1
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Kimble MT, Sane A, Reid RJ, Johnson MJ, Rothstein R, Symington LS. Strand asymmetry in the repair of replication dependent double-strand breaks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.598707. [PMID: 38948862 PMCID: PMC11212877 DOI: 10.1101/2024.06.17.598707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Single-strand breaks (SSBs) are one of the most common endogenous lesions and have the potential to give rise to cytotoxic double-strand breaks (DSBs) during DNA replication. To investigate the mechanism of replication fork collapse at SSBs and subsequent repair, we employed Cas9 nickase (nCas9) to generate site and strand-specific nicks in the budding yeast genome. We show that nCas9-induced nicks are converted to mostly double-ended DSBs during S-phase. We find that repair of replication-dependent DSBs requires homologous recombination (HR) and is independent of canonical non-homologous end joining. Consistent with a strong bias to repair these lesions using a sister chromatid template, we observe minimal induction of inter-chromosomal HR by nCas9. Using nCas9 and a gRNA to nick either the leading or lagging strand template, we carried out a genome-wide screen to identify factors necessary for the repair of replication-dependent DSBs. All the core HR genes were recovered in the screen with both gRNAs, but we recovered components of the replication-coupled nucleosome assembly (RCNA) pathway with only the gRNA targeting the leading strand template. By use of additional gRNAs, we find that the RCNA pathway is especially important to repair a leading strand fork collapse.
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2
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Acharya A, Bret H, Huang JW, Mütze M, Göse M, Kissling VM, Seidel R, Ciccia A, Guérois R, Cejka P. Mechanism of DNA unwinding by MCM8-9 in complex with HROB. Nat Commun 2024; 15:3584. [PMID: 38678026 PMCID: PMC11055865 DOI: 10.1038/s41467-024-47936-8] [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] [Received: 06/16/2023] [Accepted: 04/15/2024] [Indexed: 04/29/2024] Open
Abstract
HROB promotes the MCM8-9 helicase in DNA damage response. To understand how HROB activates MCM8-9, we defined their interaction interface. We showed that HROB makes important yet transient contacts with both MCM8 and MCM9, and binds the MCM8-9 heterodimer with the highest affinity. MCM8-9-HROB prefer branched DNA structures, and display low DNA unwinding processivity. MCM8-9 unwinds DNA as a hexamer that assembles from dimers on DNA in the presence of ATP. The hexamer involves two repeating protein-protein interfaces between the alternating MCM8 and MCM9 subunits. One of these interfaces is quite stable and forms an obligate heterodimer across which HROB binds. The other interface is labile and mediates hexamer assembly, independently of HROB. The ATPase site formed at the labile interface contributes disproportionally more to DNA unwinding than that at the stable interface. Here, we show that HROB promotes DNA unwinding downstream of MCM8-9 loading and ring formation on ssDNA.
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Affiliation(s)
- Ananya Acharya
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, 6500, Switzerland
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, 8093, Switzerland
| | - Hélène Bret
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jen-Wei Huang
- Department of Genetics and Development, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Martin Mütze
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, 04103, Germany
| | - Martin Göse
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, 04103, Germany
| | - Vera Maria Kissling
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, 8093, Switzerland
- Particles-Biology Interactions Laboratory, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), St. Gallen, 9014, Switzerland
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, 04103, Germany
| | - Alberto Ciccia
- Department of Genetics and Development, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Raphaël Guérois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, 6500, Switzerland.
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, 8093, Switzerland.
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3
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Schmit MM, Baxley RM, Wang L, Hinderlie P, Kaufman M, Simon E, Raju A, Miller JS, Bielinsky AK. A critical threshold of MCM10 is required to maintain genome stability during differentiation of induced pluripotent stem cells into natural killer cells. Open Biol 2024; 14:230407. [PMID: 38262603 PMCID: PMC10805602 DOI: 10.1098/rsob.230407] [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] [Received: 11/01/2023] [Accepted: 11/23/2023] [Indexed: 01/25/2024] Open
Abstract
Natural killer (NK) cell deficiency (NKD) is a rare disease in which NK cell function is reduced, leaving affected individuals susceptible to repeated viral infections and cancer. Recently, a patient with NKD was identified carrying compound heterozygous variants of MCM10 (minichromosome maintenance protein 10), an essential gene required for DNA replication, that caused a significant decrease in the amount of functional MCM10. NKD in this patient presented as loss of functionally mature late-stage NK cells. To understand how MCM10 deficiency affects NK cell development, we generated MCM10 heterozygous (MCM10+/-) induced pluripotent stem cell (iPSC) lines. Analyses of these cell lines demonstrated that MCM10 was haploinsufficient, similar to results in other human cell lines. Reduced levels of MCM10 in mutant iPSCs was associated with impaired clonogenic survival and increased genomic instability, including micronuclei formation and telomere erosion. The severity of these phenotypes correlated with the extent of MCM10 depletion. Significantly, MCM10+/- iPSCs displayed defects in NK cell differentiation, exhibiting reduced yields of hematopoietic stem cells (HSCs). Although MCM10+/- HSCs were able to give rise to lymphoid progenitors, these did not generate mature NK cells. The lack of mature NK cells coincided with telomere erosion, suggesting that NKD caused by these MCM10 variants arose from the accumulation of genomic instability including degradation of chromosome ends.
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Affiliation(s)
- Megan M. Schmit
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Ryan M. Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Liangjun Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Peter Hinderlie
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Marissa Kaufman
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Emily Simon
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Anjali Raju
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Jeffrey S. Miller
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
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4
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Langston LD, Georgescu RE, O'Donnell ME. Mechanism of eukaryotic origin unwinding is a dual helicase DNA shearing process. Proc Natl Acad Sci U S A 2023; 120:e2316466120. [PMID: 38109526 PMCID: PMC10756200 DOI: 10.1073/pnas.2316466120] [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] [Received: 09/23/2023] [Accepted: 11/17/2023] [Indexed: 12/20/2023] Open
Abstract
DNA replication in all cells begins with the melting of base pairs at the duplex origin to allow access to single-stranded DNA templates which are replicated by DNA polymerases. In bacteria, origin DNA is presumed to be melted by accessory proteins that allow loading of two ring-shaped replicative helicases around single-strand DNA (ssDNA) for bidirectional unwinding and DNA replication. In eukaryotes, by contrast, two replicative CMG (Cdc45-Mcm2-7-GINS) helicases are initially loaded head to head around origin double-strand DNA (dsDNA), and there does not appear to be a separate origin unwinding factor. This led us to investigate whether head-to-head CMGs use their adenosine triphosphate (ATP)-driven motors to initiate duplex DNA unwinding at the origin. Here, we show that CMG tracks on one strand of the duplex while surrounding it, and this feature allows two head-to-head CMGs to unwind dsDNA by using their respective motors to pull on opposite strands of the duplex. We further show that while CMG is capable of limited duplex unwinding on its own, the extent of unwinding is greatly and rapidly stimulated by addition of the multifunctional CMG-binding protein Mcm10 that is critical for productive initiation of DNA replication in vivo. On the basis of these findings, we propose that Mcm10 is a processivity or positioning factor that helps translate the work performed by the dual CMG motors at the origin into productive unwinding that facilitates bidirectional DNA replication.
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Affiliation(s)
- Lance D. Langston
- The Rockefeller University, New York City, NY10065
- HHMI, New York City, NY10065
| | - Roxana E. Georgescu
- The Rockefeller University, New York City, NY10065
- HHMI, New York City, NY10065
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5
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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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6
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Bellani MA, Shaik A, Majumdar I, Ling C, Seidman MM. The Response of the Replication Apparatus to Leading Template Strand Blocks. Cells 2023; 12:2607. [PMID: 37998342 PMCID: PMC10670059 DOI: 10.3390/cells12222607] [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] [Received: 10/23/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Duplication of the genome requires the replication apparatus to overcome a variety of impediments, including covalent DNA adducts, the most challenging of which is on the leading template strand. Replisomes consist of two functional units, a helicase to unwind DNA and polymerases to synthesize it. The helicase is a multi-protein complex that encircles the leading template strand and makes the first contact with a leading strand adduct. The size of the channel in the helicase would appear to preclude transit by large adducts such as DNA: protein complexes (DPC). Here we discuss some of the extensively studied pathways that support replication restart after replisome encounters with leading template strand adducts. We also call attention to recent work that highlights the tolerance of the helicase for adducts ostensibly too large to pass through the central channel.
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Affiliation(s)
| | | | | | | | - Michael M. Seidman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (M.A.B.)
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7
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Acharya A, Bret H, Huang JW, Mütze M, Göse M, Kissling V, Seidel R, Ciccia A, Guérois R, Cejka P. Mechanism of DNA unwinding by hexameric MCM8-9 in complex with HROB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544631. [PMID: 37398313 PMCID: PMC10312610 DOI: 10.1101/2023.06.12.544631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The human MCM8-9 helicase functions in concert with HROB in the context of homologous recombination, but its precise function is unknown. To gain insights into how HROB regulates MCM8-9, we first used molecular modeling and biochemistry to define their interaction interface. We show that HROB makes important contacts with both MCM8 and MCM9 subunits, which directly promotes its DNA-dependent ATPase and helicase activities. MCM8-9-HROB preferentially binds and unwinds branched DNA structures, and single-molecule experiments reveal a low DNA unwinding processivity. MCM8-9 unwinds DNA as a hexameric complex that assembles from dimers on DNA in the presence of ATP, which is prerequisite for its helicase function. The hexamer formation thus involves two repeating protein-protein interfaces forming between the alternating MCM8 and MCM9 subunits. One of these interfaces is rather stable and forms an obligate heterodimer, while the other interface is labile and mediates the assembly of the hexamer on DNA, independently of HROB. The ATPase site composed of the subunits forming the labile interface disproportionally contributes to DNA unwinding. HROB does not affect the MCM8-9 ring formation, but promotes DNA unwinding downstream by possibly coordinating ATP hydrolysis with structural transitions accompanying translocation of MCM8-9 on DNA.
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8
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Chen J, Wu S, Wang J, Han C, Zhao L, He K, Jia Y, Cui M. MCM10: An effective treatment target and a prognostic biomarker in patients with uterine corpus endometrial carcinoma. J Cell Mol Med 2023; 27:1708-1724. [PMID: 37246638 PMCID: PMC10273062 DOI: 10.1111/jcmm.17772] [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] [Received: 01/31/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/30/2023] Open
Abstract
Molecular profiling has been applied for uterine corpus endometrial carcinoma (UCEC) management for many years. The aim of this study was to explore the role of MCM10 in UCEC and construct its overall survival (OS) prediction models. Data from TCGA, GEO, cbioPotal and COSMIC databases and the methods, such as GO, KEGG, GSEA, ssGSEA and PPI, were employed to bioinformatically detect the effects of MCM10 on UCEC. RT-PCR, Western blot and immunohistochemistry were used to validate the effects of MCM10 on UCEC. Based on Cox regression analysis using the data from TCGA and our clinical data, two OS prediction models for UCEC were established. Finally, the effects of MCM10 on UCEC were detected in vitro. Our study revealed that MCM10 was variated and overexpressed in UCEC tissue and involved in DNA replication, cell cycle, DNA repair and immune microenvironment in UCEC. Moreover, silencing MCM10 significantly inhibited the proliferation of UCEC cells in vitro. Importantly, based on MCM10 expression and clinical features, the OS prediction models were constructed with good accuracy. MCM10 could be an effective treatment target and a prognostic biomarker for UCEC patients. The OS prediction models might help establish the strategies of follow-up and treatment for UCEC patients.
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Affiliation(s)
- Junyu Chen
- Department of Gynecology and ObstetricsThe Second Hospital of Jilin UniversityChangchunChina
| | - Shan Wu
- Department of Gynecology and ObstetricsThe Second Hospital of Jilin UniversityChangchunChina
- Department of Reproductive Endocrinology, Key Laboratory of Reproductive Genetics (Ministry of Education)Women's Hospital, Zhejiang University, School of MedicineHangzhouChina
| | - Junwei Wang
- Department of Obstetrics and GynecologyThe First Hospital of Jilin UniversityChangchunChina
| | - Chunying Han
- Third Department of Gynecological OncologyJilin Cancer HospitalChangchunChina
| | - Lijing Zhao
- Department of Rehabilitation, School of NursingJilin UniversityChangchunChina
| | - Kang He
- Department of Rehabilitation, School of NursingJilin UniversityChangchunChina
| | - Yan Jia
- Department of Gynecology and ObstetricsThe Second Hospital of Jilin UniversityChangchunChina
| | - Manhua Cui
- Department of Gynecology and ObstetricsThe Second Hospital of Jilin UniversityChangchunChina
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9
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Campos LV, Van Ravenstein SX, Vontalge EJ, Greer BH, Heintzman DR, Kavlashvili T, McDonald WH, Rose KL, Eichman BF, Dewar JM. RTEL1 and MCM10 overcome topological stress during vertebrate replication termination. Cell Rep 2023; 42:112109. [PMID: 36807139 PMCID: PMC10432576 DOI: 10.1016/j.celrep.2023.112109] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/30/2022] [Accepted: 01/30/2023] [Indexed: 02/19/2023] Open
Abstract
Topological stress can cause converging replication forks to stall during termination of vertebrate DNA synthesis. However, replication forks ultimately overcome fork stalling, suggesting that alternative mechanisms of termination exist. Using proteomics in Xenopus egg extracts, we show that the helicase RTEL1 and the replisome protein MCM10 are highly enriched on chromatin during fork convergence and are crucially important for fork convergence under conditions of topological stress. RTEL1 and MCM10 cooperate to promote fork convergence and do not impact topoisomerase activity but do promote fork progression through a replication barrier. Thus, RTEL1 and MCM10 play a general role in promoting progression of stalled forks, including when forks stall during termination. Our data reveal an alternate mechanism of termination involving RTEL1 and MCM10 that can be used to complete DNA synthesis under conditions of topological stress.
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Affiliation(s)
- Lillian V Campos
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | | | - Emma J Vontalge
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Briana H Greer
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Darren R Heintzman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Tamar Kavlashvili
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - W Hayes McDonald
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Kristie Lindsey Rose
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Brandt F Eichman
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - James M Dewar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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10
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The CMG helicase and cancer: a tumor "engine" and weakness with missing mutations. Oncogene 2023; 42:473-490. [PMID: 36522488 PMCID: PMC9948756 DOI: 10.1038/s41388-022-02572-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022]
Abstract
The replicative Cdc45-MCM-GINS (CMG) helicase is a large protein complex that functions in the DNA melting and unwinding steps as a component of replisomes during DNA replication in mammalian cells. Although the CMG performs this important role in cell growth, the CMG is not a simple bystander in cell cycle events. Components of the CMG, specifically the MCM precursors, are also involved in maintaining genomic stability by regulating DNA replication fork speeds, facilitating recovery from replicative stresses, and preventing consequential DNA damage. Given these important functions, MCM/CMG complexes are highly regulated by growth factors such as TGF-ß1 and by signaling factors such as Myc, Cyclin E, and the retinoblastoma protein. Mismanagement of MCM/CMG complexes when these signaling mediators are deregulated, and in the absence of the tumor suppressor protein p53, leads to increased genomic instability and is a contributor to tumorigenic transformation and tumor heterogeneity. The goal of this review is to provide insight into the mechanisms and dynamics by which the CMG is regulated during its assembly and activation in mammalian genomes, and how errors in CMG regulation due to oncogenic changes promote tumorigenesis. Finally, and most importantly, we highlight the emerging understanding of the CMG helicase as an exploitable vulnerability and novel target for therapeutic intervention in cancer.
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11
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Zhao X, Wang J, Jin D, Cheng J, Chen H, Li Z, Wang Y, Lou H, Zhu JK, Du X, Gong Z. AtMCM10 promotes DNA replication-coupled nucleosome assembly in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:203-222. [PMID: 36541721 DOI: 10.1111/jipb.13438] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Minichromosome Maintenance protein 10 (MCM10) is essential for DNA replication initiation and DNA elongation in yeasts and animals. Although the functions of MCM10 in DNA replication and repair have been well documented, the detailed mechanisms for MCM10 in these processes are not well known. Here, we identified AtMCM10 gene through a forward genetic screening for releasing a silenced marker gene. Although plant MCM10 possesses a similar crystal structure as animal MCM10, AtMCM10 is not essential for plant growth or development in Arabidopsis. AtMCM10 can directly bind to histone H3-H4 and promotes nucleosome assembly in vitro. The nucleosome density is decreased in Atmcm10, and most of the nucleosome density decreased regions in Atmcm10 are also regulated by newly synthesized histone chaperone Chromatin Assembly Factor-1 (CAF-1). Loss of both AtMCM10 and CAF-1 is embryo lethal, indicating that AtMCM10 and CAF-1 are indispensable for replication-coupled nucleosome assembly. AtMCM10 interacts with both new and parental histones. Atmcm10 mutants have lower H3.1 abundance and reduced H3K27me1/3 levels with releasing some silenced transposons. We propose that AtMCM10 deposits new and parental histones during nucleosome assembly, maintaining proper epigenetic modifications and genome stability during DNA replication.
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Affiliation(s)
- Xinjie Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dan Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jinkui Cheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hui Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yu Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jian-Kang Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Science, Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuan Du
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen, 518060, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, 518060, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
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12
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Identification of Novel Hub Genes Associated with Psoriasis Using Integrated Bioinformatics Analysis. Int J Mol Sci 2022; 23:ijms232315286. [PMID: 36499614 PMCID: PMC9737295 DOI: 10.3390/ijms232315286] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Psoriasis is a chronic, prolonged, and recurrent inflammatory skin disease and the current therapeutics can only alleviate the symptoms rather than cure it completely. Therefore, we aimed to identify the molecular signatures and specific biomarkers of psoriasis to provide novel clues for psoriasis and targeted therapy. In the present study, the Gene Expression Omnibus (GEO) database was used to retrieve three microarray datasets (GSE166388, GSE50790 and GSE42632) and to explore the differentially expressed genes (DEGs) in psoriasis using the Affy package in R software. The gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment were utilized to determine the common DEGs and their capabilities. The STRING database was used to develop DEG-encoded proteins and a protein-protein interaction network (PPI) and the Cytohubba plugin to classify hub genes. Using the NetworkAnalyst platform, we detected transcription factors (TFs), microRNAs and drug candidates interacting with hub genes. In addition, the expression levels of hub genes in HaCaT cells were detected by western blot. We screened the up- and downregulated DEGs from the transcriptome microarrays of corresponding psoriasis patients. Functional enrichment of DEGs in psoriasis was mainly associated with positive regulation of leukocyte cell-cell adhesion and T cell activation, cytokine binding, cytokine activity and the Wnt signaling pathway. Through further data processing, we obtained 57 intersecting genes in the three datasets and probed them in STRING to determine the interaction of their expressed proteins and we obtained the critical 10 hub genes in the Cytohubba plugin, including TOP2A, CDKN3, MCM10, PBK, HMMR, CEP55, ASPM, KIAA0101, ESC02, and IL-1β. Using these hub genes as targets, we obtained 35 TFs and 213 miRNAs that may regulate these genes and 33 potential therapeutic agents for psoriasis. Furthermore, the expression levels of TOP2A, MCM10, PBK, ASPM, KIAA0101 and IL-1β were observably increased in HaCaT cells. In conclusion, we identified potential biomarkers, risk factors and drugs for psoriasis.
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13
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Shaw AE, Kairamkonda S, Ghodke H, Schauer GD. Biochemical and single-molecule techniques to study accessory helicase resolution of R-loop proteins at stalled replication forks. Methods Enzymol 2022; 673:191-225. [PMID: 35965008 DOI: 10.1016/bs.mie.2022.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
R-loop proteins present a stable and robust blockade to the progression of a DNA replication fork during S-phase. The consequences of this block can include mutagenesis and other irreversible chromosomal catastrophes, causing genomic instability and disease. As such, further investigation into the molecular mechanisms underlying R-loop protein resolution is warranted. The critical role of non-replicative accessory helicases in R-loop protein resolution has increasingly come into light in recent years. Such helicases include the Pif1-family, monomeric helicases that have been studied in many different contexts and that have been ascribed to a multitude of separable protective functions in the cell. In this chapter, we present protocols to study R-loop protein resolution by Pif1 helicase at stalled replication forks using purified proteins, both at the biochemical and single-molecule level. Our system uses recombinant proteins expressed in Saccharomyces cerevisiae but could apply to practically any organism of interest due to the high interspecies homology of the proteins involved in DNA replication. The methods we outline are extensible to many systems and should be applicable to studying R-loop clearance by any Superfamily (SF) 1B helicase. These techniques will further enable mechanistic research on these critical but understudied components of the genomic maintenance program.
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Affiliation(s)
- Alisa E Shaw
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Sreeya Kairamkonda
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Harshad Ghodke
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW, Australia
| | - Grant D Schauer
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States.
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14
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Mellor C, Perez C, Sale JE. Creation and resolution of non-B-DNA structural impediments during replication. Crit Rev Biochem Mol Biol 2022; 57:412-442. [PMID: 36170051 PMCID: PMC7613824 DOI: 10.1080/10409238.2022.2121803] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 01/27/2023]
Abstract
During replication, folding of the DNA template into non-B-form secondary structures provides one of the most abundant impediments to the smooth progression of the replisome. The core replisome collaborates with multiple accessory factors to ensure timely and accurate duplication of the genome and epigenome. Here, we discuss the forces that drive non-B structure formation and the evidence that secondary structures are a significant and frequent source of replication stress that must be actively countered. Taking advantage of recent advances in the molecular and structural biology of the yeast and human replisomes, we examine how structures form and how they may be sensed and resolved during replication.
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Affiliation(s)
- Christopher Mellor
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Consuelo Perez
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Julian E Sale
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
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15
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A DNA Replication Fork-centric View of the Budding Yeast DNA Damage Response. DNA Repair (Amst) 2022; 119:103393. [DOI: 10.1016/j.dnarep.2022.103393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/23/2022]
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16
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Dimerization of Firing Factors for Replication Origin Activation in Eukaryotes: A Crucial Process for Simultaneous Assembly of Bidirectional Replication Forks? BIOLOGY 2022; 11:biology11060928. [PMID: 35741449 PMCID: PMC9219616 DOI: 10.3390/biology11060928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Chromosomal DNA must be faithfully duplicated and segregated into two daughter cells when cells divide. DNA synthesis initiates from specific regions known as the origins of replication. When it starts, a pair of the replication fork is established, and each replication fork moves away from replication origins. In each replication fork, replicative helicase unwinds DNA from a double to a single strand. This implies that two sets of active helicase are generated from each replication origin. To make this possible, two sets of replicative helicases are loaded onto replication origins as inactive dimers first. When S-phase specific cyclin-dependent kinases, S-CDKs, are activated, the inactive helicase is converted into the active helicase with the aid of other factors called firing factors. Although two sets of firing factors seem to be required to activate two sets of helicase, it is largely unknown whether two sets of firing factors function simultaneously to establish bidirectional replication forks in a coordinated way. We introduce our current understanding of firing factor dimerization and discuss its potential contribution to bidirectional replication fork formation in this review. Abstract Controlling the activity of the heterohexameric Mcm2–7 replicative helicase is crucial for regulation of replication origin activity in eukaryotes. Because bidirectional replication forks are generated from every replication origin, when origins are licensed for replication in the first step of DNA replication, two inactive Mcm2–7 heterohexiameric complexes are loaded around double stranded DNA as a head-to-head double hexamer. The helicases are subsequently activated via a ‘firing’ reaction, in which the Mcm2–7 double hexamer is converted into two active helicase units, the CMG complex, by firing factors. Dimerization of firing factors may contribute to this process by allowing simultaneous activation of two sets of helicases and thus efficient assembly of bidirectional replication forks. An example of this is dimerization of the firing factor Sld3/Treslin/Ticrr via its binding partner, Sld7/MTBP. In organisms in which no Sld7 ortholog has been identified, such as the fission yeast Schizosaccharomyces pombe, Sld3 itself has a dimerization domain, and it has been suggested that this self-interaction is crucial for the firing reaction in this organism. Dimerization induces a conformational change in Sdl3 that appears to be critical for the firing reaction. Moreover, Mcm10 also seems to be regulated by self-interaction in yeasts. Although it is not yet clear to what extent dimerization of firing factors contributes to the firing reaction in eukaryotes, we discuss the possible roles of firing factor dimerization in simultaneous helicase activation.
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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: 1] [Impact Index Per Article: 0.5] [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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18
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Wu Z, Wang Y, Li J, Wang H, Tuo X, Zheng J. MCM10 is a Prognostic Biomarker and Correlated With Immune Checkpoints in Ovarian Cancer. Front Genet 2022; 13:864578. [PMID: 35664337 PMCID: PMC9161093 DOI: 10.3389/fgene.2022.864578] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/02/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Microchromosome maintenance protein 10 (MCM10) is required for DNA replication in all eukaryotes, and it plays a key role in the development of many types of malignancies. However, we currently still do not know the relationship between MCM10 and ovarian cancer (OV) prognosis and immune checkpoints. Methods: The Gene Expression Profiling Interactive Analysis and Tumor Immunology Estimation Resource (TIMER) databases were used to investigate MCM10 expression in Fan cancer. The Kaplan-Meier Plotter and PrognoScan were used to assess the relationship between MCM10 and OV prognosis. The LinkedOmics database was used to analyze the MCM10 co-expression network and explore GO term annotation and the KEGG pathway. The relationship between MCM10 expression and immune infiltration in OV was investigated using the Tumor Immunology Estimation Resource database. cBioPortal database was used to explore the relationship between MCM10 expression and 25 immune checkpoints. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) was performed to detect MCM10 expression. The prognosis was also analyzed by distinguishing between high and low expression groups based on median expression values. Results: The results of the three data sets (220,651_s_at, 222,962_s_at and 223,570_at) in KM Plotter all indicated that the overall survivalof the high MCM10 expression group was lower than that of the low expression group OV, and the results of GSE9891 also reached the same conclusion. The expression level of MCM10 was negatively correlated with B cells and CD8+T cells, and positively correlated with CD4+T Cells and Macrophages. GO term annotation and KEGG pathway analysis showed that the co-expressed genes of MCM10 were mainly enriched in cell cycle and DNA replication. The alterations in MCM10 coexisted statistically with the immune checkpoints CTLA4, TNFSF4, TNFSF18, CD80, ICOSLG, LILRB1 and CD200. PCR results displayed that MCM10 was highly expressed in OV tissues, and the increased expression of MCM10 was significantly associated with poor overall survival. Conclusion: These results demonstrated that high expression of MCM10 was associated with poor prognosis in OV and correlated with immune checkpoints.
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Affiliation(s)
- Zhenzhen Wu
- Department of Gynecology, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Yueyuan Wang
- Department of Pathology, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Juan Li
- Department of Gynecology, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Huiling Wang
- Department of Gynecological Oncology, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Xunyuan Tuo
- Department of Gynecological Oncology, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Jing Zheng
- Department of Gynecology, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
- *Correspondence: Jing Zheng,
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19
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Malone EG, Thompson MD, Byrd AK. Role and Regulation of Pif1 Family Helicases at the Replication Fork. Int J Mol Sci 2022; 23:ijms23073736. [PMID: 35409096 PMCID: PMC8998199 DOI: 10.3390/ijms23073736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
Abstract
Pif1 helicases are a multifunctional family of DNA helicases that are important for many aspects of genomic stability in the nucleus and mitochondria. Pif1 helicases are conserved from bacteria to humans. Pif1 helicases play multiple roles at the replication fork, including promoting replication through many barriers such as G-quadruplex DNA, the rDNA replication fork barrier, tRNA genes, and R-loops. Pif1 helicases also regulate telomerase and promote replication termination, Okazaki fragment maturation, and break-induced replication. This review highlights many of the roles and regulations of Pif1 at the replication fork that promote cellular health and viability.
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Affiliation(s)
- Emory G. Malone
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (E.G.M.); (M.D.T.)
| | - Matthew D. Thompson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (E.G.M.); (M.D.T.)
| | - Alicia K. Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (E.G.M.); (M.D.T.)
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence: ; Tel.: +1-501-526-6488
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20
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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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21
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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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22
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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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23
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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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24
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CMG helicase can use ATPγS to unwind DNA: Implications for the rate-limiting step in the reaction mechanism. Proc Natl Acad Sci U S A 2022; 119:2119580119. [PMID: 35042821 PMCID: PMC8794833 DOI: 10.1073/pnas.2119580119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2021] [Indexed: 11/18/2022] Open
Abstract
The adenosine triphosphate (ATP) analog ATPγS often greatly slows or prevents enzymatic ATP hydrolysis. The eukaryotic CMG (Cdc45, Mcm2 to 7, GINS) replicative helicase is presumed unable to hydrolyze ATPγS and thus unable to perform DNA unwinding, as documented for certain other helicases. Consequently, ATPγS is often used to "preload" CMG onto forked DNA substrates without unwinding before adding ATP to initiate helicase activity. We find here that CMG does hydrolyze ATPγS and couples it to DNA unwinding. Indeed, the rate of unwinding of a 20- and 30-mer duplex fork of different sequences by CMG is only reduced 1- to 1.5-fold using ATPγS compared with ATP. These findings imply that a conformational change is the rate-limiting step during CMG unwinding, not hydrolysis. Instead of using ATPγS for loading CMG onto DNA, we demonstrate here that nonhydrolyzable adenylyl-imidodiphosphate (AMP-PNP) can be used to preload CMG onto a forked DNA substrate without unwinding.
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25
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Optimizing CMG helicase and CMG-dependent replication assays by designing DNA fork substrates and choosing nucleotide analogues for helicase preloading. Methods Enzymol 2022; 672:173-202. [DOI: 10.1016/bs.mie.2022.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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26
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Nottingham E, Mazzio E, Surapaneni SK, Kutlehria S, Mondal A, Badisa R, Safe S, Rishi AK, Singh M. Synergistic effects of methyl 2-cyano-3,11-dioxo-18beta-olean-1,-12-dien-30-oate and erlotinib on erlotinib-resistant non-small cell lung cancer cells. J Pharm Anal 2021; 11:799-807. [PMID: 35028186 PMCID: PMC8740161 DOI: 10.1016/j.jpha.2021.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 11/09/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is often characterized by an underlying mutation in the epidermal growth factor receptor (EGFR), contributing to aggressive metastatic disease. Methyl 2-cyano-3,11-dioxo-18beta-olean-1,12-dien-30-oate (CDODA-Me), a glycyrrhetinic acid derivative, reportedly improves the therapeutic response to erlotinib (ERL), an EGFR tyrosine kinase inhibitor. In the present study, we performed a series of studies to demonstrate the efficacy of CDODA-Me (2 μM) in sensitizing HCC827R (ERL-resistant) cells to ERL. Herein, we first established the selectivity of ERL-induced drug resistance in the HCC827R cells, which was sensitized when ERL was combined with CDODA-Me (2 μM), shifting the IC50 from 23.48 μM to 5.46 μM. Subsequently, whole transcriptomic microarray expression data demonstrated that the combination of ERL + CDODA-Me elicited 210 downregulated genes (0.44% of the whole transcriptome (WT)) and 174 upregulated genes (0.36% of the WT), of which approximately 80% were unique to the ERL + CDODA-Me group. Synergistic effects centered on losses to cell cycle progression transcripts, a reduction of minichromosome maintenance complex components (MCM2-7), all key components of the Cdc45·MCM2-7GINS (CMG) complex, and replicative helicases; these effects were tantamount to the upregulation of processes associated with the nuclear factor erythroid 2 like 2 translational response to oxidative stress, including sulfiredoxin 1, heme oxygenase 1, and stress-induced growth inhibitor 1. Collectively, these findings indicate that the synergistic therapeutic effects of ERL + CDODA-Me on resistant NSCLC cells are mediated via the inhibition of mitosis and induction of oxidative stress.
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Affiliation(s)
- Ebony Nottingham
- Department of Pharmaceutics, College of Pharmacy and Pharmaceutical Sciences, Florida A & M University, Tallahassee, FL, 32307, USA
| | - Elizabeth Mazzio
- Department of Pharmaceutics, College of Pharmacy and Pharmaceutical Sciences, Florida A & M University, Tallahassee, FL, 32307, USA
| | - Sunil Kumar Surapaneni
- Department of Pharmaceutics, College of Pharmacy and Pharmaceutical Sciences, Florida A & M University, Tallahassee, FL, 32307, USA
| | - Shallu Kutlehria
- Department of Pharmaceutics, College of Pharmacy and Pharmaceutical Sciences, Florida A & M University, Tallahassee, FL, 32307, USA
| | - Arindam Mondal
- Department of Pharmaceutics, College of Pharmacy and Pharmaceutical Sciences, Florida A & M University, Tallahassee, FL, 32307, USA
| | - Ramesh Badisa
- Department of Pharmaceutics, College of Pharmacy and Pharmaceutical Sciences, Florida A & M University, Tallahassee, FL, 32307, USA
| | - Stephen Safe
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine, Texas A & M University, College Station, TX, 77843, USA
| | - Arun K. Rishi
- John D. Dingell VA medical Center and Department of Oncology, Wayne State University, Detroit, MI, 48201, USA
| | - Mandip Singh
- Department of Pharmaceutics, College of Pharmacy and Pharmaceutical Sciences, Florida A & M University, Tallahassee, FL, 32307, USA
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27
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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: 8] [Impact Index Per Article: 2.7] [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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28
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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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29
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Mayle R, O'Donnell M. Expression of recombinant multi-protein complexes in Saccharomyces cerevisiae. Methods Enzymol 2021; 660:3-20. [PMID: 34742395 DOI: 10.1016/bs.mie.2021.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Baker's yeast, Saccharomyces cerevisiae, is a versatile system for expression of recombinant eukaryotic proteins. This system is simple to use and does not require extraordinary expertise nor tissue culture facilities. Proteins expressed in the yeast system provide eukaryotic post-translational modifications, making it superior to bacterial expression for factors that require post-translational modification. In addition, it is quite simple to co-express multiple genes at the same time, for recombinant production of large multi-protein complexes. In this chapter, we provide protocols for inducible expression of recombinant genes from episomal plasmid vectors, and protocols for integration of the recombinant genes into the chromosomes of yeast, which enables simple rapid growth of expression cells and induction of recombinant protein complexes in non-selectable rich media.
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Affiliation(s)
- Ryan Mayle
- Laboratory of DNA Replication, The Rockefeller University, New York, NY, United States
| | - Mike O'Donnell
- Laboratory of DNA Replication, The Rockefeller University, New York, NY, United States; Howard Hughes Medical Institute at Rockefeller University, New York, NY, United States.
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30
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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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31
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Ashour ME, Mosammaparast N. Mechanisms of damage tolerance and repair during DNA replication. Nucleic Acids Res 2021; 49:3033-3047. [PMID: 33693881 PMCID: PMC8034635 DOI: 10.1093/nar/gkab101] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/28/2021] [Accepted: 03/02/2021] [Indexed: 01/05/2023] Open
Abstract
Accurate duplication of chromosomal DNA is essential for the transmission of genetic information. The DNA replication fork encounters template lesions, physical barriers, transcriptional machinery, and topological barriers that challenge the faithful completion of the replication process. The flexibility of replisomes coupled with tolerance and repair mechanisms counteract these replication fork obstacles. The cell possesses several universal mechanisms that may be activated in response to various replication fork impediments, but it has also evolved ways to counter specific obstacles. In this review, we will discuss these general and specific strategies to counteract different forms of replication associated damage to maintain genomic stability.
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Affiliation(s)
- Mohamed Elsaid Ashour
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
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32
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Baxley RM, Leung W, Schmit MM, Matson JP, Yin L, Oram MK, Wang L, Taylor J, Hedberg J, Rogers CB, Harvey AJ, Basu D, Taylor JC, Pagnamenta AT, Dreau H, Craft J, Ormondroyd E, Watkins H, Hendrickson EA, Mace EM, Orange JS, Aihara H, Stewart GS, Blair E, Cook JG, Bielinsky AK. Bi-allelic MCM10 variants associated with immune dysfunction and cardiomyopathy cause telomere shortening. Nat Commun 2021; 12:1626. [PMID: 33712616 PMCID: PMC7955084 DOI: 10.1038/s41467-021-21878-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/11/2021] [Indexed: 12/22/2022] Open
Abstract
Minichromosome maintenance protein 10 (MCM10) is essential for eukaryotic DNA replication. Here, we describe compound heterozygous MCM10 variants in patients with distinctive, but overlapping, clinical phenotypes: natural killer (NK) cell deficiency (NKD) and restrictive cardiomyopathy (RCM) with hypoplasia of the spleen and thymus. To understand the mechanism of MCM10-associated disease, we modeled these variants in human cell lines. MCM10 deficiency causes chronic replication stress that reduces cell viability due to increased genomic instability and telomere erosion. Our data suggest that loss of MCM10 function constrains telomerase activity by accumulating abnormal replication fork structures enriched with single-stranded DNA. Terminally-arrested replication forks in MCM10-deficient cells require endonucleolytic processing by MUS81, as MCM10:MUS81 double mutants display decreased viability and accelerated telomere shortening. We propose that these bi-allelic variants in MCM10 predispose specific cardiac and immune cell lineages to prematurely arrest during differentiation, causing the clinical phenotypes observed in both NKD and RCM patients.
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Affiliation(s)
- Ryan M Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Wendy Leung
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Megan M Schmit
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jacob Peter Matson
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Lulu Yin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Marissa K Oram
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Liangjun Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - John Taylor
- Oxford Medical Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jack Hedberg
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Colette B Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Adam J Harvey
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Debashree Basu
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jenny C Taylor
- Wellcome Centre Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford NIHR Biomedical Research Centre, Oxford, OX3 7BN, UK
| | - Alistair T Pagnamenta
- Wellcome Centre Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford NIHR Biomedical Research Centre, Oxford, OX3 7BN, UK
| | - Helene Dreau
- Department of Haematology, University of Oxford, Oxford, OX3 7BN, UK
| | - Jude Craft
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Elizabeth Ormondroyd
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Emily M Mace
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Jordan S Orange
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Edward Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jeanette Gowen Cook
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
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33
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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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34
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Schmit M, Bielinsky AK. Congenital Diseases of DNA Replication: Clinical Phenotypes and Molecular Mechanisms. Int J Mol Sci 2021; 22:E911. [PMID: 33477564 PMCID: PMC7831139 DOI: 10.3390/ijms22020911] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/19/2022] Open
Abstract
Deoxyribonucleic acid (DNA) replication can be divided into three major steps: initiation, elongation and termination. Each time a human cell divides, these steps must be reiteratively carried out. Disruption of DNA replication can lead to genomic instability, with the accumulation of point mutations or larger chromosomal anomalies such as rearrangements. While cancer is the most common class of disease associated with genomic instability, several congenital diseases with dysfunctional DNA replication give rise to similar DNA alterations. In this review, we discuss all congenital diseases that arise from pathogenic variants in essential replication genes across the spectrum of aberrant replisome assembly, origin activation and DNA synthesis. For each of these conditions, we describe their clinical phenotypes as well as molecular studies aimed at determining the functional mechanisms of disease, including the assessment of genomic stability. By comparing and contrasting these diseases, we hope to illuminate how the disruption of DNA replication at distinct steps affects human health in a surprisingly cell-type-specific manner.
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Affiliation(s)
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA;
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35
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Abstract
In all cell types, a multi-protein machinery is required to accurately duplicate the large duplex DNA genome. This central life process requires five core replisome factors in all cellular life forms studied thus far. Unexpectedly, three of the five core replisome factors have no common ancestor between bacteria and eukaryotes. Accordingly, the replisome machines of bacteria and eukaryotes have important distinctions in the way that they are organized and function. This chapter outlines the major replication proteins that perform DNA duplication at replication forks, with particular attention to differences and similarities in the strategies used by eukaryotes and bacteria.
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Affiliation(s)
- Nina Y Yao
- DNA Replication Laboratory, The Rockefeller University, New York, USA, 10065
| | - Michael E O'Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, USA, 10065. .,Howard Hughes Medical Institute, The Rockefeller University, New York, USA, 10065.
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36
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Schauer GD, Spenkelink LM, Lewis JS, Yurieva O, Mueller SH, van Oijen AM, O'Donnell ME. Replisome bypass of a protein-based R-loop block by Pif1. Proc Natl Acad Sci U S A 2020; 117:30354-30361. [PMID: 33199603 PMCID: PMC7720201 DOI: 10.1073/pnas.2020189117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Efficient and faithful replication of the genome is essential to maintain genome stability. Replication is carried out by a multiprotein complex called the replisome, which encounters numerous obstacles to its progression. Failure to bypass these obstacles results in genome instability and may facilitate errors leading to disease. Cells use accessory helicases that help the replisome bypass difficult barriers. All eukaryotes contain the accessory helicase Pif1, which tracks in a 5'-3' direction on single-stranded DNA and plays a role in genome maintenance processes. Here, we reveal a previously unknown role for Pif1 in replication barrier bypass. We use an in vitro reconstituted Saccharomyces cerevisiae replisome to demonstrate that Pif1 enables the replisome to bypass an inactive (i.e., dead) Cas9 (dCas9) R-loop barrier. Interestingly, dCas9 R-loops targeted to either strand are bypassed with similar efficiency. Furthermore, we employed a single-molecule fluorescence visualization technique to show that Pif1 facilitates this bypass by enabling the simultaneous removal of the dCas9 protein and the R-loop. We propose that Pif1 is a general displacement helicase for replication bypass of both R-loops and protein blocks.
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Affiliation(s)
- Grant D Schauer
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523;
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Jacob S Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Olga Yurieva
- HHMI, Rockefeller University, New York, NY 10065
- Laboratory of DNA Replication, Rockefeller University, New York, NY 10065
| | - Stefan H Mueller
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia;
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Michael E O'Donnell
- HHMI, Rockefeller University, New York, NY 10065;
- Laboratory of DNA Replication, Rockefeller University, New York, NY 10065
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37
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Conti BA, Smogorzewska A. Mechanisms of direct replication restart at stressed replisomes. DNA Repair (Amst) 2020; 95:102947. [PMID: 32853827 PMCID: PMC7669714 DOI: 10.1016/j.dnarep.2020.102947] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 02/09/2023]
Affiliation(s)
- Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York 10065, USA.
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38
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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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39
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Structure of the polymerase ε holoenzyme and atomic model of the leading strand replisome. Nat Commun 2020; 11:3156. [PMID: 32572031 PMCID: PMC7308368 DOI: 10.1038/s41467-020-16910-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/02/2020] [Indexed: 01/01/2023] Open
Abstract
The eukaryotic leading strand DNA polymerase (Pol) ε contains 4 subunits, Pol2, Dpb2, Dpb3 and Dpb4. Pol2 is a fusion of two B-family Pols; the N-terminal Pol module is catalytic and the C-terminal Pol module is non-catalytic. Despite extensive efforts, there is no atomic structure for Pol ε holoenzyme, critical to understanding how DNA synthesis is coordinated with unwinding and the DNA path through the CMG helicase-Pol ε-PCNA clamp. We show here a 3.5-Å cryo-EM structure of yeast Pol ε revealing that the Dpb3–Dpb4 subunits bridge the two DNA Pol modules of Pol2, holding them rigid. This information enabled an atomic model of the leading strand replisome. Interestingly, the model suggests that an OB fold in Dbp2 directs leading ssDNA from CMG to the Pol ε active site. These results complete the DNA path from entry of parental DNA into CMG to exit of daughter DNA from PCNA. DNA polymerase epsilon (Pol ε) is responsible for leading strand synthesis during DNA replication. Here the authors use Cryo-EM to describe the architecture of the Pol ε holoenzyme and to provide an atomic model for the leading strand replisome.
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40
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Joo S, Chung BH, Lee M, Ha TH. Ring-shaped replicative helicase encircles double-stranded DNA during unwinding. Nucleic Acids Res 2020; 47:11344-11354. [PMID: 31665506 PMCID: PMC6868380 DOI: 10.1093/nar/gkz893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/29/2019] [Accepted: 10/23/2019] [Indexed: 11/14/2022] Open
Abstract
Ring-shaped replicative helicases are hexameric and play a key role in cellular DNA replication. Despite their importance, our understanding of the unwinding mechanism of replicative helicases is far from perfect. Bovine papillomavirus E1 is one of the best-known model systems for replicative helicases. E1 is a multifunctional initiator that senses and melts the viral origin and unwinds DNA. Here, we study the unwinding mechanism of E1 at the single-molecule level using magnetic tweezers. The result reveals that E1 as a single hexamer is a poorly processive helicase with a low unwinding rate. Tension on the DNA strands impedes unwinding, indicating that the helicase interacts strongly with both DNA strands at the junction. While investigating the interaction at a high force (26–30 pN), we discovered that E1 encircles dsDNA. By comparing with the E1 construct without a DNA binding domain, we propose two possible encircling modes of E1 during active unwinding.
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Affiliation(s)
- Sihwa Joo
- BioNanoTechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.,Department of Nanobiotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Bong H Chung
- BioNanoTechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.,Department of Nanobiotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea.,BioNano Health Guard Research Center, Daejeon 34141, Republic of Korea
| | - Mina Lee
- Center for Nano-Bio Measurement, Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea
| | - Tai H Ha
- BioNanoTechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.,Department of Nanobiotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
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41
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Wasserman MR, Schauer GD, O'Donnell ME, Liu S. Replication Fork Activation Is Enabled by a Single-Stranded DNA Gate in CMG Helicase. Cell 2020; 178:600-611.e16. [PMID: 31348887 DOI: 10.1016/j.cell.2019.06.032] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 04/05/2019] [Accepted: 06/24/2019] [Indexed: 10/26/2022]
Abstract
The eukaryotic replicative helicase CMG is a closed ring around double-stranded (ds)DNA at origins yet must transition to single-stranded (ss)DNA for helicase action. CMG must also handle repair intermediates, such as reversed forks that lack ssDNA. Here, using correlative single-molecule fluorescence and force microscopy, we show that CMG harbors a ssDNA gate that enables transitions between ss and dsDNA. When coupled to DNA polymerase, CMG remains on ssDNA, but when uncoupled, CMG employs this gate to traverse forked junctions onto dsDNA. Surprisingly, CMG undergoes rapid diffusion on dsDNA and can transition back onto ssDNA to nucleate a functional replisome. The gate-distinct from that between Mcm2/5 used for origin loading-is intrinsic to CMG; however, Mcm10 promotes strand passage by enhancing the affinity of CMG to DNA. This gating process may explain the dsDNA-to-ssDNA transition of CMG at origins and help preserve CMG on dsDNA during fork repair.
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Affiliation(s)
- Michael R Wasserman
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065, USA
| | - Grant D Schauer
- Laboratory of DNA Replication, The Rockefeller University, New York, NY 10065, USA
| | - Michael E O'Donnell
- Laboratory of DNA Replication, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065, USA.
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42
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Rad53 limits CMG helicase uncoupling from DNA synthesis at replication forks. Nat Struct Mol Biol 2020; 27:461-471. [PMID: 32341532 PMCID: PMC7225081 DOI: 10.1038/s41594-020-0407-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/06/2020] [Indexed: 12/13/2022]
Abstract
The coordination of DNA unwinding and synthesis at replication forks promotes efficient and faithful replication of chromosomal DNA. Disruption of the balance between helicase and polymerase activities during replication stress leads to fork progression defects and activation of the Rad53 checkpoint kinase, which is essential for the functional maintenance of stalled replication forks. The mechanism of Rad53-dependent fork stabilization is not known. Using reconstituted budding yeast replisomes, we show that mutational inactivation of the leading strand DNA polymerase, Pol ε, dNTP depletion, and chemical inhibition of DNA polymerases cause excessive DNA unwinding by the replicative DNA helicase, CMG, demonstrating that budding yeast replisomes lack intrinsic mechanisms that control helicase-polymerase coupling at the fork. Importantly, we find that the Rad53 kinase restricts excessive DNA unwinding at replication forks by limiting CMG helicase activity, suggesting a mechanism for fork stabilization by the replication checkpoint.
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43
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Yuan Z, Georgescu R, Bai L, Zhang D, Li H, O'Donnell ME. DNA unwinding mechanism of a eukaryotic replicative CMG helicase. Nat Commun 2020; 11:688. [PMID: 32019936 PMCID: PMC7000775 DOI: 10.1038/s41467-020-14577-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 01/17/2020] [Indexed: 11/09/2022] Open
Abstract
High-resolution structures have not been reported for replicative helicases at a replication fork at atomic resolution, a prerequisite to understanding the unwinding mechanism. The eukaryotic replicative CMG (Cdc45, Mcm2-7, GINS) helicase contains a Mcm2-7 motor ring, with the N-tier ring in front and the C-tier motor ring behind. The N-tier ring is structurally divided into a zinc finger (ZF) sub-ring followed by the oligosaccharide/oligonucleotide-binding (OB) fold ring. Here we report the cryo-EM structure of CMG on forked DNA at 3.9 Å, revealing that parental DNA enters the ZF sub-ring and strand separation occurs at the bottom of the ZF sub-ring, where the lagging strand is blocked and diverted sideways by OB hairpin-loops of Mcm3, Mcm4, Mcm6, and Mcm7. Thus, instead of employing a specific steric exclusion process, or even a separation pin, unwinding is achieved via a "dam-and-diversion tunnel" mechanism that does not require specific protein-DNA interaction. The C-tier motor ring contains spirally configured PS1 and H2I loops of Mcms 2, 3, 5, 6 that translocate on the spirally-configured leading strand, and thereby pull the preceding DNA segment through the diversion tunnel for strand separation.
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Affiliation(s)
- Zuanning Yuan
- Structural Biology Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Roxana Georgescu
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.,DNA Replication Laboratory, The Rockefeller University, New York, NY, USA
| | - Lin Bai
- Structural Biology Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Dan Zhang
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA
| | - Huilin Li
- Structural Biology Program, Van Andel Institute, Grand Rapids, MI, USA.
| | - Michael E O'Donnell
- Howard Hughes Medical Institute, Chevy Chase, MD, USA. .,DNA Replication Laboratory, The Rockefeller University, New York, NY, USA.
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44
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Zou Z, Liang T, Xu Z, Xie J, Zhang S, Chen W, Wan S, Ling Y, Zhang H. Protein interactions in T7 DNA replisome inhibit the bypass of abasic site by DNA polymerase. Mutagenesis 2019; 34:355-361. [PMID: 31318416 DOI: 10.1093/mutage/gez013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 05/14/2019] [Indexed: 11/13/2022] Open
Abstract
Abasic site as a common DNA lesion blocks DNA replication and is highly mutagenic. Protein interactions in T7 DNA replisome facilitate DNA replication and translesion DNA synthesis. However, bypass of an abasic site by T7 DNA replisome has never been investigated. In this work, we used T7 DNA replisome and T7 DNA polymerase alone as two models to study DNA replication on encountering an abasic site. Relative to unmodified DNA, abasic site strongly inhibited primer extension and completely blocked strand-displacement DNA synthesis, due to the decreased fraction of enzyme-DNA productive complex and the reduced average extension rates. Moreover, abasic site at DNA fork inhibited the binding of DNA polymerase or helicase onto fork and the binding between polymerase and helicase at fork. Notably and unexpectedly, we found DNA polymerase alone bypassed an abasic site on primer/template (P/T) substrate more efficiently than did polymerase and helicase complex bypass it at fork. The presence of gp2.5 further inhibited the abasic site bypass at DNA fork. Kinetic analysis showed that this inhibition at fork relative to that on P/T was due to the decreased fraction of productive complex instead of the average extension rates. Therefore, we found that protein interactions in T7 DNA replisome inhibited the bypass of DNA lesion, different from all the traditional concept that protein interactions or accessory proteins always promote DNA replication and DNA damage bypass, providing new insights in translesion DNA synthesis performed by DNA replisome.
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Affiliation(s)
- Zhenyu Zou
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Tingting Liang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Zhongyan Xu
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayu Xie
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Shuming Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Weina Chen
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Siqi Wan
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yihui Ling
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, China
| | - Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.,The Key Laboratory of Environment and Health Among Universities and Colleges in Fujian, School of Public Health, Fujian Medical University, Fuzhou, China
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45
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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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46
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Lewis JS, Spenkelink LM, Schauer GD, Yurieva O, Mueller SH, Natarajan V, Kaur G, Maher C, Kay C, O'Donnell ME, van Oijen AM. Tunability of DNA Polymerase Stability during Eukaryotic DNA Replication. Mol Cell 2019; 77:17-25.e5. [PMID: 31704183 DOI: 10.1016/j.molcel.2019.10.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/25/2019] [Accepted: 10/01/2019] [Indexed: 12/29/2022]
Abstract
Structural and biochemical studies have revealed the basic principles of how the replisome duplicates genomic DNA, but little is known about its dynamics during DNA replication. We reconstitute the 34 proteins needed to form the S. cerevisiae replisome and show how changing local concentrations of the key DNA polymerases tunes the ability of the complex to efficiently recycle these proteins or to dynamically exchange them. Particularly, we demonstrate redundancy of the Pol α-primase DNA polymerase activity in replication and show that Pol α-primase and the lagging-strand Pol δ can be re-used within the replisome to support the synthesis of large numbers of Okazaki fragments. This unexpected malleability of the replisome might allow it to deal with barriers and resource challenges during replication of large genomes.
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Affiliation(s)
- Jacob S Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Grant D Schauer
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Olga Yurieva
- Laboratory of DNA Replication, Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Cambridge, MA 02138, USA
| | - Stefan H Mueller
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Varsha Natarajan
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Gurleen Kaur
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Claire Maher
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Callum Kay
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Michael E O'Donnell
- Laboratory of DNA Replication, Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Cambridge, MA 02138, USA.
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia.
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47
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Abstract
The replisome quickly and accurately copies billions of DNA bases each cell division cycle. However, it can make errors, especially when the template DNA is damaged. In these cases, replication-coupled repair mechanisms remove the mistake or repair the template lesions to ensure high fidelity and complete copying of the genome. Failures in these genome maintenance activities generate mutations, rearrangements, and chromosome segregation problems that cause many human diseases. In this review, I provide a broad overview of replication-coupled repair pathways, explaining how they fix polymerase mistakes, respond to template damage that acts as obstacles to the replisome, deal with broken forks, and impact human health and disease.
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48
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Yuan Z, Georgescu R, Santos RDLA, Zhang D, Bai L, Yao NY, Zhao G, O'Donnell ME, Li H. Ctf4 organizes sister replisomes and Pol α into a replication factory. eLife 2019; 8:47405. [PMID: 31589141 PMCID: PMC6800005 DOI: 10.7554/elife.47405] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 10/04/2019] [Indexed: 12/14/2022] Open
Abstract
The current view is that eukaryotic replisomes are independent. Here we show that Ctf4 tightly dimerizes CMG helicase, with an extensive interface involving Psf2, Cdc45, and Sld5. Interestingly, Ctf4 binds only one Pol α-primase. Thus, Ctf4 may have evolved as a trimer to organize two helicases and one Pol α-primase into a replication factory. In the 2CMG–Ctf43–1Pol α-primase factory model, the two CMGs nearly face each other, placing the two lagging strands toward the center and two leading strands out the sides. The single Pol α-primase is centrally located and may prime both sister replisomes. The Ctf4-coupled-sister replisome model is consistent with cellular microscopy studies revealing two sister forks of an origin remain attached and are pushed forward from a protein platform. The replication factory model may facilitate parental nucleosome transfer during replication.
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Affiliation(s)
- Zuanning Yuan
- Structural Biology Program, Van Andel Institute, Grand Rapids, United States
| | - Roxana Georgescu
- Howard Hughes Medical Institute, Chevy Chase, United States.,DNA Replication Laboratory, The Rockefeller University, New York, United States
| | | | - Daniel Zhang
- DNA Replication Laboratory, The Rockefeller University, New York, United States
| | - Lin Bai
- Structural Biology Program, Van Andel Institute, Grand Rapids, United States
| | - Nina Y Yao
- DNA Replication Laboratory, The Rockefeller University, New York, United States
| | - Gongpu Zhao
- David Van Andel Advanced Cryo-EM Suite, Van Andel Institute, Grand Rapids, United States
| | - Michael E O'Donnell
- Howard Hughes Medical Institute, Chevy Chase, United States.,DNA Replication Laboratory, The Rockefeller University, New York, United States
| | - Huilin Li
- Structural Biology Program, Van Andel Institute, Grand Rapids, United States
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49
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Whinn KS, Kaur G, Lewis JS, Schauer GD, Mueller SH, Jergic S, Maynard H, Gan ZY, Naganbabu M, Bruchez MP, O'Donnell ME, Dixon NE, van Oijen AM, Ghodke H. Nuclease dead Cas9 is a programmable roadblock for DNA replication. Sci Rep 2019; 9:13292. [PMID: 31527759 PMCID: PMC6746809 DOI: 10.1038/s41598-019-49837-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/31/2019] [Indexed: 01/19/2023] Open
Abstract
Limited experimental tools are available to study the consequences of collisions between DNA-bound molecular machines. Here, we repurpose a catalytically inactivated Cas9 (dCas9) construct as a generic, novel, targetable protein-DNA roadblock for studying mechanisms underlying enzymatic activities on DNA substrates in vitro. We illustrate the broad utility of this tool by demonstrating replication fork arrest by the specifically bound dCas9-guideRNA complex to arrest viral, bacterial and eukaryotic replication forks in vitro.
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Affiliation(s)
- Kelsey S Whinn
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Gurleen Kaur
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Jacob S Lewis
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Grant D Schauer
- Howard Hughes Medical Institute, Rockefeller University, New York, NY, 10065, USA
| | - Stefan H Mueller
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Slobodan Jergic
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Hamish Maynard
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
| | - Zhong Yan Gan
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
| | - Matharishwan Naganbabu
- Department of Chemistry and Molecular Biosensors and Imaging Center, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania, 15213, USA
| | - Marcel P Bruchez
- Department of Chemistry and Molecular Biosensors and Imaging Center, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania, 15213, USA
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania, 15213, USA
| | - Michael E O'Donnell
- Howard Hughes Medical Institute, Rockefeller University, New York, NY, 10065, USA
| | - Nicholas E Dixon
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Antoine M van Oijen
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia.
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia.
| | - Harshad Ghodke
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia.
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia.
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50
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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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