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Laatri S, El Khayari S, Qriouet Z. Exploring the molecular aspect and updating evolutionary approaches to the DNA polymerase enzymes for biotechnological needs: A comprehensive review. Int J Biol Macromol 2024; 276:133924. [PMID: 39033894 DOI: 10.1016/j.ijbiomac.2024.133924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
DNA polymerases are essential enzymes that play a key role in living organisms, as they participate in the synthesis and maintenance of the DNA molecule. The intrinsic properties of these enzymes have been widely observed and studied to understand their functions, activities, and behavior, which has allowed their natural power in DNA synthesis to be exploited in modern biotechnology, to the point of making them true pillars of the field. In this context, the laboratory evolution of these enzymes, either by directed evolution or rational design, has led to the generation of a wide range of new DNA polymerases with novel properties, suitable for a variety of biotechnological needs. In this review, we examine DNA polymerases at the molecular level, their biotechnological use, and their evolutionary methods in relation to the novel properties sought, providing a chronological selection of evolved DNA polymerases cited in the literature that we consider to be of great interest. To our knowledge, this work is the first to bring together the molecular, functional and evolutionary aspects of the DNA polymerase enzyme. We believe it will be of great interest to researchers whose aim is to produce new lines of evolved DNA polymerases.
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Affiliation(s)
- Said Laatri
- Microbiology and Molecular Biology Laboratory, Faculty of Sciences, Mohammed V-Souissi University, Rabat 10100, Morocco.
| | | | - Zidane Qriouet
- Pharmacology and Toxicology Laboratory, Faculty of Medicine and Pharmacy, Mohammed V-Souissi University, Rabat 10100, Morocco
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2
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Zhou Q, Ding X, Du W, Wang H, Wu S, Li J, Yang S. Multi-enzymatic systems synergize new RCA technique amplified super-long dsDNA from DNA circle. Anal Chim Acta 2024; 1291:342220. [PMID: 38280785 DOI: 10.1016/j.aca.2024.342220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/05/2024] [Indexed: 01/29/2024]
Abstract
BACKGROUND In the field of DNA amplification, there are great challenges in the effectively amplify of long-chain amplification, especially amplification up to several hundred kb level. RESULTS A novel technique for the unbiased whole genome amplification from a thimbleful of DNA circles, such as low as 10 ng/ 10 μL of the circular cpDNA or low as 5 ng/ 10 μL of the plasmid, is developed, which can amplify an abundance of the whole genome sequences. Specifically, the new technique that combines rolling-amplification and triple-enzyme system presents a tightly controlled process of a series of buffers/reactions and optimized procedures, that applies from the primer-template duplexes to the Elution step. The result of this technique provides a new approach for extending RCA capacity, where it can reach 200 kb from the circular cpDNA amplification and 150 kb from the plasmid DNA amplification, that demonstrates superior breadth and evenness of genome coverage, high reproducibility, small amplification bias with the amplification efficiency. SIGNIFICANCE AND NOVELTY This new technique will develop into one of the powerful tools for isothermal DNA amplification in vitro, genome sequencing/analysis, phylogenetic analysis, physical mapping, and other molecular biology applications.
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Affiliation(s)
- Qiang Zhou
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Xianlong Ding
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Wanqing Du
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Hongjie Wang
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Shuo Wu
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Jun Li
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Shouping Yang
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
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3
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Schmaltz LF, Koag MC, Kou Y, Zhang L, Lee S. Genotoxic effects of the major alkylation damage N7-methylguanine and methyl formamidopyrimidine. Biochem J 2023; 480:573-585. [PMID: 37078496 PMCID: PMC11061863 DOI: 10.1042/bcj20220460] [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: 08/31/2022] [Revised: 03/29/2023] [Accepted: 04/19/2023] [Indexed: 04/21/2023]
Abstract
Various alkylating agents are known to preferentially modify guanine in DNA, resulting in the formation of N7-alkylguanine (N7-alkylG) and the imidazole ring opened alkyl-formamidopyrimidine (alkyl-FapyG) lesions. Evaluating the mutagenic effects of N7-alkylG has been challenging due to the instability of the positively charged N7-alkylG. To address this issue, we developed a 2'-fluorine-mediated transition-state destabilization approach, which stabilizes N7-alkylG and prevents spontaneous depurination. We also developed a postsynthetic conversion of 2'-F-N7-alkylG DNA into 2'-F-alkyl-FapyG DNA. Using these methods, we incorporated site-specific N7-methylG and methyl-FapyG into pSP189 plasmid and determined their mutagenic properties in bacterial cells using the supF-based colony screening assay. The mutation frequency of N7-methylG was found to be less than 0.5%. Our crystal structure analysis revealed that N7-methylation did not significantly alter base pairing properties, as evidenced by a correct base pairing between 2'-F-N7-methylG and dCTP in Dpo4 polymerase catalytic site. In contrast, the mutation frequency of methyl-FapyG was 6.3%, highlighting the mutagenic nature of this secondary lesion. Interestingly, all mutations arising from methyl-FapyG in the 5'-GGT(methyl-FapyG)G-3' context were single nucleotide deletions at the 5'-G of the lesion. Overall, our results demonstrate that 2'-fluorination technology is a useful tool for studying the chemically labile N7-alkylG and alkyl-FapyG lesions.
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Affiliation(s)
- Lillian F Schmaltz
- From the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Myong-Chul Koag
- From the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Yi Kou
- From the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Louis Zhang
- From the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Seongmin Lee
- From the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A
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4
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Abstract
B-family DNA polymerases (PolBs) of different groups are widespread in Archaea, and different PolBs often coexist in the same organism. Many of these PolB enzymes remain to be investigated. One of the main groups that is poorly characterized is PolB2, whose members occur in many archaea but are predicted to be inactivated forms of DNA polymerase. Here, Sulfolobus islandicus DNA polymerase 2 (Dpo2), a PolB2 enzyme, was expressed in its native host and purified. Characterization of the purified enzyme revealed that the polymerase possesses a robust nucleotide incorporation activity but is devoid of the 3'-5' exonuclease activity. Enzyme kinetics analyses showed that Dpo2 replicates undamaged DNA templates with high fidelity, which is consistent with its inefficient nucleotide insertion activity opposite different DNA lesions. Strikingly, the polymerase is highly efficient in extending mismatches and mispaired primer termini once a nucleotide is placed opposite a damaged site. This extender polymerase represents a novel type of prokaryotic PolB specialized for DNA damage repair in Archaea. IMPORTANCE In this work, we report that Sulfolobus islandicus Dpo2, a B-family DNA polymerase once predicted to be an inactive form, is a bona fide DNA polymerase functioning in translesion synthesis. S. islandicus Dpo2 is a member of a large group of B-family DNA polymerases (PolB2) that are present in many archaea and some bacteria, and they carry variations in well-conserved amino acids in the functional domains responsible for polymerization and proofreading. However, we found that this prokaryotic B-family DNA polymerase not only replicates undamaged DNA with high fidelity but also extends mismatch and DNA lesion-containing substrates with high efficiencies. With these data, we propose this enzyme functions as an extender polymerase, the first prokaryotic enzyme of this type. Our data also suggest this PolB2 enzyme represents a functional counterpart of the eukaryotic DNA polymerase Pol zeta, an enzyme that is devoted to DNA damage repair.
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5
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Kawada T, Kino K, Tokorodani K, Anabuki R, Morikawa M, Kobayashi T, Ohara K, Ohshima T, Miyazawa H. Analysis of nucleotide insertion opposite urea and translesion synthesis across urea by DNA polymerases. Genes Environ 2022; 44:7. [PMID: 35168664 PMCID: PMC8845263 DOI: 10.1186/s41021-022-00236-3] [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: 08/26/2021] [Accepted: 02/01/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract Urea (Ua) is produced in DNA as the result of oxidative damage to thymine and guanine. It was previously reported that Klenow fragment (Kf) exo− incorporated dATP opposite Ua, and that DNA polymerase β was blocked by Ua. We report here the following nucleotide incorporations opposite Ua by various DNA polymerases: DNA polymerase α, dATP and dGTP (dATP > dGTP); DNA polymerase δ, dATP; DNA polymerase ζ, dATP; Kf exo−, dATP; Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4), dGTP and dATP (dGTP > dATP); and DNA polymerase η, dCTP, dGTP, dATP, and dTTP (dCTP > dGTP > dATP > dTTP). DNA polymerases β and ε were blocked by Ua. Elongation by DNA polymerases δ and ζ stopped after inserting dATP opposite Ua. Importantly, the elongation efficiency to full-length beyond Ua using DNA polymerase η and Dpo4 were almost the same as that of natural DNA. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s41021-022-00236-3.
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Affiliation(s)
- Taishu Kawada
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
| | - Katsuhito Kino
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan.
| | - Kyousuke Tokorodani
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
| | - Ryuto Anabuki
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
| | - Masayuki Morikawa
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
| | - Takanobu Kobayashi
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
| | - Kazuaki Ohara
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
| | - Takayuki Ohshima
- Faculty of Science and Engineering, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
| | - Hiroshi Miyazawa
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
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6
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Feng X, Zhang B, Xu R, Gao Z, Liu X, Yuan G, Ishino S, Feng M, Shen Y, Ishino Y, She Q. Enzymatic Switching Between Archaeal DNA Polymerases Facilitates Abasic Site Bypass. Front Microbiol 2021; 12:802670. [PMID: 34987494 PMCID: PMC8721586 DOI: 10.3389/fmicb.2021.802670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/30/2021] [Indexed: 12/21/2022] Open
Abstract
Abasic sites are among the most abundant DNA lesions encountered by cells. Their replication requires actions of specialized DNA polymerases. Herein, two archaeal specialized DNA polymerases were examined for their capability to perform translesion DNA synthesis (TLS) on the lesion, including Sulfolobuss islandicus Dpo2 of B-family, and Dpo4 of Y-family. We found neither Dpo2 nor Dpo4 is efficient to complete abasic sites bypass alone, but their sequential actions promote lesion bypass. Enzyme kinetics studies further revealed that the Dpo4's activity is significantly inhibited at +1 to +3 site past the lesion, at which Dpo2 efficiently extends the primer termini. Furthermore, their activities are inhibited upon synthesis of 5-6 nt TLS patches. Once handed over to Dpo1, these substrates basically inactivate its exonuclease, enabling the transition from proofreading to polymerization of the replicase. Collectively, by functioning as an "extender" to catalyze further DNA synthesis past the lesion, Dpo2 bridges the activity gap between Dpo4 and Dpo1 in the archaeal TLS process, thus achieving more efficient lesion bypass.
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Affiliation(s)
- Xu Feng
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Baochang Zhang
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ruyi Xu
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zhe Gao
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiaotong Liu
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Guanhua Yuan
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Mingxia Feng
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yulong Shen
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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7
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Shi H, Kimsey IJ, Gu S, Liu HF, Pham U, Schumacher MA, Al-Hashimi HM. Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA. Nucleic Acids Res 2021; 49:12540-12555. [PMID: 34792150 PMCID: PMC8643651 DOI: 10.1093/nar/gkab936] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/25/2021] [Accepted: 11/14/2021] [Indexed: 11/17/2022] Open
Abstract
Watson–Crick base pairs (bps) are the fundamental unit of genetic information and the building blocks of the DNA double helix. However, A-T and G-C can also form alternative ‘Hoogsteen’ bps, expanding the functional complexity of DNA. We developed ‘Hoog-finder’, which uses structural fingerprints to rapidly screen Hoogsteen bps, which may have been mismodeled as Watson–Crick in crystal structures of protein–DNA complexes. We uncovered 17 Hoogsteen bps, 7 of which were in complex with 6 proteins never before shown to bind Hoogsteen bps. The Hoogsteen bps occur near mismatches, nicks and lesions and some appear to participate in recognition and damage repair. Our results suggest a potentially broad role for Hoogsteen bps in stressed regions of the genome and call for a community-wide effort to identify these bps in current and future crystal structures of DNA and its complexes.
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Affiliation(s)
- Honglue Shi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Isaac J Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Stephanie Gu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hsuan-Fu Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Uyen Pham
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hashim M Al-Hashimi
- Department of Chemistry, Duke University, Durham, NC 27710, USA.,Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
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8
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Fan C, Deng Q, Zhu TF. Bioorthogonal information storage in L-DNA with a high-fidelity mirror-image Pfu DNA polymerase. Nat Biotechnol 2021; 39:1548-1555. [PMID: 34326549 DOI: 10.1038/s41587-021-00969-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/31/2021] [Indexed: 02/07/2023]
Abstract
Natural DNA is exquisitely evolved to store genetic information. The chirally inverted L-DNA, possessing the same informational capacity but resistant to biodegradation, may serve as a robust, bioorthogonal information repository. Here we chemically synthesize a 90-kDa high-fidelity mirror-image Pfu DNA polymerase that enables accurate assembly of a kilobase-sized mirror-image gene. We use the polymerase to encode in L-DNA an 1860 paragraph by Louis Pasteur that first proposed a mirror-image world of biology. We realize chiral steganography by embedding a chimeric D-DNA/L-DNA key molecule in a D-DNA storage library, which conveys a false or secret message depending on the chirality of reading. Furthermore, we show that a trace amount of an L-DNA barcode preserved in water from a local pond remains amplifiable and sequenceable for 1 year, whereas a D-DNA barcode under the same conditions could not be amplified after 1 day. These next-generation mirror-image molecular tools may transform the development of advanced mirror-image biology systems and pave the way for the realization of the mirror-image central dogma and exploration of their applications.
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Affiliation(s)
- Chuyao Fan
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Qiang Deng
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Ting F Zhu
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.
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9
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Vaisman A, McDonald JP, Smith MR, Aspelund SL, Evans TC, Woodgate R. Identification and Characterization of Thermostable Y-Family DNA Polymerases η, ι, κ and Rev1 From a Lower Eukaryote, Thermomyces lanuginosus. Front Mol Biosci 2021; 8:778400. [PMID: 34805283 PMCID: PMC8595933 DOI: 10.3389/fmolb.2021.778400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
Y-family DNA polymerases (pols) consist of six phylogenetically separate subfamilies; two UmuC (polV) branches, DinB (pol IV, Dpo4, polκ), Rad30A/POLH (polη), and Rad30B/POLI (polι) and Rev1. Of these subfamilies, DinB orthologs are found in all three domains of life; eubacteria, archaea, and eukarya. UmuC orthologs are identified only in bacteria, whilst Rev1 and Rad30A/B orthologs are only detected in eukaryotes. Within eukaryotes, a wide array of evolutionary diversity exists. Humans possess all four Y-family pols (pols η, ι, κ, and Rev1), Schizosaccharomyces pombe has three Y-family pols (pols η, κ, and Rev1), and Saccharomyces cerevisiae only has polη and Rev1. Here, we report the cloning, expression, and biochemical characterization of the four Y-family pols from the lower eukaryotic thermophilic fungi, Thermomyces lanuginosus. Apart from the expected increased thermostability of the T. lanuginosus Y-family pols, their major biochemical properties are very similar to properties of their human counterparts. In particular, both Rad30B homologs (T. lanuginosus and human polɩ) exhibit remarkably low fidelity during DNA synthesis that is template sequence dependent. It was previously hypothesized that higher organisms had acquired this property during eukaryotic evolution, but these observations imply that polι originated earlier than previously known, suggesting a critical cellular function in both lower and higher eukaryotes.
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Affiliation(s)
- Alexandra Vaisman
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - John P McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Mallory R Smith
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Sender L Aspelund
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Thomas C Evans
- New England Biolabs Incorporated, Ipswich, MA, United States
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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10
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Strobel EJ. Efficient Linear dsDNA Tagging Using Deoxyuridine Excision*. Chembiochem 2021; 22:3214-3224. [PMID: 34547157 DOI: 10.1002/cbic.202100425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/05/2021] [Indexed: 11/06/2022]
Abstract
Site-specific strategies for exchanging segments of dsDNA are important for DNA library construction and molecular tagging. Deoxyuridine (dU) excision is an approach for generating 3' ssDNA overhangs in gene assembly and molecular cloning procedures. Unlike approaches that use a multi-base pair motif to specify a DNA cut site, dU excision requires only a dT→dU substitution. Consequently, excision sites can be embedded in biologically active DNA sequences by placing dU substitutions at non-perturbative positions. In this work, I describe a molecular tagging method that uses dU excision to exchange a segment of a dsDNA strand with a long synthetic oligonucleotide. The core workflow of this method, called deoxyUridine eXcision-tagging (dUX-tagging), is an efficient one-pot reaction: strategically positioned dU nucleotides are excised from dsDNA to generate a 3' overhang so that additional sequence can be appended by annealing and ligating a tagging oligonucleotide. The tagged DNA is then processed by one of two procedures to fill the 5' overhang and remove excess tagging oligo. To facilitate its widespread use, all dUX-tagging procedures exclusively use commercially available reagents. As a result, dUX-tagging is a concise and easily implemented approach for high-efficiency linear dsDNA tagging.
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Affiliation(s)
- Eric J Strobel
- Department of Biological Sciences, The University at Buffalo, Buffalo, NY 14260, USA
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11
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Nie QM, Sun LZ, Li HB, Chu X, Wang J. Effects of electrostatic interactions on global folding and local conformational dynamics of a multidomain Y-family DNA polymerase. Phys Chem Chem Phys 2021; 23:20841-20847. [PMID: 34533560 DOI: 10.1039/d1cp02832d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Y-family DNA polymerases specialize in translesion DNA synthesis, which is essential for replicating damaged DNA. The Y-family polymerases, which are made up of four stable domains, exhibit extensive distributions of charged residues, and are responsible for the tight formation of the protein-DNA complex. However, it is still unclear how the electrostatic interactions influence the conformational dynamics of the polymerases. Here, we focus on the case of a prototype Y-family DNA polymerase, Dpo4. Using coarse-grained models including a salt-dependent electrostatic potential, we investigate the effects of the electrostatic interactions on the folding process of Dpo4. Our simulations show that strong electrostatic interactions result in a three-state folding of Dpo4, consistent with the experimental observations. This folding process exhibits low cooperativity led by low salt concentration, where the individual domains fold one by one through one single pathway. Since the refined folding order of domains in multidomain proteins can shrink the configurational space, we suggest that the electrostatic interactions facilitate the Dpo4 folding. In addition, we study the local conformational dynamics of Dpo4 in terms of fluctuation and frustration analyses. We show that the electrostatic interactions can exaggerate the local conformational properties, which are in favor of the large-scale conformational transition of Dpo4 during the functional DNA binding. Our results underline the importance of electrostatic interactions in the conformational dynamics of Dpo4 at both the global and local scale, providing useful guidance in protein engineering at the multidomain level.
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Affiliation(s)
- Qing-Miao Nie
- Department of Applied Physics, Zhejiang University of Technology, 288, Liuhe Road, Hangzhou 310023, P. R. China
| | - Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, 288, Liuhe Road, Hangzhou 310023, P. R. China
| | - Hai-Bin Li
- Department of Applied Physics, Zhejiang University of Technology, 288, Liuhe Road, Hangzhou 310023, P. R. China
| | - Xiakun Chu
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794, USA.
| | - Jin Wang
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794, USA.
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12
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Strobel EJ. Preparation and Characterization of Internally Modified DNA Templates for Chemical Transcription Roadblocking. Bio Protoc 2021; 11:e4141. [PMID: 34604447 DOI: 10.21769/bioprotoc.4141] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/18/2021] [Accepted: 05/11/2021] [Indexed: 01/19/2023] Open
Abstract
Site-specific transcription arrest is the basis of emerging technologies that assess nascent RNA structure and function. Cotranscriptionally folded RNA can be displayed from an arrested RNA polymerase (RNAP) for biochemical manipulations by halting transcription elongation at a defined DNA template position. Most transcription "roadblocking" approaches halt transcription elongation using a protein blockade that is non-covalently attached to the template DNA. I previously developed a strategy for halting Escherichia coli RNAP at a chemical lesion, which expands the repertoire of transcription roadblocking technologies and enables sophisticated manipulations of the arrested elongation complexes. To facilitate this chemical transcription roadblocking approach, I developed a sequence-independent method for preparing internally modified dsDNA using PCR and translesion synthesis. Here, I present a detailed protocol for the preparation and characterization of internally modified dsDNA templates for chemical transcription roadblocking experiments. Graphic abstract: Precise transcription roadblocking using functionalized DNA lesions.
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Affiliation(s)
- Eric J Strobel
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
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13
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Ghodke PP, Mali JR, Patra A, Rizzo CJ, Guengerich FP, Egli M. Enzymatic bypass and the structural basis of miscoding opposite the DNA adduct 1,N 2-ethenodeoxyguanosine by human DNA translesion polymerase η. J Biol Chem 2021; 296:100642. [PMID: 33839151 PMCID: PMC8121704 DOI: 10.1016/j.jbc.2021.100642] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 11/26/2022] Open
Abstract
Etheno (ε)-adducts, e.g., 1,N2-ε−guanine (1,N2-ε-G) and 1,N6-ε−adenine (1,N6-ε-A), are formed through the reaction of DNA with metabolites of vinyl compounds or with lipid peroxidation products. These lesions are known to be mutagenic, but it is unknown how they lead to errors in DNA replication that are bypassed by DNA polymerases. Here we report the structural basis of misincorporation frequencies across from 1,N2-ε-G by human DNA polymerase (hpol) η. In single-nucleotide insertions opposite the adduct 1,N2-ε-G, hpol η preferentially inserted dGTP, followed by dATP, dTTP, and dCTP. This preference for purines was also seen in the first extension step. Analysis of full-length extension products by LC-MS/MS revealed that G accounted for 85% of nucleotides inserted opposite 1,N2-ε-G in single base insertion, and 63% of bases inserted in the first extension step. Extension from the correct nucleotide pair (C) was not observed, but the primer with A paired opposite 1,N2-ε-G was readily extended. Crystal structures of ternary hpol η insertion-stage complexes with nonhydrolyzable nucleotides dAMPnPP or dCMPnPP showed a syn orientation of the adduct, with the incoming A staggered between adducted base and the 5’-adjacent T, while the incoming C and adducted base were roughly coplanar. The formation of a bifurcated H-bond between incoming dAMPnPP and 1,N2-ε-G and T, compared with the single H-bond formed between incoming dCMPnPP and 1,N2-ε-G, may account for the observed facilitated insertion of dGTP and dATP. Thus, preferential insertion of purines by hpol η across from etheno adducts contributes to distinct outcomes in error-prone DNA replication.
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Affiliation(s)
- Pratibha P Ghodke
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Jyotirling R Mali
- Department of Chemistry, College of Arts and Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Amritraj Patra
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Carmelo J Rizzo
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA; Department of Chemistry, College of Arts and Science, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA
| | - F Peter Guengerich
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA.
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14
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Nakama T, Takezawa Y, Shionoya M. Site-specific polymerase incorporation of consecutive ligand-containing nucleotides for multiple metal-mediated base pairing. Chem Commun (Camb) 2021; 57:1392-1395. [PMID: 33438690 DOI: 10.1039/d0cc07771b] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An enzymatic method has been developed for the synthesis of DNA oligomers containing consecutive artificial ligand-type nucleotides. Three hydroxypyridone ligand-containing nucleotides forming CuII-mediated unnatural base pairs were continuously incorporated at a pre-specified position by a lesion-bypass Dpo4 polymerase. This enzymatic synthesis was applied to the development of a CuII-responsive DNAzyme. Accordingly, this research will open new routes for the construction of metal-responsive DNA architectures that are manipulated by multiple metal-mediated base pairing.
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Affiliation(s)
- Takahiro Nakama
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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15
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Miyabayashi H, Jain R, Suzuki S, Grogan DW, Kurosawa N. PolB1 Is Sufficient for DNA Replication and Repair Under Normal Growth Conditions in the Extremely Thermophilic Crenarchaeon Sulfolobus acidocaldarius. Front Microbiol 2020; 11:613375. [PMID: 33424816 PMCID: PMC7785828 DOI: 10.3389/fmicb.2020.613375] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/30/2020] [Indexed: 01/12/2023] Open
Abstract
The thermophilic crenarchaeon Sulfolobus acidocaldarius has four DNA polymerases (DNAPs): PolB1, PolB2, PolB3, and Dbh (PolY). Previous in vitro studies suggested that PolB1 is the main replicative DNAP of Sulfolobales whereas PolB2 and Y-family polymerases Dpo4 (Saccharolobus solfataricus) or Dbh are involved in DNA repair and translesion DNA synthesis. On the other hand, there are various opinions about the role of PolB3, which remains to be clearly resolved. In order to examine the roles of the DNAPs of S. acidocaldarius through in vivo experiments, we constructed polB2, polB3, and dbh deletion strains and characterized their phenotypes. Efforts to construct a polB1 deletion strain were not successful; in contrast, it was possible to isolate triple gene-deletion strains lacking polB2, polB3, and dbh. The growth of these strains was nearly the same as that of the parent strains under normal growth conditions. The polB2, polB3, and dbh single-deletion strains were sensitive to some types of DNA-damaging treatments, but exhibited normal sensitivity to UV irradiation and several other damaging treatments. Overall, the genotype which exhibited the greatest sensitivity to the DNA-damaging treatments we tested was the ΔpolB2 ΔpolB3 combination, providing the first evidence of overlapping function for these two DNAPs in vivo. The results of our study strongly suggest that PolB1 is responsible for the DNA replication of both the leading and lagging strands and is sufficient to complete the repair of most DNA damage under normal growth conditions in S. acidocaldarius.
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Affiliation(s)
- Hiroka Miyabayashi
- Department of Environmental Engineering for Symbiosis, Graduate School of Science and Engineering, Soka University, Tokyo, Japan
| | - Rupal Jain
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Shoji Suzuki
- Department of Environmental Engineering for Symbiosis, Graduate School of Science and Engineering, Soka University, Tokyo, Japan
| | - Dennis W. Grogan
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Norio Kurosawa
- Department of Environmental Engineering for Symbiosis, Graduate School of Science and Engineering, Soka University, Tokyo, Japan
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16
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Pérez-Arnaiz P, Dattani A, Smith V, Allers T. Haloferax volcanii-a model archaeon for studying DNA replication and repair. Open Biol 2020; 10:200293. [PMID: 33259746 PMCID: PMC7776575 DOI: 10.1098/rsob.200293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022] Open
Abstract
The tree of life shows the relationship between all organisms based on their common ancestry. Until 1977, it comprised two major branches: prokaryotes and eukaryotes. Work by Carl Woese and other microbiologists led to the recategorization of prokaryotes and the proposal of three primary domains: Eukarya, Bacteria and Archaea. Microbiological, genetic and biochemical techniques were then needed to study the third domain of life. Haloferax volcanii, a halophilic species belonging to the phylum Euryarchaeota, has provided many useful tools to study Archaea, including easy culturing methods, genetic manipulation and phenotypic screening. This review will focus on DNA replication and DNA repair pathways in H. volcanii, how this work has advanced our knowledge of archaeal cellular biology, and how it may deepen our understanding of bacterial and eukaryotic processes.
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Affiliation(s)
| | | | | | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
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17
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Cranford MT, Kaszubowski JD, Trakselis MA. A hand-off of DNA between archaeal polymerases allows high-fidelity replication to resume at a discrete intermediate three bases past 8-oxoguanine. Nucleic Acids Res 2020; 48:10986-10997. [PMID: 32997110 PMCID: PMC7641752 DOI: 10.1093/nar/gkaa803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/22/2020] [Accepted: 09/16/2020] [Indexed: 01/12/2023] Open
Abstract
During DNA replication, the presence of 8-oxoguanine (8-oxoG) lesions in the template strand cause the high-fidelity (HiFi) DNA polymerase (Pol) to stall. An early response to 8-oxoG lesions involves ‘on-the-fly’ translesion synthesis (TLS), in which a specialized TLS Pol is recruited and replaces the stalled HiFi Pol for lesion bypass. The length of TLS must be long enough for effective bypass, but it must also be regulated to minimize replication errors by the TLS Pol. The exact position where the TLS Pol ends and the HiFi Pol resumes (i.e. the length of the TLS patch) has not been described. We use steady-state and pre-steady-state kinetic assays to characterize lesion bypass intermediates formed by different archaeal polymerase holoenzyme complexes that include PCNA123 and RFC. After bypass of 8-oxoG by TLS PolY, products accumulate at the template position three base pairs beyond the lesion. PolY is catalytically poor for subsequent extension from this +3 position beyond 8-oxoG, but this inefficiency is overcome by rapid extension of HiFi PolB1. The reciprocation of Pol activities at this intermediate indicates a defined position where TLS Pol extension is limited and where the DNA substrate is handed back to the HiFi Pol after bypass of 8-oxoG.
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Affiliation(s)
- Matthew T Cranford
- Baylor University, Department of Chemistry and Biochemistry, One Bear Place, #97348, Waco, TX 76798, USA
| | - Joseph D Kaszubowski
- Baylor University, Department of Chemistry and Biochemistry, One Bear Place, #97348, Waco, TX 76798, USA
| | - Michael A Trakselis
- Baylor University, Department of Chemistry and Biochemistry, One Bear Place, #97348, Waco, TX 76798, USA
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18
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Chu X, Suo Z, Wang J. Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase. eLife 2020; 9:60434. [PMID: 33079059 PMCID: PMC7641590 DOI: 10.7554/elife.60434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/16/2020] [Indexed: 01/01/2023] Open
Abstract
The way in which multidomain proteins fold has been a puzzling question for decades. Until now, the mechanisms and functions of domain interactions involved in multidomain protein folding have been obscure. Here, we develop structure-based models to investigate the folding and DNA-binding processes of the multidomain Y-family DNA polymerase IV (DPO4). We uncover shifts in the folding mechanism among ordered domain-wise folding, backtracking folding, and cooperative folding, modulated by interdomain interactions. These lead to ‘U-shaped’ DPO4 folding kinetics. We characterize the effects of interdomain flexibility on the promotion of DPO4–DNA (un)binding, which probably contributes to the ability of DPO4 to bypass DNA lesions, which is a known biological role of Y-family polymerases. We suggest that the native topology of DPO4 leads to a trade-off between fast, stable folding and tight functional DNA binding. Our approach provides an effective way to quantitatively correlate the roles of protein interactions in conformational dynamics at the multidomain level.
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Affiliation(s)
- Xiakun Chu
- Department of Chemistry, State University of New York at Stony Brook, New York, United States
| | - Zucai Suo
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, United States
| | - Jin Wang
- Department of Chemistry, State University of New York at Stony Brook, New York, United States
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19
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Kathuria P, Singh P, Sharma P, Wetmore SD. Replication of the Aristolochic Acid I Adenine Adduct (ALI-N6-A) by a Model Translesion Synthesis DNA Polymerase: Structural Insights on the Induction of Transversion Mutations from Molecular Dynamics Simulations. Chem Res Toxicol 2020; 33:2573-2583. [DOI: 10.1021/acs.chemrestox.0c00183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Preetleen Kathuria
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Prebhleen Singh
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
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20
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Wu Y, Jaremko WJ, Wilson RC, Pata JD. Heterotrimeric PCNA increases the activity and fidelity of Dbh, a Y-family translesion DNA polymerase prone to creating single-base deletion mutations. DNA Repair (Amst) 2020; 96:102967. [PMID: 32961405 DOI: 10.1016/j.dnarep.2020.102967] [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: 06/10/2020] [Revised: 08/18/2020] [Accepted: 08/31/2020] [Indexed: 11/15/2022]
Abstract
Dbh is a Y-family translesion DNA polymerase from Sulfolobus acidocaldarius, an archaeal species that grows in harsh environmental conditions. Biochemically, Dbh displays a distinctive mutational profile, creating single-base deletion mutations at extraordinarily high frequencies (up to 50 %) in specific repeat sequences. In cells, however, Dbh does not appear to contribute significantly to spontaneous frameshifts in these same sequence contexts. This suggests that either the error-prone DNA synthesis activity of Dbh is reduced in vivo and/or Dbh is restricted from replicating these sequences. Here, we test the hypothesis that the propensity for Dbh to make single base deletion mutations is reduced through interaction with the S. acidocaldarius heterotrimeric sliding clamp processivity factor, PCNA-123. We first confirm that Dbh physically interacts with PCNA-123, with the interaction requiring both the PCNA-1 subunit and the C-terminal 10 amino acids of Dbh, which contain a predicted PCNA-interaction peptide (PIP) motif. This interaction stimulates the polymerase activity of Dbh, even on short, linear primer-template DNA, by increasing the rate of nucleotide incorporation. This stimulation requires an intact PCNA-123 heterotrimer and a DNA duplex length of at least 18 basepairs, the minimal length predicted from structural data to bind to both the polymerase and the clamp. Finally, we find that PCNA-123 increases the fidelity of Dbh on a single-base deletion hotspot sequence 3-fold by promoting an increase in the rate of correct, but not incorrect, nucleotide addition and propose that PCNA-123 induces Dbh to adopt a more active conformation that is less prone to creating deletions during DNA synthesis.
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Affiliation(s)
- Yifeng Wu
- Wadsworth Center, New York State Department of Health, Albany, NY, United States; Department of Biomedical Sciences, University at Albany, Albany, NY, United States
| | - William J Jaremko
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Ryan C Wilson
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Janice D Pata
- Wadsworth Center, New York State Department of Health, Albany, NY, United States; Department of Biomedical Sciences, University at Albany, Albany, NY, United States.
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21
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Feng X, Liu X, Xu R, Zhao R, Feng W, Liao J, Han W, She Q. A Unique B-Family DNA Polymerase Facilitating Error-Prone DNA Damage Tolerance in Crenarchaeota. Front Microbiol 2020; 11:1585. [PMID: 32793138 PMCID: PMC7390963 DOI: 10.3389/fmicb.2020.01585] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/17/2020] [Indexed: 12/20/2022] Open
Abstract
Sulfolobus islandicus codes for four DNA polymerases: three are of the B-family (Dpo1, Dpo2, and Dpo3), and one is of the Y-family (Dpo4). Western analysis revealed that among the four polymerases, only Dpo2 exhibited DNA damage-inducible expression. To investigate how these DNA polymerases could contribute to DNA damage tolerance in S. islandicus, we conducted genetic analysis of their encoding genes in this archaeon. Plasmid-borne gene expression revealed that Dpo2 increases cell survival upon DNA damage at the expense of mutagenesis. Gene deletion studies showed although dpo1 is essential, the remaining three genes are dispensable. Furthermore, although Dpo4 functions in housekeeping translesion DNA synthesis (TLS), Dpo2, a B-family DNA polymerase once predicted to be inactive, functions as a damage-inducible TLS enzyme solely responsible for targeted mutagenesis, facilitating GC to AT/TA conversions in the process. Together, our data indicate that Dpo2 is the main DNA polymerase responsible for DNA damage tolerance and is the primary source of targeted mutagenesis. Given that crenarchaea encoding a Dpo2 also have a low-GC composition genome, the Dpo2-dependent DNA repair pathway may be conserved in this archaeal lineage.
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Affiliation(s)
- Xu Feng
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiaotong Liu
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ruyi Xu
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ruiliang Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenqian Feng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianglan Liao
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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22
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Hogrel G, Lu Y, Alexandre N, Bossé A, Dulermo R, Ishino S, Ishino Y, Flament D. Role of RadA and DNA Polymerases in Recombination-Associated DNA Synthesis in Hyperthermophilic Archaea. Biomolecules 2020; 10:E1045. [PMID: 32674430 PMCID: PMC7407445 DOI: 10.3390/biom10071045] [Citation(s) in RCA: 4] [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: 05/29/2020] [Revised: 07/03/2020] [Accepted: 07/09/2020] [Indexed: 01/20/2023] Open
Abstract
Among the three domains of life, the process of homologous recombination (HR) plays a central role in the repair of double-strand DNA breaks and the restart of stalled replication forks. Curiously, main protein actors involved in the HR process appear to be essential for hyperthermophilic Archaea raising interesting questions about the role of HR in replication and repair strategies of those Archaea living in extreme conditions. One key actor of this process is the recombinase RadA, which allows the homologous strand search and provides a DNA substrate required for following DNA synthesis and restoring genetic information. DNA polymerase operation after the strand exchange step is unclear in Archaea. Working with Pyrococcus abyssi proteins, here we show that both DNA polymerases, family-B polymerase (PolB) and family-D polymerase (PolD), can take charge of processing the RadA-mediated recombination intermediates. Our results also indicate that PolD is far less efficient, as compared with PolB, to extend the invaded DNA at the displacement-loop (D-loop) substrate. These observations coincide with previous genetic analyses obtained on Thermococcus species showing that PolB is mainly involved in DNA repair without being essential probably because PolD could take over combined with additional partners.
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Affiliation(s)
- Gaëlle Hogrel
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| | - Yang Lu
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| | - Nicolas Alexandre
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| | - Audrey Bossé
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| | - Rémi Dulermo
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka 819-0395, Japan; (S.I.); (Y.I.)
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka 819-0395, Japan; (S.I.); (Y.I.)
| | - Didier Flament
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
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23
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Strobel EJ, Lis JT, Lucks JB. Chemical roadblocking of DNA transcription for nascent RNA display. J Biol Chem 2020; 295:6401-6412. [PMID: 32209658 DOI: 10.1074/jbc.ra120.012641] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/20/2020] [Indexed: 11/06/2022] Open
Abstract
Site-specific arrest of RNA polymerases (RNAPs) is fundamental to several technologies that assess RNA structure and function. Current in vitro transcription "roadblocking" approaches inhibit transcription elongation by blocking RNAP with a protein bound to the DNA template. One limitation of protein-mediated transcription roadblocking is that it requires inclusion of a protein factor extrinsic to the minimal in vitro transcription reaction. In this work, we developed a chemical approach for halting transcription by Escherichia coli RNAP. We first established a sequence-independent method for site-specific incorporation of chemical lesions into dsDNA templates by sequential PCR and translesion synthesis. We then show that interrupting the transcribed DNA strand with an internal desthiobiotin-triethylene glycol modification or 1,N6-etheno-2'-deoxyadenosine base efficiently and stably halts Escherichia coli RNAP transcription. By encoding an intrinsic stall site within the template DNA, our chemical transcription roadblocking approach enables display of nascent RNA molecules from RNAP in a minimal in vitro transcription reaction.
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Affiliation(s)
- Eric J Strobel
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208 .,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208
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24
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Berroyer A, Alvarado G, Larson ED. Response of Sulfolobus solfataricus Dpo4 polymerase in vitro to a DNA G-quadruplex. Mutagenesis 2020; 34:289-297. [PMID: 31169295 DOI: 10.1093/mutage/gez010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 05/06/2019] [Indexed: 12/12/2022] Open
Abstract
Repetitive DNA sequences support the formation of structures that can interrupt replication and repair, leading to breaks and mutagenesis. One particularly stable structure is G-quadruplex (G4) DNA, which is four-stranded and formed from tandemly repetitive guanine bases. When folded within a template, G4 interferes with DNA synthesis. Similar to non-duplex structures, DNA base lesions can also halt an advancing replication fork, but the Y-family polymerases solve this problem by bypassing the damage. In order to better understand how guanine-rich DNA is replicated, we have investigated the activity of the model Y-family polymerase, Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4), on guanine-rich templates in vitro. We find that Dpo4 progression on templates containing either a single GC-rich hairpin or a G4 DNA structure is greatly reduced and synthesis stalls at the structure. Human polymerase eta (hPol eta) showed the same pattern of stalling at G4; however, and in contrast to Klenow, hPol eta and Dpo4 partially synthesise into the guanine repeat. Substitution of the nucleotide selectivity residue in Dpo4 with alanine permitted ribonucleotide incorporation on unstructured templates, but this further reduced the ability of Dpo4 to synthesise across from the guanine repeats. The advancement of Dpo4 on G4 templates was highest when the reaction was supplied with only deoxycytidine triphosphate, suggesting that high-fidelity synthesis is favoured over misincorporation. Our results are consistent with a model where the Y-family polymerases pause upon encountering G4 structures but have an ability to negotiate some synthesis through tetrad-associated guanines. This suggests that the Y-family polymerases reduce mutagenesis by catalysing the accurate replication of repetitive DNA sequences, but most likely in concert with additional replication and structure resolution activities.
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Affiliation(s)
- Alexandra Berroyer
- School of Biological Sciences, Illinois State University, Normal, IL, USA
| | - Gloria Alvarado
- School of Biological Sciences, Illinois State University, Normal, IL, USA
| | - Erik D Larson
- School of Biological Sciences, Illinois State University, Normal, IL, USA
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25
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Takezawa Y, Nakama T, Shionoya M. Enzymatic Synthesis of Cu(II)-Responsive Deoxyribozymes through Polymerase Incorporation of Artificial Ligand-Type Nucleotides. J Am Chem Soc 2019; 141:19342-19350. [PMID: 31731834 DOI: 10.1021/jacs.9b08955] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metal-mediated artificial base pairs, consisting of ligand-type nucleotides and a bridging metal ion, have shown promise as functional units to develop stimuli-responsive DNA materials. Although a variety of metal-mediated base pairs have been constructed with artificial ligand-type nucleotides and various metal ions, the application of such metal-mediated base pairs has been relatively poorly explored mainly due to the cumbersome chemical synthesis of artificial DNA strands. Herein we report a facile enzymatic method to synthesize DNA strands containing a ligand-type hydroxypyridone (H) nucleotide, which forms a CuII-mediated base pair (H-CuII-H). A two-step primer extension reaction using two commercially available polymerases enabled the incorporation of a H nucleotide at an internal position of oligonucleotides. The polymerase synthesis was subsequently applied to the development of metal-responsive deoxyribozymes (DNAzymes), whose catalytic activity was regulated by the formation of a single H-CuII-H base pair in its stem region. The DNAzyme activity was reversibly switched by the alternate addition and the removal of CuII ions. Furthermore, metal-dependent orthogonal activation of a CuII-responsive H-DNAzyme and a HgII-responsive T-DNAzyme was experimentally demonstrated by utilizing both H-CuII-H as well as widely explored T-HgII-T base pairs. These results suggest that the incorporation of H-CuII-H base pairs would facilitate the rational design of metal-responsive functional DNAs. Accordingly, the facile enzymatic synthesis of artificial ligand-bearing DNAs developed in this study would significantly expand the toolbox of DNA-based supramolecular chemistry and DNA nanotechnology.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Takahiro Nakama
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
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26
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Sakhtemani R, Senevirathne V, Stewart J, Perera MLW, Pique-Regi R, Lawrence MS, Bhagwat AS. Genome-wide mapping of regions preferentially targeted by the human DNA-cytosine deaminase APOBEC3A using uracil-DNA pulldown and sequencing. J Biol Chem 2019; 294:15037-15051. [PMID: 31431505 DOI: 10.1074/jbc.ra119.008053] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 08/13/2019] [Indexed: 12/16/2022] Open
Abstract
Activation-induced deaminase (AID) and apolipoprotein B mRNA-editing enzyme catalytic subunit (APOBEC) enzymes convert cytosines to uracils, creating signature mutations that have been used to predict sites targeted by these enzymes. Mutation-based targeting maps are distorted by the error-prone or error-free repair of these uracils and by selection pressures. To directly map uracils created by AID/APOBEC enzymes, here we used uracil-DNA glycosylase and an alkoxyamine to covalently tag and sequence uracil-containing DNA fragments (UPD-Seq). We applied this technique to the genome of repair-defective, APOBEC3A-expressing bacterial cells and created a uracilation genome map, i.e. uracilome. The peak uracilated regions were in the 5'-ends of genes and operons mainly containing tRNA genes and a few protein-coding genes. We validated these findings through deep sequencing of pulldown regions and whole-genome sequencing of independent clones. The peaks were not correlated with high transcription rates or stable RNA:DNA hybrid formation. We defined the uracilation index (UI) as the frequency of occurrence of TT in UPD-Seq reads at different original TC dinucleotides. Genome-wide UI calculation confirmed that APOBEC3A modifies cytosines in the lagging-strand template during replication and in short hairpin loops. APOBEC3A's preference for tRNA genes was observed previously in yeast, and an analysis of human tumor sequences revealed that in tumors with a high percentage of APOBEC3 signature mutations, the frequency of tRNA gene mutations was much higher than in the rest of the genome. These results identify multiple causes underlying selection of cytosines by APOBEC3A for deamination, and demonstrate the utility of UPD-Seq.
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Affiliation(s)
- Ramin Sakhtemani
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | | | - Jessica Stewart
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Madusha L W Perera
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Michael S Lawrence
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Ashok S Bhagwat
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202 .,Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, Michigan 48201
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27
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28
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Archaeal DNA polymerases: new frontiers in DNA replication and repair. Emerg Top Life Sci 2018; 2:503-516. [PMID: 33525823 DOI: 10.1042/etls20180015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 09/27/2018] [Accepted: 10/08/2018] [Indexed: 11/17/2022]
Abstract
Archaeal DNA polymerases have long been studied due to their superior properties for DNA amplification in the polymerase chain reaction and DNA sequencing technologies. However, a full comprehension of their functions, recruitment and regulation as part of the replisome during genome replication and DNA repair lags behind well-established bacterial and eukaryotic model systems. The archaea are evolutionarily very broad, but many studies in the major model systems of both Crenarchaeota and Euryarchaeota are starting to yield significant increases in understanding of the functions of DNA polymerases in the respective phyla. Recent advances in biochemical approaches and in archaeal genetic models allowing knockout and epitope tagging have led to significant increases in our understanding, including DNA polymerase roles in Okazaki fragment maturation on the lagging strand, towards reconstitution of the replisome itself. Furthermore, poorly characterised DNA polymerase paralogues are finding roles in DNA repair and CRISPR immunity. This review attempts to provide a current update on the roles of archaeal DNA polymerases in both DNA replication and repair, addressing significant questions that remain for this field.
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29
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Lemor M, Kong Z, Henry E, Brizard R, Laurent S, Bossé A, Henneke G. Differential Activities of DNA Polymerases in Processing Ribonucleotides during DNA Synthesis in Archaea. J Mol Biol 2018; 430:4908-4924. [PMID: 30342933 DOI: 10.1016/j.jmb.2018.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/09/2018] [Accepted: 10/12/2018] [Indexed: 12/11/2022]
Abstract
Consistent with the fact that ribonucleotides (rNTPs) are in excess over deoxyribonucleotides (dNTPs) in vivo, recent findings indicate that replicative DNA polymerases (DNA Pols) are able to insert ribonucleotides (rNMPs) during DNA synthesis, raising crucial questions about the fidelity of DNA replication in both Bacteria and Eukarya. Here, we report that the level of rNTPs is 20-fold higher than that of dNTPs in Pyrococcus abyssi cells. Using dNTP and rNTP concentrations present in vivo, we recorded rNMP incorporation in a template-specific manner during in vitro synthesis, with the family-D DNA Pol (PolD) having the highest propensity compared with the family-B DNA Pol and the p41/p46 complex. We also showed that ribonucleotides accumulate at a relatively high frequency in the genome of wild-type Thermococcales cells, and this frequency significantly increases upon deletion of RNase HII, the major enzyme responsible for the removal of RNA from DNA. Because ribonucleotides remain in genomic DNA, we then analyzed the effects on polymerization activities by the three DNA Pols. Depending on the identity of the base and the sequence context, all three DNA Pols bypass rNMP-containing DNA templates with variable efficiency and nucleotide (mis)incorporation ability. Unexpectedly, we found that PolD correctly base-paired a single ribonucleotide opposite rNMP-containing DNA templates. An evolutionary scenario is discussed concerning rNMP incorporation into DNA and genome stability.
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Affiliation(s)
- Mélanie Lemor
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Ziqing Kong
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Etienne Henry
- CNRS, Ifremer, Univ Brest, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280, Plouzané, France
| | - Raphaël Brizard
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Sébastien Laurent
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Audrey Bossé
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Ghislaine Henneke
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France.
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30
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Vaisman A, Woodgate R. Ribonucleotide discrimination by translesion synthesis DNA polymerases. Crit Rev Biochem Mol Biol 2018; 53:382-402. [PMID: 29972306 DOI: 10.1080/10409238.2018.1483889] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The well-being of all living organisms relies on the accurate duplication of their genomes. This is usually achieved by highly elaborate replicase complexes which ensure that this task is accomplished timely and efficiently. However, cells often must resort to the help of various additional "specialized" DNA polymerases that gain access to genomic DNA when replication fork progression is hindered. One such specialized polymerase family consists of the so-called "translesion synthesis" (TLS) polymerases; enzymes that have evolved to replicate damaged DNA. To fulfill their main cellular mission, TLS polymerases often must sacrifice precision when selecting nucleotide substrates. Low base-substitution fidelity is a well-documented inherent property of these enzymes. However, incorrect nucleotide substrates are not only those which do not comply with Watson-Crick base complementarity, but also those whose sugar moiety is incorrect. Does relaxed base-selectivity automatically mean that the TLS polymerases are unable to efficiently discriminate between ribonucleoside triphosphates and deoxyribonucleoside triphosphates that differ by only a single atom? Which strategies do TLS polymerases employ to select suitable nucleotide substrates? In this review, we will collate and summarize data accumulated over the past decade from biochemical and structural studies, which aim to answer these questions.
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Affiliation(s)
- Alexandra Vaisman
- a Laboratory of Genomic Integrity , National Institute of Child Health and Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Roger Woodgate
- a Laboratory of Genomic Integrity , National Institute of Child Health and Human Development, National Institutes of Health , Bethesda , MD , USA
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31
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Variable termination sites of DNA polymerases encountering a DNA-protein cross-link. PLoS One 2018; 13:e0198480. [PMID: 29856874 PMCID: PMC5983568 DOI: 10.1371/journal.pone.0198480] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/18/2018] [Indexed: 11/19/2022] Open
Abstract
DNA-protein cross-links (DPCs) are important DNA lesions induced by endogenous crosslinking agents such as formaldehyde or acetaldehyde, as well as ionizing radiation, cancer chemotherapeutic drugs, and abortive action of some enzymes. Due to their very bulky nature, they are expected to interfere with DNA and RNA synthesis and DNA repair. DPCs are highly genotoxic and the ability of cells to deal with them is relevant for many chemotherapeutic interventions. However, interactions of DNA polymerases with DPCs have been poorly studied due to the lack of a convenient experimental model. We have used NaBH4-induced trapping of E. coli formamidopyrimidine-DNA glycosylase with DNA to construct model DNA polymerase substrates containing a DPC in single-stranded template, or in the template strand of double-stranded DNA, or in the non-template (displaced) strand of double-stranded DNA. Nine DNA polymerases belonging to families A, B, X, and Y were studied with respect to their behavior upon encountering a DPC: Klenow fragment of E. coli DNA polymerase I, Thermus aquaticus DNA polymerase I, Pyrococcus furiosus DNA polymerase, Sulfolobus solfataricus DNA polymerase IV, human DNA polymerases β, κ and λ, and DNA polymerases from bacteriophages T4 and RB69. Although none were able to fully bypass DPCs in any context, Family B DNA polymerases (T4, RB69) and Family Y DNA polymerase IV were able to elongate the primer up to the site of the cross-link if a DPC was located in single-stranded template or in the displaced strand. In other cases, DNA synthesis stopped 4-5 nucleotides before the site of the cross-link in single-stranded template or in double-stranded DNA if the polymerases could displace the downstream strand. We suggest that termination of DNA polymerases on a DPC is mostly due to the unrelieved conformational strain experienced by the enzyme when pressing against the cross-linked protein molecule.
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32
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Sano S, Miyamoto S, Kawamoto S. Rapid multiplex nucleic acid amplification test developed using paper chromatography chip and azobenzene-modified oligonucleotides. J Biosci Bioeng 2018; 126:397-403. [PMID: 29673986 DOI: 10.1016/j.jbiosc.2018.03.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/09/2018] [Accepted: 03/23/2018] [Indexed: 11/17/2022]
Abstract
Although nucleic acid amplification test (NAT) is widely used for pathogen detection, rapid NAT systems that do not require special and expensive instruments must be developed in order to enable point of care (POC)-NATs, which contribute to early initiation of treatment. As a POC-NAT system, Kaneka DNA chromatography chip (KDCC), developed using DNA tag-bound primer through modified substance, was shown to be suitable for POC testing, due to the rapid detection time, simple procedures, and low manufacturing costs. However, owing to some modifications in primer, the detection performance and amplification speed were shown to be reduced when using KDCC, counteracting the increased speed of detection. To solve these issues and improve the speed of this NAT system, we investigated a better modification substance for KDCC. Here, azobenzene-modified primers were shown to have the highest amplification speed and detection performance in KDCC, of all modifications tested in this study, showing 10-100-fold lower detection limit but maintaining the same reaction time. Additionally, rapid herpes simplex virus detection system with azobenzene modified primers was developed. We believed that this breakthrough will contribute toward enabling greater utilization of POC-NATs for medical care, especially in developing countries and clinics.
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Affiliation(s)
- Sotaro Sano
- Medical Devices Solutions Vehicle, Kaneka Corporation, 1-8 Miyamaemachi, Takasago-cho, Takasago, Hyogo 676-8688, Japan; Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan.
| | - Shigehiko Miyamoto
- Medical Devices Solutions Vehicle, Kaneka Corporation, 1-8 Miyamaemachi, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Seiji Kawamoto
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
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33
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Liyanage PS, Walker AR, Brenlla A, Cisneros GA, Romano LJ, Rueda D. Bulky Lesion Bypass Requires Dpo4 Binding in Distinct Conformations. Sci Rep 2017; 7:17383. [PMID: 29234107 PMCID: PMC5727293 DOI: 10.1038/s41598-017-17643-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/28/2017] [Indexed: 11/23/2022] Open
Abstract
Translesion DNA synthesis is an essential process that helps resume DNA replication at forks stalled near bulky adducts on the DNA. Benzo[a]pyrene (B[a]P) is a polycyclic aromatic hydrocarbon (PAH) that can be metabolically activated to benzo[a]pyrene diol epoxide (BPDE), which then can react with DNA to form carcinogenic DNA adducts. Here, we have used single-molecule florescence resonance energy transfer (smFRET) experiments, classical molecular dynamics simulations, and nucleotide incorporation assays to investigate the mechanism by which the model Y-family polymerase, Dpo4, bypasses a (+)-cis-B[a]P-N2-dG adduct in DNA. Our data show that when (+)-cis-B[a]P-N2-dG is the templating base, the B[a]P moiety is in a non-solvent exposed conformation stacked within the DNA helix, where it effectively blocks nucleotide incorporation across the adduct by Dpo4. However, when the media contains a small amount of dimethyl sulfoxide (DMSO), the adduct is able to move to a solvent-exposed conformation, which enables error-prone DNA replication past the adduct. When the primer terminates across from the adduct position, the addition of DMSO leads to the formation of an insertion complex capable of accurate nucleotide incorporation.
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Affiliation(s)
| | - Alice R Walker
- Department of Chemistry, University of North Texas, Denton, TX, 76201, USA
| | - Alfonso Brenlla
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX, 76201, USA
| | - Louis J Romano
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA.
| | - David Rueda
- Molecular Virology, Department of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK. .,Single Molecule Imaging Group, MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.
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34
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Cranford MT, Chu AM, Baguley JK, Bauer RJ, Trakselis MA. Characterization of a coupled DNA replication and translesion synthesis polymerase supraholoenzyme from archaea. Nucleic Acids Res 2017; 45:8329-8340. [PMID: 28655184 PMCID: PMC5737361 DOI: 10.1093/nar/gkx539] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/12/2017] [Indexed: 02/04/2023] Open
Abstract
The ability of the replisome to seamlessly coordinate both high fidelity and translesion DNA synthesis requires a means to regulate recruitment and binding of enzymes from solution. Co-occupancy of multiple DNA polymerases within the replisome has been observed primarily in bacteria and is regulated by posttranslational modifications in eukaryotes, and both cases are coordinated by the processivity clamp. Because of the heterotrimeric nature of the PCNA clamp in some archaea, there is potential to occupy and regulate specific polymerases at defined subunits. In addition to specific PCNA and polymerase interactions (PIP site), we have now identified and characterized a novel protein contact between the Y-family DNA polymerase and the B-family replication polymerase (YB site) bound to PCNA and DNA from Sulfolobus solfataricus. These YB contacts are essential in forming and stabilizing a supraholoenzyme (SHE) complex on DNA, effectively increasing processivity of DNA synthesis. The SHE complex can not only coordinate polymerase exchange within the complex but also provides a mechanism for recruitment of polymerases from solution based on multiequilibrium processes. Our results provide evidence for an archaeal PCNA 'tool-belt' recruitment model of multienzyme function that can facilitate both high fidelity and translesion synthesis within the replisome during DNA replication.
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Affiliation(s)
- Matthew T Cranford
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Aurea M Chu
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Joshua K Baguley
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Robert J Bauer
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA
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35
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Jiang W, Zhang B, Fan C, Wang M, Wang J, Deng Q, Liu X, Chen J, Zheng J, Liu L, Zhu TF. Mirror-image polymerase chain reaction. Cell Discov 2017; 3:17037. [PMID: 29051832 PMCID: PMC5643884 DOI: 10.1038/celldisc.2017.37] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 09/03/2017] [Accepted: 09/03/2017] [Indexed: 01/30/2023] Open
Abstract
The construction of mirror-image biological systems may open the next frontier for biomedical technology development and discovery. Here we have designed and chemically synthesized a mutant version of the thermostable Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) consisting of d-amino acids. With a total peptide length of 358 amino acid residues, it is the largest chemically synthesized d-amino acid protein reported to date. We show that the d-polymerase is able to amplify a 120-bp l-DNA sequence coding for the Escherichia coli 5S ribosomal RNA gene rrfB by mirror-image polymerase chain reaction, and that both the natural and mirror-image systems operate with strict chiral specificity. The development of efficient miPCR systems may lead to many practical applications, such as mirror-image systematic evolution of ligands by exponential enrichment for the selection of therapeutically promising nuclease-resistant l-nucleic acid aptamers.
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Affiliation(s)
- Wenjun Jiang
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Baochang Zhang
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Chuyao Fan
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Min Wang
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Jiaxing Wang
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Qiang Deng
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Xianyu Liu
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Ji Chen
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Jishen Zheng
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Lei Liu
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Ting F Zhu
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
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Hintze BJ, Richardson JS, Richardson DC. Mismodeled purines: implicit alternates and hidden Hoogsteens. Acta Crystallogr D Struct Biol 2017; 73:852-859. [PMID: 28994414 PMCID: PMC5633910 DOI: 10.1107/s2059798317013729] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/25/2017] [Indexed: 12/14/2022] Open
Abstract
Hoogsteen base pairs are seen in DNA crystal structures, but only rarely. This study tests whether Hoogsteens or other syn purines are either under-modeled or over-modeled, which are known problems for rare conformations. Candidate purines needing a syn/anti 180° flip were identified by diagnostic patterns of difference electron-density peaks. Manual inspection narrowed 105 flip candidates to 20 convincing cases, all at ≤2.7 Å resolution. Rebuilding and refinement confirmed that 14 of these were authentic purine flips. Seven examples are modeled as Watson-Crick base pairs but should be Hoogsteens (commonest at duplex termini), and three had the opposite issue. Syn/anti flips were also needed for some single-stranded purines. Five of the 20 convincing cases arose from an unmodeled alternate duplex running in the opposite direction. These are in semi-palindromic DNA sequences bound by a homodimeric protein and show flipped-purine-like difference peaks at residues where the palindrome is imperfect. This study documents types of incorrect modeling which are worth avoiding. However, the primary conclusions are that such mistakes are infrequent, the bias towards fitting anti purines is very slight, and the occurrence rate of Hoogsteen base pairs in DNA crystal structures remains unchanged from earlier estimates at ∼0.3%.
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Trakselis MA, Cranford MT, Chu AM. Coordination and Substitution of DNA Polymerases in Response to Genomic Obstacles. Chem Res Toxicol 2017; 30:1956-1971. [PMID: 28881136 DOI: 10.1021/acs.chemrestox.7b00190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability for DNA polymerases (Pols) to overcome a variety of obstacles in its path to maintain genomic stability during replication is a complex endeavor. It requires the coordination of multiple Pols with differing specificities through molecular control and access to the replisome. Although a number of contacts directly between Pols and accessory proteins have been identified, forming the basis of a variety of holoenzyme complexes, the dynamics of Pol active site substitutions remain uncharacterized. Substitutions can occur externally by recruiting new Pols to replisome complexes through an "exchange" of enzyme binding or internally through a "switch" in the engagement of DNA from preformed associated enzymes contained within supraholoenzyme complexes. Models for how high fidelity (HiFi) replication Pols can be substituted by translesion synthesis (TLS) Pols at sites of damage during active replication will be discussed. These substitution mechanisms may be as diverse as the number of Pol families and types of damage; however, common themes can be recognized across species. Overall, Pol substitutions will be controlled by explicit protein contacts, complex multiequilibrium processes, and specific kinetic activities. Insight into how these dynamic processes take place and are regulated will be of utmost importance for our greater understanding of the specifics of TLS as well as providing for future novel chemotherapeutic and antimicrobial strategies.
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Affiliation(s)
- Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
| | - Matthew T Cranford
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
| | - Aurea M Chu
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
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Increased Processivity, Misincorporation, and Nucleotide Incorporation Efficiency in Sulfolobus solfataricus Dpo4 Thumb Domain Mutants. Appl Environ Microbiol 2017; 83:AEM.01013-17. [PMID: 28710267 DOI: 10.1128/aem.01013-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/04/2017] [Indexed: 01/21/2023] Open
Abstract
The present study aimed to increase the processivity of Sulfolobus solfataricus DNA polymerase Dpo4. Protein engineering and bioinformatics were used to compile a library of potential Dpo4 mutation sites. Ten potential mutants were identified and constructed. A primer extension assay was used to evaluate the processivity of Dpo4 mutants. Thumb (A181D) and finger (E63K) domain mutants showed a processivity of 20 and 19 nucleotides (nt), respectively. A little finger domain mutant (I248Y) exhibited a processivity of 17 nt, only 1 nt more than wild-type Dpo4. Furthermore, the A181D mutant showed lower fidelity and higher nucleotide incorporation efficiency (4.74 × 10-4 s-1 μM-1) than E63K and I248Y mutants. When tasked with bypassing damage, the A181D mutant exhibited a 3.81-fold and 2.62-fold higher catalytic efficiency (kcat/Km ) at incorporating dCTP and dATP, respectively, than wild-type Dpo4. It also showed a 55% and 91.5% higher catalytic efficiency when moving beyond the damaged 8-oxoG:C and 8-oxoG:A base pairs, respectively, compared to wild-type Dpo4. Protein engineering and bioinformatics methods can effectively increase the processivity and translesion synthesis ability of Dpo4.IMPORTANCE DNA polymerases with poor fidelity can be exploited to store data and record changes in response to the intracellular environment. Sulfolobus solfataricus Dpo4 is such an enzyme, although its use is hindered by its low processivity. In this work, we used a bioinformatics and protein engineering approach to generate Dpo4 mutants with improved processivity. We identified the Dpo4 thumb domain as the most relevant in controlling processivity.
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Pech A, Achenbach J, Jahnz M, Schülzchen S, Jarosch F, Bordusa F, Klussmann S. A thermostable d-polymerase for mirror-image PCR. Nucleic Acids Res 2017; 45:3997-4005. [PMID: 28158820 PMCID: PMC5605242 DOI: 10.1093/nar/gkx079] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/27/2017] [Indexed: 01/13/2023] Open
Abstract
Biological evolution resulted in a homochiral world in which nucleic acids consist exclusively of d-nucleotides and proteins made by ribosomal translation of l-amino acids. From the perspective of synthetic biology, however, particularly anabolic enzymes that could build the mirror-image counterparts of biological macromolecules such as l-DNA or l-RNA are lacking. Based on a convergent synthesis strategy, we have chemically produced and characterized a thermostable mirror-image polymerase that efficiently replicates and amplifies mirror-image (l)-DNA. This artificial enzyme, dubbed d-Dpo4-3C, is a mutant of Sulfolobus solfataricus DNA polymerase IV consisting of 352 d-amino acids. d-Dpo4-3C was reliably deployed in classical polymerase chain reactions (PCR) and it was used to assemble a first mirror-image gene coding for the protein Sso7d. We believe that this d-polymerase provides a valuable tool to further investigate the mysteries of biological (homo)chirality and to pave the way for potential novel life forms running on a mirror-image genome.
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Affiliation(s)
- Andreas Pech
- NOXXON Pharma AG, Weinbergweg 23, 06120 Halle (Saale), Germany
| | - John Achenbach
- NOXXON Pharma AG, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Michael Jahnz
- NOXXON Pharma AG, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | | | - Florian Jarosch
- NOXXON Pharma AG, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Frank Bordusa
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Sven Klussmann
- NOXXON Pharma AG, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
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40
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Lee YA, Lee YC, Geacintov NE, Shafirovich V. Translesion synthesis past guanine(C8)-thymine(N3) intrastrand cross-links catalyzed by selected A- and Y-family polymerases. MOLECULAR BIOSYSTEMS 2017; 12:1892-900. [PMID: 27102383 DOI: 10.1039/c6mb00160b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Oxidatively generated guanine radicals in DNA can undergo various nucleophilic reactions including the formation of C8-guanine cross-links with adjacent or nearby N3-thymines in DNA in the presence of O2. These G[8-3]T lesions have been identified in the DNA of human cells exposed to oxidative stress, and are most likely genotoxic if not removed by cellular defence mechanisms. The abilities of several representative polymerases to bypass the G[8-3]T lesions in two different sequence contexts, G*T* and G*CT*, were assessed in vitro. The polymerase BF (bacillus fragment) from Bacillus stearothermophilus, the Y-family archaeal polymerases Dpo4 from Sulfolobus sulfataricus P2, and human DNA pol κ and pol η were selected for the study. The A-family polymerase BF was strongly blocked, while relatively weak translesion synthesis was observed in the case of Y-family polymerases Dpo4 and pol κ. Primer extension catalyzed by pol η was also partially stalled at various positions at or near the G[8-3]T cross-linked bases, but a significant and distributive primer extension was observed beyond the sites of the lesions with the efficiency being consistently greater in the case of G*CT* than in the case of G*T* lesions. The results obtained with pol η are compared with translesion synthesis past other intrastrand cross-linked lesions with previously published results of others that include the isomeric G[8-5m]T lesions generated by ionizing radiation, the cis-syn cyclobutane pyrimidine dimer and the 6-4 photoproduct generated by UV irradiation, and the Pt-G*G* lesions derived from the reactions of the chemotherapeutic agent cisplatin with DNA.
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Affiliation(s)
- Young-Ae Lee
- Department of Chemistry, Yeungnam University, Gyeongsan, 38541, Korea
| | - Yuan-Cho Lee
- Chemistry Department, New York University, 31 Washington Place, New York, NY10003-5180, USA.
| | - Nicholas E Geacintov
- Chemistry Department, New York University, 31 Washington Place, New York, NY10003-5180, USA.
| | - Vladimir Shafirovich
- Chemistry Department, New York University, 31 Washington Place, New York, NY10003-5180, USA.
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41
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DNA binding strength increases the processivity and activity of a Y-Family DNA polymerase. Sci Rep 2017; 7:4756. [PMID: 28684739 PMCID: PMC5500549 DOI: 10.1038/s41598-017-02578-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/12/2017] [Indexed: 11/09/2022] Open
Abstract
DNA polymerase (pol) processivity, i.e., the bases a polymerase extends before falling off the DNA, and activity are important for copying difficult DNA sequences, including simple repeats. Y-family pols would be appealing for copying difficult DNA and incorporating non-natural dNTPs, due to their low fidelity and loose active site, but are limited by poor processivity and activity. In this study, the binding between Dbh and DNA was investigated to better understand how to rationally design enhanced processivity in a Y-family pol. Guided by structural simulation, a fused pol Sdbh with non-specific dsDNA binding protein Sso7d in the N-terminus was designed. This modification increased in vitro processivity 4-fold as compared to the wild-type Dbh. Additionally, bioinformatics was used to identify amino acid mutations that would increase stabilization of Dbh bound to DNA. The variant SdbhM76I further improved the processivity of Dbh by 10 fold. The variant SdbhKSKIP241–245RVRKS showed higher activity than Dbh on the incorporation of dCTP (correct) and dATP (incorrect) opposite the G (normal) or 8-oxoG(damaged) template base. These results demonstrate the capability to rationally design increases in pol processivity and catalytic efficiency through computational DNA binding predictions and the addition of non-specific DNA binding domains.
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42
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Identification and characterization of a heterotrimeric archaeal DNA polymerase holoenzyme. Nat Commun 2017; 8:15075. [PMID: 28462924 PMCID: PMC5418573 DOI: 10.1038/ncomms15075] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/27/2017] [Indexed: 11/26/2022] Open
Abstract
Since their initial characterization over 30 years ago, it has been believed that the archaeal B-family DNA polymerases are single-subunit enzymes. This contrasts with the multi-subunit B-family replicative polymerases of eukaryotes. Here we reveal that the highly studied PolB1 from Sulfolobus solfataricus exists as a heterotrimeric complex in cell extracts. Two small subunits, PBP1 and PBP2, associate with distinct surfaces of the larger catalytic subunit and influence the enzymatic properties of the DNA polymerase. Thus, multi-subunit replicative DNA polymerase holoenzymes are present in all three domains of life. We reveal the architecture of the assembly by a combination of cross-linking coupled with mass spectrometry, X-ray crystallography and single-particle electron microscopy. The small subunits stabilize the holoenzyme assembly and the acidic tail of one small subunit mitigates the ability of the enzyme to perform strand-displacement synthesis, with important implications for lagging strand DNA synthesis. The current model for B-family DNA polymerases in archaea is one of single-subunit enzymes in contrast to the multi-subunit complexes in eukaryotes. Here the authors show that PolB1 from Sulfolobus solfataricus exists as a heterotrimeric complex in cell extracts.
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43
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Lee E, Fowler JD, Suo Z, Wu Z. Backbone assignment of the binary complex of the full length Sulfolobus solfataricus DNA polymerase IV and DNA. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:39-43. [PMID: 27738883 DOI: 10.1007/s12104-016-9717-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/08/2016] [Indexed: 05/03/2023]
Abstract
Sulfolobus solfataricus DNA polymerase IV (Dpo4), a model Y-family DNA polymerase, bypasses a wide range of DNA lesions in vitro and in vivo. In this paper, we report the backbone chemical shift assignments of the full length Dpo4 in its binary complex with a 14/14-mer DNA substrate. Upon DNA binding, several β-stranded regions in the isolated catalytic core and little finger/linker fragments of Dpo4 become more structured. This work serves as a foundation for our ongoing investigation of conformational dynamics of Dpo4 and future determination of the first solution structures of a DNA polymerase and its binary and ternary complexes.
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Affiliation(s)
- Eunjeong Lee
- Department of Chemistry and Biochemistry, The Ohio State University, 876 Biological Sciences, 484 West 12th Ave., Columbus, OH, 43210, USA
| | - Jason D Fowler
- Department of Chemistry and Biochemistry, The Ohio State University, 876 Biological Sciences, 484 West 12th Ave., Columbus, OH, 43210, USA
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University, 876 Biological Sciences, 484 West 12th Ave., Columbus, OH, 43210, USA
| | - Zhengrong Wu
- Department of Chemistry and Biochemistry, The Ohio State University, 876 Biological Sciences, 484 West 12th Ave., Columbus, OH, 43210, USA.
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44
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Total chemical synthesis of a thermostable enzyme capable of polymerase chain reaction. Cell Discov 2017; 3:17008. [PMID: 28265464 PMCID: PMC5335361 DOI: 10.1038/celldisc.2017.8] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/06/2017] [Indexed: 01/30/2023] Open
Abstract
Polymerase chain reaction (PCR) has been a defining tool in modern biology. Towards realizing mirror-image PCR, we have designed and chemically synthesized a mutant version of the 352-residue thermostable Sulfolobus solfataricus P2 DNA polymerase IV with l-amino acids and tested its PCR activity biochemically. To the best of our knowledge, this enzyme is the largest chemically synthesized protein reported to date. We show that with optimization of PCR conditions, the fully synthetic polymerase is capable of amplifying template sequences of up to 1.5 kb. The establishment of this synthetic route for chemically synthesizing DNA polymerase IV is a stepping stone towards building a d-enzyme system for mirror-image PCR, which may open up an avenue for the creation of many mirror-image molecular tools such as mirror-image systematic evolution of ligands by exponential enrichment.
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45
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Westphal K, Zdrowowicz M, Zylicz-Stachula A, Rak J. Chemically–enzymatic synthesis of photosensitive DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 167:228-235. [DOI: 10.1016/j.jphotobiol.2017.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/20/2016] [Accepted: 01/03/2017] [Indexed: 01/24/2023]
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46
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Song YS, Shu YG, Zhou X, Ou-Yang ZC, Li M. Proofreading of DNA polymerase: a new kinetic model with higher-order terminal effects. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:025101. [PMID: 27842005 DOI: 10.1088/0953-8984/29/2/025101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The fidelity of DNA replication by DNA polymerase (DNAP) has long been an important issue in biology. While numerous experiments have revealed details of the molecular structure and working mechanism of DNAP which consists of both a polymerase site and an exonuclease (proofreading) site, there were quite a few theoretical studies on the fidelity issue. The first model which explicitly considered both sites was proposed in the 1970s and the basic idea was widely accepted by later models. However, all these models did not systematically investigate the dominant factor on DNAP fidelity, i.e. the higher-order terminal effects through which the polymerization pathway and the proofreading pathway coordinate to achieve high fidelity. In this paper, we propose a new and comprehensive kinetic model of DNAP based on some recent experimental observations, which includes previous models as special cases. We present a rigorous and unified treatment of the corresponding steady-state kinetic equations of any-order terminal effects, and derive analytical expressions for fidelity in terms of kinetic parameters under bio-relevant conditions. These expressions offer new insights on how the higher-order terminal effects contribute substantially to the fidelity in an order-by-order way, and also show that the polymerization-and-proofreading mechanism is dominated only by very few key parameters. We then apply these results to calculate the fidelity of some real DNAPs, which are in good agreements with previous intuitive estimates given by experimentalists.
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Affiliation(s)
- Yong-Shun Song
- School of Physical Sciences, University of Chinese Academy of Sciences, No 19A Yuquan Road, Beijing 100049, People's Republic of China
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47
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Raper AT, Reed AJ, Gadkari VV, Suo Z. Advances in Structural and Single-Molecule Methods for Investigating DNA Lesion Bypass and Repair Polymerases. Chem Res Toxicol 2016; 30:260-269. [PMID: 28092942 DOI: 10.1021/acs.chemrestox.6b00342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Innovative advances in X-ray crystallography and single-molecule biophysics have yielded unprecedented insight into the mechanisms of DNA lesion bypass and damage repair. Time-dependent X-ray crystallography has been successfully applied to view the bypass of 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), a major oxidative DNA lesion, and the incorporation of the triphosphate form, 8-oxo-dGTP, catalyzed by human DNA polymerase β. Significant findings of these studies are highlighted here, and their contributions to the current mechanistic understanding of mutagenic translesion DNA synthesis (TLS) and base excision repair are discussed. In addition, single-molecule Förster resonance energy transfer (smFRET) techniques have recently been adapted to investigate nucleotide binding and incorporation opposite undamaged dG and 8-oxoG by Sulfolobus solfataricus DNA polymerase IV (Dpo4), a model Y-family DNA polymerase. The mechanistic response of Dpo4 to a DNA lesion and the complex smFRET technique are described here. In this perspective, we also describe how time-dependent X-ray crystallography and smFRET can be used to achieve the spatial and temporal resolutions necessary to answer some of the mechanistic questions that remain in the fields of TLS and DNA damage repair.
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Affiliation(s)
- Austin T Raper
- Department of Chemistry and Biochemistry and The Ohio State Biochemistry Program, The Ohio State University , Columbus, Ohio 43210, United States
| | - Andrew J Reed
- Department of Chemistry and Biochemistry and The Ohio State Biochemistry Program, The Ohio State University , Columbus, Ohio 43210, United States
| | - Varun V Gadkari
- Department of Chemistry and Biochemistry and The Ohio State Biochemistry Program, The Ohio State University , Columbus, Ohio 43210, United States
| | - Zucai Suo
- Department of Chemistry and Biochemistry and The Ohio State Biochemistry Program, The Ohio State University , Columbus, Ohio 43210, United States
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48
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Gao X, Huang H. Synthesis of N 7-Alkyl-9-deaza-2'-deoxyguanosines Containing Polar N 7 Chains. Examples of Chemically Stable Analogues of N 7-Hydroxyethyl and N 7-Oxoethyl Adducts of 2'-Deoxyguanosine. J Org Chem 2016; 81:11697-11705. [PMID: 27805399 DOI: 10.1021/acs.joc.6b02110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Development of chemically stable analogues of unstable DNA lesions enables accurate study of polymerase bypass. We report the design and synthesis of N7-hydroxyethyl-9-deaza-2'-deoxyguanosine and N7-oxoethyl-9-deaza-2'-deoxyguanosine as the analogues of N7-hydroxyethyl-2'-deoxyguanosine and N7-oxoethyl-2'-deoxyguanosine, respectively. We also developed the synthesis of these two nucleosides whose N7 side chains are protected by TBS for the convenience of conversion to phosphoramidites.
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Affiliation(s)
- Xun Gao
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology , Newark, New Jersey 07102, United States
| | - Haidong Huang
- 4Catalyzer, 530 Old Whitfield Street, Guilford, Connecticut 06437, United States
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49
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Manderville RA, Wetmore SD. Understanding the Mutagenicity of O-Linked and C-Linked Guanine DNA Adducts: A Combined Experimental and Computational Approach. Chem Res Toxicol 2016; 30:177-188. [DOI: 10.1021/acs.chemrestox.6b00323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Richard A. Manderville
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Stacey D. Wetmore
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, AB, Canada T1K 3M4
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50
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Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation. Proc Natl Acad Sci U S A 2016; 113:E4005-14. [PMID: 27339134 DOI: 10.1073/pnas.1602591113] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Viral RNA-dependent RNA polymerases (RdRPs) play essential roles in viral genome replication and transcription. We previously reported several structural states of the poliovirus RdRP nucleotide addition cycle (NAC) that revealed a unique palm domain-based active site closure mechanism and proposed a six-state NAC model including a hypothetical state representing translocation intermediates. Using the RdRP from another human enterovirus, enterovirus 71, here we report seven RdRP elongation complex structures derived from a crystal lattice that allows three NAC events. These structures suggested a key order of events in initial NTP binding and NTP-induced active site closure and revealed a bona fide translocation intermediate featuring asymmetric movement of the template-product duplex. Our work provides essential missing links in understanding NTP recognition and translocation mechanisms in viral RdRPs and emphasizes the uniqueness of the viral RdRPs compared with other processive polymerases.
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