1
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Truchon AR, Chase EE, Stark AR, Wilhelm SW. The diel disconnect between cell growth and division in Aureococcus is interrupted by giant virus infection. Front Microbiol 2024; 15:1426193. [PMID: 39234538 PMCID: PMC11371579 DOI: 10.3389/fmicb.2024.1426193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/05/2024] [Indexed: 09/06/2024] Open
Abstract
Viruses of eukaryotic algae have become an important research focus due to their role(s) in nutrient cycling and top-down control of algal blooms. Omics-based studies have identified a boon of genomic and transcriptional potential among the Nucleocytoviricota, a phylum of large dsDNA viruses which have been shown to infect algal and non-algal eukaryotes. However, little is still understood regarding the infection cycle of these viruses, particularly in how they take over a metabolically active host and convert it into a virocell state. Of particular interest are the roles light and the diel cycle in virocell development. Yet despite such a large proportion of Nucleocytoviricota infecting phototrophs, little work has been done to tie infection dynamics to the presence, and absence, of light. Here, we examine the role of the diel cycle on the physiological and transcriptional state of the pelagophyte Aureococcus anophagefferens while undergoing infection by Kratosvirus quantuckense strain AaV. Our observations demonstrate how infection by the virus interrupts the diel growth and division of this cell strain, and that infection further complicates the system by enhancing export of cell biomass.
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Affiliation(s)
- Alexander R Truchon
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | - Emily E Chase
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | - Ashton R Stark
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
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2
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De March M. Crystal structure of the 3'→5' exonuclease from Methanocaldococcus jannaschii. Biochem Biophys Res Commun 2024; 712-713:149893. [PMID: 38657529 DOI: 10.1016/j.bbrc.2024.149893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024]
Abstract
RecJ exonucleases are members of the DHH phosphodiesterase family ancestors of eukaryotic Cdc45, the key component of the CMG (Cdc45-MCM-GINS) complex at the replication fork. They are involved in DNA replication and repair, RNA maturation and Okazaki fragment degradation. Bacterial RecJs resect 5'-end ssDNA. Conversely, archaeal RecJs are more versatile being able to hydrolyse in both directions and acting on ssDNA as well as on RNA. In Methanocaldococcus jannaschii two RecJs were previously characterized: RecJ1 is a 5'→3' DNA exonuclease, MjaRecJ2 works only on 3'-end DNA/RNA with a preference for RNA. Here, I present the crystal structure of MjaRecJ2, solved at a resolution of 2.8 Å, compare it with the other RecJ structures, in particular the 5'→3' TkoGAN and the bidirectional PfuRecJ, and discuss its characteristics in light of the more recent knowledge on RecJs. This work adds new structural data that might improve the knowledge of these class of proteins.
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Affiliation(s)
- Matteo De March
- Structural Biology Laboratory, Elettra Sincrotrone Trieste S.c.p.A., 34149, Trieste, Italy; Department of Environmental and Biological Sciences, University of Nova Gorica, SI-5000, Nova Gorica, Slovenia.
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3
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Wang WW, Yi GS, Zhou H, Zhao YX, Wang QS, He JH, Yu F, Xiao X, Liu XP. The structure of the archaeal nuclease RecJ2 implicates its catalytic mechanism and inability to interact with GINS. J Biol Chem 2024; 300:107379. [PMID: 38762184 PMCID: PMC11193018 DOI: 10.1016/j.jbc.2024.107379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/20/2024] Open
Abstract
Bacterial RecJ exhibits 5'→3' exonuclease activity that is specific to ssDNA; however, archaeal RecJs show 5' or 3' exonuclease activity. The hyperthermophilic archaea Methanocaldococcus jannaschii encodes the 5'-exonuclease MjRecJ1 and the 3'-exonuclease MjRecJ2. In addition to nuclease activity, archaeal RecJ interacts with GINS, a structural subcomplex of the replicative DNA helicase complex. However, MjRecJ1 and MjRecJ2 do not interact with MjGINS. Here, we report the structural basis for the inability of the MjRecJ2 homologous dimer to interact with MjGINS and its efficient 3' hydrolysis polarity for short dinucleotides. Based on the crystal structure of MjRecJ2, we propose that the interaction surface of the MjRecJ2 dimer overlaps the potential interaction surface for MjGINS and blocks the formation of the MjRecJ2-GINS complex. Exposing the interaction surface of the MjRecJ2 dimer restores its interaction with MjGINS. The cocrystal structures of MjRecJ2 with substrate dideoxynucleotides or product dCMP/CMP show that MjRecJ2 has a short substrate binding patch, which is perpendicular to the longer patch of bacterial RecJ. Our results provide new insights into the function and diversification of archaeal RecJ/Cdc45 proteins.
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Affiliation(s)
- Wei-Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Gang-Shun Yi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Huan Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Xuan Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Sanya, China
| | - Qi-Sheng Wang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Hua He
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China; The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Feng Yu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Sanya, China; Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Xi-Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Sanya, China; Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.
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4
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Radhakrishnan A, Sharma C, Malviya VN, Srivastav R. Deciphering the molecular functionality of Cdc45 in replisomal complex. Biochem Biophys Rep 2024; 37:101643. [PMID: 38298211 PMCID: PMC10828582 DOI: 10.1016/j.bbrep.2024.101643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
The members of DHH superfamily have been reported with diverse substrate spectrum and play pivotal roles in replication, repair, and RNA metabolism. This family comprises phosphatases, phosphoesterase and bifunctional enzymes having nanoRNase and phosphatase activities. Cell cycle factor Cdc45, a member of this superfamily, is crucial for movement of the replication fork during DNA replication and an important component of the replisome. The specific protein-protein interactions of Cdc45 with other factors along with helicase moderate the faithful DNA replication process. However, the exact biochemical functions of this factor are still unknown and need further investigation. Here, we studied the biochemical roles of Cdc45 and its molecular interactions within the replisomal complex. The alteration in the level of protein, observed when DNA damage is induced in-vivo, suggests its association with DNA replication stress. We analyzed protein Cdc45, providing new insights about the molecular and biochemical functionality of this replisomal factor.
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Affiliation(s)
| | - Chandresh Sharma
- Translational Health Science and Technology Institute, Haryana, India
| | - Viveka Nand Malviya
- Department of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Gottingen, Germany
| | - Rajpal Srivastav
- Amity Institute of Biotechnology, Amity University Uttar Pardesh, Noida, India
- Department of Science & Technology, Ministry of Science & Technology, New Delhi, India
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5
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Schons-Fonseca L, Lazova MD, Smith JL, Anderson ME, Grossman AD. Beneficial and detrimental genes in the cellular response to replication arrest. PLoS Genet 2022; 18:e1010564. [PMID: 36574412 PMCID: PMC9836290 DOI: 10.1371/journal.pgen.1010564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/12/2023] [Accepted: 12/09/2022] [Indexed: 12/28/2022] Open
Abstract
DNA replication is essential for all living organisms. Several events can disrupt replication, including DNA damage (e.g., pyrimidine dimers, crosslinking) and so-called "roadblocks" (e.g., DNA-binding proteins or transcription). Bacteria have several well-characterized mechanisms for repairing damaged DNA and then restoring functional replication forks. However, little is known about the repair of stalled or arrested replication forks in the absence of chemical alterations to DNA. Using a library of random transposon insertions in Bacillus subtilis, we identified 35 genes that affect the ability of cells to survive exposure to an inhibitor that arrests replication elongation, but does not cause chemical alteration of the DNA. Genes identified include those involved in iron-sulfur homeostasis, cell envelope biogenesis, and DNA repair and recombination. In B. subtilis, and many bacteria, two nucleases (AddAB and RecJ) are involved in early steps in repairing replication forks arrested by chemical damage to DNA and loss of either nuclease causes increased sensitivity to DNA damaging agents. These nucleases resect DNA ends, leading to assembly of the recombinase RecA onto the single-stranded DNA. Notably, we found that disruption of recJ increased survival of cells following replication arrest, indicating that in the absence of chemical damage to DNA, RecJ is detrimental to survival. In contrast, and as expected, disruption of addA decreased survival of cells following replication arrest, indicating that AddA promotes survival. The different phenotypes of addA and recJ mutants appeared to be due to differences in assembly of RecA onto DNA. RecJ appeared to promote too much assembly of RecA filaments. Our results indicate that in the absence of chemical damage to DNA, RecA is dispensable for cells to survive replication arrest and that the stable RecA nucleofilaments favored by the RecJ pathway may lead to cell death by preventing proper processing of the arrested replication fork.
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Affiliation(s)
- Luciane Schons-Fonseca
- Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts, United States of America
| | - Milena D. Lazova
- Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts, United States of America
| | - Janet L. Smith
- Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts, United States of America
| | - Mary E. Anderson
- Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts, United States of America
| | - Alan D. Grossman
- Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts, United States of America
- * E-mail:
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6
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Kim WD, Huber RJ. An altered transcriptome underlies cln5-deficiency phenotypes in Dictyostelium discoideum. Front Genet 2022; 13:1045738. [DOI: 10.3389/fgene.2022.1045738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022] Open
Abstract
Mutations in CLN5 cause a subtype of neuronal ceroid lipofuscinosis (NCL) called CLN5 disease. The NCLs, commonly referred to as Batten disease, are a family of neurodegenerative lysosomal storage diseases that affect all ages and ethnicities globally. Previous research showed that CLN5 participates in a variety of cellular processes. However, the precise function of CLN5 in the cell and the pathway(s) regulating its function are not well understood. In the model organism Dictyostelium discoideum, loss of the CLN5 homolog, cln5, impacts various cellular and developmental processes including cell proliferation, cytokinesis, aggregation, cell adhesion, and terminal differentiation. In this study, we used comparative transcriptomics to identify differentially expressed genes underlying cln5-deficiency phenotypes during growth and the early stages of multicellular development. During growth, genes associated with protein ubiquitination/deubiquitination, cell cycle progression, and proteasomal degradation were affected, while genes linked to protein and carbohydrate catabolism were affected during early development. We followed up this analysis by showing that loss of cln5 alters the intracellular and extracellular amounts of proliferation repressors during growth and increases the extracellular amount of conditioned medium factor, which regulates cAMP signalling during the early stages of development. Additionally, cln5- cells displayed increased intracellular and extracellular amounts of discoidin, which is involved in cell-substrate adhesion and migration. Previous work in mammalian models reported altered lysosomal enzyme activity due to mutation or loss of CLN5. Here, we detected altered intracellular activities of various carbohydrate enzymes and cathepsins during cln5- growth and starvation. Notably, cln5- cells displayed reduced β-hexosaminidase activity, which aligns with previous work showing that D. discoideum Cln5 and human CLN5 can cleave the substrate acted upon by β-hexosaminidase. Finally, consistent with the differential expression of genes associated with proteasomal degradation in cln5- cells, we also observed elevated amounts of a proteasome subunit and reduced proteasome 20S activity during cln5- growth and starvation. Overall, this study reveals the impact of cln5-deficiency on gene expression in D. discoideum, provides insight on the genes and proteins that play a role in regulating Cln5-dependent processes, and sheds light on the molecular mechanisms underlying CLN5 disease.
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7
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Zhang L, Lin T, Yin Y, Chen M. Biochemical and functional characterization of a thermostable RecJ exonuclease from Thermococcus gammatolerans. Int J Biol Macromol 2022; 204:617-626. [PMID: 35150781 DOI: 10.1016/j.ijbiomac.2022.02.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 01/18/2023]
Abstract
RecJ is ubiquitous in bacteria and Archaea, and play an important role in DNA replication and repair. Currently, our understanding on biochemical function of archaeal RecJ is incomplete due to the limited reports. The genome of the hyperthermophilic and radioresistant euryarchaeon Thermococcus gammatolerans encodes one putative RecJ protein (Tga-RecJ). Herein, we report biochemical characteristics and catalytic mechanism of Tga-RecJ. Tga-RecJ can degrade ssDNA in the 5'-3' direction at high temperature as observed in Thermococcus kodakarensis RecJ and Pyrococcus furiosus RecJ, the two closest homologs of the enzyme. In contrasted to P. furiosus RecJ, Tga-RecJ lacks 3'-5' ssRNA exonuclease activity. Furthermore, maximum activity of Tga-RecJ is observed at 50 °C ~ 70 °C and pH 7.0-9.0 with Mn2+, and the enzyme is the most thermostable among the reported RecJ proteins. Additionally, the rates for hydrolyzing ssDNA by Tga-RecJ were estimated by kinetic analyses at 50 °C ~ 70 °C, thus revealing its activation energy (10.5 ± 0.6 kcal/mol), which is the first report on energy barrier for ssDNA degradation by RecJ. Mutational studies showed that the mutations of residues D36, D83, D105, H106, H107 and D166 in Tga-RecJ to alanine almost completely abolish its activity, thereby suggesting that these residues are essential for catalysis.
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Affiliation(s)
- Likui Zhang
- Guangling College, Yangzhou University, China; College of Environmental Science and Engineering, Marine Science & Technology Institute, Yangzhou University, China.
| | - Tan Lin
- College of Environmental Science and Engineering, Marine Science & Technology Institute, Yangzhou University, China
| | - Youcheng Yin
- College of Environmental Science and Engineering, Marine Science & Technology Institute, Yangzhou University, China
| | - Min Chen
- College of Environmental Science and Engineering, Marine Science & Technology Institute, Yangzhou University, China.
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8
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Abstract
The faithful and timely copying of DNA by molecular machines known as replisomes depends on a disparate suite of enzymes and scaffolding factors working together in a highly orchestrated manner. Large, dynamic protein-nucleic acid assemblies that selectively morph between distinct conformations and compositional states underpin this critical cellular process. In this article, we discuss recent progress outlining the physical basis of replisome construction and progression in eukaryotes.
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Affiliation(s)
- Ilan Attali
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA;
| | - Michael R Botchan
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA;
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9
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Knapp KM, Fellows B, Aggarwal S, Dalal A, Bicknell LS. A synonymous variant in a non-canonical exon of CDC45 disrupts splicing in two affected sibs with Meier-Gorlin syndrome with craniosynostosis. Eur J Med Genet 2021; 64:104182. [PMID: 33639314 DOI: 10.1016/j.ejmg.2021.104182] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 12/10/2020] [Accepted: 01/23/2021] [Indexed: 11/30/2022]
Abstract
Disruption of the initiation of DNA replication is significantly associated with Meier-Gorlin syndrome (MGORS), an autosomal recessive condition of reduced growth, microtia and patellar a/hypoplasia. Biallelic mutations in CDC45, a member of the pre-initiation complex in DNA replication, cause a spectrum of phenotypes ranging from MGORS with craniosynostosis, through to isolated short stature and craniosynostosis. Here we report two affected sibs with MGORS and craniosynostosis, with biallelic variants in CDC45 identified by 10X Chromium whole genome sequencing. One variant is a frameshift mutation, predicted to be pathogenic, and is inherited in trans with a synonymous variant in a non-canonical exon (exon 7) of CDC45. An in vitro splicing assay showed that while the canonical CDC45 exon 6-exon 8 transcript (with skipping of exon 7; numbering as per NM001178010.2) remained as the predominant transcript, the variant allele induced the use of novel splice acceptor sites in intron 6, all of which produced transcripts harbouring premature stop codons. This perturbation of canonical splicing provides evidence that this synonymous variant is indeed a deleterious alteration in this family. This report adds to the initial patient cohort in which several synonymous variants were also described, further highlighting the contribution of this variant type in CDC45. It also reiterates the true potential pathogenicity of synonymous variants, which is a mutation type that is commonly ignored in variant prioritization strategies.
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Affiliation(s)
- Karen M Knapp
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Bridget Fellows
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India; Department of Medical Genetics, Kasturba Medical College, Manipal, Karnataka, India
| | - Louise S Bicknell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
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10
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Pérez-Arnaiz P, Dattani A, Smith V, Allers T. Haloferax volcanii-a model archaeon for studying DNA replication and repair. Open Biol 2020; 10:200293. [PMID: 33259746 PMCID: PMC7776575 DOI: 10.1098/rsob.200293] [Citation(s) in RCA: 5] [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: 09/11/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022] Open
Abstract
The tree of life shows the relationship between all organisms based on their common ancestry. Until 1977, it comprised two major branches: prokaryotes and eukaryotes. Work by Carl Woese and other microbiologists led to the recategorization of prokaryotes and the proposal of three primary domains: Eukarya, Bacteria and Archaea. Microbiological, genetic and biochemical techniques were then needed to study the third domain of life. Haloferax volcanii, a halophilic species belonging to the phylum Euryarchaeota, has provided many useful tools to study Archaea, including easy culturing methods, genetic manipulation and phenotypic screening. This review will focus on DNA replication and DNA repair pathways in H. volcanii, how this work has advanced our knowledge of archaeal cellular biology, and how it may deepen our understanding of bacterial and eukaryotic processes.
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Affiliation(s)
| | | | | | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
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11
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Feng L, Chang CC, Song D, Jiang C, Song Y, Wang CF, Deng W, Zou YJ, Chen HF, Xiao X, Wang FP, Liu XP. The trimeric Hef-associated nuclease HAN is a 3'→5' exonuclease and is probably involved in DNA repair. Nucleic Acids Res 2019; 46:9027-9043. [PMID: 30102394 PMCID: PMC6158738 DOI: 10.1093/nar/gky707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 08/01/2018] [Indexed: 12/26/2022] Open
Abstract
Nucleases play important roles in nucleic acid metabolism. Some archaea encode a conserved protein known as Hef-associated nuclease (HAN). In addition to its C-terminal DHH nuclease domain, HAN also has three N-terminal domains, including a DnaJ-Zinc-finger, ribosomal protein S1-like, and oligonucleotide/oligosaccharide-binding fold. To further understand HAN’s function, we biochemically characterized the enzymatic properties of HAN from Pyrococcus furiosus (PfuHAN), solved the crystal structure of its DHH nuclease domain, and examined its role in DNA repair. Our results show that PfuHAN is a Mn2+-dependent 3′-exonuclease specific to ssDNA and ssRNA with no activity on blunt and 3′-recessive double-stranded DNA. Domain truncation confirmed that the intrinsic nuclease activity is dependent on the C-terminal DHH nuclease domain. The crystal structure of the DHH nuclease domain adopts a trimeric topology, with each subunit adopting a classical DHH phosphoesterase fold. Yeast two hybrid assay confirmed that the DHH domain interacts with the IDR peptide of Hef nuclease. Knockout of the han gene or its C-terminal DHH nuclease domain in Haloferax volcanii resulted in increased sensitivity to the DNA damage reagent MMS. Our results imply that HAN nuclease might be involved in repairing stalled replication forks in archaea.
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Affiliation(s)
- Lei Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Chen-Chen Chang
- Institute of Precision Medicine,The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine
| | - Dong Song
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Chuang Jiang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Yang Song
- Institute of Precision Medicine,The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine
| | - Chao-Fan Wang
- Institute of Precision Medicine,The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine
| | - Wei Deng
- Institute of Precision Medicine,The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine
| | - Ya-Juan Zou
- Instrumental Analysis Center, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Feng-Ping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Xi-Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
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12
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Li MJ, Yi GS, Yu F, Zhou H, Chen JN, Xu CY, Wang FP, Xiao X, He JH, Liu XP. The crystal structure of Pyrococcus furiosus RecJ implicates it as an ancestor of eukaryotic Cdc45. Nucleic Acids Res 2019; 45:12551-12564. [PMID: 30053256 PMCID: PMC5716160 DOI: 10.1093/nar/gkx887] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/01/2017] [Indexed: 12/27/2022] Open
Abstract
RecJ nucleases specifically degrade single-stranded (ss) DNA in the 5′ to 3′ direction. Archaeal RecJ is different from bacterial RecJ in sequence, domain organization, and substrate specificity. The RecJ from archaea Pyrococcus furiosus (PfuRecJ) also hydrolyzes RNA strands in the 3′ to 5′ direction. Like eukaryotic Cdc45 protein, archaeal RecJ forms a complex with MCM helicase and GINS. Here, we report the crystal structures of PfuRecJ and the complex of PfuRecJ and two CMPs. PfuRecJ bind one or two divalent metal ions in its crystal structure. A channel consisting of several positively charged residues is identified in the complex structure, and might be responsible for binding substrate ssDNA and/or releasing single nucleotide products. The deletion of the complex interaction domain (CID) increases the values of kcat/Km of 5′ exonuclease activity on ssDNA and 3′ exonuclease activity on ssRNA by 5- and 4-fold, respectively, indicating that the CID functions as a regulator of enzymatic activity. The DHH domain of PfuRecJ interacts with the C-terminal beta-sheet domain of the GINS51 subunit in the tetrameric GINS complex. The relationship of archaeal and bacterial RecJs, as well as eukaryotic Cdc45, is discussed based on biochemical and structural results.
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Affiliation(s)
- Min-Jun Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Gang-Shun Yi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
| | - Feng Yu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Huan Zhou
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Jia-Nan Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
| | - Chun-Yan Xu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Feng-Ping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
| | - Jian-Hua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Xi-Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
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13
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Nagata M, Ishino S, Yamagami T, Ishino Y. Replication protein A complex in Thermococcus kodakarensis interacts with DNA polymerases and helps their effective strand synthesis. Biosci Biotechnol Biochem 2019; 83:695-704. [DOI: 10.1080/09168451.2018.1559722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
ABSTRACT
Replication protein A (RPA) is an essential component of DNA metabolic processes. RPA binds to single-stranded DNA (ssDNA) and interacts with multiple DNA-binding proteins. In this study, we showed that two DNA polymerases, PolB and PolD, from the hyperthermophilic archaeon Thermococcus kodakarensis interact directly with RPA in vitro. RPA was expected to play a role in resolving the secondary structure, which may stop the DNA synthesis reaction, in the template ssDNA. Our in vitro DNA synthesis assay showed that the pausing was resolved by RPA for both PolB and PolD. These results supported the fact that RPA interacts with DNA polymerases as a member of the replisome and is involved in the normal progression of DNA replication forks.
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Affiliation(s)
- Mariko Nagata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Yamagami
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
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14
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Rios-Morales RY, Chan SH, Bell SP. Initiation-specific alleles of the Cdc45 helicase-activating protein. PLoS One 2019; 14:e0214426. [PMID: 30913274 PMCID: PMC6435160 DOI: 10.1371/journal.pone.0214426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/12/2019] [Indexed: 11/19/2022] Open
Abstract
The committed step in DNA replication initiation is the activation of the Mcm2-7 replicative DNA helicase. Two activators, Cdc45 and GINS, associate with Mcm2-7 at origins of replication to form the CMG complex, which is the active eukaryotic replicative helicase. These activators function during both replication initiation and elongation, however, it remains unclear whether Cdc45 performs the same function(s) during both events. Here, we describe the genetic and biochemical characterization of seven Cdc45 mutations. Three of these mutations are temperature-sensitive lethal mutations in CDC45. Intriguingly, these mutants are defective for DNA replication initiation but not elongation. Consistent with an initiation defect, all three temperature-sensitive mutants are defective for CMG formation. Two of the lethal mutants are located within the RecJ-like domain of Cdc45 confirming the importance of this region for Cdc45 function. The remaining two lethal mutations localize to an intrinsically disordered region (IDR) of Cdc45 that is found in all eukaryotes. Despite the lethality of these IDR substitution mutants, Cdc45 lacking the IDR retains full function. Together, our data provide insights into the functional importance of Cdc45 domains and suggest that the requirements for Cdc45 function during DNA replication initiation are distinct from those involved in replication elongation.
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Affiliation(s)
- Ramon Y. Rios-Morales
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Sze Ham Chan
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Stephen P. Bell
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- * E-mail:
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15
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The archaeal RecJ-like proteins: nucleases and ex-nucleases with diverse roles in replication and repair. Emerg Top Life Sci 2018; 2:493-501. [PMID: 33525824 DOI: 10.1042/etls20180017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/16/2018] [Accepted: 08/23/2018] [Indexed: 11/17/2022]
Abstract
RecJ proteins belong to the DHH superfamily of phosphoesterases that has members in all three domains of life. In bacteria, the archetypal RecJ is a 5' → 3' ssDNA exonuclease that functions in homologous recombination, base excision repair and mismatch repair, while in eukaryotes, the RecJ-like protein Cdc45 (which has lost its nuclease activity) is a key component of the CMG (Cdc45-MCM-GINS) complex, the replicative DNA helicase that unwinds double-stranded DNA at the replication fork. In archaea, database searching identifies genes encoding one or more RecJ family proteins in almost all sequenced genomes. Biochemical analysis has confirmed that some but not all of these proteins are components of archaeal CMG complexes and has revealed a surprising diversity in mode of action and substrate preference. In addition to this, some archaea encode catalytically inactive RecJ-like proteins, and others a mix of active and inactive proteins, with the inactive proteins being confined to structural roles only. Here, I summarise current knowledge of the structure and function of the archaeal RecJ-like proteins, focusing on similarities and differences between proteins from different archaeal species, between proteins within species and between the archaeal proteins and their bacterial and eukaryotic relatives. Models for RecJ-like function are described and key areas for further study highlighted.
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16
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Goswami P, Abid Ali F, Douglas ME, Locke J, Purkiss A, Janska A, Eickhoff P, Early A, Nans A, Cheung AMC, Diffley JFX, Costa A. Structure of DNA-CMG-Pol epsilon elucidates the roles of the non-catalytic polymerase modules in the eukaryotic replisome. Nat Commun 2018; 9:5061. [PMID: 30498216 PMCID: PMC6265327 DOI: 10.1038/s41467-018-07417-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/28/2018] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic origin firing depends on assembly of the Cdc45-MCM-GINS (CMG) helicase. A key step is the recruitment of GINS that requires the leading-strand polymerase Pol epsilon, composed of Pol2, Dpb2, Dpb3, Dpb4. While a truncation of the catalytic N-terminal Pol2 supports cell division, Dpb2 and C-terminal Pol2 (C-Pol2) are essential for viability. Dpb2 and C-Pol2 are non-catalytic modules, shown or predicted to be related to an exonuclease and DNA polymerase, respectively. Here, we present the cryo-EM structure of the isolated C-Pol2/Dpb2 heterodimer, revealing that C-Pol2 contains a DNA polymerase fold. We also present the structure of CMG/C-Pol2/Dpb2 on a DNA fork, and find that polymerase binding changes both the helicase structure and fork-junction engagement. Inter-subunit contacts that keep the helicase-polymerase complex together explain several cellular phenotypes. At least some of these contacts are preserved during Pol epsilon-dependent CMG assembly on path to origin firing, as observed with DNA replication reconstituted in vitro. Eukaryotic origin firing depends on assembly of the Cdc45-MCM-GINS (CMG) helicase, which requires the leading-strand polymerase Pol ɛ. Here the authors present a structural analysis of a CMG Pol ɛ on a DNA fork, providing insight on the steps leading productive helicase engagement to the DNA junction.
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Affiliation(s)
- Panchali Goswami
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ferdos Abid Ali
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Max E Douglas
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Julia Locke
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Andrew Purkiss
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Agnieszka Janska
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Patrik Eickhoff
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Anne Early
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alan M C Cheung
- Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology, University College London, London, UK.,Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
| | - John F X Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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17
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Possible function of the second RecJ-like protein in stalled replication fork repair by interacting with Hef. Sci Rep 2017; 7:16949. [PMID: 29209094 PMCID: PMC5717133 DOI: 10.1038/s41598-017-17306-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/20/2017] [Indexed: 01/03/2023] Open
Abstract
RecJ was originally identified in Escherichia coli and plays an important role in the DNA repair and recombination pathways. Thermococcus kodakarensis, a hyperthermophilic archaeon, has two RecJ-like nucleases. These proteins are designated as GAN (GINS-associated nuclease) and HAN (Hef-associated nuclease), based on the protein they interact with. GAN is probably a counterpart of Cdc45 in the eukaryotic CMG replicative helicase complex. HAN is considered mainly to function with Hef for restoration of the stalled replication fork. In this study, we characterized HAN to clarify its functions in Thermococcus cells. HAN showed single-strand specific 3′ to 5′ exonuclease activity, which was stimulated in the presence of Hef. A gene disruption analysis revealed that HAN was non-essential for viability, but the ΔganΔhan double mutant did not grow under optimal conditions at 85 °C. This deficiency was not fully recovered by introducing the mutant han gene, encoding the nuclease-deficient HAN protein, back into the genome. These results suggest that the unstable replicative helicase complex without GAN performs ineffective fork progression, and thus the stalled fork repair system including HAN becomes more important. The nuclease activity of HAN is required for the function of this protein in T. kodakarensis.
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18
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Nagata M, Ishino S, Yamagami T, Ogino H, Simons JR, Kanai T, Atomi H, Ishino Y. The Cdc45/RecJ-like protein forms a complex with GINS and MCM, and is important for DNA replication in Thermococcus kodakarensis. Nucleic Acids Res 2017; 45:10693-10705. [PMID: 28977567 PMCID: PMC5737688 DOI: 10.1093/nar/gkx740] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/12/2017] [Indexed: 01/18/2023] Open
Abstract
The archaeal minichromosome maintenance (MCM) has DNA helicase activity, which is stimulated by GINS in several archaea. In the eukaryotic replicative helicase complex, Cdc45 forms a complex with MCM and GINS, named as CMG (Cdc45-MCM-GINS). Cdc45 shares sequence similarity with bacterial RecJ. A Cdc45/RecJ-like protein from Thermococcus kodakarensis shows a bacterial RecJ-like exonuclease activity, which is stimulated by GINS in vitro. Therefore, this archaeal Cdc45/RecJ is designated as GAN, from GINS-associated nuclease. In this study, we identified the CMG-like complex in T. kodakarensis cells. The GAN·GINS complex stimulated the MCM helicase, but MCM did not affect the nuclease activity of GAN in vitro. The gene disruption analysis showed that GAN was non-essential for its viability but the Δgan mutant did not grow at 93°C. Furthermore, the Δgan mutant showed a clear retardation in growth as compared with the parent cells under optimal conditions at 85°C. These deficiencies were recovered by introducing the gan gene encoding the nuclease deficient GAN protein back to the genome. These results suggest that the replicative helicase complex without GAN may become unstable and ineffective in replication fork progression. The nuclease activity of GAN is not related to the growth defects of the Δgan mutant cells.
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Affiliation(s)
- Mariko Nagata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Fukuoka 812-8581, Japan
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Fukuoka 812-8581, Japan
| | - Takeshi Yamagami
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Fukuoka 812-8581, Japan
| | - Hiromi Ogino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Fukuoka 812-8581, Japan
| | - Jan-Robert Simons
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Kyoto 615-8510, Japan
| | - Tamotsu Kanai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Kyoto 615-8510, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Kyoto 615-8510, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Fukuoka 812-8581, Japan
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19
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Two Archaeal RecJ Nucleases from Methanocaldococcus jannaschii Show Reverse Hydrolysis Polarity: Implication to Their Unique Function in Archaea. Genes (Basel) 2017; 8:genes8090211. [PMID: 28837073 PMCID: PMC5615345 DOI: 10.3390/genes8090211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 12/05/2022] Open
Abstract
Bacterial nuclease RecJ, which exists in almost all bacterial species, specifically degrades single-stranded (ss) DNA in the 5′ to 3′ direction. Some archaeal phyla, except Crenarchaea, also encode RecJ homologs. Compared with bacterial RecJ, archaeal RecJ exhibits a largely different amino acid sequence and domain organization. Archaeal RecJs from Thermococcus kodakarensis and Pyrococcus furiosus show 5′→3′ exonuclease activity on ssDNA. Interestingly, more than one RecJ exists in some Euryarchaeota classes, such as Methanomicrobia, Methanococci, Methanomicrobia, Methanobacteria, and Archaeoglobi. Here we report the biochemical characterization of two RecJs from Methanocaldococcus jannaschii, the long RecJ1 (MJ0977) and short RecJ2 (MJ0831) to understand their enzymatic properties. RecJ1 is a 5′→3′ exonuclease with a preference to ssDNA; however, RecJ2 is a 3′→5′ exonuclease with a preference to ssRNA. The 5′ terminal phosphate promotes RecJ1 activity, but the 3′ terminal phosphate inhibits RecJ2 nuclease. Go-Ichi-Ni-San (GINS) complex does not interact with two RecJs and does not promote their nuclease activities. Finally, we discuss the diversity, function, and molecular evolution of RecJ in archaeal taxonomy. Our analyses provide insight into the function and evolution of conserved archaeal RecJ/eukaryotic Cdc45 protein.
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20
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Szambowska A, Tessmer I, Prus P, Schlott B, Pospiech H, Grosse F. Cdc45-induced loading of human RPA onto single-stranded DNA. Nucleic Acids Res 2017; 45:3217-3230. [PMID: 28100698 PMCID: PMC5389570 DOI: 10.1093/nar/gkw1364] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 01/02/2017] [Indexed: 11/14/2022] Open
Abstract
Cell division cycle protein 45 (Cdc45) is an essential component of the eukaryotic replicative DNA helicase. We found that human Cdc45 forms a complex with the single-stranded DNA (ssDNA) binding protein RPA. Moreover, it actively loads RPA onto nascent ssDNA. Pull-down assays and surface plasmon resonance studies revealed that Cdc45-bound RPA complexed with ssDNA in the 8–10 nucleotide binding mode, but dissociated when RPA covered a 30-mer. Real-time analysis of RPA-ssDNA binding demonstrated that Cdc45 catalytically loaded RPA onto ssDNA. This placement reaction required physical contacts of Cdc45 with the RPA70A subdomain. Our results imply that Cdc45 controlled stabilization of the 8-nt RPA binding mode, the subsequent RPA transition into 30-mer mode and facilitated an ordered binding to ssDNA. We propose that a Cdc45-mediated loading guarantees a seamless deposition of RPA on newly emerging ssDNA at the nascent replication fork.
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Affiliation(s)
- Anna Szambowska
- Research Group Biochemistry, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef Schneider Strasse 2, D-97080 Würzburg, Germany
| | - Piotr Prus
- Biocenter Oulu, P.O. Box 5000, 90014 University of Oulu, Finland
| | - Bernhard Schlott
- Research Group Biochemistry, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany.,Proteomics Core Facility, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Helmut Pospiech
- Research Group Biochemistry, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany.,Faculty of Biochemistry and Molecular Medicine, P.O. Box 5000, 90014 University of Oulu, Finland
| | - Frank Grosse
- Research Group Biochemistry, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany.,Center for Molecular Biomedicine, Friedrich-Schiller University, Biochemistry Department, Jena, Germany
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21
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Eukaryotic Replicative Helicase Subunit Interaction with DNA and Its Role in DNA Replication. Genes (Basel) 2017; 8:genes8040117. [PMID: 28383499 PMCID: PMC5406864 DOI: 10.3390/genes8040117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/23/2017] [Accepted: 03/31/2017] [Indexed: 01/30/2023] Open
Abstract
The replicative helicase unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. In eukaryotes, the replicative helicase is composed of the Cdc45 protein, the heterohexameric ring-shaped Mcm2-7 complex, and the tetrameric GINS complex (CMG). The CMG proteins bind directly to DNA, as demonstrated by experiments with purified proteins. The mechanism and function of these DNA-protein interactions are presently being investigated, and a number of important discoveries relating to how the helicase proteins interact with DNA have been reported recently. While some of the protein-DNA interactions directly relate to the unwinding function of the enzyme complex, other protein-DNA interactions may be important for minichromosome maintenance (MCM) loading, origin melting or replication stress. This review describes our current understanding of how the eukaryotic replicative helicase subunits interact with DNA structures in vitro, and proposed models for the in vivo functions of replicative helicase-DNA interactions are also described.
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22
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Ogino H, Ishino S, Kohda D, Ishino Y. The RecJ2 protein in the thermophilic archaeon Thermoplasma acidophilum is a 3'-5' exonuclease that associates with a DNA replication complex. J Biol Chem 2017; 292:7921-7931. [PMID: 28302716 DOI: 10.1074/jbc.m116.767921] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 03/15/2017] [Indexed: 11/06/2022] Open
Abstract
RecJ/cell division cycle 45 (Cdc45) proteins are widely conserved in the three domains of life, i.e. in bacteria, Eukarya, and Archaea. Bacterial RecJ is a 5'-3' exonuclease and functions in DNA repair pathways by using its 5'-3' exonuclease activity. Eukaryotic Cdc45 has no identified enzymatic activity but participates in the CMG complex, so named because it is composed of Cdc45, minichromosome maintenance protein complex (MCM) proteins 2-7, and GINS complex proteins (Sld5, Psf11-3). Eukaryotic Cdc45 and bacterial/archaeal RecJ share similar amino acid sequences and are considered functional counterparts. In Archaea, a RecJ homolog in Thermococcus kodakarensis was shown to associate with GINS and accelerate its nuclease activity and was, therefore, designated GAN (GINS-associated nuclease); however, to date, no archaeal RecJ·MCM·GINS complex has been isolated. The thermophilic archaeon Thermoplasma acidophilum has two RecJ-like proteins, designated TaRecJ1 and TaRecJ2. TaRecJ1 exhibited DNA-specific 5'-3' exonuclease activity, whereas TaRecJ2 had 3'-5' exonuclease activity and preferred RNA over DNA. TaRecJ2, but not TaRecJ1, formed a stable complex with TaGINS in a 2:1 molar ratio. Furthermore, the TaRecJ2·TaGINS complex stimulated activity of TaMCM (T. acidophilum MCM) helicase in vitro, and the TaRecJ2·TaMCM·TaGINS complex was also observed in vivo However, TaRecJ2 did not interact with TaMCM directly and was not required for the helicase activation in vitro These findings suggest that the function of archaeal RecJ in DNA replication evolved divergently from Cdc45 despite conservation of the CMG-like complex formation between Archaea and Eukarya.
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Affiliation(s)
- Hiromi Ogino
- From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashiku, Fukuoka 812-8581, Japan and
| | - Sonoko Ishino
- From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashiku, Fukuoka 812-8581, Japan and
| | - Daisuke Kohda
- the Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Yoshizumi Ishino
- From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashiku, Fukuoka 812-8581, Japan and .,the Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashiku, Fukuoka 812-8582, Japan
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23
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Abstract
Cellular DNA replication factories depend on ring-shaped hexameric helicases to aid DNA synthesis by processively unzipping the parental DNA helix. Replicative helicases are loaded onto DNA by dedicated initiator, loader, and accessory proteins during the initiation of DNA replication in a tightly regulated, multistep process. We discuss here the molecular choreography of DNA replication initiation across the three domains of life, highlighting similarities and differences in the strategies used to deposit replicative helicases onto DNA and to melt the DNA helix in preparation for replisome assembly. Although initiators and loaders are phylogenetically related, the mechanisms they use for accomplishing similar tasks have diverged considerably and in an unpredictable manner.
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Affiliation(s)
- Franziska Bleichert
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Michael R Botchan
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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24
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Parker MW, Botchan MR, Berger JM. Mechanisms and regulation of DNA replication initiation in eukaryotes. Crit Rev Biochem Mol Biol 2017; 52:107-144. [PMID: 28094588 DOI: 10.1080/10409238.2016.1274717] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cellular DNA replication is initiated through the action of multiprotein complexes that recognize replication start sites in the chromosome (termed origins) and facilitate duplex DNA melting within these regions. In a typical cell cycle, initiation occurs only once per origin and each round of replication is tightly coupled to cell division. To avoid aberrant origin firing and re-replication, eukaryotes tightly regulate two events in the initiation process: loading of the replicative helicase, MCM2-7, onto chromatin by the origin recognition complex (ORC), and subsequent activation of the helicase by its incorporation into a complex known as the CMG. Recent work has begun to reveal the details of an orchestrated and sequential exchange of initiation factors on DNA that give rise to a replication-competent complex, the replisome. Here, we review the molecular mechanisms that underpin eukaryotic DNA replication initiation - from selecting replication start sites to replicative helicase loading and activation - and describe how these events are often distinctly regulated across different eukaryotic model organisms.
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Affiliation(s)
- Matthew W Parker
- a Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Michael R Botchan
- b Department of Molecular and Cell Biology , University of California Berkeley , Berkeley , CA , USA
| | - James M Berger
- a Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , MD , USA
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25
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Bell SD. Initiation of DNA Replication in the Archaea. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:99-115. [PMID: 29357055 DOI: 10.1007/978-981-10-6955-0_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Organisms within the archaeal domain of life possess a simplified version of the eukaryotic DNA replication machinery. While some archaea possess a bacterial-like mode of DNA replication with single origins of replication per chromosome, the majority of species characterized to date possess chromosomes with multiple replication origins. Genetic, structural, and biochemical studies have revealed the nature of archaeal origin specification. Recent work has begun to shed light on the mechanisms of replication initiation in these organisms.
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Affiliation(s)
- Stephen D Bell
- Department of Molecular and Cellular Biochemistry, Department of Biology, Indiana University, Bloomington, IN, USA.
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26
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Bai L, Yuan Z, Sun J, Georgescu R, O'Donnell ME, Li H. Architecture of the Saccharomyces cerevisiae Replisome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:207-228. [PMID: 29357060 DOI: 10.1007/978-981-10-6955-0_10] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Eukaryotic replication proteins are highly conserved, and thus study of Saccharomyces cerevisiae replication can inform about this central process in higher eukaryotes including humans. The S. cerevisiae replisome is a large and dynamic assembly comprised of ~50 proteins. The core of the replisome is composed of 31 different proteins including the 11-subunit CMG helicase; RFC clamp loader pentamer; PCNA clamp; the heteroligomeric DNA polymerases ε, δ, and α-primase; and the RPA heterotrimeric single strand binding protein. Many additional protein factors either travel with or transiently associate with these replisome proteins at particular times during replication. In this chapter, we summarize several recent structural studies on the S. cerevisiae replisome and its subassemblies using single particle electron microscopy and X-ray crystallography. These recent structural studies have outlined the overall architecture of a core replisome subassembly and shed new light on the mechanism of eukaryotic replication.
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Affiliation(s)
- Lin Bai
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Zuanning Yuan
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, USA
- Biochemistry and Structural Biology Graduate Program, Stony Brook University, Stony Brook, NY, USA
| | - Jingchuan Sun
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Roxana Georgescu
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Michael E O'Donnell
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Huilin Li
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, USA.
- Biochemistry and Structural Biology Graduate Program, Stony Brook University, Stony Brook, NY, USA.
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27
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Pellegrini L. Structural insights into Cdc45 function: was there a nuclease at the heart of the ancestral replisome? Biophys Chem 2016; 225:10-14. [PMID: 27919598 PMCID: PMC5484177 DOI: 10.1016/j.bpc.2016.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/10/2016] [Accepted: 11/10/2016] [Indexed: 01/28/2023]
Abstract
The role of Cdc45 in genomic duplication has remained unclear since its initial identification as an essential replication factor. Recent structural studies of Cdc45 and the evolutionarily-related archaeal GAN and bacterial RecJ nucleases have provided fresh insight into its function as co-activator of the MCM helicase. The CMG helicase of the last archaeal/eukaryotic ancestor might have harboured a single-stranded DNA nuclease activity, conserved in some modern archaea.
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Affiliation(s)
- Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
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28
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Xu Y, Gristwood T, Hodgson B, Trinidad JC, Albers SV, Bell SD. Archaeal orthologs of Cdc45 and GINS form a stable complex that stimulates the helicase activity of MCM. Proc Natl Acad Sci U S A 2016; 113:13390-13395. [PMID: 27821767 PMCID: PMC5127375 DOI: 10.1073/pnas.1613825113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The regulated recruitment of Cdc45 and GINS is key to activating the eukaryotic MCM(2-7) replicative helicase. We demonstrate that the homohexameric archaeal MCM helicase associates with orthologs of GINS and Cdc45 in vivo and in vitro. Association of these factors with MCM robustly stimulates the MCM helicase activity. In contrast to the situation in eukaryotes, archaeal Cdc45 and GINS form an extremely stable complex before binding MCM. Further, the archaeal GINS•Cdc45 complex contains two copies of Cdc45. Our analyses give insight into the function and evolution of the conserved core of the archaeal/eukaryotic replisome.
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Affiliation(s)
- Yuli Xu
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405
- Biology Department, Indiana University, Bloomington, IN 47405
| | - Tamzin Gristwood
- Sir William Dunn School of Pathology, Oxford OX13RE, United Kingdom
| | - Ben Hodgson
- Sir William Dunn School of Pathology, Oxford OX13RE, United Kingdom
| | | | - Sonja-Verena Albers
- Max Planck Institute für terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - Stephen D Bell
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405;
- Biology Department, Indiana University, Bloomington, IN 47405
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29
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Oyama T, Ishino S, Shirai T, Yamagami T, Nagata M, Ogino H, Kusunoki M, Ishino Y. Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication. Nucleic Acids Res 2016; 44:9505-9517. [PMID: 27599844 PMCID: PMC5100581 DOI: 10.1093/nar/gkw789] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/29/2016] [Indexed: 12/29/2022] Open
Abstract
In eukaryotic DNA replication initiation, hexameric MCM (mini-chromosome maintenance) unwinds the template double-stranded DNA to form the replication fork. MCM is activated by two proteins, Cdc45 and GINS, which constitute the ‘CMG’ unwindosome complex together with the MCM core. The archaeal DNA replication system is quite similar to that of eukaryotes, but only limited knowledge about the DNA unwinding mechanism is available, from a structural point of view. Here, we describe the crystal structure of an archaeal GAN (GINS-associated nuclease) from Thermococcus kodakaraensis, the homolog of eukaryotic Cdc45, in both the free form and the complex with the C-terminal domain of the cognate Gins51 subunit (Gins51C). This first archaeal GAN structure exhibits a unique, ‘hybrid’ structure between the bacterial RecJ and the eukaryotic Cdc45. GAN possesses the conserved DHH and DHH1 domains responsible for the exonuclease activity, and an inserted CID (CMG interacting domain)-like domain structurally comparable to that in Cdc45, suggesting its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication. A structural comparison of the GAN–Gins51C complex with the GINS tetramer suggests that GINS uses the mobile Gins51C as a hook to bind GAN for CMG formation.
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Affiliation(s)
- Takuji Oyama
- Faculty of Life and Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Tsuyoshi Shirai
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Takeshi Yamagami
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Mariko Nagata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Hiromi Ogino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Masami Kusunoki
- Faculty of Life and Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
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30
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Pellegrini L, Costa A. New Insights into the Mechanism of DNA Duplication by the Eukaryotic Replisome. Trends Biochem Sci 2016; 41:859-871. [PMID: 27555051 DOI: 10.1016/j.tibs.2016.07.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 11/26/2022]
Abstract
The DNA replication machinery, or replisome, is a macromolecular complex that combines DNA unwinding, priming and synthesis activities. In eukaryotic cells, the helicase and polymerases are multi-subunit, highly-dynamic assemblies whose structural characterization requires an integrated approach. Recent studies have combined single-particle electron cryo-microscopy and protein crystallography to gain insights into the mechanism of DNA duplication by the eukaryotic replisome. We review current understanding of how replication fork unwinding by the CMG helicase is coupled to leading-strand synthesis by polymerase (Pol) ɛ and lagging-strand priming by Pol α/primase, and discuss emerging principles of replisome organization.
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Affiliation(s)
- Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - Alessandro Costa
- Macromolecular Machines Laboratory, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, UK.
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31
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Fenwick AL, Kliszczak M, Cooper F, Murray J, Sanchez-Pulido L, Twigg SRF, Goriely A, McGowan SJ, Miller KA, Taylor IB, Logan C, Bozdogan S, Danda S, Dixon J, Elsayed SM, Elsobky E, Gardham A, Hoffer MJV, Koopmans M, McDonald-McGinn DM, Santen GWE, Savarirayan R, de Silva D, Vanakker O, Wall SA, Wilson LC, Yuregir OO, Zackai EH, Ponting CP, Jackson AP, Wilkie AOM, Niedzwiedz W, Bicknell LS. Mutations in CDC45, Encoding an Essential Component of the Pre-initiation Complex, Cause Meier-Gorlin Syndrome and Craniosynostosis. Am J Hum Genet 2016; 99:125-38. [PMID: 27374770 PMCID: PMC5005452 DOI: 10.1016/j.ajhg.2016.05.019] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/09/2016] [Indexed: 11/19/2022] Open
Abstract
DNA replication precisely duplicates the genome to ensure stable inheritance of genetic information. Impaired licensing of origins of replication during the G1 phase of the cell cycle has been implicated in Meier-Gorlin syndrome (MGS), a disorder defined by the triad of short stature, microtia, and a/hypoplastic patellae. Biallelic partial loss-of-function mutations in multiple components of the pre-replication complex (preRC; ORC1, ORC4, ORC6, CDT1, or CDC6) as well as de novo stabilizing mutations in the licensing inhibitor, GMNN, cause MGS. Here we report the identification of mutations in CDC45 in 15 affected individuals from 12 families with MGS and/or craniosynostosis. CDC45 encodes a component of both the pre-initiation (preIC) and CMG helicase complexes, required for initiation of DNA replication origin firing and ongoing DNA synthesis during S-phase itself, respectively, and hence is functionally distinct from previously identified MGS-associated genes. The phenotypes of affected individuals range from syndromic coronal craniosynostosis to severe growth restriction, fulfilling diagnostic criteria for Meier-Gorlin syndrome. All mutations identified were biallelic and included synonymous mutations altering splicing of physiological CDC45 transcripts, as well as amino acid substitutions expected to result in partial loss of function. Functionally, mutations reduce levels of full-length transcripts and protein in subject cells, consistent with partial loss of CDC45 function and a predicted limited rate of DNA replication and cell proliferation. Our findings therefore implicate the preIC as an additional protein complex involved in the etiology of MGS and connect the core cellular machinery of genome replication with growth, chondrogenesis, and cranial suture homeostasis.
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Affiliation(s)
- Aimee L Fenwick
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Maciej Kliszczak
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Fay Cooper
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jennie Murray
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Luis Sanchez-Pulido
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Anne Goriely
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Simon J McGowan
- Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Kerry A Miller
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Indira B Taylor
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Clare Logan
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sevcan Bozdogan
- Department of Medical Genetics, Mersin University, Mersin, 33343 Cukurova, Turkey
| | - Sumita Danda
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, Tamil Nadu 632004, India
| | - Joanne Dixon
- Genetic Health Service NZ-South Island Hub, Christchurch Hospital, Christchurch, Canterbury 8140, New Zealand
| | - Solaf M Elsayed
- Children's Hospital, Ain Shams University, Cairo 11566, Egypt
| | - Ezzat Elsobky
- Children's Hospital, Ain Shams University, Cairo 11566, Egypt
| | - Alice Gardham
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Mariette J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Marije Koopmans
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Donna M McDonald-McGinn
- Clinical Genetics, The Children's Hospital of Philadelphia, 34th & Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Ravi Savarirayan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Deepthi de Silva
- Department of Physiology, Faculty of Medicine, University of Kelaniya, Ragama, Gampaha GQ 11010, Sri Lanka
| | - Olivier Vanakker
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Steven A Wall
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Louise C Wilson
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Ozge Ozalp Yuregir
- Genetic Diagnosis Center, Adana Numune Training and Research Hospital, Cukurova, Adana, 01170, Turkey
| | - Elaine H Zackai
- Clinical Genetics, The Children's Hospital of Philadelphia, 34th & Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Chris P Ponting
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Andrew P Jackson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Wojciech Niedzwiedz
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Louise S Bicknell
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK; Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, Otago 9016, New Zealand.
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32
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Simon AC, Sannino V, Costanzo V, Pellegrini L. Structure of human Cdc45 and implications for CMG helicase function. Nat Commun 2016; 7:11638. [PMID: 27189187 PMCID: PMC4873980 DOI: 10.1038/ncomms11638] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/14/2016] [Indexed: 01/05/2023] Open
Abstract
Cell division cycle protein 45 (Cdc45) is required for DNA synthesis during genome duplication, as a component of the Cdc45-MCM-GINS (CMG) helicase. Despite its essential biological function, its biochemical role in DNA replication has remained elusive. Here we report the 2.1-Å crystal structure of human Cdc45, which confirms its evolutionary link with the bacterial RecJ nuclease and reveals several unexpected features that underpin its function in eukaryotic DNA replication. These include a long-range interaction between N- and C-terminal DHH domains, blocking access to the DNA-binding groove of its RecJ-like fold, and a helical insertion in its N-terminal DHH domain, which appears poised for replisome interactions. In combination with available electron microscopy data, we validate by mutational analysis the mechanism of Cdc45 association with the MCM ring and GINS co-activator, critical for CMG assembly. These findings provide an indispensable molecular basis to rationalize the essential role of Cdc45 in genomic duplication. The cell cycle division protein Cdc45 is required for genome duplication in eukaryotes. Here, the authors determine the crystal structure of human Cdc45 and combine it with functional data to improve our understanding of its role in DNA replication.
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Affiliation(s)
- Aline C Simon
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Vincenzo Sannino
- DNA Metabolism Laboratory, FIRC Institute of Molecular Oncology Foundation, 20139 Milan, Italy
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, FIRC Institute of Molecular Oncology Foundation, 20139 Milan, Italy
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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33
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Abid Ali F, Costa A. The MCM Helicase Motor of the Eukaryotic Replisome. J Mol Biol 2016; 428:1822-32. [PMID: 26829220 DOI: 10.1016/j.jmb.2016.01.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/23/2016] [Indexed: 10/22/2022]
Abstract
The MCM motor of the CMG helicase powers ahead of the eukaryotic replication machinery to unwind DNA, in a process that requires ATP hydrolysis. The reconstitution of DNA replication in vitro has established the succession of events that lead to replication origin activation by the MCM and recent studies have started to elucidate the structural basis of duplex DNA unwinding. Despite the exciting progress, how the MCM translocates on DNA remains a matter of debate.
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Affiliation(s)
- Ferdos Abid Ali
- Architecture and Dynamics of Macromolecular Machines, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, United Kingdom
| | - Alessandro Costa
- Architecture and Dynamics of Macromolecular Machines, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, United Kingdom.
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34
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Abstract
The cellular replicating machine, or "replisome," is composed of numerous different proteins. The core replication proteins in all cell types include a helicase, primase, DNA polymerases, sliding clamp, clamp loader, and single-strand binding (SSB) protein. The core eukaryotic replisome proteins evolved independently from those of bacteria and thus have distinct architectures and mechanisms of action. The core replisome proteins of the eukaryote include: an 11-subunit CMG helicase, DNA polymerase alpha-primase, leading strand DNA polymerase epsilon, lagging strand DNA polymerase delta, PCNA clamp, RFC clamp loader, and the RPA SSB protein. There are numerous other proteins that travel with eukaryotic replication forks, some of which are known to be involved in checkpoint regulation or nucleosome handling, but most have unknown functions and no bacterial analogue. Recent studies have revealed many structural and functional insights into replisome action. Also, the first structure of a replisome from any cell type has been elucidated for a eukaryote, consisting of 20 distinct proteins, with quite unexpected results. This review summarizes the current state of knowledge of the eukaryotic core replisome proteins, their structure, individual functions, and how they are organized at the replication fork as a machine.
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Affiliation(s)
- D Zhang
- The Rockefeller University, New York, NY, United States
| | - M O'Donnell
- The Rockefeller University, New York, NY, United States; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, United States.
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35
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Cheng K, Xu H, Chen X, Wang L, Tian B, Zhao Y, Hua Y. Structural basis for DNA 5´-end resection by RecJ. eLife 2016; 5:e14294. [PMID: 27058167 PMCID: PMC4846377 DOI: 10.7554/elife.14294] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/07/2016] [Indexed: 12/18/2022] Open
Abstract
The resection of DNA strand with a 5´ end at double-strand breaks is an essential step in recombinational DNA repair. RecJ, a member of DHH family proteins, is the only 5´ nuclease involved in the RecF recombination pathway. Here, we report the crystal structures of Deinococcus radiodurans RecJ in complex with deoxythymidine monophosphate (dTMP), ssDNA, the C-terminal region of single-stranded DNA-binding protein (SSB-Ct) and a mechanistic insight into the RecF pathway. A terminal 5´-phosphate-binding pocket above the active site determines the 5´-3´ polarity of the deoxy-exonuclease of RecJ; a helical gateway at the entrance to the active site admits ssDNA only; and the continuous stacking interactions between protein and nine nucleotides ensure the processive end resection. The active site of RecJ in the N-terminal domain contains two divalent cations that coordinate the nucleophilic water. The ssDNA makes a 180° turn at the scissile phosphate. The C-terminal domain of RecJ binds the SSB-Ct, which explains how RecJ and SSB work together to efficiently process broken DNA ends for homologous recombination.
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Affiliation(s)
- Kaiying Cheng
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Hong Xu
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Xuanyi Chen
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Liangyan Wang
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Bing Tian
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Ye Zhao
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Yuejin Hua
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
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36
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Yuan Z, Bai L, Sun J, Georgescu R, Liu J, O'Donnell ME, Li H. Structure of the eukaryotic replicative CMG helicase suggests a pumpjack motion for translocation. Nat Struct Mol Biol 2016; 23:217-24. [PMID: 26854665 PMCID: PMC4812828 DOI: 10.1038/nsmb.3170] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/06/2016] [Indexed: 01/06/2023]
Abstract
The CMG helicase is composed of Cdc45, Mcm2-7 and GINS. Here we report the structure of the Saccharomyces cerevisiae CMG, determined by cryo-EM at a resolution of 3.7-4.8 Å. The structure reveals that GINS and Cdc45 scaffold the N tier of the helicase while enabling motion of the AAA+ C tier. CMG exists in two alternating conformations, compact and extended, thus suggesting that the helicase moves like an inchworm. The N-terminal regions of Mcm2-7, braced by Cdc45-GINS, form a rigid platform upon which the AAA+ C domains make longitudinal motions, nodding up and down like an oil-rig pumpjack attached to a stable platform. The Mcm ring is remodeled in CMG relative to the inactive Mcm2-7 double hexamer. The Mcm5 winged-helix domain is inserted into the central channel, thus blocking entry of double-stranded DNA and supporting a steric-exclusion DNA-unwinding model.
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Affiliation(s)
- Zuanning Yuan
- Department of Biochemistry &Cell Biology, Stony Brook University, Stony Brook, New York, USA.,Biology Department, Brookhaven National Laboratory, Upton, New York, USA
| | - Lin Bai
- Biology Department, Brookhaven National Laboratory, Upton, New York, USA
| | - Jingchuan Sun
- Biology Department, Brookhaven National Laboratory, Upton, New York, USA
| | - Roxana Georgescu
- DNA Replication Laboratory, Rockefeller University, New York, New York, USA.,Howard Hughes Medical Institute, Rockefeller University, New York, New York, USA
| | - Jun Liu
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, Texas, USA
| | - Michael E O'Donnell
- DNA Replication Laboratory, Rockefeller University, New York, New York, USA.,Howard Hughes Medical Institute, Rockefeller University, New York, New York, USA
| | - Huilin Li
- Department of Biochemistry &Cell Biology, Stony Brook University, Stony Brook, New York, USA.,Biology Department, Brookhaven National Laboratory, Upton, New York, USA
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37
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Cheng K, Zhao Y, Chen X, Li T, Wang L, Xu H, Tian B, Hua Y. A Novel C-Terminal Domain of RecJ is Critical for Interaction with HerA in Deinococcus radiodurans. Front Microbiol 2015; 6:1302. [PMID: 26648913 PMCID: PMC4663267 DOI: 10.3389/fmicb.2015.01302] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/06/2015] [Indexed: 01/09/2023] Open
Abstract
Homologous recombination (HR) generates error-free repair products, which plays an important role in double strand break repair and replication fork rescue processes. DNA end resection, the critical step in HR, is usually performed by a series of nuclease/helicase. RecJ was identified as a 5'-3' exonuclease involved in bacterial DNA end resection. Typical RecJ possesses a conserved DHH domain, a DHHA1 domain, and an oligonucleotide/oligosaccharide-binding (OB) fold. However, RecJs from Deinococcus-Thermus phylum, such as Deinococcus radiodurans RecJ (DrRecJ), possess an extra C-terminal domain (CTD), of which the function has not been characterized. Here, we showed that a CTD-deletion of DrRecJ (DrRecJΔC) could not restore drrecJ mutant growth and mitomycin C (MMC)-sensitive phenotypes, indicating that this domain is essential for DrRecJ in vivo. DrRecJΔC displayed reduced DNA nuclease activity and DNA binding ability. Direct interaction was identified between DrRecJ-CTD and DrHerA, which stimulates DrRecJ nuclease activity by enhancing its DNA binding affinity. Moreover, DrNurA nuclease, another partner of DrHerA, inhibited the stimulation of DrHerA on DrRecJ nuclease activity by interaction with DrHerA. Opposing growth and MMC-resistance phenotypes between the recJ and nurA mutants were observed. A novel modulation mechanism among DrRecJ, DrHerA, and DrNurA was also suggested.
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Affiliation(s)
- Kaiying Cheng
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
| | - Ye Zhao
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
| | - Xuanyi Chen
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
| | - Tao Li
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
| | - Liangyan Wang
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
| | - Hong Xu
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
| | - Bing Tian
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
| | - Yuejin Hua
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
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Gerhardt J, Guler GD, Fanning E. Human DNA helicase B interacts with the replication initiation protein Cdc45 and facilitates Cdc45 binding onto chromatin. Exp Cell Res 2015; 334:283-93. [PMID: 25933514 DOI: 10.1016/j.yexcr.2015.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 04/17/2015] [Accepted: 04/20/2015] [Indexed: 10/23/2022]
Abstract
The chromosomal DNA replication in eukaryotic cells begins at replication initation sites, which are marked by the assembly of the pre-replication complexes in early G1. At the G1/S transition, recruitment of additional replication initiation proteins enables origin DNA unwinding and loading of DNA polymerases. We found that depletion of the human DNA helicase B (HDHB) inhibits the initiation of DNA replication, suggesting a role of HDHB in the beginning of the DNA synthesis. To gain insight into the function of HDHB during replication initiation, we examined the physical interactions of purified recombinant HDHB with key initiation proteins. HDHB interacts directly with two initiation factors TopBP1 and Cdc45. In addition we found that both, the N-terminus and helicase domain of HDHB bind to the N-terminus of Cdc45. Furthermore depletion of HDHB from human cells diminishes Cdc45 association with chromatin, suggesting that HDHB may facilitate Cdc45 recruitment at G1/S in human cells.
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Affiliation(s)
- Jeannine Gerhardt
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Gulfem D Guler
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Ellen Fanning
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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Petojevic T, Pesavento JJ, Costa A, Liang J, Wang Z, Berger JM, Botchan MR. Cdc45 (cell division cycle protein 45) guards the gate of the Eukaryote Replisome helicase stabilizing leading strand engagement. Proc Natl Acad Sci U S A 2015; 112:E249-58. [PMID: 25561522 PMCID: PMC4311868 DOI: 10.1073/pnas.1422003112] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
DNA replication licensing is now understood to be the pathway that leads to the assembly of double hexamers of minichromosome maintenance (Mcm2-7) at origin sites. Cell division control protein 45 (Cdc45) and GINS proteins activate the latent Mcm2-7 helicase by inducing allosteric changes through binding, forming a Cdc45/Mcm2-7/GINS (CMG) complex that is competent to unwind duplex DNA. The CMG has an active gate between subunits Mcm2 and Mcm5 that opens and closes in response to nucleotide binding. The consequences of inappropriate Mcm2/5 gate actuation and the role of a side channel formed between GINS/Cdc45 and the outer edge of the Mcm2-7 ring for unwinding have remained unexplored. Here we uncover a novel function for Cdc45. Cross-linking studies trace the path of the DNA with the CMG complex at a fork junction between duplex and single strands with the bound CMG in an open or closed gate conformation. In the closed state, the lagging strand does not pass through the side channel, but in the open state, the leading strand surprisingly interacts with Cdc45. Mutations in the recombination protein J fold of Cdc45 that ablate this interaction diminish helicase activity. These data indicate that Cdc45 serves as a shield to guard against occasional slippage of the leading strand from the core channel.
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Affiliation(s)
- Tatjana Petojevic
- Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, CA 94720; Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - James J Pesavento
- Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, CA 94720
| | - Alessandro Costa
- Clare Hall Laboratories, London Research Institute, South Mimms, Herts EN6 3LD, United Kingdom; and
| | - Jingdan Liang
- Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, CA 94720
| | - Zhijun Wang
- Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, CA 94720
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205
| | - Michael R Botchan
- Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, CA 94720;
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40
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Ahmad M, Tuteja R. Emerging importance of mismatch repair components including UvrD helicase and their cross-talk with the development of drug resistance in malaria parasite. Mutat Res 2014; 770:54-60. [PMID: 25771870 DOI: 10.1016/j.mrfmmm.2014.09.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/14/2014] [Accepted: 09/17/2014] [Indexed: 06/04/2023]
Abstract
Human malaria is an important parasitic infection responsible for a significant number of deaths worldwide, particularly in tropical and subtropical regions. The recent scenario has worsened mainly because of the emergence of drug-resistant malaria parasites having the potential to spread across the world. Drug-resistant parasites possess a defective mismatch repair (MMR); therefore, it is essential to explore its mechanism in detail to determine the underlying cause. Recently, artemisinin-resistant parasites have been reported to exhibit nonsynonymous single nucleotide polymorphisms in genes involved in MMR pathways such as MutL homolog (MLH) and UvrD. Plasmodium falciparum MLH is an endonuclease required to restore the defective MMR in drug-resistant W2 strain of P. falciparum. Although the role of helicases in eukaryotic MMR has been questioned, the identification and characterization of the UvrD helicase and their cross-talk with MLH in P. falciparum suggests the possible involvement of UvrD in MMR. A comparative genome-wide analysis revealed the presence of the UvrD helicase in Plasmodium species, while it is absent in human host. Therefore, PfUvrD may emerge as a suitable drug target to control malaria. This review study is focused on recent developments in MMR biochemistry, emerging importance of the UvrD helicase, possibility of its involvement in MMR and the emerging cross-talk between MMR components and drug resistance in malaria parasite.
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Affiliation(s)
- Moaz Ahmad
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Renu Tuteja
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Ogino H, Ishino S, Oyama T, Kohda D, Ishino Y. Disordered interdomain region of Gins is important for functional tetramer formation to stimulate MCM helicase in Thermoplasma acidophilum. Biosci Biotechnol Biochem 2014; 79:432-8. [PMID: 25419910 DOI: 10.1080/09168451.2014.982503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The eukaryotic MCM is activated by forming the CMG complex with Cdc45 and GINS to work as a replicative helicase. The eukaryotic GINS consists of four different proteins to form tetrameric complex. In contrast, the TaGins51 protein from the thermophilic archaeon, Thermoplasma acidophilum forms a homotetramer (TaGINS), and interacts with the cognate MCM (TaMCM) to stimulate the DNA-binding, ATPase, and helicase activities of TaMCM. All Gins proteins from Archaea and Eukarya contain α-helical A- and β-stranded B-domains. Here, we found that TaGins51 forms the tetramer without the B-domain. However, the A-domain without the linker region between the A- and B-domains could not form a stable tetramer, and furthermore, the A-domain by itself could not stimulate the TaMCM activity. These results suggest that the formation of the Gins51 tetramer is necessary for MCM activation, and the disordered linker region between the two domains is critical for the functional complex formation.
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Affiliation(s)
- Hiromi Ogino
- a Department of Bioscience & Biotechnology , Graduate School of Bioresource & Bioenvironmental Sciences, Kyushu University , Fukuoka , Japan
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42
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Tognetti S, Riera A, Speck C. Switch on the engine: how the eukaryotic replicative helicase MCM2-7 becomes activated. Chromosoma 2014; 124:13-26. [PMID: 25308420 DOI: 10.1007/s00412-014-0489-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 12/17/2022]
Abstract
A crucial step during eukaryotic initiation of DNA replication is the correct loading and activation of the replicative DNA helicase, which ensures that each replication origin fires only once. Unregulated DNA helicase loading and activation, as it occurs in cancer, can cause severe DNA damage and genomic instability. The essential mini-chromosome maintenance proteins 2-7 (MCM2-7) represent the core of the eukaryotic replicative helicase that is loaded at DNA replication origins during G1-phase of the cell cycle. The MCM2-7 helicase activity, however, is only triggered during S-phase once the holo-helicase Cdc45-MCM2-7-GINS (CMG) has been formed. A large number of factors and several kinases interact and contribute to CMG formation and helicase activation, though the exact mechanisms remain unclear. Crucially, upon DNA damage, this reaction is temporarily halted to ensure genome integrity. Here, we review the current understanding of helicase activation; we focus on protein interactions during CMG formation, discuss structural changes during helicase activation, and outline similarities and differences of the prokaryotic and eukaryotic helicase activation process.
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Affiliation(s)
- Silvia Tognetti
- DNA Replication Group, Institute of Clinical Science, Imperial College, London, W12 0NN, UK
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43
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Costa A, Renault L, Swuec P, Petojevic T, Pesavento JJ, Ilves I, MacLellan-Gibson K, Fleck RA, Botchan MR, Berger JM. DNA binding polarity, dimerization, and ATPase ring remodeling in the CMG helicase of the eukaryotic replisome. eLife 2014; 3:e03273. [PMID: 25117490 PMCID: PMC4359367 DOI: 10.7554/elife.03273] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/08/2014] [Indexed: 01/29/2023] Open
Abstract
The Cdc45/Mcm2-7/GINS (CMG) helicase separates DNA strands during replication in eukaryotes. How the CMG is assembled and engages DNA substrates remains unclear. Using electron microscopy, we have determined the structure of the CMG in the presence of ATPγS and a DNA duplex bearing a 3' single-stranded tail. The structure shows that the MCM subunits of the CMG bind preferentially to single-stranded DNA, establishes the polarity by which DNA enters into the Mcm2-7 pore, and explains how Cdc45 helps prevent DNA from dissociating from the helicase. The Mcm2-7 subcomplex forms a cracked-ring, right-handed spiral when DNA and nucleotide are bound, revealing unexpected congruencies between the CMG and both bacterial DnaB helicases and the AAA+ motor of the eukaryotic proteasome. The existence of a subpopulation of dimeric CMGs establishes the subunit register of Mcm2-7 double hexamers and together with the spiral form highlights how Mcm2-7 transitions through different conformational and assembly states as it matures into a functional helicase.
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Affiliation(s)
- Alessandro Costa
- London Research Institute, Cancer Research UK, London, United Kingdom
| | - Ludovic Renault
- London Research Institute, Cancer Research UK, London, United Kingdom Department of Imaging, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Paolo Swuec
- London Research Institute, Cancer Research UK, London, United Kingdom
| | - Tatjana Petojevic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - James J Pesavento
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Ivar Ilves
- Institute of Technology, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Kirsty MacLellan-Gibson
- Department of Imaging, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Roland A Fleck
- Department of Imaging, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Michael R Botchan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States
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44
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Activation of the MCM helicase from the thermophilic archaeon, Thermoplasma acidophilum by interactions with GINS and Cdc6-2. Extremophiles 2014; 18:915-24. [PMID: 25107272 DOI: 10.1007/s00792-014-0673-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/06/2014] [Indexed: 01/25/2023]
Abstract
In DNA replication studies, the mechanism for regulation of the various steps from initiation to elongation is a crucial subject to understand cell cycle control. The eukaryotic minichromosome maintenance (MCM) protein complex is recruited to the replication origin by Cdc6 and Cdt1 to form the pre-replication complex, and participates in forming the CMG complex formation with Cdc45 and GINS to work as the active helicase. Intriguingly, Thermoplasma acidophilum, as well as many other archaea, has only one Gins protein homolog, contrary to the heterotetramer of the eukaryotic GINS made of four different proteins. The Gins51 protein reportedly forms a homotetramer (TaGINS) and physically interacts with TaMCM. In addition, TaCdc6-2, one of the two Cdc6/Orc1 homologs in T. acidophilum reportedly stimulates the ATPase and helicase activities of TaMCM in vitro. Here, we found a reaction condition, in which TaGINS stimulated the ATPase and helicase activities of TaMCM in a concentration dependent manner. Furthermore, the stimulation of the TaMCM helicase activity by TaGINS was enhanced by the addition of TaCdc6-2. A gel retardation assay revealed that TaMCM, TaGINS, and TaCdc6-2 form a complex on ssDNA. However, glutaraldehyde-crosslinking was necessary to detect the shifted band, indicating that the ternary complex of TaMCM-TaGINS-TaCdc6-2 is not stable in vitro. Immunoprecipitation experiment supported a weak interaction of these three proteins in vivo. Activation of the replicative helicase by a mechanism including a Cdc6-like protein suggests the divergent evolution after the division into Archaea and Eukarya.
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45
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Itou H, Muramatsu S, Shirakihara Y, Araki H. Crystal structure of the homology domain of the eukaryotic DNA replication proteins Sld3/Treslin. Structure 2014; 22:1341-1347. [PMID: 25126958 DOI: 10.1016/j.str.2014.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 06/05/2014] [Accepted: 07/03/2014] [Indexed: 11/30/2022]
Abstract
The initiation of eukaryotic chromosomal DNA replication requires the formation of an active replicative helicase at the replication origins of chromosomal DNA. Yeast Sld3 and its metazoan counterpart Treslin are the hub proteins mediating protein associations critical for the helicase formation. Here, we show the crystal structure of the central domain of Sld3 that is conserved in Sld3/Treslin family of proteins. The domain consists of two segments with 12 helices and is sufficient to bind to Cdc45, the essential helicase component. The structure model of the Sld3-Cdc45 complex, which is crucial for the formation of the active helicase, is proposed.
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Affiliation(s)
- Hiroshi Itou
- Structural Biology Center, National Institute of Genetics, Yata1111, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, SOKENDAI, Yata1111, Mishima, Shizuoka 411-8540, Japan.
| | - Sachiko Muramatsu
- Division of Microbial Genetics, National Institute of Genetics, Yata1111, Mishima, Shizuoka 411-8540, Japan
| | - Yasuo Shirakihara
- Structural Biology Center, National Institute of Genetics, Yata1111, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, SOKENDAI, Yata1111, Mishima, Shizuoka 411-8540, Japan
| | - Hiroyuki Araki
- Division of Microbial Genetics, National Institute of Genetics, Yata1111, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, SOKENDAI, Yata1111, Mishima, Shizuoka 411-8540, Japan.
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46
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Diversity of the DNA replication system in the Archaea domain. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:675946. [PMID: 24790526 PMCID: PMC3984812 DOI: 10.1155/2014/675946] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 02/16/2014] [Indexed: 12/11/2022]
Abstract
The precise and timely duplication of the genome is essential for cellular life. It is achieved by DNA replication, a complex process that is conserved among the three domains of life. Even though the cellular structure of archaea closely resembles that of bacteria, the information processing machinery of archaea is evolutionarily more closely related to the eukaryotic system, especially for the proteins involved in the DNA replication process. While the general DNA replication mechanism is conserved among the different domains of life, modifications in functionality and in some of the specialized replication proteins are observed. Indeed, Archaea possess specific features unique to this domain. Moreover, even though the general pattern of the replicative system is the same in all archaea, a great deal of variation exists between specific groups.
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47
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Kristensen TP, Maria Cherian R, Gray FC, MacNeill SA. The haloarchaeal MCM proteins: bioinformatic analysis and targeted mutagenesis of the β7-β8 and β9-β10 hairpin loops and conserved zinc binding domain cysteines. Front Microbiol 2014; 5:123. [PMID: 24723920 PMCID: PMC3972481 DOI: 10.3389/fmicb.2014.00123] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 03/10/2014] [Indexed: 11/13/2022] Open
Abstract
The hexameric MCM complex is the catalytic core of the replicative helicase in eukaryotic and archaeal cells. Here we describe the first in vivo analysis of archaeal MCM protein structure and function relationships using the genetically tractable haloarchaeon Haloferax volcanii as a model system. Hfx. volcanii encodes a single MCM protein that is part of the previously identified core group of haloarchaeal MCM proteins. Three structural features of the N-terminal domain of the Hfx. volcanii MCM protein were targeted for mutagenesis: the β7-β8 and β9-β10 β-hairpin loops and putative zinc binding domain. Five strains carrying single point mutations in the β7-β8 β-hairpin loop were constructed, none of which displayed impaired cell growth under normal conditions or when treated with the DNA damaging agent mitomycin C. However, short sequence deletions within the β7-β8 β-hairpin were not tolerated and neither was replacement of the highly conserved residue glutamate 187 with alanine. Six strains carrying paired alanine substitutions within the β9-β10 β-hairpin loop were constructed, leading to the conclusion that no individual amino acid within that hairpin loop is absolutely required for MCM function, although one of the mutant strains displays greatly enhanced sensitivity to mitomycin C. Deletions of two or four amino acids from the β9-β10 β-hairpin were tolerated but mutants carrying larger deletions were inviable. Similarly, it was not possible to construct mutants in which any of the conserved zinc binding cysteines was replaced with alanine, underlining the likely importance of zinc binding for MCM function. The results of these studies demonstrate the feasibility of using Hfx. volcanii as a model system for reverse genetic analysis of archaeal MCM protein function and provide important confirmation of the in vivo importance of conserved structural features identified by previous bioinformatic, biochemical and structural studies.
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Affiliation(s)
- Tatjana P Kristensen
- Department of Biology, University of Copenhagen, Københavns Biocenter Copenhagen N, Denmark
| | - Reeja Maria Cherian
- Department of Biology, University of Copenhagen, Københavns Biocenter Copenhagen N, Denmark
| | - Fiona C Gray
- Department of Biology, University of Copenhagen, Københavns Biocenter Copenhagen N, Denmark
| | - Stuart A MacNeill
- Department of Biology, University of Copenhagen, Københavns Biocenter Copenhagen N, Denmark ; School of Biology, University of St. Andrews North Haugh, St. Andrews, Fife, UK
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48
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Szambowska A, Tessmer I, Kursula P, Usskilat C, Prus P, Pospiech H, Grosse F. DNA binding properties of human Cdc45 suggest a function as molecular wedge for DNA unwinding. Nucleic Acids Res 2013; 42:2308-19. [PMID: 24293646 PMCID: PMC3936751 DOI: 10.1093/nar/gkt1217] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The cell division cycle protein 45 (Cdc45) represents an essential replication factor that, together with the Mcm2-7 complex and the four subunits of GINS, forms the replicative DNA helicase in eukaryotes. Recombinant human Cdc45 (hCdc45) was structurally characterized and its DNA-binding properties were determined. Synchrotron radiation circular dichroism spectroscopy, dynamic light scattering, small-angle X-ray scattering and atomic force microscopy revealed that hCdc45 exists as an alpha-helical monomer and possesses a structure similar to its bacterial homolog RecJ. hCdc45 bound long (113-mer or 80-mer) single-stranded DNA fragments with a higher affinity than shorter ones (34-mer). hCdc45 displayed a preference for 3′ protruding strands and bound tightly to single-strand/double-strand DNA junctions, such as those presented by Y-shaped DNA, bubbles and displacement loops, all of which appear transiently during the initiation of DNA replication. Collectively, our findings suggest that hCdc45 not only binds to but also slides on DNA with a 3′–5′ polarity and, thereby acts as a molecular ‘wedge’ to initiate DNA strand displacement.
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Affiliation(s)
- Anna Szambowska
- Research Group Biochemistry, Leibniz Institute for Age Research -Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany, Laboratory of Molecular Biology IBB PAS, Affiliated with University of Gdansk, Wita Stwosza 59 Gdansk, Poland, Rudolf Virchow Center, DFG Research Center for Experimental Biomedicine, Josef Schneider Strasse 2, 7080 Wurzburg, Germany, Department of Biochemistry, Oulu, P.O. Box 3000, University of Oulu, Oulu 90014, Finland, Department of Chemistry, University of Hamburg/DESY, Notkestrasse 85, 22607 Hamburg, Germany, Biocenter Oulu, P.O. Box 3000, University of Oulu, Oulu 90014, Finland and Center for Molecular Biomedicine, Friedrich-Schiller University, Biochemistry Department, Jena, Germany
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49
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Bell SD, Botchan MR. The minichromosome maintenance replicative helicase. Cold Spring Harb Perspect Biol 2013; 5:a012807. [PMID: 23881943 DOI: 10.1101/cshperspect.a012807] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The eukaryotic replicative helicase, the minichromosome maintenance (MCM) complex, is composed of six distinct, but related, subunits MCM(2-7). The relationship between the sequences of the subunits indicates that they are derived from a common ancestor and indeed, present-day archaea possess a homohexameric MCM. Recent progress in the biochemical and structural studies of both eukaryal and archaeal MCM complexes are beginning to shed light on the mechanisms of action of this key component of the replisome.
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Affiliation(s)
- Stephen D Bell
- Molecular and Cellular Biochemistry Department, Biology Department, Indiana University, Bloomington, Indiana 47405
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50
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Abstract
Recent advances in the characterization of the archaeal DNA replication system together with comparative genomic analysis have led to the identification of several previously uncharacterized archaeal proteins involved in replication and currently reveal a nearly complete correspondence between the components of the archaeal and eukaryotic replication machineries. It can be inferred that the archaeal ancestor of eukaryotes and even the last common ancestor of all extant archaea possessed replication machineries that were comparable in complexity to the eukaryotic replication system. The eukaryotic replication system encompasses multiple paralogs of ancestral components such that heteromeric complexes in eukaryotes replace archaeal homomeric complexes, apparently along with subfunctionalization of the eukaryotic complex subunits. In the archaea, parallel, lineage-specific duplications of many genes encoding replication machinery components are detectable as well; most of these archaeal paralogs remain to be functionally characterized. The archaeal replication system shows remarkable plasticity whereby even some essential components such as DNA polymerase and single-stranded DNA-binding protein are displaced by unrelated proteins with analogous activities in some lineages.
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Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
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