1
|
Zhang T, Rawal Y, Jiang H, Kwon Y, Sung P, Greenberg RA. Break-induced replication orchestrates resection-dependent template switching. Nature 2023; 619:201-208. [PMID: 37316655 PMCID: PMC10937050 DOI: 10.1038/s41586-023-06177-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 05/05/2023] [Indexed: 06/16/2023]
Abstract
Break-induced telomere synthesis (BITS) is a RAD51-independent form of break-induced replication that contributes to alternative lengthening of telomeres1,2. This homology-directed repair mechanism utilizes a minimal replisome comprising proliferating cell nuclear antigen (PCNA) and DNA polymerase-δ to execute conservative DNA repair synthesis over many kilobases. How this long-tract homologous recombination repair synthesis responds to complex secondary DNA structures that elicit replication stress remains unclear3-5. Moreover, whether the break-induced replisome orchestrates additional DNA repair events to ensure processivity is also unclear. Here we combine synchronous double-strand break induction with proteomics of isolated chromatin segments (PICh) to capture the telomeric DNA damage response proteome during BITS1,6. This approach revealed a replication stress-dominated response, highlighted by repair synthesis-driven DNA damage tolerance signalling through RAD18-dependent PCNA ubiquitination. Furthermore, the SNM1A nuclease was identified as the major effector of ubiquitinated PCNA-dependent DNA damage tolerance. SNM1A recognizes the ubiquitin-modified break-induced replisome at damaged telomeres, and this directs its nuclease activity to promote resection. These findings show that break-induced replication orchestrates resection-dependent lesion bypass, with SNM1A nuclease activity serving as a critical effector of ubiquitinated PCNA-directed recombination in mammalian cells.
Collapse
Affiliation(s)
- Tianpeng Zhang
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yashpal Rawal
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Haoyang Jiang
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Roger A Greenberg
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
2
|
Genetic Predisposition to Colorectal Cancer: How Many and Which Genes to Test? Int J Mol Sci 2023; 24:ijms24032137. [PMID: 36768460 PMCID: PMC9916931 DOI: 10.3390/ijms24032137] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/25/2023] Open
Abstract
Colorectal cancer is one of the most common tumors, and genetic predisposition is one of the key risk factors in the development of this malignancy. Lynch syndrome and familial adenomatous polyposis are the best-known genetic diseases associated with hereditary colorectal cancer. However, some other genetic disorders confer an increased risk of colorectal cancer, such as Li-Fraumeni syndrome (TP53 gene), MUTYH-associated polyposis (MUTYH gene), Peutz-Jeghers syndrome (STK11 gene), Cowden syndrome (PTEN gene), and juvenile polyposis syndrome (BMPR1A and SMAD4 genes). Moreover, the recent advances in molecular techniques, in particular Next-Generation Sequencing, have led to the identification of many new genes involved in the predisposition to colorectal cancers, such as RPS20, POLE, POLD1, AXIN2, NTHL1, MSH3, RNF43 and GREM1. In this review, we summarized the past and more recent findings in the field of cancer predisposition genes, with insights into the role of the encoded proteins and into the associated genetic disorders. Furthermore, we discussed the possible clinical utility of genetic testing in terms of prevention protocols and therapeutic approaches.
Collapse
|
3
|
Common Markers and Small Molecule Inhibitors in Golgi Studies. Methods Mol Biol 2022; 2557:453-493. [PMID: 36512231 PMCID: PMC10178357 DOI: 10.1007/978-1-0716-2639-9_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this chapter, we provide a detailed guide for the application of commonly used small molecules to study Golgi structure and function in vitro. Furthermore, we have curated a concise, validated list of endomembrane markers typically used in downstream assays to examine the consequent effect on the Golgi via microscopy and western blot after drug treatment. This chapter will be useful for researchers beginning their foray into the field of intracellular trafficking and Golgi biology.
Collapse
|
4
|
Kitazono I, Akahane T, Kobayashi Y, Yanazume S, Tabata K, Tasaki T, Noguchi H, Kirishima M, Higashi M, Kobayashi H, Tanimoto A. Pelvic Carcinosarcoma Showing a Diverse Histology and Hierarchical Gene Mutation with a Common POLE Mutation to Endometrial Endometroid Carcinoma: A Case Report. Int J Surg Pathol 2022; 30:891-899. [PMID: 35360975 DOI: 10.1177/10668969221088880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
POLE mutation-type endometrial cancer is characterized by an extremely high tumor mutation burden. Most POLE mutation-type endometrial cancers are histologically endometrioid carcinomas, and POLE mutation-type carcinosarcomas are rare among endometrial cancers. We report a case of endometrial and pelvic cancer in a 53-year-old woman who was analyzed using next-generating sequencing. The endometrial lesion harbored a p.T457del POLE mutation with an elevated tumor mutation burden and low microsatellite instability. The pelvic lesion showed divergent histological features, consisting of high-grade endometrioid carcinoma, neuroendocrine carcinoma, and chondrosarcoma. In addition to the common POLE mutation detected in the endometrial lesion, the pelvic lesion in each element showed additional gene mutations in a hierarchical manner. Therefore, it is indicated that the p.T457del POLE mutation is a pathogenic mutation and may be related to POLE mutation-induced carcinogenesis and divergent morphogenesis in endometrial cancer.
Collapse
Affiliation(s)
- Ikumi Kitazono
- Department of Pathology, 208512Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Toshiaki Akahane
- Department of Pathology, 208512Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Center for Human Genome and Gene Analysis, Kagoshima University Hospital, 9-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Yusuke Kobayashi
- Course of Advanced Cancer Medicine for Gynecologic Cancer, 208512Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Shintaro Yanazume
- Department of Obstetrics and Gynecology, 208512Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kazuhiro Tabata
- Department of Pathology, 208512Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Takashi Tasaki
- Department of Pathology, 208512Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hirotsugu Noguchi
- Department of Pathology, 208512Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Mari Kirishima
- Department of Pathology, 208512Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Michiyo Higashi
- Department of Pathology, 208512Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hiroaki Kobayashi
- Course of Advanced Cancer Medicine for Gynecologic Cancer, 208512Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Department of Obstetrics and Gynecology, 208512Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Akihide Tanimoto
- Department of Pathology, 208512Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Center for Human Genome and Gene Analysis, Kagoshima University Hospital, 9-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| |
Collapse
|
5
|
Cadherin‑16 inhibits thyroid carcinoma cell proliferation and invasion. Oncol Lett 2022; 23:145. [PMID: 35350592 PMCID: PMC8941525 DOI: 10.3892/ol.2022.13265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/04/2022] [Indexed: 11/11/2022] Open
Abstract
Cadherin-16 (CDH16), a member of the cadherin family of adhesion molecules, serves an important role in the formation and maintenance of the thyroid follicular lumen. Decreased expression of CDH16 has been reported to be associated with tumor stage in papillary thyroid cancer (PTC); however, previous analyses have been limited and the biological role of CDH16 in different subtypes of TC is unknown. To investigate the role of CDH16 in the occurrence and development of TC, bioinformatic analysis of three TC subtypes (PTC, follicular cell-derived TC and anaplastic TC) was performed using an extended data set from the Gene Expression Omnibus database, with additional confirmation using data from The Cancer Genome Atlas, as well as biopsies from 35 patients with PTC and TC or follicular cell lines. According to the dataset analysis, CDH16 was downregulated in PTC and follicular cell-derived and anaplastic TC; the downregulation in PTC was independent of DNA copy number variation. Furthermore, low expression levels of CDH16 were significantly correlated with tumor size, lymph node metastasis status and disease stage in 35 patients with PTC. Gene Set Enrichment Analysis suggested that CDH16 participated in DNA replication and cell adhesion pathways. To evaluate CDH16 activity, CDH16 was overexpressed in TC-derived BCPAP cells. CDH16 overexpression inhibited cell proliferation, migration and invasion and induced apoptosis by downregulating proteins associated with DNA replication and cell adhesion. These results support the identification of CDH16 as a valuable target for TC prognosis and therapy and, to the best of our knowledge, represent the first direct demonstration of its mechanistic role in TC.
Collapse
|
6
|
ATM immunohistochemistry as a potential marker for the differential diagnosis of no specific molecular profile subtype and POLE-mutation subtype endometrioid carcinoma. Pathol Res Pract 2022; 230:153743. [DOI: 10.1016/j.prp.2021.153743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/12/2021] [Accepted: 12/16/2021] [Indexed: 12/21/2022]
|
7
|
Wang Y, Chen Y, Wang C, Yang M, Wang Y, Bao L, Wang JE, Kim B, Chan KY, Xu W, Capota E, Ortega J, Nijhawan D, Li GM, Luo W, Wang Y. MIF is a 3' flap nuclease that facilitates DNA replication and promotes tumor growth. Nat Commun 2021; 12:2954. [PMID: 34012010 PMCID: PMC8134555 DOI: 10.1038/s41467-021-23264-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 04/20/2021] [Indexed: 11/13/2022] Open
Abstract
How cancer cells cope with high levels of replication stress during rapid proliferation is currently unclear. Here, we show that macrophage migration inhibitory factor (MIF) is a 3’ flap nuclease that translocates to the nucleus in S phase. Poly(ADP-ribose) polymerase 1 co-localizes with MIF to the DNA replication fork, where MIF nuclease activity is required to resolve replication stress and facilitates tumor growth. MIF loss in cancer cells leads to mutation frequency increases, cell cycle delays and DNA synthesis and cell growth inhibition, which can be rescued by restoring MIF, but not nuclease-deficient MIF mutant. MIF is significantly upregulated in breast tumors and correlates with poor overall survival in patients. We propose that MIF is a unique 3’ nuclease, excises flaps at the immediate 3’ end during DNA synthesis and favors cancer cells evading replication stress-induced threat for their growth. Replication stress is associated with cancer formation and progression. Here the authors reveal that the macrophage migration inhibitory factor (MIF) functions as 3’ flap nuclease involved in resolving replication stress affecting overall tumor progression.
Collapse
Affiliation(s)
- Yijie Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yan Chen
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chenliang Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Mingming Yang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yanan Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Lei Bao
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jennifer E Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - BongWoo Kim
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kara Y Chan
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Weizhi Xu
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Emanuela Capota
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Janice Ortega
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Deepak Nijhawan
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Guo-Min Li
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Weibo Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yingfei Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA. .,Department of Neurology, UT Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
8
|
Stepchenkova EI, Zhuk AS, Cui J, Tarakhovskaya ER, Barbari SR, Shcherbakova PV, Polev DE, Fedorov R, Poliakov E, Rogozin IB, Lada AG, Pavlov YI. Compensation for the absence of the catalytically active half of DNA polymerase ε in yeast by positively selected mutations in CDC28. Genetics 2021; 218:6222163. [PMID: 33844024 DOI: 10.1093/genetics/iyab060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/02/2021] [Indexed: 11/14/2022] Open
Abstract
Current eukaryotic replication models postulate that leading and lagging DNA strands are replicated predominantly by dedicated DNA polymerases. The catalytic subunit of the leading strand DNA polymerase ε, Pol2, consists of two halves made of two different ancestral B-family DNA polymerases. Counterintuitively, the catalytically active N-terminal half is dispensable, while the inactive C-terminal part is required for viability. Despite extensive studies of yeast Saccharomyces cerevisiae strains lacking the active N-terminal half, it is still unclear how these strains survive and recover. We designed a robust method for constructing mutants with only the C-terminal part of Pol2. Strains without the active polymerase part show severe growth defects, sensitivity to replication inhibitors, chromosomal instability, and elevated spontaneous mutagenesis. Intriguingly, the slow-growing mutant strains rapidly accumulate fast-growing clones. Analysis of genomic DNA sequences of these clones revealed that the adaptation to the loss of the catalytic N-terminal part of Pol2 occurs by a positive selection of mutants with improved growth. Elevated mutation rates help generate sufficient numbers of these variants. Single nucleotide changes in the cell cycle-dependent kinase gene, CDC28, improve the growth of strains lacking the N-terminal part of Pol2, and rescue their sensitivity to replication inhibitors and, in parallel, lower mutation rates. Our study predicts that changes in mammalian homologs of cyclin-dependent kinases may contribute to cellular responses to the leading strand polymerase defects.
Collapse
Affiliation(s)
- Elena I Stepchenkova
- Laboratory of Mutagenesis and Genetic Toxicology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, Saint-Petersburg 199034, Russia.,Department of Genetics and Biotechnology, Saint-Petersburg State University, Saint-Petersburg 199034, Russia.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Anna S Zhuk
- ITMO University, Saint-Petersburg 191002, Russia
| | - Jian Cui
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Elena R Tarakhovskaya
- Laboratory of Mutagenesis and Genetic Toxicology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, Saint-Petersburg 199034, Russia.,Department of Plant Physiology and Biochemistry, Saint-Petersburg State University, Saint-Petersburg 199034, Russia
| | - Stephanie R Barbari
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Dmitrii E Polev
- Research Resource Center "Biobank," Research Park, Saint-Petersburg State University, Saint-Petersburg 198504, Russia
| | - Roman Fedorov
- Department of Mathematics, University of Pittsburgh, PA 15213, USA
| | - Eugenia Poliakov
- Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Artem G Lada
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, CA 92697, USA
| | - Youri I Pavlov
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Saint-Petersburg 199034, Russia.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Microbiology and Pathology, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
9
|
Pavlov YI, Zhuk AS, Stepchenkova EI. DNA Polymerases at the Eukaryotic Replication Fork Thirty Years after: Connection to Cancer. Cancers (Basel) 2020; 12:E3489. [PMID: 33255191 PMCID: PMC7760166 DOI: 10.3390/cancers12123489] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
Recent studies on tumor genomes revealed that mutations in genes of replicative DNA polymerases cause a predisposition for cancer by increasing genome instability. The past 10 years have uncovered exciting details about the structure and function of replicative DNA polymerases and the replication fork organization. The principal idea of participation of different polymerases in specific transactions at the fork proposed by Morrison and coauthors 30 years ago and later named "division of labor," remains standing, with an amendment of the broader role of polymerase δ in the replication of both the lagging and leading DNA strands. However, cancer-associated mutations predominantly affect the catalytic subunit of polymerase ε that participates in leading strand DNA synthesis. We analyze how new findings in the DNA replication field help elucidate the polymerase variants' effects on cancer.
Collapse
Affiliation(s)
- Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases and Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Genetics and Biotechnology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia;
| | - Anna S. Zhuk
- International Laboratory of Computer Technologies, ITMO University, 197101 Saint Petersburg, Russia;
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia;
- Laboratory of Mutagenesis and Genetic Toxicology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, 199034 Saint Petersburg, Russia
| |
Collapse
|
10
|
Watts LP, Natsume T, Saito Y, Garzon J, Dong Q, Boteva L, Gilbert N, Kanemaki MT, Hiraga SI, Donaldson AD. The RIF1-long splice variant promotes G1 phase 53BP1 nuclear bodies to protect against replication stress. eLife 2020; 9:e58020. [PMID: 33141022 PMCID: PMC7671687 DOI: 10.7554/elife.58020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 11/02/2020] [Indexed: 12/13/2022] Open
Abstract
Human cells lacking RIF1 are highly sensitive to replication inhibitors, but the reasons for this sensitivity have been enigmatic. Here, we show that RIF1 must be present both during replication stress and in the ensuing recovery period to promote cell survival. Of two isoforms produced by alternative splicing, we find that RIF1-Long alone can protect cells against replication inhibition, but RIF1-Short is incapable of mediating protection. Consistent with this isoform-specific role, RIF1-Long is required to promote the formation of the 53BP1 nuclear bodies that protect unrepaired damage sites in the G1 phase following replication stress. Overall, our observations show that RIF1 is needed at several cell cycle stages after replication insult, with the RIF1-Long isoform playing a specific role during the ensuing G1 phase in damage site protection.
Collapse
Affiliation(s)
- Lotte P Watts
- Institute of Medical Sciences, University of AberdeenAberdeenUnited Kingdom
| | - Toyoaki Natsume
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS)MishimaJapan
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI)MishimaJapan
| | - Yuichiro Saito
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS)MishimaJapan
| | - Javier Garzon
- Institute of Medical Sciences, University of AberdeenAberdeenUnited Kingdom
| | - Qianqian Dong
- Institute of Medical Sciences, University of AberdeenAberdeenUnited Kingdom
| | - Lora Boteva
- MRC Human Genetics Unit, The University of EdinburghEdinburghUnited Kingdom
| | - Nick Gilbert
- MRC Human Genetics Unit, The University of EdinburghEdinburghUnited Kingdom
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS)MishimaJapan
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI)MishimaJapan
| | - Shin-ichiro Hiraga
- Institute of Medical Sciences, University of AberdeenAberdeenUnited Kingdom
| | - Anne D Donaldson
- Institute of Medical Sciences, University of AberdeenAberdeenUnited Kingdom
| |
Collapse
|
11
|
Guilliam TA, Yeeles JTP. An updated perspective on the polymerase division of labor during eukaryotic DNA replication. Crit Rev Biochem Mol Biol 2020; 55:469-481. [PMID: 32883112 DOI: 10.1080/10409238.2020.1811630] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In eukaryotes three DNA polymerases (Pols), α, δ, and ε, are tasked with bulk DNA synthesis of nascent strands during genome duplication. Most evidence supports a model where Pol α initiates DNA synthesis before Pol ε and Pol δ replicate the leading and lagging strands, respectively. However, a number of recent reports, enabled by advances in biochemical and genetic techniques, have highlighted emerging roles for Pol δ in all stages of leading-strand synthesis; initiation, elongation, and termination, as well as fork restart. By focusing on these studies, this review provides an updated perspective on the division of labor between the replicative polymerases during DNA replication.
Collapse
Affiliation(s)
- Thomas A Guilliam
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Joseph T P Yeeles
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| |
Collapse
|
12
|
Acharya N, Khandagale P, Thakur S, Sahu JK, Utkalaja BG. Quaternary structural diversity in eukaryotic DNA polymerases: monomeric to multimeric form. Curr Genet 2020; 66:635-655. [PMID: 32236653 DOI: 10.1007/s00294-020-01071-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/13/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022]
Abstract
Sixteen eukaryotic DNA polymerases have been identified and studied so far. Based on the sequence similarity of the catalytic subunits of DNA polymerases, these have been classified into four A, B, X and Y families except PrimPol, which belongs to the AEP family. The quaternary structure of these polymerases also varies depending upon whether they are composed of one or more subunits. Therefore, in this review, we used a quaternary structure-based classification approach to group DNA polymerases as either monomeric or multimeric and highlighted functional significance of their accessory subunits. Additionally, we have briefly summarized various DNA polymerase discoveries from a historical perspective, emphasized unique catalytic mechanism of each DNA polymerase and highlighted recent advances in understanding their cellular functions.
Collapse
Affiliation(s)
- Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India.
| | - Prashant Khandagale
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Shweta Thakur
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Jugal Kishor Sahu
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Bhabasha Gyanadeep Utkalaja
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| |
Collapse
|
13
|
Li HD, Cuevas I, Zhang M, Lu C, Alam MM, Fu YX, You MJ, Akbay EA, Zhang H, Castrillon DH. Polymerase-mediated ultramutagenesis in mice produces diverse cancers with high mutational load. J Clin Invest 2018; 128:4179-4191. [PMID: 30124468 PMCID: PMC6118636 DOI: 10.1172/jci122095] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/03/2018] [Indexed: 12/26/2022] Open
Abstract
Mutations underlie all cancers, and their identification and study are the foundation of cancer biology. We describe what we believe to be a novel approach to mutagenesis and cancer studies based on the DNA polymerase ε (POLE) ultramutator phenotype recently described in human cancers, in which a single amino acid substitution (most commonly P286R) in the proofreading domain results in error-prone DNA replication. We engineered a conditional PoleP286R allele in mice. PoleP286R/+ embryonic fibroblasts exhibited a striking mutator phenotype and immortalized more efficiently. PoleP286R/+ mice were born at Mendelian ratios but rapidly developed lethal cancers of diverse lineages, yielding the most cancer-prone monoallelic model described to date, to our knowledge. Comprehensive whole-genome sequencing analyses showed that the cancers were driven by high base substitution rates in the range of human cancers, overcoming a major limitation of previous murine cancer models. These data establish polymerase-mediated ultramutagenesis as an efficient in vivo approach for the generation of diverse animal cancer models that recapitulate the high mutational loads inherent to human cancers.
Collapse
Affiliation(s)
- Hao-Dong Li
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Ileana Cuevas
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Musi Zhang
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Changzheng Lu
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Md Maksudul Alam
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Yang-Xin Fu
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - M. James You
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Esra A. Akbay
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - He Zhang
- Lyda Hill Department of Bioinformatics, UTSW Medical Center, Dallas, Texas, USA
| | - Diego H. Castrillon
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| |
Collapse
|
14
|
Itkonen HM, Kantelinen J, Vaara M, Parkkinen S, Schlott B, Grosse F, Nyström M, Syväoja JE, Pospiech H. Human DNA polymerase α interacts with mismatch repair proteins MSH2 and MSH6. FEBS Lett 2016; 590:4233-4241. [DOI: 10.1002/1873-3468.12475] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/20/2016] [Accepted: 10/26/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Harri M. Itkonen
- Research group Biochemistry; Leibniz Institute on Aging - Fritz Lipmann Institute; Jena Germany
- Department of Biology; University of Eastern Finland; Joensuu Finland
- Prostate Cancer Research Group; Nordic EMBL Partnership; Centre for Molecular Medicine Norway; University of Oslo; Blindern Norway
| | - Jukka Kantelinen
- Department of Biosciences; Division of Genetics; University of Helsinki; Finland
| | - Markku Vaara
- Department of Biology; University of Eastern Finland; Joensuu Finland
| | - Sinikka Parkkinen
- Department of Biology; University of Eastern Finland; Joensuu Finland
| | - Bernhard Schlott
- Research group Biochemistry; Leibniz Institute on Aging - Fritz Lipmann Institute; Jena Germany
- Service group Proteomics; Leibniz Institute on Aging - Fritz Lipmann Institute; Jena Germany
| | - Frank Grosse
- Research group Biochemistry; Leibniz Institute on Aging - Fritz Lipmann Institute; Jena Germany
| | - Minna Nyström
- Department of Biosciences; Division of Genetics; University of Helsinki; Finland
| | - Juhani E. Syväoja
- Institute of Biomedicine; University of Eastern Finland; Kuopio Finland
| | - Helmut Pospiech
- Research group Biochemistry; Leibniz Institute on Aging - Fritz Lipmann Institute; Jena Germany
- Faculty of Biochemistry and Molecular Medicine; University of Oulu; Finland
| |
Collapse
|
15
|
Lujan SA, Williams JS, Kunkel TA. DNA Polymerases Divide the Labor of Genome Replication. Trends Cell Biol 2016; 26:640-654. [PMID: 27262731 DOI: 10.1016/j.tcb.2016.04.012] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/27/2016] [Accepted: 04/29/2016] [Indexed: 01/14/2023]
Abstract
DNA polymerases synthesize DNA in only one direction, but large genomes require RNA priming and bidirectional replication from internal origins. We review here the physical, chemical, and evolutionary constraints underlying these requirements. We then consider the roles of the major eukaryotic replicases, DNA polymerases α, δ, and ɛ, in replicating the nuclear genome. Pol α has long been known to extend RNA primers at origins and on Okazaki fragments that give rise to the nascent lagging strand. Taken together, more recent results of mutation and ribonucleotide incorporation mapping, electron microscopy, and immunoprecipitation of nascent DNA now lead to a model wherein Pol ɛ and Pol δ, respectively, synthesize the majority of the nascent leading and lagging strands of undamaged DNA.
Collapse
Affiliation(s)
- Scott A Lujan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Jessica S Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
| |
Collapse
|
16
|
Abstract
The machines that decode and regulate genetic information require the translation, transcription and replication pathways essential to all living cells. Thus, it might be expected that all cells share the same basic machinery for these pathways that were inherited from the primordial ancestor cell from which they evolved. A clear example of this is found in the translation machinery that converts RNA sequence to protein. The translation process requires numerous structural and catalytic RNAs and proteins, the central factors of which are homologous in all three domains of life, bacteria, archaea and eukarya. Likewise, the central actor in transcription, RNA polymerase, shows homology among the catalytic subunits in bacteria, archaea and eukarya. In contrast, while some "gears" of the genome replication machinery are homologous in all domains of life, most components of the replication machine appear to be unrelated between bacteria and those of archaea and eukarya. This review will compare and contrast the central proteins of the "replisome" machines that duplicate DNA in bacteria, archaea and eukarya, with an eye to understanding the issues surrounding the evolution of the DNA replication apparatus.
Collapse
Affiliation(s)
- Nina Y Yao
- a DNA Replication Laboratory, The Rockefeller University , New York , NY , USA and
| | - Mike E O'Donnell
- a DNA Replication Laboratory, The Rockefeller University , New York , NY , USA and.,b Howard Hughes Medical Institute, The Rockefeller University , New York , NY , USA
| |
Collapse
|
17
|
Linn S. Radicals in Berkeley? J Biol Chem 2015; 290:8748-57. [PMID: 25713083 DOI: 10.1074/jbc.x115.644989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In a previous autobiographical sketch for DNA Repair (Linn, S. (2012) Life in the serendipitous lane: excitement and gratification in studying DNA repair. DNA Repair 11, 595-605), I wrote about my involvement in research on mechanisms of DNA repair. In this Reflections, I look back at how I became interested in free radical chemistry and biology and outline some of our bizarre (at the time) observations. Of course, these studies could never have succeeded without the exceptional aid of my mentors: my teachers; the undergraduate and graduate students, postdoctoral fellows, and senior lab visitors in my laboratory; and my faculty and staff colleagues here at Berkeley. I am so indebted to each and every one of these individuals for their efforts to overcome my ignorance and set me on the straight and narrow path to success in research. I regret that I cannot mention and thank each of these mentors individually.
Collapse
Affiliation(s)
- Stuart Linn
- From the Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202
| |
Collapse
|
18
|
Replicative DNA polymerase δ but not ε proofreads errors in Cis and in Trans. PLoS Genet 2015; 11:e1005049. [PMID: 25742645 PMCID: PMC4351087 DOI: 10.1371/journal.pgen.1005049] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 02/02/2015] [Indexed: 01/18/2023] Open
Abstract
It is now well established that in yeast, and likely most eukaryotic organisms, initial DNA replication of the leading strand is by DNA polymerase ε and of the lagging strand by DNA polymerase δ. However, the role of Pol δ in replication of the leading strand is uncertain. In this work, we use a reporter system in Saccharomyces cerevisiae to measure mutation rates at specific base pairs in order to determine the effect of heterozygous or homozygous proofreading-defective mutants of either Pol ε or Pol δ in diploid strains. We find that wild-type Pol ε molecules cannot proofread errors created by proofreading-defective Pol ε molecules, whereas Pol δ can not only proofread errors created by proofreading-defective Pol δ molecules, but can also proofread errors created by Pol ε-defective molecules. These results suggest that any interruption in DNA synthesis on the leading strand is likely to result in completion by Pol δ and also explain the higher mutation rates observed in Pol δ-proofreading mutants compared to Pol ε-proofreading defective mutants. For strains reverting via AT→GC, TA→GC, CG→AT, and GC→AT mutations, we find in addition a strong effect of gene orientation on mutation rate in proofreading-defective strains and demonstrate that much of this orientation dependence is due to differential efficiencies of mispair elongation. We also find that a 3′-terminal 8 oxoG, unlike a 3′-terminal G, is efficiently extended opposite an A and is not subject to proofreading. Proofreading mutations have been shown to result in tumor formation in both mice and humans; the results presented here can help explain the properties exhibited by those proofreading mutants. Many DNA polymerases are able to proofread their errors: after incorporation of a wrong base, the resulting mispair invokes an exonuclease activity of the polymerase that removes the mispaired base and allows replication to continue. Elimination of the proofreading activity thus results in much higher mutation rates. We demonstrate that the two major replicative DNA polymerases in yeast, Pol δ and Pol ε, have different proofreading abilities. In diploid cells, Pol ε is not able to proofread errors created by other Pol ε molecules, whereas Pol δ can proofread not only errors created by other Pol δ molecules but also errors created by Pol ε molecules. We also find that mispaired bases not corrected by proofreading have much different likelihoods of being extended, depending on the particular base-base mismatch. In humans, defects in Pol δ or Pol ε proofreading can lead to cancer, and these results help explain the formation of those tumors and the finding that Pol ε mutants seem to be found as frequently, or more so, in human tumors as Pol δ mutants.
Collapse
|
19
|
Garbacz M, Araki H, Flis K, Bebenek A, Zawada AE, Jonczyk P, Makiela-Dzbenska K, Fijalkowska IJ. Fidelity consequences of the impaired interaction between DNA polymerase epsilon and the GINS complex. DNA Repair (Amst) 2015; 29:23-35. [PMID: 25758782 DOI: 10.1016/j.dnarep.2015.02.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 01/08/2023]
Abstract
DNA polymerase epsilon interacts with the CMG (Cdc45-MCM-GINS) complex by Dpb2p, the non-catalytic subunit of DNA polymerase epsilon. It is postulated that CMG is responsible for targeting of Pol ɛ to the leading strand. We isolated a mutator dpb2-100 allele which encodes the mutant form of Dpb2p. We showed previously that Dpb2-100p has impaired interactions with Pol2p, the catalytic subunit of Pol ɛ. Here, we present that Dpb2-100p has strongly impaired interaction with the Psf1 and Psf3 subunits of the GINS complex. Our in vitro results suggest that while dpb2-100 does not alter Pol ɛ's biochemical properties including catalytic efficiency, processivity or proofreading activity - it moderately decreases the fidelity of DNA synthesis. As the in vitro results did not explain the strong in vivo mutator effect of the dpb2-100 allele we analyzed the mutation spectrum in vivo. The analysis of the mutation rates in the dpb2-100 mutant indicated an increased participation of the error-prone DNA polymerase zeta in replication. However, even in the absence of Pol ζ activity the presence of the dpb2-100 allele was mutagenic, indicating that a significant part of mutagenesis is Pol ζ-independent. A strong synergistic mutator effect observed for transversions in the triple mutant dpb2-100 pol2-4 rev3Δ as compared to pol2-4 rev3Δ and dpb2-100 rev3Δ suggests that in the presence of the dpb2-100 allele the number of replication errors is enhanced. We hypothesize that in the dpb2-100 strain, where the interaction between Pol ɛ and GINS is weakened, the access of Pol δ to the leading strand may be increased. The increased participation of Pol δ on the leading strand in the dpb2-100 mutant may explain the synergistic mutator effect observed in the dpb2-100 pol3-5DV double mutant.
Collapse
Affiliation(s)
- Marta Garbacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Mutagenesis and DNA Repair, Pawinskiego 5A, Warsaw 02-106, Poland
| | - Hiroyuki Araki
- National Institute of Genetics, Division of Microbial Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Krzysztof Flis
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Mutagenesis and DNA Repair, Pawinskiego 5A, Warsaw 02-106, Poland
| | - Anna Bebenek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Molecular Biology, Pawinskiego 5A, Warsaw 02-106, Poland
| | - Anna E Zawada
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Mutagenesis and DNA Repair, Pawinskiego 5A, Warsaw 02-106, Poland
| | - Piotr Jonczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Mutagenesis and DNA Repair, Pawinskiego 5A, Warsaw 02-106, Poland
| | - Karolina Makiela-Dzbenska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Mutagenesis and DNA Repair, Pawinskiego 5A, Warsaw 02-106, Poland.
| | - Iwona J Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Mutagenesis and DNA Repair, Pawinskiego 5A, Warsaw 02-106, Poland.
| |
Collapse
|
20
|
Villani G, Shevelev I, Orlando E, Pospiech H, Syvaoja JE, Markkanen E, Hubscher U, Le Gac NT. Gap-directed translesion DNA synthesis of an abasic site on circular DNA templates by a human replication complex. PLoS One 2014; 9:e93908. [PMID: 24710081 PMCID: PMC3977967 DOI: 10.1371/journal.pone.0093908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/08/2014] [Indexed: 12/02/2022] Open
Abstract
DNA polymerase ε (pol ε) is believed to be the leading strand replicase in eukaryotes whereas pols λ and β are thought to be mainly involved in re-synthesis steps of DNA repair. DNA elongation by the human pol ε is halted by an abasic site (apurinic/apyrimidinic (AP) site). We have previously reported that human pols λ, β and η can perform translesion synthesis (TLS) of an AP site in the presence of pol ε. In the case of pol λ and β, this TLS requires the presence of a gap downstream from the product synthetized by the ε replicase. However, since these studies were conducted exclusively with a linear DNA template, we decided to test whether the structure of the template could influence the capacity of the pols ε, λ, β and η to perform TLS of an AP site. Therefore, we have investigated the replication of damaged “minicircle” DNA templates. In addition, replication of circular DNA requires, beyond DNA pols, the processivity clamp PCNA, the clamp loader replication factor C (RFC), and the accessory proteins replication protein A (RPA). Finally we have compared the capacity of unmodified versus monoubiquitinated PCNA in sustaining TLS by pols λ and η on a circular template. Our results indicate that in vitro gap-directed TLS synthesis by pols λ and β in the presence of pol ε, RPA and PCNA is unaffected by the structure of the DNA template. Moreover, monoubiquitination of PCNA does not affect TLS by pol λ while it appears to slightly stimulate TLS by pol η.
Collapse
Affiliation(s)
- Giuseppe Villani
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
| | - Igor Shevelev
- Leibniz Institute for Age Research - Fritz Lipman Institute, Jena, Germany
- Department of Biochemistry, University of Oulu, Oulu, Finland
| | - Eleonora Orlando
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
| | - Helmut Pospiech
- Leibniz Institute for Age Research - Fritz Lipman Institute, Jena, Germany
- Department of Biochemistry, University of Oulu, Oulu, Finland
| | - Juhani E. Syvaoja
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Enni Markkanen
- Biochemistry Group, Department of Oncology, Gray Institute for Radiation Oncology and Biology, Oxford, United Kingdom
| | - Ulrich Hubscher
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, Zürich, Switzerland
| | - Nicolas Tanguy Le Gac
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- * E-mail:
| |
Collapse
|
21
|
Agbor AA, Göksenin AY, LeCompte KG, Hans SH, Pursell ZF. Human Pol ε-dependent replication errors and the influence of mismatch repair on their correction. DNA Repair (Amst) 2013; 12:954-63. [PMID: 24051051 PMCID: PMC4520434 DOI: 10.1016/j.dnarep.2013.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 08/19/2013] [Accepted: 08/20/2013] [Indexed: 12/30/2022]
Abstract
Mutations in human DNA polymerase (Pol) ε, one of three eukaryotic Pols required for DNA replication, have recently been found associated with an ultramutator phenotype in tumors from somatic colorectal and endometrial cancers and in a familial colorectal cancer. Possibly, Pol ε mutations reduce the accuracy of DNA synthesis, thereby increasing the mutational burden and contributing to tumor development. To test this possibility in vivo, we characterized an active site mutant allele of human Pol ε that exhibits a strong mutator phenotype in vitro when the proofreading exonuclease activity of the enzyme is inactive. This mutant has a strong bias toward mispairs opposite template pyrimidine bases, particularly T • dTTP mispairs. Expression of mutant Pol ε in human cells lacking functional mismatch repair caused an increase in mutation rate primarily due to T • dTTP mispairs. Functional mismatch repair eliminated the increased mutagenesis. The results indicate that the mutant Pol ε causes replication errors in vivo, and is at least partially dominant over the endogenous, wild type Pol ε. Since tumors from familial and somatic colorectal patients arise with Pol ε mutations in a single allele, are microsatellite stable and have a large increase in base pair substitutions, our data are consistent with a Pol ε mutation requiring additional factors to promote tumor development.
Collapse
Affiliation(s)
- Anderson Ayuk Agbor
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - A. Yasemin Göksenin
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Kimberly G. LeCompte
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Samuel H. Hans
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Zachary F. Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| |
Collapse
|
22
|
Aria V, De Felice M, Di Perna R, Uno S, Masai H, Syväoja JE, van Loon B, Hübscher U, Pisani FM. The human Tim-Tipin complex interacts directly with DNA polymerase epsilon and stimulates its synthetic activity. J Biol Chem 2013; 288:12742-52. [PMID: 23511638 DOI: 10.1074/jbc.m112.398073] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Tim-Tipin complex plays an important role in the S phase checkpoint and replication fork stability in metazoans, but the molecular mechanism underlying its biological function is poorly understood. Here, we present evidence that the recombinant human Tim-Tipin complex (and Tim alone) markedly enhances the synthetic activity of DNA polymerase ε. In contrast, no significant effect on the synthetic ability of human DNA polymerase α and δ by Tim-Tipin was observed. Surface plasmon resonance measurements and co-immunoprecipitation experiments revealed that recombinant DNA polymerase ε directly interacts with either Tim or Tipin. In addition, the results of DNA band shift assays suggest that the Tim-Tipin complex (or Tim alone) is able to associate with DNA polymerase ε bound to a 40-/80-mer DNA ligand. Our results are discussed in view of the molecular dynamics at the human DNA replication fork.
Collapse
Affiliation(s)
- Valentina Aria
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Lee MYWT, Zhang S, Lin SHS, Chea J, Wang X, LeRoy C, Wong A, Zhang Z, Lee EYC. Regulation of human DNA polymerase delta in the cellular responses to DNA damage. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:683-698. [PMID: 23047826 DOI: 10.1002/em.21743] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 08/28/2012] [Accepted: 08/29/2012] [Indexed: 06/01/2023]
Abstract
The p12 subunit of polymerase delta (Pol δ) is degraded in response to DNA damage induced by UV, alkylating agents, oxidative, and replication stresses. This leads to the conversion of the Pol δ4 holoenzyme to the heterotrimer, Pol δ3. We review studies that establish that Pol δ3 formation is an event that could have a major impact on cellular processes in genomic surveillance, DNA replication, and DNA repair. p12 degradation is dependent on the apical ataxia telangiectasia and Rad3 related (ATR) kinase and is mediated by the ubiquitin-proteasome system. Pol δ3 exhibits properties of an "antimutator" polymerase, suggesting that it could contribute to an increased surveillance against mutagenesis, for example, when Pol δ carries out bypass synthesis past small base lesions that engage in spurious base pairing. Chromatin immunoprecipitation analysis and examination of the spatiotemporal recruitment of Pol δ to sites of DNA damage show that Pol δ3 is the primary form of Pol δ associated with cyclobutane pyrimidine dimer lesions and therefore should be considered as the operative form of Pol δ engaged in DNA repair. We propose a model for the switching of Pol δ with translesion polymerases, incorporating the salient features of the recently determined structure of monoubiquitinated proliferating cell nuclear antigen and emphasizing the role of Pol δ3. Because of the critical role of Pol δ activity in DNA replication and repair, the formation of Pol δ3 in response to DNA damage opens the prospect that pleiotropic effects may ensue. This opens the horizons for future exploration of how this novel response to DNA damage contributes to genomic stability.
Collapse
Affiliation(s)
- Marietta Y W T Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Göksenin AY, Zahurancik W, LeCompte KG, Taggart DJ, Suo Z, Pursell ZF. Human DNA polymerase ε is able to efficiently extend from multiple consecutive ribonucleotides. J Biol Chem 2012; 287:42675-84. [PMID: 23093410 PMCID: PMC3522268 DOI: 10.1074/jbc.m112.422733] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Replicative DNA polymerases (Pols) help to maintain the high fidelity of replication in large part through their strong selectivity against mispaired deoxyribonucleotides. It has recently been demonstrated that several replicative Pols from yeast have surprisingly low selectivity for deoxyribonucleotides over their analogous ribonucleotides. In human cells, ribonucleotides are found in great abundance over deoxyribonucleotides, raising the possibility that ribonucleotides are incorporated in the human genome at significant levels during normal cellular functions. To address this possibility, the ability of human DNA polymerase ϵ to incorporate ribonucleotides was tested. At physiological concentrations of nucleotides, human Pol ϵ readily inserts and extends from incorporated ribonucleotides. Almost half of inserted ribonucleotides escape proofreading by 3′ → 5′ exonuclease-proficient Pol ϵ, indicating that ribonucleotide incorporation by Pol ϵ is likely a significant event in human cells. Human Pol ϵ is also efficient at extending from primers terminating in up to five consecutive ribonucleotides. This efficient extension appears to result from reduced exonuclease activity on primers containing consecutive 3′-terminal ribonucleotides. These biochemical properties suggest that Pol ϵ is a likely source of ribonucleotides in human genomic DNA.
Collapse
Affiliation(s)
- A Yasemin Göksenin
- Department of Biochemistry and Molecular Biology and the Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana 70112, USA
| | | | | | | | | | | |
Collapse
|
25
|
Life in the serendipitous lane: excitement and gratification in studying DNA repair. DNA Repair (Amst) 2012; 11:595-605. [PMID: 22870513 DOI: 10.1016/j.dnarep.2011.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
26
|
Aziz K, Nowsheen S, Pantelias G, Iliakis G, Gorgoulis VG, Georgakilas AG. Targeting DNA damage and repair: embracing the pharmacological era for successful cancer therapy. Pharmacol Ther 2011; 133:334-50. [PMID: 22197993 DOI: 10.1016/j.pharmthera.2011.11.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 11/30/2011] [Indexed: 12/19/2022]
Abstract
DNA is under constant assault from genotoxic agents which creates different kinds of DNA damage. The precise replication of the genome and the continuous surveillance of its integrity are critical for survival and the avoidance of carcinogenesis. Cells have evolved an arsenal of repair pathways and cell cycle checkpoints to detect and repair DNA damage. When repair fails, typically cell cycle progression is halted and apoptosis is initiated. Here, we review the different sources and types of DNA damage including DNA replication stress and oxidative stress, the repair pathways that cells utilize to repair damaged DNA, and discuss their biological significance, especially with reference to cancer induction and cancer therapy. We also describe the main methodologies currently used for the detection of DNA damage with their strengths and limitations. We conclude with an outline as to how this information can be used to identify novel pharmacological targets for DNA repair pathways or enhancers of DNA damage to develop improved treatment strategies that will benefit cancer patients.
Collapse
Affiliation(s)
- K Aziz
- Department of Radiation Oncology & Molecular Radiation Sciences, Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21231, USA
| | | | | | | | | | | |
Collapse
|
27
|
Dimitrova DS. DNA replication initiation patterns and spatial dynamics of the human ribosomal RNA gene loci. J Cell Sci 2011; 124:2743-52. [DOI: 10.1242/jcs.082230] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Typically, only a fraction of the ≥600 ribosomal RNA (rRNA) gene copies in human cells are transcriptionally active. Expressed rRNA genes coalesce in specialized nuclear compartments – the nucleoli – and are believed to replicate during the first half of S phase. Paradoxically, attempts to visualize replicating rDNA during early S phase have failed. Here, I show that, in human (HeLa) cells, early-replicating rDNA is detectable at the nucleolar periphery and, more rarely, even outside nucleoli. Early-replicated rDNA relocates to the nucleolar interior and reassociates with the transcription factor UBF, implying that it predominantly represents expressed rDNA units. Contrary to the established model for active gene loci, replication initiates randomly throughout the early-replicating rDNA. By contrast, mostly silent rDNA copies replicate inside the nucleoli during mid and late S phase. At this stage, replication origins are fired preferentially within the non-transcribed intergenic spacers (NTSs), and ongoing rDNA transcription is required to maintain this specific initiation pattern. I propose that the unexpected spatial dynamics of the early-replicating rDNA repeats serve to ensure streamlined efficient replication of the most heavily transcribed genomic loci while simultaneously reducing the risk of chromosome breaks and rDNA hyper-recombination.
Collapse
|
28
|
Villani G, Hubscher U, Gironis N, Parkkinen S, Pospiech H, Shevelev I, di Cicco G, Markkanen E, Syväoja JE, Tanguy Le Gac N. In vitro gap-directed translesion DNA synthesis of an abasic site involving human DNA polymerases epsilon, lambda, and beta. J Biol Chem 2011; 286:32094-104. [PMID: 21757740 DOI: 10.1074/jbc.m111.246611] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA polymerase (pol) ε is thought to be the leading strand replicase in eukaryotes, whereas pols λ and β are believed to be mainly involved in re-synthesis steps of DNA repair. DNA elongation by the human pol ε is halted by an abasic site (apurinic/apyrimidinic (AP) site). In this study, we present in vitro evidence that human pols λ, β, and η can perform translesion synthesis (TLS) of an AP site in the presence of pol ε, likely by initiating the 3'OHs created at the lesion by the arrested pol ε. However, in the case of pols λ and β, this TLS requires the presence of a DNA gap downstream from the product synthesized by the pol ε, and the optimal gap for efficient TLS is different for the two polymerases. The presence of gaps did not affect the TLS capacity of human pol η. Characterization of the reaction products showed that pol β inserted dAMP opposite the AP site, whereas gap filling synthesis by pol λ resulted in single or double deletions opposite the lesion. The synthesis up to the AP site by pol ε and the subsequent TLS by pols λ and β are not influenced by human processivity factor proliferating cell nuclear antigen and human single-stranded DNA-binding protein replication protein A. The bypass capacity of pol λ at the AP site is greatly reduced when a truncated form of the enzyme, which has lost the BRCA1 C-terminal and proline-rich domains, is used. Collectively, our in vitro results support the existence of a mechanism of gap-directed TLS at an AP site involving a switch between the replicative pol ε and the repair pols λ and β.
Collapse
Affiliation(s)
- Giuseppe Villani
- Institut de Pharmacologie et de Biologie Structurale, CNRS-Université Paul Sabatier Toulouse III, UMR 5089, 205 Route de Narbonne, 31077 Toulouse Cedex, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Kaczanowski A, Kiersnowska M. Inactivation of a macronuclear intra-S-phase checkpoint in Tetrahymena thermophila with caffeine affects the integrity of the micronuclear genome. Protist 2011; 162:616-36. [PMID: 21601521 DOI: 10.1016/j.protis.2011.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 01/23/2011] [Indexed: 01/16/2023]
Abstract
Aphidicolin (APH), an inhibitor of DNA polymerase α, arrested cell divisions in Tetrahymena thermophila. Surprisingly, low concentrations of APH induced an increase of macronuclear DNA content and cell size in non-dividing cells. In spite of the cell size increase, most proliferation of basal bodies, ciliogenesis and development of new oral primordia were prevented by the APH treatment. The division arrest induced by APH was partly overridden by caffeine (CAF) treatment, which caused the fragmentation ("pulverization") of the chromosomes in G2 micronuclei. Somatic progeny of dividers with pulverized micronuclei (APH+CAF strains) contained aneuploid and amicronucleate cells. The amicronucleate cells, after losing their oral structures and most of their cilia, and undergoing progressive disorganization of cortical structures, assumed an irregular shape ("crinkled") and were nonviable. "Crinkled" cells were not formed after APH + CAF treatment of the amicronuclear BI3840 strain, which contains some mic-specific sequences in its macronucleus. Most of the APH +CAF strains had a typical "*"- like conjugation phenotype: they did not produce pronuclei, but received them unilaterally from their mates and retained old macronuclei. However, 4 among 100 APH+CAF clones induced arrest at meiotic metaphase I in their wt mates. It is likely that the origin of such clones was enhanced by chromosome pulverization.
Collapse
|
30
|
Korona DA, Lecompte KG, Pursell ZF. The high fidelity and unique error signature of human DNA polymerase epsilon. Nucleic Acids Res 2010; 39:1763-73. [PMID: 21036870 PMCID: PMC3061053 DOI: 10.1093/nar/gkq1034] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bulk replicative DNA synthesis in eukaryotes is highly accurate and efficient, primarily because of two DNA polymerases (Pols): Pols δ and ε. The high fidelity of these enzymes is due to their intrinsic base selectivity and proofreading exonuclease activity which, when coupled with post-replication mismatch repair, helps to maintain human mutation rates at less than one mutation per genome duplication. Conditions that reduce polymerase fidelity result in increased mutagenesis and can lead to cancer in mice. Whereas yeast Pol ε has been well characterized, human Pol ε remains poorly understood. Here, we present the first report on the fidelity of human Pol ε. We find that human Pol ε carries out DNA synthesis with high fidelity, even in the absence of its 3′→5′ exonucleolytic proofreading and is significantly more accurate than yeast Pol ε. Though its spectrum of errors is similar to that of yeast Pol ε, there are several notable exceptions. These include a preference of the human enzyme for T→A over A→T transversions. As compared with other replicative DNA polymerases, human Pol ε is particularly accurate when copying homonucleotide runs of 4–5 bases. The base pair substitution specificity and high fidelity for frameshift errors observed for human Pol ε are distinct from the errors made by human Pol δ.
Collapse
Affiliation(s)
- Dagmara A Korona
- Department of Biochemistry and Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | | | | |
Collapse
|
31
|
Effect of 8-oxoguanine and abasic site DNA lesions on in vitro elongation by human DNA polymerase in the presence of replication protein A and proliferating-cell nuclear antigen. Biochem J 2010; 429:573-82. [PMID: 20528769 DOI: 10.1042/bj20100405] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DNA pol (polymerase) is thought to be the leading strand replicase in eukaryotes. In the present paper, we show that human DNA pol can efficiently bypass an 8-oxo-G (7,8-dihydro-8-oxoguanine) lesion on the template strand by inserting either dCMP or dAMP opposite to it, but it cannot bypass an abasic site. During replication, DNA pols associate with accessory proteins that may alter their bypass ability. We investigated the role of the human DNA sliding clamp PCNA (proliferating-cell nuclear antigen) and of the human single-stranded DNA-binding protein RPA (replication protein A) in the modulation of the DNA synthesis and translesion capacity of DNA pol . RPA inhibited the elongation by human DNA pol on templates annealed to short primers. PCNA did not influence the elongation by DNA pol and had no effect on inhibition of elongation caused by RPA. RPA inhibition was considerably reduced when the length of the primers was increased. On templates bearing the 8-oxo-G lesion, this inhibitory effect was more pronounced on DNA replication beyond the lesion, suggesting that RPA may prevent extension by DNA pol after incorporation opposite an 8-oxo-G. Neither PCNA nor RPA had any effect on the inability of DNA pol to replicate past the AP site, independent of the primer length.
Collapse
|
32
|
Pavlov YI, Shcherbakova PV. DNA polymerases at the eukaryotic fork-20 years later. Mutat Res 2009; 685:45-53. [PMID: 19682465 DOI: 10.1016/j.mrfmmm.2009.08.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 08/05/2009] [Indexed: 10/20/2022]
Abstract
Function of the eukaryotic genome depends on efficient and accurate replication of anti-parallel DNA strands. Eukaryotic DNA polymerases have different properties adapted to perform a wide spectrum of DNA transactions. Here we focus on major players in the bulk replication, DNA polymerases of the B-family. We review the organization of the replication fork in eukaryotes in a historical perspective, analyze contemporary models and propose a new integrative model of the fork.
Collapse
Affiliation(s)
- Youri I Pavlov
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA.
| | | |
Collapse
|
33
|
Dai H, Liu J, Malkas LH, Catalano J, Alagharu S, Hickey RJ. Chromium reduces the in vitro activity and fidelity of DNA replication mediated by the human cell DNA synthesome. Toxicol Appl Pharmacol 2009; 236:154-65. [PMID: 19371627 PMCID: PMC2804861 DOI: 10.1016/j.taap.2008.12.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Revised: 12/17/2008] [Accepted: 12/18/2008] [Indexed: 11/22/2022]
Abstract
Hexavalent chromium Cr(VI) is known to be a carcinogenic metal ion, with a complicated mechanism of action. It can be found within our environment in soil and water contaminated by manufacturing processes. Cr(VI) ion is readily taken up by cells, and is recognized to be both genotoxic and cytotoxic; following its reduction to the stable trivalent form of the ion, chromium(Cr(III)), within cells. This form of the ion is known to impede the activity of cellular DNA polymerase and polymerase-mediated DNA replication. Here, we report the effects of chromium on the activity and fidelity of the DNA replication process mediated by the human cell DNA synthesome. The DNA synthesome is a functional multiprotein complex that is fully competent to carry-out each phase of the DNA replication process. The IC(50) of Cr(III) toward the activity of DNA synthesome-associated DNA polymerases alpha, delta and epsilon is 15, 45 and 125 muM, respectively. Cr(III) inhibits synthesome-mediated DNA synthesis (IC(50)=88 muM), and significantly reduces the fidelity of synthesome-mediated DNA replication. The mutation frequency induced by the different concentrations of Cr(III) ion used in our assays ranges from 2-13 fold higher than that which occurs spontaneously, and the types of mutations include single nucleotide substitutions, insertions, and deletions. Single nucleotide substitutions are the predominant type of mutation, and they occur primarily at GC base-pairs. Cr(III) ion produces a lower number of transition and a higher number of transversion mutations than occur spontaneously. Unlike Cr(III), Cr(VI) ion has little effect on the in vitro DNA synthetic activity and fidelity of the DNA synthesome, but does significantly inhibit DNA synthesis in intact cells. Cell growth and proliferation is also arrested by increasing concentrations of Cr(VI) ion. Our studies provide evidence indicating that the chromium ion induced decrease in the fidelity and activity of synthesome mediated DNA replication correlates with the genotoxic and cytotoxic effects of this metal ion; and promotes cell killing via inhibition of the DNA polymerase activity mediating the DNA replication and repair processes utilized by human cells.
Collapse
Affiliation(s)
- Heqiao Dai
- Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, Indiana University Cancer Research Institute, 1044 W. Walnut Street R4-170 Indianapolis, IN 46202, USA
| | - Jianying Liu
- Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, Indiana University Cancer Research Institute, 1044 W. Walnut Street R4-170 Indianapolis, IN 46202, USA
| | - Linda H. Malkas
- Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, Indiana University Cancer Research Institute, 1044 W. Walnut Street R4-170 Indianapolis, IN 46202, USA
| | - Jennifer Catalano
- Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, Indiana University Cancer Research Institute, 1044 W. Walnut Street R4-170 Indianapolis, IN 46202, USA
| | - Srilakshmi Alagharu
- Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, Indiana University Cancer Research Institute, 1044 W. Walnut Street R4-170 Indianapolis, IN 46202, USA
| | - Robert J. Hickey
- Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, Indiana University Cancer Research Institute, 1044 W. Walnut Street R4-170 Indianapolis, IN 46202, USA
| |
Collapse
|
34
|
|
35
|
Pursell ZF, Kunkel TA. DNA polymerase epsilon: a polymerase of unusual size (and complexity). PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2008; 82:101-45. [PMID: 18929140 PMCID: PMC3694787 DOI: 10.1016/s0079-6603(08)00004-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zachary F. Pursell
- Laboratory of Molecular Genetics and Laboratory of Structural Biology National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709
| | - Thomas A. Kunkel
- Laboratory of Molecular Genetics and Laboratory of Structural Biology National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709
| |
Collapse
|
36
|
Fowler JD, Suo Z. Biochemical, structural, and physiological characterization of terminal deoxynucleotidyl transferase. Chem Rev 2007; 106:2092-110. [PMID: 16771444 DOI: 10.1021/cr040445w] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jason D Fowler
- Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | |
Collapse
|
37
|
Ogi T, Lehmann AR. The Y-family DNA polymerase kappa (pol kappa) functions in mammalian nucleotide-excision repair. Nat Cell Biol 2006; 8:640-2. [PMID: 16738703 DOI: 10.1038/ncb1417] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Accepted: 04/20/2006] [Indexed: 11/08/2022]
Abstract
DNA polymerase kappa (pol kappa) is a member of the Y-family of DNA polymerases that are thought to function in translesion synthesis (TLS) past different types of DNA damage. Here, we show that pol kappa-deficient mouse cells have substantially reduced (but not absent) levels of nucleotide excision repair (NER) of UV damage, as measured by several methods. Our results provide evidence for an unexpected role for pol kappa in mammalian NER.
Collapse
Affiliation(s)
- Tomoo Ogi
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | | |
Collapse
|
38
|
Nasheuer HP, Pospiech H, Syväoja J. Progress Towards the Anatomy of the Eukaryotic DNA Replication Fork. Genome Integr 2006. [DOI: 10.1007/7050_016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
|
39
|
Mitkova AV, Biswas-Fiss EE, Biswas SB. Modulation of DNA synthesis in Saccharomyces cerevisiae nuclear extract by DNA polymerases and the origin recognition complex. J Biol Chem 2004; 280:6285-92. [PMID: 15590683 DOI: 10.1074/jbc.m410129200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have analyzed the modulation of DNA synthesis on a supercoiled plasmid DNA template by DNA polymerases (pol), minichromosome maintenance protein complex (Mcm), topoisomerases, and the origin recognition complex (ORC) using an in vitro assay system. Antisera specific against the four-subunit pol alpha, the catalytic subunit of pol delta, and the Mcm467 complex each inhibited DNA synthesis. However, DNA synthesis in this system appeared to be independent of polepsilon. Consequently, DNA synthesis in the in vitro system appeared to depend only on two polymerases, alpha and delta, as well as the Mcm467 DNA helicase. This system requires supercoiled plasmid DNA template and DNA synthesis absolutely required DNA topoisomerase I. In addition, we also report here a novel finding that purified recombinant six subunit ORC significantly stimulated the DNA synthesis on a supercoiled plasmid DNA template containing an autonomously replicating sequence, ARS1.
Collapse
Affiliation(s)
- Atanaska V Mitkova
- Department of Molecular Biology, GSBS & SOM, University of Medicine & Dentistry of New Jersey, Stratford, New Jersey 08084, USA
| | | | | |
Collapse
|
40
|
Jokela M, Eskelinen A, Pospiech H, Rouvinen J, Syväoja JE. Characterization of the 3' exonuclease subunit DP1 of Methanococcus jannaschii replicative DNA polymerase D. Nucleic Acids Res 2004; 32:2430-40. [PMID: 15121900 PMCID: PMC419447 DOI: 10.1093/nar/gkh558] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The B-subunits associated with the replicative DNA polymerases are conserved from Archaea to humans, whereas the corresponding catalytic subunits are not related. The latter belong to the B and D DNA polymerase families in eukaryotes and archaea, respectively. Sequence analysis places the B-subunits within the calcineurin-like phosphoesterase superfamily. Since residues implicated in metal binding and catalysis are well conserved in archaeal family D DNA polymerases, it has been hypothesized that the B-subunit could be responsible for the 3'-5' proofreading exonuclease activity of these enzymes. To test this hypothesis we expressed Methanococcus jannaschii DP1 (MjaDP1), the B-subunit of DNA polymerase D, in Escherichia coli, and demonstrate that MjaDP1 functions alone as a moderately active, thermostable, Mn2+-dependent 3'-5' exonuclease. The putative polymerase subunit DP2 is not required. The nuclease activity is strongly reduced by single amino acid mutations in the phosphoesterase domain indicating the requirement of this domain for the activity. MjaDP1 acts as a unidirectional, non-processive exonuclease preferring mispaired nucleotides and single-stranded DNA, suggesting that MjaDP1 functions as the proofreading exonuclease of archaeal family D DNA polymerase.
Collapse
Affiliation(s)
- Maarit Jokela
- Biocenter Oulu and Department of Biochemistry, PO Box 3000, FIN-90014 University of Oulu, Finland
| | | | | | | | | |
Collapse
|
41
|
Kaufmann G, Nethanel T. Did an early version of the eukaryal replisome enable the emergence of chromatin? PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2004; 77:173-209. [PMID: 15196893 DOI: 10.1016/s0079-6603(04)77005-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Gabriel Kaufmann
- Biochemistry Department, Tel Aviv University, Ramat Aviv 69978, Israel
| | | |
Collapse
|
42
|
Zhang N, Lu X, Legerski RJ. Partial reconstitution of human interstrand cross-link repair in vitro: characterization of the roles of RPA and PCNA. Biochem Biophys Res Commun 2003; 309:71-8. [PMID: 12943665 DOI: 10.1016/s0006-291x(03)01535-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The repair of DNA interstrand cross-links (ICLs) remains largely ill-defined in higher eukaryotic cells. Previously, we have developed assays that can be used to monitor the early stages of processing of ICLs in vitro. Here, we have used P11 phosphocellulose chromatography to fractionate HeLa nuclear extracts and have subsequently reconstituted these assays with the resulting fractions. RPA and PCNA were found in a single fraction, and were the only factors in this fraction required for the reconstitution of these assays. The roles of RPA and PCNA in the formation of incisions at ICLs and in the subsequent DNA synthesis step were assessed. RPA was found to be essential for both stages of ICL processing indicating that it is required for lesion recognition and/or for the subsequent endonucleolytic processing. PCNA is required for the DNA synthesis stage and although it is not critical for the incision stage of the reaction it does enhance this step presumably by a stimulation of lesion recognition by MutSbeta. These findings define novel roles for RPA and PCNA in the processing of ICLs in mammalian cells.
Collapse
Affiliation(s)
- Nianxiang Zhang
- Department of Molecular Genetics, The University of Texas M.D. Anderson Cancer Center, Houston 77030, USA
| | | | | |
Collapse
|
43
|
Yamada K, Takezawa J, Ezaki O. Translesion replication in cisplatin-treated xeroderma pigmentosum variant cells is also caffeine-sensitive: features of the error-prone DNA polymerase(s) involved in UV-mutagenesis. DNA Repair (Amst) 2003; 2:909-24. [PMID: 12893087 DOI: 10.1016/s1568-7864(03)00092-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Patients with xeroderma pigmentosum variant (XP-V) have a higher risk to skin cancer and XP-V cells are extremely mutable by ultraviolet (UV). The defective gene encodes a DNA polymerase (Poleta) which catalyzed relatively accurate translesion synthesis past the cyclobutane dimer of UV-lesions instead of the replicative polymerase(s) that stalled just before the lesion. Pulse-chase studies have shown that translesion replication in XP-V cells is delayed, but does not completely cease. Taking these results together, error-prone polymerase(s) are plausively involved in the UV-mutagenesis in XP-V devoid of Poleta. However, less is known about the polymerase(s) in vivo. Using an alkaline sucrose density gradient centrifugation (ASDG) technique, translesion replication is detected in the two XP-V strains XP30RO and XP115LO. As reported by Lehmann et al. [Proc. Natl. Acad. Sci. U.S.A. 72 (1975): 219] in XP-V; (i) smaller replication products were accumulated after UV irradiation; (ii) the elongation of these products was delayed; (iii) the elongation was markedly inhibited by caffeine. XP-V cells UV-irradiated at mid-S phase were normally S-arrested, and no "override" by caffeine (i.e. abrogation of the S-checkpoint) was observed by flow cytometry, suggesting that caffeine does not act via cdc kinase here; (iv) butylphenyldeoxyguanosine (BuPGdR) inhibited elongation of replication products only in UV-irradiated XP-V cells; (v) dideoxycytidine or dideoxyinosine had no effect on this process in either normal or XP-V cells. Next, similar phenomena to UV (all of above i to v) were observed also in cisplatin-treated XP-V cells. Pol eta was indicated to participate in cisplatin-induced translesion replication in normal cells. Summing up the above results, the polymerase(s) which work in translesion replication in XP-V are probably BuPGdR-sensitive, insensitive to dideoxynucleotides and can bypass also cisplatin-lesions. To date, several polymerases capable of lesion-bypass synthesis have been isolated. The features presented here are quite useful for identifying the error-prone polymerase(s) involved in UV-mutagenesis.
Collapse
Affiliation(s)
- Kouichi Yamada
- Division of Clinical Nutrition, The National Institute of Health and Nutrition, Shinjuku-ku, 162-8636 Tokyo, Japan.
| | | | | |
Collapse
|
44
|
Raji NS, Krishna TH, Rao KS. DNA-polymerase alpha, beta, delta and epsilon activities in isolated neuronal and astroglial cell fractions from developing and aging rat cerebral cortex. Int J Dev Neurosci 2002; 20:491-6. [PMID: 12392752 DOI: 10.1016/s0736-5748(02)00079-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The relative proportions of DNA-polymerases alpha, beta, delta and epsilon (pols alpha, beta, delta and epsilon ) activities in isolated neuronal and astroglial cell fractions from developing, adult and aging rat brain cerebral cortex, were examined. This was achieved through a protocol that takes advantage of the reported differential sensitivities of different DNA-polymerases towards certain inhibitors like butylphenyl and butylanilino nucleotide analogs, 2',3'-dideoxythymidine triphosphate (ddTTP), monoclonal antibody of human alpha polymerase and the use of two template primers as substrates. The results indicate that while DNA-polymerase beta (pol beta) is the predominant enzyme, significant levels of DNA-polymerases alpha and delta/epsilon (pols alpha and delta/epsilon ) are also present in both cell types at all the post-natal ages studied. A notable difference regarding the relative abundance of DNA-polymerases other than beta is the higher percentage of pol delta/epsilon in neurons and a more sustained pol alpha activity through the life span in astroglia. The presence of detectable proportion of DNA-polymerases other than beta (particularly the delta/epsilon type) may be taken to indicate their role in long patch base excision repair as well as in other modes of DNA repair.
Collapse
Affiliation(s)
- N S Raji
- ICMR Center for Research on Aging and Brain, Department of Biochemistry, School of Life Sciences, University of Hyderabad, 500046, India
| | | | | |
Collapse
|
45
|
Porter ME. Positive and negative effects of deletions and mutations within the 5' flanking sequences of Plasmodium falciparum DNA polymerase delta. Mol Biochem Parasitol 2002; 122:9-19. [PMID: 12076766 DOI: 10.1016/s0166-6851(02)00064-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The DNA polymerase delta gene from Plasmodium falciparum is associated with a 1.76 kb 5' untranslated region and a promoter containing long homopolymeric (dA:dT) tracts and intrinsic DNA curvature. Here, a comprehensive deletion and mutational analysis of the DNA Pol(delta) upstream sequences has been undertaken to define functionally important regions. Removal of promoter-proximal DNA was shown to upregulate luciferase reporter gene expression and the ATG-proximal portion of the 5' untranslated region was required in conjunction with the promoter for reporter activity. In contrast to the ATG-proximal 5' untranslated region, deletion of the central part of the untranslated region had a positive effect on expression. Disruption of a homopolymeric (dA:dT) tract adjacent to the main transcription start site both derepressed gene expression and reduced the intrinsic curvature of DNA fragments containing this sequence.
Collapse
Affiliation(s)
- Megan E Porter
- Institute of Cell and Molecular Biology, Darwin Building, The King's Buildings, University of Edinburgh, UK.
| |
Collapse
|
46
|
Kanuri M, Minko IG, Nechev LV, Harris TM, Harris CM, Lloyd RS. Error prone translesion synthesis past gamma-hydroxypropano deoxyguanosine, the primary acrolein-derived adduct in mammalian cells. J Biol Chem 2002; 277:18257-65. [PMID: 11889127 DOI: 10.1074/jbc.m112419200] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
8-Hydroxy-5,6,7,8-tetrahydropyrimido[1,2-a]purin- 10(3H)-one,3-(2'-deoxyriboside) (1,N(2)-gamma-hydroxypropano deoxyguanosine, gamma-HOPdG) is a major DNA adduct that forms as a result of exposure to acrolein, an environmental pollutant and a product of endogenous lipid peroxidation. gamma-HOPdG has been shown previously not to be a miscoding lesion when replicated in Escherichia coli. In contrast to those prokaryotic studies, in vivo replication and mutagenesis assays in COS-7 cells using single stranded DNA containing a specific gamma-HOPdG adduct, revealed that the gamma-HOPdG adduct was significantly mutagenic. Analyses revealed both transversion and transition types of mutations at an overall mutagenic frequency of 7.4 x 10(-2)/translesion synthesis. In vitro gamma-HOPdG strongly blocks DNA synthesis by two major polymerases, pol delta and pol epsilon. Replicative blockage of pol delta by gamma-HOPdG could be diminished by the addition of proliferating cell nuclear antigen, leading to highly mutagenic translesion bypass across this adduct. The differential functioning and processing capacities of the mammalian polymerases may be responsible for the higher mutation frequencies observed in this study when compared with the accurate and efficient nonmutagenic bypass observed in the bacterial system.
Collapse
Affiliation(s)
- Manorama Kanuri
- Sealy Center for Molecular Science, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | | | | | | | | | | |
Collapse
|
47
|
Quélo AH, Bryant JA, Verbelen JP. Endoreduplication is not inhibited but induced by aphidicolin in cultured cells of tobacco. JOURNAL OF EXPERIMENTAL BOTANY 2002; 53:669-75. [PMID: 11886886 DOI: 10.1093/jexbot/53.369.669] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Endoreduplication is a common process in plants that allows cells to increase their DNA content. In the tobacco cell cultures studied in this work it can be induced by simple hormone deprivation. Mesophyll protoplast-derived cells cultured in the presence of NAA (auxin) and BAP (cytokinin) keep on dividing, while elongation and concomitant DNA endoreduplication are induced and maintained in a medium containing only NAA. If aphidicolin is given to the two types of culture, no effect is observed on elongating, endoreduplicating cells. However, the cells programmed for division switch to elongation and DNA endoreduplication. Thus aphidicolin, an inhibitor of the replicative DNA polymerases, alpha and delta, does not inhibit endoreduplication, and furthermore actually induces it when the mitotic cell cycle is blocked. DNA duplication and cell growth can only be completely blocked if ddTTP, an inhibitor of DNA polymerase-beta, is given together with aphidicolin. This result implies that an aphidicolin-resistant DNA polymerase, such as the repair-associated DNA polymerase-beta, can mediate DNA synthesis during endoreduplication and can substitute for polymerases-alpha and -delta when the latter are inhibited. Similar results are obtained in cultures of the BY-2 cell line by withdrawing auxins from the culture medium. In this cell line endoreduplication is induced only in a small proportion of the cells. A greater proportion of the cells are blocked in the G(2) phase of the cell cycle.
Collapse
Affiliation(s)
- Anne-Hélène Quélo
- Department of Biology, University of Antwerp U.I.A., Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | | | | |
Collapse
|
48
|
Fuss J, Linn S. Human DNA polymerase epsilon colocalizes with proliferating cell nuclear antigen and DNA replication late, but not early, in S phase. J Biol Chem 2002; 277:8658-66. [PMID: 11741962 DOI: 10.1074/jbc.m110615200] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
DNA polymerase epsilon (pol epsilon) has been implicated in DNA replication, DNA repair, and cell cycle control, but its precise roles are unclear. When the subcellular localization of human pol epsilon was examined by indirect immunofluorescence, pol epsilon appeared in discrete nuclear foci that colocalized with proliferating cell nuclear antigen (PCNA) foci and sites of DNA synthesis only late in S phase. Early in S phase, pol epsilon foci were adjacent to PCNA foci. In contrast to PCNA foci that were only present in S phase, pol epsilon foci were present throughout mitosis and the G(1) phase of cycling cells. It is hypothesized from these observations that pol epsilon and PCNA have separate but associated functions early in S phase and that pol epsilon participates with PCNA in DNA replication late in S phase.
Collapse
Affiliation(s)
- Jill Fuss
- Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, California 94720-3206, USA
| | | |
Collapse
|
49
|
Jackson AL, Loeb LA. The contribution of endogenous sources of DNA damage to the multiple mutations in cancer. Mutat Res 2001; 477:7-21. [PMID: 11376682 DOI: 10.1016/s0027-5107(01)00091-4] [Citation(s) in RCA: 412] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
There is increasing evidence that most human cancers contain multiple mutations. By the time a tumor is clinically detectable it may have accumulated tens of thousands of mutations. In normal cells, mutations are rare events occurring at a rate of 10(-10) mutations per nucleotide per cell per generation. We have argued that the mutation rates exhibited by normal human cells are insufficient to account for the large number of mutations found in human cancers, and therefore, that an early event in tumorigenesis is the development of a mutator phenotype. In normal cells, spontaneous and induced DNA damage is balanced by multiple pathways for DNA repair, and most DNA damage is repaired without error. However, in tumor cells this balance may be shifted such that damage overwhelms the repair capacity, resulting in the accumulation of multiple mutations. Our hypothesis is that multiple random mutations occur during carcinogenesis. The sequential mutations that are observed in some human tumors result from selective events required for tumor progression. We consider the possibility that endogenous sources of DNA damage, in particular oxidative DNA damage, may contribute to genomic instability and to a mutator phenotype in some tumors. Endogenous and environmental sources of reactive oxygen species (ROS) are abundant. In tumor cells, antioxidant or DNA repair capacity may be insufficient to compensate for the production of ROS, and these endogenous ROS may be capable of damaging DNA and inducing mutations in critical DNA stability genes. The possibility that oxidative DNA damage could be a significant source of the genomic instability characteristic of human cancers is exciting, because it may be feasible to modulate the extent of oxidative damage through antioxidant therapy. The use of antioxidants to reduce the extent of molecular damage by ROS could delay the progression of cancer.
Collapse
Affiliation(s)
- A L Jackson
- Department of Pathology, University of Washington, Seattle, Washington, WA 98195, USA
| | | |
Collapse
|
50
|
Dua R, Edwards S, Levy DL, Campbell JL. Subunit interactions within the Saccharomyces cerevisiae DNA polymerase epsilon (pol epsilon ) complex. Demonstration of a dimeric pol epsilon. J Biol Chem 2000; 275:28816-25. [PMID: 10878005 DOI: 10.1074/jbc.m002376200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Saccharomyces cerevisiae DNA polymerase epsilon (pol epsilon) is essential for chromosomal replication. A major form of pol epsilon purified from yeast consists of at least four subunits: Pol2p, Dpb2p, Dpb3p, and Dpb4p. We have investigated the protein/protein interactions between these polypeptides by using expression of individual subunits in baculovirus-infected Sf9 insect cells and by using the yeast two-hybrid assay. The essential subunits, Pol2p and Dpb2p, interact directly in the absence of the other two subunits, and the C-terminal half of POL2, the only essential portion of Pol2p, is sufficient for interaction with Dpb2p. Dpb3p and Dpb4p, non-essential subunits, also interact directly with each other in the absence of the other two subunits. We propose that Pol2p.Dpb2p and Dpb3p.Dpb4p complexes interact with each other and document several interactions between individual members of the two respective complexes. We present biochemical evidence to support the proposal that pol epsilon may be dimeric in vivo. Gel filtration of the Pol2p.Dpb2p complexes reveals a novel heterotetrameric form, consisting of two heterodimers of Pol2p.Dpb2p. Dpb2p, but not Pol2p, exists as a homodimer, and thus the Pol2p dimerization may be mediated by Dpb2p. The pol2-E and pol2-F mutations that cause replication defects in vivo weaken the interaction between Pol2p and Dpb2p and also reduce dimerization of Pol2p. This suggests, but does not prove, that dimerization may also occur in vivo and be essential for DNA replication.
Collapse
Affiliation(s)
- R Dua
- Braun Laboratories, California Institute of Technology, Pasadena, California 91125, USA
| | | | | | | |
Collapse
|