] [Indexed: 11/23/2022] Open
Abstract
Elongating nuclear RNA polymerases (Pols) frequently pause, backtrack, and are then reactivated by endonucleolytic cleavage. Pol backtracking and RNA cleavage are also crucial for proofreading, which contributes to transcription fidelity. RNA polymerase I (Pol I) of the yeast Saccharomyces cerevisiae synthesizes exclusively 35S rRNA, the precursor transcript of mature ribosomal 5.8S, 18S, and 25S rRNA. Pol I contains the specific heterodimeric subunits Rpa34.5/49 and subunit Rpa12.2, which have been implicated in RNA cleavage and elongation activity, respectively. These subunits are associated with the Pol I lobe structure and encompass different structural domains, but the contribution of these domains to RNA elongation is unclear. Here, we used Pol I mutants or reconstituted Pol I enzymes to study the effects of these subunits and/or their distinct domains on RNA cleavage, backtracking, and transcription fidelity in defined in vitro systems. Our findings suggest that the presence of the intact C-terminal domain of Rpa12.2 is sufficient to support the cleavage reaction, but that the N-terminal domains of Rpa12.2 and the heterodimer facilitate backtracking and RNA cleavage. Since both N-terminal and C-terminal domains of Rpa12.2 were also required to faithfully incorporate NTPs in the growing RNA chain, efficient backtracking and RNA cleavage might be a prerequisite for transcription fidelity. We propose that RNA Pols containing efficient RNA cleavage activity are able to add and remove nucleotides until the matching nucleotide supports RNA chain elongation, whereas cleavage-deficient enzymes can escape this proofreading process by incorporating incorrect nucleotides.
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15
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Yu Q, Kolomeisky AB, Igoshin OA. The energy cost and optimal design of networks for biological discrimination. J R Soc Interface 2022; 19:20210883. [PMID: 35259959 PMCID: PMC8905179 DOI: 10.1098/rsif.2021.0883] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many biological processes discriminate between correct and incorrect substrates through the kinetic proofreading mechanism that enables lower error at the cost of higher energy dissipation. Elucidating physico-chemical constraints for global minimization of dissipation and error is important for understanding enzyme evolution. Here, we identify theoretically a fundamental error-cost bound that tightly constrains the performance of proofreading networks under any parameter variations preserving the rate discrimination between substrates. The bound is kinetically controlled, i.e. completely determined by the difference between the transition state energies on the underlying free energy landscape. The importance of the bound is analysed for three biological processes. DNA replication by T7 DNA polymerase is shown to be nearly optimized, i.e. its kinetic parameters place it in the immediate proximity of the error-cost bound. The isoleucyl-tRNA synthetase (IleRS) of E. coli also operates close to the bound, but further optimization is prevented by the need for reaction speed. In contrast, E. coli ribosome operates in a high-dissipation regime, potentially in order to speed up protein production. Together, these findings establish a fundamental error-dissipation relation in biological proofreading networks and provide a theoretical framework for studying error-dissipation trade-off in other systems with biological discrimination.
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Affiliation(s)
- Qiwei Yu
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Anatoly B Kolomeisky
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.,Department of Chemistry, Rice University, Houston, TX 77005, USA.,Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX 77005, USA.,Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA
| | - Oleg A Igoshin
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.,Department of Chemistry, Rice University, Houston, TX 77005, USA.,Department of Bioengineering, Rice University, Houston, TX 77005, USA.,Department of Biosciences, Rice University, Houston, TX 77005, USA
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16
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Abstract
RNA polymerase III (Pol III) is a large multisubunit complex conserved in all eukaryotes that plays an essential role in producing a variety of short non-coding RNAs, such as tRNA, 5S rRNA and U6 snRNA transcripts. Pol III comprises of 17 subunits in both yeast and human with a 10-subunit core and seven peripheral subunits. Because of its size and complexity, Pol III has posed a formidable challenge to structural biologists. The first atomic cryogenic electron microscopy structure of yeast Pol III leading to the canonical view was reported in 2015. Within the last few years, the optimization of endogenous extract and purification procedure and the technical and methodological advances in cryogenic electron microscopy, together allow us to have a first look at the unprecedented details of human Pol III organization. Here, we look back on the structural studies of human Pol III and discuss them in the light of our current understanding of its role in eukaryotic transcription.
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Affiliation(s)
- Qianmin Wang
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Precision Medicine, Shanghai, China
| | - Ming Lei
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Precision Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Wu
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Precision Medicine, Shanghai, China
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17
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Zuo X, Chou T. Density- and elongation speed-dependent error correction in RNA polymerization. Phys Biol 2021; 19. [PMID: 34937012 DOI: 10.1088/1478-3975/ac45e2] [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: 03/08/2021] [Accepted: 12/22/2021] [Indexed: 11/11/2022]
Abstract
Backtracking of RNA polymerase (RNAP) is an important pausing mechanism during DNA transcription that is part of the error correction process that enhances transcription fidelity. We model the backtracking mechanism of RNA polymerase, which usually happens when the polymerase tries to incorporate a noncognate or "mismatched" nucleotide triphosphate. Previous models have made simplifying assumptions such as neglecting the trailing polymerase behind the backtracking polymerase or assuming that the trailing polymerase is stationary. We derive exact analytic solutions of a stochastic model that includes locally interacting RNAPs by explicitly showing how a trailing RNAP influences the probability that an error is corrected or incorporated by the leading backtracking RNAP. We also provide two related methods for computing the mean times for error correction and incorporation given an initial local RNAP configuration. Using these results, we propose an effective interacting-RNAP lattice that can be readily simulated.
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Affiliation(s)
- Xinzhe Zuo
- Department of Mathematics, University of California - Los Angeles, Los Angeles, CA 90095-1555, USA, Los Angeles, California, 90095, UNITED STATES
| | - Tom Chou
- Department of Mathematics, University of California - Los Angeles, Los Angeles, CA 90095-1555, USA, Los Angeles, California, 90095, UNITED STATES
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18
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Long C, Romero ME, La Rocco D, Yu J. Dissecting nucleotide selectivity in viral RNA polymerases. Comput Struct Biotechnol J 2021; 19:3339-3348. [PMID: 34104356 PMCID: PMC8175102 DOI: 10.1016/j.csbj.2021.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 01/18/2023] Open
Abstract
Designing antiviral therapeutics is of great concern per current pandemics caused by novel coronavirus or SARS-CoV-2. The core polymerase enzyme in the viral replication/transcription machinery is generally conserved and serves well for drug target. In this work we briefly review structural biology and computational clues on representative single-subunit viral polymerases that are more or less connected with SARS-CoV-2 RNA dependent RNA polymerase (RdRp), in particular, to elucidate how nucleotide substrates and potential drug analogs are selected in the viral genome synthesis. To do that, we first survey two well studied RdRps from Polio virus and hepatitis C virus in regard to structural motifs and key residues that have been identified for the nucleotide selectivity. Then we focus on related structural and biochemical characteristics discovered for the SARS-CoV-2 RdRp. To further compare, we summarize what we have learned computationally from phage T7 RNA polymerase (RNAP) on its stepwise nucleotide selectivity, and extend discussion to a structurally similar human mitochondria RNAP, which deserves special attention as it cannot be adversely affected by antiviral treatments. We also include viral phi29 DNA polymerase for comparison, which has both helicase and proofreading activities on top of nucleotide selectivity for replication fidelity control. The helicase and proofreading functions are achieved by protein components in addition to RdRp in the coronavirus replication-transcription machine, with the proofreading strategy important for the fidelity control in synthesizing a comparatively large viral genome.
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Affiliation(s)
- Chunhong Long
- School of Science, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | | | - Daniel La Rocco
- Department of Physics, University of California, Berkeley, CA 94720, USA
| | - Jin Yu
- Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92697, USA
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19
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Song Y, Hyeon C. Thermodynamic uncertainty relation to assess biological processes. J Chem Phys 2021; 154:130901. [PMID: 33832251 DOI: 10.1063/5.0043671] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We review the trade-offs between speed, fluctuations, and thermodynamic cost involved with biological processes in nonequilibrium states and discuss how optimal these processes are in light of the universal bound set by the thermodynamic uncertainty relation (TUR). The values of the uncertainty product Q of TUR, which can be used as a measure of the precision of enzymatic processes realized for a given thermodynamic cost, are suboptimal when the substrate concentration is at the Michaelis constant, and some of the key biological processes are found to work around this condition. We illustrate the utility of Q in assessing how close the molecular motors and biomass producing machineries are to the TUR bound, and for the cases of biomass production (or biological copying processes), we discuss how their optimality quantified in terms of Q is balanced with the error rate in the information transfer process. We also touch upon the trade-offs in other error-minimizing processes in biology, such as gene regulation and chaperone-assisted protein folding. A spectrum of Q recapitulating the biological processes surveyed here provides glimpses into how biological systems are evolved to optimize and balance the conflicting functional requirements.
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Affiliation(s)
- Yonghyun Song
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, South Korea
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20
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Handa S, Reyna A, Wiryaman T, Ghosh P. Determinants of adenine-mutagenesis in diversity-generating retroelements. Nucleic Acids Res 2021; 49:1033-1045. [PMID: 33367793 PMCID: PMC7826257 DOI: 10.1093/nar/gkaa1240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 02/01/2023] Open
Abstract
Diversity-generating retroelements (DGRs) vary protein sequences to the greatest extent known in the natural world. These elements are encoded by constituents of the human microbiome and the microbial ‘dark matter’. Variation occurs through adenine-mutagenesis, in which genetic information in RNA is reverse transcribed faithfully to cDNA for all template bases but adenine. We investigated the determinants of adenine-mutagenesis in the prototypical Bordetella bacteriophage DGR through an in vitro system composed of the reverse transcriptase bRT, Avd protein, and a specific RNA. We found that the catalytic efficiency for correct incorporation during reverse transcription by the bRT-Avd complex was strikingly low for all template bases, with the lowest occurring for adenine. Misincorporation across a template adenine was only somewhat lower in efficiency than correct incorporation. We found that the C6, but not the N1 or C2, purine substituent was a key determinant of adenine-mutagenesis. bRT-Avd was insensitive to the C6 amine of adenine but recognized the C6 carbonyl of guanine. We also identified two bRT amino acids predicted to nonspecifically contact incoming dNTPs, R74 and I181, as promoters of adenine-mutagenesis. Our results suggest that the overall low catalytic efficiency of bRT-Avd is intimately tied to its ability to carry out adenine-mutagenesis.
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Affiliation(s)
- Sumit Handa
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
| | - Andres Reyna
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
| | - Timothy Wiryaman
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
| | - Partho Ghosh
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
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21
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Galstyan V, Husain K, Xiao F, Murugan A, Phillips R. Proofreading through spatial gradients. eLife 2020; 9:60415. [PMID: 33357378 PMCID: PMC7813546 DOI: 10.7554/elife.60415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/24/2020] [Indexed: 12/01/2022] Open
Abstract
Key enzymatic processes use the nonequilibrium error correction mechanism called kinetic proofreading to enhance their specificity. The applicability of traditional proofreading schemes, however, is limited because they typically require dedicated structural features in the enzyme, such as a nucleotide hydrolysis site or multiple intermediate conformations. Here, we explore an alternative conceptual mechanism that achieves error correction by having substrate binding and subsequent product formation occur at distinct physical locations. The time taken by the enzyme–substrate complex to diffuse from one location to another is leveraged to discard wrong substrates. This mechanism does not have the typical structural requirements, making it easier to overlook in experiments. We discuss how the length scales of molecular gradients dictate proofreading performance, and quantify the limitations imposed by realistic diffusion and reaction rates. Our work broadens the applicability of kinetic proofreading and sets the stage for studying spatial gradients as a possible route to specificity.
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Affiliation(s)
- Vahe Galstyan
- Biochemistry and Molecular Biophysics Option, California Institute of Technology, Pasadena, United States
| | - Kabir Husain
- Department of Physics and the James Franck Institute, University of Chicago, Chicago, United States
| | - Fangzhou Xiao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Arvind Murugan
- Department of Physics and the James Franck Institute, University of Chicago, Chicago, United States
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Department of Physics, California Institute of Technology, Pasadena, United States
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22
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Andreychuk YV, Zadorsky SP, Zhuk AS, Stepchenkova EI, Inge-Vechtomov SG. Relationship between Type I and Type II Template Processes: Amyloids and Genome Stability. Mol Biol 2020. [DOI: 10.1134/s0026893320050027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Abstract
Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.
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Affiliation(s)
- Sara Osman
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
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24
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Cheung PPH, Jiang B, Booth GT, Chong TH, Unarta IC, Wang Y, Suarez GD, Wang J, Lis JT, Huang X. Identifying Transcription Error-Enriched Genomic Loci Using Nuclear Run-on Circular-Sequencing Coupled with Background Error Modeling. J Mol Biol 2020; 432:3933-3949. [PMID: 32325070 DOI: 10.1016/j.jmb.2020.04.011] [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: 12/07/2019] [Revised: 04/08/2020] [Accepted: 04/08/2020] [Indexed: 01/30/2023]
Abstract
RNA polymerase transcribes certain genomic loci with higher errors rates. These transcription error-enriched genomic loci (TEELs) have implications in disease. Current deep-sequencing methods cannot distinguish TEELs from post-transcriptional modifications, stochastic transcription errors, and technical noise, impeding efforts to elucidate the mechanisms linking TEELs to disease. Here, we describe background error model-coupled precision nuclear run-on circular-sequencing (EmPC-seq) to discern genomic regions enriched for transcription misincorporations. EmPC-seq innovatively combines a nuclear run-on assay for capturing nascent RNA before post-transcriptional modifications, a circular-sequencing step that sequences the same nascent RNA molecules multiple times to improve accuracy, and a statistical model for distinguishing error-enriched regions among stochastic polymerase errors. Applying EmPC-seq to the ribosomal RNA transcriptome, we show that TEELs of RNA polymerase I are not randomly distributed but clustered together, with higher error frequencies at nascent transcript 3' ends. Our study establishes a reliable method of identifying TEELs with nucleotide precision, which can help elucidate their molecular origins.
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Affiliation(s)
- Peter Pak-Hang Cheung
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China; Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Biaobin Jiang
- Division of Life Science, Department of Chemical and Biological Engineering, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong; The HKUST Jockey Club Institute for Advanced Study (IAS), The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Tin Hang Chong
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China
| | - Ilona Christy Unarta
- Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Yuqing Wang
- Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Gianmarco D Suarez
- Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Jiguang Wang
- Division of Life Science, Department of Chemical and Biological Engineering, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; The HKUST Jockey Club Institute for Advanced Study (IAS), The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Xuhui Huang
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China; Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong; Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
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25
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Kum DB, Mishra N, Vrancken B, Thibaut HJ, Wilder-Smith A, Lemey P, Neyts J, Dallmeier K. Limited evolution of the yellow fever virus 17d in a mouse infection model. Emerg Microbes Infect 2020; 8:1734-1746. [PMID: 31797751 PMCID: PMC6896426 DOI: 10.1080/22221751.2019.1694394] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
By infecting mice with the yellow fever virus vaccine strain 17D (YFV-17D; Stamaril®), the dose dependence and evolutionary consequences of neurotropic yellow fever infection was assessed. Highly susceptible AG129 mice were used to allow for a maximal/unlimited expansion of the viral populations. Infected mice uniformly developed neurotropic disease; the virus was isolated from their brains, plaque purified and sequenced. Viral RNA populations were overall rather homogenous [Shannon entropies 0−0.15]. The remaining, yet limited intra-host population diversity (0−11 nucleotide exchanges per genome) appeared to be a consequence of pre-existing clonal heterogeneities (quasispecies) of Stamaril®. In parallel, mice were infected with a molecular clone of YFV-17D which was in vivo launched from a plasmid. Such plasmid-launched YFV-17D had a further reduced and almost clonal evolution. The limited intra-host evolution during unrestricted expansion in a highly susceptible host is relevant for vaccine and drug development against flaviviruses in general. Firstly, a propensity for limited evolution even upon infection with a (very) low inoculum suggests that fractional dosing as implemented in current YF-outbreak control may pose only a limited risk of reversion to pathogenic vaccine-derived virus variants. Secondly, it also largely lowers the chance of antigenic drift and development of resistance to antivirals.
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Affiliation(s)
- Dieudonné Buh Kum
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium.,Aligos Belgium, Leuven, Belgium
| | - Niraj Mishra
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Bram Vrancken
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Annelies Wilder-Smith
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom.,Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
| | - Philippe Lemey
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
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26
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Takahashi S, Okura H, Chilka P, Ghosh S, Sugimoto N. Molecular crowding induces primer extension by RNA polymerase through base stacking beyond Watson–Crick rules. RSC Adv 2020; 10:33052-33058. [PMID: 35515060 PMCID: PMC9056655 DOI: 10.1039/d0ra06502a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 08/27/2020] [Indexed: 12/16/2022] Open
Abstract
The polymerisation of nucleic acids is essential for copying genetic information correctly to the next generations, whereas mispolymerisation could promote genetic diversity. It is possible that in the prebiotic era, polymerases might have used mispolymerisation to accelerate the diversification of genetic information. Even in the current era, polymerases of RNA viruses frequently cause mutations. In this study, primer extension under different molecular crowding conditions was measured using T7 RNA polymerase as a model for the reaction in the prebiotic world. Interestingly, molecular crowding using 20 wt% poly(ethylene glycol) 2000 preferentially promoted the primer extensions with ATP and GTP by T7 RNA polymerase, regardless of Watson–Crick base-pairing rules. This indicates that molecular crowding decreases the dielectric constants in solution, resulting in enhancement of stacking interactions between the primer and an incorporated nucleotide. These findings suggest that molecular crowding could accelerate genetic diversity in the prebiotic world and may promote transcription error of RNA viruses in the current era. Primer extension by T7 RNA polymerase showed preference of monomer through base stacking beyond Watson–Crick rules under molecular crowding condition.![]()
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Affiliation(s)
- Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe 650-0047
- Japan
| | - Hiromichi Okura
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe 650-0047
- Japan
| | - Pallavi Chilka
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe 650-0047
- Japan
| | - Saptarshi Ghosh
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe 650-0047
- Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe 650-0047
- Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST)
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27
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Abstract
Kinetic proofreading is an error correction mechanism present in the processes of the central dogma and beyond and typically requires the free energy of nucleotide hydrolysis for its operation. Though the molecular players of many biological proofreading schemes are known, our understanding of how energy consumption is managed to promote fidelity remains incomplete. In our work, we introduce an alternative conceptual scheme called "the piston model of proofreading" in which enzyme activation through hydrolysis is replaced with allosteric activation achieved through mechanical work performed by a piston on regulatory ligands. Inspired by Feynman's ratchet and pawl mechanism, we consider a mechanical engine designed to drive the piston actions powered by a lowering weight, whose function is analogous to that of ATP synthase in cells. Thanks to its mechanical design, the piston model allows us to tune the "knobs" of the driving engine and probe the graded changes and trade-offs between speed, fidelity, and energy dissipation. It provides an intuitive explanation of the conditions necessary for optimal proofreading and reveals the unexpected capability of allosteric molecules to beat the Hopfield limit of fidelity by leveraging the diversity of states available to them. The framework that we have built for the piston model can also serve as a basis for additional studies of driven biochemical systems.
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Affiliation(s)
- Vahe Galstyan
- Biochemistry and Molecular Biophysics Option , California Institute of Technology , Pasadena , California 91125 , United States
| | - Rob Phillips
- Department of Physics , California Institute of Technology , Pasadena , California 91125 , United States.,Department of Applied Physics , California Institute of Technology , Pasadena , California 91125 , United States.,Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
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28
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Czaja AJ. Examining pathogenic concepts of autoimmune hepatitis for cues to future investigations and interventions. World J Gastroenterol 2019; 25:6579-6606. [PMID: 31832000 PMCID: PMC6906207 DOI: 10.3748/wjg.v25.i45.6579] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Multiple pathogenic mechanisms have been implicated in autoimmune hepatitis, but they have not fully explained susceptibility, triggering events, and maintenance or escalation of the disease. Furthermore, they have not identified a critical defect that can be targeted. The goals of this review are to examine the diverse pathogenic mechanisms that have been considered in autoimmune hepatitis, indicate investigational opportunities to validate their contribution, and suggest interventions that might evolve to modify their impact. English abstracts were identified in PubMed by multiple search terms. Full length articles were selected for review, and secondary and tertiary bibliographies were developed. Genetic and epigenetic factors can affect susceptibility by influencing the expression of immune regulatory genes. Thymic dysfunction, possibly related to deficient production of programmed cell death protein-1, can allow autoreactive T cells to escape deletion, and alterations in the intestinal microbiome may help overcome immune tolerance and affect gender bias. Environmental factors may trigger the disease or induce epigenetic changes in gene function. Molecular mimicry, epitope spread, bystander activation, neo-antigen production, lymphocytic polyspecificity, and disturbances in immune inhibitory mechanisms may maintain or escalate the disease. Interventions that modify epigenetic effects on gene expression, alter intestinal dysbiosis, eliminate deleterious environmental factors, and target critical pathogenic mechanisms are therapeutic possibilities that might reduce risk, individualize management, and improve outcome. In conclusion, diverse pathogenic mechanisms have been implicated in autoimmune hepatitis, and they may identify a critical factor or sequence that can be validated and used to direct future management and preventive strategies.
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Affiliation(s)
- Albert J Czaja
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, United States
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29
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Kang JY, Mishanina TV, Landick R, Darst SA. Mechanisms of Transcriptional Pausing in Bacteria. J Mol Biol 2019; 431:4007-4029. [PMID: 31310765 DOI: 10.1016/j.jmb.2019.07.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 12/21/2022]
Abstract
Pausing by RNA polymerase (RNAP) during transcription regulates gene expression in all domains of life. In this review, we recap the history of transcriptional pausing discovery, summarize advances in our understanding of the underlying causes of pausing since then, and describe new insights into the pausing mechanisms and pause modulation by transcription factors gained from structural and biochemical experiments. The accumulated evidence to date suggests that upon encountering a pause signal in the nucleic-acid sequence being transcribed, RNAP rearranges into an elemental, catalytically inactive conformer unable to load NTP substrate. The conformation, and as a consequence lifetime, of an elemental paused RNAP is modulated by backtracking, nascent RNA structure, binding of transcription regulators, or a combination of these mechanisms. We conclude the review by outlining open questions and directions for future research in the field of transcriptional pausing.
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Affiliation(s)
- Jin Young Kang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejon 34141, Republic of Korea.
| | - Tatiana V Mishanina
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Seth A Darst
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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30
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Long C, E C, Da LT, Yu J. Determining selection free energetics from nucleotide pre-insertion to insertion in viral T7 RNA polymerase transcription fidelity control. Nucleic Acids Res 2019; 47:4721-4735. [PMID: 30916310 PMCID: PMC6511863 DOI: 10.1093/nar/gkz213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/10/2019] [Accepted: 03/18/2019] [Indexed: 01/01/2023] Open
Abstract
An elongation cycle of a transcribing RNA polymerase (RNAP) usually consists of multiple kinetics steps, so there exist multiple kinetic checkpoints where non-cognate nucleotides can be selected against. We conducted comprehensive free energy calculations on various nucleotide insertions for viral T7 RNAP employing all-atom molecular dynamics simulations. By comparing insertion free energy profiles between the non-cognate nucleotide species (rGTP and dATP) and a cognate one (rATP), we obtained selection free energetics from the nucleotide pre-insertion to the insertion checkpoints, and further inferred the selection energetics down to the catalytic stage. We find that the insertion of base mismatch rGTP proceeds mainly through an off-path along which both pre-insertion screening and insertion inhibition play significant roles. In comparison, the selection against dATP is found to go through an off-path pre-insertion screening along with an on-path insertion inhibition. Interestingly, we notice that two magnesium ions switch roles of leave and stay during the dATP on-path insertion. Finally, we infer that substantial selection energetic is still required to catalytically inhibit the mismatched rGTP to achieve an elongation error rate ∼10-4 or lower; while no catalytic selection seems to be further needed against dATP to obtain an error rate ∼10-2.
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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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31
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Sauguet L. The Extended "Two-Barrel" Polymerases Superfamily: Structure, Function and Evolution. J Mol Biol 2019; 431:4167-4183. [PMID: 31103775 DOI: 10.1016/j.jmb.2019.05.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 01/14/2023]
Abstract
DNA and RNA polymerases (DNAP and RNAP) play central roles in genome replication, maintenance and repair, as well as in the expression of genes through their transcription. Multisubunit RNAPs carry out transcription and are represented, without exception, in all cellular life forms as well as in nucleo-cytoplasmic DNA viruses. Since their discovery, multisubunit RNAPs have been the focus of intense structural and functional studies revealing that they all share a well-conserved active-site region called the two-barrel catalytic core. The two-barrel core hosts the polymerase active site, which is located at the interface between two double-psi β-barrel domains that contribute distinct amino acid residues to the active site in an asymmetrical fashion. Recently, sequencing and structural studies have added a surprising variety of DNA and RNA to the two-barrel superfamily, including the archaeal replicative DNAP (PolD), which extends the family to DNA-dependent DNAPs involved in replication. While all these polymerases share a minimal core that must have been present in their common ancestor, the two-barrel polymerase superfamily now encompasses a remarkable diversity of enzymes, including DNA-dependent RNAPs, RNA-dependent RNAPs, and DNA-dependent DNAPs, which participate in critical biological processes such as DNA transcription, DNA replication, and gene silencing. The present review will discuss both common features and differences among the extended two-barrel polymerase superfamily, focusing on the newly discovered members. Comparing their structures provides insights into the molecular mechanisms evolved by the contemporary two-barrel polymerases to accomplish their different biological functions.
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Affiliation(s)
- Ludovic Sauguet
- Institut Pasteur, Unité de Dynamique Structurale des Macromolécules, 75015 Paris, France.
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32
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Lin G, Weiss SC, Vergara S, Camacho C, Calero G. Transcription with a laser: Radiation-damage-free diffraction of RNA Polymerase II crystals. Methods 2019; 159-160:23-28. [PMID: 31029767 DOI: 10.1016/j.ymeth.2019.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/04/2019] [Accepted: 04/21/2019] [Indexed: 12/27/2022] Open
Abstract
Well-diffracting crystals are essential to obtain relevant structural data that will lead to understanding of RNA Polymerase II (Pol II) transcriptional processes at a molecular level. Here we present a strategy to study Pol II crystals using negative stain transmission electron microscopy (TEM) and a methodology to optimize radiation damage free data collection using free electron laser (FEL) at the Linac Coherent Light Source (LCLS). The use of negative stain TEM allowed visualization and optimization of crystal diffraction by monitoring the lattice quality of crystallization conditions. Nano crystals bearing perfect lattices were seeded and used to grow larger crystals for FEL data collection. Moreover, the use of in house designed crystal loops together with ultra-violet (UV) microscopy for crystal detection facilitated data collection. Such strategy permitted collection of multiple crystals of radiation-free-damage data, resulting in the highest resolution of wild type (WT) Pol II crystals ever observed.
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Affiliation(s)
- Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States
| | - Simon C Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States
| | - Sandra Vergara
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States
| | - Carlos Camacho
- Department of Computanional and Systems Biology, University of Pittsburgh School of Medicine, United States
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States.
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33
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Lockwood S, Brayton KA, Daily JA, Broschat SL. Whole Proteome Clustering of 2,307 Proteobacterial Genomes Reveals Conserved Proteins and Significant Annotation Issues. Front Microbiol 2019; 10:383. [PMID: 30873148 PMCID: PMC6403173 DOI: 10.3389/fmicb.2019.00383] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/13/2019] [Indexed: 11/24/2022] Open
Abstract
We clustered 8.76 M protein sequences deduced from 2,307 completely sequenced Proteobacterial genomes resulting in 707,311 clusters of one or more sequences of which 224,442 ranged in size from 2 to 2,894 sequences. To our knowledge this is the first study of this scale. We were surprised to find that no single cluster contained a representative sequence from all the organisms in the study. Given the minimal genome concept, we expected to find a shared set of proteins. To determine why the clusters did not have universal representation we chose four essential proteins, the chaperonin GroEL, DNA dependent RNA polymerase subunits beta and beta′ (RpoB/RpoB′), and DNA polymerase I (PolA), representing fundamental cellular functions, and examined their cluster distribution. We found these proteins to be remarkably conserved with certain caveats. Although the groEL gene was universally conserved in all the organisms in the study, the protein was not represented in all the deduced proteomes. The genes for RpoB and RpoB′ were missing from two genomes and merged in 88, and the sequences were sufficiently divergent that they formed separate clusters for 18 RpoB proteins (seven clusters) and 14 RpoB′ proteins (three clusters). For PolA, 52 organisms lacked an identifiable sequence, and seven sequences were sufficiently divergent that they formed five separate clusters. Interestingly, organisms lacking an identifiable PolA and those with divergent RpoB/RpoB′ were predominantly endosymbionts. Furthermore, we present a range of examples of annotation issues that caused the deduced proteins to be incorrectly represented in the proteome. These annotation issues made our task of determining protein conservation more difficult than expected and also represent a significant obstacle for high-throughput analyses.
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Affiliation(s)
- Svetlana Lockwood
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, United States
| | - Kelly A Brayton
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, United States.,Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States.,Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, United States
| | - Jeff A Daily
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Shira L Broschat
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, United States.,Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States.,Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, United States
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34
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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: 5] [Impact Index Per Article: 0.8] [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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35
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Yu H, Xue C, Long M, Jia H, Xue G, Du S, Coello Y, Ishibashi T. TEFM Enhances Transcription Elongation by Modifying mtRNAP Pausing Dynamics. Biophys J 2018; 115:2295-2300. [PMID: 30514634 DOI: 10.1016/j.bpj.2018.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/25/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022] Open
Abstract
Regulation of transcription elongation is one of the key mechanisms employed to control gene expression. The single-subunit mitochondrial RNA polymerase (mtRNAP) transcribes mitochondrial genes, such as those related to ATP synthesis. We investigated how mitochondrial transcription elongation factor (TEFM) enhances mtRNAP transcription elongation using a single-molecule optical-tweezers transcription assay, which follows transcription dynamics in real time and allows the separation of pause-free elongation from transcriptional pauses. We found that TEFM enhances the stall force of mtRNAP. Although TEFM does not change the pause-free elongation rate, it enhances mtRNAP transcription elongation by reducing the frequency of long-lived pauses and shortening their durations. Furthermore, we demonstrate how mtRNAP passes through the conserved sequence block II, which is the key sequence for the switch between DNA replication and transcription in mitochondria. Our findings elucidate how both TEFM and mitochondrial genomic DNA sequences directly control the transcription elongation dynamics of mtRNAP.
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Affiliation(s)
- Hongwu Yu
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Cheng Xue
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Mengping Long
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Huiqiang Jia
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Guosheng Xue
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China; Department of Physics, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Shengwang Du
- Department of Physics, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China; Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Yves Coello
- Departamento de Ciencias, Sección Química, Pontificia Universidad Católica del Perú PUCP, Lima, Peru
| | - Toyotaka Ishibashi
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China.
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36
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Wei X, Zhang J. On the Origin of Compositional Features of Ribosomes. Genome Biol Evol 2018; 10:2010-2016. [PMID: 30059996 PMCID: PMC6097593 DOI: 10.1093/gbe/evy169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 01/08/2023] Open
Abstract
Ribosomes are highly abundant in cells and comprise, besides RNAs of varying lengths, 55–80 similarly sized, short proteins. This seemingly unusual composition is thought to have resulted from selection for rapid autocatalytic ribosome production. Here, we demonstrate that ribosomal protein-splitting mutations cannot accelerate ribosome production. The autocatalytic explanation is also unnecessary, because protein lengths generally decline with expression levels. Although ribosomal proteins are shorter than expected from their expression levels, they are not outliers among members of large protein complexes in mean protein length or coefficient of variation. These observations are explainable because 1) shortening proteins lowers their synthetic cost and reduces the waste from mistranslation-induced protein dysfunction and degradation, 2) such benefits rise with expression levels, and 3) members of large complexes participate in more protein–protein interactions so are less tolerant to mistranslation. These and other considerations suggest that the compositional features of ribosomes originate from cellular energy economics.
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Affiliation(s)
- Xinzhu Wei
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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37
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Arias-Gonzalez JR. Thermodynamic framework for information in nanoscale systems with memory. J Chem Phys 2018; 147:205101. [PMID: 29195281 DOI: 10.1063/1.5004793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Information is represented by linear strings of symbols with memory that carry errors as a result of their stochastic nature. Proofreading and edition are assumed to improve certainty although such processes may not be effective. Here, we develop a thermodynamic theory for material chains made up of nanoscopic subunits with symbolic meaning in the presence of memory. This framework is based on the characterization of single sequences of symbols constructed under a protocol and is used to derive the behavior of ensembles of sequences similarly constructed. We then analyze the role of proofreading and edition in the presence of memory finding conditions to make revision an effective process, namely, to decrease the entropy of the chain. Finally, we apply our formalism to DNA replication and RNA transcription finding that Watson and Crick hybridization energies with which nucleotides are branched to the template strand during the copying process are optimal to regulate the fidelity in proofreading. These results are important in applications of information theory to a variety of solid-state physical systems and other biomolecular processes.
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Affiliation(s)
- J Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia, C/Faraday 9, Cantoblanco, 28049 Madrid, Spain and CNB-CSIC-IMDEA Nanociencia Associated Unit "Unidad de Nanobiotecnología," Cantoblanco, 28049 Madrid, Spain
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38
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Balancing Non-Equilibrium Driving with Nucleotide Selectivity at Kinetic Checkpoints in Polymerase Fidelity Control. ENTROPY 2018; 20:e20040306. [PMID: 33265397 PMCID: PMC7512825 DOI: 10.3390/e20040306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/17/2018] [Accepted: 04/21/2018] [Indexed: 02/08/2023]
Abstract
High fidelity gene transcription and replication require kinetic discrimination of nucleotide substrate species by RNA and DNA polymerases under chemical non-equilibrium conditions. It is known that sufficiently large free energy driving force is needed for each polymerization or elongation cycle to maintain far-from-equilibrium to achieve low error rates. Considering that each cycle consists of multiple kinetic steps with different transition rates, one expects that the kinetic modulations by polymerases are not evenly conducted at each step. We show that accelerations at different kinetic steps impact quite differently to the overall elongation characteristics. In particular, for forward transitions that discriminate cognate and non-cognate nucleotide species to serve as kinetic selection checkpoints, the transition cannot be accelerated too quickly nor retained too slowly to obtain low error rates, as balancing is needed between the nucleotide selectivity and the non-equilibrium driving. Such a balance is not the same as the speed-accuracy tradeoff in which high accuracy is always obtained at sacrifice of speed. For illustration purposes, we used three-state and five-state models of nucleotide addition in the polymerase elongation and show how the non-equilibrium steady state characteristics change upon variations on stepwise forward or backward kinetics. Notably, by using the multi-step elongation schemes and parameters from T7 RNA polymerase transcription elongation, we demonstrate that individual transitions serving as selection checkpoints need to proceed at moderate rates in order to sustain the necessary non-equilibrium drives as well as to allow nucleotide selections for an optimal error control. We also illustrate why rate-limiting conformational transitions of the enzyme likely play a significant role in the error reduction.
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39
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Czaja AJ. Epigenetic changes and their implications in autoimmune hepatitis. Eur J Clin Invest 2018; 48. [PMID: 29383703 DOI: 10.1111/eci.12899] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/25/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND The genetic risk of autoimmune hepatitis is insufficient to explain the observed risk, and epigenetic changes may explain disparities in disease occurrence in different populations within and between countries. The goal of this review was to examine how epigenetic changes induced by the environment or inherited as a phenotypic trait may affect autoimmune hepatitis and be amenable to therapeutic intervention. MATERIALS AND METHODS Pertinent abstracts were identified in PubMed by multiple search terms. The number of abstracts reviewed was 1689, and the number of full-length articles reviewed exceeded 150. RESULTS Activation of pro-inflammatory genes in autoimmune disease is associated with hypomethylation of deoxyribonucleic acid and modification of histones within chromatin. Organ-specific microribonucleic acids can silence genes by marking messenger ribonucleic acids for degradation, and they can promote inflammatory activity or immunosuppression. High circulating levels of the microribonucleic acids 21 and 122 have been demonstrated in autoimmune hepatitis, and they may increase production of pro-inflammatory cytokines. Microribonucleic acids are also essential for maintaining regulatory T cells. Drugs, pollutants, infections, diet and ageing can induce inheritable epigenetic changes favouring autoimmunity. Reversal is feasible by manipulating enzymes, transcription factors, gene-silencing molecules and toxic exposures or by administering methyl donors and correcting vitamin D deficiency. Gene targets, site specificity, efficacy and consequences are uncertain. CONCLUSIONS Potentially reversible epigenetic changes may affect the occurrence and outcome of autoimmune hepatitis, and investigations are warranted to determine the nature of these changes, key genomic targets, and feasible interventions and their consequences.
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Affiliation(s)
- Albert J Czaja
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
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40
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Selisko B, Papageorgiou N, Ferron F, Canard B. Structural and Functional Basis of the Fidelity of Nucleotide Selection by Flavivirus RNA-Dependent RNA Polymerases. Viruses 2018; 10:v10020059. [PMID: 29385764 PMCID: PMC5850366 DOI: 10.3390/v10020059] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 01/25/2018] [Accepted: 01/27/2018] [Indexed: 12/22/2022] Open
Abstract
Viral RNA-dependent RNA polymerases (RdRps) play a central role not only in viral replication, but also in the genetic evolution of viral RNAs. After binding to an RNA template and selecting 5'-triphosphate ribonucleosides, viral RdRps synthesize an RNA copy according to Watson-Crick base-pairing rules. The copy process sometimes deviates from both the base-pairing rules specified by the template and the natural ribose selectivity and, thus, the process is error-prone due to the intrinsic (in)fidelity of viral RdRps. These enzymes share a number of conserved amino-acid sequence strings, called motifs A-G, which can be defined from a structural and functional point-of-view. A co-relation is gradually emerging between mutations in these motifs and viral genome evolution or observed mutation rates. Here, we review our current knowledge on these motifs and their role on the structural and mechanistic basis of the fidelity of nucleotide selection and RNA synthesis by Flavivirus RdRps.
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Affiliation(s)
- Barbara Selisko
- CNRS, Aix-Marseille Université, AFMB, UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France.
| | - Nicolas Papageorgiou
- CNRS, Aix-Marseille Université, AFMB, UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France.
| | - François Ferron
- CNRS, Aix-Marseille Université, AFMB, UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France.
| | - Bruno Canard
- CNRS, Aix-Marseille Université, AFMB, UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France.
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Simple In Vitro Assay To Evaluate the Incorporation Efficiency of Ribonucleotide Analog 5'-Triphosphates into RNA by Human Mitochondrial DNA-Dependent RNA Polymerase. Antimicrob Agents Chemother 2018; 62:AAC.01830-17. [PMID: 29180528 PMCID: PMC5786792 DOI: 10.1128/aac.01830-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/21/2017] [Indexed: 01/27/2023] Open
Abstract
There is a growing body of evidence suggesting that some ribonucleoside/ribonucleotide analogs may be incorporated into mitochondrial RNA by human mitochondrial DNA-dependent RNA polymerase (POLRMT) and disrupt mitochondrial RNA synthesis. An assessment of the incorporation efficiency of a ribonucleotide analog 5′-triphosphate by POLRMT may be used to evaluate the potential mitochondrial toxicity of the analog early in the development process. In this report, we provide a simple method to prepare active recombinant POLRMT. A robust in vitro nonradioactive primer extension assay was developed to assay the incorporation efficiency of ribonucleotide analog 5′-triphosphates. Our results show that many ribonucleotide analogs, including some antiviral compounds currently in various preclinical or clinical development stages, can be incorporated into newly synthesized RNA by POLRMT and that the incorporation of some of them can lead to chain termination. The discrimination (D) values of ribonucleotide analog 5′-triphosphates over those of natural ribonucleotide triphosphates (rNTPs) were measured to evaluate the incorporation efficiency of the ribonucleotide analog 5′-triphosphates by POLRMT. The discrimination values of natural rNTPs under the condition of misincorporation by POLRMT were used as a reference to evaluate the potential mitochondrial toxicity of ribonucleotide analogs. We propose the following criteria for the potential mitochondrial toxicity of ribonucleotide analogs based on D values: a safe compound has a D value of >105; a potentially toxic compound has a D value of >104 but <105; and a toxic compound has a D value of <104. This report provides a simple screening method that should assist investigators in designing ribonucleoside-based drugs having lower mitochondrial toxicity.
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42
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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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43
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Dong J, Wu T, Xiao Y, Chen L, Xu L, Li M, Zhao M. Target-triggered transcription machinery for ultra-selective and sensitive fluorescence detection of nucleoside triphosphates in one minute. Biosens Bioelectron 2017; 100:333-340. [PMID: 28942346 DOI: 10.1016/j.bios.2017.09.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/06/2017] [Accepted: 09/17/2017] [Indexed: 01/02/2023]
Abstract
Nucleoside triphosphates (NTPs) play important roles in living organisms. However, no fluorescent assays are currently available to simply and rapidly detect multiple NTPs with satisfactory selectivity, sensitivity and low cost. Here we demonstrate for the first time a target-triggered in-vitro transcription machinery for ultra-selective, sensitive and instant fluorescence detection of multiple NTPs. The machinery assembles RNA polymerase, DNA template and non-target NTPs to convert the target NTP into equivalent RNA signal sequences which are monitored by the fluorescence enhancement of molecular beacon. The machinery offers excellent selectivity for the target NTP against NDP, NMP and dNTP. Notably, to accelerate the kinetics of the machinery while maintain its high specificity, we investigated the sequence of DNA templates systematically and established a set of guidelines for the design of the optimum DNA templates, which allowed for instant detection of the target NTP at fmol level in less than 1min. Furthermore, the machinery could be transformed into logic gates to study the coeffects of two NTPs in biosynthesis and real-time monitoring systems to reflect the distribution of NTP in nucleotide pools. These results provide very useful and low-cost tools for both biochemical tests and point-of-care analysis.
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Affiliation(s)
- Jiantong Dong
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tongbo Wu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yu Xiao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lu Chen
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lei Xu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Mengyuan Li
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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44
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Lukačišin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One 2017; 12:e0174066. [PMID: 28301878 PMCID: PMC5354634 DOI: 10.1371/journal.pone.0174066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 03/02/2017] [Indexed: 01/22/2023] Open
Abstract
RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking.
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Affiliation(s)
- Martin Lukačišin
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America
- IST Austria, Klosterneuburg, Austria
| | - Matthieu Landon
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America
- Department of Genetics, Harvard Medical School, Boston, MA, United States of America
- Ecole des Mines de Paris, Mines Paristech, Paris, France
| | - Rishi Jajoo
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America
- * E-mail:
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45
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E C, Duan B, Yu J. Nucleotide Selectivity at a Preinsertion Checkpoint of T7 RNA Polymerase Transcription Elongation. J Phys Chem B 2017; 121:3777-3786. [PMID: 28199109 DOI: 10.1021/acs.jpcb.6b11668] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleotide selection is crucial for transcription fidelity control, in particular, for viral T7 RNA polymerase (RNAP) lack of proofreading activity. It has been recognized that multiple kinetic checkpoints exist prior to full nucleotide incorporation. In this work, we implemented intensive atomistic molecular dynamics (MD) simulations to quantify how strong the nucleotide selection is at the initial checkpoint of an elongation cycle of T7 RNAP. The incoming nucleotides bind into a preinsertion site where a critical tyrosine residue locates nearby to assist the nucleotide selection. We calculated the relative binding free energy between a noncognate nucleotide and a cognate one at a preinsertion configuration via alchemical simulations, showing that a small selection free energy or the binding free energy difference (∼3 kBT) exists between the two nucleotides. Indeed, another preinsertion configuration favored by the noncognate nucleotides was identified, which appears to be off path for further nucleotide insertion and additionally assists the nucleotide selection. By chemical master equation (CME) approach, we show that the small selection free energy at the preinsertion site along with the off-path noncognate nucleotide filtering can help substantially to reduce the error rate and to maintain the elongation rate high in the T7 RNAP transcription.
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Affiliation(s)
- Chao E
- Beijing Computational Science Research Center , Beijing 100193, China
| | - Baogen Duan
- Beijing Computational Science Research Center , Beijing 100193, China
| | - Jin Yu
- Beijing Computational Science Research Center , Beijing 100193, China
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46
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Tam CP, Fahrenbach AC, Björkbom A, Prywes N, Izgu EC, Szostak JW. Downstream Oligonucleotides Strongly Enhance the Affinity of GMP to RNA Primer-Template Complexes. J Am Chem Soc 2017; 139:571-574. [PMID: 28055190 PMCID: PMC7547879 DOI: 10.1021/jacs.6b09760] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Indexed: 11/29/2022]
Abstract
Origins of life hypotheses often invoke a transitional phase of nonenzymatic template-directed RNA replication prior to the emergence of ribozyme-catalyzed copying of genetic information. Here, using NMR and ITC, we interrogate the binding affinity of guanosine 5'-monophosphate (GMP) for primer-template complexes when either another GMP, or a helper oligonucleotide, can bind downstream. Binding of GMP to a primer-template complex cannot be significantly enhanced by the possibility of downstream monomer binding, because the affinity of the downstream monomer is weaker than that of the first monomer. Strikingly, GMP binding affinity can be enhanced by ca. 2 orders of magnitude when a helper oligonucleotide is stably bound downstream of the monomer binding site. We compare these thermodynamic parameters to those previously reported for T7 RNA polymerase-mediated replication to help address questions of binding affinity in related nonenzymatic processes.
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Affiliation(s)
- Chun Pong Tam
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Albert C. Fahrenbach
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Earth
Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Anders Björkbom
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Biosciences, Åbo Akademi University, Åbo FI-20520, Finland
| | - Noam Prywes
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Enver Cagri Izgu
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
- Earth
Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
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47
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Hantsche M, Cramer P. Strukturelle Grundlage der Transkription: 10 Jahre nach dem Chemie-Nobelpreis. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Merle Hantsche
- Abteilung für Molekularbiologie; Max-Planck-Institut für biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Deutschland
| | - Patrick Cramer
- Abteilung für Molekularbiologie; Max-Planck-Institut für biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Deutschland
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48
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Rao M, Okreglak V, Chio US, Cho H, Walter P, Shan SO. Multiple selection filters ensure accurate tail-anchored membrane protein targeting. eLife 2016; 5. [PMID: 27925580 PMCID: PMC5214336 DOI: 10.7554/elife.21301] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/06/2016] [Indexed: 11/13/2022] Open
Abstract
Accurate protein localization is crucial to generate and maintain organization in all cells. Achieving accuracy is challenging, as the molecular signals that dictate a protein's cellular destination are often promiscuous. A salient example is the targeting of an essential class of tail-anchored (TA) proteins, whose sole defining feature is a transmembrane domain near their C-terminus. Here we show that the Guided Entry of Tail-anchored protein (GET) pathway selects TA proteins destined to the endoplasmic reticulum (ER) utilizing distinct molecular steps, including differential binding by the co-chaperone Sgt2 and kinetic proofreading after ATP hydrolysis by the targeting factor Get3. Further, the different steps select for distinct physicochemical features of the TA substrate. The use of multiple selection filters may be general to protein biogenesis pathways that must distinguish correct and incorrect substrates based on minor differences.
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Affiliation(s)
- Meera Rao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Voytek Okreglak
- Howard Hughes Medical Institute, University of California, San Francisco, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, United States
| | - Un Seng Chio
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Hyunju Cho
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Peter Walter
- Howard Hughes Medical Institute, University of California, San Francisco, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, United States
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
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49
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Hantsche M, Cramer P. The Structural Basis of Transcription: 10 Years After the Nobel Prize in Chemistry. Angew Chem Int Ed Engl 2016; 55:15972-15981. [DOI: 10.1002/anie.201608066] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Merle Hantsche
- Abteilung für Molekularbiologie; Max Planck Institut für biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
| | - Patrick Cramer
- Abteilung für Molekularbiologie; Max Planck Institut für biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
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50
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Abstract
Our genome is protected from the introduction of mutations by high fidelity replication and an extensive network of DNA damage response and repair mechanisms. However, the expression of our genome, via RNA and protein synthesis, allows for more diversity in translating genetic information. In addition, the splicing process has become less stringent over evolutionary time allowing for a substantial increase in the diversity of transcripts generated. The result is a diverse transcriptome and proteome that harbor selective advantages over a more tightly regulated system. Here, we describe mechanisms in place that both safeguard the genome and promote translational diversity, with emphasis on post-transcriptional RNA processing.
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Affiliation(s)
- Brian Magnuson
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, and Translational Oncology Program, University of Michigan, Ann Arbor, USA; Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Karan Bedi
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, and Translational Oncology Program, University of Michigan, Ann Arbor, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, and Translational Oncology Program, University of Michigan, Ann Arbor, USA; Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, USA.
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