1
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Sakuma K, Sasaki E, Kimura K, Komori K, Shimizu Y, Yatabe Y, Aoki M. HNRNPLL stabilizes mRNA for DNA replication proteins and promotes cell cycle progression in colorectal cancer cells. Cancer Sci 2018; 109:2458-2468. [PMID: 29869816 PMCID: PMC6113449 DOI: 10.1111/cas.13660] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 06/01/2018] [Indexed: 12/21/2022] Open
Abstract
Heterogeneous nuclear ribonucleoprotein L‐like (HNRNPLL), an RNA‐binding protein that regulates alternative splicing of pre‐mRNA, has been shown to regulate differentiation of lymphocytes, as well as metastasis of colorectal cancer cells. Here, we show that HNRNPLL promotes cell cycle progression and, hence, proliferation of colorectal cancer cells. Functional annotation analysis of those genes whose expression levels were changed threefold or more in RNA sequencing analysis between SW480 cells overexpressing HNRNPLL and those knocked down for HNRNPLL revealed enrichment of DNA replication‐related genes by HNRNPLL overexpression. Among 13 genes detected in the DNA replication pathway, PCNA,RFC3 and FEN1 showed reproducible upregulation by HNRNPLL overexpression both at mRNA and at protein levels in SW480 and HT29 cells. Importantly, knockdown of any of these genes alone suppressed the proliferation‐promoting effect induced by HNRNPLL overexpression. RNA‐immunoprecipitation assay presented a binding of FLAG‐tagged HNRNPLL to mRNA of these genes, and HNRNPLL overexpression significantly suppressed the downregulation of these genes during 12 h of actinomycin D treatment, suggesting a role of HNRNPLL in mRNA stability. Finally, analysis of a public RNA sequencing dataset of clinical samples suggested a link between overexpression of HNRNPLL and that of PCNA,RFC3 and FEN1. This link was further supported by immunohistochemistry of colorectal cancer clinical samples, whereas expression of CDKN1A, which is known to inhibit the cooperative function of PCNA, RFC3 and FEN1, was negatively associated with HNRNPLL expression. These results indicate that HNRNPLL stabilizes mRNA encoding regulators of DNA replication and promotes colorectal cancer cell proliferation.
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Affiliation(s)
- Keiichiro Sakuma
- Division of Pathophysiology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Eiichi Sasaki
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Kenya Kimura
- Department of Surgery, Hekinan Municipal Hospital, Hekinan, Japan
| | - Koji Komori
- Department of Gastroenterological Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yasuhiro Shimizu
- Department of Gastroenterological Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Masahiro Aoki
- Division of Pathophysiology, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Cancer Genetics, Program in Function Construction Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
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2
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Sisakova A, Altmannova V, Sebesta M, Krejci L. Role of PCNA and RFC in promoting Mus81-complex activity. BMC Biol 2017; 15:90. [PMID: 28969641 PMCID: PMC5625722 DOI: 10.1186/s12915-017-0429-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 09/15/2017] [Indexed: 01/23/2023] Open
Abstract
Background Proper DNA replication is essential for faithful transmission of the genome. However, replication stress has serious impact on the integrity of the cell, leading to stalling or collapse of replication forks, and has been determined as a driving force of carcinogenesis. Mus81-Mms4 complex is a structure-specific endonuclease previously shown to be involved in processing of aberrant replication intermediates and promotes POLD3-dependent DNA synthesis via break-induced replication. However, how replication components might be involved in this process is not known. Results Herein, we show the interaction and robust stimulation of Mus81-Mms4 nuclease activity by heteropentameric replication factor C (RFC) complex, the processivity factor of replicative DNA polymerases that is responsible for loading of proliferating cell nuclear antigen (PCNA) during DNA replication and repair. This stimulation is enhanced by RFC-dependent ATP hydrolysis and by PCNA loading on the DNA. Moreover, this stimulation is not specific to Rfc1, the largest of subunit of this complex, thus indicating that alternative clamp loaders may also play a role in the stimulation. We also observed a targeting of Mus81 by RFC to the nick-containing DNA substrate and we provide further evidence that indicates cooperation between Mus81 and the RFC complex in the repair of DNA lesions generated by various DNA-damaging agents. Conclusions Identification of new interacting partners and modulators of Mus81-Mms4 nuclease, RFC, and PCNA imply the cooperation of these factors in resolution of stalled replication forks and branched DNA structures emanating from the restarted replication forks under conditions of replication stress. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0429-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandra Sisakova
- Department of Biology, Masaryk University, Kamenice 5/A7, CZ-62500, Brno, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500, Brno, Czech Republic.,International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Pekarska 53, CZ-656 91, Brno, Czech Republic
| | - Veronika Altmannova
- Department of Biology, Masaryk University, Kamenice 5/A7, CZ-62500, Brno, Czech Republic.,International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Pekarska 53, CZ-656 91, Brno, Czech Republic
| | - Marek Sebesta
- Department of Biology, Masaryk University, Kamenice 5/A7, CZ-62500, Brno, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500, Brno, Czech Republic.,Present address: Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Lumir Krejci
- Department of Biology, Masaryk University, Kamenice 5/A7, CZ-62500, Brno, Czech Republic. .,National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500, Brno, Czech Republic. .,International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Pekarska 53, CZ-656 91, Brno, Czech Republic.
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3
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Kwon B, Munashingha PR, Shin YK, Lee CH, Li B, Seo YS. Physical and functional interactions between nucleosomes and Rad27, a critical component of DNA processing during DNA metabolism. FEBS J 2016; 283:4247-4262. [DOI: 10.1111/febs.13934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/22/2016] [Accepted: 10/17/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Buki Kwon
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology; Yuseong-gu Daejeon Korea
| | - Palinda Ruvan Munashingha
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology; Yuseong-gu Daejeon Korea
| | - Yong-Keol Shin
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology; Yuseong-gu Daejeon Korea
| | - Chul-Hwan Lee
- Department of Molecular Biology; UT Southwestern Medical Center; Dallas TX USA
| | - Bing Li
- Department of Molecular Biology; UT Southwestern Medical Center; Dallas TX USA
| | - Yeon-Soo Seo
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology; Yuseong-gu Daejeon Korea
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4
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Sebesta M, Urulangodi M, Stefanovie B, Szakal B, Pacesa M, Lisby M, Branzei D, Krejci L. Esc2 promotes Mus81 complex-activity via its SUMO-like and DNA binding domains. Nucleic Acids Res 2016; 45:215-230. [PMID: 27694623 PMCID: PMC5224511 DOI: 10.1093/nar/gkw882] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/30/2016] [Accepted: 09/22/2016] [Indexed: 01/17/2023] Open
Abstract
Replication across damaged DNA templates is accompanied by transient formation of sister chromatid junctions (SCJs). Cells lacking Esc2, an adaptor protein containing no known enzymatic domains, are defective in the metabolism of these SCJs. However, how Esc2 is involved in the metabolism of SCJs remains elusive. Here we show interaction between Esc2 and a structure-specific endonuclease Mus81-Mms4 (the Mus81 complex), their involvement in the metabolism of SCJs, and the effects Esc2 has on the enzymatic activity of the Mus81 complex. We found that Esc2 specifically interacts with the Mus81 complex via its SUMO-like domains, stimulates enzymatic activity of the Mus81 complex in vitro, and is involved in the Mus81 complex-dependent resolution of SCJs in vivo. Collectively, our data point to the possibility that the involvement of Esc2 in the metabolism of SCJs is, in part, via modulation of the activity of the Mus81 complex.
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Affiliation(s)
- Marek Sebesta
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic.,Department of Biology, Masaryk University, Kamenice 5/A7, CZ-62500 Brno, Czech Republic.,IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, IT-20139 Milan, Italy
| | | | - Barbora Stefanovie
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic.,Department of Biology, Masaryk University, Kamenice 5/A7, CZ-62500 Brno, Czech Republic.,International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Pekarska 53, CZ-656 91 Brno, Czech Republic
| | - Barnabas Szakal
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, IT-20139 Milan, Italy
| | - Martin Pacesa
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
| | - Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Dana Branzei
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, IT-20139 Milan, Italy
| | - Lumir Krejci
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic .,Department of Biology, Masaryk University, Kamenice 5/A7, CZ-62500 Brno, Czech Republic.,International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Pekarska 53, CZ-656 91 Brno, Czech Republic
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5
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Deshmukh AL, Kumar C, Singh DK, Maurya P, Banerjee D. Dynamics of replication proteins during lagging strand synthesis: A crossroads for genomic instability and cancer. DNA Repair (Amst) 2016; 42:72-81. [DOI: 10.1016/j.dnarep.2016.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/22/2016] [Accepted: 04/22/2016] [Indexed: 01/18/2023]
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6
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Sulfolobus replication factor C stimulates the activity of DNA polymerase B1. J Bacteriol 2014; 196:2367-75. [PMID: 24748616 DOI: 10.1128/jb.01552-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Replication factor C (RFC) is known to function in loading proliferating cell nuclear antigen (PCNA) onto primed DNA, allowing PCNA to tether DNA polymerase for highly processive DNA synthesis in eukaryotic and archaeal replication. In this report, we show that an RFC complex from the hyperthermophilic archaea of the genus Sulfolobus physically interacts with DNA polymerase B1 (PolB1) and enhances both the polymerase and 3'-5' exonuclease activities of PolB1 in an ATP-independent manner. Stimulation of the PolB1 activity by RFC is independent of the ability of RFC to bind DNA but is consistent with the ability of RFC to facilitate DNA binding by PolB1 through protein-protein interaction. These results suggest that Sulfolobus RFC may play a role in recruiting DNA polymerase for efficient primer extension, in addition to clamp loading, during DNA replication.
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7
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Qian L, Yuan F, Rodriguez-Tello P, Padgaonkar S, Zhang Y. Human Fanconi anemia complementation group a protein stimulates the 5' flap endonuclease activity of FEN1. PLoS One 2013; 8:e82666. [PMID: 24349332 PMCID: PMC3857783 DOI: 10.1371/journal.pone.0082666] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 10/26/2013] [Indexed: 11/28/2022] Open
Abstract
In eukaryotic cells, Flap endonuclease 1 (FEN1) is a major structure-specific endonuclease that processes 5’ flapped structures during maturation of lagging strand DNA synthesis, long patch base excision repair, and rescue of stalled replication forks. Here we report that fanconi anemia complementation group A protein (FANCA), a protein that recognizes 5’ flap structures and is involved in DNA repair and maintenance of replication forks, constantly stimulates FEN1-mediated incision of both DNA and RNA flaps. Kinetic analyses indicate that FANCA stimulates FEN1 by increasing the turnover rate of FEN1 and altering its substrate affinity. More importantly, six pathogenic FANCA mutants are significantly less efficient than the wild-type at stimulating FEN1 endonuclease activity, implicating that regulation of FEN1 by FANCA contributes to the maintenance of genomic stability.
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Affiliation(s)
- Liangyue Qian
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Fenghua Yuan
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Paola Rodriguez-Tello
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Suyog Padgaonkar
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Yanbin Zhang
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- * E-mail:
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8
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Mulvey CM, Tudzarova S, Crawford M, Williams GH, Stoeber K, Godovac-Zimmermann J. Subcellular proteomics reveals a role for nucleo-cytoplasmic trafficking at the DNA replication origin activation checkpoint. J Proteome Res 2013; 12:1436-53. [PMID: 23320540 PMCID: PMC4261602 DOI: 10.1021/pr3010919] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Depletion of DNA replication initiation factors such as CDC7 kinase triggers the origin activation checkpoint in healthy cells and leads to a protective cell cycle arrest at the G1 phase of the mitotic cell division cycle. This protective mechanism is thought to be defective in cancer cells. To investigate how this checkpoint is activated and maintained in healthy cells, we conducted a quantitative SILAC analysis of the nuclear- and cytoplasmic-enriched compartments of CDC7-depleted fibroblasts and compared them to a total cell lysate preparation. Substantial changes in total abundance and/or subcellular location were detected for 124 proteins, including many essential proteins associated with DNA replication/cell cycle. Similar changes in protein abundance and subcellular distribution were observed for various metabolic processes, including oxidative stress, iron metabolism, protein translation and the tricarboxylic acid cycle. This is accompanied by reduced abundance of two karyopherin proteins, suggestive of reduced nuclear import. We propose that altered nucleo-cytoplasmic trafficking plays a key role in the regulation of cell cycle arrest. The results increase understanding of the mechanisms underlying maintenance of the DNA replication origin activation checkpoint and are consistent with our proposal that cell cycle arrest is an actively maintained process that appears to be distributed over various subcellular locations.
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Affiliation(s)
- Claire M. Mulvey
- Division of Medicine, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Slavica Tudzarova
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Mark Crawford
- Division of Medicine, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Gareth H. Williams
- Research Department of Pathology and UCL Cancer Institute, Rockefeller Building, University College London, University Street, London WC1E 6JJ, United Kingdom
| | - Kai Stoeber
- Research Department of Pathology and UCL Cancer Institute, Rockefeller Building, University College London, University Street, London WC1E 6JJ, United Kingdom
| | - Jasminka Godovac-Zimmermann
- Division of Medicine, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
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9
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Wang Y, Cheng Z, Huang J, Shi Q, Hong Y, Copenhaver GP, Gong Z, Ma H. The DNA replication factor RFC1 is required for interference-sensitive meiotic crossovers in Arabidopsis thaliana. PLoS Genet 2012; 8:e1003039. [PMID: 23144629 PMCID: PMC3493451 DOI: 10.1371/journal.pgen.1003039] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 09/05/2012] [Indexed: 11/18/2022] Open
Abstract
During meiotic recombination, induced double-strand breaks (DSBs) are processed into crossovers (COs) and non-COs (NCO); the former are required for proper chromosome segregation and fertility. DNA synthesis is essential in current models of meiotic recombination pathways and includes only leading strand DNA synthesis, but few genes crucial for DNA synthesis have been tested genetically for their functions in meiosis. Furthermore, lagging strand synthesis has been assumed to be unnecessary. Here we show that the Arabidopsis thaliana DNA REPLICATION FACTOR C1 (RFC1) important for lagging strand synthesis is necessary for fertility, meiotic bivalent formation, and homolog segregation. Loss of meiotic RFC1 function caused abnormal meiotic chromosome association and other cytological defects; genetic analyses with other meiotic mutations indicate that RFC1 acts in the MSH4-dependent interference-sensitive pathway for CO formation. In a rfc1 mutant, residual pollen viability is MUS81-dependent and COs exhibit essentially no interference, indicating that these COs form via the MUS81-dependent interference-insensitive pathway. We hypothesize that lagging strand DNA synthesis is important for the formation of double Holliday junctions, but not alternative recombination intermediates. That RFC1 is found in divergent eukaryotes suggests a previously unrecognized and highly conserved role for DNA synthesis in discriminating between recombination pathways. Meiotic recombination is important for pairing and sustained association of homologous chromosomes (homologs), thereby ensuring proper homolog segregation and normal fertility. DNA synthesis is thought to be required for meiotic recombination, but few genes coding for DNA synthesis factors have been studied for possible meiotic functions because their essential roles in the mitotic cell cycle make it difficult to study their meiotic functions due to the lethality of corresponding null mutations. Current models for meiotic recombination only include leading strand DNA synthesis. We found that the Arabidopsis gene encoding the DNA REPLICATION FACTOR C1 (RFC1) important for lagging strand synthesis promotes meiotic recombination via a specific pathway for crossovers (COs) that involves the formation of double Holliday Junction (dHJ) intermediates. Therefore, lagging strand DNA synthesis is likely important for meiotic recombination. Because DNA synthesis is a highly conserved process and meiotic recombination is highly similar among budding yeast, mammals, and flowering plants, the proposed function of lagging strand synthesis for meiotic recombination might be a general feature of meiosis.
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Affiliation(s)
- Yingxiang Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhihao Cheng
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiyue Huang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Qian Shi
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yue Hong
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Gregory P. Copenhaver
- Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- * E-mail:
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10
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Shin YK, Amangyeld T, Nguyen TA, Munashingha PR, Seo YS. Human MUS81 complexes stimulate flap endonuclease 1. FEBS J 2012; 279:2412-30. [PMID: 22551069 DOI: 10.1111/j.1742-4658.2012.08620.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The yeast heterodimeric Mus81-Mms4 complex possesses a structure-specific endonuclease activity that is critical for the restart of stalled replication forks and removal of toxic recombination intermediates. Previously, we reported that Mus81-Mms4 and Rad27 (yeast FEN1, another structure-specific endonuclease) showed mutual stimulation of nuclease activity. In this study, we investigated the interactions between human FEN1 and MUS81-EME1 or MUS81-EME2, the human homologs of the yeast Mus81-Mms4 complex. We found that both MUS81-EME1 and MUS81-EME2 increased the activity of FEN1, but FEN1 did not stimulate the activity of MUS81-EME1/EME2. The MUS81 subunit alone and its N-terminal half were able to bind to FEN1 and stimulate its endonuclease activity. A truncated FEN1 fragment lacking the C-terminal region that retained catalytic activity was not stimulated by MUS81. Michaelis-Menten kinetic analysis revealed that MUS81 increased the interaction between FEN1 and its substrates, resulting in increased turnover. We also showed that, after DNA damage in human cells, FEN1 co-localizes with MUS81. These findings indicate that the human proteins and yeast homologs act similarly, except that the human FEN1 does not stimulate the nuclease activities of MUS81-EME1 or MUS81-EME2. Thus, the mammalian MUS81 complexes and FEN1 collaborate to remove the various flap structures that arise during many DNA transactions, including Okazaki fragment processing.
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Affiliation(s)
- Yong-Keol Shin
- Department of Biological Sciences, Center for DNA Replication and Genome Instability, Korea Advanced Institute of Science and Technology, Daejeon, Korea
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11
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Munashingha PR, Lee CH, Kang YH, Shin YK, Nguyen TA, Seo YS. The trans-autostimulatory activity of Rad27 suppresses dna2 defects in Okazaki fragment processing. J Biol Chem 2012; 287:8675-87. [PMID: 22235122 DOI: 10.1074/jbc.m111.326470] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Dna2 and Rad27 (yeast Fen1) are the two endonucleases critical for Okazaki fragment processing during lagging strand DNA synthesis that have been shown to interact genetically and physically. In this study, we addressed the functional consequences of these interactions by examining whether purified Rad27 of Saccharomyces cerevisiae affects the enzymatic activity of Dna2 and vice versa. For this purpose, we constructed Rad27DA (catalytically defective enzyme with an Asp to Ala substitution at amino acid 179) and found that it significantly stimulated the endonuclease activity of wild type Dna2, but failed to do so with Dna2Δ405N that lacks the N-terminal 405 amino acids. This was an unexpected finding because dna2Δ405N cells were still partially suppressed by overexpression of rad27DA in vivo. Further analyses revealed that Rad27 is a trans-autostimulatory enzyme, providing an explanation why overexpression of Rad27, regardless of its catalytic activity, suppressed dna2 mutants as long as an endogenous wild type Rad27 is available. We found that the C-terminal 16-amino acid fragment of Rad27, a highly polybasic region due to the presence of multiple positively charged lysine and arginine residues, was sufficient and necessary for the stimulation of both Rad27 and Dna2. Our findings provide further insight into how Dna2 and Rad27 jointly affect the processing of Okazaki fragments in eukaryotes.
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Affiliation(s)
- Palinda Ruvan Munashingha
- Center for DNA Replication and Genome Instability, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
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12
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Balakrishnan L, Gloor JW, Bambara RA. Reconstitution of eukaryotic lagging strand DNA replication. Methods 2010; 51:347-57. [PMID: 20178844 DOI: 10.1016/j.ymeth.2010.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 02/15/2010] [Accepted: 02/17/2010] [Indexed: 11/17/2022] Open
Abstract
Eukaryotic DNA replication is a complex process requiring the proper functioning of a multitude of proteins to create error-free daughter DNA strands and maintain genome integrity. Even though synthesis and joining of Okazaki fragments on the lagging strand involves only half the DNA in the nucleus, the complexity associated with processing these fragments is about twice that needed for leading strand synthesis. Flap endonuclease 1 (FEN1) is the central component of the Okazaki fragment maturation pathway. FEN1 cleaves flaps that are displaced by DNA polymerase delta (pol delta), to create a nick that is effectively joined by DNA ligase I. The Pif1 helicase and Dna2 helicase/nuclease contribute to the maturation process by elongating the flap displaced by pol delta. Though the reason for generating long flaps is still a matter of debate, genetic studies have shown that Dna2 and Pif1 are both important components of DNA replication. Our current knowledge of the exact enzymatic steps that govern Okazaki fragment maturation has heavily derived from reconstitution reactions in vitro, which have augmented genetic information, to yield current mechanistic models. In this review, we describe both the design of specific DNA substrates that simulate intermediates of fragment maturation and protocols for reconstituting partial and complete lagging strand replication.
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Affiliation(s)
- Lata Balakrishnan
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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13
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Lee CH, Shin YK, Phung TTH, Bae JS, Kang YH, Nguyen TA, Kim JH, Kim DH, Kang MJ, Bae SH, Seo YS. Involvement of Vts1, a structure-specific RNA-binding protein, in Okazaki fragment processing in yeast. Nucleic Acids Res 2009; 38:1583-95. [PMID: 20007605 PMCID: PMC2836565 DOI: 10.1093/nar/gkp1135] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The non-essential VTS1 gene of Saccharomyces cerevisiae is highly conserved in eukaryotes and encodes a sequence- and structure-specific RNA-binding protein. The Vts1 protein has been implicated in post-transcriptional regulation of a specific set of mRNAs that contains its-binding site at their 3'-untranslated region. In this study, we identified VTS1 as a multi-copy suppressor of dna2-K1080E, a lethal mutant allele of DNA2 that lacks DNA helicase activity. The suppression was allele-specific, since overexpression of Vts1 did not suppress the temperature-dependent growth defects of dna2Delta405N devoid of the N-terminal 405-amino-acid residues. Purified recombinant Vts1 stimulated the endonuclease activity of wild-type Dna2, but not the endonuclease activity of Dna2Delta405N, indicating that the activation requires the N-terminal domain of Dna2. Stimulation of Dna2 endonuclease activity by Vts1 appeared to be the direct cause of suppression, since the multi-copy expression of Dna2-K1080E suppressed the lethality observed with its single-copy expression. We found that vts1Delta dna2Delta405N and vts1Deltadna2-7 double mutant cells displayed synergistic growth defects, in support of a functional interaction between two genes. Our results provide both in vivo and in vitro evidence that Vts1 is involved in lagging strand synthesis by modulating the Dna2 endonuclease activity that plays an essential role in Okazaki fragment processing.
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Affiliation(s)
- Chul-Hwan Lee
- Center for DNA Replication and Genome Instability, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
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