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Wu J, Zheng H, Gong P. Crystal structure of African swine fever virus pE301R reveals a ring-shaped trimeric DNA sliding clamp. J Biol Chem 2023:104872. [PMID: 37257822 PMCID: PMC10320598 DOI: 10.1016/j.jbc.2023.104872] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023] Open
Abstract
African swine fever virus (ASFV) is an important animal pathogen that is causing a current ASF pandemic and affecting pork industry globally. ASFV encodes at least 150 proteins, and the functions of many of them remain to be clarified. The ASFV protein E301R (pE301R) was predicted to be a DNA sliding clamp protein homolog working as a DNA replication processivity factor. However, structural evidence was lacking to support the existence of a ring-shaped sliding clamp in large eukaryotic DNA viruses. Here we have solved a high-resolution crystal structure of pE301R and identified a canonical ring-shaped clamp comprising a pE301R trimer. Interestingly, this complete-toroidal structure is different from those of the monomeric clamp protein homolog, herpes simplex virus UL42, and the C-shaped dimeric human cytomegalovirus UL44, but highly homologous to that of the eukaryotic clamp homolog proliferating cell nuclear antigen. Moreover, pE301R has a unique N-terminal extension (NE) that is important in maintaining the trimeric form of the protein in solution, while specific features in length and surface electrostatic potential of its inter-domain connector (IDC) implies specificity in interactions with binding partners such as the viral DNA polymerase. Thus, our data pave the way for further dissection of the processivity clamp protein structural and functional diversity and ASFV DNA replication mechanisms.
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Affiliation(s)
- Jiqin Wu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.262 Jin Long Street, Wuhan, Hubei, 430207, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.262 Jin Long Street, Wuhan, Hubei, 430207, China; Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, 300350, China; Hubei Jiangxia Laboratory, Wuhan, Hubei 430207, China.
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2
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Blaine HC, Burke JT, Ravi J, Stallings CL. DciA Helicase Operators Exhibit Diversity across Bacterial Phyla. J Bacteriol 2022; 204:e0016322. [PMID: 35880876 PMCID: PMC9380583 DOI: 10.1128/jb.00163-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/21/2022] [Indexed: 01/28/2023] Open
Abstract
A fundamental requirement for life is the replication of an organism's DNA. Studies in Escherichia coli and Bacillus subtilis have set the paradigm for DNA replication in bacteria. During replication initiation in E. coli and B. subtilis, the replicative helicase is loaded onto the DNA at the origin of replication by an ATPase helicase loader. However, most bacteria do not encode homologs to the helicase loaders in E. coli and B. subtilis. Recent work has identified the DciA protein as a predicted helicase operator that may perform a function analogous to the helicase loaders in E. coli and B. subtilis. DciA proteins, which are defined by the presence of a DUF721 domain (termed the DciA domain herein), are conserved in most bacteria but have only been studied in mycobacteria and gammaproteobacteria (Pseudomonas aeruginosa and Vibrio cholerae). Sequences outside the DciA domain in Mycobacterium tuberculosis DciA are essential for protein function but are not conserved in the P. aeruginosa and V. cholerae homologs, raising questions regarding the conservation and evolution of DciA proteins across bacterial phyla. To comprehensively define the DciA protein family, we took a computational evolutionary approach and analyzed the domain architectures and sequence properties of DciA domain-containing proteins across the tree of life. These analyses identified lineage-specific domain architectures among DciA homologs, as well as broadly conserved sequence-structural motifs. The diversity of DciA proteins represents the evolution of helicase operation in bacterial DNA replication and highlights the need for phylum-specific analyses of this fundamental biological process. IMPORTANCE Despite the fundamental importance of DNA replication for life, this process remains understudied in bacteria outside Escherichia coli and Bacillus subtilis. In particular, most bacteria do not encode the helicase-loading proteins that are essential in E. coli and B. subtilis for DNA replication. Instead, most bacteria encode a DciA homolog that likely constitutes the predominant mechanism of helicase operation in bacteria. However, it is still unknown how DciA structure and function compare across diverse phyla that encode DciA proteins. In this study, we performed computational evolutionary analyses to uncover tremendous diversity among DciA homologs. These studies provide a significant advance in our understanding of an essential component of the bacterial DNA replication machinery.
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Affiliation(s)
- Helen C. Blaine
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Joseph T. Burke
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- Genomics and Molecular Genetics Undergraduate Program, Michigan State University, East Lansing, Michigan, USA
| | - Janani Ravi
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Christina L. Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, Missouri, USA
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3
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Gaubitz C, Liu X, Pajak J, Stone NP, Hayes JA, Demo G, Kelch BA. Cryo-EM structures reveal high-resolution mechanism of a DNA polymerase sliding clamp loader. eLife 2022; 11:e74175. [PMID: 35179493 PMCID: PMC8893722 DOI: 10.7554/elife.74175] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Sliding clamps are ring-shaped protein complexes that are integral to the DNA replication machinery of all life. Sliding clamps are opened and installed onto DNA by clamp loader AAA+ ATPase complexes. However, how a clamp loader opens and closes the sliding clamp around DNA is still unknown. Here, we describe structures of the Saccharomyces cerevisiae clamp loader Replication Factor C (RFC) bound to its cognate sliding clamp Proliferating Cell Nuclear Antigen (PCNA) en route to successful loading. RFC first binds to PCNA in a dynamic, closed conformation that blocks both ATPase activity and DNA binding. RFC then opens the PCNA ring through a large-scale 'crab-claw' expansion of both RFC and PCNA that explains how RFC prefers initial binding of PCNA over DNA. Next, the open RFC:PCNA complex binds DNA and interrogates the primer-template junction using a surprising base-flipping mechanism. Our structures indicate that initial PCNA opening and subsequent closure around DNA do not require ATP hydrolysis, but are driven by binding energy. ATP hydrolysis, which is necessary for RFC release, is triggered by interactions with both PCNA and DNA, explaining RFC's switch-like ATPase activity. Our work reveals how a AAA+ machine undergoes dramatic conformational changes for achieving binding preference and substrate remodeling.
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Affiliation(s)
- Christl Gaubitz
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Xingchen Liu
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Joshua Pajak
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Nicholas P Stone
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Janelle A Hayes
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Gabriel Demo
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester MA & Central European Institute of Technology, Masaryk UniversityBrnoCzech Republic
| | - Brian A Kelch
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
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4
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Liu B, Li S, Liu Y, Chen H, Hu Z, Wang Z, Zhao Y, Zhang L, Ma B, Wang H, Matthews S, Wang Y, Zhang K. Bacteriophage Twort protein Gp168 is a β-clamp inhibitor by occupying the DNA sliding channel. Nucleic Acids Res 2021; 49:11367-11378. [PMID: 34614154 PMCID: PMC8565349 DOI: 10.1093/nar/gkab875] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/22/2022] Open
Abstract
Bacterial chromosome replication is mainly catalyzed by DNA polymerase III, whose beta subunits enable rapid processive DNA replication. Enabled by the clamp-loading complex, the two beta subunits form a ring-like clamp around DNA and keep the polymerase sliding along. Given the essential role of β-clamp, its inhibitors have been explored for antibacterial purposes. Similarly, β-clamp is an ideal target for bacteriophages to shut off host DNA synthesis during host takeover. The Gp168 protein of phage Twort is such an example, which binds to the β-clamp of Staphylococcus aureus and prevents it from loading onto DNA causing replication arrest. Here, we report a cryo-EM structure of the clamp–Gp168 complex at 3.2-Å resolution. In the structure of the complex, the Gp168 dimer occupies the DNA sliding channel of β-clamp and blocks its loading onto DNA, which represents a new inhibitory mechanism against β-clamp function. Interestingly, the key residues responsible for this interaction on the β-clamp are well conserved among bacteria. We therefore demonstrate that Gp168 is potentially a cross-species β-clamp inhibitor, as it forms complex with the Bacillus subtilis β-clamp. Our findings reveal an alternative mechanism for bacteriophages to inhibit β-clamp and provide a new strategy to combat bacterial drug resistance.
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Affiliation(s)
- Bing Liu
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China.,Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Shanshan Li
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Yang Liu
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China
| | - Huan Chen
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China
| | - Zhenyue Hu
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China
| | - Zhihao Wang
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China.,Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Yimin Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Biyun Ma
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China
| | - Hongliang Wang
- Department of Pathogen Biology and Immunology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Steve Matthews
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Yawen Wang
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China
| | - Kaiming Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
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5
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Chang HR, Jung E, Cho S, Jeon YJ, Kim Y. Targeting Non-Oncogene Addiction for Cancer Therapy. Biomolecules 2021; 11:129. [PMID: 33498235 PMCID: PMC7909239 DOI: 10.3390/biom11020129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
While Next-Generation Sequencing (NGS) and technological advances have been useful in identifying genetic profiles of tumorigenesis, novel target proteins and various clinical biomarkers, cancer continues to be a major global health threat. DNA replication, DNA damage response (DDR) and repair, and cell cycle regulation continue to be essential systems in targeted cancer therapies. Although many genes involved in DDR are known to be tumor suppressor genes, cancer cells are often dependent and addicted to these genes, making them excellent therapeutic targets. In this review, genes implicated in DNA replication, DDR, DNA repair, cell cycle regulation are discussed with reference to peptide or small molecule inhibitors which may prove therapeutic in cancer patients. Additionally, the potential of utilizing novel synthetic lethal genes in these pathways is examined, providing possible new targets for future therapeutics. Specifically, we evaluate the potential of TONSL as a novel gene for targeted therapy. Although it is a scaffold protein with no known enzymatic activity, the strategy used for developing PCNA inhibitors can also be utilized to target TONSL. This review summarizes current knowledge on non-oncogene addiction, and the utilization of synthetic lethality for developing novel inhibitors targeting non-oncogenic addiction for cancer therapy.
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Affiliation(s)
- Hae Ryung Chang
- Department of Biological Sciences and Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea; (E.J.); (S.C.)
| | - Eunyoung Jung
- Department of Biological Sciences and Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea; (E.J.); (S.C.)
| | - Soobin Cho
- Department of Biological Sciences and Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea; (E.J.); (S.C.)
| | - Young-Jun Jeon
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea;
| | - Yonghwan Kim
- Department of Biological Sciences and Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea; (E.J.); (S.C.)
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6
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Abstract
In all cell types, a multi-protein machinery is required to accurately duplicate the large duplex DNA genome. This central life process requires five core replisome factors in all cellular life forms studied thus far. Unexpectedly, three of the five core replisome factors have no common ancestor between bacteria and eukaryotes. Accordingly, the replisome machines of bacteria and eukaryotes have important distinctions in the way that they are organized and function. This chapter outlines the major replication proteins that perform DNA duplication at replication forks, with particular attention to differences and similarities in the strategies used by eukaryotes and bacteria.
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Affiliation(s)
- Nina Y Yao
- DNA Replication Laboratory, The Rockefeller University, New York, USA, 10065
| | - Michael E O'Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, USA, 10065. .,Howard Hughes Medical Institute, The Rockefeller University, New York, USA, 10065.
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7
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Chen Y, Qian J, You L, Zhang X, Jiao J, Liu Y, Zhao J. Subunit Interaction Differences Between the Replication Factor C Complexes in Arabidopsis and Rice. FRONTIERS IN PLANT SCIENCE 2018; 9:779. [PMID: 29971074 PMCID: PMC6018503 DOI: 10.3389/fpls.2018.00779] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/22/2018] [Indexed: 06/01/2023]
Abstract
Replication factor C (RFC) is a multisubunit complex that opens the sliding clamp and loads it onto the DNA chain in an ATP-dependent manner and is thus critical for high-speed DNA synthesis. In yeast (Saccharomyces cerevisiae) and humans, biochemical studies and structural analysis revealed interaction patterns between the subunits and architectures of the clamp loaders. Mutations of ScRFC1/2/3/4/5 lead to loss of cell viability and defective replication. However, the functions of RFC subunits in higher plants are unclear, except for AtRFC1/3/4, and the interaction and arrangement of the subunits have not been studied. Here, we identified rfc2-1/+, rfc3-2/+, and rfc5-1/+ mutants in Arabidopsis, and found that embryos and endosperm arrested at the 2/4-celled embryo proper stage and 6-8 nuclei stages, respectively. Subcellular localization analysis revealed that AtRFC1 and OsRFC1/4/5 proteins were localized in the nucleus, while AtRFC2/3/4/5 and OsRFC2/3 proteins were present both in the nucleus and cytoplasm. By using yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) techniques, we demonstrated the interactions of Arabidopsis and rice (Oryza sativa) RFC subunits, and proposed arrangements of the five subunits within the RFC complex, which were AtRFC5-AtRFC4-AtRFC3/2-AtRFC2/3-AtRFC1 and OsRFC5-OsRFC2-OsRFC3-OsRFC4-OsRFC1, respectively. In addition, AtRFC1 could interact with AtRFC2/3/4/5 in the presence of other subunits, while OsRFC1 directly interacted with the other four subunits. To further characterize the regions required for complex formation, truncated RFC proteins of the subunits were created. The results showed that C-termini of the RFC subunits are required for complex formation. Our studies indicate that the localization and interactions of RFCs in Arabidopsis and rice are distinctly discrepant.
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8
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Watanabe S, Fujiyama H, Takafuji T, Kayama K, Matsumoto M, Nakayama KI, Yoshida K, Sugimoto N, Fujita M. Glutamate-rich WD40 repeat containing 1 regulates ribosomal protein L23 levels via the ubiquitin-proteasome system. J Cell Sci 2018; 131:jcs.213009. [DOI: 10.1242/jcs.213009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 06/11/2018] [Indexed: 01/01/2023] Open
Abstract
GRWD1 is a Cdt1-binding protein that promotes MCM loading through its histone chaperone activity. GRWD1 acts as a tumor-promoting factor by downregulating p53 via the RPL11-MDM2-p53 axis. Here, we identified GRWD1-interacting proteins using a proteomics approach and showed that GRWD1 interacts with various proteins involved in transcription, translation, DNA replication and repair, chromatin organization, and ubiquitin-mediated proteolysis. We focused on the ribosomal protein RPL23, which positively regulates nucleolar stress responses through MDM2 binding and inhibition, thereby functioning as a tumor suppressor. Overexpression of GRWD1 decreased RPL23 protein levels and stability; this effect was restored by the proteasome inhibitor MG132. EDD, an E3 ubiquitin ligase that interacts with GRWD1, also downregulated RPL23, and the decrease was further enhanced by co-expression of GRWD1. Conversely, siRNA-mediated GRWD1 knockdown upregulated RPL23. Co-expression of GRWD1 and EDD promoted RPL23 ubiquitination. These data suggest that GRWD1 acts together with EDD to negatively regulate RPL23 via the ubiquitin-proteasome system. GRWD1 reversed the RPL23-mediated inhibition of anchorage-independent growth in cancer cells. Our data suggest that GRWD1-induced RPL23 proteolysis plays a role in p53 downregulation and tumorigenesis.
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Affiliation(s)
- Shinya Watanabe
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroki Fujiyama
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Takuya Takafuji
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kota Kayama
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Keiichi I. Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kazumasa Yoshida
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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9
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Control of Genome Integrity by RFC Complexes; Conductors of PCNA Loading onto and Unloading from Chromatin during DNA Replication. Genes (Basel) 2017; 8:genes8020052. [PMID: 28134787 PMCID: PMC5333041 DOI: 10.3390/genes8020052] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/21/2017] [Indexed: 11/23/2022] Open
Abstract
During cell division, genome integrity is maintained by faithful DNA replication during S phase, followed by accurate segregation in mitosis. Many DNA metabolic events linked with DNA replication are also regulated throughout the cell cycle. In eukaryotes, the DNA sliding clamp, proliferating cell nuclear antigen (PCNA), acts on chromatin as a processivity factor for DNA polymerases. Since its discovery, many other PCNA binding partners have been identified that function during DNA replication, repair, recombination, chromatin remodeling, cohesion, and proteolysis in cell-cycle progression. PCNA not only recruits the proteins involved in such events, but it also actively controls their function as chromatin assembles. Therefore, control of PCNA-loading onto chromatin is fundamental for various replication-coupled reactions. PCNA is loaded onto chromatin by PCNA-loading replication factor C (RFC) complexes. Both RFC1-RFC and Ctf18-RFC fundamentally function as PCNA loaders. On the other hand, after DNA synthesis, PCNA must be removed from chromatin by Elg1-RFC. Functional defects in RFC complexes lead to chromosomal abnormalities. In this review, we summarize the structural and functional relationships among RFC complexes, and describe how the regulation of PCNA loading/unloading by RFC complexes contributes to maintaining genome integrity.
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10
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Kelch BA, Makino DL, O'Donnell M, Kuriyan J. Clamp loader ATPases and the evolution of DNA replication machinery. BMC Biol 2012; 10:34. [PMID: 22520345 PMCID: PMC3331839 DOI: 10.1186/1741-7007-10-34] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 04/20/2012] [Indexed: 11/19/2022] Open
Abstract
Clamp loaders are pentameric ATPases of the AAA+ family that operate to ensure processive DNA replication. They do so by loading onto DNA the ring-shaped sliding clamps that tether the polymerase to the DNA. Structural and biochemical analysis of clamp loaders has shown how, despite differences in composition across different branches of life, all clamp loaders undergo the same concerted conformational transformations, which generate a binding surface for the open clamp and an internal spiral chamber into which the DNA at the replication fork can slide, triggering ATP hydrolysis, release of the clamp loader, and closure of the clamp round the DNA. We review here the current understanding of the clamp loader mechanism and discuss the implications of the differences between clamp loaders from the different branches of life.
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Affiliation(s)
- Brian A Kelch
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
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11
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Mueser TC, Hinerman JM, Devos JM, Boyer RA, Williams KJ. Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives. Virol J 2010; 7:359. [PMID: 21129204 PMCID: PMC3012046 DOI: 10.1186/1743-422x-7-359] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 12/03/2010] [Indexed: 12/13/2022] Open
Abstract
The bacteriophage T4 encodes 10 proteins, known collectively as the replisome, that are responsible for the replication of the phage genome. The replisomal proteins can be subdivided into three activities; the replicase, responsible for duplicating DNA, the primosomal proteins, responsible for unwinding and Okazaki fragment initiation, and the Okazaki repair proteins. The replicase includes the gp43 DNA polymerase, the gp45 processivity clamp, the gp44/62 clamp loader complex, and the gp32 single-stranded DNA binding protein. The primosomal proteins include the gp41 hexameric helicase, the gp61 primase, and the gp59 helicase loading protein. The RNaseH, a 5' to 3' exonuclease and T4 DNA ligase comprise the activities necessary for Okazaki repair. The T4 provides a model system for DNA replication. As a consequence, significant effort has been put forth to solve the crystallographic structures of these replisomal proteins. In this review, we discuss the structures that are available and provide comparison to related proteins when the T4 structures are unavailable. Three of the ten full-length T4 replisomal proteins have been determined; the gp59 helicase loading protein, the RNase H, and the gp45 processivity clamp. The core of T4 gp32 and two proteins from the T4 related phage RB69, the gp43 polymerase and the gp45 clamp are also solved. The T4 gp44/62 clamp loader has not been crystallized but a comparison to the E. coli gamma complex is provided. The structures of T4 gp41 helicase, gp61 primase, and T4 DNA ligase are unknown, structures from bacteriophage T7 proteins are discussed instead. To better understand the functionality of T4 DNA replication, in depth structural analysis will require complexes between proteins and DNA substrates. A DNA primer template bound by gp43 polymerase, a fork DNA substrate bound by RNase H, gp43 polymerase bound to gp32 protein, and RNase H bound to gp32 have been crystallographically determined. The preparation and crystallization of complexes is a significant challenge. We discuss alternate approaches, such as small angle X-ray and neutron scattering to generate molecular envelopes for modeling macromolecular assemblies.
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Affiliation(s)
| | - Jennifer M Hinerman
- Department of Molecular Genetics, Biochemistry & Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Juliette M Devos
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
| | | | - Kandace J Williams
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine, Toledo OH, USA
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12
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Maradeo ME, Garg A, Skibbens RV. Rfc5p regulates alternate RFC complex functions in sister chromatid pairing reactions in budding yeast. Cell Cycle 2010; 9:4370-8. [PMID: 20980821 DOI: 10.4161/cc.9.21.13634] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Sister chromatid pairing reactions, termed cohesion establishment, occur during S-phase and appear to be regulated by Replication Factor C (RFC) complexes. For instance, RFCs that contain Ctf18p exhibit pro-establishment activities while those that contain Elg1p exhibit anti-establishment activities. It remains unknown whether Ctf18p-RFC and Elg1p-RFC functions are simply opposing or instead reveal complicated and non-parallel regulatory mechanisms. To better understand the nature of these novel pathways, we analyzed the small RFC subunit Rfc5p that is common to both Ctf18p-RFC and Elg1p-RFC. Despite this commonality, the data show that diminished Rfc5p function rescues ctf7/eco1 mutant cell phenotypes, revealing that Rfc5p promotes anti-establishment activities. This rescue is specific to establishment pathways in that rfc5-1 greatly accentuates growth defects when expressed in scc2 (deposition), mcd1/scc1 or smc3 (cohesion maintenance) mutated cells. Our results reveal for the first time a role for small RFC subunits in directing RFC complex functions-in this case towards anti-establishment pathways. We further report that Pds5p exhibits both establishment and anti-establishment functions in cohesion. This duality suggests that categorizations of establishment and anti-establishment activities require further examination.
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Affiliation(s)
- Marie E Maradeo
- Dept. of Biological Sciences, Lehigh University, Bethlehem, PA, USA
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13
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Makiela-Dzbenska K, Jaszczur M, Banach-Orlowska M, Jonczyk P, Schaaper RM, Fijalkowska IJ. Role of Escherichia coli DNA polymerase I in chromosomal DNA replication fidelity. Mol Microbiol 2009; 74:1114-27. [PMID: 19843230 DOI: 10.1111/j.1365-2958.2009.06921.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have investigated the possible role of Escherichia coli DNA polymerase (Pol) I in chromosomal replication fidelity. This was done by substituting the chromosomal polA gene by the polAexo variant containing an inactivated 3'-->5' exonuclease, which serves as a proofreader for this enzyme's misinsertion errors. Using this strain, activities of Pol I during DNA replication might be detectable as increases in the bacterial mutation rate. Using a series of defined lacZ reversion alleles in two orientations on the chromosome as markers for mutagenesis, 1.5- to 4-fold increases in mutant frequencies were observed. In general, these increases were largest for lac orientations favouring events during lagging strand DNA replication. Further analysis of these effects in strains affected in other E. coli DNA replication functions indicated that this polAexo mutator effect is best explained by an effect that is additive compared with other error-producing events at the replication fork. No evidence was found that Pol I participates in the polymerase switching between Pol II, III and IV at the fork. Instead, our data suggest that the additional errors produced by polAexo are created during the maturation of Okazaki fragments in the lagging strand.
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Affiliation(s)
- Karolina Makiela-Dzbenska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, Warsaw, Poland
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14
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Castrec B, Rouillon C, Henneke G, Flament D, Querellou J, Raffin JP. Binding to PCNA in Euryarchaeal DNA Replication requires two PIP motifs for DNA polymerase D and one PIP motif for DNA polymerase B. J Mol Biol 2009; 394:209-18. [PMID: 19781553 DOI: 10.1016/j.jmb.2009.09.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Revised: 09/16/2009] [Accepted: 09/17/2009] [Indexed: 01/07/2023]
Abstract
Replicative DNA polymerases possess a canonical C-terminal proliferating cell nuclear antigen (PCNA)-binding motif termed the PCNA-interacting protein (PIP) box. We investigated the role of the PIP box on the functional interactions of the two DNA polymerases, PabPol B (family B) and PabPol D (family D), from the hyperthermophilic euryarchaeon Pyrococcus abyssi, with its cognate PCNA. The PIP box was essential for interactions of PabPol B with PCNA, as shown by surface plasmon resonance and primer extension studies. In contrast, binding of PabPol D to PCNA was affected only partially by removing the PIP motif. We identified a second palindromic PIP box motif at the N-terminus of the large subunit of PabPol D that was required for the interactions of PabPol D with PCNA. Thus, two PIP motifs were needed for PabPol D for binding to PabPCNA. Moreover, the C-terminus of PabPCNA was essential for stimulation of PabPol D activity but not for stimulation of PabPol B activity. Neither DNA polymerase interacted with the PabPCNA interdomain connecting loop. Our data suggest that distinct processes are involved in PabPol D and PabPol B binding to PCNA, raising the possibility that Archaea require two mechanisms for recruiting replicative DNA polymerases at the replication fork.
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Affiliation(s)
- Benoît Castrec
- Université de Bretagne Occidentale, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, BP 70, F-29280 Plouzané, France
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15
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Perumal SK, Yue H, Hu Z, Spiering MM, Benkovic SJ. Single-molecule studies of DNA replisome function. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:1094-112. [PMID: 19665592 DOI: 10.1016/j.bbapap.2009.07.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 07/08/2009] [Accepted: 07/28/2009] [Indexed: 11/16/2022]
Abstract
Fast and accurate replication of DNA is accomplished by the interactions of multiple proteins in the dynamic DNA replisome. The DNA replisome effectively coordinates the leading and lagging strand synthesis of DNA. These complex, yet elegantly organized, molecular machines have been studied extensively by kinetic and structural methods to provide an in-depth understanding of the mechanism of DNA replication. Owing to averaging of observables, unique dynamic information of the biochemical pathways and reactions is concealed in conventional ensemble methods. However, recent advances in the rapidly expanding field of single-molecule analyses to study single biomolecules offer opportunities to probe and understand the dynamic processes involved in large biomolecular complexes such as replisomes. This review will focus on the recent developments in the biochemistry and biophysics of DNA replication employing single-molecule techniques and the insights provided by these methods towards a better understanding of the intricate mechanisms of DNA replication.
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Affiliation(s)
- Senthil K Perumal
- 414 Wartik Laboratory, Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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16
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Abstract
Replisomes are the protein assemblies that replicate DNA. They function as molecular motors to catalyze template-mediated polymerization of nucleotides, unwinding of DNA, the synthesis of RNA primers, and the assembly of proteins on DNA. The replisome of bacteriophage T7 contains a minimum of proteins, thus facilitating its study. This review describes the molecular motors and coordination of their activities, with emphasis on the T7 replisome. Nucleotide selection, movement of the polymerase, binding of the processivity factor, unwinding of DNA, and RNA primer synthesis all require conformational changes and protein contacts. Lagging-strand synthesis is mediated via a replication loop whose formation and resolution is dictated by switches to yield Okazaki fragments of discrete size. Both strands are synthesized at identical rates, controlled by a molecular brake that halts leading-strand synthesis during primer synthesis. The helicase serves as a reservoir for polymerases that can initiate DNA synthesis at the replication fork. We comment on the differences in other systems where applicable.
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Affiliation(s)
- Samir M Hamdan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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17
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The Elg1-RFC clamp-loading complex performs a role in sister chromatid cohesion. PLoS One 2009; 4:e4707. [PMID: 19262753 PMCID: PMC2650802 DOI: 10.1371/journal.pone.0004707] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 02/02/2009] [Indexed: 11/19/2022] Open
Abstract
It is widely accepted that of the four Replication Factor C (RFC) complexes (defined by the associations of either Rfc1p, Ctf18p, Elg1p or Rad24p with Rfc2p-Rfc5p), only Ctf18-RFC functions in sister chromatid cohesion. This model is based on findings that CTF18 deletion is lethal in combination with mutations in either CTF7ECO1 or MCD1 sister chromatid cohesion genes and that ctf18 mutant cells exhibit cohesion defects. Here, we report that Elg1-RFC not only participates in cohesion but performs a function that is distinct from that of Ctf18-RFC. The results show that deletion of ELG1 rescues both ctf7eco1 mutant cell temperature sensitivity and cohesion defects. Moreover, over-expression of ELG1 enhances ctf7eco1 mutant cell phenotypes. These findings suggest that the balance of Ctf7pEco1p activity depends on both Ctf18-RFC and Elg1-RFC. We also report that ELG1 deletion produces cohesion defects and intensifies the conditional phenotype of mcd1 mutant cells, further supporting a role for Elg1-RFC in cohesion. Attesting to the specificity of these interactions, deletion of RAD24 neither suppressed nor exacerbated cohesion defects in either ctf7eco1 or mcd1 mutant cells. While parallel analyses failed to uncover a similar role in cohesion for Rad24-RFC, it is well known that Rad24-RFC, Elg1-RFC and Ctf18-RFC play key roles in DNA damage responses. We tested and found that Ctf7pEco1p plays a significant role in Rad24-RFC-based DNA response pathways. In combination, these findings challenge current views and document new and distinct roles for RFC complexes in cohesion and for Ctf7pEco1p in DNA repair.
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18
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Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit. J Mol Biol 2008; 382:859-69. [PMID: 18691598 PMCID: PMC2614274 DOI: 10.1016/j.jmb.2008.07.058] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Accepted: 07/22/2008] [Indexed: 01/07/2023]
Abstract
The crystal structure of the catalytic alpha-subunit of the DNA polymerase III (Pol IIIalpha) holoenzyme bound to primer-template DNA and an incoming deoxy-nucleoside 5'-triphosphate has been determined at 4.6-A resolution. The polymerase interacts with the sugar-phosphate backbone of the DNA across its minor groove, which is made possible by significant movements of the thumb, finger, and beta-binding domains relative to their orientations in the unliganded polymerase structure. Additionally, the DNA and incoming nucleotide are bound to the active site of Pol IIIalpha nearly identically as they are in their complex with DNA polymerase beta, thereby proving that the eubacterial replicating polymerase, but not the eukaryotic replicating polymerase, is homologous to DNA polymerase beta. Finally, superimposing a recent structure of the clamp bound to DNA on this Pol IIIalpha complex with DNA places a loop of the beta-binding domain into the appropriate clamp cleft and supports a mechanism of polymerase switching.
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19
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Kato JI. Regulatory Network of the Initiation of Chromosomal Replication inEscherichia coli. Crit Rev Biochem Mol Biol 2008; 40:331-42. [PMID: 16338685 DOI: 10.1080/10409230500366090] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The bacterial chromosome is replicated once during the division cycle, a process ensured by the tight regulation of initiation at oriC. In prokaryotes, the initiator protein DnaA plays an essential role at the initiation step, and feedback control is critical in regulating initiation. Three systems have been identified that exert feedback control in Escherichia coli, all of which are necessary for tight strict regulation of the initiation step. In particular, the ATP-dependent control of DnaA activity is essential. A missing link in initiator activity regulation has been identified, facilitating analysis of the reaction mechanism. Furthermore, key components of this regulatory network have also been described. Because the eukaryotic initiator complex, ORC, is also regulated by ATP, the bacterial system provides an important model for understanding initiation in eukaryotes. This review summarizes recent studies on the regulation of initiator activity.
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Affiliation(s)
- Jun-ichi Kato
- Department of Biology, Graduate School of Science, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo, Japan
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20
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uvsF RFC1, the large subunit of replication factor C in Aspergillus nidulans, is essential for DNA replication, functions in UV repair and is upregulated in response to MMS-induced DNA damage. Fungal Genet Biol 2008; 45:1227-34. [PMID: 18655840 DOI: 10.1016/j.fgb.2008.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 06/26/2008] [Accepted: 06/26/2008] [Indexed: 11/22/2022]
Abstract
uvsF201 was the first highly UV-sensitive repair-defective mutation isolated in Aspergillus nidulans. It showed epistasis only with postreplication repair mutations, but caused lethal interactions with many other repair-defective strains. Unexpectedly, closest homology of uvsF was found to the large subunit of human DNA replication factor RFC that is essential for DNA replication. Sequencing of the uvsF201 region identified changes at two close base pairs and the corresponding amino acids in the 5'-region of uvsF(RFC1). This viable mutant represents a novel and possibly important type. Additional sequencing of the uvsF region confirmed a mitochondrial ribosomal protein gene, mrpA(L16), closely adjacent, head-to-head with a 0.2kb joint promoter region. MMS-induced transcription of both the genes, but especially uvsF(RFC1), providing evidence for a function in DNA damage response.
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21
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McInerney P, Johnson A, Katz F, O'Donnell M. Characterization of a triple DNA polymerase replisome. Mol Cell 2007; 27:527-38. [PMID: 17707226 DOI: 10.1016/j.molcel.2007.06.019] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Revised: 05/15/2007] [Accepted: 06/12/2007] [Indexed: 11/20/2022]
Abstract
The replicase of all cells is thought to utilize two DNA polymerases for coordinated synthesis of leading and lagging strands. The DNA polymerases are held to DNA by circular sliding clamps. We demonstrate here that the E. coli DNA polymerase III holoenzyme assembles into a particle that contains three DNA polymerases. The three polymerases appear capable of simultaneous activity. Furthermore, the trimeric replicase is fully functional at a replication fork with helicase, primase, and sliding clamps; it produces slightly shorter Okazaki fragments than replisomes containing two DNA polymerases. We propose that two polymerases can function on the lagging strand and that the third DNA polymerase can act as a reserve enzyme to overcome certain types of obstacles to the replication fork.
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Affiliation(s)
- Peter McInerney
- Laboratory of DNA Replication, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021, USA
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22
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Li F, Liu Q, Chen YY, Yu ZN, Zhang ZP, Zhou YF, Deng JY, Bi LJ, Zhang XE. Escherichia coli mismatch repair protein MutL interacts with the clamp loader subunits of DNA polymerase III. Mutat Res 2007; 637:101-10. [PMID: 17765269 DOI: 10.1016/j.mrfmmm.2007.07.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 07/09/2007] [Accepted: 07/17/2007] [Indexed: 11/15/2022]
Abstract
It has been hypothesized that DNA mismatch repair (MMR) is coupled with DNA replication; however, the involvement of DNA polymerase III subunits in bacterial DNA MMR has not been clearly elucidated. In an effort to better understand the relationship between these 2 systems, the potential interactions between the Escherichia coli MMR protein and the clamp loader subunits of E. coli DNA polymerase III were analyzed by far western blotting and then confirmed and characterized by surface plasmon resonance (SPR) imaging. The results showed that the MMR key protein MutL could directly interact with both the individual subunits delta, delta', and gamma and the complex of these subunits (clamp loader). Kinetic parameters revealed that the interactions are strong and stable, suggesting that MutL might be involved in the recruitment of the clamp loader during the resynthesis step in MMR. The interactions between MutL, the delta and gamma subunits, and the clamp loader were observed to be modulated by ATP. Deletion analysis demonstrated that both the N-terminal residues (1-293) and C-terminal residues (556-613) of MutL are required for interacting with the subunits delta and delta'. Based on these findings and the available information, the network of interactions between the MMR components and the DNA polymerase III subunits was established; this network provides strong evidence to support the notion that DNA replication and MMR are highly associated with each other.
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Affiliation(s)
- Feng Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agriculture University, Wuhan, China
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23
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Shiomi Y, Masutani C, Hanaoka F, Kimura H, Tsurimoto T. A Second Proliferating Cell Nuclear Antigen Loader Complex, Ctf18-Replication Factor C, Stimulates DNA Polymerase η Activity. J Biol Chem 2007; 282:20906-14. [PMID: 17545166 DOI: 10.1074/jbc.m610102200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Replication factor C (RFC) loads the clamp protein PCNA onto DNA structures. Ctf18-RFC, which consists of the chromosome cohesion factors Ctf18, Dcc1, and Ctf8 and four small RFC subunits, functions as a second proliferating cell nuclear antigen (PCNA) loader. To identify potential targets of Ctf18-RFC, human cell extracts were assayed for DNA polymerase activity specifically stimulated by Ctf18-RFC in conjunction with PCNA. After several chromatography steps, an activity stimulated by Ctf18-RFC but not by RFC was identified. Liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis revealed the presence of two DNA polymerases, eta and lambda, in the most purified fraction, but experiments with purified recombinant proteins demonstrated that only polymerase (pol) eta was responsible for activity. Ctf18-RFC alone stimulated pol eta, and the addition of PCNA cooperatively increased stimulation. Furthermore, Ctf18-RFC interacted physically with pol eta, as indicated by co-precipitation in human cells. We propose that this novel loader-DNA polymerase interaction allows DNA replication forks to overcome interference by various template structures, including damaged DNA and DNA-protein complexes that maintain chromosome cohesion.
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Affiliation(s)
- Yasushi Shiomi
- Department of Biology, School of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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24
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Rouillon C, Henneke G, Flament D, Querellou J, Raffin JP. DNA Polymerase Switching on Homotrimeric PCNA at the Replication Fork of the Euryarchaea Pyrococcus abyssi. J Mol Biol 2007; 369:343-55. [PMID: 17442344 DOI: 10.1016/j.jmb.2007.03.054] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Revised: 03/15/2007] [Accepted: 03/19/2007] [Indexed: 12/28/2022]
Abstract
DNA replication in Archaea, as in other organisms, involves large protein complexes called replisomes. In the Euryarchaeota subdomain, only two putative replicases have been identified, and their roles in leading and lagging strand DNA synthesis are still poorly understood. In this study, we focused on the coupling of proliferating cell nuclear antigen (PCNA)-loading mechanisms with DNA polymerase function in the Euryarchaea Pyrococcus abyssi. PCNA spontaneously loaded onto primed DNA, and replication factor C dramatically increased this loading. Surprisingly, the family B DNA polymerase (Pol B) also increased PCNA loading, probably by stabilizing the clamp on primed DNA via an essential motif. In contrast, on an RNA-primed DNA template, the PCNA/Pol B complex was destabilized in the presence of dNTPs, allowing the family D DNA polymerase (Pol D) to perform RNA-primed DNA synthesis. Then, Pol D is displaced by Pol B to perform processive DNA synthesis, at least on the leading strand.
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Affiliation(s)
- Christophe Rouillon
- IFREMER, UMR 6197, Laboratoire de Microbiologie et Environnements Extrêmes, BP 70, F-29280 Plouzané, France
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25
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Jergic S, Ozawa K, Williams NK, Su XC, Scott DD, Hamdan SM, Crowther JA, Otting G, Dixon NE. The unstructured C-terminus of the tau subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the alpha subunit. Nucleic Acids Res 2007; 35:2813-24. [PMID: 17355988 PMCID: PMC1888804 DOI: 10.1093/nar/gkm079] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The τ subunit of Escherichia coli DNA polymerase III holoenzyme interacts with the α subunit through its C-terminal Domain V, τC16. We show that the extreme C-terminal region of τC16 constitutes the site of interaction with α. The τC16 domain, but not a derivative of it with a C-terminal deletion of seven residues (τC16Δ7), forms an isolable complex with α. Surface plasmon resonance measurements were used to determine the dissociation constant (KD) of the α−τC16 complex to be ∼260 pM. Competition with immobilized τC16 by τC16 derivatives for binding to α gave values of KD of 7 μM for the α−τC16Δ7 complex. Low-level expression of the genes encoding τC16 and τC16▵7, but not τC16Δ11, is lethal to E. coli. Suppression of this lethal phenotype enabled selection of mutations in the 3′ end of the τC16 gene, that led to defects in α binding. The data suggest that the unstructured C-terminus of τ becomes folded into a helix–loop–helix in its complex with α. An N-terminally extended construct, τC24, was found to bind DNA in a salt-sensitive manner while no binding was observed for τC16, suggesting that the processivity switch of the replisome functionally involves Domain IV of τ.
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Affiliation(s)
- Slobodan Jergic
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Kiyoshi Ozawa
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Neal K. Williams
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Xun-Cheng Su
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Daniel D. Scott
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Samir M. Hamdan
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Jeffrey A. Crowther
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Nicholas E. Dixon
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
- *To whom correspondence should be addressed. +61 2 42214346+61 2 42214287
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26
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Neuwald AF. Hypothesis: bacterial clamp loader ATPase activation through DNA-dependent repositioning of the catalytic base and of a trans-acting catalytic threonine. Nucleic Acids Res 2006; 34:5280-90. [PMID: 17012286 PMCID: PMC1636414 DOI: 10.1093/nar/gkl519] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The prokaryotic DNA polymerase III clamp loader complex loads the β clamp onto DNA to link the replication complex to DNA during processive synthesis and unloads it again once synthesis is complete. This minimal complex consists of one δ, one δ′ and three γ subunits, all of which possess an AAA+ module—though only the γ subunit exhibits ATPase activity. Here clues to underlying clamp loader mechanisms are obtained through Bayesian inference of various categories of selective constraints imposed on the γ and δ′ subunits. It is proposed that a conserved histidine is ionized via electron transfer involving structurally adjacent residues within the sensor 1 region of γ's AAA+ module. The resultant positive charge on this histidine inhibits ATPase activity by drawing the negatively charged catalytic base away from the active site. It is also proposed that this arrangement is disrupted upon interaction of DNA with basic residues in γ implicated previously in DNA binding, regarding which a lysine that is near the sensor 1 region and that is highly conserved both in bacterial and in eukaryotic clamp loader ATPases appears to play a critical role. γ ATPases also appear to utilize a trans-acting threonine that is donated by helix 6 of an adjacent γ or δ′ subunit and that assists in the activation of a water molecule for nucleophilic attack on the γ phosphorous atom of ATP. As eukaryotic and archaeal clamp loaders lack most of these key residues, it appears that eubacteria utilize a fundamentally different mechanism for clamp loader activation than do these other organisms.
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Affiliation(s)
- Andrew F Neuwald
- Cold Spring Harbor Laboratory, 1 Bungtown Road PO Box 100, Cold Spring Harbor, NY 11724, USA
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27
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Johnson A, Yao NY, Bowman GD, Kuriyan J, O'Donnell M. The replication factor C clamp loader requires arginine finger sensors to drive DNA binding and proliferating cell nuclear antigen loading. J Biol Chem 2006; 281:35531-43. [PMID: 16980295 DOI: 10.1074/jbc.m606090200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Replication factor C (RFC) is an AAA+ heteropentamer that couples the energy of ATP binding and hydrolysis to the loading of the DNA polymerase processivity clamp, proliferating cell nuclear antigen (PCNA), onto DNA. RFC consists of five subunits in a spiral arrangement (RFC-A, -B, -C, -D, and -E, corresponding to subunits RFC1, RFC4, RFC3, RFC2, and RFC5, respectively). The RFC subunits are AAA+ family proteins and the complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginines act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis. In this study, the arginine fingers in RFC were mutated to examine the steps in the PCNA loading mechanism that occur after RFC binds ATP. This report finds that the ATP sites of RFC function in distinct steps during loading of PCNA onto DNA. ATP binding to RFC powers recruitment and opening of PCNA and activates a gamma-phosphate sensor in ATP site C that promotes DNA association. ATP hydrolysis in site D is uniquely stimulated by PCNA, and we propose that this event is coupled to PCNA closure around DNA, which starts an ordered hydrolysis around the ring. PCNA closure severs contact to RFC subunits D and E (RFC2 and RFC5), and the gamma-phosphate sensor of ATP site C is switched off, resulting in low affinity of RFC for DNA and ejection of RFC from the site of PCNA loading.
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Affiliation(s)
- Aaron Johnson
- Laboratory of DNA Replication, Howard Hughes Medical Institute and Rockefeller University, New York, New York 10021, USA
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28
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López de Saro FJ, Marinus MG, Modrich P, O'Donnell M. The beta sliding clamp binds to multiple sites within MutL and MutS. J Biol Chem 2006; 281:14340-9. [PMID: 16546997 DOI: 10.1074/jbc.m601264200] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The MutL and MutS proteins are the central components of the DNA repair machinery that corrects mismatches generated by DNA polymerases during synthesis. We find that MutL interacts directly with the beta sliding clamp, a ring-shaped dimeric protein that confers processivity to DNA polymerases by tethering them to their substrates. Interestingly, the interaction of MutL with beta only occurs in the presence of single-stranded DNA. We find that the interaction occurs via a loop in MutL near the ATP-binding site. The binding site of MutL on beta locates to the hydrophobic pocket between domains two and three of the clamp. Site-specific replacement of two residues in MutL diminished interaction with beta without disrupting MutL function with helicase II. In vivo studies reveal that this mutant MutL is no longer functional in mismatch repair. In addition, the human MLH1 has a close match to the proliferating cell nuclear antigen clamp binding motif in the region that corresponds to the beta interaction site in Escherichia coli MutL, and a peptide corresponding to this site binds proliferating cell nuclear antigen. The current report also examines in detail the interaction of beta with MutS. We find that two distinct regions of MutS interact with beta. One is located near the C terminus and the other is close to the N terminus, within the mismatch binding domain. Complementation studies using genes encoding different MutS mutants reveal that the N-terminal beta interaction motif on MutS is essential for activity in vivo, but the C-terminal interaction site for beta is not. In light of these results, we propose roles for the beta clamp in orchestrating the sequence of events that lead to mismatch repair in the cell.
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29
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Affiliation(s)
- Mike O'Donnell
- Laboratory of DNA Replication, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10021, USA.
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30
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Affiliation(s)
- David Jeruzalmi
- Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.
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31
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Abstract
DNA replicases are multicomponent machines that have evolved clever strategies to perform their function. Although the structure of DNA is elegant in its simplicity, the job of duplicating it is far from simple. At the heart of the replicase machinery is a heteropentameric AAA+ clamp-loading machine that couples ATP hydrolysis to load circular clamp proteins onto DNA. The clamps encircle DNA and hold polymerases to the template for processive action. Clamp-loader and sliding clamp structures have been solved in both prokaryotic and eukaryotic systems. The heteropentameric clamp loaders are circular oligomers, reflecting the circular shape of their respective clamp substrates. Clamps and clamp loaders also function in other DNA metabolic processes, including repair, checkpoint mechanisms, and cell cycle progression. Twin polymerases and clamps coordinate their actions with a clamp loader and yet other proteins to form a replisome machine that advances the replication fork.
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Affiliation(s)
- Aaron Johnson
- Howard Hughes Medical Institute, New York City, New York 10021-6399, USA.
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32
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Banach-Orlowska M, Fijalkowska IJ, Schaaper RM, Jonczyk P. DNA polymerase II as a fidelity factor in chromosomal DNA synthesis in Escherichia coli. Mol Microbiol 2005; 58:61-70. [PMID: 16164549 DOI: 10.1111/j.1365-2958.2005.04805.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Escherichia coli DNA polymerase III holoenzyme (HE) is the main replicase responsible for replication of the bacterial chromosome. E. coli contains four additional polymerases, and it is a relevant question whether these might also contribute to chromosomal replication and its fidelity. Here, we have investigated the role of DNA polymerase II (Pol II) (polB gene product). Mismatch repair-defective strains containing the polBex1 allele--encoding a polymerase-proficient but exonucleolytically defective Pol II--displayed a mutator activity for four different chromosomal lac mutational markers. The mutator effect was dependent on the chromosomal orientation of the lacZ gene. The results indicate that Pol II plays a role in chromosomal replication and that its role is not equal in leading- versus lagging-strand replication. In particular, the role of Pol II appeared larger in the lagging strand. When combined with dnaQ or dnaE mutator alleles, polBex1 showed strong, near multiplicative effects. The results fit a model in which Pol II acts as proofreader for HE-produced misinsertion errors. A second role of Pol II is to protect mismatched 3' termini against the mutagenic action of polymerase IV (dinB product). Overall, Pol II may be considered a main player in the polymerase trafficking at the replication fork.
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Affiliation(s)
- Magdalena Banach-Orlowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, Warsaw, Poland
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33
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Tsurimoto T, Shinozaki A, Yano M, Seki M, Enomoto T. Human Werner helicase interacting protein 1 (WRNIP1) functions as a novel modulator for DNA polymerase delta. Genes Cells 2005; 10:13-22. [PMID: 15670210 DOI: 10.1111/j.1365-2443.2004.00812.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Human WRNIP1, a Werner DNA helicase interacting protein 1, was expressed in insect cells and E. coli. The purified protein behaved as a homo-oligomeric complex with a native molecular mass indicative of an octamer, and the complex copurified with an ATPase activity that was stimulated by double-stranded DNA ends. As suggested by genetic studies of budding yeast WRNIP1/Mgs1, the purified human WRNIP1 complex interacted physically with human DNA polymerase delta (pol delta), stimulating its DNA synthesis activity more than fivefold in the presence or absence of proliferating cell nuclear antigen. Analysis of reaction products demonstrated the stimulation to be partly due to an increased processivity of pol delta but more importantly to an increase in its initiation frequency. Addition of ATP to reactions partially suppressed stimulation by WRNIP1. Furthermore, a mutant WRNIP1 lacking ATPase activity could stimulate pol delta normally but was insensitive to suppression by ATP. These results indicate that WRNIP1 functions as a modulator for initiation or restart events during pol delta-mediated DNA synthesis and that its ATPase activity is utilized to sense DNA ends and to regulate the extent of stimulation.
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Affiliation(s)
- Toshiki Tsurimoto
- Department of Biology, School of Sciences, Kyushu University, Fukuoka 812-8581, Japan.
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34
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Abstract
Replication of genomic DNA is a universal process that proceeds in distinct stages, from initiation to elongation and finally to termination. Each stage involves multiple stable or transient interactions between protein subunits with functions that are more or less conserved in all organisms. In Escherichia coli, initiation of bidirectional replication at the origin (oriC) occurs through the concerted actions of the DnaA replication initiator protein, the hexameric DnaB helicase, the DnaC?helicase loading partner and the DnaG primase, leading to establishment of two replication forks. Elongation of RNA primers at each fork proceeds simultaneously on both strands by actions of the multimeric replicase, DNA polymerase III holoenzyme. The fork that arrives first in the terminus region is halted by its encounter with a correctly-oriented complex of the Tus replication terminator protein bound at one of several Ter sites, where it is trapped until the other fork arrives. We summarize current understanding of interactions among the various proteins that act in the different stages of replication of the chromosome of E. coli, and make some comparisons with the analogous proteins in Bacillus subtilis and the coliphages T4 and T7.
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Affiliation(s)
- Patrick M Schaeffer
- Research School of Chemistry, Australian National University, Canberra, Australia
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35
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Chaperon DN. A method for the construction of in frame substitutions in operons: deletion of the essential Escherichia coli holB gene coding for a subunit of the DNA polymerase III holoenzyme. J Microbiol Methods 2005; 65:127-34. [PMID: 16083981 DOI: 10.1016/j.mimet.2005.06.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2005] [Revised: 06/29/2005] [Accepted: 06/29/2005] [Indexed: 11/22/2022]
Abstract
To investigate the putative five-gene operon at 24.9 min on the Escherichia coli genome, which comprises the genes pabC, yceG, tmk, holB and ycfH, a method for the construction of an in frame deletion strain of the essential E. coli holB gene was developed. HolB, also referred to as delta prime or delta', is a subunit of the DNA polymerase III (Pol III) holoenzyme. The holB gene was replaced by the kanamycin resistance gene kka1, coding for amino glycoside 3'-phosphotransferase kanamycin kinase. The kanamycin resistance gene was expressed under the control of the promoter(s) of the putative five-gene operon. The holB gene is essential for bacterial growth and the deletion of holB exhibits no polar effects on the adjacent genes tmk or ycfH in terms of cell viability. The method of the holB null construction presented in this work allows for a simplified studying of interactions between the different subunits of DNA polymerase III.
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Affiliation(s)
- David-Nicolas Chaperon
- Département de Biochimie Médicale, Centre Médical Universitaire, 1, rue Michel-Servet, CH-1211 Genève-4, Switzerland
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36
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Skibbens RV. Unzipped and loaded: the role of DNA helicases and RFC clamp-loading complexes in sister chromatid cohesion. J Cell Biol 2005; 169:841-6. [PMID: 15955849 PMCID: PMC2171654 DOI: 10.1083/jcb.200503129] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2005] [Accepted: 05/13/2005] [Indexed: 11/22/2022] Open
Abstract
It is well known that the products of chromosome replication are paired to ensure that the sisters segregate away from each other during mitosis. A key issue is how cells pair sister chromatids but preclude the catastrophic pairing of nonsister chromatids. The identification of both replication factor C and DNA helicases as critical for sister chromatid pairing has brought new insights into this fundamental process.
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Affiliation(s)
- Robert V Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA.
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37
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Saito M, Oyama T, Shirai T. Detection of subunit interfacial modifications by tracing the evolution of clamp–loader complex. Protein Eng Des Sel 2005; 18:139-45. [PMID: 15820979 DOI: 10.1093/protein/gzi016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The archaeal and eukaryal clamp-loader and clamp proteins were investigated with the evolutionary trace method. The molecular phylogeny of the proteins suggested that the hetero-pentameric complex of the archaeal clamp-loader with two subunits (RFCL and RFCS) was not a preserved ancestral type, but a degenerated version of the eukaryal complex of five subunits (RFC1-5). The evolutionary trace of amino acid replacements during the course of subunit differentiation revealed that the replacements had accumulated preferentially at the subunit interface regions. Some of the interfacial modifications that might be responsible for the specific interaction between the subunits were conserved in the current complex.
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Affiliation(s)
- Mihoko Saito
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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38
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Goedken ER, Kazmirski SL, Bowman GD, O'Donnell M, Kuriyan J. Mapping the interaction of DNA with the Escherichia coli DNA polymerase clamp loader complex. Nat Struct Mol Biol 2005; 12:183-90. [PMID: 15665871 DOI: 10.1038/nsmb889] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2004] [Accepted: 11/27/2004] [Indexed: 11/09/2022]
Abstract
Sliding clamps are loaded onto DNA by ATP-dependent clamp loader complexes. A recent crystal structure of a clamp loader-clamp complex suggested an unexpected mechanism for DNA recognition, in which the ATPase subunits of the loader spiral around primed DNA. We report the results of fluorescence-based assays that probe the mechanism of the Escherichia coli clamp loader and show that conserved residues clustered within the inner surface of the modeled clamp loader spiral are critical for DNA recognition, DNA-dependent ATPase activity and clamp release. Duplex DNA with a 5'-overhang single-stranded region (corresponding to correctly primed DNA) stimulates clamp release, as does blunt-ended duplex DNA, whereas duplex DNA with a 3' overhang and single-stranded DNA are ineffective. These results provide evidence for the recognition of DNA within an inner chamber formed by the spiral organization of the ATPase domains of the clamp loader.
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Affiliation(s)
- Eric R Goedken
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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39
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Bruck I, Georgescu RE, O'Donnell M. Conserved interactions in the Staphylococcus aureus DNA PolC chromosome replication machine. J Biol Chem 2005; 280:18152-62. [PMID: 15647255 DOI: 10.1074/jbc.m413595200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The PolC holoenzyme replicase of the Gram-positive Staphylococcus aureus pathogen has been reconstituted from pure subunits. We compared individual S. aureus replicase subunits with subunits from the Gram-negative Escherichia coli polymerase III holoenzyme for activity and interchangeability. The central organizing subunit, tau, is smaller than its Gram-negative homolog, yet retains the ability to bind single-stranded DNA and contains DNA-stimulated ATPase activity comparable with E. coli tau. S. aureus tau also stimulates PolC, although they do not form as stabile a complex as E. coli polymerase III.tau. We demonstrate that the extreme C-terminal residues of PolC bind to and function with beta clamps from different bacteria. Hence, this polymerase-clamp interaction is highly conserved. Additionally, the S. aureus delta wrench of the clamp loader binds to E. coli beta. The S. aureus clamp loader is even capable of loading E. coli and Streptococcus pyogenes beta clamps onto DNA. Interestingly, S. aureus PolC lacks functionality with heterologous beta clamps when they are loaded onto DNA by the S. aureus clamp loader, suggesting that the S. aureus clamp loader may have difficulty ejecting from heterologous clamps. Nevertheless, these overall findings underscore the conservation in structure and function of Gram-positive and Gram-negative replicases despite >1 billion years of evolutionary distance between them.
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Affiliation(s)
- Irina Bruck
- Howard Hughes Medical Institute and Rockefeller University, New York, New York 10021, USA
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40
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Su'etsugu M, Shimuta TR, Ishida T, Kawakami H, Katayama T. Protein associations in DnaA-ATP hydrolysis mediated by the Hda-replicase clamp complex. J Biol Chem 2004; 280:6528-36. [PMID: 15611053 DOI: 10.1074/jbc.m412060200] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Escherichia coli, the activity of ATP-bound DnaA protein in initiating chromosomal replication is negatively controlled in a replication-coordinated manner. The RIDA (regulatory inactivation of DnaA) system promotes DnaA-ATP hydrolysis to produce the inactivated form DnaA-ADP in a manner depending on the Hda protein and the DNA-loaded form of the beta-sliding clamp, a subunit of the replicase holoenzyme. A highly functional form of Hda was purified and shown to form a homodimer in solution, and two Hda dimers were found to associate with a single clamp molecule. Purified mutant Hda proteins were used in a staged in vitro RIDA system followed by a pull-down assay to show that Hda-clamp binding is a prerequisite for DnaA-ATP hydrolysis and that binding is mediated by an Hda N-terminal motif. Arg(168) in the AAA(+) Box VII motif of Hda plays a role in stable homodimer formation and in DnaA-ATP hydrolysis, but not in clamp binding. Furthermore, the DnaA N-terminal domain is required for the functional interaction of DnaA with the Hda-clamp complex. Single cells contain approximately 50 Hda dimers, consistent with the results of in vitro experiments. These findings and the features of AAA(+) proteins, including DnaA, suggest the following model. DnaA-ATP is hydrolyzed at a binding interface between the AAA(+) domains of DnaA and Hda; the DnaA N-terminal domain supports this interaction; and the interaction of DnaA-ATP with the Hda-clamp complex occurs in a catalytic mode.
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Affiliation(s)
- Masayuki Su'etsugu
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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41
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Miyata T, Oyama T, Mayanagi K, Ishino S, Ishino Y, Morikawa K. The clamp-loading complex for processive DNA replication. Nat Struct Mol Biol 2004; 11:632-6. [PMID: 15208692 DOI: 10.1038/nsmb788] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 05/04/2004] [Indexed: 11/09/2022]
Abstract
DNA polymerase requires two processing factors, sliding clamps and clamp loaders, to direct rapid and accurate duplication of genomic DNA. In eukaryotes, proliferating cell nuclear antigen (PCNA), the ring-shaped sliding clamp, encircles double-stranded DNA within its central hole and tethers the DNA polymerases onto DNA. Replication factor C (RFC) acts as the clamp loader, which correctly installs the sliding clamp onto DNA strands in an ATP-dependent manner. Here we report the three-dimensional structure of an archaeal clamp-loading complex (RFC-PCNA-DNA) determined by single-particle EM. The three-dimensional structure of the complex, reconstituted in vitro using a nonhydrolyzable ATP analog, reveals two components, a closed ring and a horseshoe-shaped element, which correspond to PCNA and RFC, respectively. The atomic structure of PCNA fits well into the closed ring, suggesting that this ternary complex represents a state just after the PCNA ring has closed to encircle the DNA duplex.
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Affiliation(s)
- Tomoko Miyata
- Department of Structural Biology, Biomolecular Engineering Research Institute, Suita, Osaka 565-0874, Japan
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42
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López de Saro F, Georgescu RE, Leu F, O'Donnell M. Protein trafficking on sliding clamps. Philos Trans R Soc Lond B Biol Sci 2004; 359:25-30. [PMID: 15065653 PMCID: PMC1693307 DOI: 10.1098/rstb.2003.1361] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The sliding clamps of chromosomal replicases are acted upon by both the clamp loader and DNA polymerase. Several other proteins and polymerases also interact with the clamp. These proteins bind the clamp at the same spot and use it in sequential fashion. First the clamp loader must bind the clamp in order to load it onto DNA, but directly thereafter the clamp loader must clear away from the clamp so it can be used by the replicative DNA polymerase. At the end of replication, the replicase is ejected from the clamp, which presumably allows the clamp to interact with yet other proteins after its use by the replicase. This paper describes how different proteins in the Escherichia coli replicase, DNA polymerase III holoenzyme, coordinate their traffic flow on the clamp. The mechanism by which traffic flow on the beta clamp is directed is based on competition of the proteins for the clamp, where DNA structure modulates the competition. It seems likely that the principles will generalize to a traffic flow of other factors on these circular clamp proteins.
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43
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Goedken ER, Levitus M, Johnson A, Bustamante C, O'Donnell M, Kuriyan J. Fluorescence measurements on the E.coli DNA polymerase clamp loader: implications for conformational changes during ATP and clamp binding. J Mol Biol 2004; 336:1047-59. [PMID: 15037068 DOI: 10.1016/j.jmb.2003.12.074] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2003] [Revised: 12/19/2003] [Accepted: 12/19/2003] [Indexed: 10/26/2022]
Abstract
Sliding clamps are ring-shaped proteins that tether DNA polymerases to their templates during processive DNA replication. The action of ATP-dependent clamp loader complexes is required to open the circular clamps and to load them onto DNA. The crystal structure of the pentameric clamp loader complex from Escherichia coli (the gamma complex), determined in the absence of nucleotides, revealed a highly asymmetric and extended form of the clamp loader. Consideration of this structure suggested that a compact and more symmetrical inactive form may predominate in solution in the absence of crystal packing forces. This model has the N-terminal domains of the delta and delta' subunits of the clamp loader close to each other in the inactive state, with the clamp loader opening in a crab-claw-like fashion upon ATP-binding. We have used fluorescence resonance energy transfer (FRET) to investigate the structural changes in the E.coli clamp loader complex that result from ATP-binding and interactions between the clamp loader and the beta clamp. FRET measurements using fluorophores placed in the N-terminal domains of the delta and delta' subunits indicate that the distances between these subunits in solution are consistent with the previously crystallized extended form of the clamp loader. Furthermore, the addition of nucleotide and clamp to the labeled clamp loader does not appreciably alter these FRET distances. Our results suggest that the changes that occur in the relative positioning of the delta and delta' subunits when ATP binds to and activates the complex are subtle, and that crab-claw-like movements are not a significant component of the clamp loader mechanism.
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Affiliation(s)
- Eric R Goedken
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
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44
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Shiomi Y, Shinozaki A, Sugimoto K, Usukura J, Obuse C, Tsurimoto T. The reconstituted human Chl12-RFC complex functions as a second PCNA loader. Genes Cells 2004; 9:279-90. [PMID: 15066120 DOI: 10.1111/j.1356-9597.2004.00724.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sister chromatid cohesion factor Chl12 shares amino acid sequence similarity with RFC1, the largest subunit of replication factor C (RFC), and forms a clamp loader complex in association with the RFC small subunits RFCs2-5. It has been shown that the human Chl12-RFC complex, reconstituted with a baculovirus expression system, specifically interacts with human proliferating cell nuclear antigen (PCNA). The purified Chl12-RFC complex is structurally indistinguishable from RFC, as shown by electron microscopy, and it exhibits DNA-stimulated ATPase activity that is further enhanced by PCNA, and by DNA binding activity on specific primer/template DNA structures. Furthermore, the complex loads PCNA onto a circular DNA substrate, and stimulates DNA polymerase delta DNA synthesis on a primed M13 single-stranded template in the presence of purified replication proteins. However, it cannot substitute for RFC in promoting simian virus 40 DNA replication in vitro with crude fractions. These results demonstrate that the human Chl12-RFC complex is a second PCNA loader and that its roles in replication are clearly distinguishable from those of RFC.
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Affiliation(s)
- Yasushi Shiomi
- Department of Biology, School of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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45
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McInerney P, O'Donnell M. Functional uncoupling of twin polymerases: mechanism of polymerase dissociation from a lagging-strand block. J Biol Chem 2004; 279:21543-51. [PMID: 15014081 DOI: 10.1074/jbc.m401649200] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Replication forks are constantly subjected to events that lead to fork stalling, stopping, or collapse. Using a synthetic rolling circle DNA substrate, we demonstrate that a block to the lagging-strand polymerase does not compromise helicase or leading-strand polymerase activity. In fact, lagging-strand synthesis also continues. Thus, the blocked lagging-strand enzyme quickly dissociates from the block site and resumes synthesis on new primed sites. Furthermore, studies in which the lagging polymerase is continuously blocked show that the leading polymerase continues unabated even as it remains attached to the lagging-strand enzyme. Hence, upon encounter of a block to the lagging stand, the polymerases functionally uncouple yet remain physically associated. Further study reveals that naked single-stranded DNA results in disruption of a stalled polymerase from its beta-DNA substrate. Thus, as the replisome advances, the single-stranded DNA loop that accumulates on the lagging-strand template releases the stalled lagging-strand polymerase from beta after SSB protein is depleted. The lagging-strand polymerase is then free to continue Okazaki fragment production.
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Affiliation(s)
- Peter McInerney
- Laboratory of DNA Replication, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021, USA
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46
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Abstract
Cells have high-fidelity polymerases whose task is to accurately replicate the genome, and low-fidelity polymerases with specialized functions. Although some of these low-fidelity polymerases are exceptional in their ability to replicate damaged DNA and restore the undamaged sequence, they are error prone on undamaged DNA. In fact, these error-prone polymerases are sometimes used in circumstances where the capacity to make errors has a selective advantage. The mutagenic potential of the error-prone polymerases requires that their expression, activity, and access to undamaged DNA templates be regulated. Here we review these specialized polymerases with an emphasis on their biological roles.
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Affiliation(s)
- Alison J Rattray
- Gene Regulation and Chromosome Biology Laboratory, NCI-Frederick, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA.
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47
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Abstract
Genome sequences of a number of archaea have revealed an apparent paradox in the phylogenies of the bacteria, archaea, and eukarya, as well as an intriguing set of problems to be resolved in the study of DNA replication. The archaea, long thought to be bacteria, are not only different enough to merit their own domain but also appear to be an interesting mosaic of bacterial, eukaryal, and unique features. Most archaeal proteins participating in DNA replication are more similar in sequence to those found in eukarya than to analogous replication proteins in bacteria. However, archaea have only a subset of the eukaryal replication machinery, apparently needing fewer polypeptides and structurally simpler complexes. The archaeal replication apparatus also contains features not found in other organisms owing, in part, to the broad range of environmental conditions, some extreme, in which members of this domain thrive. In this review the current knowledge of the mechanisms governing DNA replication in archaea is summarized and the similarities and differences of those of bacteria and eukarya are highlighted.
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Affiliation(s)
- Beatrice Grabowski
- University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA.
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48
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López de Saro FJ, Georgescu RE, Goodman MF, O'Donnell M. Competitive processivity-clamp usage by DNA polymerases during DNA replication and repair. EMBO J 2004; 22:6408-18. [PMID: 14633999 PMCID: PMC291844 DOI: 10.1093/emboj/cdg603] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Protein clamps are ubiquitous and essential components of DNA metabolic machineries, where they serve as mobile platforms that interact with a large variety of proteins. In this report we identify residues that are required for binding of the beta-clamp to DNA polymerase III of Escherichia coli, a polymerase of the Pol C family. We show that the alpha polymerase subunit of DNA polymerase III interacts with the beta-clamp via its extreme seven C-terminal residues, some of which are conserved. Moreover, interaction of Pol III with the clamp takes place at the same site as that of the delta-subunit of the clamp loader, providing the basis for a switch between the clamp loading machinery and the polymerase itself. Escherichia coli DNA polymerases I, II, IV and V (UmuC) interact with beta at the same site. Given the limited amounts of clamps in the cell, these results suggest that clamp binding may be competitive and regulated, and that the different polymerases may use the same clamp sequentially during replication and repair.
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Affiliation(s)
- Francisco J López de Saro
- Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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49
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Abstract
In this essay, we consider helicases, defined as enzymes that use the free energies of binding and hydrolysis of ATP to drive the unwinding of double-stranded nucleic acids, and ask how they function within, and are "coupled" to, the macromolecular machines of gene expression. To illustrate the principles of the integration of helicases into such machines, we consider the macromolecular complexes that direct and control DNA replication and DNA-dependent RNA transcription, and use these systems to illustrate how machines centered around coupled polymerase-helicase systems can be regulated by small changes in the interactions of their functional components.
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Affiliation(s)
- Peter H von Hippel
- Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene 97403, USA.
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50
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Kaufmann G, Nethanel T. Did an early version of the eukaryal replisome enable the emergence of chromatin? PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2004; 77:173-209. [PMID: 15196893 DOI: 10.1016/s0079-6603(04)77005-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Gabriel Kaufmann
- Biochemistry Department, Tel Aviv University, Ramat Aviv 69978, Israel
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