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Zhang T, Wang X, Zhang Q, Yang D, Zhang X, Liu H, Wang Q, Dong Z, Zhao J. Interactive effects of multiple antibiotic residues and ocean acidification on physiology and metabolome of the bay scallops Argopecten irradians irradians. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168941. [PMID: 38056652 DOI: 10.1016/j.scitotenv.2023.168941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 12/08/2023]
Abstract
Coastal areas are confronted with compounding threats arising from both climatic and non-climatic stressors. Antibiotic pollution and ocean acidification are two prevalently concurrent environmental stressors. Yet their interactive effects on marine biota have not been investigated adequately and the compound hazard remain obscure. In this study, bay scallops Argopecten irradians irradians were exposed to multiple antibiotics (sulfamethoxazole, tetracycline, oxytetracycline, norfloxacin, and erythromycin, each at a concentration of 1 μg/L) combined with/without acidic seawater (pH 7.6) for 35 days. The single and interactive effects of the two stressors on A. irradians irradians were determined from multidimensional bio-responses, including energetic physiological traits as well as the molecular underpinning (metabolome and expressions of key genes). Results showed that multiple antibiotics predominantly enhanced the process of DNA repair and replication via disturbing the purine metabolism pathway. This alternation is perhaps to cope with the DNA damage induced by oxidative stress. Ocean acidification mainly disrupted energy metabolism and ammonia metabolism of the scallops, as evidenced by the increased ammonia excretion rate, the decreased O:N ratio, and perturbations in amino acid metabolism pathways. Moreover, the antagonistic effects of multiple antibiotics and ocean acidification caused alternations in the relative abundance of neurotransmitter and gene expression of neurotransmitter receptors, which may lead to neurological disorders in scallops. Overall, the revealed alternations in physiological traits, metabolites and gene expressions provide insightful information for the health status of bivalves in a natural environmental condition under the climate change scenarios.
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Affiliation(s)
- Tianyu Zhang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264117, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xin Wang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264117, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Qianqian Zhang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264117, PR China
| | - Dinglong Yang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264117, PR China
| | - Xiaoli Zhang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264117, PR China
| | - Hui Liu
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264117, PR China
| | - Qing Wang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264117, PR China
| | - Zhijun Dong
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264117, PR China
| | - Jianmin Zhao
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264117, PR China; Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264117, PR China.
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2
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Gold NM, Okeke MN, He Y. Involvement of Inheritance in Determining Telomere Length beyond Environmental and Lifestyle Factors. Aging Dis 2023:AD.2023.1023. [PMID: 37962459 DOI: 10.14336/ad.2023.1023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
All linear chromosomal ends have specific DNA-protein complexes called telomeres. Telomeres serve as a "molecular clock" to estimate the potential length of cell replication. Shortening of telomere length (TL) is associated with cellular senescence, aging, and various age-related diseases in humans. Here we reviewed the structure, function, and regulation of telomeres and the age-related diseases associated with telomere attrition. Among the various determinants of TL, we highlight the connection between TL and heredity to provide a new overview of genetic determinants for TL. Studies across multiple species have shown that maternal and paternal TL influence the TL of their offspring, and this may affect life span and their susceptibility to age-related diseases. Hence, we reviewed the linkage between TL and parental influences and the proposed mechanisms involved. More in-depth studies on the genetic mechanism for TL attrition are needed due to the potential application of this knowledge in human medicine to prevent premature frailty at its earliest stage, as well as promote health and longevity.
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Affiliation(s)
- Naheemat Modupeola Gold
- Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- State Key Laboratory of Genetic, Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Michael Ngozi Okeke
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Nanomedical Technology Research, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yonghan He
- Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- State Key Laboratory of Genetic, Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Cohen-Paes A, de Alcântara AL, de Souza Menezes E, Moreira FC, Fernandes MR, Guerreiro JF, Ribeiro-Dos-Santos Â, Dos Santos SEB, dos Santos NPC. Characterization of DNA Polymerase Genes in Amazonian Amerindian Populations. Genes (Basel) 2022; 14:53. [PMID: 36672794 PMCID: PMC9859017 DOI: 10.3390/genes14010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 12/28/2022] Open
Abstract
Due to their continuing geographic isolation, the Amerindian populations of the Brazilian Amazon present a different genetic profile when compared to other continental populations. Few studies have investigated genetic variants present in these populations, especially in the context of next-generation sequencing. Knowledge of the molecular profile of a population is one of the bases for inferences about human evolutionary history, in addition, it has the ability to assist in the validation of molecular biomarkers of susceptibility to complex and rare diseases, and in the improvement of specific precision medicine protocols applied to these populations and to populations with high Amerindian ancestry, such as Brazilians. DNA polymerases play essential roles in DNA replication, repair, recombination, or damage repair, and their influence on various clinical phenotypes has been demonstrated in the specialized literature. Thus, the aim of this study is to characterize the molecular profile of POLA1, POLE, POLG, POLQ, and REV3L genes in Amerindian populations from the Brazilian Amazon, comparing these findings with genomic data from five continental populations described in the gnomAD database, and with data from the Brazilian population described in ABraOM. We performed the whole exome sequencing (WES) of 63 Indigenous individuals. Our study described for the first time the allele frequency of 45 variants already described in the other continental populations, but never before described in the investigated Amerindian populations. Our results also describe eight unique variants of the investigated Amerindians populations, with predictions of moderate, modifier and high clinical impact. Our findings demonstrate the unique genetic profile of the Indigenous population of the Brazilian Amazon, reinforcing the need for further studies on these populations, and may contribute to the creation of public policies that optimize not only the quality of life of this population, but also of the Brazilian population.
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Affiliation(s)
- Amanda Cohen-Paes
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, PA, Brazil
| | | | - Elisa de Souza Menezes
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, PA, Brazil
| | | | | | - João Farias Guerreiro
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, PA, Brazil
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
| | - Sidney Emanuel Batista Dos Santos
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, PA, Brazil
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
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Lisova AE, Baranovskiy AG, Morstadt LM, Babayeva ND, Tahirov T. Human DNA polymerase α has a strong mutagenic potential at the initial steps of DNA synthesis. Nucleic Acids Res 2022; 50:12266-12273. [PMID: 36454017 PMCID: PMC9757036 DOI: 10.1093/nar/gkac1101] [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: 08/12/2022] [Revised: 09/16/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022] Open
Abstract
DNA polymerase α (Polα) is essential for DNA replication initiation and makes a notable contribution to genome mutagenesis. The activity and fidelity of Polα during the early steps of DNA replication have not been well studied. Here we show that at the beginning of DNA synthesis, when extending the RNA primer received from primase, Polα is more mutagenic than during the later DNA elongation steps. Kinetic and binding studies revealed substantially higher activity and affinity to the template:primer when Polα interacts with ribonucleotides of a chimeric RNA-DNA primer. Polα activity greatly varies during first six steps of DNA synthesis, and the bias in the rates of correct and incorrect dNTP incorporation leads to impaired fidelity, especially upon the second step of RNA primer extension. Furthermore, increased activity and stability of Polα/template:primer complexes containing RNA-DNA primers result in higher efficiency of mismatch extension.
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Affiliation(s)
| | | | - Lucia M Morstadt
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nigar D Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Tahir H Tahirov
- To whom correspondence should be addressed. Tel: +1 402 559 7608; Fax: +1 402 559 3739;
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5
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Osia B, Twarowski J, Jackson T, Lobachev K, Liu L, Malkova A. Migrating bubble synthesis promotes mutagenesis through lesions in its template. Nucleic Acids Res 2022; 50:6870-6889. [PMID: 35748867 PMCID: PMC9262586 DOI: 10.1093/nar/gkac520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/23/2022] [Accepted: 06/10/2022] [Indexed: 12/24/2022] Open
Abstract
Break-induced replication (BIR) proceeds via a migrating D-loop for hundreds of kilobases and is highly mutagenic. Previous studies identified long single-stranded (ss) nascent DNA that accumulates during leading strand synthesis to be a target for DNA damage and a primary source of BIR-induced mutagenesis. Here, we describe a new important source of mutagenic ssDNA formed during BIR: the ssDNA template for leading strand BIR synthesis formed during D-loop migration. Specifically, we demonstrate that this D-loop bottom template strand (D-BTS) is susceptible to APOBEC3A (A3A)-induced DNA lesions leading to mutations associated with BIR. Also, we demonstrate that BIR-associated ssDNA promotes an additional type of genetic instability: replication slippage between microhomologies stimulated by inverted DNA repeats. Based on our results we propose that these events are stimulated by both known sources of ssDNA formed during BIR, nascent DNA formed by leading strand synthesis, and the D-BTS that we describe here. Together we report a new source of mutagenesis during BIR that may also be shared by other homologous recombination pathways driven by D-loop repair synthesis.
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Affiliation(s)
| | | | - Tyler Jackson
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kirill Lobachev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GE 30332, USA
| | - Liping Liu
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
| | - Anna Malkova
- To whom correspondence should be addressed. Tel: +1 319 384 1285;
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6
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Baranovskiy AG, Babayeva ND, Lisova AE, Morstadt LM, Tahirov TH. Structural and functional insight into mismatch extension by human DNA polymerase α. Proc Natl Acad Sci U S A 2022; 119:e2111744119. [PMID: 35467978 PMCID: PMC9169922 DOI: 10.1073/pnas.2111744119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 03/08/2022] [Indexed: 12/11/2022] Open
Abstract
Human DNA polymerase α (Polα) does not possess proofreading ability and plays an important role in genome replication and mutagenesis. Polα extends the RNA primers generated by primase and provides a springboard for loading other replication factors. Here we provide the structural and functional analysis of the human Polα interaction with a mismatched template:primer. The structure of the human Polα catalytic domain in the complex with an incoming deoxycytidine triphosphate (dCTP) and the template:primer containing a T-C mismatch at the growing primer terminus was solved at a 2.9 Å resolution. It revealed the absence of significant distortions in the active site and in the conformation of the substrates, except the primer 3′-end. The T-C mismatch acquired a planar geometry where both nucleotides moved toward each other by 0.4 Å and 0.7 Å, respectively, and made one hydrogen bond. The binding studies conducted at a physiological salt concentration revealed that Polα has a low affinity to DNA and is not able to discriminate against a mispaired template:primer in the absence of deoxynucleotide triphosphate (dNTP). Strikingly, in the presence of cognate dNTP, Polα showed a more than 10-fold higher selectivity for a correct duplex versus a mismatched one. According to pre-steady-state kinetic studies, human Polα extends the T-C mismatch with a 249-fold lower efficiency due to reduction of the polymerization rate constant by 38-fold and reduced affinity to the incoming nucleotide by 6.6-fold. Thus, a mismatch at the postinsertion site affects all factors important for primer extension: affinity to both substrates and the rate of DNA polymerization.
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Affiliation(s)
- Andrey G. Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Nigar D. Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Alisa E. Lisova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Lucia M. Morstadt
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Tahir H. Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
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7
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Abstract
B-family DNA polymerases (PolBs) of different groups are widespread in Archaea, and different PolBs often coexist in the same organism. Many of these PolB enzymes remain to be investigated. One of the main groups that is poorly characterized is PolB2, whose members occur in many archaea but are predicted to be inactivated forms of DNA polymerase. Here, Sulfolobus islandicus DNA polymerase 2 (Dpo2), a PolB2 enzyme, was expressed in its native host and purified. Characterization of the purified enzyme revealed that the polymerase possesses a robust nucleotide incorporation activity but is devoid of the 3'-5' exonuclease activity. Enzyme kinetics analyses showed that Dpo2 replicates undamaged DNA templates with high fidelity, which is consistent with its inefficient nucleotide insertion activity opposite different DNA lesions. Strikingly, the polymerase is highly efficient in extending mismatches and mispaired primer termini once a nucleotide is placed opposite a damaged site. This extender polymerase represents a novel type of prokaryotic PolB specialized for DNA damage repair in Archaea. IMPORTANCE In this work, we report that Sulfolobus islandicus Dpo2, a B-family DNA polymerase once predicted to be an inactive form, is a bona fide DNA polymerase functioning in translesion synthesis. S. islandicus Dpo2 is a member of a large group of B-family DNA polymerases (PolB2) that are present in many archaea and some bacteria, and they carry variations in well-conserved amino acids in the functional domains responsible for polymerization and proofreading. However, we found that this prokaryotic B-family DNA polymerase not only replicates undamaged DNA with high fidelity but also extends mismatch and DNA lesion-containing substrates with high efficiencies. With these data, we propose this enzyme functions as an extender polymerase, the first prokaryotic enzyme of this type. Our data also suggest this PolB2 enzyme represents a functional counterpart of the eukaryotic DNA polymerase Pol zeta, an enzyme that is devoted to DNA damage repair.
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Abstract
The homologous recombination (HR) pathway has been implicated as the predominant mechanism for the repair of chromosomal DNA double-strand breaks (DSBs) of the malarial parasite. Although the extrachromosomal mitochondrial genome of this parasite experiences a greater number of DSBs due to its close proximity to the electron transport chain, nothing is known about the proteins involved in the repair of the mitochondrial genome. We investigated the involvement of nucleus-encoded HR proteins in the repair of the mitochondrial genome, as this genome does not code for any DNA repair proteins. Here, we provide evidence that the nucleus-encoded "recombinosome" of the parasite is also involved in mitochondrial genome repair. First, two crucial HR proteins, namely, Plasmodium falciparum Rad51 (PfRad51) and P. falciparum Bloom helicase (PfBlm) are located in the mitochondria. They are recruited to the mitochondrial genome at the schizont stage, a stage that is prone to DSBs due to exposure to various endogenous and physiologic DNA-damaging agents. Second, the recruitment of these two proteins to the damaged mitochondrial genome coincides with the DNA repair kinetics. Moreover, both the proteins exit the mitochondrial DNA (mtDNA) once the genome is repaired. Most importantly, the specific chemical inhibitors of PfRad51 and PfBlm block the repair of UV-induced DSBs of the mitochondrial genome. Additionally, overexpression of these two proteins resulted in a kinetically faster repair. Given the essentiality of the mitochondrial genome, blocking its repair by inhibiting the HR pathway could offer a novel strategy for curbing malaria. IMPORTANCE The impact of malaria on global public health and the world economy continues to surge despite decades of vaccine research and drug development efforts. An alarming rise in resistance toward all the commercially available antimalarial drugs and the lack of an effective malaria vaccine brings us to the urge to identify novel intervention strategies for curbing malaria. Here, we uncover the molecular mechanism behind the repair of the most deleterious form of DNA lesions on the parasitic mitochondrial genome. Given that the single-copy mitochondrion is an indispensable organelle of the malaria parasite, we propose that targeting the mitochondrial DNA repair pathways should be exploited as a potential malaria control strategy. The establishment of the parasitic homologous recombination machinery as the predominant repair mechanism of the mitochondrial DNA double-strand breaks underscores the importance of this pathway as a novel druggable target.
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9
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Ying J, Yang L, Yin JC, Xia G, Xing M, Chen X, Pang J, Wu Y, Bao H, Wu X, Shao Y, Zhu L, Cheng X. Additive effects of variants of unknown significance in replication repair-associated DNA polymerase genes on mutational burden and prognosis across diverse cancers. J Immunother Cancer 2021; 9:jitc-2021-002336. [PMID: 34479923 PMCID: PMC8420654 DOI: 10.1136/jitc-2021-002336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Defects in replication repair-associated DNA polymerases often manifest an ultra-high tumor mutational burden (TMB), which is associated with higher probabilities of response to immunotherapies. The functional and clinical implications of different polymerase variants remain unclear. METHODS Targeted next-generation sequencing using a 425-cancer gene panel, which covers all exonic regions of three polymerase genes (POLE, POLD1, and POLH), was conducted in a cohort of 12,266 patients across 16 different tumor types from January 2017 to January 2019. Prognostication of POL variant-positive patients was performed using a cohort of 4679 patients from the The Cancer Genome Atlas (TCGA) datasets. RESULTS The overall prevalence of somatic and germline polymerase variants was 4.2% (95% CI 3.8% to 4.5%) and 0.7% (95% CI 0.5% to 0.8%), respectively, with highest frequencies in endometrial, urinary, prostate, and colorectal cancers (CRCs). While most germline polymerase variants showed no clear functional consequences, we identified a candidate p.T466A affecting the exonuclease domain of POLE, which might be underlying the early onset in a case with childhood CRC. Low frequencies of known hot-spot somatic mutations in POLE were detected and were associated with younger age, the male sex, and microsatellite stability. In both the panel and TCGA cohorts, POLE drivers exhibited high frequencies of alterations in genes in the DNA damage and repair (DDR) pathways, including BRCA2, ATM, MSH6, and ATR. Variants of unknown significance (VUS) of different polymerase domains showed variable penetrance with those in the exonuclease domain of POLE and POLD1 displaying high TMB. VUS in POL genes exhibited an additive effect as carriers of multiple VUS had exponentially increased TMB and prolonged overall survival. Similar to cases with driver mutations, the TMB-high POL VUS samples showed DDR pathway involvement and polymerase hypermutation signatures. Combinatorial analysis of POL and DDR pathway status further supported the potential additive effects of POL VUS and DDR pathway genes and revealed distinct prognostic subclasses that were independent of cancer type and TMB. CONCLUSIONS Our results demonstrate the pathogenicity and additive prognostic value of POL VUS and DDR pathway gene alterations and suggest that genetic testing may be warranted in patients with diverse solid tumors.
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Affiliation(s)
- Jieer Ying
- Department of Abdominal Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Lin Yang
- Department of Medical Oncology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiani C Yin
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Guojie Xia
- Department of Medical Oncology, Traditional Chinese Medical Hospital of Huzhou, Huzhou, China
| | - Minyan Xing
- Department of Medical Oncology, The First Affiliated Hospital of Zhejiang University, Haining, Zhejiang, China
| | - Xiaoxi Chen
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Jiaohui Pang
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Yong Wu
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Hua Bao
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Xue Wu
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China.,School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lingjun Zhu
- Department of Oncology, Sir Run Run Hospital Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiangdong Cheng
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China .,Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
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10
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Manigrasso J, De Vivo M, Palermo G. Controlled Trafficking of Multiple and Diverse Cations Prompts Nucleic Acid Hydrolysis. ACS Catal 2021; 11:8786-8797. [PMID: 35145762 DOI: 10.1021/acscatal.1c01825] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Recent in crystallo reaction intermediates have detailed how nucleic acid hydrolysis occurs in the RNA ribonuclease H1 (RNase H1), a fundamental metalloenzyme involved in maintaining the human genome. At odds with the previous characterization, these in crystallo structures unexpectedly captured multiple metal ions (K+ and Mg2+) transiently bound in the vicinity of the two-metal-ion active site. Using multi-microsecond all-atom molecular dynamics and free-energy simulations, we investigated the functional implications of the dynamic exchange of multiple K+ and Mg2+ ions at the RNase H1 reaction center. We found that such ions are timely positioned at non-overlapping locations near the active site, at different stages of catalysis, being crucial for both reactants' alignment and leaving group departure. We also found that this cation trafficking is tightly regulated by variations of the solution's ionic strength and is aided by two conserved second-shell residues, E188 and K196, suggesting a mechanism for the cations' recruitment during catalysis. These results indicate that controlled trafficking of multi-cation dynamics, opportunely prompted by second-shell residues, is functionally essential to the complex enzymatic machinery of the RNase H1. These findings revise the current knowledge on the RNase H1 catalysis and open new catalytic possibilities for other similar metalloenzymes including, but not limited to, CRISPR-Cas9, group II intron ribozyme and the human spliceosome.
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Affiliation(s)
- Jacopo Manigrasso
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Genoa, 16163, Italy.,Department of Bioengineering, University of California Riverside, Riverside, CA 52512, United States
| | - Marco De Vivo
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Genoa, 16163, Italy
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, Riverside, CA 52512, United States.,Department of Chemistry, University of California Riverside, Riverside, CA 52512, United States
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11
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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.
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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
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12
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Koonin EV, Krupovic M, Ishino S, Ishino Y. The replication machinery of LUCA: common origin of DNA replication and transcription. BMC Biol 2020; 18:61. [PMID: 32517760 PMCID: PMC7281927 DOI: 10.1186/s12915-020-00800-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Origin of DNA replication is an enigma because the replicative DNA polymerases (DNAPs) are not homologous among the three domains of life, Bacteria, Archaea, and Eukarya. The homology between the archaeal replicative DNAP (PolD) and the large subunits of the universal RNA polymerase (RNAP) responsible for transcription suggests a parsimonious evolutionary scenario. Under this model, RNAPs and replicative DNAPs evolved from a common ancestor that functioned as an RNA-dependent RNA polymerase in the RNA-protein world that predated the advent of DNA replication. The replicative DNAP of the Last Universal Cellular Ancestor (LUCA) would be the ancestor of the archaeal PolD.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, 75015, Paris, France
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
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13
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Khandagale P, Thakur S, Acharya N. Identification of PCNA-interacting protein motifs in human DNA polymerase δ. Biosci Rep 2020; 40:BSR20200602. [PMID: 32314787 PMCID: PMC7189476 DOI: 10.1042/bsr20200602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/07/2020] [Accepted: 04/14/2020] [Indexed: 01/22/2023] Open
Abstract
DNA polymerase δ (Polδ) is a highly processive essential replicative DNA polymerase. In humans, the Polδ holoenzyme consists of p125, p50, p68 and p12 subunits and recently, we showed that the p12 subunit exists as a dimer. Extensive biochemical studies suggest that all the subunits of Polδ interact with the processivity factor proliferating cell nuclear antigen (PCNA) to carry out a pivotal role in genomic DNA replication. While PCNA-interacting protein motif (PIP) motifs in p68, p50 and p12 have been mapped, same in p125, the catalytic subunit of the holoenzyme, remains elusive. Therefore, in the present study by using multiple approaches we have conclusively mapped a non-canonical PIP motif from residues 999VGGLLAFA1008 in p125, which binds to the inter-domain-connecting loop (IDCL) of PCNA with high affinity. Collectively, including previous studies, we conclude that similar to Saccharomyces cerevisiae Polδ, each of the human Polδ subunits possesses motif to interact with PCNA and significantly contributes toward the processive nature of this replicative DNA polymerase.
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Affiliation(s)
- 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
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India
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14
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Donati E, Genna V, De Vivo M. Recruiting Mechanism and Functional Role of a Third Metal Ion in the Enzymatic Activity of 5' Structure-Specific Nucleases. J Am Chem Soc 2020; 142:2823-2834. [PMID: 31939291 PMCID: PMC7993637 DOI: 10.1021/jacs.9b10656] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Enzymes of the 5′ structure-specific
nuclease family are crucial for DNA repair, replication, and recombination.
One such enzyme is the human exonuclease 1 (hExo1) metalloenzyme,
which cleaves DNA strands, acting primarily as a processive 5′-3′
exonuclease and secondarily as a 5′-flap endonuclease. Recently,
in crystallo reaction intermediates have elucidated how hExo1 exerts
hydrolysis of DNA phosphodiester bonds. These hExo1 structures show
a third metal ion intermittently bound close to the two-metal-ion
active site, to which recessed ends or 5′-flap substrates bind.
Evidence of this third ion has been observed in several nucleic-acid-processing
metalloenzymes. However, there is still debate over what triggers
the (un)binding of this transient third ion during catalysis and whether
this ion has a catalytic function. Using extended molecular dynamics
and enhanced sampling free-energy simulations, we observed that the
carboxyl side chain of Glu89 (located along the arch motif in hExo1)
flips frequently from the reactant state to the product state. The
conformational flipping of Glu89 allows one metal ion to be recruited
from the bulk and promptly positioned near the catalytic center. This
is in line with the structural evidence. Additionally, our simulations
show that the third metal ion assists the departure, through the mobile
arch, of the nucleotide monophosphate product from the catalytic site.
Structural comparisons of nuclease enzymes suggest that this Glu(Asp)-mediated
mechanism for third ion recruitment and nucleic acid hydrolysis may
be shared by other 5′ structure-specific nucleases.
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Affiliation(s)
- Elisa Donati
- Laboratory of Molecular Modelling & Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genoa , Italy
| | - Vito Genna
- Laboratory of Molecular Modelling & Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genoa , Italy
| | - Marco De Vivo
- Laboratory of Molecular Modelling & Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genoa , Italy
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15
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Elango R, Osia B, Harcy V, Malc E, Mieczkowski PA, Roberts SA, Malkova A. Repair of base damage within break-induced replication intermediates promotes kataegis associated with chromosome rearrangements. Nucleic Acids Res 2019; 47:9666-9684. [PMID: 31392335 PMCID: PMC6765108 DOI: 10.1093/nar/gkz651] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/12/2019] [Accepted: 08/02/2019] [Indexed: 02/01/2023] Open
Abstract
Break induced replication (BIR) is a double strand break repair pathway that can promote genetic instabilities similar to those observed in cancer. Instead of a replication fork, BIR is driven by a migration bubble where asynchronous synthesis between leading and lagging strands leads to accumulation of single-stranded DNA (ssDNA) that promotes mutation. However, the details of the mechanism of mutagenesis, including the identity of the participating proteins, remain unknown. Using yeast as a model, we demonstrate that mutagenic ssDNA is formed at multiple positions along the BIR track and that Pol ζ is responsible for the majority of both spontaneous and damage-induced base substitutions during BIR. We also report that BIR creates a potent substrate for APOBEC3A (A3A) cytidine deaminase that can promote formation of mutation clusters along the entire track of BIR. Finally, we demonstrate that uracil glycosylase initiates the bypass of DNA damage induced by A3A in the context of BIR without formation of base substitutions, but instead this pathway frequently leads to chromosomal rearrangements. Together, the expression of A3A during BIR in yeast recapitulates the main features of APOBEC-induced kataegis in human cancers, suggesting that BIR might represent an important source of these hyper-mutagenic events.
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Affiliation(s)
- Rajula Elango
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
| | - Beth Osia
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
| | - Victoria Harcy
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Ewa Malc
- Department of Genetics, Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Piotr A Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Steven A Roberts
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
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16
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Khandagale P, Peroumal D, Manohar K, Acharya N. Human DNA polymerase delta is a pentameric holoenzyme with a dimeric p12 subunit. Life Sci Alliance 2019; 2:2/2/e201900323. [PMID: 30885984 PMCID: PMC6424025 DOI: 10.26508/lsa.201900323] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 01/07/2023] Open
Abstract
The subunit p12 of human DNA polymerase delta (hPolδ) can dimerize, facilitating its interaction with PCNA and suggesting that hPolδ exists in a pentameric form in the cell. Human DNA polymerase delta (Polδ), a holoenzyme consisting of p125, p50, p68, and p12 subunits, plays an essential role in DNA replication, repair, and recombination. Herein, using multiple physicochemical and cellular approaches, we found that the p12 protein forms a dimer in solution. In vitro reconstitution and pull down of cellular Polδ by tagged p12 substantiate the pentameric nature of this critical holoenzyme. Furthermore, a consensus proliferating nuclear antigen (PCNA) interaction protein motif at the extreme carboxyl-terminal tail and a homodimerization domain at the amino terminus of the p12 subunit were identified. Mutational analyses of these motifs in p12 suggest that dimerization facilitates p12 binding to the interdomain connecting loop of PCNA. In addition, we observed that oligomerization of the smallest subunit of Polδ is evolutionarily conserved as Cdm1 of Schizosaccharomyces pombe also dimerizes. Thus, we suggest that human Polδ is a pentameric complex with a dimeric p12 subunit, and discuss implications of p12 dimerization in enzyme architecture and PCNA interaction during DNA replication.
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Affiliation(s)
- Prashant Khandagale
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Doureradjou Peroumal
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Kodavati Manohar
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
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17
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Sakamoto AN. Translesion Synthesis in Plants: Ultraviolet Resistance and Beyond. FRONTIERS IN PLANT SCIENCE 2019; 10:1208. [PMID: 31649692 PMCID: PMC6794406 DOI: 10.3389/fpls.2019.01208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 09/03/2019] [Indexed: 05/06/2023]
Abstract
Plant genomes sustain various forms of DNA damage that stall replication forks. Translesion synthesis (TLS) is one of the pathways to overcome stalled replication in which specific polymerases (TLS polymerase) perform bypass synthesis across DNA damage. This article gives a brief overview of plant TLS polymerases. In Arabidopsis, DNA polymerase (Pol) ζ, η, κ, θ, and λ and Reversionless1 (Rev1) are shown to be involved in the TLS. For example, AtPolη bypasses ultraviolet (UV)-induced cyclobutane pyrimidine dimers in vitro. Disruption of AtPolζ or AtPolη increases root stem cell death after UV irradiation. These results suggest that AtPolζ and ATPolη bypass UV-induced damage, prevent replication arrest, and allow damaged cells to survive and grow. In general, TLS polymerases have low fidelity and often induce mutations. Accordingly, disruption of AtPolζ or AtRev1 reduces somatic mutation frequency, whereas disruption of AtPolη elevates it, suggesting that plants have both mutagenic and less mutagenic TLS activities. The stalled replication fork can be resolved by a strand switch pathway involving a DNA helicase Rad5. Disruption of both AtPolζ and AtRAD5a shows synergistic or additive effects in the sensitivity to DNA-damaging agents. Moreover, AtPolζ or AtRev1 disruption elevates homologous recombination frequencies in somatic tissues. These results suggest that the Rad5-dependent pathway and TLS are parallel. Plants grown in the presence of heat shock protein 90 (HSP90) inhibitor showed lower mutation frequencies, suggesting that HSP90 regulates mutagenic TLS in plants. Hypersensitivities of TLS-deficient plants to γ-ray and/or crosslink damage suggest that plant TLS polymerases have multiple roles, as reported in other organisms.
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18
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Baranovskiy AG, Duong VN, Babayeva ND, Zhang Y, Pavlov YI, Anderson KS, Tahirov TH. Activity and fidelity of human DNA polymerase α depend on primer structure. J Biol Chem 2018; 293:6824-6843. [PMID: 29555682 DOI: 10.1074/jbc.ra117.001074] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/09/2018] [Indexed: 12/13/2022] Open
Abstract
DNA polymerase α (Polα) plays an important role in genome replication. In a complex with primase, Polα synthesizes chimeric RNA-DNA primers necessary for replication of both chromosomal DNA strands. During RNA primer extension with deoxyribonucleotides, Polα needs to use double-stranded helical substrates having different structures. Here, we provide a detailed structure-function analysis of human Polα's interaction with dNTPs and DNA templates primed with RNA, chimeric RNA-DNA, or DNA. We report the crystal structures of two ternary complexes of the Polα catalytic domain containing dCTP, a DNA template, and either a DNA or an RNA primer. Unexpectedly, in the ternary complex with a DNA:DNA duplex and dCTP, the "fingers" subdomain of Polα is in the open conformation. Polα induces conformational changes in the DNA and hybrid duplexes to produce the universal double helix form. Pre-steady-state kinetic studies indicated for both duplex types that chemical catalysis rather than product release is the rate-limiting step. Moreover, human Polα extended DNA primers with higher efficiency but lower processivity than it did with RNA and chimeric primers. Polα has a substantial propensity to make errors during DNA synthesis, and we observed that its fidelity depends on the type of sugar at the primer 3'-end. A detailed structural comparison of Polα with other replicative DNA polymerases disclosed common features and some differences, which may reflect the specialization of each polymerase in genome replication.
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Affiliation(s)
- Andrey G Baranovskiy
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and
| | - Vincent N Duong
- the Departments of Pharmacology and Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Nigar D Babayeva
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and
| | - Yinbo Zhang
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and
| | - Youri I Pavlov
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and.,the Departments of Biochemistry and Molecular Biology, Pathology and Microbiology, and Genetics and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198 and
| | - Karen S Anderson
- the Departments of Pharmacology and Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Tahir H Tahirov
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and
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19
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Rogozin IB, Goncearenco A, Lada AG, De S, Yurchenko V, Nudelman G, Panchenko AR, Cooper DN, Pavlov YI. DNA polymerase η mutational signatures are found in a variety of different types of cancer. Cell Cycle 2018; 17:348-355. [PMID: 29139326 DOI: 10.1080/15384101.2017.1404208] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA polymerase (pol) η is a specialized error-prone polymerase with at least two quite different and contrasting cellular roles: to mitigate the genetic consequences of solar UV irradiation, and promote somatic hypermutation in the variable regions of immunoglobulin genes. Misregulation and mistargeting of pol η can compromise genome integrity. We explored whether the mutational signature of pol η could be found in datasets of human somatic mutations derived from normal and cancer cells. A substantial excess of single and tandem somatic mutations within known pol η mutable motifs was noted in skin cancer as well as in many other types of human cancer, suggesting that somatic mutations in A:T bases generated by DNA polymerase η are a common feature of tumorigenesis. Another peculiarity of pol ηmutational signatures, mutations in YCG motifs, led us to speculate that error-prone DNA synthesis opposite methylated CpG dinucleotides by misregulated pol η in tumors might constitute an additional mechanism of cytosine demethylation in this hypermutable dinucleotide.
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Affiliation(s)
- Igor B Rogozin
- a National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA
| | - Alexander Goncearenco
- a National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA
| | - Artem G Lada
- b Department Microbiology and Molecular Genetics , University of California , Davis , CA , USA
| | - Subhajyoti De
- c Rutgers Cancer Institute of New Jersey , Rutgers University , New Brunswick , NJ , USA
| | - Vyacheslav Yurchenko
- d Life Science Research Center , University of Ostrava, 71000 Ostrava , Czech Republic
| | - German Nudelman
- e Systems Biology Center , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , USA
| | - Anna R Panchenko
- a National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA
| | - David N Cooper
- f Institute of Medical Genetics, School of Medicine , Cardiff University , UK
| | - Youri I Pavlov
- g Eppley Institute for Research in Cancer and Allied Diseases , University of Nebraska Medical Center , Omaha , NE 68198, USA.,h Departments of Microbiology and Pathology , University of Nebraska Medical Center , Omaha , NE , USA.,i Biochemistry and Molecular Biology , University of Nebraska Medical Center , Omaha , NE , USA.,j Genetics, Cell Biology and Anatomy , University of Nebraska Medical Center , Omaha , NE , USA
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20
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Lada AG, Stepchenkova EI, Zhuk AS, Kliver SF, Rogozin IB, Polev DE, Dhar A, Pavlov YI. Recombination Is Responsible for the Increased Recovery of Drug-Resistant Mutants with Hypermutated Genomes in Resting Yeast Diploids Expressing APOBEC Deaminases. Front Genet 2017; 8:202. [PMID: 29312434 PMCID: PMC5733079 DOI: 10.3389/fgene.2017.00202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 11/22/2017] [Indexed: 12/11/2022] Open
Abstract
DNA editing deaminases (APOBECs) are implicated in generation of mutations in somatic cells during tumorigenesis. APOBEC-dependent mutagenesis is thought to occur during transient exposure of unprotected single-stranded DNA. Mutations frequently occur in clusters (kataegis). We investigated mechanisms of mutant generation in growing and resting diploid yeast expressing APOBEC from sea lamprey, PmCDA1, whose kataegistic effect was previously shown to be associated with transcription. We have found that the frequency of canavanine-resistant mutants kept raising after growth cessation, while the profile of transcription remained unchanged. Surprisingly, the overall number of mutations in the genomes did not elevate in resting cells. Thus, mutations were accumulated during vigorous growth stage with both intense replication and transcription. We found that the elevated recovery of can1 mutant clones in non-growing cells is the result of loss of heterozygosity (LOH) leading to clusters of homozygous mutations in the chromosomal regions distal to the reporter gene. We confirmed that recombination frequency in resting cells was elevated by orders of magnitude, suggesting that cells were transiently committed to meiotic levels of recombination, a process referred to in yeast genetics as return-to-growth. In its extreme, on day 6 of starvation, a few mutant clones were haploid, likely resulting from completed meiosis. Distribution of mutations along chromosomes indicated that PmCDA1 was active during ongoing recombination events and sometimes produced characteristic kataegis near initial breakpoints. AID and APOBEC1 behaved similar to PmCDA1. We conclude that replication, transcription, and mitotic recombination contribute to the recovered APOBEC-induced mutations in resting diploids. The mechanism is relevant to the initial stages of oncogenic transformation in terminally differentiated cells, when recombination may lead to the LOH exposing recessive mutations induced by APOBECs in cell's history and to acquisition of new mutations near original break.
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Affiliation(s)
- Artem G Lada
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, United States
| | - Elena I Stepchenkova
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Anna S Zhuk
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Sergei F Kliver
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States.,Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Dmitrii E Polev
- Research Resource Center "Biobank", Research Park, Saint-Petersburg State University, Saint Petersburg, Russia
| | - Alok Dhar
- Department of Genetics, Cell Biology and Anatomy and Vice Chancellor of Research Core, University of Nebraska Medical Center, Omaha, NE, United States
| | - Youri I Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
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21
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Baranovskiy AG, Siebler HM, Pavlov YI, Tahirov TH. Iron-Sulfur Clusters in DNA Polymerases and Primases of Eukaryotes. Methods Enzymol 2017; 599:1-20. [PMID: 29746236 PMCID: PMC5947875 DOI: 10.1016/bs.mie.2017.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Research during the past decade witnessed the discovery of [4Fe-4S] clusters in several members of the eukaryotic DNA replication machinery. The presence of clusters was confirmed by UV-visible absorption, electron paramagnetic resonance spectroscopy, and metal analysis for primase and the B-family DNA polymerases δ and ζ. The crystal structure of primase revealed that the [4Fe-4S] cluster is buried inside the protein and fulfills a structural role. Although [4Fe-4S] clusters are firmly established in the C-terminal domains of catalytic subunits of DNA polymerases δ and ζ, no structures are currently available and their precise roles have not been ascertained. The [4Fe-4S] clusters in the polymerases and primase play a structural role ensuring proper protein folding and stability. In DNA polymerases δ and ζ, they can potentially play regulatory role by sensing hurdles during DNA replication and assisting with DNA polymerase switches by oscillation between oxidized-reduced states.
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Affiliation(s)
- Andrey G Baranovskiy
- Eppley Institute for Research in Cancer, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, United States
| | | | - Youri I Pavlov
- Eppley Institute for Research in Cancer, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, United States.
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, United States.
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22
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Chatterjee N, Walker GC. Mechanisms of DNA damage, repair, and mutagenesis. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:235-263. [PMID: 28485537 PMCID: PMC5474181 DOI: 10.1002/em.22087] [Citation(s) in RCA: 987] [Impact Index Per Article: 141.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 03/16/2017] [Indexed: 05/08/2023]
Abstract
Living organisms are continuously exposed to a myriad of DNA damaging agents that can impact health and modulate disease-states. However, robust DNA repair and damage-bypass mechanisms faithfully protect the DNA by either removing or tolerating the damage to ensure an overall survival. Deviations in this fine-tuning are known to destabilize cellular metabolic homeostasis, as exemplified in diverse cancers where disruption or deregulation of DNA repair pathways results in genome instability. Because routinely used biological, physical and chemical agents impact human health, testing their genotoxicity and regulating their use have become important. In this introductory review, we will delineate mechanisms of DNA damage and the counteracting repair/tolerance pathways to provide insights into the molecular basis of genotoxicity in cells that lays the foundation for subsequent articles in this issue. Environ. Mol. Mutagen. 58:235-263, 2017. © 2017 Wiley Periodicals, Inc.
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23
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McVey M, Khodaverdian VY, Meyer D, Cerqueira PG, Heyer WD. Eukaryotic DNA Polymerases in Homologous Recombination. Annu Rev Genet 2017; 50:393-421. [PMID: 27893960 DOI: 10.1146/annurev-genet-120215-035243] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Homologous recombination (HR) is a central process to ensure genomic stability in somatic cells and during meiosis. HR-associated DNA synthesis determines in large part the fidelity of the process. A number of recent studies have demonstrated that DNA synthesis during HR is conservative, less processive, and more mutagenic than replicative DNA synthesis. In this review, we describe mechanistic features of DNA synthesis during different types of HR-mediated DNA repair, including synthesis-dependent strand annealing, break-induced replication, and meiotic recombination. We highlight recent findings from diverse eukaryotic organisms, including humans, that suggest both replicative and translesion DNA polymerases are involved in HR-associated DNA synthesis. Our focus is to integrate the emerging literature about DNA polymerase involvement during HR with the unique aspects of these repair mechanisms, including mutagenesis and template switching.
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Affiliation(s)
- Mitch McVey
- Department of Biology, Tufts University, Medford, Massachusetts 02155;
| | | | - Damon Meyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616; .,College of Health Sciences, California Northstate University, Rancho Cordova, California 95670
| | - Paula Gonçalves Cerqueira
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616;
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616; .,Department of Molecular and Cellular Biology, University of California, Davis, California 95616
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24
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Abstract
The human primosome is a 340-kilodalton complex of primase (DNA-dependent RNA polymerase) and DNA polymerase α, which initiates genome replication by synthesizing chimeric RNA-DNA primers for DNA polymerases δ and ϵ. Accumulated biochemical and structural data reveal the complex mechanism of concerted primer synthesis by two catalytic centers. First, primase generates an RNA primer through three steps: initiation, consisting of dinucleotide synthesis from two nucleotide triphosphates; elongation, resulting in dinucleotide extension; and termination, owing to primase inhibition by a mature 9-mer primer. Then Polα, which works equally well on DNA:RNA and DNA:DNA double helices, intramolecularly catches the template primed by a 9mer RNA and extends the primer with dNTPs. All primosome transactions are highly coordinated by autoregulation through the alternating activation/inhibition of the catalytic centers. This coordination is mediated by the small C-terminal domain of the primase accessory subunit, which forms a tight complex with the template:primer, shuttles between the primase and DNA polymerase active sites, and determines their access to the substrate.
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25
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Turab Naqvi AA, Rahman S, Rubi, Zeya F, Kumar K, Choudhary H, Jamal MS, Kim J, Hassan MI. Genome analysis of Chlamydia trachomatis for functional characterization of hypothetical proteins to discover novel drug targets. Int J Biol Macromol 2016; 96:234-240. [PMID: 27993657 DOI: 10.1016/j.ijbiomac.2016.12.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/05/2016] [Accepted: 12/15/2016] [Indexed: 01/28/2023]
Abstract
C. trachomatis is a Gram-negative bacterium that causes trachoma and sexually transmitted disease (STD) Chlamydia in humans. Chlamydial genital infections are the most frequent among all communicable diseases. The D/UW-3/Cx strain of C. trachomatis contains 935 genes and three pseudogenes. Out of these genes, 887 genes code for proteins while six for rRNA, 37 tRNA, and three genes translate into other RNAs. The proteome of C. trachomatis made of 887 proteins contains 269 Hypothetical proteins (HPs) that are subjected to functional characterization. This study suggests some known methods of functional characterization of such HPs. All of these methods are explicitly used to assign functions to the HPs with the accuracy of more than 90%. After extensive analysis of all the HPs, we have successfully assigned functions to 89 HPs with high precision. In the newly assigned HPs, there are enzymes, transporters, binding proteins, proteins involved in biosynthesis and regulatory processes and proteins with miscellaneous functions. The study suggests that the functionally annotated HPs may play a vital role in the growth and pathogenesis of this organism. Therefore, they can be considered potential drug targets.
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Affiliation(s)
- Ahmad Abu Turab Naqvi
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 712-749, South Korea
| | - Rubi
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Firdaus Zeya
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Kundan Kumar
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Hani Choudhary
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, Center of Innovation in Personalized Medicine, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Sarwar Jamal
- King Fahd Medical Research Center, King Abdulaziz University, P.O. Box: 80216, Jeddah 21589, Saudi Arabia
| | - Jihoe Kim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 712-749, South Korea.
| | - Md Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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Defect of Fe-S cluster binding by DNA polymerase δ in yeast suppresses UV-induced mutagenesis, but enhances DNA polymerase ζ - dependent spontaneous mutagenesis. DNA Repair (Amst) 2016; 49:60-69. [PMID: 28034630 DOI: 10.1016/j.dnarep.2016.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 11/30/2016] [Accepted: 11/30/2016] [Indexed: 11/21/2022]
Abstract
Eukaryotic genomes are duplicated by a complex machinery, utilizing high fidelity replicative B-family DNA polymerases (pols) α, δ and ε. Specialized error-prone pol ζ, the fourth B-family member, is recruited when DNA synthesis by the accurate trio is impeded by replication stress or DNA damage. The damage tolerance mechanism dependent on pol ζ prevents DNA/genome instability and cell death at the expense of increased mutation rates. The pol switches occurring during this specialized replication are not fully understood. The loss of pol ζ results in the absence of induced mutagenesis and suppression of spontaneous mutagenesis. Disruption of the Fe-S cluster motif that abolish the interaction of the C-terminal domain (CTD) of the catalytic subunit of pol ζ with its accessory subunits, which are shared with pol δ, leads to a similar defect in induced mutagenesis. Intriguingly, the pol3-13 mutation that affects the Fe-S cluster in the CTD of the catalytic subunit of pol δ also leads to defective induced mutagenesis, suggesting the possibility that Fe-S clusters are essential for the pol switches during replication of damaged DNA. We confirmed that yeast strains with the pol3-13 mutation are UV-sensitive and defective in UV-induced mutagenesis. However, they have increased spontaneous mutation rates. We found that this increase is dependent on functional pol ζ. In the pol3-13 mutant strain with defective pol δ, there is a sharp increase in transversions and complex mutations, which require functional pol ζ, and an increase in the occurrence of large deletions, whose size is controlled by pol ζ. Therefore, the pol3-13 mutation abrogates pol ζ-dependent induced mutagenesis, but allows for pol ζ recruitment for the generation of spontaneous mutations and prevention of larger deletions. These results reveal differential control of the two major types of pol ζ-dependent mutagenesis by the Fe-S cluster present in replicative pol δ.
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Cellular responses to replication stress: Implications in cancer biology and therapy. DNA Repair (Amst) 2016; 49:9-20. [PMID: 27908669 DOI: 10.1016/j.dnarep.2016.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 12/11/2022]
Abstract
DNA replication is essential for cell proliferation. Any obstacles during replication cause replication stress, which may lead to genomic instability and cancer formation. In this review, we summarize the physiological DNA replication process and the normal cellular response to replication stress. We also outline specialized therapies in clinical trials based on current knowledge and future perspectives in the field.
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28
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Evolutionary switches between two serine codon sets are driven by selection. Proc Natl Acad Sci U S A 2016; 113:13109-13113. [PMID: 27799560 DOI: 10.1073/pnas.1615832113] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Serine is the only amino acid that is encoded by two disjoint codon sets so that a tandem substitution of two nucleotides is required to switch between the two sets. Previously published evidence suggests that, for the most evolutionarily conserved serines, the codon set switch occurs by simultaneous substitution of two nucleotides. Here we report a genome-wide reconstruction of the evolution of serine codons in triplets of closely related species from diverse prokaryotes and eukaryotes. The results indicate that the great majority of codon set switches proceed by two consecutive nucleotide substitutions, via a threonine or cysteine intermediate, and are driven by selection. These findings imply a strong pressure of purifying selection in protein evolution, which in the case of serine codon set switches occurs via an initial deleterious substitution quickly followed by a second, compensatory substitution. The result is frequent reversal of amino acid replacements and, at short evolutionary distances, pervasive homoplasy.
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Huang J, Copenhaver GP, Ma H, Wang Y. New insights into the role of DNA synthesis in meiotic recombination. Sci Bull (Beijing) 2016. [DOI: 10.1007/s11434-016-1126-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Baranovskiy AG, Babayeva ND, Zhang Y, Gu J, Suwa Y, Pavlov YI, Tahirov TH. Mechanism of Concerted RNA-DNA Primer Synthesis by the Human Primosome. J Biol Chem 2016; 291:10006-20. [PMID: 26975377 DOI: 10.1074/jbc.m116.717405] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Indexed: 12/31/2022] Open
Abstract
The human primosome, a 340-kilodalton complex of primase and DNA polymerase α (Polα), synthesizes chimeric RNA-DNA primers to be extended by replicative DNA polymerases δ and ϵ. The intricate mechanism of concerted primer synthesis by two catalytic centers was an enigma for over three decades. Here we report the crystal structures of two key complexes, the human primosome and the C-terminal domain of the primase large subunit (p58C) with bound DNA/RNA duplex. These structures, along with analysis of primase/polymerase activities, provide a plausible mechanism for all transactions of the primosome including initiation, elongation, accurate counting of RNA primer length, primer transfer to Polα, and concerted autoregulation of alternate activation/inhibition of the catalytic centers. Our findings reveal a central role of p58C in the coordinated actions of two catalytic domains in the primosome and ultimately could impact the design of anticancer drugs.
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Affiliation(s)
- Andrey G Baranovskiy
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center and
| | - Nigar D Babayeva
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center and
| | - Yinbo Zhang
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center and the Departments of Biochemistry and Molecular Biology and
| | - Jianyou Gu
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center and
| | - Yoshiaki Suwa
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center and
| | - Youri I Pavlov
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center and the Departments of Biochemistry and Molecular Biology and Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Tahir H Tahirov
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center and
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Sakofsky CJ, Ayyar S, Deem AK, Chung WH, Ira G, Malkova A. Translesion Polymerases Drive Microhomology-Mediated Break-Induced Replication Leading to Complex Chromosomal Rearrangements. Mol Cell 2015; 60:860-72. [PMID: 26669261 DOI: 10.1016/j.molcel.2015.10.041] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 09/14/2015] [Accepted: 10/28/2015] [Indexed: 01/06/2023]
Abstract
Complex genomic rearrangements (CGRs) are a hallmark of many human diseases. Recently, CGRs were suggested to result from microhomology-mediated break-induced replication (MMBIR), a replicative mechanism involving template switching at positions of microhomology. Currently, the cause of MMBIR and the proteins mediating this process remain unknown. Here, we demonstrate in yeast that a collapse of homology-driven break-induced replication (BIR) caused by defective repair DNA synthesis in the absence of Pif1 helicase leads to template switches involving 0-6 nt of homology, followed by resolution of recombination intermediates into chromosomal rearrangements. Importantly, we show that these microhomology-mediated template switches, indicative of MMBIR, are driven by translesion synthesis (TLS) polymerases Polζ and Rev1. Thus, an interruption of BIR involving fully homologous chromosomes in yeast triggers a switch to MMBIR catalyzed by TLS polymerases. Overall, our study provides important mechanistic insights into the initiation of MMBIR associated with genomic rearrangements, similar to those promoting diseases in humans.
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Affiliation(s)
| | - Sandeep Ayyar
- Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN 46202, USA
| | - Angela K Deem
- Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN 46202, USA
| | - Woo-Hyun Chung
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Grzegorz Ira
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
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32
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Suzuki M, Kino K, Kawada T, Oyoshi T, Morikawa M, Kobayashi T, Miyazawa H. Contiguous 2,2,4-triamino-5(2H)-oxazolone obstructs DNA synthesis by DNA polymerases α, β, η, ι, κ, REV1 and Klenow Fragment exo-, but not by DNA polymerase ζ. J Biochem 2015; 159:323-9. [PMID: 26491064 PMCID: PMC4763079 DOI: 10.1093/jb/mvv103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 09/10/2015] [Indexed: 12/18/2022] Open
Abstract
Guanine is the most easily oxidized of the four DNA bases, and contiguous guanines (GG) in a sequence are more readily oxidized than a single guanine in a sequence. Continued oxidation of GGs results in a contiguous oxidized guanine lesion. Two contiguous 2,5-diamino-4H-imidazol-4-ones, an oxidized form of guanine that hydrolyses to 2,2,4-triamino-5(2H)-oxazolone (Oz), are detected following the oxidation of GG. In this study, we analysed translesion synthesis (TLS) across two contiguous Oz molecules (OzOz) using Klenow Fragment exo− (KF exo−) and DNA polymerases (Pols) α, β, ζ, η, ι, κ and REV1. We found that KF exo− and Pols α, β, ι and REV1 inserted one nucleotide opposite the 3′ Oz of OzOz and stalled at the subsequent extension, and that Pol κ incorporated no nucleotide. Pol η only inefficiently elongated the primer up to full-length across OzOz; the synthesis of most DNA strands stalled at the 3′ or 5′ Oz of OzOz. Surprisingly, however, Pol ζ efficiently extended the primer up to full-length across OzOz, unlike the other DNA polymerases, but catalysed error-prone nucleotide incorporation. We therefore believe that Pol ζ is required for efficient TLS of OzOz. These results show that OzOz obstructs DNA synthesis by DNA polymerases except Pol ζ.
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Affiliation(s)
- Masayo Suzuki
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1, Shido, Sanuki, Kagawa 769-2193, Japan and
| | - Katsuhito Kino
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1, Shido, Sanuki, Kagawa 769-2193, Japan and
| | - Taishu Kawada
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1, Shido, Sanuki, Kagawa 769-2193, Japan and
| | - Takanori Oyoshi
- Faculty of Science, Department of Chemistry, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan
| | - Masayuki Morikawa
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1, Shido, Sanuki, Kagawa 769-2193, Japan and
| | - Takanobu Kobayashi
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1, Shido, Sanuki, Kagawa 769-2193, Japan and
| | - Hiroshi Miyazawa
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1, Shido, Sanuki, Kagawa 769-2193, Japan and
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Błażej P, Miasojedow B, Grabińska M, Mackiewicz P. Optimization of Mutation Pressure in Relation to Properties of Protein-Coding Sequences in Bacterial Genomes. PLoS One 2015; 10:e0130411. [PMID: 26121655 PMCID: PMC4488281 DOI: 10.1371/journal.pone.0130411] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 05/19/2015] [Indexed: 12/22/2022] Open
Abstract
Most mutations are deleterious and require energetically costly repairs. Therefore, it seems that any minimization of mutation rate is beneficial. On the other hand, mutations generate genetic diversity indispensable for evolution and adaptation of organisms to changing environmental conditions. Thus, it is expected that a spontaneous mutational pressure should be an optimal compromise between these two extremes. In order to study the optimization of the pressure, we compared mutational transition probability matrices from bacterial genomes with artificial matrices fulfilling the same general features as the real ones, e.g., the stationary distribution and the speed of convergence to the stationarity. The artificial matrices were optimized on real protein-coding sequences based on Evolutionary Strategies approach to minimize or maximize the probability of non-synonymous substitutions and costs of amino acid replacements depending on their physicochemical properties. The results show that the empirical matrices have a tendency to minimize the effects of mutations rather than maximize their costs on the amino acid level. They were also similar to the optimized artificial matrices in the nucleotide substitution pattern, especially the high transitions/transversions ratio. We observed no substantial differences between the effects of mutational matrices on protein-coding sequences in genomes under study in respect of differently replicated DNA strands, mutational cost types and properties of the referenced artificial matrices. The findings indicate that the empirical mutational matrices are rather adapted to minimize mutational costs in the studied organisms in comparison to other matrices with similar mathematical constraints.
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Affiliation(s)
- Paweł Błażej
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Błażej Miasojedow
- Section of Mathematical Statistics, The Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warszawa, Poland
| | - Małgorzata Grabińska
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Paweł Mackiewicz
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
- * E-mail:
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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.
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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
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Disruption of Transcriptional Coactivator Sub1 Leads to Genome-Wide Re-distribution of Clustered Mutations Induced by APOBEC in Active Yeast Genes. PLoS Genet 2015; 11:e1005217. [PMID: 25941824 PMCID: PMC4420506 DOI: 10.1371/journal.pgen.1005217] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/13/2015] [Indexed: 12/21/2022] Open
Abstract
Mutations in genomes of species are frequently distributed non-randomly, resulting in mutation clusters, including recently discovered kataegis in tumors. DNA editing deaminases play the prominent role in the etiology of these mutations. To gain insight into the enigmatic mechanisms of localized hypermutagenesis that lead to cluster formation, we analyzed the mutational single nucleotide variations (SNV) data obtained by whole-genome sequencing of drug-resistant mutants induced in yeast diploids by AID/APOBEC deaminase and base analog 6-HAP. Deaminase from sea lamprey, PmCDA1, induced robust clusters, while 6-HAP induced a few weak ones. We found that PmCDA1, AID, and APOBEC1 deaminases preferentially mutate the beginning of the actively transcribed genes. Inactivation of transcription initiation factor Sub1 strongly reduced deaminase-induced can1 mutation frequency, but, surprisingly, did not decrease the total SNV load in genomes. However, the SNVs in the genomes of the sub1 clones were re-distributed, and the effect of mutation clustering in the regions of transcription initiation was even more pronounced. At the same time, the mutation density in the protein-coding regions was reduced, resulting in the decrease of phenotypically detected mutants. We propose that the induction of clustered mutations by deaminases involves: a) the exposure of ssDNA strands during transcription and loss of protection of ssDNA due to the depletion of ssDNA-binding proteins, such as Sub1, and b) attainment of conditions favorable for APOBEC action in subpopulation of cells, leading to enzymatic deamination within the currently expressed genes. This model is applicable to both the initial and the later stages of oncogenic transformation and explains variations in the distribution of mutations and kataegis events in different tumor cells. Genomes of tumors are heavily enriched with mutations. Some of these mutations are distributed non-randomly, forming mutational clusters. Editing cytosine deaminases from APOBEC superfamily are responsible for the formation of many of these clusters. We have expressed APOBEC enzyme in diploid yeast cells and found that most of the mutations occur in the beginning of the active genes, where transcription starts. Clusters of mutations overlapped with promoters/transcription start sites. This is likely due to the weaker protection of ssDNA, an ultimate APOBEC deaminase enzyme target, in the beginning of the genes. This hypothesis was reinforced by the finding that inactivation of Sub1 transcription initiation factor, which is found predominantly in the regions of transcription initiation, leads to further increase in mutagenesis in the beginning of the genes. Interestingly, the total number of mutations in the genomes of Sub1-deficient clones did not change, despite the 100-fold decrease in frequency of mutants in a reporter gene. Thus, the drastic change in genome-wide distribution of mutations can be caused by inactivation of a single gene. We propose that the loss of ssDNA protection factors causes formation of mutation clusters in human cancer.
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Jung M, Shin MK, Jung YK, Yoo HS. Modulation of macrophage activities in proliferation, lysosome, and phagosome by the nonspecific immunostimulator, mica. PLoS One 2015; 10:e0117838. [PMID: 25668030 PMCID: PMC4323240 DOI: 10.1371/journal.pone.0117838] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/02/2015] [Indexed: 11/18/2022] Open
Abstract
It was reported that the aluminosilicate material mica activated macrophages and showed its immunostimulating effects. However, the mechanisms by which it exerts these effects are unclear. To address this, we evaluated the effects of mica fine particles (MFP, 804.1 ± 0.02 nm) on the murine macrophage cell line, RAW 264.7. Specifically, RAW 264.7 cells were treated with 100 and 500 μg/mL MFP and their proliferative response was determined using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Changes in global gene expression upon MFP treatment for 12 and 48 h were also determined using microarrays. Following the MFP treatment, RAW 264.7 cells showed a low level of proliferation compared to nontreated cells (p < 0.01). There was a change in an expression level of 1,128 genes after 48 h treatment. Specifically, genes associated with the cell cycle, DNA replication, and pyrimidine and purine metabolisms, were down-regulated in cells treated with MFP, which resulted in reduction of cell proliferation. MFP treatment also up-regulated genes associated with lysosome and phagosome function, which are both required for macrophage activities. We speculate that activation of macrophages by mica is in part derived from up-regulation of these pathways.
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Affiliation(s)
- Myunghwan Jung
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Min-Kyoung Shin
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Yeon-Kwon Jung
- Seobong BioBesstech Co., Ltd., Yeoksam-dong, Kangnam-gu, Seoul, Republic of Korea
| | - Han Sang Yoo
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, Republic of Korea
- * E-mail:
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37
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Chen W, Zhang L. The pattern of DNA cleavage intensity around indels. Sci Rep 2015; 5:8333. [PMID: 25660536 PMCID: PMC4321175 DOI: 10.1038/srep08333] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/07/2015] [Indexed: 12/22/2022] Open
Abstract
Indels (insertions and deletions) are the second most common form of genetic variations in the eukaryotic genomes and are responsible for a multitude of genetic diseases. Despite its significance, detailed molecular mechanisms for indel generation are still unclear. Here we examined 2,656,597 small human and mouse germline indels, 16,742 human somatic indels, 10,599 large human insertions, and 5,822 large chimpanzee insertions and systematically analyzed the patterns of DNA cleavage intensities in the 200 base pair regions surrounding these indels. Our results show that DNA cleavage intensities close to the start and end points of indels are significantly lower than other regions, for both small human germline and somatic indels and also for mouse small indels. Compared to small indels, the patterns of DNA cleavage intensity around large indels are more complex, and there are two low intensity regions near each end of the indels that are approximately 13 bp apart from each other. Detailed analyses of a subset of indels show that there is slight difference in cleavage intensity distribution between insertion indels and deletion indels that could be contributed by their respective enrichment of different repetitive elements. These results will provide new insight into indel generation mechanisms.
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Affiliation(s)
- Wei Chen
- 1] Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan, China 063000 [2] Department of Computer Science, Virginia Tech, Blacksburg VA 24060
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg VA 24060
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38
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Ghodgaonkar MM, Kehl P, Ventura I, Hu L, Bignami M, Jiricny J. Phenotypic characterization of missense polymerase-δ mutations using an inducible protein-replacement system. Nat Commun 2014; 5:4990. [PMID: 25241845 DOI: 10.1038/ncomms5990] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 08/14/2014] [Indexed: 01/12/2023] Open
Abstract
Next-generation sequencing has revolutionized the search for disease-causing genetic alterations. Unfortunately, the task of distinguishing the handful of causative mutations from rare variants remains daunting. We now describe an assay that permits the analysis of all types of mutations in any gene of choice through the generation of stable human cell lines, in which the endogenous protein has been inducibly replaced with its genetic variant. Here we studied the phenotype of variants of the essential replicative polymerase-δ carrying missense mutations in its active site, similar to those recently identified in familial colon cancer patients. We show that expression of the mutants but not the wild-type protein endows the engineered cells with a mutator phenotype and that the mutations affect the fidelity and/or the exonuclease activity of the isolated enzyme in vitro. This proof-of-principle study demonstrates the general applicability of this experimental approach in the study of genotype-phenotype correlations.
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Affiliation(s)
- Medini Manohar Ghodgaonkar
- Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Patrick Kehl
- Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Ilenia Ventura
- 1] Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland [2] Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome 11061, Italy
| | - Liyan Hu
- Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Margherita Bignami
- 1] Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland [2] Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome 11061, Italy
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
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Generalized portrait of cancer metabolic pathways inferred from a list of genes overexpressed in cancer. GENETICS RESEARCH INTERNATIONAL 2014; 2014:646193. [PMID: 25243088 PMCID: PMC4163292 DOI: 10.1155/2014/646193] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/15/2014] [Indexed: 12/17/2022]
Abstract
More than half a century from postulated Warburg theory of cancer cells origin, a question of changed metabolism in cancer is again taking the central place. Generalized picture of cancer metabolism was replaced by analysis of signaling and oncogenes in each type of cancer for several decades. However, now empowered with wealth of knowledge about tumor suppressors, oncogenes, and signaling pathways, reprogramming of cellular metabolism (e.g., increased glycolysis to respiration ratio in cancer cells) reemerged as an important element of cancer progression. To analyze level of expression of various proteins including metabolic enzymes across various cancers we used dbEST and Unigene data. We delineated a list of genes that are overexpressed in different types of cancer. We also grouped overexpressed enzymes into KEGG pathways and analyzed adjacent pathways to describe enzymatic reactions that take place in cancer cells and to identify major players that are abundant in cancer protein machinery. Glycolysis/gluconeogenesis and oxidative phosphorylation are the most abundant pathways although several other pathways are enriched in genes from our list. Ubiquitously overexpressed genes could be marked as nonspecific cancer-associated genes when analyzing genes that are overexpressed in certain types of cancer. Thus the list of overexpressed genes may be a useful tool for cancer research.
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Doublié S, Zahn KE. Structural insights into eukaryotic DNA replication. Front Microbiol 2014; 5:444. [PMID: 25202305 PMCID: PMC4142720 DOI: 10.3389/fmicb.2014.00444] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 08/04/2014] [Indexed: 12/23/2022] Open
Abstract
Three DNA polymerases of the B family function at the replication fork in eukaryotic cells: DNA polymerases α, δ, and ε. DNA polymerase α, an heterotetramer composed of two primase subunits and two polymerase subunits, initiates replication. DNA polymerases δ and ε elongate the primers generated by pol α. The DNA polymerase from bacteriophage RB69 has served as a model for eukaryotic B family polymerases for some time. The recent crystal structures of pol δ, α, and ε revealed similarities but also a number of unexpected differences between the eukaryotic polymerases and their bacteriophage counterpart, and also among the three yeast polymerases. This review will focus on their shared structural elements as well as the features that are unique to each of these polymerases.
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Affiliation(s)
- Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont Burlington, VT, USA
| | - Karl E Zahn
- Department of Microbiology and Molecular Genetics, University of Vermont Burlington, VT, USA
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Zhang Y, Baranovskiy AG, Tahirov TH, Pavlov YI. The C-terminal domain of the DNA polymerase catalytic subunit regulates the primase and polymerase activities of the human DNA polymerase α-primase complex. J Biol Chem 2014; 289:22021-34. [PMID: 24962573 DOI: 10.1074/jbc.m114.570333] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The initiation of DNA synthesis during replication of the human genome is accomplished primarily by the DNA polymerase α-primase complex, which makes the RNA-DNA primers accessible to processive DNA pols. The structural information needed to understand the mechanism of regulation of this complex biochemical reaction is incomplete. The presence of two enzymes in one complex poses the question of how these two enzymes cooperate during priming of DNA synthesis. Yeast two-hybrid and direct pulldown assays revealed that the N-terminal domain of the large subunit of primase (p58N) directly interacts with the C-terminal domain of the catalytic subunit of polα (p180C). We found that a complex of the C-terminal domain of the catalytic subunit of polα with the second subunit (p180C-p70) stimulated primase activity, whereas the whole catalytically active heterodimer of polα (p180ΔN-p70) inhibited RNA synthesis by primase. Conversely, the polα catalytic domain without the C-terminal part (p180ΔN-core) possessed a much higher propensity to extend the RNA primer than the two-subunit polα (p180ΔN-p70), suggesting that p180C and/or p70 are involved in the negative regulation of DNA pol activity. We conclude that the interaction between p180C, p70, and p58 regulates the proper primase and polymerase function. The composition of the template DNA is another important factor determining the activity of the complex. We have found that polα activity strongly depends on the sequence of the template and that homopyrimidine runs create a strong barrier for DNA synthesis by polα.
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Affiliation(s)
- Yinbo Zhang
- From the Eppley Institute for Research in Cancer and Allied Diseases, Department of Biochemistry and Molecular Biology, and
| | | | - Tahir H Tahirov
- From the Eppley Institute for Research in Cancer and Allied Diseases,
| | - Youri I Pavlov
- From the Eppley Institute for Research in Cancer and Allied Diseases, Department of Biochemistry and Molecular Biology, and Department of Pathology and Microbiology, University of Nebraska Medical Center, Nebraska Medical Center, Omaha, Nebraska 68198-6805
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Siebler HM, Lada AG, Baranovskiy AG, Tahirov TH, Pavlov YI. A novel variant of DNA polymerase ζ, Rev3ΔC, highlights differential regulation of Pol32 as a subunit of polymerase δ versus ζ in Saccharomyces cerevisiae. DNA Repair (Amst) 2014; 24:138-149. [PMID: 24819597 DOI: 10.1016/j.dnarep.2014.04.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/17/2014] [Accepted: 04/24/2014] [Indexed: 10/25/2022]
Abstract
Unrepaired DNA lesions often stall replicative DNA polymerases and are bypassed by translesion synthesis (TLS) to prevent replication fork collapse. Mechanisms of TLS are lesion- and species-specific, with a prominent role of specialized DNA polymerases with relaxed active sites. After nucleotide(s) are incorporated across from the altered base(s), the aberrant primer termini are typically extended by DNA polymerase ζ (pol ζ). As a result, pol ζ is responsible for most DNA damage-induced mutations. The mechanisms of sequential DNA polymerase switches in vivo remain unclear. The major replicative DNA polymerase δ (pol δ) shares two accessory subunits, called Pol31/Pol32 in yeast, with pol ζ. Inclusion of Pol31/Pol32 in the pol δ/pol ζ holoenzymes requires a [4Fe-4S] cluster in C-termini of the catalytic subunits. Disruption of this cluster in Pol ζ or deletion of POL32 attenuates induced mutagenesis. Here we describe a novel mutation affecting the catalytic subunit of pol ζ, rev3ΔC, which provides insight into the regulation of pol switches. Strains with Rev3ΔC, lacking the entire C-terminal domain and therefore the platform for Pol31/Pol32 binding, are partially proficient in Pol32-dependent UV-induced mutagenesis. This suggests an additional role of Pol32 in TLS, beyond being a pol ζ subunit, related to pol δ. In search for members of this regulatory pathway, we examined the effects of Maintenance of Genome Stability 1 (Mgs1) protein on mutagenesis in the absence of Rev3-Pol31/Pol32 interaction. Mgs1 may compete with Pol32 for binding to PCNA. Mgs1 overproduction suppresses induced mutagenesis, but had no effect on UV-mutagenesis in the rev3ΔC strain, suggesting that Mgs1 exerts its inhibitory effect by acting specifically on Pol32 bound to pol ζ. The evidence for differential regulation of Pol32 in pol δ and pol ζ emphasizes the complexity of polymerase switches.
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Affiliation(s)
- Hollie M Siebler
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
| | - Artem G Lada
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
| | - Youri I Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
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Heitzer E, Tomlinson I. Replicative DNA polymerase mutations in cancer. Curr Opin Genet Dev 2014; 24:107-13. [PMID: 24583393 PMCID: PMC4003352 DOI: 10.1016/j.gde.2013.12.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 12/20/2013] [Indexed: 12/18/2022]
Abstract
Three DNA polymerases - Pol α, Pol δ and Pol ɛ - are essential for DNA replication. After initiation of DNA synthesis by Pol α, Pol δ or Pol ɛ take over on the lagging and leading strand respectively. Pol δ and Pol ɛ perform the bulk of replication with very high fidelity, which is ensured by Watson-Crick base pairing and 3'exonuclease (proofreading) activity. Yeast models have shown that mutations in the exonuclease domain of Pol δ and Pol ɛ homologues can cause a mutator phenotype. Recently, we identified germline exonuclease domain mutations (EDMs) in human POLD1 and POLE that predispose to 'polymerase proofreading associated polyposis' (PPAP), a disease characterised by multiple colorectal adenomas and carcinoma, with high penetrance and dominant inheritance. Moreover, somatic EDMs in POLE have also been found in sporadic colorectal and endometrial cancers. Tumors with EDMs are microsatellite stable and show an 'ultramutator' phenotype, with a dramatic increase in base substitutions.
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Affiliation(s)
- Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Harrachgasse 21/8, A-8010 Graz, Austria.
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK; Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
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45
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A short review on the implications of base excision repair pathway for neurons: relevance to neurodegenerative diseases. Mitochondrion 2013; 16:38-49. [PMID: 24220222 DOI: 10.1016/j.mito.2013.10.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 10/31/2013] [Accepted: 10/31/2013] [Indexed: 12/13/2022]
Abstract
Oxidative DNA damage results from the attack by reactive oxygen and nitrogen species (ROS/RNS) on human genome. This includes base modifications such as oxidized bases, abasic (AP) sites, and single-strand breaks (SSBs), all of which are repaired by the base excision repair (BER) pathway, one among the six known repair pathways. BER-pathway in mammalian cells involves several evolutionarily conserved proteins and is also linked to genome replication and transcription. The BER-pathway enzymes, namely, DNA glycosylases (DGs) and the end-processing proteins such as abasic endonuclease (APE1), form complexes with downstream repair enzymes via protein-protein and DNA-protein interactions. An emerging concept for BER proteins is their involvement in non-canonical functions associated to RNA metabolism, which is opening new interesting perspectives. Various mechanisms that are underlined in maintaining neuronal cell genome integrity are identified, but are inconclusive in providing protection against oxidative damage in neurodegenerative disorders, main emphasis is given towards the role played by the proteins of BER-pathway that is discussed. In addition, mechanisms of action of BER-pathway in nuclear vs. mitochondria as well as the non-canonical functions are discussed in connection to human neurodegenerative diseases.
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46
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Gening LV, Lakhin AV, Stelmashook EV, Isaev NK, Tarantul VZ. Inhibition of Mn2+-induced error-prone DNA synthesis with Cd2+ and Zn2+. BIOCHEMISTRY (MOSCOW) 2013; 78:1137-45. [DOI: 10.1134/s0006297913100088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Belan E. LINEs of evidence: noncanonical DNA replication as an epigenetic determinant. Biol Direct 2013; 8:22. [PMID: 24034780 PMCID: PMC3868326 DOI: 10.1186/1745-6150-8-22] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 09/06/2013] [Indexed: 12/17/2022] Open
Abstract
LINE-1 (L1) retrotransposons are repetitive elements in mammalian genomes. They are
capable of synthesizing DNA on their own RNA templates by harnessing reverse
transcriptase (RT) that they encode. Abundantly expressed full-length L1s and their
RT are found to globally influence gene expression profiles, differentiation state,
and proliferation capacity of early embryos and many types of cancer, albeit by yet
unknown mechanisms. They are essential for the progression of early development and
the establishment of a cancer-related undifferentiated state. This raises important
questions regarding the functional significance of L1 RT in these cell systems.
Massive nuclear L1-linked reverse transcription has been shown to occur in mouse
zygotes and two-cell embryos, and this phenomenon is purported to be DNA replication
independent. This review argues against this claim with the goal of understanding the
nature of this phenomenon and the role of L1 RT in early embryos and cancers.
Available L1 data are revisited and integrated with relevant findings accumulated in
the fields of replication timing, chromatin organization, and epigenetics, bringing
together evidence that strongly supports two new concepts. First, noncanonical
replication of a portion of genomic full-length L1s by means of L1 RNP-driven reverse
transcription is proposed to co-exist with DNA polymerase-dependent replication of
the rest of the genome during the same round of DNA replication in embryonic and
cancer cell systems. Second, the role of this mechanism is thought to be epigenetic;
it might promote transcriptional competence of neighboring genes linked to
undifferentiated states through the prevention of tethering of involved L1s to the
nuclear periphery. From the standpoint of these concepts, several hitherto
inexplicable phenomena can be explained. Testing methods for the model are
proposed.
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Affiliation(s)
- Ekaterina Belan
- Genetics Laboratory, Royal University Hospital, Saskatoon, SK S7N 0W8, Canada.
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Matsui I, Matsui E, Yamasaki K, Yokoyama H. Domain structures and inter-domain interactions defining the holoenzyme architecture of archaeal d-family DNA polymerase. Life (Basel) 2013; 3:375-85. [PMID: 25369811 PMCID: PMC4187176 DOI: 10.3390/life3030375] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 06/26/2013] [Accepted: 06/27/2013] [Indexed: 02/01/2023] Open
Abstract
Archaea-specific D-family DNA polymerase (PolD) forms a dimeric heterodimer consisting of two large polymerase subunits and two small exonuclease subunits. According to the protein-protein interactions identified among the domains of large and small subunits of PolD, a symmetrical model for the domain topology of the PolD holoenzyme is proposed. The experimental evidence supports various aspects of the model. The conserved amphipathic nature of the N-terminal putative α-helix of the large subunit plays a key role in the homodimeric assembly and the self-cyclization of the large subunit and is deeply involved in the archaeal PolD stability and activity. We also discuss the evolutional transformation from archaeal D-family to eukaryotic B-family polymerase on the basis of the structural information.
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Affiliation(s)
- Ikuo Matsui
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan.
| | - Eriko Matsui
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan.
| | - Kazuhiko Yamasaki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan.
| | - Hideshi Yokoyama
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan.
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Saini N, Zhang Y, Nishida Y, Sheng Z, Choudhury S, Mieczkowski P, Lobachev KS. Fragile DNA motifs trigger mutagenesis at distant chromosomal loci in saccharomyces cerevisiae. PLoS Genet 2013; 9:e1003551. [PMID: 23785298 PMCID: PMC3681665 DOI: 10.1371/journal.pgen.1003551] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 04/23/2013] [Indexed: 11/19/2022] Open
Abstract
DNA sequences capable of adopting non-canonical secondary structures have been associated with gross-chromosomal rearrangements in humans and model organisms. Previously, we have shown that long inverted repeats that form hairpin and cruciform structures and triplex-forming GAA/TTC repeats induce the formation of double-strand breaks which trigger genome instability in yeast. In this study, we demonstrate that breakage at both inverted repeats and GAA/TTC repeats is augmented by defects in DNA replication. Increased fragility is associated with increased mutation levels in the reporter genes located as far as 8 kb from both sides of the repeats. The increase in mutations was dependent on the presence of inverted or GAA/TTC repeats and activity of the translesion polymerase Polζ. Mutagenesis induced by inverted repeats also required Sae2 which opens hairpin-capped breaks and initiates end resection. The amount of breakage at the repeats is an important determinant of mutations as a perfect palindromic sequence with inherently increased fragility was also found to elevate mutation rates even in replication-proficient strains. We hypothesize that the underlying mechanism for mutagenesis induced by fragile motifs involves the formation of long single-stranded regions in the broken chromosome, invasion of the undamaged sister chromatid for repair, and faulty DNA synthesis employing Polζ. These data demonstrate that repeat-mediated breaks pose a dual threat to eukaryotic genome integrity by inducing chromosomal aberrations as well as mutations in flanking genes.
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Affiliation(s)
- Natalie Saini
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America,
| | - Yu Zhang
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America,
| | - Yuri Nishida
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America,
| | - Ziwei Sheng
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America,
| | - Shilpa Choudhury
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America,
| | - Piotr Mieczkowski
- Department of Genetics, School of Medicine, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kirill S. Lobachev
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America,
- * E-mail:
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Wienk H, Slootweg JC, Speerstra S, Kaptein R, Boelens R, Folkers GE. The Fanconi anemia associated protein FAAP24 uses two substrate specific binding surfaces for DNA recognition. Nucleic Acids Res 2013; 41:6739-49. [PMID: 23661679 PMCID: PMC3711432 DOI: 10.1093/nar/gkt354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
To maintain the integrity of the genome, multiple DNA repair systems exist to repair damaged DNA. Recognition of altered DNA, including bulky adducts, pyrimidine dimers and interstrand crosslinks (ICL), partially depends on proteins containing helix-hairpin-helix (HhH) domains. To understand how ICL is specifically recognized by the Fanconi anemia proteins FANCM and FAAP24, we determined the structure of the HhH domain of FAAP24. Although it resembles other HhH domains, the FAAP24 domain contains a canonical hairpin motif followed by distorted motif. The HhH domain can bind various DNA substrates; using nuclear magnetic resonance titration experiments, we demonstrate that the canonical HhH motif is required for double-stranded DNA (dsDNA) binding, whereas the unstructured N-terminus can interact with single-stranded DNA. Both DNA binding surfaces are used for binding to ICL-like single/double-strand junction-containing DNA substrates. A structural model for FAAP24 bound to dsDNA has been made based on homology with the translesion polymerase iota. Site-directed mutagenesis, sequence conservation and charge distribution support the dsDNA-binding model. Analogous to other HhH domain-containing proteins, we suggest that multiple FAAP24 regions together contribute to binding to single/double-strand junction, which could contribute to specificity in ICL DNA recognition.
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Affiliation(s)
- Hans Wienk
- Bijvoet Center For Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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