1
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He Q, Wang F, Yao NY, O'Donnell ME, Li H. Structures of the human leading strand Polε-PCNA holoenzyme. Nat Commun 2024; 15:7847. [PMID: 39245668 PMCID: PMC11381554 DOI: 10.1038/s41467-024-52257-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 09/02/2024] [Indexed: 09/10/2024] Open
Abstract
In eukaryotes, the leading strand DNA is synthesized by Polε and the lagging strand by Polδ. These replicative polymerases have higher processivity when paired with the DNA clamp PCNA. While the structure of the yeast Polε catalytic domain has been determined, how Polε interacts with PCNA is unknown in any eukaryote, human or yeast. Here we report two cryo-EM structures of human Polε-PCNA-DNA complex, one in an incoming nucleotide bound state and the other in a nucleotide exchange state. The structures reveal an unexpected three-point interface between the Polε catalytic domain and PCNA, with the conserved PIP (PCNA interacting peptide)-motif, the unique P-domain, and the thumb domain each interacting with a different protomer of the PCNA trimer. We propose that the multi-point interface prevents other PIP-containing factors from recruiting to PCNA while PCNA functions with Polε. Comparison of the two states reveals that the finger domain pivots around the [4Fe-4S] cluster-containing tip of the P-domain to regulate nucleotide exchange and incoming nucleotide binding.
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Affiliation(s)
- Qing He
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Feng Wang
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Nina Y Yao
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Michael E O'Donnell
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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2
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You Z, Masai H. Assembly, Activation, and Helicase Actions of MCM2-7: Transition from Inactive MCM2-7 Double Hexamers to Active Replication Forks. BIOLOGY 2024; 13:629. [PMID: 39194567 DOI: 10.3390/biology13080629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024]
Abstract
In this review, we summarize the processes of the assembly of multi-protein replisomes at the origins of replication. Replication licensing, the loading of inactive minichromosome maintenance double hexamers (dhMCM2-7) during the G1 phase, is followed by origin firing triggered by two serine-threonine kinases, Cdc7 (DDK) and CDK, leading to the assembly and activation of Cdc45/MCM2-7/GINS (CMG) helicases at the entry into the S phase and the formation of replisomes for bidirectional DNA synthesis. Biochemical and structural analyses of the recruitment of initiation or firing factors to the dhMCM2-7 for the formation of an active helicase and those of origin melting and DNA unwinding support the steric exclusion unwinding model of the CMG helicase.
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Affiliation(s)
- Zhiying You
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan
| | - Hisao Masai
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
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3
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Schmid EW, Walter JC. Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588596. [PMID: 38645019 PMCID: PMC11030396 DOI: 10.1101/2024.04.09.588596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Protein-protein interactions (PPIs) are ubiquitous in biology, yet a comprehensive structural characterization of the PPIs underlying biochemical processes is lacking. Although AlphaFold-Multimer (AF-M) has the potential to fill this knowledge gap, standard AF-M confidence metrics do not reliably separate relevant PPIs from an abundance of false positive predictions. To address this limitation, we used machine learning on well curated datasets to train a Structure Prediction and Omics informed Classifier called SPOC that shows excellent performance in separating true and false PPIs, including in proteome-wide screens. We applied SPOC to an all-by-all matrix of nearly 300 human genome maintenance proteins, generating ~40,000 predictions that can be viewed at predictomes.org, where users can also score their own predictions with SPOC. High confidence PPIs discovered using our approach suggest novel hypotheses in genome maintenance. Our results provide a framework for interpreting large scale AF-M screens and help lay the foundation for a proteome-wide structural interactome.
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Affiliation(s)
- Ernst W. Schmid
- Department of Biological Chemistry & Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Johannes C. Walter
- Department of Biological Chemistry & Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
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4
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Williams SL, Casas‐Delucchi CS, Raguseo F, Guneri D, Li Y, Minamino M, Fletcher EE, Yeeles JTP, Keyser UF, Waller ZAE, Di Antonio M, Coster G. Replication-induced DNA secondary structures drive fork uncoupling and breakage. EMBO J 2023; 42:e114334. [PMID: 37781931 PMCID: PMC10646557 DOI: 10.15252/embj.2023114334] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023] Open
Abstract
Sequences that form DNA secondary structures, such as G-quadruplexes (G4s) and intercalated-Motifs (iMs), are abundant in the human genome and play various physiological roles. However, they can also interfere with replication and threaten genome stability. Multiple lines of evidence suggest G4s inhibit replication, but the underlying mechanism remains unclear. Moreover, evidence of how iMs affect the replisome is lacking. Here, we reconstitute replication of physiologically derived structure-forming sequences to find that a single G4 or iM arrest DNA replication. Direct single-molecule structure detection within solid-state nanopores reveals structures form as a consequence of replication. Combined genetic and biophysical characterisation establishes that structure stability and probability of structure formation are key determinants of replisome arrest. Mechanistically, replication arrest is caused by impaired synthesis, resulting in helicase-polymerase uncoupling. Significantly, iMs also induce breakage of nascent DNA. Finally, stalled forks are only rescued by a specialised helicase, Pif1, but not Rrm3, Sgs1, Chl1 or Hrq1. Altogether, we provide a mechanism for quadruplex structure formation and resolution during replication and highlight G4s and iMs as endogenous sources of replication stress.
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Affiliation(s)
- Sophie L Williams
- Genome Replication Lab, Division of Cancer Biology, Institute of Cancer ResearchChester Beatty LaboratoriesLondonUK
| | - Corella S Casas‐Delucchi
- Genome Replication Lab, Division of Cancer Biology, Institute of Cancer ResearchChester Beatty LaboratoriesLondonUK
| | - Federica Raguseo
- Chemistry DepartmentImperial College London, MSRHLondonUK
- Institute of Chemical Biology, MSRHLondonUK
| | | | - Yunxuan Li
- Cavendish LaboratoryUniversity of CambridgeCambridgeUK
| | | | | | | | | | | | - Marco Di Antonio
- Chemistry DepartmentImperial College London, MSRHLondonUK
- Institute of Chemical Biology, MSRHLondonUK
- Francis Crick InstituteLondonUK
| | - Gideon Coster
- Genome Replication Lab, Division of Cancer Biology, Institute of Cancer ResearchChester Beatty LaboratoriesLondonUK
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5
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Xu Z, Feng J, Yu D, Huo Y, Ma X, Lam WH, Liu Z, Li XD, Ishibashi T, Dang S, Zhai Y. Synergism between CMG helicase and leading strand DNA polymerase at replication fork. Nat Commun 2023; 14:5849. [PMID: 37730685 PMCID: PMC10511561 DOI: 10.1038/s41467-023-41506-0] [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: 12/21/2021] [Accepted: 09/07/2023] [Indexed: 09/22/2023] Open
Abstract
The replisome that replicates the eukaryotic genome consists of at least three engines: the Cdc45-MCM-GINS (CMG) helicase that separates duplex DNA at the replication fork and two DNA polymerases, one on each strand, that replicate the unwound DNA. Here, we determined a series of cryo-electron microscopy structures of a yeast replisome comprising CMG, leading-strand polymerase Polε and three accessory factors on a forked DNA. In these structures, Polε engages or disengages with the motor domains of the CMG by occupying two alternative positions, which closely correlate with the rotational movement of the single-stranded DNA around the MCM pore. During this process, the polymerase remains stably coupled to the helicase using Psf1 as a hinge. This synergism is modulated by a concerted rearrangement of ATPase sites to drive DNA translocation. The Polε-MCM coupling is not only required for CMG formation to initiate DNA replication but also facilitates the leading-strand DNA synthesis mediated by Polε. Our study elucidates a mechanism intrinsic to the replisome that coordinates the activities of CMG and Polε to negotiate any roadblocks, DNA damage, and epigenetic marks encountered during translocation along replication forks.
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Affiliation(s)
- Zhichun Xu
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Jianrong Feng
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Daqi Yu
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Yunjing Huo
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Xiaohui Ma
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Wai Hei Lam
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Toyotaka Ishibashi
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Shangyu Dang
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
- HKUST-Shenzhen Research Institute, 518057, Nanshan, Shenzhen, China.
| | - Yuanliang Zhai
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
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6
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Dmowski M, Makiela-Dzbenska K, Sharma S, Chabes A, Fijalkowska IJ. Impairment of the non-catalytic subunit Dpb2 of DNA Pol ɛ results in increased involvement of Pol δ on the leading strand. DNA Repair (Amst) 2023; 129:103541. [PMID: 37481989 DOI: 10.1016/j.dnarep.2023.103541] [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: 03/31/2023] [Revised: 05/29/2023] [Accepted: 07/05/2023] [Indexed: 07/25/2023]
Abstract
The generally accepted model assumes that leading strand synthesis is performed by Pol ε, while lagging-strand synthesis is catalyzed by Pol δ. Pol ε has been shown to target the leading strand by interacting with the CMG helicase [Cdc45 Mcm2-7 GINS(Psf1-3, Sld5)]. Proper functioning of the CMG-Pol ɛ, the helicase-polymerase complex is essential for its progression and the fidelity of DNA replication. Dpb2p, the essential non-catalytic subunit of Pol ε plays a key role in maintaining the correct architecture of the replisome by acting as a link between Pol ε and the CMG complex. Using a temperature-sensitive dpb2-100 mutant previously isolated in our laboratory, and a genetic system which takes advantage of a distinct mutational signature of the Pol δ-L612M variant which allows detection of the involvement of Pol δ in the replication of particular DNA strands we show that in yeast cells with an impaired Dpb2 subunit, the contribution of Pol δ to the replication of the leading strand is significantly increased.
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Affiliation(s)
- Michal Dmowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland.
| | - Karolina Makiela-Dzbenska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Iwona J Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland.
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7
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Rouillon C, Eckhardt BV, Kollenstart L, Gruss F, Verkennis AE, Rondeel I, Krijger PHL, Ricci G, Biran A, van Laar T, Delvaux de Fenffe CM, Luppens G, Albanese P, Sato K, Scheltema RA, de Laat W, Knipscheer P, Dekker N, Groth A, Mattiroli F. CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands. Nucleic Acids Res 2023; 51:3770-3792. [PMID: 36942484 PMCID: PMC10164577 DOI: 10.1093/nar/gkad171] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 02/18/2023] [Accepted: 02/23/2023] [Indexed: 03/23/2023] Open
Abstract
During every cell cycle, both the genome and the associated chromatin must be accurately replicated. Chromatin Assembly Factor-1 (CAF-1) is a key regulator of chromatin replication, but how CAF-1 functions in relation to the DNA replication machinery is unknown. Here, we reveal that this crosstalk differs between the leading and lagging strand at replication forks. Using biochemical reconstitutions, we show that DNA and histones promote CAF-1 recruitment to its binding partner PCNA and reveal that two CAF-1 complexes are required for efficient nucleosome assembly under these conditions. Remarkably, in the context of the replisome, CAF-1 competes with the leading strand DNA polymerase epsilon (Polϵ) for PCNA binding. However, CAF-1 does not affect the activity of the lagging strand DNA polymerase Delta (Polδ). Yet, in cells, CAF-1 deposits newly synthesized histones equally on both daughter strands. Thus, on the leading strand, chromatin assembly by CAF-1 cannot occur simultaneously to DNA synthesis, while on the lagging strand these processes may be coupled. We propose that these differences may facilitate distinct parental histone recycling mechanisms and accommodate the inherent asymmetry of DNA replication.
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Affiliation(s)
- Clément Rouillon
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bruna V Eckhardt
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leonie Kollenstart
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Fabian Gruss
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Inge Rondeel
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Giulia Ricci
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alva Biran
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Theo van Laar
- Kavli Institute of Nanoscience Delft, TU Delft, The Netherlands
| | | | - Georgiana Luppens
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
| | - Pascal Albanese
- Utrecht Institute for Pharmaceutical Sciences, Utrecht University, the Netherlands
| | - Koichi Sato
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Richard A Scheltema
- Utrecht Institute for Pharmaceutical Sciences, Utrecht University, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Nynke H Dekker
- Kavli Institute of Nanoscience Delft, TU Delft, The Netherlands
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Francesca Mattiroli
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
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8
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Vipat S, Gupta D, Jonchhe S, Anderspuk H, Rothenberg E, Moiseeva TN. The non-catalytic role of DNA polymerase epsilon in replication initiation in human cells. Nat Commun 2022; 13:7099. [PMID: 36402816 PMCID: PMC9675812 DOI: 10.1038/s41467-022-34911-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022] Open
Abstract
DNA polymerase epsilon (PolE) in an enzyme essential for DNA replication. Deficiencies and mutations in PolE cause severe developmental abnormalities and cancers. Paradoxically, the catalytic domain of yeast PolE catalytic subunit is dispensable for survival, and its non-catalytic essential function is linked with replicative helicase (CMG) assembly. Less is known about the PolE role in replication initiation in human cells. Here we use an auxin-inducible degron system to study the effect of POLE1 depletion on replication initiation in U2OS cells. POLE1-depleted cells were able to assemble CMG helicase and initiate DNA synthesis that failed shortly after. Expression of POLE1 non-catalytic domain rescued this defect resulting in slow, but continuous DNA synthesis. We propose a model where in human U2OS cells POLE1/POLE2 are dispensable for CMG assembly, but essential during later steps of replication initiation. Our study provides some insights into the role of PolE in replication initiation in human cells.
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Affiliation(s)
- Sameera Vipat
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, 12618, Estonia
| | - Dipika Gupta
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Sagun Jonchhe
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Hele Anderspuk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, 12618, Estonia
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Tatiana N Moiseeva
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, 12618, Estonia.
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9
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Du H, Jolly A, Grochowski CM, Yuan B, Dawood M, Jhangiani SN, Li H, Muzny D, Fatih JM, Coban-Akdemir Z, Carlin ME, Scheuerle AE, Witzl K, Posey JE, Pendleton M, Harrington E, Juul S, Hastings PJ, Bi W, Gibbs RA, Sedlazeck FJ, Lupski JR, Carvalho CMB, Liu P. The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation. Genome Med 2022; 14:122. [PMID: 36303224 PMCID: PMC9609164 DOI: 10.1186/s13073-022-01123-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/10/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The multiple de novo copy number variant (MdnCNV) phenotype is described by having four or more constitutional de novo CNVs (dnCNVs) arising independently throughout the human genome within one generation. It is a rare peri-zygotic mutational event, previously reported to be seen once in every 12,000 individuals referred for genome-wide chromosomal microarray analysis due to congenital abnormalities. These rare families provide a unique opportunity to understand the genetic factors of peri-zygotic genome instability and the impact of dnCNV on human diseases. METHODS Chromosomal microarray analysis (CMA), array-based comparative genomic hybridization, short- and long-read genome sequencing (GS) were performed on the newly identified MdnCNV family to identify de novo mutations including dnCNVs, de novo single-nucleotide variants (dnSNVs), and indels. Short-read GS was performed on four previously published MdnCNV families for dnSNV analysis. Trio-based rare variant analysis was performed on the newly identified individual and four previously published MdnCNV families to identify potential genetic etiologies contributing to the peri-zygotic genomic instability. Lin semantic similarity scores informed quantitative human phenotype ontology analysis on three MdnCNV families to identify gene(s) driving or contributing to the clinical phenotype. RESULTS In the newly identified MdnCNV case, we revealed eight de novo tandem duplications, each ~ 1 Mb, with microhomology at 6/8 breakpoint junctions. Enrichment of de novo single-nucleotide variants (SNV; 6/79) and de novo indels (1/12) was found within 4 Mb of the dnCNV genomic regions. An elevated post-zygotic SNV mutation rate was observed in MdnCNV families. Maternal rare variant analyses identified three genes in distinct families that may contribute to the MdnCNV phenomenon. Phenotype analysis suggests that gene(s) within dnCNV regions contribute to the observed proband phenotype in 3/3 cases. CNVs in two cases, a contiguous gene duplication encompassing PMP22 and RAI1 and another duplication affecting NSD1 and SMARCC2, contribute to the clinically observed phenotypic manifestations. CONCLUSIONS Characteristic features of dnCNVs reported here are consistent with a microhomology-mediated break-induced replication (MMBIR)-driven mechanism during the peri-zygotic period. Maternal genetic variants in DNA repair genes potentially contribute to peri-zygotic genomic instability. Variable phenotypic features were observed across a cohort of three MdnCNV probands, and computational quantitative phenotyping revealed that two out of three had evidence for the contribution of more than one genetic locus to the proband's phenotype supporting the hypothesis of de novo multilocus pathogenic variation (MPV) in those families.
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Affiliation(s)
- Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christopher M Grochowski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics Laboratory, Houston, TX, 77021, USA
- Seattle Children's Hospital, Seattle, WA, 98105, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Mary Esther Carlin
- Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Angela E Scheuerle
- Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Division of Genetics Diagnostics, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Karin Witzl
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, 1000, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | | | | | - Sissel Juul
- Oxford Nanopore Technologies Inc, New York, NY, 10013, USA
| | - P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, BCM, Houston, TX, 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics Laboratory, Houston, TX, 77021, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fritz J Sedlazeck
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Texas Children's Hospital, Houston, TX, 77030, USA.
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Pacific Northwest Research Institute, 720 Broadway, Seattle, WA, 98122, USA.
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Baylor Genetics Laboratory, Houston, TX, 77021, USA.
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10
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Lisova AE, Baranovskiy AG, Morstadt LM, Babayeva ND, Stepchenkova EI, Tahirov TH. The iron-sulfur cluster is essential for DNA binding by human DNA polymerase ε. Sci Rep 2022; 12:17436. [PMID: 36261579 PMCID: PMC9581978 DOI: 10.1038/s41598-022-21550-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/28/2022] [Indexed: 01/13/2023] Open
Abstract
DNA polymerase ε (Polε) is a key enzyme for DNA replication in eukaryotes. Recently it was shown that the catalytic domain of yeast Polε (PolεCD) contains a [4Fe-4S] cluster located at the base of the processivity domain (P-domain) and coordinated by four conserved cysteines. In this work, we show that human PolεCD (hPolεCD) expressed in bacterial cells also contains an iron-sulfur cluster. In comparison, recombinant hPolεCD produced in insect cells contains significantly lower level of iron. The iron content of purified hPolECD samples correlates with the level of DNA-binding molecules, which suggests an important role of the iron-sulfur cluster in hPolε interaction with DNA. Indeed, mutation of two conserved cysteines that coordinate the cluster abolished template:primer binding as well as DNA polymerase and proofreading exonuclease activities. We propose that the cluster regulates the conformation of the P-domain, which, like a gatekeeper, controls access to a DNA-binding cleft for a template:primer. The binding studies demonstrated low affinity of hPolεCD to DNA and a strong effect of salt concentration on stability of the hPolεCD/DNA complex. Pre-steady-state kinetic studies have shown a maximal polymerization rate constant of 51.5 s-1 and a relatively low affinity to incoming dNTP with an apparent KD of 105 µM.
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Affiliation(s)
- Alisa E Lisova
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Andrey G Baranovskiy
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Lucia M Morstadt
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Nigar D Babayeva
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Elena I Stepchenkova
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Department of Genetics and Biotechnology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Saint-Petersburg State University, Russian Academy of Sciences, St. Petersburg, Russia
| | - Tahir H Tahirov
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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11
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Fujisawa R, Polo Rivera C, Labib KPM. Multiple UBX proteins reduce the ubiquitin threshold of the mammalian p97-UFD1-NPL4 unfoldase. eLife 2022; 11:e76763. [PMID: 35920641 PMCID: PMC9377798 DOI: 10.7554/elife.76763] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022] Open
Abstract
The p97/Cdc48 ATPase and its ubiquitin receptors Ufd1-Npl4 are essential to unfold ubiquitylated proteins in many areas of eukaryotic cell biology. In yeast, Cdc48-Ufd1-Npl4 is controlled by a quality control mechanism, whereby substrates must be conjugated to at least five ubiquitins. Here, we show that mammalian p97-UFD1-NPL4 is governed by a complex interplay between additional p97 cofactors and the number of conjugated ubiquitins. Using reconstituted assays for the disassembly of ubiquitylated CMG (Cdc45-MCM-GINS) helicase by human p97-UFD1-NPL4, we show that the unfoldase has a high ubiquitin threshold for substrate unfolding, which can be reduced by the UBX proteins UBXN7, FAF1, or FAF2. Our data indicate that the UBX proteins function by binding to p97-UFD1-NPL4 and stabilising productive interactions between UFD1-NPL4 and K48-linked chains of at least five ubiquitins. Stimulation by UBXN7 is dependent upon known ubiquitin-binding motifs, whereas FAF1 and FAF2 use a previously uncharacterised coiled-coil domain to reduce the ubiquitin threshold of p97-UFD1-NPL4. We show that deleting the Ubnx7 and Faf1 genes impairs CMG disassembly during S-phase and mitosis and sensitises cells to reduced ubiquitin ligase activity. These findings indicate that multiple UBX proteins are important for the efficient unfolding of ubiquitylated proteins by p97-UFD1-NPL4 in mammalian cells.
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Affiliation(s)
- Ryo Fujisawa
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Cristian Polo Rivera
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Karim PM Labib
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of DundeeDundeeUnited Kingdom
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12
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Casas-Delucchi CS, Daza-Martin M, Williams SL, Coster G. The mechanism of replication stalling and recovery within repetitive DNA. Nat Commun 2022; 13:3953. [PMID: 35853874 PMCID: PMC9296464 DOI: 10.1038/s41467-022-31657-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 06/27/2022] [Indexed: 11/09/2022] Open
Abstract
Accurate chromosomal DNA replication is essential to maintain genomic stability. Genetic evidence suggests that certain repetitive sequences impair replication, yet the underlying mechanism is poorly defined. Replication could be directly inhibited by the DNA template or indirectly, for example by DNA-bound proteins. Here, we reconstitute replication of mono-, di- and trinucleotide repeats in vitro using eukaryotic replisomes assembled from purified proteins. We find that structure-prone repeats are sufficient to impair replication. Whilst template unwinding is unaffected, leading strand synthesis is inhibited, leading to fork uncoupling. Synthesis through hairpin-forming repeats is rescued by replisome-intrinsic mechanisms, whereas synthesis of quadruplex-forming repeats requires an extrinsic accessory helicase. DNA-induced fork stalling is mechanistically similar to that induced by leading strand DNA lesions, highlighting structure-prone repeats as an important potential source of replication stress. Thus, we propose that our understanding of the cellular response to replication stress may also be applied to DNA-induced replication stalling.
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Affiliation(s)
- Corella S Casas-Delucchi
- Genome Replication lab, Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Manuel Daza-Martin
- Genome Replication lab, Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Sophie L Williams
- Genome Replication lab, Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Gideon Coster
- Genome Replication lab, Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK.
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13
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Lisova AE, Baranovskiy AG, Morstadt LM, Babayeva ND, Tahirov TH. Efficient discrimination against RNA-containing primers by human DNA polymerase ε. Sci Rep 2022; 12:10163. [PMID: 35715491 PMCID: PMC9205888 DOI: 10.1038/s41598-022-14602-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/09/2022] [Indexed: 01/13/2023] Open
Abstract
DNA polymerase ε (Polε) performs bulk synthesis of DNA on the leading strand during genome replication. Polε binds two substrates, a template:primer and dNTP, and catalyzes a covalent attachment of dNMP to the 3' end of the primer. Previous studies have shown that Polε easily inserts and extends ribonucleotides, which may promote mutagenesis and genome instability. In this work, we analyzed the mechanisms of discrimination against RNA-containing primers by human Polε (hPolε), performing binding and kinetic studies at near-physiological salt concentration. Pre-steady-state kinetic studies revealed that hPolεCD extends RNA primers with approximately 3300-fold lower efficiency in comparison to DNA, and addition of one dNMP to the 3' end of an RNA primer increases activity 36-fold. Likewise, addition of one rNMP to the 3' end of a DNA primer reduces activity 38-fold. The binding studies conducted in the presence of 0.15 M NaCl revealed that human hPolεCD has low affinity to DNA (KD of 1.5 µM). Strikingly, a change of salt concentration from 0.1 M to 0.15 M reduces the stability of the hPolεCD/DNA complex by 25-fold. Upon template:primer binding, the incoming dNTP and magnesium ions make hPolε discriminative against RNA and chimeric RNA-DNA primers. In summary, our studies revealed that hPolε discrimination against RNA-containing primers is based on the following factors: incoming dNTP, magnesium ions, a steric gate for the primer 2'OH, and the rigid template:primer binding pocket near the catalytic site. In addition, we showed the importance of conducting functional studies at near-physiological salt concentration.
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Affiliation(s)
- Alisa E Lisova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Lucia M Morstadt
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Nigar D Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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14
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Zaffar E, Ferreira P, Sanchez-Pulido L, Boos D. The Role of MTBP as a Replication Origin Firing Factor. BIOLOGY 2022; 11:biology11060827. [PMID: 35741348 PMCID: PMC9219753 DOI: 10.3390/biology11060827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 12/12/2022]
Abstract
The initiation step of replication at replication origins determines when and where in the genome replication machines, replisomes, are generated. Tight control of replication initiation helps facilitate the two main tasks of genome replication, to duplicate the genome accurately and exactly once each cell division cycle. The regulation of replication initiation must ensure that initiation occurs during the S phase specifically, that no origin fires more than once per cell cycle, that enough origins fire to avoid non-replicated gaps, and that the right origins fire at the right time but only in favorable circumstances. Despite its importance for genetic homeostasis only the main molecular processes of eukaryotic replication initiation and its cellular regulation are understood. The MTBP protein (Mdm2-binding protein) is so far the last core replication initiation factor identified in metazoan cells. MTBP is the orthologue of yeast Sld7. It is essential for origin firing, the maturation of pre-replicative complexes (pre-RCs) into replisomes, and is emerging as a regulation focus targeted by kinases and by regulated degradation. We present recent insight into the structure and cellular function of the MTBP protein in light of recent structural and biochemical studies revealing critical molecular details of the eukaryotic origin firing reaction. How the roles of MTBP in replication and other cellular processes are mutually connected and are related to MTBP's contribution to tumorigenesis remains largely unclear.
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Affiliation(s)
- Eman Zaffar
- Molecular Genetics II, Centre for Medical Biotechnology, University of Duisburg-Essen, 45141 Essen, Germany; (E.Z.); (P.F.)
| | - Pedro Ferreira
- Molecular Genetics II, Centre for Medical Biotechnology, University of Duisburg-Essen, 45141 Essen, Germany; (E.Z.); (P.F.)
| | - Luis Sanchez-Pulido
- Medical Research Council Human Genetics Unit, IGC, University of Edinburgh, Edinburgh EH9 3JR, UK;
| | - Dominik Boos
- Molecular Genetics II, Centre for Medical Biotechnology, University of Duisburg-Essen, 45141 Essen, Germany; (E.Z.); (P.F.)
- Correspondence: ; Tel.: +49-201-183-4132
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15
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Batra S, Devbhandari S, Remus D. CMG helicase activity on G4-containing DNA templates. Methods Enzymol 2022; 672:233-260. [PMID: 35934477 PMCID: PMC9578012 DOI: 10.1016/bs.mie.2022.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
G-quadruplexes (G4s) are non-canonical nucleic acid structures that form in G-rich regions of the genome and threaten genome stability by interfering with DNA replication. However, the underlying mechanisms are poorly understood. We have recently found that G4s can stall eukaryotic replication forks by blocking the progression of replicative DNA helicase, CMG. In this paper, we detail the methodology of DNA unwinding assays to investigate the impact of G4s on CMG progression. The method details the purification of recombinantly expressed CMG from the budding yeast, Saccharomyces cerevisiae, purification of synthetic oligonucleotides, and covers various aspects of DNA substrate preparation, reaction setup and result interpretation. The use of synthetic oligonucleotides provides the advantage of allowing to control the formation of G4 structures in DNA substrates. The methods discussed here can be adapted for the study of other DNA helicases and provide a general template for the assembly of DNA substrates with distinct G4 structures.
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Affiliation(s)
- Sahil Batra
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Sujan Devbhandari
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Dirk Remus
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
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16
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Abstract
DNA replication in eukaryotic cells initiates from large numbers of sites called replication origins. Initiation of replication from these origins must be tightly controlled to ensure the entire genome is precisely duplicated in each cell cycle. This is accomplished through the regulation of the first two steps in replication: loading and activation of the replicative DNA helicase. Here we describe what is known about the mechanism and regulation of these two reactions from a genetic, biochemical, and structural perspective, focusing on recent progress using proteins from budding yeast. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London, UK;
| | - John F X Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, London, UK;
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17
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Multiple roles of Pol epsilon in eukaryotic chromosome replication. Biochem Soc Trans 2022; 50:309-320. [PMID: 35129614 PMCID: PMC9022971 DOI: 10.1042/bst20210082] [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: 10/15/2021] [Revised: 12/23/2021] [Accepted: 01/06/2022] [Indexed: 11/17/2022]
Abstract
Pol epsilon is a tetrameric assembly that plays distinct roles during eukaryotic chromosome replication. It catalyses leading strand DNA synthesis; yet this function is dispensable for viability. Its non-catalytic domains instead play an essential role in the assembly of the active replicative helicase and origin activation, while non-essential histone-fold subunits serve a critical function in parental histone redeposition onto newly synthesised DNA. Furthermore, Pol epsilon plays a structural role in linking the RFC–Ctf18 clamp loader to the replisome, supporting processive DNA synthesis, DNA damage response signalling as well as sister chromatid cohesion. In this minireview, we discuss recent biochemical and structural work that begins to explain various aspects of eukaryotic chromosome replication, with a focus on the multiple roles of Pol epsilon in this process.
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18
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Increased contribution of DNA polymerase delta to the leading strand replication in yeast with an impaired CMG helicase complex. DNA Repair (Amst) 2022; 110:103272. [DOI: 10.1016/j.dnarep.2022.103272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/24/2021] [Accepted: 01/04/2022] [Indexed: 11/19/2022]
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19
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Jones ML, Baris Y, Taylor MRG, Yeeles JTP. Structure of a human replisome shows the organisation and interactions of a DNA replication machine. EMBO J 2021; 40:e108819. [PMID: 34694004 PMCID: PMC8634136 DOI: 10.15252/embj.2021108819] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 02/01/2023] Open
Abstract
The human replisome is an elaborate arrangement of molecular machines responsible for accurate chromosome replication. At its heart is the CDC45-MCM-GINS (CMG) helicase, which, in addition to unwinding the parental DNA duplex, arranges many proteins including the leading-strand polymerase Pol ε, together with TIMELESS-TIPIN, CLASPIN and AND-1 that have key and varied roles in maintaining smooth replisome progression. How these proteins are coordinated in the human replisome is poorly understood. We have determined a 3.2 Å cryo-EM structure of a human replisome comprising CMG, Pol ε, TIMELESS-TIPIN, CLASPIN and AND-1 bound to replication fork DNA. The structure permits a detailed understanding of how AND-1, TIMELESS-TIPIN and Pol ε engage CMG, reveals how CLASPIN binds to multiple replisome components and identifies the position of the Pol ε catalytic domain. Furthermore, the intricate network of contacts contributed by MCM subunits and TIMELESS-TIPIN with replication fork DNA suggests a mechanism for strand separation.
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20
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Jenkyn-Bedford M, Jones ML, Baris Y, Labib KPM, Cannone G, Yeeles JTP, Deegan TD. A conserved mechanism for regulating replisome disassembly in eukaryotes. Nature 2021; 600:743-747. [PMID: 34700328 PMCID: PMC8695382 DOI: 10.1038/s41586-021-04145-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/14/2021] [Indexed: 11/28/2022]
Abstract
Replisome disassembly is the final step of eukaryotic DNA replication and is triggered by ubiquitylation of the CDC45-MCM-GINS (CMG) replicative helicase1-3. Despite being driven by evolutionarily diverse E3 ubiquitin ligases in different eukaryotes (SCFDia2 in budding yeast1, CUL2LRR1 in metazoa4-7), replisome disassembly is governed by a common regulatory principle, in which ubiquitylation of CMG is suppressed before replication termination, to prevent replication fork collapse. Recent evidence suggests that this suppression is mediated by replication fork DNA8-10. However, it is unknown how SCFDia2 and CUL2LRR1 discriminate terminated from elongating replisomes, to selectively ubiquitylate CMG only after termination. Here we used cryo-electron microscopy to solve high-resolution structures of budding yeast and human replisome-E3 ligase assemblies. Our structures show that the leucine-rich repeat domains of Dia2 and LRR1 are structurally distinct, but bind to a common site on CMG, including the MCM3 and MCM5 zinc-finger domains. The LRR-MCM interaction is essential for replisome disassembly and, crucially, is occluded by the excluded DNA strand at replication forks, establishing the structural basis for the suppression of CMG ubiquitylation before termination. Our results elucidate a conserved mechanism for the regulation of replisome disassembly in eukaryotes, and reveal a previously unanticipated role for DNA in preserving replisome integrity.
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Affiliation(s)
| | | | | | - Karim P M Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, UK
| | | | | | - Tom D Deegan
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
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21
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McClure AW, Diffley JF. Rad53 checkpoint kinase regulation of DNA replication fork rate via Mrc1 phosphorylation. eLife 2021; 10:69726. [PMID: 34387546 PMCID: PMC8387023 DOI: 10.7554/elife.69726] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/12/2021] [Indexed: 12/18/2022] Open
Abstract
The Rad53 DNA checkpoint protein kinase plays multiple roles in the budding yeast cell response to DNA replication stress. Key amongst these is its enigmatic role in safeguarding DNA replication forks. Using DNA replication reactions reconstituted with purified proteins, we show Rad53 phosphorylation of Sld3/7 or Dbf4-dependent kinase blocks replication initiation whilst phosphorylation of Mrc1 or Mcm10 slows elongation. Mrc1 phosphorylation is necessary and sufficient to slow replication forks in complete reactions; Mcm10 phosphorylation can also slow replication forks, but only in the absence of unphosphorylated Mrc1. Mrc1 stimulates the unwinding rate of the replicative helicase, CMG, and Rad53 phosphorylation of Mrc1 prevents this. We show that a phosphorylation-mimicking Mrc1 mutant cannot stimulate replication in vitro and partially rescues the sensitivity of a rad53 null mutant to genotoxic stress in vivo. Our results show that Rad53 protects replication forks in part by antagonising Mrc1 stimulation of CMG unwinding.
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Affiliation(s)
- Allison W McClure
- Chromosome Replication Laboratory, The Francis Crick Institute, London, United Kingdom
| | - John Fx Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, London, United Kingdom
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22
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Guilliam TA. Mechanisms for Maintaining Eukaryotic Replisome Progression in the Presence of DNA Damage. Front Mol Biosci 2021; 8:712971. [PMID: 34295925 PMCID: PMC8290200 DOI: 10.3389/fmolb.2021.712971] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/25/2021] [Indexed: 12/04/2022] Open
Abstract
The eukaryotic replisome coordinates template unwinding and nascent-strand synthesis to drive DNA replication fork progression and complete efficient genome duplication. During its advancement along the parental template, each replisome may encounter an array of obstacles including damaged and structured DNA that impede its progression and threaten genome stability. A number of mechanisms exist to permit replisomes to overcome such obstacles, maintain their progression, and prevent fork collapse. A combination of recent advances in structural, biochemical, and single-molecule approaches have illuminated the architecture of the replisome during unperturbed replication, rationalised the impact of impediments to fork progression, and enhanced our understanding of DNA damage tolerance mechanisms and their regulation. This review focusses on these studies to provide an updated overview of the mechanisms that support replisomes to maintain their progression on an imperfect template.
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Affiliation(s)
- Thomas A. Guilliam
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
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23
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Willhoft O, Costa A. A structural framework for DNA replication and transcription through chromatin. Curr Opin Struct Biol 2021; 71:51-58. [PMID: 34218162 DOI: 10.1016/j.sbi.2021.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
In eukaryotic cells, DNA replication and transcription machineries uncoil nucleosomes along the double helix, to achieve the exposure of the single-stranded DNA template for nucleic acid synthesis. The replisome and RNA polymerases then redeposit histones onto DNA behind the advancing molecular motor, in a process that is crucial for epigenetic inheritance and homeostasis, respectively. Here, we compare and contrast the mechanisms by which these molecular machines advance through nucleosome arrays and discuss how chromatin remodellers can facilitate DNA replication and transcription.
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Affiliation(s)
- Oliver Willhoft
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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24
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Henrikus SS, Costa A. Towards a Structural Mechanism for Sister Chromatid Cohesion Establishment at the Eukaryotic Replication Fork. BIOLOGY 2021; 10:466. [PMID: 34073213 PMCID: PMC8229022 DOI: 10.3390/biology10060466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/23/2022]
Abstract
Cohesion between replicated chromosomes is essential for chromatin dynamics and equal segregation of duplicated genetic material. In the G1 phase, the ring-shaped cohesin complex is loaded onto duplex DNA, enriching at replication start sites, or "origins". During the same phase of the cell cycle, and also at the origin sites, two MCM helicases are loaded as symmetric double hexamers around duplex DNA. During the S phase, and through the action of replication factors, cohesin switches from encircling one parental duplex DNA to topologically enclosing the two duplicated DNA filaments, which are known as sister chromatids. Despite its vital importance, the structural mechanism leading to sister chromatid cohesion establishment at the replication fork is mostly elusive. Here we review the current understanding of the molecular interactions between the replication machinery and cohesin, which support sister chromatid cohesion establishment and cohesin function. In particular, we discuss how cryo-EM is shedding light on the mechanisms of DNA replication and cohesin loading processes. We further expound how frontier cryo-EM approaches, combined with biochemistry and single-molecule fluorescence assays, can lead to understanding the molecular basis of sister chromatid cohesion establishment at the replication fork.
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Affiliation(s)
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK;
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25
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Zach R, Carr AM. Increased expression of Polδ does not alter the canonical replication program in vivo. Wellcome Open Res 2021; 6:44. [PMID: 33796794 PMCID: PMC7974630 DOI: 10.12688/wellcomeopenres.16600.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2021] [Indexed: 01/08/2023] Open
Abstract
Background: In vitro experiments utilising the reconstituted Saccharomyces cerevisiae eukaryotic replisome indicated that the efficiency of the leading strand replication is impaired by a moderate increase in Polδ concentration. It was hypothesised that the slower rate of the leading strand synthesis characteristic for reactions containing two-fold and four-fold increased concentration of Polδ represented a consequence of a relatively rare event, during which Polδ stochastically outcompeted Polε and, in an inefficient manner, temporarily facilitated extension of the leading strand. Inspired by this observation, we aimed to determine whether similarly increased Polδ levels influence replication dynamics in vivo using the fission yeast Schizosaccharomyces pombe as a model system. Methods: To generate S. pombe strains over-expressing Polδ, we utilised Cre-Lox mediated cassette exchange and integrated one or three extra genomic copies of all four Polδ genes. To estimate expression of respective Polδ genes in Polδ-overexpressing mutants, we measured relative transcript levels of cdc1 + , cdc6 + (or cdc6 L591G ), cdc27 + and cdm1 + by reverse transcription followed by quantitative PCR (RT-qPCR). To assess the impact of Polδ over-expression on cell physiology and replication dynamics, we used standard cell biology techniques and polymerase usage sequencing. Results: We provide an evidence that two-fold and four-fold over-production of Polδ does not significantly alter growth rate, cellular morphology and S-phase duration. Polymerase usage sequencing analysis further indicates that increased Polδ expression does not change activities of Polδ, Polε and Polα at replication initiation sites and across replication termination zones. Additionally, we show that mutants over-expressing Polδ preserve WT-like distribution of replication origin efficiencies. Conclusions: Our experiments do not disprove the existence of opportunistic polymerase switches; however, the data indicate that, if stochastic replacement of Polε for Polδ does occur i n vivo, it represents a rare phenomenon that does not significantly influence canonical replication program.
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Affiliation(s)
- Róbert Zach
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Antony M. Carr
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
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26
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Stepchenkova EI, Zhuk AS, Cui J, Tarakhovskaya ER, Barbari SR, Shcherbakova PV, Polev DE, Fedorov R, Poliakov E, Rogozin IB, Lada AG, Pavlov YI. Compensation for the absence of the catalytically active half of DNA polymerase ε in yeast by positively selected mutations in CDC28. Genetics 2021; 218:6222163. [PMID: 33844024 DOI: 10.1093/genetics/iyab060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/02/2021] [Indexed: 11/14/2022] Open
Abstract
Current eukaryotic replication models postulate that leading and lagging DNA strands are replicated predominantly by dedicated DNA polymerases. The catalytic subunit of the leading strand DNA polymerase ε, Pol2, consists of two halves made of two different ancestral B-family DNA polymerases. Counterintuitively, the catalytically active N-terminal half is dispensable, while the inactive C-terminal part is required for viability. Despite extensive studies of yeast Saccharomyces cerevisiae strains lacking the active N-terminal half, it is still unclear how these strains survive and recover. We designed a robust method for constructing mutants with only the C-terminal part of Pol2. Strains without the active polymerase part show severe growth defects, sensitivity to replication inhibitors, chromosomal instability, and elevated spontaneous mutagenesis. Intriguingly, the slow-growing mutant strains rapidly accumulate fast-growing clones. Analysis of genomic DNA sequences of these clones revealed that the adaptation to the loss of the catalytic N-terminal part of Pol2 occurs by a positive selection of mutants with improved growth. Elevated mutation rates help generate sufficient numbers of these variants. Single nucleotide changes in the cell cycle-dependent kinase gene, CDC28, improve the growth of strains lacking the N-terminal part of Pol2, and rescue their sensitivity to replication inhibitors and, in parallel, lower mutation rates. Our study predicts that changes in mammalian homologs of cyclin-dependent kinases may contribute to cellular responses to the leading strand polymerase defects.
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Affiliation(s)
- Elena I Stepchenkova
- Laboratory of Mutagenesis and Genetic Toxicology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, Saint-Petersburg 199034, Russia.,Department of Genetics and Biotechnology, Saint-Petersburg State University, Saint-Petersburg 199034, Russia.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Anna S Zhuk
- ITMO University, Saint-Petersburg 191002, Russia
| | - Jian Cui
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Elena R Tarakhovskaya
- Laboratory of Mutagenesis and Genetic Toxicology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, Saint-Petersburg 199034, Russia.,Department of Plant Physiology and Biochemistry, Saint-Petersburg State University, Saint-Petersburg 199034, Russia
| | - Stephanie R Barbari
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Dmitrii E Polev
- Research Resource Center "Biobank," Research Park, Saint-Petersburg State University, Saint-Petersburg 198504, Russia
| | - Roman Fedorov
- Department of Mathematics, University of Pittsburgh, PA 15213, USA
| | - Eugenia Poliakov
- Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Artem G Lada
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, CA 92697, USA
| | - Youri I Pavlov
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Saint-Petersburg 199034, Russia.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Microbiology and Pathology, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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27
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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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28
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Zach R, Carr AM. Increased expression of Polδ does not alter the canonical replication program in vivo. Wellcome Open Res 2021; 6:44. [PMID: 33796794 PMCID: PMC7974630 DOI: 10.12688/wellcomeopenres.16600.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 11/20/2022] Open
Abstract
Background: In vitro experiments utilising the reconstituted Saccharomyces cerevisiae eukaryotic replisome indicated that the efficiency of the leading strand replication is impaired by a moderate increase in Polδ concentration. It was hypothesised that the slower rate of the leading strand synthesis characteristic for reactions containing two-fold and four-fold increased concentration of Polδ represented a consequence of a relatively rare event, during which Polδ stochastically outcompeted Polε and, in an inefficient manner, temporarily facilitated extension of the leading strand. Inspired by this observation, we aimed to determine whether similarly increased Polδ levels influence replication dynamics in vivo using the fission yeast Schizosaccharomyces pombe as a model system. Methods: To generate S. pombe strains over-expressing Polδ, we utilised Cre-Lox mediated cassette exchange and integrated one or three extra genomic copies of all four Polδ genes. To estimate expression of respective Polδ genes in Polδ-overexpressing mutants, we measured relative transcript levels of cdc1 + , cdc6 + (or cdc6 L591G ), cdc27 + and cdm1 + by reverse transcription followed by quantitative PCR (RT-qPCR). To assess the impact of Polδ over-expression on cell physiology and replication dynamics, we used standard cell biology techniques and polymerase usage sequencing. Results: We provide an evidence that two-fold and four-fold over-production of Polδ does not significantly alter growth rate, cellular morphology and S-phase duration. Polymerase usage sequencing analysis further indicates that increased Polδ expression does not change activities of Polδ, Polε and Polα at replication initiation sites and across replication termination zones. Additionally, we show that mutants over-expressing Polδ preserve WT-like distribution of replication origin efficiencies. Conclusions: Our experiments do not disprove the existence of opportunistic polymerase switches; however, the data indicate that, if stochastic replacement of Polε for Polδ does occur i n vivo, it represents a rare phenomenon that does not significantly influence canonical replication program.
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Affiliation(s)
- Róbert Zach
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Antony M. Carr
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
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29
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Caught in the act: structural dynamics of replication origin activation and fork progression. Biochem Soc Trans 2021; 48:1057-1066. [PMID: 32369549 PMCID: PMC7329347 DOI: 10.1042/bst20190998] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 01/03/2023]
Abstract
This review discusses recent advances in single-particle cryo-EM and single-molecule approaches used to visualise eukaryotic DNA replication reactions reconstituted in vitro. We comment on the new challenges facing structural biologists, as they turn to describing the dynamic cascade of events that lead to replication origin activation and fork progression.
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30
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Anatomy of a twin DNA replication factory. Biochem Soc Trans 2020; 48:2769-2778. [PMID: 33300972 PMCID: PMC7752080 DOI: 10.1042/bst20200640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 11/30/2022]
Abstract
The replication of DNA in chromosomes is initiated at sequences called origins at which two replisome machines are assembled at replication forks that move in opposite directions. Interestingly, in vivo studies observe that the two replication forks remain fastened together, often referred to as a replication factory. Replication factories containing two replisomes are well documented in cellular studies of bacteria (Escherichia coli and Bacillus subtilis) and the eukaryote, Saccharomyces cerevisiae. This basic twin replisome factory architecture may also be preserved in higher eukaryotes. Despite many years of documenting the existence of replication factories, the molecular details of how the two replisome machines are tethered together has been completely unknown in any organism. Recent structural studies shed new light on the architecture of a eukaryote replisome factory, which brings with it a new twist on how a replication factory may function.
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31
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Denkiewicz-Kruk M, Jedrychowska M, Endo S, Araki H, Jonczyk P, Dmowski M, Fijalkowska IJ. Recombination and Pol ζ Rescue Defective DNA Replication upon Impaired CMG Helicase-Pol ε Interaction. Int J Mol Sci 2020; 21:ijms21249484. [PMID: 33322195 PMCID: PMC7762974 DOI: 10.3390/ijms21249484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/06/2020] [Accepted: 12/09/2020] [Indexed: 11/22/2022] Open
Abstract
The CMG complex (Cdc45, Mcm2–7, GINS (Psf1, 2, 3, and Sld5)) is crucial for both DNA replication initiation and fork progression. The CMG helicase interaction with the leading strand DNA polymerase epsilon (Pol ε) is essential for the preferential loading of Pol ε onto the leading strand, the stimulation of the polymerase, and the modulation of helicase activity. Here, we analyze the consequences of impaired interaction between Pol ε and GINS in Saccharomyces cerevisiae cells with the psf1-100 mutation. This significantly affects DNA replication activity measured in vitro, while in vivo, the psf1-100 mutation reduces replication fidelity by increasing slippage of Pol ε, which manifests as an elevated number of frameshifts. It also increases the occurrence of single-stranded DNA (ssDNA) gaps and the demand for homologous recombination. The psf1-100 mutant shows elevated recombination rates and synthetic lethality with rad52Δ. Additionally, we observe increased participation of DNA polymerase zeta (Pol ζ) in DNA synthesis. We conclude that the impaired interaction between GINS and Pol ε requires enhanced involvement of error-prone Pol ζ, and increased participation of recombination as a rescue mechanism for recovery of impaired replication forks.
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Affiliation(s)
- Milena Denkiewicz-Kruk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
| | - Malgorzata Jedrychowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
| | - Shizuko Endo
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan; (S.E.); (H.A.)
| | - Hiroyuki Araki
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan; (S.E.); (H.A.)
| | - Piotr Jonczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
| | - Michal Dmowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
- Correspondence: (M.D.); (I.J.F.); Tel.: +48-22-5921128 (M.D.); +48-22-5921113 (I.J.F.)
| | - Iwona J. Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
- Correspondence: (M.D.); (I.J.F.); Tel.: +48-22-5921128 (M.D.); +48-22-5921113 (I.J.F.)
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32
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Stokes K, Winczura A, Song B, Piccoli GD, Grabarczyk DB. Ctf18-RFC and DNA Pol ϵ form a stable leading strand polymerase/clamp loader complex required for normal and perturbed DNA replication. Nucleic Acids Res 2020; 48:8128-8145. [PMID: 32585006 PMCID: PMC7641331 DOI: 10.1093/nar/gkaa541] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 12/28/2022] Open
Abstract
The eukaryotic replisome must faithfully replicate DNA and cope with replication fork blocks and stalling, while simultaneously promoting sister chromatid cohesion. Ctf18-RFC is an alternative PCNA loader that links all these processes together by an unknown mechanism. Here, we use integrative structural biology combined with yeast genetics and biochemistry to highlight the specific functions that Ctf18-RFC plays within the leading strand machinery via an interaction with the catalytic domain of DNA Pol ϵ. We show that a large and unusually flexible interface enables this interaction to occur constitutively throughout the cell cycle and regardless of whether forks are replicating or stalled. We reveal that, by being anchored to the leading strand polymerase, Ctf18-RFC can rapidly signal fork stalling to activate the S phase checkpoint. Moreover, we demonstrate that, independently of checkpoint signaling or chromosome cohesion, Ctf18-RFC functions in parallel to Chl1 and Mrc1 to protect replication forks and cell viability.
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Affiliation(s)
- Katy Stokes
- University of Warwick, Warwick Medical School, Coventry, UK
| | | | - Boyuan Song
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, Josef-Schneider-Str. 2, Würzburg 97080, Germany.,Department of Biochemistry, Biocenter, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | | | - Daniel B Grabarczyk
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, Josef-Schneider-Str. 2, Würzburg 97080, Germany
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33
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Kazlauskas D, Krupovic M, Guglielmini J, Forterre P, Venclovas Č. Diversity and evolution of B-family DNA polymerases. Nucleic Acids Res 2020; 48:10142-10156. [PMID: 32976577 PMCID: PMC7544198 DOI: 10.1093/nar/gkaa760] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022] Open
Abstract
B-family DNA polymerases (PolBs) represent the most common replicases. PolB enzymes that require RNA (or DNA) primed templates for DNA synthesis are found in all domains of life and many DNA viruses. Despite extensive research on PolBs, their origins and evolution remain enigmatic. Massive accumulation of new genomic and metagenomic data from diverse habitats as well as availability of new structural information prompted us to conduct a comprehensive analysis of the PolB sequences, structures, domain organizations, taxonomic distribution and co-occurrence in genomes. Based on phylogenetic analysis, we identified a new, widespread group of bacterial PolBs that are more closely related to the catalytically active N-terminal half of the eukaryotic PolEpsilon (PolEpsilonN) than to Escherichia coli Pol II. In Archaea, we characterized six new groups of PolBs. Two of them show close relationships with eukaryotic PolBs, the first one with PolEpsilonN, and the second one with PolAlpha, PolDelta and PolZeta. In addition, structure comparisons suggested common origin of the catalytically inactive C-terminal half of PolEpsilon (PolEpsilonC) and PolAlpha. Finally, in certain archaeal PolBs we discovered C-terminal Zn-binding domains closely related to those of PolAlpha and PolEpsilonC. Collectively, the obtained results allowed us to propose a scenario for the evolution of eukaryotic PolBs.
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Affiliation(s)
- Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Mart Krupovic
- Archaeal Virology Unit, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France
| | - Julien Guglielmini
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Patrick Forterre
- Archaeal Virology Unit, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
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34
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Kapadia N, El-Hajj ZW, Zheng H, Beattie TR, Yu A, Reyes-Lamothe R. Processive Activity of Replicative DNA Polymerases in the Replisome of Live Eukaryotic Cells. Mol Cell 2020; 80:114-126.e8. [DOI: 10.1016/j.molcel.2020.08.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 07/02/2020] [Accepted: 08/19/2020] [Indexed: 12/14/2022]
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35
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Eickhoff P, Kose HB, Martino F, Petojevic T, Abid Ali F, Locke J, Tamberg N, Nans A, Berger JM, Botchan MR, Yardimci H, Costa A. Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome. Cell Rep 2020; 28:2673-2688.e8. [PMID: 31484077 PMCID: PMC6737378 DOI: 10.1016/j.celrep.2019.07.104] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/15/2019] [Accepted: 07/26/2019] [Indexed: 01/12/2023] Open
Abstract
In the eukaryotic replisome, DNA unwinding by the Cdc45-MCM-Go-Ichi-Ni-San (GINS) (CMG) helicase requires a hexameric ring-shaped ATPase named minichromosome maintenance (MCM), which spools single-stranded DNA through its central channel. Not all six ATPase sites are required for unwinding; however, the helicase mechanism is unknown. We imaged ATP-hydrolysis-driven translocation of the CMG using cryo-electron microscopy (cryo-EM) and found that the six MCM subunits engage DNA using four neighboring protomers at a time, with ATP binding promoting DNA engagement. Morphing between different helicase states leads us to suggest a non-symmetric hand-over-hand rotary mechanism, explaining the asymmetric requirements of ATPase function around the MCM ring of the CMG. By imaging of a higher-order replisome assembly, we find that the Mrc1-Csm3-Tof1 fork-stabilization complex strengthens the interaction between parental duplex DNA and the CMG at the fork, which might support the coupling between DNA translocation and fork unwinding. Vertical DNA movement through the MCM ring requires rotation inside the pore Structural asymmetries in MCM-DNA are captured during ATPase-powered translocation Asymmetric rotation explains selective ATPase site requirements for translocation The fork-stabilization complex strengthens parental-DNA engagement by the MCM
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Affiliation(s)
- Patrik Eickhoff
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Hazal B Kose
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Fabrizio Martino
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Tatjana Petojevic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ferdos Abid Ali
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Julia Locke
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Nele Tamberg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - James M Berger
- 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
| | - Hasan Yardimci
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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36
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Guilliam TA, Yeeles JTP. An updated perspective on the polymerase division of labor during eukaryotic DNA replication. Crit Rev Biochem Mol Biol 2020; 55:469-481. [PMID: 32883112 DOI: 10.1080/10409238.2020.1811630] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In eukaryotes three DNA polymerases (Pols), α, δ, and ε, are tasked with bulk DNA synthesis of nascent strands during genome duplication. Most evidence supports a model where Pol α initiates DNA synthesis before Pol ε and Pol δ replicate the leading and lagging strands, respectively. However, a number of recent reports, enabled by advances in biochemical and genetic techniques, have highlighted emerging roles for Pol δ in all stages of leading-strand synthesis; initiation, elongation, and termination, as well as fork restart. By focusing on these studies, this review provides an updated perspective on the division of labor between the replicative polymerases during DNA replication.
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Affiliation(s)
- Thomas A Guilliam
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Joseph T P Yeeles
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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37
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Deegan TD, Mukherjee PP, Fujisawa R, Polo Rivera C, Labib K. CMG helicase disassembly is controlled by replication fork DNA, replisome components and a ubiquitin threshold. eLife 2020; 9:e60371. [PMID: 32804080 PMCID: PMC7462611 DOI: 10.7554/elife.60371] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/14/2020] [Indexed: 12/20/2022] Open
Abstract
The eukaryotic replisome assembles around the CMG helicase, which stably associates with DNA replication forks throughout elongation. When replication terminates, CMG is ubiquitylated on its Mcm7 subunit and disassembled by the Cdc48/p97 ATPase. Until now, the regulation that restricts CMG ubiquitylation to termination was unknown, as was the mechanism of disassembly. By reconstituting these processes with purified budding yeast proteins, we show that ubiquitylation is tightly repressed throughout elongation by the Y-shaped DNA structure of replication forks. Termination removes the repressive DNA structure, whereupon long K48-linked ubiquitin chains are conjugated to CMG-Mcm7, dependent on multiple replisome components that bind to the ubiquitin ligase SCFDia2. This mechanism pushes CMG beyond a '5-ubiquitin threshold' that is inherent to Cdc48, which specifically unfolds ubiquitylated Mcm7 and thereby disassembles CMG. These findings explain the exquisite regulation of CMG disassembly and provide a general model for the disassembly of ubiquitylated protein complexes by Cdc48.
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Affiliation(s)
- Tom D Deegan
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Progya P Mukherjee
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Ryo Fujisawa
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Cristian Polo Rivera
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Karim Labib
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of DundeeDundeeUnited Kingdom
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38
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Liu L, Zhang Y, Zhang J, Wang JH, Cao Q, Li Z, Campbell JL, Dong MQ, Lou H. Characterization of the dimeric CMG/pre-initiation complex and its transition into DNA replication forks. Cell Mol Life Sci 2020; 77:3041-3058. [PMID: 31728581 PMCID: PMC11104849 DOI: 10.1007/s00018-019-03333-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/17/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
The pre-initiation complex (pre-IC) has been proposed for two decades as an intermediate right before the maturation of the eukaryotic DNA replication fork. However, its existence and biochemical nature remain enigmatic. Here, through combining several enrichment strategies, we are able to isolate an endogenous dimeric CMG-containing complex (designated as d-CMG) distinct from traditional single CMG (s-CMG) and in vitro reconstituted dimeric CMG. D-CMG is assembled upon entry into the S phase and shortly matures into s-CMG/replisome, leading to the fact that only ~ 5% of the total CMG-containing complexes can be detected as d-CMG in vivo. Mass spectra reveal that RPA and DNA Pol α/primase co-purify with s-CMG, but not with d-CMG. Consistently, the former fraction is able to catalyze DNA unwinding and de novo synthesis, while the latter catalyzes neither. The two CMGs in d-CMG display flexibly orientated conformations under an electronic microscope. When DNA Pol α-primase is inactivated, d-CMG % rose up to 29%, indicating an incomplete pre-IC/fork transition. These findings reveal biochemical properties of the d-CMG/pre-IC and provide in vivo evidence to support the pre-IC/fork transition as a bona fide step in replication initiation.
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Affiliation(s)
- Lu Liu
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China
| | - Yue Zhang
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China
| | - Jingjing Zhang
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China
| | - Jian-Hua Wang
- National Institute of Biological Sciences (NIBS), Beijing, 102206, China
| | - Qinhong Cao
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China
| | - Zhen Li
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China
| | - Judith L Campbell
- Braun Laboratories, California Institute of Technology, Pasadena, 91125, CA, USA
| | - Meng-Qiu Dong
- National Institute of Biological Sciences (NIBS), Beijing, 102206, China
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China.
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Cerritelli SM, Iranzo J, Sharma S, Chabes A, Crouch RJ, Tollervey D, El Hage A. High density of unrepaired genomic ribonucleotides leads to Topoisomerase 1-mediated severe growth defects in absence of ribonucleotide reductase. Nucleic Acids Res 2020; 48:4274-4297. [PMID: 32187369 PMCID: PMC7192613 DOI: 10.1093/nar/gkaa103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/12/2022] Open
Abstract
Cellular levels of ribonucleoside triphosphates (rNTPs) are much higher than those of deoxyribonucleoside triphosphates (dNTPs), thereby influencing the frequency of incorporation of ribonucleoside monophosphates (rNMPs) by DNA polymerases (Pol) into DNA. RNase H2-initiated ribonucleotide excision repair (RER) efficiently removes single rNMPs in genomic DNA. However, processing of rNMPs by Topoisomerase 1 (Top1) in absence of RER induces mutations and genome instability. Here, we greatly increased the abundance of genomic rNMPs in Saccharomyces cerevisiae by depleting Rnr1, the major subunit of ribonucleotide reductase, which converts ribonucleotides to deoxyribonucleotides. We found that in strains that are depleted of Rnr1, RER-deficient, and harbor an rNTP-permissive replicative Pol mutant, excessive accumulation of single genomic rNMPs severely compromised growth, but this was reversed in absence of Top1. Thus, under Rnr1 depletion, limited dNTP pools slow DNA synthesis by replicative Pols and provoke the incorporation of high levels of rNMPs in genomic DNA. If a threshold of single genomic rNMPs is exceeded in absence of RER and presence of limited dNTP pools, Top1-mediated genome instability leads to severe growth defects. Finally, we provide evidence showing that accumulation of RNA/DNA hybrids in absence of RNase H1 and RNase H2 leads to cell lethality under Rnr1 depletion.
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Affiliation(s)
- Susana M Cerritelli
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jaime Iranzo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå SE-901 87, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå SE-901 87, Sweden
| | - Robert J Crouch
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - David Tollervey
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Aziz El Hage
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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40
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Le TT, Gao X, Park SH, Lee J, Inman JT, Lee JH, Killian JL, Badman RP, Berger JM, Wang MD. Synergistic Coordination of Chromatin Torsional Mechanics and Topoisomerase Activity. Cell 2020; 179:619-631.e15. [PMID: 31626768 PMCID: PMC6899335 DOI: 10.1016/j.cell.2019.09.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/16/2019] [Accepted: 09/24/2019] [Indexed: 12/23/2022]
Abstract
DNA replication in eukaryotes generates DNA supercoiling, which may intertwine (braid) daughter chromatin fibers to form precatenanes, posing topological challenges during chromosome segregation. The mechanisms that limit precatenane formation remain unclear. By making direct torque measurements, we demonstrate that the intrinsic mechanical properties of chromatin play a fundamental role in dictating precatenane formation and regulating chromatin topology. Whereas a single chromatin fiber is torsionally soft, a braided fiber is torsionally stiff, indicating that supercoiling on chromatin substrates is preferentially directed in front of the fork during replication. We further show that topoisomerase II relaxation displays a strong preference for a single chromatin fiber over a braided fiber. These results suggest a synergistic coordination-the mechanical properties of chromatin inherently suppress precatenane formation during replication elongation by driving DNA supercoiling ahead of the fork, where supercoiling is more efficiently removed by topoisomerase II. VIDEO ABSTRACT.
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Affiliation(s)
- Tung T Le
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Xiang Gao
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Seong Ha Park
- Biophysics Program, Cornell University, Ithaca, NY 14853, USA
| | - Jaeyoon Lee
- Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - James T Inman
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Joyce H Lee
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jessica L Killian
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Ryan P Badman
- Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michelle D Wang
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA.
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41
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DNA replication protein Cdc45 directly interacts with PCNA via its PIP box in Leishmania donovani and the Cdc45 PIP box is essential for cell survival. PLoS Pathog 2020; 16:e1008190. [PMID: 32413071 PMCID: PMC7255605 DOI: 10.1371/journal.ppat.1008190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/28/2020] [Accepted: 04/16/2020] [Indexed: 12/22/2022] Open
Abstract
DNA replication protein Cdc45 is an integral part of the eukaryotic replicative helicase whose other components are the Mcm2-7 core, and GINS. We identified a PIP box motif in Leishmania donovani Cdc45. This motif is typically linked to interaction with the eukaryotic clamp proliferating cell nuclear antigen (PCNA). The homotrimeric PCNA can potentially bind upto three different proteins simultaneously via a loop region present in each monomer. Multiple binding partners have been identified from among the replication machinery in other eukaryotes, and the concerted /sequential binding of these partners are central to the fidelity of the replication process. Though conserved in Cdc45 across Leishmania species and Trypanosoma cruzi, the PIP box is absent in Trypanosoma brucei Cdc45. Here we investigate the possibility of Cdc45-PCNA interaction and the role of such an interaction in the in vivo context. Having confirmed the importance of Cdc45 in Leishmania DNA replication we establish that Cdc45 and PCNA interact stably in whole cell extracts, also interacting with each other directly in vitro. The interaction is mediated via the Cdc45 PIP box. This PIP box is essential for Leishmania survival. The importance of the Cdc45 PIP box is also examined in Schizosaccharomyces pombe, and it is found to be essential for cell survival here as well. Our results implicate a role for the Leishmania Cdc45 PIP box in recruiting or stabilizing PCNA on chromatin. The Cdc45-PCNA interaction might help tether PCNA and associated replicative DNA polymerase to the DNA template, thus facilitating replication fork elongation. Though multiple replication proteins that associate with PCNA have been identified in other eukaryotes, this is the first report demonstrating a direct interaction between Cdc45 and PCNA, and while our analysis suggests the interaction may not occur in human cells, it indicates that it may not be confined to trypanosomatids.
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42
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DNA polymerase ε relies on a unique domain for efficient replisome assembly and strand synthesis. Nat Commun 2020; 11:2437. [PMID: 32415104 PMCID: PMC7228970 DOI: 10.1038/s41467-020-16095-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 04/14/2020] [Indexed: 12/21/2022] Open
Abstract
DNA polymerase epsilon (Pol ε) is required for genome duplication and tumor suppression. It supports both replisome assembly and leading strand synthesis; however, the underlying mechanisms remain to be elucidated. Here we report that a conserved domain within the Pol ε catalytic core influences both of these replication steps in budding yeast. Modeling cancer-associated mutations in this domain reveals its unexpected effect on incorporating Pol ε into the four-member pre-loading complex during replisome assembly. In addition, genetic and biochemical data suggest that the examined domain supports Pol ε catalytic activity and symmetric movement of replication forks. Contrary to previously characterized Pol ε cancer variants, the examined mutants cause genome hyper-rearrangement rather than hyper-mutation. Our work thus suggests a role of the Pol ε catalytic core in replisome formation, a reliance of Pol ε strand synthesis on a unique domain, and a potential tumor-suppressive effect of Pol ε in curbing genome re-arrangements.
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43
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Baretić D, Jenkyn-Bedford M, Aria V, Cannone G, Skehel M, Yeeles JTP. Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork. Mol Cell 2020; 78:926-940.e13. [PMID: 32369734 PMCID: PMC7276988 DOI: 10.1016/j.molcel.2020.04.012] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 12/15/2022]
Abstract
The eukaryotic replisome, organized around the Cdc45-MCM-GINS (CMG) helicase, orchestrates chromosome replication. Multiple factors associate directly with CMG, including Ctf4 and the heterotrimeric fork protection complex (Csm3/Tof1 and Mrc1), which has important roles including aiding normal replication rates and stabilizing stalled forks. How these proteins interface with CMG to execute these functions is poorly understood. Here we present 3 to 3.5 Å resolution electron cryomicroscopy (cryo-EM) structures comprising CMG, Ctf4, and the fork protection complex at a replication fork. The structures provide high-resolution views of CMG-DNA interactions, revealing a mechanism for strand separation, and show Csm3/Tof1 “grip” duplex DNA ahead of CMG via a network of interactions important for efficient replication fork pausing. Although Mrc1 was not resolved in our structures, we determine its topology in the replisome by cross-linking mass spectrometry. Collectively, our work reveals how four highly conserved replisome components collaborate with CMG to facilitate replisome progression and maintain genome stability. Cryo-EM structure of Csm3/Tof1 and Ctf4 bound to the eukaryotic CMG helicase Csm3/Tof1 are positioned at the front of the replisome where they grip duplex DNA High-resolution views of CMG-DNA contacts suggest a mechanism for strand separation Mrc1 binds across one side of CMG contacting the front and back of the replisome
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Affiliation(s)
- Domagoj Baretić
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
| | | | - Valentina Aria
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
| | - Giuseppe Cannone
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
| | - Mark Skehel
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
| | - Joseph T P Yeeles
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK.
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44
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Guilliam TA, Yeeles JTP. Reconstitution of translesion synthesis reveals a mechanism of eukaryotic DNA replication restart. Nat Struct Mol Biol 2020; 27:450-460. [PMID: 32341533 DOI: 10.1038/s41594-020-0418-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/16/2020] [Indexed: 12/23/2022]
Abstract
Leading-strand template aberrations cause helicase-polymerase uncoupling and impede replication fork progression, but the details of how uncoupled forks are restarted remain uncertain. Using purified proteins from Saccharomyces cerevisiae, we have reconstituted translesion synthesis (TLS)-mediated restart of a eukaryotic replisome following collision with a cyclobutane pyrimidine dimer. We find that TLS functions 'on the fly' to promote resumption of rapid replication fork rates, despite lesion bypass occurring uncoupled from the Cdc45-MCM-GINS (CMG) helicase. Surprisingly, the main lagging-strand polymerase, Pol δ, binds the leading strand upon uncoupling and inhibits TLS. Pol δ is also crucial for efficient recoupling of leading-strand synthesis to CMG following lesion bypass. Proliferating cell nuclear antigen monoubiquitination positively regulates TLS to overcome Pol δ inhibition. We reveal that these mechanisms of negative and positive regulation also operate on the lagging strand. Our observations have implications for both fork restart and the division of labor during leading-strand synthesis generally.
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Affiliation(s)
- Thomas A Guilliam
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Joseph T P Yeeles
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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45
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Wooten M, Li Y, Snedeker J, Nizami ZF, Gall JG, Chen X. Superresolution imaging of chromatin fibers to visualize epigenetic information on replicative DNA. Nat Protoc 2020; 15:1188-1208. [PMID: 32051613 PMCID: PMC7255620 DOI: 10.1038/s41596-019-0283-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022]
Abstract
During DNA replication, the genetic information of a cell is copied. Subsequently, identical genetic information is segregated reliably to the two daughter cells through cell division. Meanwhile, DNA replication is intrinsically linked to the process of chromatin duplication, which is required for regulating gene expression and establishing cell identities. Understanding how chromatin is established, maintained or changed during DNA replication represents a fundamental question in biology. Recently, we developed a method to directly visualize chromatin components at individual replication forks undergoing DNA replication. This method builds upon the existing chromatin fiber technique and combines it with cell type-specific chromatin labeling and superresolution microscopy. In this method, a short pulse of nucleoside analog labels replicative regions in the cells of interest. Chromatin fibers are subsequently isolated and attached to a glass slide, after which a laminar flow of lysis buffer extends the lysed chromatin fibers parallel with the direction of the flow. Fibers are then immunostained for different chromatin-associated proteins and mounted for visualization using superresolution microscopy. Replication foci, or 'bubbles,' are identified by the presence of the incorporated nucleoside analog. For researchers experienced in molecular biology and superresolution microscopy, this protocol typically takes 2-3 d from sample preparation to data acquisition, with an additional day for data processing and quantification.
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Affiliation(s)
- Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Yingying Li
- Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Jonathan Snedeker
- Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Zehra F Nizami
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD, USA.
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46
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Defects in the GINS complex increase the instability of repetitive sequences via a recombination-dependent mechanism. PLoS Genet 2019; 15:e1008494. [PMID: 31815930 PMCID: PMC6922473 DOI: 10.1371/journal.pgen.1008494] [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: 08/02/2019] [Revised: 12/19/2019] [Accepted: 10/25/2019] [Indexed: 12/16/2022] Open
Abstract
Faithful replication and repair of DNA lesions ensure genome maintenance. During replication in eukaryotic cells, DNA is unwound by the CMG helicase complex, which is composed of three major components: the Cdc45 protein, Mcm2-7, and the GINS complex. The CMG in complex with DNA polymerase epsilon (CMG-E) participates in the establishment and progression of the replisome. Impaired functioning of the CMG-E was shown to induce genomic instability and promote the development of various diseases. Therefore, CMG-E components play important roles as caretakers of the genome. In Saccharomyces cerevisiae, the GINS complex is composed of the Psf1, Psf2, Psf3, and Sld5 essential subunits. The Psf1-1 mutant form fails to interact with Psf3, resulting in impaired replisome assembly and chromosome replication. Here, we show increased instability of repeat tracts (mononucleotide, dinucleotide, trinucleotide and longer) in yeast psf1-1 mutants. To identify the mechanisms underlying this effect, we analyzed repeated sequence instability using derivatives of psf1-1 strains lacking genes involved in translesion synthesis, recombination, or mismatch repair. Among these derivatives, deletion of RAD52, RAD51, MMS2, POL32, or PIF1 significantly decreased DNA repeat instability. These results, together with the observed increased amounts of single-stranded DNA regions and Rfa1 foci suggest that recombinational mechanisms make important contributions to repeat tract instability in psf1-1 cells. We propose that defective functioning of the CMG-E complex in psf1-1 cells impairs the progression of DNA replication what increases the contribution of repair mechanisms such as template switch and break-induced replication. These processes require sequence homology search which in case of a repeated DNA tract may result in misalignment leading to its expansion or contraction. Processes that ensure genome stability are crucial for all organisms to avoid mutations and decrease the risk of diseases. The coordinated activity of mechanisms underlying the maintenance of high-fidelity DNA duplication and repair is critical to deal with the malfunction of replication forks or DNA damage. Repeated sequences in DNA are particularly prone to instability; these sequences undergo expansions or contractions, leading in humans to various neurological, neurodegenerative, and neuromuscular disorders. A mutant form of one of the noncatalytic subunits of active DNA helicase complex impairs DNA replication. Here, we show that this form also significantly increases the instability of mononucleotide, dinucleotide, trinucleotide and longer repeat tracts. Our results suggest that in cells that harbor a mutated variant of the helicase complex, continuation of DNA replication is facilitated by recombination processes, and this mechanism can be highly mutagenic during repair synthesis through repetitive regions, especially regions that form secondary structures. Our results indicate that proper functioning of the DNA helicase complex is crucial for maintenance of the stability of repeated DNA sequences, especially in the context of recently described disorders in which mutations or deregulation of the human homologs of genes encoding DNA helicase subunits were observed.
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47
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Winczura A, Appanah R, Tatham MH, Hay RT, De Piccoli G. The S phase checkpoint promotes the Smc5/6 complex dependent SUMOylation of Pol2, the catalytic subunit of DNA polymerase ε. PLoS Genet 2019; 15:e1008427. [PMID: 31765407 PMCID: PMC6876773 DOI: 10.1371/journal.pgen.1008427] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/16/2019] [Indexed: 12/31/2022] Open
Abstract
Replication fork stalling and accumulation of single-stranded DNA trigger the S phase checkpoint, a signalling cascade that, in budding yeast, leads to the activation of the Rad53 kinase. Rad53 is essential in maintaining cell viability, but its targets of regulation are still partially unknown. Here we show that Rad53 drives the hyper-SUMOylation of Pol2, the catalytic subunit of DNA polymerase ε, principally following replication forks stalling induced by nucleotide depletion. Pol2 is the main target of SUMOylation within the replisome and its modification requires the SUMO-ligase Mms21, a subunit of the Smc5/6 complex. Moreover, the Smc5/6 complex co-purifies with Pol ε, independently of other replisome components. Finally, we map Pol2 SUMOylation to a single site within the N-terminal catalytic domain and identify a SUMO-interacting motif at the C-terminus of Pol2. These data suggest that the S phase checkpoint regulate Pol ε during replication stress through Pol2 SUMOylation and SUMO-binding ability.
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Affiliation(s)
- Alicja Winczura
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Rowin Appanah
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Michael H. Tatham
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, United Kingdom
| | - Ronald T. Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, United Kingdom
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48
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Perera HM, Behrmann MS, Hoang JM, Griffin WC, Trakselis MA. Contacts and context that regulate DNA helicase unwinding and replisome progression. Enzymes 2019; 45:183-223. [PMID: 31627877 DOI: 10.1016/bs.enz.2019.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hexameric DNA helicases involved in the separation of duplex DNA at the replication fork have a universal architecture but have evolved from two separate protein families. The consequences are that the regulation, translocation polarity, strand specificity, and architectural orientation varies between phage/bacteria to that of archaea/eukaryotes. Once assembled and activated for single strand DNA translocation and unwinding, the DNA polymerase couples tightly to the helicase forming a robust replisome complex. However, this helicase-polymerase interaction can be challenged by various forms of endogenous or exogenous agents that can stall the entire replisome or decouple DNA unwinding from synthesis. The consequences of decoupling can be severe, leading to a build-up of ssDNA requiring various pathways for replication fork restart. All told, the hexameric helicase sits prominently at the front of the replisome constantly responding to a variety of obstacles that require transient unwinding/reannealing, traversal of more stable blocks, and alternations in DNA unwinding speed that regulate replisome progression.
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Affiliation(s)
- Himasha M Perera
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Megan S Behrmann
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Joy M Hoang
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Wezley C Griffin
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States.
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49
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A quest for coordination among activities at the replisome. Biochem Soc Trans 2019; 47:1067-1075. [PMID: 31395754 DOI: 10.1042/bst20180402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 11/17/2022]
Abstract
Faithful DNA replication is required for transmission of the genetic material across generations. The basic mechanisms underlying this process are shared among all organisms: progressive unwinding of the long double-stranded DNA; synthesis of RNA primers; and synthesis of a new DNA chain. These activities are invariably performed by a multi-component machine called the replisome. A detailed description of this molecular machine has been achieved in prokaryotes and phages, with the replication processes in eukaryotes being comparatively less known. However, recent breakthroughs in the in vitro reconstitution of eukaryotic replisomes have resulted in valuable insight into their functions and mechanisms. In conjunction with the developments in eukaryotic replication, an emerging overall view of replisomes as dynamic protein ensembles is coming into fruition. The purpose of this review is to provide an overview of the recent insights into the dynamic nature of the bacterial replisome, revealed through single-molecule techniques, and to describe some aspects of the eukaryotic replisome under this framework. We primarily focus on Escherichia coli and Saccharomyces cerevisiae (budding yeast), since a significant amount of literature is available for these two model organisms. We end with a description of the methods of live-cell fluorescence microscopy for the characterization of replisome dynamics.
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50
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Lee MYWT, Zhang S, Wang X, Chao HH, Zhao H, Darzynkiewicz Z, Zhang Z, Lee EYC. Two forms of human DNA polymerase δ: Who does what and why? DNA Repair (Amst) 2019; 81:102656. [PMID: 31326365 DOI: 10.1016/j.dnarep.2019.102656] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
DNA polymerase δ (Pol δ) plays a central role in lagging strand DNA synthesis in eukaryotic cells, as well as an important role in DNA repair processes. Human Pol δ4 is a heterotetramer of four subunits, the smallest of which is p12. Pol δ3 is a trimeric form that is generated in vivo by the degradation of the p12 subunit in response to DNA damage, and during entry into S-phase. The biochemical properties of the two forms of Pol δ, as well as the changes in their distribution during the cell cycle, are reviewed from the perspective of understanding their respective cellular functions. Biochemical and cellular studies support a role for Pol δ3 in gap filling during DNA repair, and in Okazaki fragment synthesis during DNA replication. Recent studies of cells in which p12 expression is ablated, and are therefore null for Pol δ4, show that Pol δ4 is not required for cell viability. These cells have a defect in homologous recombination, revealing a specific role for Pol δ4 that cannot be performed by Pol δ3. Pol δ4 activity is required for D-loop displacement synthesis in HR. The reasons why Pol δ4 but not Pol δ3 can perform this function are discussed, as well as the question of whether helicase action is needed for efficient D-loop displacement synthesis. Pol δ4 is largely present in the G1 and G2/M phases of the cell cycle and is low in S phase. This is discussed in relation to the availability of Pol δ4 as an additional layer of regulation for HR activity during cell cycle progression.
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Affiliation(s)
- Marietta Y W T Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, USA.
| | - Sufang Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, USA
| | - Xiaoxiao Wang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, USA
| | - Hsiao Hsiang Chao
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, USA
| | - Hong Zhao
- Department of Pathology, New York Medical College, Valhalla, USA
| | | | - Zhongtao Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, USA
| | - Ernest Y C Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, USA
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