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Gao S, Hou P, Oh J, Wang D, Greenberg MM. Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG. J Am Chem Soc 2024; 146:6274-6282. [PMID: 38393762 DOI: 10.1021/jacs.3c14476] [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] [Indexed: 02/25/2024]
Abstract
Oxidative DNA lesions cause significant detrimental effects on a living species. Two major DNA lesions resulting from dG oxidation, 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodGuo) and formamidopyrimidine (Fapy·dG), are produced from a common chemical intermediate. Fapy·dG is formed in comparable yields under oxygen-deficient conditions. Replicative bypass of Fapy·dG in human cells is more mutagenic than that of 8-OxodGuo. Despite the biological importance of transcriptional mutagenesis, there are no reports of the effects of Fapy·dG on RNA polymerase II (Pol II) activity. Here we perform comprehensive kinetic studies to investigate the impact of Fapy·dG on three key transcriptional fidelity checkpoint steps by Pol II: insertion, extension, and proofreading steps. The ratios of error-free versus error-prone incorporation opposite Fapy·dG are significantly reduced in comparison with undamaged dG. Similarly, Fapy·dG:A mispair is extended with comparable efficiency as that of the error-free, Fapy·dG:C base pair. The α- and β-configurational isomers of Fapy·dG have distinct effects on Pol II insertion and extension. Pol II can preferentially cleave error-prone products by proofreading. To further understand the structural basis of transcription processing of Fapy·dG, five different structures were solved, including Fapy·dG template-loading state (apo), error-free cytidine triphosphate (CTP) binding state (prechemistry), error-prone ATP binding state (prechemistry), error-free Fapy·dG:C product state (postchemistry), and error-prone Fapy·dG:A product state (postchemistry), revealing distinctive nucleotide binding and product states. Taken together, our study provides a comprehensive mechanistic framework for better understanding how Fapy·dG lesions impact transcription and subsequent pathological consequences.
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Affiliation(s)
- Shijun Gao
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Peini Hou
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Department of Regulatory Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California 92093, United States
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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2
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Gong W, Li S. Rpb7 represses transcription-coupled nucleotide excision repair. J Biol Chem 2023; 299:104969. [PMID: 37380080 PMCID: PMC10382679 DOI: 10.1016/j.jbc.2023.104969] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/30/2023] Open
Abstract
Transcription-coupled repair (TCR) is a subpathway of nucleotide excision repair (NER) that is regulated by multiple facilitators, such as Rad26, and repressors, such as Rpb4 and Spt4/Spt5. How these factors interplay with each other and with core RNA polymerase II (RNAPII) remains largely unknown. In this study, we identified Rpb7, an essential RNAPII subunit, as another TCR repressor and characterized its repression of TCR in the AGP2, RPB2, and YEF3 genes, which are transcribed at low, moderate, and high rates, respectively. The Rpb7 region that interacts with the KOW3 domain of Spt5 represses TCR largely through the same common mechanism as Spt4/Spt5, as mutations in this region mildly enhance the derepression of TCR by spt4Δ only in the YEF3 gene but not in the AGP2 or RPB2 gene. The Rpb7 regions that interact with Rpb4 and/or the core RNAPII repress TCR largely independently of Spt4/Spt5, as mutations in these regions synergistically enhance the derepression of TCR by spt4Δ in all the genes analyzed. The Rpb7 regions that interact with Rpb4 and/or the core RNAPII may also play positive roles in other (non-NER) DNA damage repair and/or tolerance mechanisms, as mutations in these regions can cause UV sensitivity that cannot be attributed to derepression of TCR. Our study reveals a novel function of Rpb7 in TCR regulation and suggests that this RNAPII subunit may have broader roles in DNA damage response beyond its known function in transcription.
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Affiliation(s)
- Wenzhi Gong
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA.
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3
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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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4
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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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5
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Oh J, Jia T, Xu J, Chong J, Dervan PB, Wang D. RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder. Proc Natl Acad Sci U S A 2022; 119:e2114065119. [PMID: 35022237 PMCID: PMC8784135 DOI: 10.1073/pnas.2114065119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023] Open
Abstract
Elongating RNA polymerase II (Pol II) can be paused or arrested by a variety of obstacles. These obstacles include DNA lesions, DNA-binding proteins, and small molecules. Hairpin pyrrole-imidazole (Py-Im) polyamides bind to the minor groove of DNA in a sequence-specific manner and induce strong transcriptional arrest. Remarkably, this Py-Im-induced Pol II transcriptional arrest is persistent and cannot be rescued by transcription factor TFIIS. In contrast, TFIIS can effectively rescue the transcriptional arrest induced by a nucleosome barrier. The structural basis of Py-Im-induced transcriptional arrest and why TFIIS cannot rescue this arrest remain elusive. Here we determined the X-ray crystal structures of four distinct Pol II elongation complexes (Pol II ECs) in complex with hairpin Py-Im polyamides as well as of the hairpin Py-Im polyamides-dsDNA complex. We observed that the Py-Im oligomer directly interacts with RNA Pol II residues, introduces compression of the downstream DNA duplex, prevents Pol II forward translocation, and induces Pol II backtracking. These results, together with biochemical studies, provide structural insight into the molecular mechanism by which Py-Im blocks transcription. Our structural study reveals why TFIIS fails to promote Pol II bypass of Py-Im-induced transcriptional arrest.
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Affiliation(s)
- Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Tiezheng Jia
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Peter B Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125;
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093;
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
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6
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Agapov A, Olina A, Kulbachinskiy A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3018-3041. [PMID: 35323981 PMCID: PMC8989532 DOI: 10.1093/nar/gkac174] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 02/26/2022] [Accepted: 03/03/2022] [Indexed: 11/14/2022] Open
Abstract
Cellular DNA is continuously transcribed into RNA by multisubunit RNA polymerases (RNAPs). The continuity of transcription can be disrupted by DNA lesions that arise from the activities of cellular enzymes, reactions with endogenous and exogenous chemicals or irradiation. Here, we review available data on translesion RNA synthesis by multisubunit RNAPs from various domains of life, define common principles and variations in DNA damage sensing by RNAP, and consider existing controversies in the field of translesion transcription. Depending on the type of DNA lesion, it may be correctly bypassed by RNAP, or lead to transcriptional mutagenesis, or result in transcription stalling. Various lesions can affect the loading of the templating base into the active site of RNAP, or interfere with nucleotide binding and incorporation into RNA, or impair RNAP translocation. Stalled RNAP acts as a sensor of DNA damage during transcription-coupled repair. The outcome of DNA lesion recognition by RNAP depends on the interplay between multiple transcription and repair factors, which can stimulate RNAP bypass or increase RNAP stalling, and plays the central role in maintaining the DNA integrity. Unveiling the mechanisms of translesion transcription in various systems is thus instrumental for understanding molecular pathways underlying gene regulation and genome stability.
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Affiliation(s)
- Aleksei Agapov
- Correspondence may also be addressed to Aleksei Agapov. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
| | - Anna Olina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute” Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- To whom correspondence should be addressed. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
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7
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Jin X, Yan ZH, Lu L, Lu S, Zhang G, Lin W. Peripheral Immune Cells Exhaustion and Functional Impairment in Patients With Chronic Hepatitis B. Front Med (Lausanne) 2021; 8:759292. [PMID: 34782855 PMCID: PMC8589627 DOI: 10.3389/fmed.2021.759292] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/17/2021] [Indexed: 12/30/2022] Open
Abstract
After infection of hepatitis B virus (HBV), the virus induces a variety of immune disorders in the host, leading to immune escape and, finally, the chronicity of the disease. This study investigated immune cell defects and functional impairment in patients with chronic hepatitis B (CHB). We analyzed the percentage, function, and phenotypes of various immune cell subpopulations in the peripheral blood along with the concentrations of cytokines in the plasma. We compared the results between patients with CHB and healthy individuals. It was found that in patients with CHB, the cell function was impaired and, there was increased expression of inhibitory receptors, such as NKG2A and PD-1 in both NK and T cells. The impairment of function was mainly in cytokine secretion, and the cytotoxicity was not significantly diminished. We also found that the proportion of dendritic cells (DC) decreased and regulatory B cells (Breg) increased in CHB. In addition, the Breg cells were negatively correlated with T cell cytokine and positively correlated with ALT and HBV viral load. Taken together, various disorders and functional impairments were found in the immune cells of peripheral blood in CHB patients, especially NK and T cells. These cells showed exhaustion and the increase of regulatory B cells may be one of the reasons for this phenomenon.
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Affiliation(s)
- Xin Jin
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Zhi-Han Yan
- Department of Hepatology, Wuxi Fifth People's Hospital, Wuxi, China
| | - Lingna Lu
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Shengjia Lu
- Department of Infectious Diseases, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Guoping Zhang
- Department of Clinical Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Wei Lin
- Department of Otolaryngology, Tongde Hospital of Zhejiang Province, Hangzhou, China
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Oh J, Xu J, Chong J, Wang D. Molecular basis of transcriptional pausing, stalling, and transcription-coupled repair initiation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194659. [PMID: 33271312 DOI: 10.1016/j.bbagrm.2020.194659] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022]
Abstract
Transcription elongation by RNA polymerase II (Pol II) is constantly challenged by numerous types of obstacles that lead to transcriptional pausing or stalling. These obstacles include DNA lesions, DNA epigenetic modifications, DNA binding proteins, and non-B form DNA structures. In particular, lesion-induced prolonged transcriptional blockage or stalling leads to genome instability, cellular dysfunction, and cell death. Transcription-coupled nucleotide excision repair (TC-NER) pathway is the first line of defense that detects and repairs these transcription-blocking DNA lesions. In this review, we will first summarize the recent research progress toward understanding the molecular basis of transcriptional pausing and stalling by different kinds of obstacles. We will then discuss new insights into Pol II-mediated lesion recognition and the roles of CSB in TC-NER.
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Affiliation(s)
- Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, United States; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States.
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9
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Agapov A, Esyunina D, Kulbachinskiy A. Gre-family factors modulate DNA damage sensing by Deinococcus radiodurans RNA polymerase. RNA Biol 2019; 16:1711-1720. [PMID: 31416390 DOI: 10.1080/15476286.2019.1656027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Deinococcus radiodurans is a highly stress resistant bacterium that encodes universal as well as lineage-specific factors involved in DNA transcription and repair. However, the effects of DNA lesions on RNA synthesis by D. radiodurans RNA polymerase (RNAP) have never been studied. We investigated the ability of this RNAP to transcribe damaged DNA templates and demonstrated that various lesions significantly affect the efficiency and fidelity of RNA synthesis. DNA modifications that disrupt correct base-pairing can strongly inhibit transcription and increase nucleotide misincorporation by D. radiodurans RNAP. The universal transcription factor GreA and Deinococcus-specific factor Gfh1 stimulate RNAP stalling at various DNA lesions, depending on the type of the lesion and the presence of Mn2+ ions, abundant divalent cations in D. radiodurans. Furthermore, Gfh1 stimulates the action of the Mfd translocase, which removes transcription elongation complexes paused at the sites of DNA lesions. Thus, Gre-family factors in D. radiodurans might have evolved to increase the efficiency of DNA damage recognition by the transcription and repair machineries in this bacterium.
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Affiliation(s)
- Aleksei Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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Oh J, Xu J, Chong J, Wang D. Structural and biochemical analysis of DNA lesion-induced RNA polymerase II arrest. Methods 2019; 159-160:29-34. [PMID: 30797902 DOI: 10.1016/j.ymeth.2019.02.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/30/2019] [Accepted: 02/19/2019] [Indexed: 11/16/2022] Open
Abstract
Transcription, catalyzed by RNA polymerase II (Pol II) in eukaryotes, is the first step in gene expression. RNA Pol II is a 12-subunit enzyme complex regulated by many different transcription factors during transcription initiation, elongation, and termination. During elongation, Pol II encounters various types of obstacles that can cause transcriptional pausing and arrest. Through decades of research on transcriptional pausing, it is widely known that Pol II can distinguish between different types of obstacles by its active site. A major class of obstacles is DNA lesions. While some DNA lesions can cause transient transcriptional pausing, which can be bypassed by Pol II itself or with the help from other elongation factors, bulky DNA damage can cause prolonged transcriptional pausing and arrest, which signals for transcription coupled repair. Using biochemical and structural biology approaches, the outcomes of many different types of DNA lesions, DNA modifications, and DNA binding molecules to transcription were studied. In this mini review, we will describe the in vitro transcription assays with Pol II to investigate the impacts of various DNA lesions on transcriptional outcomes and the crystallization method of lesion-arrested Pol II complex. These methods can provide a general platform for the structural and biochemical analysis of Pol II transcriptional pausing and bypass mechanisms.
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Affiliation(s)
- Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States; Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, United States.
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11
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Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair. DNA Repair (Amst) 2018; 71:43-55. [PMID: 30174298 DOI: 10.1016/j.dnarep.2018.08.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Eukaryotic transcription-coupled nucleotide excision repair (TC-NER) is a pathway that removes DNA lesions capable of blocking RNA polymerase II (Pol II) transcription from the template strand. This process is initiated by lesion-arrested Pol II and the recruitment of Cockayne Syndrome B protein (CSB). In this review, we will focus on the lesion recognition steps of eukaryotic TC-NER and summarize the recent research progress toward understanding the structural basis of Pol II-mediated lesion recognition and Pol II-CSB interactions. We will discuss the roles of CSB in both TC-NER initiation and transcription elongation. Finally, we propose an updated model of tripartite lesion recognition and verification for TC-NER in which CSB ensures Pol II-mediated recognition of DNA lesions for TC-NER.
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12
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Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis. Proc Natl Acad Sci U S A 2017; 114:E7082-E7091. [PMID: 28784758 DOI: 10.1073/pnas.1708748114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Alkylated DNA lesions, induced by both exogenous chemical agents and endogenous metabolites, interfere with the efficiency and accuracy of DNA replication and transcription. However, the molecular mechanisms of DNA alkylation-induced transcriptional stalling and mutagenesis remain unknown. In this study, we systematically investigated how RNA polymerase II (pol II) recognizes and bypasses regioisomeric O2-, N3-, and O4-ethylthymidine (O2-, N3-, and O4-EtdT) lesions. We observed distinct pol II stalling profiles for the three regioisomeric EtdT lesions. Intriguingly, pol II stalling at O2-EtdT and N3-EtdT sites is exacerbated by TFIIS-stimulated proofreading activity. Assessment for the impact of the EtdT lesions on individual fidelity checkpoints provided further mechanistic insights, where the transcriptional lesion bypass routes for the three EtdT lesions are controlled by distinct fidelity checkpoints. The error-free transcriptional lesion bypass route is strongly favored for the minor-groove O2-EtdT lesion. In contrast, a dominant error-prone route stemming from GMP misincorporation was observed for the major-groove O4-EtdT lesion. For the N3-EtdT lesion that disrupts base pairing, multiple transcriptional lesion bypass routes were found. Importantly, the results from the present in vitro transcriptional studies are well correlated with in vivo transcriptional mutagenesis analysis. Finally, we identified a minor-groove-sensing motif from pol II (termed Pro-Gate loop). The Pro-Gate loop faces toward the minor groove of RNA:DNA hybrid and is involved in modulating the translocation of minor-groove alkylated DNA template after nucleotide incorporation opposite the lesion. Taken together, this work provides important mechanistic insights into transcriptional stalling, lesion bypass, and mutagenesis of alkylated DNA lesions.
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13
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Abstract
Transcription-coupled DNA repair (TCR) acts on lesions in the transcribed strand of active genes. Helix distorting adducts and other forms of DNA damage often interfere with the progression of the transcription apparatus. Prolonged stalling of RNA polymerase can promote genome instability and also induce cell cycle arrest and apoptosis. These generally unfavorable events are counteracted by RNA polymerase-mediated recruitment of specific proteins to the sites of DNA damage to perform TCR and eventually restore transcription. In this perspective we discuss the decision-making process to employ TCR and we elucidate the intricate biochemical pathways leading to TCR in E. coli and human cells.
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Affiliation(s)
- Bibhusita Pani
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA.
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14
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Kolbanovskiy M, Chowdhury MA, Nadkarni A, Broyde S, Geacintov NE, Scicchitano DA, Shafirovich V. The Nonbulky DNA Lesions Spiroiminodihydantoin and 5-Guanidinohydantoin Significantly Block Human RNA Polymerase II Elongation in Vitro. Biochemistry 2017; 56:3008-3018. [PMID: 28514164 DOI: 10.1021/acs.biochem.7b00295] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The most common, oxidatively generated lesion in cellular DNA is 8-oxo-7,8-dihydroguanine, which can be oxidized further to yield highly mutagenic spiroiminodihydantoin (Sp) and 5-guanidinohydantoin (Gh) in DNA. In human cell-free extracts, both lesions can be excised by base excision repair and global genomic nucleotide excision repair. However, it is not known if these lesions can be removed by transcription-coupled DNA repair (TCR), a pathway that clears lesions from DNA that impede RNA synthesis. To determine if Sp or Gh impedes transcription, which could make each a viable substrate for TCR, either an Sp or a Gh lesion was positioned on the transcribed strand of DNA under the control of a promoter that supports transcription by human RNA polymerase II. These constructs were incubated in HeLa nuclear extracts that contained active RNA polymerase II, and the resulting transcripts were resolved by denaturing polyacrylamide gel electrophoresis. The structurally rigid Sp strongly blocks transcription elongation, permitting 1.6 ± 0.5% nominal lesion bypass. In contrast, the conformationally flexible Gh poses less of a block to human RNAPII, allowing 9 ± 2% bypass. Furthermore, fractional lesion bypass for Sp and Gh is minimally affected by glycosylase activity found in the HeLa nuclear extract. These data specifically suggest that both Sp and Gh may well be susceptible to TCR because each poses a significant block to human RNA polymerase II progression. A more general principle is also proposed: Conformational flexibility may be an important structural feature of DNA lesions that enhances their transcriptional bypass.
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Affiliation(s)
- Marina Kolbanovskiy
- Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003-5180, United States
| | - Moinuddin A Chowdhury
- Department of Biology, New York University , 100 Washington Square East, New York, New York 10003-5180, United States
| | - Aditi Nadkarni
- Department of Biology, New York University , 100 Washington Square East, New York, New York 10003-5180, United States
| | - Suse Broyde
- Department of Biology, New York University , 100 Washington Square East, New York, New York 10003-5180, United States
| | - Nicholas E Geacintov
- Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003-5180, United States
| | - David A Scicchitano
- Department of Biology, New York University , 100 Washington Square East, New York, New York 10003-5180, United States.,Division of Science, New York University Abu Dhabi , P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Vladimir Shafirovich
- Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003-5180, United States
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15
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Small RNA-mediated repair of UV-induced DNA lesions by the DNA DAMAGE-BINDING PROTEIN 2 and ARGONAUTE 1. Proc Natl Acad Sci U S A 2017; 114:E2965-E2974. [PMID: 28325872 DOI: 10.1073/pnas.1618834114] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
As photosynthetic organisms, plants need to prevent irreversible UV-induced DNA lesions. Through an unbiased, genome-wide approach, we have uncovered a previously unrecognized interplay between Global Genome Repair and small interfering RNAs (siRNAs) in the recognition of DNA photoproducts, prevalently in intergenic regions. Genetic and biochemical approaches indicate that, upon UV irradiation, the DNA DAMAGE-BINDING PROTEIN 2 (DDB2) and ARGONAUTE 1 (AGO1) of Arabidopsis thaliana form a chromatin-bound complex together with 21-nt siRNAs, which likely facilitates recognition of DNA damages in an RNA/DNA complementary strand-specific manner. The biogenesis of photoproduct-associated siRNAs involves the noncanonical, concerted action of RNA POLYMERASE IV, RNA-DEPENDENT RNA POLYMERASE-2, and DICER-LIKE-4. Furthermore, the chromatin association/dissociation of the DDB2-AGO1 complex is under the control of siRNA abundance and DNA damage signaling. These findings reveal unexpected nuclear functions for DCL4 and AGO1, and shed light on the interplay between small RNAs and DNA repair recognition factors at damaged sites.
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16
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Li W, Li S. Facilitators and Repressors of Transcription-coupled DNA Repair in Saccharomyces cerevisiae. Photochem Photobiol 2016; 93:259-267. [PMID: 27796045 DOI: 10.1111/php.12655] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 09/12/2016] [Indexed: 12/11/2022]
Abstract
Nucleotide excision repair is a well-conserved DNA repair pathway that removes bulky and/or helix-distorting DNA lesions, such as UV-induced cyclobutane pyrimidine dimers and pyrimidine (6-4) pyrimidone photoproducts. Transcription-coupled repair (TCR) is a subpathway of nucleotide excision repair that is dedicated to rapid removal of DNA lesions in the transcribed strand of actively transcribed genes. In eukaryotic cells, TCR is triggered by RNA polymerase II (RNAP II). Rad26, a DNA-dependent ATPase, Rpb9, a nonessential subunit of RNAP II, and Sen1, a 5' to 3' RNA/DNA and DNA helicase, have been shown to facilitate TCR in Saccharomyces cerevisiae. In contrast, a number of factors have also been found to repress TCR in the yeast. These TCR repressors include Rpb4, another nonessential subunit of RNAP II, Spt4/5, a transcription elongation factor complex, and the RNAP II-associated factor 1 complex (PAFc). It appears that the eukaryotic TCR process involves intricate interplays of RNAP II with TCR facilitators and repressors. In this minireview, we summarize recent advances in TCR in S. cerevisiae.
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Affiliation(s)
- Wentao Li
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
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17
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Shin JH, Xu L, Wang D. RNA polymerase II acts as a selective sensor for DNA lesions and endogenous DNA modifications. Transcription 2016; 7:57-62. [PMID: 27105138 PMCID: PMC4984683 DOI: 10.1080/21541264.2016.1168506] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 12/31/2022] Open
Abstract
During transcription elongation, RNA polymerase II (pol II) travels along the DNA template across thousands to millions of nucleotides and accurately synthesizes the complementary RNA transcripts. Apart from its canonical function as a key enzyme for DNA-dependent RNA synthesis, pol II also functions as a selective sensor to recognize DNA lesions or epigenetic modifications.
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Affiliation(s)
- Ji Hyun Shin
- Department of Cellular and Molecular Medicine, School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA, USA
| | - Liang Xu
- Department of Cellular and Molecular Medicine, School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA, USA
| | - Dong Wang
- Department of Cellular and Molecular Medicine, School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA, USA
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18
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Hwang CS, Xu L, Wang W, Ulrich S, Zhang L, Chong J, Shin JH, Huang X, Kool ET, McKenna CE, Wang D. Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution. Nucleic Acids Res 2016; 44:3820-8. [PMID: 27060150 PMCID: PMC4857003 DOI: 10.1093/nar/gkw220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 03/18/2016] [Accepted: 03/21/2016] [Indexed: 02/07/2023] Open
Abstract
RNA polymerase II (pol II) utilizes a complex interaction network to select and incorporate correct nucleoside triphosphate (NTP) substrates with high efficiency and fidelity. Our previous 'synthetic nucleic acid substitution' strategy has been successfully applied in dissecting the function of nucleic acid moieties in pol II transcription. However, how the triphosphate moiety of substrate influences the rate of P-O bond cleavage and formation during nucleotide incorporation is still unclear. Here, by employing β,γ-bridging atom-'substituted' NTPs, we elucidate how the methylene substitution in the pyrophosphate leaving group affects cognate and non-cognate nucleotide incorporation. Intriguingly, the effect of the β,γ-methylene substitution on the non-cognate UTP/dT scaffold (∼3-fold decrease in kpol) is significantly different from that of the cognate ATP/dT scaffold (∼130-fold decrease in kpol). Removal of the wobble hydrogen bonds in U:dT recovers a strong response to methylene substitution of UTP. Our kinetic and modeling studies are consistent with a unique altered transition state for bond formation and cleavage for UTP/dT incorporation compared with ATP/dT incorporation. Collectively, our data reveals the functional interplay between NTP triphosphate moiety and base pair hydrogen bonding recognition during nucleotide incorporation.
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Affiliation(s)
- Candy S Hwang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0744, USA
| | - Liang Xu
- Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
| | - Wei Wang
- Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
| | - Sébastien Ulrich
- Department of Chemistry, Stanford University, Stanford, CA 94305-5017, USA Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, 34296 Montpellier cedex 5, France
| | - Lu Zhang
- Department of Chemistry, Division of Biomedical Engineering, Center of Systems Biology and Human Health, School of Science and Institute for Advance Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jenny Chong
- Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
| | - Ji Hyun Shin
- Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
| | - Xuhui Huang
- Department of Chemistry, Division of Biomedical Engineering, Center of Systems Biology and Human Health, School of Science and Institute for Advance Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305-5017, USA
| | - Charles E McKenna
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0744, USA
| | - Dong Wang
- Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
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19
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Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue. Nat Commun 2016; 7:11244. [PMID: 27091704 PMCID: PMC4838855 DOI: 10.1038/ncomms11244] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 03/03/2016] [Indexed: 12/19/2022] Open
Abstract
The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3′-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3′-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation. RNA Polymerase II can detect and cleave mis-incorporated nucleotides by a proofreading mechanism that requires backtracking of the enzyme. Here the authors show that Pol II backtracking occurs in a stepwise mode that involves two intermediate states where the fraying of the terminal RNA nucleotide is a prerequisite.
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20
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Transcription coupled nucleotide excision repair in the yeast Saccharomyces cerevisiae: The ambiguous role of Rad26. DNA Repair (Amst) 2015; 36:43-48. [DOI: 10.1016/j.dnarep.2015.09.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Francia S. Non-Coding RNA: Sequence-Specific Guide for Chromatin Modification and DNA Damage Signaling. Front Genet 2015; 6:320. [PMID: 26617633 PMCID: PMC4643122 DOI: 10.3389/fgene.2015.00320] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/09/2015] [Indexed: 12/19/2022] Open
Abstract
Chromatin conformation shapes the environment in which our genome is transcribed into RNA. Transcription is a source of DNA damage, thus it often occurs concomitantly to DNA damage signaling. Growing amounts of evidence suggest that different types of RNAs can, independently from their protein-coding properties, directly affect chromatin conformation, transcription and splicing, as well as promote the activation of the DNA damage response (DDR) and DNA repair. Therefore, transcription paradoxically functions to both threaten and safeguard genome integrity. On the other hand, DNA damage signaling is known to modulate chromatin to suppress transcription of the surrounding genetic unit. It is thus intriguing to understand how transcription can modulate DDR signaling while, in turn, DDR signaling represses transcription of chromatin around the DNA lesion. An unexpected player in this field is the RNA interference (RNAi) machinery, which play roles in transcription, splicing and chromatin modulation in several organisms. Non-coding RNAs (ncRNAs) and several protein factors involved in the RNAi pathway are well known master regulators of chromatin while only recent reports show their involvement in DDR. Here, we discuss the experimental evidence supporting the idea that ncRNAs act at the genomic loci from which they are transcribed to modulate chromatin, DDR signaling and DNA repair.
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Affiliation(s)
- Sofia Francia
- IFOM - FIRC Institute of Molecular Oncology Milan, Italy ; Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche Pavia, Italy
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22
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Hu J, Zhu Y, Tong H, Shen X, Chen L, Ran J. A detailed study of homogeneous agarose/hydroxyapatite nanocomposites for load-bearing bone tissue. Int J Biol Macromol 2015; 82:134-43. [PMID: 26434527 DOI: 10.1016/j.ijbiomac.2015.09.077] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/13/2015] [Accepted: 09/30/2015] [Indexed: 11/25/2022]
Abstract
Agarose/hydroxyapatite (agar/HA) nanocomposites for load-bearing bone substitutes were successfully fabricated via a novel in situ precipitation method. Observation via SEM and TEM revealed that the spherical inorganic nanoparticles of approximately 50 nm were well dispersed in the organic matrix, and the crystallographic area combined closely with the amorphous area. The uniform dispersion of HA nanoparticles had prominent effect on improving the mechanical properties of the agar/HA nanocomposites (the highest elastic modulus: 1104.42 MPa; the highest compressive strength: 400.039 MPa), which proved to be potential load-bearing bone substitutes. The thermal stability of agarose and nanocomposites was also studied. The MG63 osteoblast-like cells on the composite disks displayed fusiform and polygonal morphology in the presence of HA, suggesting that the cell maturation was promoted. The results of cell proliferation and cell differentiation indicated that the cells cultured on the agar/HA composite disks significantly increased the alkaline phosphatase activity and calcium deposition. The structural role of agarose in the composite system was investigated to better understand the effect of biopolymer on structure and properties of the composites. The optimal properties were the result of a comprehensive synergy of the components.
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Affiliation(s)
- Jingxiao Hu
- Key Laboratory of Analytical Chemistry for Biology and Medicine, Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 430072, PR China
| | - Youjia Zhu
- Department of Stomatology, Zhongnan Hospital, Wuhan University, 430071, PR China.
| | - Hua Tong
- Key Laboratory of Analytical Chemistry for Biology and Medicine, Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 430072, PR China; Suzhou Research Institute of Wuhan University, Suzhou, Jiangsu 215123, PR China
| | - Xinyu Shen
- Key Laboratory of Analytical Chemistry for Biology and Medicine, Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 430072, PR China.
| | - Li Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine, Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 430072, PR China
| | - Jiabing Ran
- Key Laboratory of Analytical Chemistry for Biology and Medicine, Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 430072, PR China
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23
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Xu L, Wang W, Chong J, Shin JH, Xu J, Wang D. RNA polymerase II transcriptional fidelity control and its functional interplay with DNA modifications. Crit Rev Biochem Mol Biol 2015; 50:503-19. [PMID: 26392149 DOI: 10.3109/10409238.2015.1087960] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Accurate genetic information transfer is essential for life. As a key enzyme involved in the first step of gene expression, RNA polymerase II (Pol II) must maintain high transcriptional fidelity while it reads along DNA template and synthesizes RNA transcript in a stepwise manner during transcription elongation. DNA lesions or modifications may lead to significant changes in transcriptional fidelity or transcription elongation dynamics. In this review, we will summarize recent progress toward understanding the molecular basis of RNA Pol II transcriptional fidelity control and impacts of DNA lesions and modifications on Pol II transcription elongation.
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Affiliation(s)
- Liang Xu
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Wei Wang
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Jenny Chong
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Ji Hyun Shin
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Jun Xu
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Dong Wang
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
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24
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T-cell exhaustion in chronic hepatitis B infection: current knowledge and clinical significance. Cell Death Dis 2015; 6:e1694. [PMID: 25789969 PMCID: PMC4385920 DOI: 10.1038/cddis.2015.42] [Citation(s) in RCA: 245] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/02/2015] [Accepted: 01/19/2015] [Indexed: 12/14/2022]
Abstract
Hepatitis B virus (HBV) infection is the major cause of inflammatory liver disease, of which the clinical recovery and effective anti-viral therapy is associated with the sustained viral control of effector T cells. In humans, chronic HBV infection often shows weak or absent virus-specific T-cell reactivity, which is described as the ‘exhaustion' state characterized by poor effector cytotoxic activity, impaired cytokine production and sustained expression of multiple inhibitory receptors, such as programmed cell death-1 (PD-1), lymphocyte activation gene-3, cytotoxic T lymphocyte-associated antigen-4 and CD244. As both CD4+ and CD8+ T cells participate in the immune responses against chronic hepatitis virus through distinct manners, compelling evidences have been proposed, which restore the anti-viral function of these exhausted T cells by blocking those inhibitory receptors with its ligand and will pave the way for the development of more effective immunotherapeutic and prophylactic strategies for the treatment of chronic infectious diseases. A large number of studies have stated the essentiality of T-cell exhaustion in virus-infected diseases, such as LCMV, hepatitis C virus (HCV), human immunodeficiency virus infections and cancers. Besides, the functional restoration of HCV- and HIV-specific CD8+ T cells by PD-1 blockade has already been repeatedly verified, and also for the immunological control of tumors in humans, blocking the PD-1 pathway could be a major immunotherapeutic strategy. Although the specific molecular pathways of T-cell exhaustion remain ambiguous, several transcriptional pathways have been implicated in T-cell exhaustion recently; among them Blimp-1, T-bet and NFAT2 were able to regulate exhausted T cells during chronic viral infection, suggesting a distinct lineage fate for this sub-population of T cells. This paper summarizes the current literature relevant to T-cell exhaustion in patients with HBV-related chronic hepatitis, the options for identifying new potential therapeutic targets to treat HBV infection and highlights priorities for further study.
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25
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Blosser TR, Loeff L, Westra ER, Vlot M, Künne T, Sobota M, Dekker C, Brouns SJJ, Joo C. Two distinct DNA binding modes guide dual roles of a CRISPR-Cas protein complex. Mol Cell 2015; 58:60-70. [PMID: 25752578 DOI: 10.1016/j.molcel.2015.01.028] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/29/2014] [Accepted: 01/20/2015] [Indexed: 12/21/2022]
Abstract
Small RNA-guided protein complexes play an essential role in CRISPR-mediated immunity in prokaryotes. While these complexes initiate interference by flagging cognate invader DNA for destruction, recent evidence has implicated their involvement in new CRISPR memory formation, called priming, against mutated invader sequences. The mechanism by which the target recognition complex mediates these disparate responses-interference and priming-remains poorly understood. Using single-molecule FRET, we visualize how bona fide and mutated targets are differentially probed by E. coli Cascade. We observe that the recognition of bona fide targets is an ordered process that is tightly controlled for high fidelity. Mutated targets are recognized with low fidelity, which is featured by short-lived and PAM- and seed-independent binding by any segment of the crRNA. These dual roles of Cascade in immunity with distinct fidelities underpin CRISPR-Cas robustness, allowing for efficient degradation of bona fide targets and priming of mutated DNA targets.
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Affiliation(s)
- Timothy R Blosser
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, 2628 CJ, Delft, The Netherlands
| | - Luuk Loeff
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, 2628 CJ, Delft, The Netherlands
| | - Edze R Westra
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB, Wageningen, The Netherlands
| | - Marnix Vlot
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB, Wageningen, The Netherlands
| | - Tim Künne
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB, Wageningen, The Netherlands
| | - Małgorzata Sobota
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB, Wageningen, The Netherlands
| | - Cees Dekker
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, 2628 CJ, Delft, The Netherlands
| | - Stan J J Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB, Wageningen, The Netherlands
| | - Chirlmin Joo
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, 2628 CJ, Delft, The Netherlands
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26
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Li W, Selvam K, Ko T, Li S. Transcription bypass of DNA lesions enhances cell survival but attenuates transcription coupled DNA repair. Nucleic Acids Res 2014; 42:13242-53. [PMID: 25389266 PMCID: PMC4245964 DOI: 10.1093/nar/gku1150] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Transcription-coupled DNA repair (TCR) is a subpathway of nucleotide excision repair (NER) dedicated to rapid removal of DNA lesions in the transcribed strand of actively transcribed genes. The precise nature of the TCR signal and how the repair machinery gains access to lesions imbedded in stalled RNA polymerase II (RNAP II) complexes in eukaryotic cells are still enigmatic. RNAP II has an intrinsic capacity for transcription bypass of DNA lesions by incorporation or misincorporation of nucleotides across the lesions. It has been suggested that transcription bypass of lesions, which exposes the lesions, may be required for TCR. Here, we show that E1103G mutation of Rpb1, the largest subunit of RNAP II, which promotes transcription bypass of UV-induced cyclobutane pyrimidine dimers (CPDs), increases survival of UV irradiated yeast cells but attenuates TCR. The increased cell survival is independent of any NER subpathways. In contrast, G730D mutation of Rpb1, which impairs transcription bypass of CPDs, enhances TCR. Our results suggest that transcription bypass of lesions attenuates TCR but enhances cell tolerance to DNA lesions. Efficient stalling of RNAP II is essential for efficient TCR.
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Affiliation(s)
- Wentao Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Kathiresan Selvam
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Tengyu Ko
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
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