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Zhang H. Mechanisms of mutagenesis induced by DNA lesions: multiple factors affect mutations in translesion DNA synthesis. Crit Rev Biochem Mol Biol 2020; 55:219-251. [PMID: 32448001 DOI: 10.1080/10409238.2020.1768205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Environmental mutagens lead to mutagenesis. However, the mechanisms are very complicated and not fully understood. Environmental mutagens produce various DNA lesions, including base-damaged or sugar-modified DNA lesions, as well as epigenetically modified DNA. DNA polymerases produce mutation spectra in translesion DNA synthesis (TLS) through misincorporation of incorrect nucleotides, frameshift deletions, blockage of DNA replication, imbalance of leading- and lagging-strand DNA synthesis, and genome instability. Motif or subunit in DNA polymerases further affects the mutations in TLS. Moreover, protein interactions and accessory proteins in DNA replisome also alter mutations in TLS, demonstrated by several representative DNA replisomes. Finally, in cells, multiple DNA polymerases or cellular proteins collaborate in TLS and reduce in vivo mutagenesis. Summaries and perspectives were listed. This review shows mechanisms of mutagenesis induced by DNA lesions and the effects of multiple factors on mutations in TLS in vitro and in vivo.
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Affiliation(s)
- Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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Zou Z, Liang T, Xu Z, Xie J, Zhang S, Chen W, Wan S, Ling Y, Zhang H. Protein interactions in T7 DNA replisome inhibit the bypass of abasic site by DNA polymerase. Mutagenesis 2019; 34:355-361. [PMID: 31318416 DOI: 10.1093/mutage/gez013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 05/14/2019] [Indexed: 11/13/2022] Open
Abstract
Abasic site as a common DNA lesion blocks DNA replication and is highly mutagenic. Protein interactions in T7 DNA replisome facilitate DNA replication and translesion DNA synthesis. However, bypass of an abasic site by T7 DNA replisome has never been investigated. In this work, we used T7 DNA replisome and T7 DNA polymerase alone as two models to study DNA replication on encountering an abasic site. Relative to unmodified DNA, abasic site strongly inhibited primer extension and completely blocked strand-displacement DNA synthesis, due to the decreased fraction of enzyme-DNA productive complex and the reduced average extension rates. Moreover, abasic site at DNA fork inhibited the binding of DNA polymerase or helicase onto fork and the binding between polymerase and helicase at fork. Notably and unexpectedly, we found DNA polymerase alone bypassed an abasic site on primer/template (P/T) substrate more efficiently than did polymerase and helicase complex bypass it at fork. The presence of gp2.5 further inhibited the abasic site bypass at DNA fork. Kinetic analysis showed that this inhibition at fork relative to that on P/T was due to the decreased fraction of productive complex instead of the average extension rates. Therefore, we found that protein interactions in T7 DNA replisome inhibited the bypass of DNA lesion, different from all the traditional concept that protein interactions or accessory proteins always promote DNA replication and DNA damage bypass, providing new insights in translesion DNA synthesis performed by DNA replisome.
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Affiliation(s)
- Zhenyu Zou
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Tingting Liang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Zhongyan Xu
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayu Xie
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Shuming Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Weina Chen
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Siqi Wan
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yihui Ling
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, China
| | - Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.,The Key Laboratory of Environment and Health Among Universities and Colleges in Fujian, School of Public Health, Fujian Medical University, Fuzhou, China
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Zou Z, Chen Z, Cai Y, Yang H, Du K, Li B, Jiang Y, Zhang H. Consecutive ribonucleoside monophosphates on template inhibit DNA replication by T7 DNA polymerase or by T7 polymerase and helicase complex. Biochimie 2018; 151:128-138. [DOI: 10.1016/j.biochi.2018.05.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 05/31/2018] [Indexed: 12/19/2022]
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Zou Z, Chen Z, Xue Q, Xu Y, Xiong J, Yang P, Le S, Zhang H. Protein Interactions in the T7 DNA Replisome Facilitate DNA Damage Bypass. Chembiochem 2018; 19:1740-1749. [PMID: 29900646 DOI: 10.1002/cbic.201800203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Indexed: 01/07/2023]
Abstract
The DNA replisome inevitably encounters DNA damage during DNA replication. The T7 DNA replisome contains a DNA polymerase (gp5), the processivity factor thioredoxin (trx), a helicase-primase (gp4), and a ssDNA-binding protein (gp2.5). T7 protein interactions mediate this DNA replication. However, whether the protein interactions could promote DNA damage bypass is still little addressed. In this study, we investigated strand-displacement DNA synthesis past 8-oxoG or O6 -MeG lesions at the synthetic DNA fork by the T7 DNA replisome. DNA damage does not obviously affect the binding affinities between helicase, polymerase, and DNA fork. Relative to unmodified G, both 8-oxoG and O6 -MeG-as well as GC-rich template sequence clusters-inhibit strand-displacement DNA synthesis and produce partial extension products. Relative to the gp4 ΔC-tail, gp4 promotes DNA damage bypass. The presence of gp2.5 also promotes it. Thus, the interactions of polymerase with helicase and ssDNA-binding protein facilitate DNA damage bypass. Accessory proteins in other complicated DNA replisomes also facilitate bypassing DNA damage in similar manner. This work provides new mechanistic information relating to DNA damage bypass by the DNA replisome.
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Affiliation(s)
- Zhenyu Zou
- Public Health Laboratory Sciences and Toxicology, West China School of Public Health, Sichuan University, No.17 People's South Road, Chengdu, 6100041, P. R. China
| | - Ze Chen
- Public Health Laboratory Sciences and Toxicology, West China School of Public Health, Sichuan University, No.17 People's South Road, Chengdu, 6100041, P. R. China
| | - Qizhen Xue
- Public Health Laboratory Sciences and Toxicology, West China School of Public Health, Sichuan University, No.17 People's South Road, Chengdu, 6100041, P. R. China
| | - Ying Xu
- Public Health Laboratory Sciences and Toxicology, West China School of Public Health, Sichuan University, No.17 People's South Road, Chengdu, 6100041, P. R. China
| | - Jingyuan Xiong
- Public Health Laboratory Sciences and Toxicology, West China School of Public Health, Sichuan University, No.17 People's South Road, Chengdu, 6100041, P. R. China
| | - Ping Yang
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, 511439, P. R. China
| | - Shuai Le
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Huidong Zhang
- Public Health Laboratory Sciences and Toxicology, West China School of Public Health, Sichuan University, No.17 People's South Road, Chengdu, 6100041, P. R. China
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Peralta-Castro A, Baruch-Torres N, Brieba LG. Plant organellar DNA primase-helicase synthesizes RNA primers for organellar DNA polymerases using a unique recognition sequence. Nucleic Acids Res 2017; 45:10764-10774. [PMID: 28977480 PMCID: PMC5737085 DOI: 10.1093/nar/gkx745] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/24/2017] [Indexed: 11/14/2022] Open
Abstract
DNA primases recognize single-stranded DNA (ssDNA) sequences to synthesize RNA primers during lagging-strand replication. Arabidopsis thaliana encodes an ortholog of the DNA primase-helicase from bacteriophage T7, dubbed AtTwinkle, that localizes in chloroplasts and mitochondria. Herein, we report that AtTwinkle synthesizes RNA primers from a 5′-(G/C)GGA-3′ template sequence. Within this sequence, the underlined nucleotides are cryptic, meaning that they are essential for template recognition but are not instructional during RNA synthesis. Thus, in contrast to all primases characterized to date, the sequence recognized by AtTwinkle requires two nucleotides (5′-GA-3′) as a cryptic element. The divergent zinc finger binding domain (ZBD) of the primase module of AtTwinkle may be responsible for template sequence recognition. During oligoribonucleotide synthesis, AtTwinkle shows a strong preference for rCTP as its initial ribonucleotide and a moderate preference for rGMP or rCMP incorporation during elongation. RNA products synthetized by AtTwinkle are efficiently used as primers for plant organellar DNA polymerases. In sum, our data strongly suggest that AtTwinkle primes organellar DNA polymerases during lagging strand synthesis in plant mitochondria and chloroplast following a primase-mediated mechanism. This mechanism contrasts to lagging-strand DNA replication in metazoan mitochondria, in which transcripts synthesized by mitochondrial RNA polymerase prime mitochondrial DNA polymerase γ.
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Affiliation(s)
- Antolín Peralta-Castro
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, CP 36821, México
| | - Noe Baruch-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, CP 36821, México
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, CP 36821, México
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Liu B, Xue Q, Tang Y, Cao J, Guengerich FP, Zhang H. Mechanisms of mutagenesis: DNA replication in the presence of DNA damage. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2016; 768:53-67. [PMID: 27234563 PMCID: PMC5237373 DOI: 10.1016/j.mrrev.2016.03.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 02/07/2016] [Accepted: 03/14/2016] [Indexed: 10/22/2022]
Abstract
Environmental mutagens cause DNA damage that disturbs replication and produces mutations, leading to cancer and other diseases. We discuss mechanisms of mutagenesis resulting from DNA damage, from the level of DNA replication by a single polymerase to the complex DNA replisome of some typical model organisms (including bacteriophage T7, T4, Sulfolobus solfataricus, Escherichia coli, yeast and human). For a single DNA polymerase, DNA damage can affect replication in three major ways: reducing replication fidelity, causing frameshift mutations, and blocking replication. For the DNA replisome, protein interactions and the functions of accessory proteins can yield rather different results even with a single DNA polymerase. The mechanism of mutation during replication performed by the DNA replisome is a long-standing question. Using new methods and techniques, the replisomes of certain organisms and human cell extracts can now be investigated with regard to the bypass of DNA damage. In this review, we consider the molecular mechanism of mutagenesis resulting from DNA damage in replication at the levels of single DNA polymerases and complex DNA replisomes, including translesion DNA synthesis.
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Affiliation(s)
- Binyan Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - Qizhen Xue
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - Yong Tang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - F Peter Guengerich
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Huidong Zhang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China.
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Abstract
I spent my childhood and adolescence in North and South Carolina, attended Duke University, and then entered Duke Medical School. One year in the laboratory of George Schwert in the biochemistry department kindled my interest in biochemistry. After one year of residency on the medical service of Duke Hospital, chaired by Eugene Stead, I joined the group of Arthur Kornberg at Stanford Medical School as a postdoctoral fellow. Two years later I accepted a faculty position at Harvard Medical School, where I remain today. During these 50 years, together with an outstanding group of students, postdoctoral fellows, and collaborators, I have pursued studies on DNA replication. I have experienced the excitement of discovering a number of important enzymes in DNA replication that, in turn, triggered an interest in the dynamics of a replisome. My associations with industry have been stimulating and fostered new friendships. I could not have chosen a better career.
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Affiliation(s)
- Charles C Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115;
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