1
|
Zhang M, Li W, Feng J, Gong Z, Yao Y, Zheng C. Integrative transcriptomics and proteomics analysis constructs a new molecular model for ovule abortion in the female-sterile line of Pinus tabuliformis Carr. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 294:110462. [PMID: 32234230 DOI: 10.1016/j.plantsci.2020.110462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 06/11/2023]
Abstract
Ovule development is critical to plant reproduction and free nuclear mitosis of megagametophyte (FNMM) is vital for ovule development. However, most results of ovule development were based on the studies in angiosperms, and its molecular regulation remained largely unknown in gymnosperms, particularly, during FNMM. In this context, we studied the genome-wide difference between sterile line (SL) and fertile line (FL) ovules using transcriptomics and proteomics approaches in Pinus tabuliformis Carr. Comparative analyses revealed that genes involved in DNA replication, DNA damage repair, Cell cycle, Apoptosis and Energy metabolism were highlighted. Further results showed the low expressions of MCM 2-7, RRM1, etc. perhaps led to abnormal DNA replication and damage repair, and the significantly different expressions of PARP2, CCs1, CCs3, etc. implied that the accumulated DNA double-stranded breaks were failed to be repaired and the cell cycle was arrested at G2/M in SL ovules, potentially resulting in the occurrence of apoptosis. Moreover, the deficiency of ETF-QO might hinder FNMM. Consequently, FNMM stopped and ovule aborted in SL ovules. Our results suggested a selective regulatory mechanism led to FNMM half-stop and ovule abortion in P. tabuliformis and these insights could be exploited to investigate the molecular regulations of ovule development in woody gymnosperms.
Collapse
Affiliation(s)
- Min Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China
| | - Wenhai Li
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China
| | - Jun Feng
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China
| | - Zaixin Gong
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China
| | - Yang Yao
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China
| | - Caixia Zheng
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China.
| |
Collapse
|
2
|
Oh DY, Matsumoto Y, Kitajiri SI, Kim NKD, Kim MY, Kim AR, Lee M, Lee C, Tomkinson AE, Katsuno T, Kim SY, Shin HW, Han JH, Lee S, Park WY, Choi BY. POLD1 variants leading to reduced polymerase activity can cause hearing loss without syndromic features. Hum Mutat 2020; 41:913-920. [PMID: 31944473 DOI: 10.1002/humu.23984] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 12/17/2019] [Accepted: 01/13/2020] [Indexed: 11/08/2022]
Abstract
DNA polymerase δ, whose catalytic subunit is encoded by POLD1, is responsible for synthesizing the lagging strand of DNA. Single heterozygous POLD1 mutations in domains with polymerase and exonuclease activities have been reported to cause syndromic deafness as a part of multisystem metabolic disorder or predisposition to cancer. However, the phenotypes of diverse combinations of POLD1 genotypes have not been elucidated in humans. We found that five members of a multiplex family segregating autosomal recessive nonsyndromic sensorineural hearing loss (NS-SNHL) have revealed novel compound heterozygous POLD1 variants (p.Gly1100Arg and a presumptive null function variant, p.Ser197Hisfs*54). The recombinant p.Gly1100Arg polymerase δ showed a reduced polymerase activity by 30-40%, but exhibited normal exonuclease activity. The polymerase activity in cell extracts from the affected subject carrying the two POLD1 mutant alleles was about 33% of normal controls. We suggest that significantly decreased polymerase δ activity, but not a complete absence, with normal exonuclease activity could lead to NS-SNHL.
Collapse
Affiliation(s)
- Doo-Yi Oh
- Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Yoshihiro Matsumoto
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico.,Department of Environmental Biology, Chubu University College of Bioscience and Biotechnology, Kasugai, Aichi, Japan
| | - Shin-Ichiro Kitajiri
- Department of Otolaryngology-Head and Neck Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Nayoung K D Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Min Young Kim
- Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Ah Reum Kim
- Department of Otorhinolaryngology, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul, Korea
| | - Mingyu Lee
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Korea.,Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
| | - Chung Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Seoul, Korea
| | - Alan E Tomkinson
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico
| | - Tatsuya Katsuno
- Department of Otolaryngology-Head and Neck Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - So Young Kim
- Department of Otorhinolaryngology, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul, Korea
| | - Hyun-Woo Shin
- Department of Otorhinolaryngology, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul, Korea.,Department of Pharmacology, Seoul National University College of Medicine, Seoul, Korea.,Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Seungmin Lee
- Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,Department of Molecular Cell Biology, School of Medicine, Sungkyunkwan University, Seoul, Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, Korea
| |
Collapse
|
3
|
Hoitsma NM, Whitaker AM, Schaich MA, Smith MR, Fairlamb MS, Freudenthal BD. Structure and function relationships in mammalian DNA polymerases. Cell Mol Life Sci 2020; 77:35-59. [PMID: 31722068 PMCID: PMC7050493 DOI: 10.1007/s00018-019-03368-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/11/2019] [Accepted: 10/31/2019] [Indexed: 12/19/2022]
Abstract
DNA polymerases are vital for the synthesis of new DNA strands. Since the discovery of DNA polymerase I in Escherichia coli, a diverse library of mammalian DNA polymerases involved in DNA replication, DNA repair, antibody generation, and cell checkpoint signaling has emerged. While the unique functions of these DNA polymerases are differentiated by their association with accessory factors and/or the presence of distinctive catalytic domains, atomic resolution structures of DNA polymerases in complex with their DNA substrates have revealed mechanistic subtleties that contribute to their specialization. In this review, the structure and function of all 15 mammalian DNA polymerases from families B, Y, X, and A will be reviewed and discussed with special emphasis on the insights gleaned from recently published atomic resolution structures.
Collapse
Affiliation(s)
- Nicole M Hoitsma
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Amy M Whitaker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Matthew A Schaich
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Mallory R Smith
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Max S Fairlamb
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| |
Collapse
|
4
|
Suzuki M, Kino K, Kawada T, Morikawa M, Kobayashi T, Miyazawa H. Analysis of nucleotide insertion opposite 2,2,4-triamino-5(2H)-oxazolone by eukaryotic B- and Y-family DNA polymerases. Chem Res Toxicol 2015; 28:1307-16. [PMID: 26010525 DOI: 10.1021/acs.chemrestox.5b00114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Mutations induced by oxidative DNA damage can cause diseases such as cancer. In particular, G:C-T:A and G:C-C:G transversions are caused by oxidized guanine and have been observed in the p53 and K-ras genes. We focused on an oxidized form of guanine, 2,2,4-triamino-5(2H)-oxazolone (Oz), as a cause of G:C-C:G transversions based on our earlier elucidation that DNA polymerases (Pols) α, β, γ, ε, η, I, and IV incorporate dGTP opposite Oz. The nucleotide insertion and extension of Pols δ, ζ, ι, κ, and REV1, belonging to the B- and Y-families of DNA polymerases, were analyzed for the first time. Pol δ incorporated dGTP, in common with other replicative DNA polymerases. Pol ζ incorporated dGTP and dATP, and the efficiency of elongation up to full-length beyond Oz was almost the same as that beyond G. Although nucleotide incorporation by Pols ι or κ was also error-prone, they did not extend the primer. On the other hand, the polymerase REV1 predominantly incorporated dCTP opposite Oz more efficiently than opposite 8-oxo-7,8-dihydroguanine, guanidinohydantoin, or tetrahydrofuran. Here, we demonstrate that Pol ζ can efficiently replicate DNA containing Oz and that REV1 can prevent G:C-C:G transversions caused by Oz.
Collapse
Affiliation(s)
- Masayo Suzuki
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1, Shido, Sanuki, Kagawa 769-2193, Japan
| | - Katsuhito Kino
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1, Shido, Sanuki, Kagawa 769-2193, Japan
| | - Taishu Kawada
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1, Shido, Sanuki, Kagawa 769-2193, Japan
| | - Masayuki Morikawa
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1, Shido, Sanuki, Kagawa 769-2193, Japan
| | - Takanobu Kobayashi
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1, Shido, Sanuki, Kagawa 769-2193, Japan
| | - Hiroshi Miyazawa
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1, Shido, Sanuki, Kagawa 769-2193, Japan
| |
Collapse
|
5
|
Killelea T, Ralec C, Bossé A, Henneke G. PCR performance of a thermostable heterodimeric archaeal DNA polymerase. Front Microbiol 2014; 5:195. [PMID: 24847315 PMCID: PMC4019886 DOI: 10.3389/fmicb.2014.00195] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 04/12/2014] [Indexed: 11/17/2022] Open
Abstract
DNA polymerases are versatile tools used in numerous important molecular biological core technologies like the ubiquitous polymerase chain reaction (PCR), cDNA cloning, genome sequencing, and nucleic acid based diagnostics. Taking into account the multiple DNA amplification techniques in use, different DNA polymerases must be optimized for each type of application. One of the current tendencies is to reengineer or to discover new DNA polymerases with increased performance and broadened substrate spectra. At present, there is a great demand for such enzymes in applications, e.g., forensics or paleogenomics. Current major limitations hinge on the inability of conventional PCR enzymes, such as Taq, to amplify degraded or low amounts of template DNA. Besides, a wide range of PCR inhibitors can also impede reactions of nucleic acid amplification. Here we looked at the PCR performances of the proof-reading D-type DNA polymerase from P. abyssi, Pab-polD. Fragments, 3 kilobases in length, were specifically PCR-amplified in its optimized reaction buffer. Pab-polD showed not only a greater resistance to high denaturation temperatures than Taq during cycling, but also a superior tolerance to the presence of potential inhibitors. Proficient proof-reading Pab-polD enzyme could also extend a primer containing up to two mismatches at the 3' primer termini. Overall, we found valuable biochemical properties in Pab-polD compared to the conventional Taq, which makes the enzyme ideally suited for cutting-edge PCR-applications.
Collapse
Affiliation(s)
- Tom Killelea
- Université de Bretagne Occidentale, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France
| | - Céline Ralec
- Université de Bretagne Occidentale, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France
| | - Audrey Bossé
- Université de Bretagne Occidentale, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France
| | - Ghislaine Henneke
- Université de Bretagne Occidentale, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France
| |
Collapse
|
6
|
Waisertreiger ISR, Liston VG, Menezes MR, Kim HM, Lobachev KS, Stepchenkova EI, Tahirov TH, Rogozin IB, Pavlov YI. Modulation of mutagenesis in eukaryotes by DNA replication fork dynamics and quality of nucleotide pools. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:699-724. [PMID: 23055184 PMCID: PMC3893020 DOI: 10.1002/em.21735] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/13/2012] [Accepted: 08/15/2012] [Indexed: 06/01/2023]
Abstract
The rate of mutations in eukaryotes depends on a plethora of factors and is not immediately derived from the fidelity of DNA polymerases (Pols). Replication of chromosomes containing the anti-parallel strands of duplex DNA occurs through the copying of leading and lagging strand templates by a trio of Pols α, δ and ϵ, with the assistance of Pol ζ and Y-family Pols at difficult DNA template structures or sites of DNA damage. The parameters of the synthesis at a given location are dictated by the quality and quantity of nucleotides in the pools, replication fork architecture, transcription status, regulation of Pol switches, and structure of chromatin. The result of these transactions is a subject of survey and editing by DNA repair.
Collapse
Affiliation(s)
- Irina S.-R. Waisertreiger
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Victoria G. Liston
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Miriam R. Menezes
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Hyun-Min Kim
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Kirill S. Lobachev
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Elena I. Stepchenkova
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
- Saint Petersburg Branch of Vavilov Institute of General Genetics, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
- Department of Genetics, Saint Petersburg University, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
| | - Tahir H. Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Igor B. Rogozin
- National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD 20894, U.S.A
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
| | - Youri. I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
- Department of Genetics, Saint Petersburg University, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
| |
Collapse
|
7
|
Abstract
DNA polymerase δ (Pol δ) is a member of the B-family DNA polymerases and is one of the major replicative DNA polymerases in eukaryotes. In addition to chromosomal DNA replication it is also involved in DNA repair and recombination. Pol δ is a multi-subunit complex comprised of a catalytic subunit and accessory subunits. The latter subunits play a critical role in the regulation of Pol δ functions. Recent progress in the structural characterization of Pol δ, together with a vast number of biochemical and functional studies, provides the basis for understanding the intriguing mechanisms of its regulation during DNA replication, repair and recombination. In this chapter we review the current state of the Pol δ structure-function relationship with an emphasis on the role of its accessory subunits.
Collapse
Affiliation(s)
- Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198-7696, USA,
| |
Collapse
|
8
|
Brocas C, Charbonnier JB, Dhérin C, Gangloff S, Maloisel L. Stable interactions between DNA polymerase δ catalytic and structural subunits are essential for efficient DNA repair. DNA Repair (Amst) 2010; 9:1098-111. [PMID: 20813592 DOI: 10.1016/j.dnarep.2010.07.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 07/19/2010] [Accepted: 07/23/2010] [Indexed: 11/24/2022]
Abstract
Eukaryotic DNA polymerase δ (Pol δ) activity is crucial for chromosome replication and DNA repair and thus, plays an essential role in genome stability. In Saccharomyces cerevisiae, Pol δ is a heterotrimeric complex composed of the catalytic subunit Pol3, the structural B subunit Pol31, and Pol32, an additional auxiliary subunit. Pol3 interacts with Pol31 thanks to its C-terminal domain (CTD) and this interaction is of functional importance both in DNA replication and DNA repair. Interestingly, deletion of the last four C-terminal Pol3 residues, LSKW, in the pol3-ct mutant does not affect DNA replication but leads to defects in homologous recombination and in break-induced replication (BIR) repair pathways. The defect associated with pol3-ct could result from a defective interaction between Pol δ and a protein involved in recombination. However, we show that the LSKW motif is required for the interaction between Pol3 C-terminal end and Pol31. This loss of interaction is relevant in vivo since we found that pol3-ct confers HU sensitivity on its own and synthetic lethality with a POL32 deletion. Moreover, pol3-ct shows genetic interactions, both suppression and synthetic lethality, with POL31 mutant alleles. Structural analyses indicate that the B subunit of Pol δ displays a major conserved region at its surface and that pol31 alleles interacting with pol3-ct, correspond to substitutions of Pol31 amino acids that are situated in this particular region. Superimposition of our Pol31 model on the 3D architecture of the phylogenetically related DNA polymerase α (Pol α) suggests that Pol3 CTD interacts with the conserved region of Pol31, thus providing a molecular basis to understand the defects associated with pol3-ct. Taken together, our data highlight a stringent dependence on Pol δ complex stability in DNA repair.
Collapse
Affiliation(s)
- Clémentine Brocas
- CEA, DSV, iRCM, Bâtiment 05/BP6, Fontenay-aux-Roses, F-92265, France
| | | | | | | | | |
Collapse
|
9
|
Sanchez Garcia J, Baranovskiy AG, Knatko EV, Gray FC, Tahirov TH, MacNeill SA. Functional mapping of the fission yeast DNA polymerase delta B-subunit Cdc1 by site-directed and random pentapeptide insertion mutagenesis. BMC Mol Biol 2009; 10:82. [PMID: 19686603 PMCID: PMC2734569 DOI: 10.1186/1471-2199-10-82] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 08/17/2009] [Indexed: 11/25/2022] Open
Abstract
Background DNA polymerase δ plays an essential role in chromosomal DNA replication in eukaryotic cells, being responsible for synthesising the bulk of the lagging strand. In fission yeast, Pol δ is a heterotetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1. Pol3 binds directly to the B-subunit, Cdc1, which in turn binds the C-subunit, Cdc27. Human Pol δ comprises the same four subunits, and the crystal structure was recently reported of a complex of human p50 and the N-terminal domain of p66, the human orthologues of Cdc1 and Cdc27, respectively. Results To gain insights into the structure and function of Cdc1, random and directed mutagenesis techniques were used to create a collection of thirty alleles encoding mutant Cdc1 proteins. Each allele was tested for function in fission yeast and for binding of the altered protein to Pol3 and Cdc27 using the two-hybrid system. Additionally, the locations of the amino acid changes in each protein were mapped onto the three-dimensional structure of human p50. The results obtained from these studies identify amino acid residues and regions within the Cdc1 protein that are essential for interaction with Pol3 and Cdc27 and for in vivo function. Mutations specifically defective in Pol3-Cdc1 interactions allow the identification of a possible Pol3 binding surface on Cdc1. Conclusion In the absence of a three-dimensional structure of the entire Pol δ complex, the results of this study highlight regions in Cdc1 that are vital for protein function in vivo and provide valuable clues to possible protein-protein interaction surfaces on the Cdc1 protein that will be important targets for further study.
Collapse
Affiliation(s)
- Javier Sanchez Garcia
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3JR, UK.
| | | | | | | | | | | |
Collapse
|
10
|
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
|
11
|
Schmitt MW, Matsumoto Y, Loeb LA. High fidelity and lesion bypass capability of human DNA polymerase delta. Biochimie 2009; 91:1163-72. [PMID: 19540301 DOI: 10.1016/j.biochi.2009.06.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Accepted: 06/09/2009] [Indexed: 11/27/2022]
Abstract
DNA polymerase delta (Pol delta) is one of the main replicative DNA polymerases in human cells and therefore is a critical determinant of the overall accuracy of DNA synthesis. Here we document the fidelity of a human Pol delta holoenzyme and systematically score the types of mutations that the enzyme generates in a forward mutation assay. We find that human Pol delta is highly accurate, catalyzing less than one nucleotide mis-insertion per 220,000 nucleotides polymerized. Inactivation of proofreading or mutation of a conserved active site residue significantly elevates the frequency of incorporation errors, demonstrating the contribution of both the base selection and proofreading domains to the overall accuracy of synthesis by Pol delta. The highly selective nature of the polymerase active site is also indicated by the stalling of Pol delta upon encountering multiple types of DNA lesions. However, DNA damage is not an absolute block to Pol delta progression. We propose that partial lesion bypass by Pol delta represents a balance between stalling to allow for repair of mutagenic lesions by specialized repair proteins and bypass of damage to allow for successful completion of DNA synthesis by Pol delta in the presence of weakly blocking DNA adducts.
Collapse
Affiliation(s)
- Michael W Schmitt
- Department of Biochemistry and Pathology, Joseph Gottstein Memorial Cancer Research Laboratory, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | | |
Collapse
|
12
|
Fazlieva R, Spittle CS, Morrissey D, Hayashi H, Yan H, Matsumoto Y. Proofreading exonuclease activity of human DNA polymerase delta and its effects on lesion-bypass DNA synthesis. Nucleic Acids Res 2009; 37:2854-66. [PMID: 19282447 PMCID: PMC2685094 DOI: 10.1093/nar/gkp155] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Replicative DNA polymerases possess 3′ → 5′ exonuclease activity to reduce misincorporation of incorrect nucleotides by proofreading during replication. To examine if this proofreading activity modulates DNA synthesis of damaged templates, we constructed a series of recombinant human DNA polymerase δ (Pol δ) in which one or two of the three conserved Asp residues in the exonuclease domain are mutated, and compared their properties with that of the wild-type enzyme. While all the mutant enzymes lost more than 95% exonuclease activity and severely decreased the proofreading activity than the wild-type, the bypass efficiency of damaged templates was varied: two mutant enzymes, D515V and D402A/D515A, gave higher bypass efficiencies on templates containing an abasic site, but another mutant, D316N/D515A, showed a lower bypass efficiency than the wild-type. All the enzymes including the wild-type inserted an adenine opposite the abasic site, whereas these enzymes inserted cytosine and adenine opposite an 8-oxoguanine with a ratio of 6:4. These results indicate that the exonuclease activity of human Pol δ modulates its intrinsic bypass efficiency on the damaged template, but does not affect the choice of nucleotide to be inserted.
Collapse
Affiliation(s)
- Ruzaliya Fazlieva
- Medical Science Division, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | | | | | | | | | | |
Collapse
|
13
|
Masuda Y, Suzuki M, Piao J, Gu Y, Tsurimoto T, Kamiya K. Dynamics of human replication factors in the elongation phase of DNA replication. Nucleic Acids Res 2007; 35:6904-16. [PMID: 17932049 PMCID: PMC2175312 DOI: 10.1093/nar/gkm822] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In eukaryotic cells, DNA replication is carried out by coordinated actions of many proteins, including DNA polymerase δ (pol δ), replication factor C (RFC), proliferating cell nuclear antigen (PCNA) and replication protein A. Here we describe dynamic properties of these proteins in the elongation step on a single-stranded M13 template, providing evidence that pol δ has a distributive nature over the 7 kb of the M13 template, repeating a frequent dissociation–association cycle at growing 3′-hydroxyl ends. Some PCNA could remain at the primer terminus during this cycle, while the remainder slides out of the primer terminus or is unloaded once pol δ has dissociated. RFC remains around the primer terminus through the elongation phase, and could probably hold PCNA from which pol δ has detached, or reload PCNA from solution to restart DNA synthesis. Furthermore, we suggest that a subunit of pol δ, POLD3, plays a crucial role in the efficient recycling of PCNA during dissociation–association cycles of pol δ. Based on these observations, we propose a model for dynamic processes in elongation complexes.
Collapse
Affiliation(s)
- Yuji Masuda
- Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan.
| | | | | | | | | | | |
Collapse
|
14
|
Pavlov YI, Shcherbakova PV, Rogozin IB. Roles of DNA Polymerases in Replication, Repair, and Recombination in Eukaryotes. INTERNATIONAL REVIEW OF CYTOLOGY 2006; 255:41-132. [PMID: 17178465 DOI: 10.1016/s0074-7696(06)55002-8] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The functioning of the eukaryotic genome depends on efficient and accurate DNA replication and repair. The process of replication is complicated by the ongoing decomposition of DNA and damage of the genome by endogenous and exogenous factors. DNA damage can alter base coding potential resulting in mutations, or block DNA replication, which can lead to double-strand breaks (DSB) and to subsequent chromosome loss. Replication is coordinated with DNA repair systems that operate in cells to remove or tolerate DNA lesions. DNA polymerases can serve as sensors in the cell cycle checkpoint pathways that delay cell division until damaged DNA is repaired and replication is completed. Eukaryotic DNA template-dependent DNA polymerases have different properties adapted to perform an amazingly wide spectrum of DNA transactions. In this review, we discuss the structure, the mechanism, and the evolutionary relationships of DNA polymerases and their possible functions in the replication of intact and damaged chromosomes, DNA damage repair, and recombination.
Collapse
Affiliation(s)
- Youri I Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, Departments of Biochemistry and Molecular Biology, and Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-6805, USA
| | | | | |
Collapse
|
15
|
Abstract
DNA replicases are multicomponent machines that have evolved clever strategies to perform their function. Although the structure of DNA is elegant in its simplicity, the job of duplicating it is far from simple. At the heart of the replicase machinery is a heteropentameric AAA+ clamp-loading machine that couples ATP hydrolysis to load circular clamp proteins onto DNA. The clamps encircle DNA and hold polymerases to the template for processive action. Clamp-loader and sliding clamp structures have been solved in both prokaryotic and eukaryotic systems. The heteropentameric clamp loaders are circular oligomers, reflecting the circular shape of their respective clamp substrates. Clamps and clamp loaders also function in other DNA metabolic processes, including repair, checkpoint mechanisms, and cell cycle progression. Twin polymerases and clamps coordinate their actions with a clamp loader and yet other proteins to form a replisome machine that advances the replication fork.
Collapse
Affiliation(s)
- Aaron Johnson
- Howard Hughes Medical Institute, New York City, New York 10021-6399, USA.
| | | |
Collapse
|
16
|
Abstract
Three DNA polymerases are thought to function at the eukaryotic DNA replication fork. Currently, a coherent model has been derived for the composition and activities of the lagging strand machinery. RNA-DNA primers are initiated by DNA polymerase ot-primase. Loading of the proliferating cell nuclear antigen, PCNA, dissociates DNA polymerase ca and recruits DNA polymerase S and the flap endonuclease FEN1 for elongation and in preparation for its requirement during maturation, respectively. Nick translation by the strand displacement action of DNA polymerase 8, coupled with the nuclease action of FEN1, results in processive RNA degradation until a proper DNA nick is reached for closure by DNA ligase I. In the event of excessive strand displacement synthesis, other factors, such as the Dna2 nuclease/helicase, are required to trim excess flaps. Paradoxically, the composition and activity of the much simpler leading strand machinery has not been clearly established. The burden of evidence suggests that DNA polymerase E normally replicates this strand,but under conditions of dysfunction, DNA polymerase 8 may substitute.
Collapse
Affiliation(s)
- Parie Garg
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | | |
Collapse
|
17
|
Sanchez Garcia J, Ciufo LF, Yang X, Kearsey SE, MacNeill SA. The C-terminal zinc finger of the catalytic subunit of DNA polymerase delta is responsible for direct interaction with the B-subunit. Nucleic Acids Res 2004; 32:3005-16. [PMID: 15173383 PMCID: PMC434430 DOI: 10.1093/nar/gkh623] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2004] [Revised: 05/06/2004] [Accepted: 05/06/2004] [Indexed: 11/14/2022] Open
Abstract
DNA polymerase delta (Pol delta) plays a central role in eukaryotic chromosomal DNA replication, repair and recombination. In fission yeast, Pol delta is a tetrameric enzyme, comprising the catalytic subunit Pol3 and three smaller subunits, Cdc1, Cdc27 and Cdm1. Previous studies have demonstrated a direct interaction between Pol3 and Cdc1, the B-subunit of the complex. Here it is shown that removal of the tandem zinc finger modules located at the C-terminus of Pol3 by targeted proteolysis renders the Pol3 protein non-functional in vivo, and that the C-terminal zinc finger module ZnF2 is both necessary and sufficient for binding to the B-subunit in vivo and in vitro. Extensive mutagenesis of the ZnF2 module identifies important residues for B-subunit binding. In particular, disruption of the ZnF2 module by substitution of the putative metal-coordinating cysteines with alanine abolishes B-subunit binding and in vivo function. Finally, evidence is presented suggesting that the ZnF region is post-translationally modified in fission yeast cells.
Collapse
Affiliation(s)
- Javier Sanchez Garcia
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | | | | | | | | |
Collapse
|
18
|
Abstract
Any living cell is faced with the fundamental task of keeping the genome intact in order to develop in an organized manner, to function in a complex environment, to divide at the right time, and to die when it is appropriate. To achieve this goal, an efficient machinery is required to maintain the genetic information encoded in DNA during cell division, DNA repair, DNA recombination, and the bypassing of damage in DNA. DNA polymerases (pols) alpha, beta, gamma, delta, and epsilon are the key enzymes required to maintain the integrity of the genome under all these circumstances. In the last few years the number of known pols, including terminal transferase and telomerase, has increased to at least 19. A particular pol might have more than one functional task in a cell and a particular DNA synthetic event may require more than one pol, which suggests that nature has provided various safety mechanisms. This multi-functional feature is especially valid for the variety of novel pols identified in the last three years. These are the lesion-replicating enzymes pol zeta, pol eta, pol iota, pol kappa, and Rev1, and a group of pols called pol theta;, pol lambda, pol micro, pol sigma, and pol phi that fulfill a variety of other tasks.
Collapse
Affiliation(s)
- Ulrich Hubscher
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
| | | | | |
Collapse
|
19
|
Bermudez VP, MacNeill SA, Tappin I, Hurwitz J. The influence of the Cdc27 subunit on the properties of the Schizosaccharomyces pombe DNA polymerase delta. J Biol Chem 2002; 277:36853-62. [PMID: 12124382 DOI: 10.1074/jbc.m202897200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Schizosaccharomyces pombe DNA polymerase (pol) delta contains four subunits, pol 3, Cdc1, Cdc27, and Cdm1. In this report, we examined the role of Cdc27 on the structure and activity of pol delta. We show that the four-subunit complex is monomeric in structure, in contrast to the previous report that it was a dimer (Zuo, S., Bermudez, V., Zhang, G., Kelman, Z., and Hurwitz, J. (2000) J. Biol. Chem. 275, 5153-5162). This discrepancy between the earlier and recent observations was traced to the marked asymmetric shape of Cdc27. Cdc27 contains two critical domains that govern its role in activating pol delta. The N-terminal region (amino acids (aa) 1-160) binds to Cdc1 and its extreme C-terminal end (aa 362-369) interacts with proliferating cell nuclear antigen (PCNA). Mutants of S. pombe pol delta, containing truncated Cdc27 derivatives deficient in binding to PCNA, supported DNA replication less processively than the wild-type complex. Fusion of a minimal PCNA-binding motif (aa 352-372) to C-terminally truncated Cdc27 derivatives restored processive DNA synthesis in vitro. In vivo, the introduction of these fused Cdc27 derivatives into cdc27Delta cells conferred viability. These data support the model in which Cdc27 plays an essential role in DNA replication by recruiting PCNA to the pol delta holoenzyme.
Collapse
Affiliation(s)
- Vladimir P Bermudez
- Memorial Sloan-Kettering Cancer Center, Program of Molecular Biology, New York, New York 10021, USA
| | | | | | | |
Collapse
|
20
|
Ducoux M, Urbach S, Baldacci G, Hübscher U, Koundrioukoff S, Christensen J, Hughes P. Mediation of proliferating cell nuclear antigen (PCNA)-dependent DNA replication through a conserved p21(Cip1)-like PCNA-binding motif present in the third subunit of human DNA polymerase delta. J Biol Chem 2001; 276:49258-66. [PMID: 11595739 DOI: 10.1074/jbc.m106990200] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The subunit that mediates binding of proliferating cell nuclear antigen (PCNA) to human DNA polymerase delta has not been clearly defined. We show that the third subunit of human DNA polymerase delta, p66, interacts with PCNA through a canonical PCNA-binding sequence located in its C terminus. Conversely, p66 interacts with the domain-interconnecting loop of PCNA, a region previously shown to be important for DNA polymerase delta activity and for binding of the cell cycle inhibitor p21(Cip1). In accordance with this, a peptide containing the PCNA-binding domain of p21(Cip1) inhibited p66 binding to PCNA and the activity of native three-subunit DNA polymerase delta. Furthermore, pull-down assays showed that DNA polymerase delta requires p66 for interaction with PCNA. More importantly, only reconstituted three-subunit DNA polymerase delta displayed PCNA-dependent DNA replication that could be inhibited by the PCNA-binding domain of p21(Cip1). Direct participation of p66 in PCNA-dependent DNA replication in vivo is demonstrated by co-localization of p66 with PCNA and DNA polymerase delta within DNA replication foci. Finally, in vitro phosphorylation of p66 by cyclin-dependent kinases suggests that p66 activity may be subject to cell cycle-dependent regulation. These results suggest that p66 is the chief mediator of PCNA-dependent DNA synthesis by DNA polymerase delta.
Collapse
Affiliation(s)
- M Ducoux
- Institut Curie, UMR 2027 du CNRS, Génotoxicologie et Cycle Cellulaire, Bâtiment 110, Centre Universitaire, 91405 Orsay Cedex, France
| | | | | | | | | | | | | |
Collapse
|
21
|
Johansson E, Majka J, Burgers PM. Structure of DNA polymerase delta from Saccharomyces cerevisiae. J Biol Chem 2001; 276:43824-8. [PMID: 11568188 DOI: 10.1074/jbc.m108842200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA polymerase delta (Pol delta) from Saccharomyces cerevisiae consists of three subunits, Pol3 (125 kDa), Pol31 (55 kDa), and Pol32 (40 kDa), present at a 1:1:1 stoichiometry in purified preparations. Previously, based on gel filtration studies of Pol delta, we suggested that the enzyme may be a dimer of catalytic cores, with dimerization mediated by the Pol32 subunit (Burgers, P. M., and Gerik, K. J. (1998) J. Biol. Chem. 273, 19756-19762). We now report on extensive gel filtration, glycerol gradient sedimentation, and analytical equilibrium centrifugation studies of Pol delta and of several subassemblies of Pol delta. The hydrodynamic parameters of these assemblies indicate that (i) Pol32 is a rod-shaped protein with a frictional ratio f/f(0) = 2.22; (ii) any complex containing Pol32 also has an extremely asymmetric shape; (iii) the results of these studies are independent of concentration (varied between 0.1-20 microm); (iv) all complexes are monomeric under the conditions studied (up to 20 microm). Moreover, a two-hybrid analysis of the Pol32 subunit did not detect a Pol32-Pol32 interaction in vivo. Therefore, we conclude that the assembly structure of Pol delta is that of a monomer.
Collapse
Affiliation(s)
- E Johansson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | | | | |
Collapse
|
22
|
Organization, Replication, Transposition, and Repair of DNA. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|