251
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Musiałek MW, Rybaczek D. Behavior of replication origins in Eukaryota - spatio-temporal dynamics of licensing and firing. Cell Cycle 2015; 14:2251-64. [PMID: 26030591 DOI: 10.1080/15384101.2015.1056421] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Although every organism shares some common features of replication, this process varies greatly among eukaryotic species. Current data show that mathematical models of the organization of origins based on possibility theory may be applied (and remain accurate) in every model organism i.e. from yeast to humans. The major differences lie within the dynamics of origin firing and the regulation mechanisms that have evolved to meet new challenges throughout the evolution of the organism. This article elaborates on the relations between chromatin structure, organization of origins, their firing times and the impact that these features can have on genome stability, showing both differences and parallels inside the eukaryotic domain.
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Key Words
- APC, anaphase promoting complex
- ARS, autonomously replicating sequences
- ATR, ataxia telangiectasia mutated and Rad3-related kinase
- C-Frag, chromosome fragmentation
- CDK, cyclin-dependent kinase
- CDT, C-terminus domain
- CEN, centromere
- CFSs, chromosome fragile sites
- CIN, chromosome instability
- CMG, Cdc45-MCM-GINS complex
- Cdc45, cell division control protein 45
- Cdc6, cell division control protein 6
- Cdt1, chromatin licensing and DNA replication factor 1
- Chk1, checkpoint kinase 1
- Clb2, G2/mitotic-specific cyclin Clb2
- DCR, Ddb1-Cu14a-Roc1 complex
- DDK, Dbf-4-dependent kinase
- DSBs, double strand breaks
- Dbf4, protein Dbf4 homolog A
- Dfp1, Hsk1-Dfp1 kinase complex regulatory subunit Dfp1
- Dpb11, DNA replication regulator Dpb11
- E2F, E2F transcription factor
- EL, early to late origins transition
- ETG1, E2F target gene 1/replisome factor
- Fkh, fork head domain protein
- GCN5, histone acetyltransferase GCN5
- GINS, go-ichi-ni-san
- LE, late to early origins transition
- MCM2–7, minichromosome maintenance helicase complex
- NDT, N-terminus domain
- ORC, origin recognition complex
- ORCA, origin recognition complex subunit A
- PCC, premature chromosome condensation
- PCNA, proliferating cell nuclear antigen
- RO, replication origin
- RPD3, histone deacetylase 3
- RTC, replication timing control
- Rif1, replication timing regulatory factor 1
- SCF, Skp1-Cullin-F-Box ligase
- SIR, sulfite reductase
- Sld2, replication regulator Sld2
- Sld3, replication regulator Sld3
- Swi6, chromatin-associated protein swi6
- Taz1, telomere length regulator taz1
- YKU70, yeast Ku protein.
- dormant origins
- mathematical models of replication
- ori, origin
- origin competence
- origin efficiency
- origin firing
- origin licensing
- p53, tumor suppressor protein p53
- replication timing
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Affiliation(s)
- Marcelina W Musiałek
- a Department of Cytophysiology ; Institute of Experimental Biology; Faculty of Biology and Environmental Protection; University of Łódź ; Łódź , Poland
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252
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Duzdevich D, Warner MD, Ticau S, Ivica NA, Bell SP, Greene EC. The dynamics of eukaryotic replication initiation: origin specificity, licensing, and firing at the single-molecule level. Mol Cell 2015; 58:483-94. [PMID: 25921072 DOI: 10.1016/j.molcel.2015.03.017] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/20/2015] [Accepted: 03/11/2015] [Indexed: 12/23/2022]
Abstract
Eukaryotic replication initiation is highly regulated and dynamic. It begins with the origin recognition complex (ORC) binding DNA sites called origins of replication. ORC, together with Cdc6 and Cdt1, mediate pre-replicative complex (pre-RC) assembly by loading a double hexamer of Mcm2-7: the core of the replicative helicase. Here, we use single-molecule imaging to directly visualize Saccharomyces cerevisiae pre-RC assembly and replisome firing in real time. We show that ORC can locate and stably bind origins within large tracts of non-origin DNA and that Cdc6 drives ordered pre-RC assembly. We further show that the dynamics of the ORC-Cdc6 interaction dictate Mcm2-7 loading specificity and that Mcm2-7 double hexamers form preferentially at a native origin sequence. Finally, we demonstrate that single Mcm2-7 hexamers propagate bidirectionally, monotonically, and processively as constituents of active replisomes.
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Affiliation(s)
- Daniel Duzdevich
- Department of Biological Sciences, Columbia University, New York, NY 10032, USA
| | - Megan D Warner
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Simina Ticau
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nikola A Ivica
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stephen P Bell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, and the Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA.
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253
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Georgescu RE, Schauer GD, Yao NY, Langston LD, Yurieva O, Zhang D, Finkelstein J, O'Donnell ME. Reconstitution of a eukaryotic replisome reveals suppression mechanisms that define leading/lagging strand operation. eLife 2015; 4:e04988. [PMID: 25871847 PMCID: PMC4413876 DOI: 10.7554/elife.04988] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 04/13/2015] [Indexed: 12/17/2022] Open
Abstract
We have reconstituted a eukaryotic leading/lagging strand replisome comprising 31 distinct polypeptides. This study identifies a process unprecedented in bacterial replisomes. While bacteria and phage simply recruit polymerases to the fork, we find that suppression mechanisms are used to position the distinct eukaryotic polymerases on their respective strands. Hence, Pol ε is active with CMG on the leading strand, but it is unable to function on the lagging strand, even when Pol δ is not present. Conversely, Pol δ-PCNA is the only enzyme capable of extending Okazaki fragments in the presence of Pols ε and α. We have shown earlier that Pol δ-PCNA is suppressed on the leading strand with CMG (Georgescu et al., 2014). We propose that CMG, the 11-subunit helicase, is responsible for one or both of these suppression mechanisms that spatially control polymerase occupancy at the fork.
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Affiliation(s)
- Roxana E Georgescu
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, United States
| | - Grant D Schauer
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, United States
| | - Nina Y Yao
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, United States
| | - Lance D Langston
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, United States
| | - Olga Yurieva
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, United States
| | - Dan Zhang
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, United States
| | - Jeff Finkelstein
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, United States
| | - Mike E O'Donnell
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, United States
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254
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Abstract
To ensure duplication of the entire genome, eukaryotic DNA replication initiates from thousands of replication origins. The replication forks move through the chromatin until they encounter forks from neighboring origins. During replication fork termination forks converge, the replisomes disassemble and topoisomerase II resolves the daughter DNA molecules. If not resolved efficiently, terminating forks result in genomic instability through the formation of pathogenic structures. Our recent findings shed light onto the mechanism of replisome disassembly upon replication fork termination. We have shown that termination-specific polyubiquitylation of the replicative helicase component – Mcm7, leads to dissolution of the active helicase in a process dependent on the p97/VCP/Cdc48 segregase. The inhibition of terminating helicase disassembly resulted in a replication termination defect. In this extended view we present hypothetical models of replication fork termination and discuss remaining and emerging questions in the DNA replication termination field.
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Key Words
- CMG, Cdc45, Mcm2–7, GINS complex
- CRL, cullin-RING ligase
- D loop, displacement loop
- DDR, DNA damage response
- DNA replication
- DSB, double strand break
- DUB, deubiquitylating enzyme
- ER, endoplasmic reticulum
- ERAD, endoplasmic reticulum associated protein degradation
- GINS, Go-Ichi-Ni-San, complex made of Sld5, Psf1, Psf2, Psf3
- ICL, intra-strand crosslink
- MCM, Minichromosome maintenance
- Mcm2–7
- OriC, chromosomal replication origin
- R loop, RNA:DNA hybrid
- RING, really interesting gene
- RPC, Replisome Progression Complex
- Ter, termination site
- Tus-Ter, terminus utilisation substance - termination
- Xenopus
- p97 segregase
- replication termination
- replicative helicase
- replisome
- ubiquitin
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Affiliation(s)
- Rachael Bailey
- a School of Cancer Sciences; University of Birmingham ; Birmingham , UK
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255
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Belsky JA, MacAlpine HK, Lubelsky Y, Hartemink AJ, MacAlpine DM. Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly. Genes Dev 2015; 29:212-24. [PMID: 25593310 PMCID: PMC4298139 DOI: 10.1101/gad.247924.114] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Start sites of DNA replication are marked by the origin recognition complex (ORC), which coordinates Mcm2–7 helicase loading to form the prereplicative complex (pre-RC). Belsky et al. “footprinted” nucleosomes, transcription factors, and replication proteins at multiple points during the Saccharomyces cerevisiae cell cycle. This revealed a precise ORC-dependent footprint at 269 origins in G2. A separate class of inefficient origins exhibited protein occupancy only in G1. The local chromatin environment restricts the loading of the Mcm2–7 double hexamer either upstream of or downstream from the ACS. Start sites of DNA replication are marked by the origin recognition complex (ORC), which coordinates Mcm2–7 helicase loading to form the prereplicative complex (pre-RC). Although pre-RC assembly is well characterized in vitro, the process is poorly understood within the local chromatin environment surrounding replication origins. To reveal how the chromatin architecture modulates origin selection and activation, we “footprinted” nucleosomes, transcription factors, and replication proteins at multiple points during the Saccharomyces cerevisiae cell cycle. Our nucleotide-resolution protein occupancy profiles resolved a precise ORC-dependent footprint at 269 origins in G2. A separate class of inefficient origins exhibited protein occupancy only in G1, suggesting that stable ORC chromatin association in G2 is a determinant of origin efficiency. G1 nucleosome remodeling concomitant with pre-RC assembly expanded the origin nucleosome-free region and enhanced activation efficiency. Finally, the local chromatin environment restricts the loading of the Mcm2–7 double hexamer either upstream of or downstream from the ARS consensus sequence (ACS).
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Affiliation(s)
- Jason A Belsky
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA; Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA
| | - Heather K MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA;
| | - Yoav Lubelsky
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Alexander J Hartemink
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA; Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA; Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA;
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256
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Urban JM, Foulk MS, Casella C, Gerbi SA. The hunt for origins of DNA replication in multicellular eukaryotes. F1000PRIME REPORTS 2015; 7:30. [PMID: 25926981 PMCID: PMC4371235 DOI: 10.12703/p7-30] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Origins of DNA replication (ORIs) occur at defined regions in the genome. Although DNA sequence defines the position of ORIs in budding yeast, the factors for ORI specification remain elusive in metazoa. Several methods have been used recently to map ORIs in metazoan genomes with the hope that features for ORI specification might emerge. These methods are reviewed here with analysis of their advantages and shortcomings. The various factors that may influence ORI selection for initiation of DNA replication are discussed.
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Affiliation(s)
- John M. Urban
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
| | - Michael S. Foulk
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
- Department of Biology, Mercyhurst University501 East 38th Street, Erie, PA 16546USA
| | - Cinzia Casella
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
- Institute for Molecular Medicine, University of Southern DenmarkJB Winsloews Vej 25, 5000 Odense CDenmark
| | - Susan A. Gerbi
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
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257
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Georgescu R, Langston L, O'Donnell M. A proposal: Evolution of PCNA's role as a marker of newly replicated DNA. DNA Repair (Amst) 2015; 29:4-15. [PMID: 25704660 DOI: 10.1016/j.dnarep.2015.01.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 01/28/2015] [Accepted: 01/30/2015] [Indexed: 11/26/2022]
Abstract
Processivity clamps that hold DNA polymerases to DNA for processivity were the first proteins known to encircle the DNA duplex. At the time, polymerase processivity was thought to be the only function of ring shaped processivity clamps. But studies from many laboratories have identified numerous proteins that bind and function with sliding clamps. Among these processes are mismatch repair and nucleosome assembly. Interestingly, there exist polymerases that are highly processive and do not require clamps. Hence, DNA polymerase processivity does not intrinsically require that sliding clamps evolved for this purpose. We propose that polymerases evolved to require clamps as a way of ensuring that clamps are deposited on newly replicated DNA. These clamps are then used on the newly replicated daughter strands, for processes important to genomic integrity, such as mismatch repair and the assembly of nucleosomes to maintain epigenetic states of replicating cells during development.
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Affiliation(s)
- Roxana Georgescu
- Rockefeller University and HHMI, 1230 York Avenue, Box 228, New York, NY 10065, United States
| | - Lance Langston
- Rockefeller University and HHMI, 1230 York Avenue, Box 228, New York, NY 10065, United States
| | - Mike O'Donnell
- Rockefeller University and HHMI, 1230 York Avenue, Box 228, New York, NY 10065, United States.
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258
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Kotsantis P, Jones RM, Higgs MR, Petermann E. Cancer therapy and replication stress: forks on the road to perdition. Adv Clin Chem 2015; 69:91-138. [PMID: 25934360 DOI: 10.1016/bs.acc.2014.12.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Deregulated DNA replication occurs in cancer where it contributes to genomic instability. This process is a target of cytotoxic therapies. Chemotherapies exploit high DNA replication in cancer cells by modifying the DNA template or by inhibiting vital enzymatic activities that lead to slowing or stalling replication fork progression. Stalled replication forks can be converted into toxic DNA double-strand breaks resulting in cell death, i.e., replication stress. While likely crucial for many cancer treatments, replication stress is poorly understood due to its complexity. While we still know relatively little about the role of replication stress in cancer therapy, technical advances in recent years have shed new light on the effect that cancer therapeutics have on replication forks and the molecular mechanisms that lead from obstructed fork progression to cell death. This chapter will give an overview of our current understanding of replication stress in the context of cancer therapy.
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Affiliation(s)
- Panagiotis Kotsantis
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Rebecca M Jones
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Martin R Higgs
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Eva Petermann
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom.
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259
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Dhingra N, Bruck I, Smith S, Ning B, Kaplan DL. Dpb11 protein helps control assembly of the Cdc45·Mcm2-7·GINS replication fork helicase. J Biol Chem 2015; 290:7586-601. [PMID: 25659432 DOI: 10.1074/jbc.m115.640383] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dpb11 is required for the initiation of DNA replication in budding yeast. Dpb11 binds to S-phase cyclin-dependent kinase-phosphorylated Sld2 and Sld3 to form a ternary complex during S phase. The replication fork helicase in eukaryotes is composed of Cdc45, Mcm2-7, and GINS. We show here, using purified proteins from budding yeast, that Dpb11 alone binds to Mcm2-7 and that Dpb11 also competes with GINS for binding to Mcm2-7. Furthermore, Dpb11 binds directly to single-stranded DNA (ssDNA), and ssDNA inhibits the Dpb11 interaction with Mcm2-7. We also found that Dpb11 can recruit Cdc45 to Mcm2-7. We identified a mutant of the BRCT4 motif of Dpb11 that remains bound to Mcm2-7 in the presence of ssDNA (dpb11-m1,m2,m3,m5), and this mutant exhibits a DNA replication defect when expressed in budding yeast cells. Expression of this mutant results in increased interaction between Dpb11 and Mcm2-7 during S phase, impaired GINS interaction with Mcm2-7 during S phase, and decreased replication protein A (RPA) interaction with origin DNA during S phase. We propose a model in which Dpb11 first recruits Cdc45 to Mcm2-7. Dpb11, although bound to Cdc45·Mcm2-7, can block the interaction between GINS and Mcm2-7. Upon extrusion of ssDNA from the central channel of Mcm2-7, Dpb11 dissociates from Mcm2-7, and Dpb11 binds to ssDNA, thereby allowing GINS to bind to Cdc45·Mcm2-7. Finally, we propose that Dpb11 functions with Sld2 and Sld3 to help control the assembly of the replication fork helicase.
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Affiliation(s)
- Nalini Dhingra
- From the Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235 and
| | - Irina Bruck
- the Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306-4300
| | - Skye Smith
- the Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306-4300
| | - Boting Ning
- From the Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235 and
| | - Daniel L Kaplan
- the Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306-4300
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260
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Morino M, Tanaka M, Shiomi Y, Nishitani H. Imaging analysis to determine chromatin binding of the licensing factor MCM2-7 in mammalian cells. Methods Mol Biol 2015; 1170:529-37. [PMID: 24906334 DOI: 10.1007/978-1-4939-0888-2_29] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
S-CDK and DDK protein kinases initiate DNA replication at replication origins. Prior to the activation of these kinases, origins must become competent for replication by loading MCM2-7 DNA helicase on chromatin. This process is known as replication licensing or pre-replicative complex (pre-RC) formation. After the onset of S phase, however, licensing is inhibited to prevent re-replication of DNA. In this chapter, we describe a method to analyze origin licensing by imaging the chromatin-bound licensing factor MCM2-7. In a normal cell cycle, MCM2-7 is loaded at the end of mitosis or early G1 phase. As S phase progresses, MCM2-7 is dissociated from the replicated regions. When DNA replication is completed, cells in G2 phase have no chromatin-bound MCM2-7. The analysis of chromatin-bound MCM2-7 in each cell provides an insight into cell cycle stage and condition for cell cycle.
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Affiliation(s)
- Masayuki Morino
- Graduate School of Life Science, University of Hyogo, Kamigori, Ako-gun, Hyogo, 678-1297, Japan
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261
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Petojevic T, Pesavento JJ, Costa A, Liang J, Wang Z, Berger JM, Botchan MR. Cdc45 (cell division cycle protein 45) guards the gate of the Eukaryote Replisome helicase stabilizing leading strand engagement. Proc Natl Acad Sci U S A 2015; 112:E249-58. [PMID: 25561522 PMCID: PMC4311868 DOI: 10.1073/pnas.1422003112] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
DNA replication licensing is now understood to be the pathway that leads to the assembly of double hexamers of minichromosome maintenance (Mcm2-7) at origin sites. Cell division control protein 45 (Cdc45) and GINS proteins activate the latent Mcm2-7 helicase by inducing allosteric changes through binding, forming a Cdc45/Mcm2-7/GINS (CMG) complex that is competent to unwind duplex DNA. The CMG has an active gate between subunits Mcm2 and Mcm5 that opens and closes in response to nucleotide binding. The consequences of inappropriate Mcm2/5 gate actuation and the role of a side channel formed between GINS/Cdc45 and the outer edge of the Mcm2-7 ring for unwinding have remained unexplored. Here we uncover a novel function for Cdc45. Cross-linking studies trace the path of the DNA with the CMG complex at a fork junction between duplex and single strands with the bound CMG in an open or closed gate conformation. In the closed state, the lagging strand does not pass through the side channel, but in the open state, the leading strand surprisingly interacts with Cdc45. Mutations in the recombination protein J fold of Cdc45 that ablate this interaction diminish helicase activity. These data indicate that Cdc45 serves as a shield to guard against occasional slippage of the leading strand from the core channel.
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Affiliation(s)
- Tatjana Petojevic
- Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, CA 94720; Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - James J Pesavento
- Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, CA 94720
| | - Alessandro Costa
- Clare Hall Laboratories, London Research Institute, South Mimms, Herts EN6 3LD, United Kingdom; and
| | - Jingdan Liang
- Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, CA 94720
| | - Zhijun Wang
- Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, CA 94720
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205
| | - Michael R Botchan
- Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, CA 94720;
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262
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Zegerman P. Evolutionary conservation of the CDK targets in eukaryotic DNA replication initiation. Chromosoma 2015; 124:309-21. [PMID: 25575982 DOI: 10.1007/s00412-014-0500-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 11/27/2014] [Accepted: 12/01/2014] [Indexed: 10/24/2022]
Abstract
A fundamental requirement for all organisms is the faithful duplication and transmission of the genetic material. Failure to accurately copy and segregate the genome during cell division leads to loss of genetic information and chromosomal abnormalities. Such genome instability is the hallmark of the earliest stages of tumour formation. Cyclin-dependent kinase (CDK) plays a vital role in regulating the duplication of the genome within the eukaryotic cell cycle. Importantly, this kinase is deregulated in many cancer types and is an emerging target of chemotherapeutics. In this review, I will consider recent advances concerning the role of CDK in replication initiation across eukaryotes. The implications for strict CDK-dependent regulation of genome duplication in the context of the cell cycle will be discussed.
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Affiliation(s)
- Philip Zegerman
- Department of Biochemistry, Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, The Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, CB2 1QN, UK,
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263
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Copeland NA, Sercombe HE, Wilson RHC, Coverley D. Cyclin A/CDK2 phosphorylation of CIZ1 blocks replisome formation and initiation of mammalian DNA replication. J Cell Sci 2015; 128:1518-27. [DOI: 10.1242/jcs.161919] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/23/2015] [Indexed: 12/25/2022] Open
Abstract
CIZ1 is a nuclear matrix protein that cooperates with cyclin A/CDK2 to promote mammalian DNA replication. We show here that cyclin A/CDK2 also negatively regulates CIZ1 activity via phosphorylation at threonines 144, 192, and 293. Phosphomimetic mutants do not promote DNA replication in cell-free and cell-based assays, and also have a dominant negative effect on replisome formation at the level of PCNA recruitment. Phosphorylation blocks direct interaction with cyclin A/CDK2, and recruitment of endogenous cyclin A to the nuclear matrix. In contrast, phosphomimetic CIZ1 retains nuclear matrix binding capability, and interaction with CDC6 is not affected. Phospho-threonine 192-specific antibodies confirm that CIZ1 is phosphorylated during S-phase and G2, and show that phosphorylation at this site occurs at post-initiation concentrations of cyclin A/CDK2. Together the data suggest that CIZ1 is a kinase sensor that promotes initiation of DNA replication at low kinase levels, when in a hypophosphorylated state that is permissive for cyclin A-CDK2 interaction and delivery to licensed origins, but blocks delivery at higher kinase levels when it is itself phosphorylated.
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264
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Hamm DC, Bondra ER, Harrison MM. Transcriptional activation is a conserved feature of the early embryonic factor Zelda that requires a cluster of four zinc fingers for DNA binding and a low-complexity activation domain. J Biol Chem 2014; 290:3508-18. [PMID: 25538246 DOI: 10.1074/jbc.m114.602292] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Delayed transcriptional activation of the zygotic genome is a nearly universal phenomenon in metazoans. Immediately following fertilization, development is controlled by maternally deposited products, and it is not until later stages that widespread activation of the zygotic genome occurs. Although the mechanisms driving this genome activation are currently unknown, the transcriptional activator Zelda (ZLD) has been shown to be instrumental in driving this process in Drosophila melanogaster. Here we define functional domains of ZLD required for both DNA binding and transcriptional activation. We show that the C-terminal cluster of four zinc fingers mediates binding to TAGteam DNA elements in the promoters of early expressed genes. All four zinc fingers are required for this activity, and splice isoforms lacking three of the four zinc fingers fail to activate transcription. These truncated splice isoforms dominantly suppress activation by the full-length, embryonically expressed isoform. We map the transcriptional activation domain of ZLD to a central region characterized by low complexity. Despite relatively little sequence conservation within this domain, ZLD orthologs from Drosophila virilis, Anopheles gambiae, and Nasonia vitripennis activate transcription in D. melanogaster cells. Transcriptional activation by these ZLD orthologs suggests that ZLD functions through conserved interactions with a protein cofactor(s). We have identified distinct DNA-binding and activation domains within the critical transcription factor ZLD that controls the initial activation of the zygotic genome.
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Affiliation(s)
- Danielle C Hamm
- From the Department of Biomolecular Chemistry, University of Wisconsin Madison, Wisconsin 53706
| | - Eliana R Bondra
- From the Department of Biomolecular Chemistry, University of Wisconsin Madison, Wisconsin 53706
| | - Melissa M Harrison
- From the Department of Biomolecular Chemistry, University of Wisconsin Madison, Wisconsin 53706
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265
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Sun J, Fernandez-Cid A, Riera A, Tognetti S, Yuan Z, Stillman B, Speck C, Li H. Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function. Genes Dev 2014; 28:2291-303. [PMID: 25319829 PMCID: PMC4201289 DOI: 10.1101/gad.242313.114] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex (pre-RC) that contains a Mcm2–7 double hexamer. In this study, Sun et al. examined the helicase loading reaction in the presence of ATP, revealing the basic architecture of a number of pre-RC assembly reaction intermediates, including a newly identified ORC–Cdc6–Mcm2–7–Mcm2–7 complex. The detailed architecture of the Mcm2–7 double hexamer was also established. Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm2–7 (minichromosome maintenance proteins 2–7) double hexamer. During S phase, each Mcm2–7 hexamer forms the core of a replicative DNA helicase. However, the mechanisms of origin licensing and helicase activation are poorly understood. The helicase loaders ORC–Cdc6 function to recruit a single Cdt1–Mcm2–7 heptamer to replication origins prior to Cdt1 release and ORC–Cdc6–Mcm2–7 complex formation, but how the second Mcm2–7 hexamer is recruited to promote double-hexamer formation is not well understood. Here, structural evidence for intermediates consisting of an ORC–Cdc6–Mcm2–7 complex and an ORC–Cdc6–Mcm2–7–Mcm2–7 complex are reported, which together provide new insights into DNA licensing. Detailed structural analysis of the loaded Mcm2–7 double-hexamer complex demonstrates that the two hexamers are interlocked and misaligned along the DNA axis and lack ATP hydrolysis activity that is essential for DNA helicase activity. Moreover, we show that the head-to-head juxtaposition of the Mcm2–7 double hexamer generates a new protein interaction surface that creates a multisubunit-binding site for an S-phase protein kinase that is known to activate DNA replication. The data suggest how the double hexamer is assembled and how helicase activity is regulated during DNA licensing, with implications for cell cycle control of DNA replication and genome stability.
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Affiliation(s)
- Jingchuan Sun
- Biosciences Department, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Alejandra Fernandez-Cid
- DNA Replication Group, MRC Clinical Sciences Centre, Imperial College Faculty of Medicine, London W12 0NN, United Kingdom
| | - Alberto Riera
- DNA Replication Group, MRC Clinical Sciences Centre, Imperial College Faculty of Medicine, London W12 0NN, United Kingdom
| | - Silvia Tognetti
- DNA Replication Group, MRC Clinical Sciences Centre, Imperial College Faculty of Medicine, London W12 0NN, United Kingdom
| | - Zuanning Yuan
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Christian Speck
- DNA Replication Group, MRC Clinical Sciences Centre, Imperial College Faculty of Medicine, London W12 0NN, United Kingdom;
| | - Huilin Li
- Biosciences Department, Brookhaven National Laboratory, Upton, New York 11973, USA; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794, USA
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266
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Bruck I, Kaplan DL. The Dbf4-Cdc7 kinase promotes Mcm2-7 ring opening to allow for single-stranded DNA extrusion and helicase assembly. J Biol Chem 2014; 290:1210-21. [PMID: 25471369 DOI: 10.1074/jbc.m114.608232] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The replication fork helicase in eukaryotes is composed of Cdc45, Mcm2-7, and GINS (CMG). The Dbf4-Cdc7 kinase phosphorylates Mcm2 in vitro, but the in vivo role for Dbf4-Cdc7 phosphorylation of Mcm2 is unclear. We find that budding yeast Dbf4-Cdc7 phosphorylates Mcm2 in vivo under normal conditions during S phase. Inhibiting Dbf4-Cdc7 phosphorylation of Mcm2 confers a dominant-negative phenotype with a severe growth defect. Inhibiting Dbf4-Cdc7 phosphorylation of Mcm2 under wild-type expression conditions also results in impaired DNA replication, substantially decreased single-stranded formation at an origin, and markedly disrupted interaction between GINS and Mcm2-7 during S phase. In vitro, Dbf4-Cdc7 kinase (DDK) phosphorylation of Mcm2 substantially weakens the interaction between Mcm2 and Mcm5, and Dbf4-Cdc7 phosphorylation of Mcm2 promotes Mcm2-7 ring opening. The extrusion of ssDNA from the central channel of Mcm2-7 triggers GINS attachment to Mcm2-7. Thus, Dbf4-Cdc7 phosphorylation of Mcm2 may open the Mcm2-7 ring at the Mcm2-Mcm5 interface, allowing for single-stranded DNA extrusion and subsequent GINS assembly with Mcm2-7.
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Affiliation(s)
- Irina Bruck
- From the Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306
| | - Daniel L Kaplan
- From the Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306
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267
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Moreno SP, Bailey R, Campion N, Herron S, Gambus A. Polyubiquitylation drives replisome disassembly at the termination of DNA replication. Science 2014; 346:477-81. [PMID: 25342805 DOI: 10.1126/science.1253585] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Resolution of replication forks during termination of DNA replication is essential for accurate duplication of eukaryotic genomes. Here we present evidence consistent with the idea that polyubiquitylation of a replisome component (Mcm7) leads to its disassembly at the converging terminating forks because of the action of the p97/VCP/Cdc48 protein remodeler. Using Xenopus laevis egg extract, we have shown that blocking polyubiquitylation results in the prolonged association of the active helicase with replicating chromatin. The Mcm7 subunit is the only component of the active helicase that we find polyubiquitylated during replication termination. The observed polyubiquitylation is followed by disassembly of the active helicase dependent on p97/VCP/Cdc48. Altogether, our data provide insight into the mechanism of replisome disassembly during eukaryotic DNA replication termination.
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Affiliation(s)
- Sara Priego Moreno
- School of Cancer Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - Rachael Bailey
- School of Cancer Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - Nicholas Campion
- School of Cancer Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - Suzanne Herron
- School of Cancer Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - Agnieszka Gambus
- School of Cancer Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK.
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268
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Keller H, Kiosze K, Sachsenweger J, Haumann S, Ohlenschläger O, Nuutinen T, Syväoja JE, Görlach M, Grosse F, Pospiech H. The intrinsically disordered amino-terminal region of human RecQL4: multiple DNA-binding domains confer annealing, strand exchange and G4 DNA binding. Nucleic Acids Res 2014; 42:12614-27. [PMID: 25336622 PMCID: PMC4227796 DOI: 10.1093/nar/gku993] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/20/2014] [Accepted: 10/06/2014] [Indexed: 01/01/2023] Open
Abstract
Human RecQL4 belongs to the ubiquitous RecQ helicase family. Its N-terminal region represents the only homologue of the essential DNA replication initiation factor Sld2 of Saccharomyces cerevisiae, and also participates in the vertebrate initiation of DNA replication. Here, we utilized a random screen to identify N-terminal fragments of human RecQL4 that could be stably expressed in and purified from Escherichia coli. Biophysical characterization of these fragments revealed that the Sld2 homologous RecQL4 N-terminal domain carries large intrinsically disordered regions. The N-terminal fragments were sufficient for the strong annealing activity of RecQL4. Moreover, this activity appeared to be the basis for an ATP-independent strand exchange activity. Both activities relied on multiple DNA-binding sites with affinities to single-stranded, double-stranded and Y-structured DNA. Finally, we found a remarkable affinity of the N-terminus for guanine quadruplex (G4) DNA, exceeding the affinities for other DNA structures by at least 60-fold. Together, these findings suggest that the DNA interactions mediated by the N-terminal region of human RecQL4 represent a central function at the replication fork. The presented data may also provide a mechanistic explanation for the role of elements with a G4-forming propensity identified in the vicinity of vertebrate origins of DNA replication.
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Affiliation(s)
- Heidi Keller
- Research Group Biochemistry, Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Kristin Kiosze
- Research Group Biochemistry, Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Juliane Sachsenweger
- Research Group Biochemistry, Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Sebastian Haumann
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Oliver Ohlenschläger
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Tarmo Nuutinen
- Department of Biology, University of Eastern Finland, PO Box 111, FI-80101 Joensuu, Finland
| | - Juhani E Syväoja
- Institute of Biomedicine, University of Eastern Finland, PO Box 1627, FI-70211 Kuopio, Finland
| | - Matthias Görlach
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Frank Grosse
- Research Group Biochemistry, Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany Center for Molecular Biomedicine, Friedrich-Schiller University, Jena, Germany
| | - Helmut Pospiech
- Research Group Biochemistry, Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany Faculty of Biochemistry and Molecular Medicine, PO Box 5000, FI-90014 University of Oulu, Finland
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269
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Bochman ML. Roles of DNA helicases in the maintenance of genome integrity. Mol Cell Oncol 2014; 1:e963429. [PMID: 27308340 PMCID: PMC4905024 DOI: 10.4161/23723548.2014.963429] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/25/2014] [Accepted: 09/01/2014] [Indexed: 11/19/2022]
Abstract
Genome integrity is achieved and maintained by the sum of all of the processes in the cell that ensure the faithful duplication and repair of DNA, as well as its genetic transmission from one cell division to the next. As central players in virtually all of the DNA transactions that occur in vivo, DNA helicases (molecular motors that unwind double-stranded DNA to produce single-stranded substrates) represent a crucial enzyme family that is necessary for genomic stability. Indeed, mutations in many human helicase genes are linked to a variety of diseases with symptoms that can be generally described as genomic instability, such as predispositions to cancers. This review focuses on the roles of both DNA replication helicases and recombination/repair helicases in maintaining genome integrity and provides a brief overview of the diseases related to defects in these enzymes.
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Affiliation(s)
- Matthew L Bochman
- Molecular and Cellular Biochemistry Department; Indiana University ; Bloomington, IN USA
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270
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CMG helicase and DNA polymerase ε form a functional 15-subunit holoenzyme for eukaryotic leading-strand DNA replication. Proc Natl Acad Sci U S A 2014; 111:15390-5. [PMID: 25313033 DOI: 10.1073/pnas.1418334111] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA replication in eukaryotes is asymmetric, with separate DNA polymerases (Pol) dedicated to bulk synthesis of the leading and lagging strands. Pol α/primase initiates primers on both strands that are extended by Pol ε on the leading strand and by Pol δ on the lagging strand. The CMG (Cdc45-MCM-GINS) helicase surrounds the leading strand and is proposed to recruit Pol ε for leading-strand synthesis, but to date a direct interaction between CMG and Pol ε has not been demonstrated. While purifying CMG helicase overexpressed in yeast, we detected a functional complex between CMG and native Pol ε. Using pure CMG and Pol ε, we reconstituted a stable 15-subunit CMG-Pol ε complex and showed that it is a functional polymerase-helicase on a model replication fork in vitro. On its own, the Pol2 catalytic subunit of Pol ε is inefficient in CMG-dependent replication, but addition of the Dpb2 protein subunit of Pol ε, known to bind the Psf1 protein subunit of CMG, allows stable synthesis with CMG. Dpb2 does not affect Pol δ function with CMG, and thus we propose that the connection between Dpb2 and CMG helps to stabilize Pol ε on the leading strand as part of a 15-subunit leading-strand holoenzyme we refer to as CMGE. Direct binding between Pol ε and CMG provides an explanation for specific targeting of Pol ε to the leading strand and provides clear mechanistic evidence for how strand asymmetry is maintained in eukaryotes.
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271
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Tognetti S, Riera A, Speck C. Switch on the engine: how the eukaryotic replicative helicase MCM2-7 becomes activated. Chromosoma 2014; 124:13-26. [PMID: 25308420 DOI: 10.1007/s00412-014-0489-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 12/17/2022]
Abstract
A crucial step during eukaryotic initiation of DNA replication is the correct loading and activation of the replicative DNA helicase, which ensures that each replication origin fires only once. Unregulated DNA helicase loading and activation, as it occurs in cancer, can cause severe DNA damage and genomic instability. The essential mini-chromosome maintenance proteins 2-7 (MCM2-7) represent the core of the eukaryotic replicative helicase that is loaded at DNA replication origins during G1-phase of the cell cycle. The MCM2-7 helicase activity, however, is only triggered during S-phase once the holo-helicase Cdc45-MCM2-7-GINS (CMG) has been formed. A large number of factors and several kinases interact and contribute to CMG formation and helicase activation, though the exact mechanisms remain unclear. Crucially, upon DNA damage, this reaction is temporarily halted to ensure genome integrity. Here, we review the current understanding of helicase activation; we focus on protein interactions during CMG formation, discuss structural changes during helicase activation, and outline similarities and differences of the prokaryotic and eukaryotic helicase activation process.
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Affiliation(s)
- Silvia Tognetti
- DNA Replication Group, Institute of Clinical Science, Imperial College, London, W12 0NN, UK
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272
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Duxin JP, Dewar JM, Yardimci H, Walter JC. Repair of a DNA-protein crosslink by replication-coupled proteolysis. Cell 2014; 159:346-57. [PMID: 25303529 PMCID: PMC4229047 DOI: 10.1016/j.cell.2014.09.024] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/18/2014] [Accepted: 09/11/2014] [Indexed: 12/24/2022]
Abstract
DNA-protein crosslinks (DPCs) are caused by environmental, endogenous, and chemotherapeutic agents and pose a severe threat to genome stability. We use Xenopus egg extracts to recapitulate DPC repair in vitro and show that this process is coupled to DNA replication. A DPC on the leading strand template arrests the replisome by stalling the CMG helicase. The DPC is then degraded on DNA, yielding a peptide-DNA adduct that is bypassed by CMG. The leading strand subsequently resumes synthesis, stalls again at the adduct, and then progresses past the adduct using DNA polymerase ζ. A DPC on the lagging strand template only transiently stalls the replisome, but it too is degraded, allowing Okazaki fragment bypass. Our experiments describe a versatile, proteolysis-based mechanism of S phase DPC repair that avoids replication fork collapse.
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Affiliation(s)
- Julien P Duxin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - James M Dewar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Hasan Yardimci
- Cancer Research UK, London Research Institute, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, UK
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute.
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273
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Mazouzi A, Velimezi G, Loizou JI. DNA replication stress: causes, resolution and disease. Exp Cell Res 2014; 329:85-93. [PMID: 25281304 DOI: 10.1016/j.yexcr.2014.09.030] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/20/2014] [Accepted: 09/22/2014] [Indexed: 12/17/2022]
Abstract
DNA replication is a fundamental process of the cell that ensures accurate duplication of the genetic information and subsequent transfer to daughter cells. Various pertubations, originating from endogenous or exogenous sources, can interfere with proper progression and completion of the replication process, thus threatening genome integrity. Coordinated regulation of replication and the DNA damage response is therefore fundamental to counteract these challenges and ensure accurate synthesis of the genetic material under conditions of replication stress. In this review, we summarize the main sources of replication stress and the DNA damage signaling pathways that are activated in order to preserve genome integrity during DNA replication. We also discuss the association of replication stress and DNA damage in human disease and future perspectives in the field.
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Affiliation(s)
- Abdelghani Mazouzi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Georgia Velimezi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria.
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274
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Miller JM, Arachea BT, Epling LB, Enemark EJ. Analysis of the crystal structure of an active MCM hexamer. eLife 2014; 3:e03433. [PMID: 25262915 PMCID: PMC4359371 DOI: 10.7554/elife.03433] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/28/2014] [Indexed: 12/26/2022] Open
Abstract
In a previous Research article (Froelich et al., 2014), we suggested an MCM helicase activation mechanism, but were limited in discussing the ATPase domain because it was absent from the crystal structure. Here we present the crystal structure of a nearly full-length MCM hexamer that is helicase-active and thus has all features essential for unwinding DNA. The structure is a chimera of Sulfolobus solfataricus N-terminal domain and Pyrococcus furiosus ATPase domain. We discuss three major findings: 1) a novel conformation for the A-subdomain that could play a role in MCM regulation; 2) interaction of a universally conserved glutamine in the N-terminal Allosteric Communication Loop with the AAA+ domain helix-2-insert (h2i); and 3) a recessed binding pocket for the MCM ssDNA-binding motif influenced by the h2i. We suggest that during helicase activation, the h2i clamps down on the leading strand to facilitate strand retention and regulate ATP hydrolysis. DOI:http://dx.doi.org/10.7554/eLife.03433.001
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Affiliation(s)
- Justin M Miller
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States
| | - Buenafe T Arachea
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States
| | - Leslie B Epling
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States
| | - Eric J Enemark
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States
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275
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Wu M, Lu W, Santos RE, Frattini MG, Kelly TJ. Geminin inhibits a late step in the formation of human pre-replicative complexes. J Biol Chem 2014; 289:30810-30821. [PMID: 25231993 PMCID: PMC4215257 DOI: 10.1074/jbc.m114.552935] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The initial step in initiation of eukaryotic DNA replication involves the assembly of pre-replicative complexes (pre-RCs) at origins of replication during the G1 phase of the cell cycle. In metazoans initiation is inhibited by the regulatory factor Geminin. We have purified the human pre-RC proteins, studied their interactions in vitro with each other and with origin DNA, and analyzed the effects of HsGeminin on formation of DNA-protein complexes. The formation of an initial complex containing the human origin recognition complex (HsORC), HsCdt1, HsCdc6, and origin DNA is cooperative, involving all possible binary interactions among the components. Maximal association of HsMCM2-7, a component of the replicative helicase, requires HsORC, HsCdc6, HsCdt1, and ATP, and is driven by interactions of HsCdt1 and HsCdc6 with multiple HsMCM2-7 subunits. Formation of stable complexes, resistant to high salt, requires ATP hydrolysis. In the absence of HsMCM proteins, HsGeminin inhibits the association of HsCdt1 with DNA or with HsORC-HsCdc6-DNA complexes. However, HsGeminin does not inhibit recruitment of HsMCM2-7 to DNA to form complexes containing all of the pre-RC proteins. In fact, HsGeminin itself is a component of such complexes, and interacts directly with the HsMcm3 and HsMcm5 subunits of HsMCM2-7, as well as with HsCdt1. Although HsGeminin does not prevent the initial formation of DNA-protein complexes containing the pre-RC proteins, it strongly inhibits the formation of stable pre-RCs that are resistant to high salt. We suggest that bound HsGeminin prevents transition of the pre-RC to a state that is competent for initiation of DNA replication.
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Affiliation(s)
- Min Wu
- Program in Molecular Biology and Memorial Sloan-Kettering Cancer Center, New York, New York 10065
| | - Wenyan Lu
- Program in Molecular Biology and Memorial Sloan-Kettering Cancer Center, New York, New York 10065
| | - Ruth E Santos
- Program in Molecular Biology and Memorial Sloan-Kettering Cancer Center, New York, New York 10065
| | - Mark G Frattini
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10065.
| | - Thomas J Kelly
- Program in Molecular Biology and Memorial Sloan-Kettering Cancer Center, New York, New York 10065.
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276
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Long DT, Joukov V, Budzowska M, Walter JC. BRCA1 promotes unloading of the CMG helicase from a stalled DNA replication fork. Mol Cell 2014; 56:174-85. [PMID: 25219499 DOI: 10.1016/j.molcel.2014.08.012] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 06/30/2014] [Accepted: 08/07/2014] [Indexed: 11/19/2022]
Abstract
The tumor suppressor protein BRCA1 promotes homologous recombination (HR), a high-fidelity mechanism to repair DNA double-strand breaks (DSBs) that arise during normal replication and in response to DNA-damaging agents. Recent genetic experiments indicate that BRCA1 also performs an HR-independent function during the repair of DNA interstrand crosslinks (ICLs). Here we show that BRCA1 is required to unload the CMG helicase complex from chromatin after replication forks collide with an ICL. Eviction of the stalled helicase allows leading strands to be extended toward the ICL, followed by endonucleolytic processing of the crosslink, lesion bypass, and DSB repair. Our results identify BRCA1-dependent helicase unloading as a critical, early event in ICL repair.
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Affiliation(s)
- David T Long
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Vladimir Joukov
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Magda Budzowska
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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277
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Coster G, Frigola J, Beuron F, Morris EP, Diffley JFX. Origin licensing requires ATP binding and hydrolysis by the MCM replicative helicase. Mol Cell 2014; 55:666-77. [PMID: 25087873 PMCID: PMC4157578 DOI: 10.1016/j.molcel.2014.06.034] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/11/2014] [Accepted: 06/26/2014] [Indexed: 01/24/2023]
Abstract
Loading of the six related Minichromosome Maintenance (MCM) proteins as head-to-head double hexamers during DNA replication origin licensing is crucial for ensuring once-per-cell-cycle DNA replication in eukaryotic cells. Assembly of these prereplicative complexes (pre-RCs) requires the Origin Recognition Complex (ORC), Cdc6, and Cdt1. ORC, Cdc6, and MCM are members of the AAA+ family of ATPases, and pre-RC assembly requires ATP hydrolysis. Here we show that ORC and Cdc6 mutants defective in ATP hydrolysis are competent for origin licensing. However, ATP hydrolysis by Cdc6 is required to release nonproductive licensing intermediates. We show that ATP binding stabilizes the wild-type MCM hexamer. Moreover, by analyzing MCM containing mutant subunits, we show that ATP binding and hydrolysis by MCM are required for Cdt1 release and double hexamer formation. This work alters our view of how ATP is used by licensing factors to assemble pre-RCs.
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Affiliation(s)
- Gideon Coster
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Herts. EN6 3LD, UK
| | - Jordi Frigola
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Herts. EN6 3LD, UK
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - John F X Diffley
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Herts. EN6 3LD, UK.
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278
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Herridge RP, Day RC, Macknight RC. The role of the MCM2-7 helicase complex during Arabidopsis seed development. PLANT MOLECULAR BIOLOGY 2014; 86:69-84. [PMID: 24947836 DOI: 10.1007/s11103-014-0213-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 06/08/2014] [Indexed: 05/27/2023]
Abstract
The MINICHROMOSOME MAINTENANCE 2-7 (MCM2-7) complex, a ring-shaped heterohexamer, unwinds the DNA double helix ahead of the other replication machinery. Although there is evidence that individual components might have other roles, the essential nature of the MCM2-7 complex in DNA replication has made it difficult to uncover these. Here, we present a detailed analysis of Arabidopsis thaliana mcm2-7 mutants and reveal phenotypic differences. The MCM2-7 genes are coordinately expressed during development, although MCM7 is expressed at a higher level in the egg cell. Consistent with a role in the egg cell, heterozygous mcm7 mutants resulted in frequent ovule abortion, a phenotype that does not occur in other mcm mutants. All mutants showed a maternal effect, whereby seeds inheriting a maternal mutant allele occasionally aborted later in seed development with defects in embryo patterning, endosperm nuclear size, and cellularization, a phenotype that is variable between subunit mutants. We provide evidence that this maternal effect is due to the necessity of a maternal store of MCM protein in the central cell that is sufficient for maintaining seed viability and size in the absence of de novo MCM transcription. Reducing MCM levels using endosperm-specific RNAi constructs resulted in the up-regulation of DNA repair transcripts, consistent with the current hypothesis that excess MCM2-7 complexes are loaded during G1 phase, and are required during S phase to overcome replicative stress or DNA damage. Overall, this study demonstrates the importance of the MCM2-7 subunits during seed development and suggests that there are functional differences between the subunits.
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Affiliation(s)
- Rowan P Herridge
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
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279
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The Mcm2-7 replicative helicase: a promising chemotherapeutic target. BIOMED RESEARCH INTERNATIONAL 2014; 2014:549719. [PMID: 25243149 PMCID: PMC4163376 DOI: 10.1155/2014/549719] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/08/2014] [Accepted: 08/10/2014] [Indexed: 02/05/2023]
Abstract
Numerous eukaryotic replication factors have served as chemotherapeutic targets. One replication factor that has largely escaped drug development is the Mcm2-7 replicative helicase. This heterohexameric complex forms the licensing system that assembles the replication machinery at origins during initiation, as well as the catalytic core of the CMG (Cdc45-Mcm2-7-GINS) helicase that unwinds DNA during elongation. Emerging evidence suggests that Mcm2-7 is also part of the replication checkpoint, a quality control system that monitors and responds to DNA damage. As the only replication factor required for both licensing and DNA unwinding, Mcm2-7 is a major cellular regulatory target with likely cancer relevance. Mutations in at least one of the six MCM genes are particularly prevalent in squamous cell carcinomas of the lung, head and neck, and prostrate, and MCM mutations have been shown to cause cancer in mouse models. Moreover various cellular regulatory proteins, including the Rb tumor suppressor family members, bind Mcm2-7 and inhibit its activity. As a preliminary step toward drug development, several small molecule inhibitors that target Mcm2-7 have been recently discovered. Both its structural complexity and essential role at the interface between DNA replication and its regulation make Mcm2-7 a potential chemotherapeutic target.
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280
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Costa A, Renault L, Swuec P, Petojevic T, Pesavento JJ, Ilves I, MacLellan-Gibson K, Fleck RA, Botchan MR, Berger JM. DNA binding polarity, dimerization, and ATPase ring remodeling in the CMG helicase of the eukaryotic replisome. eLife 2014; 3:e03273. [PMID: 25117490 PMCID: PMC4359367 DOI: 10.7554/elife.03273] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/08/2014] [Indexed: 01/29/2023] Open
Abstract
The Cdc45/Mcm2-7/GINS (CMG) helicase separates DNA strands during replication in eukaryotes. How the CMG is assembled and engages DNA substrates remains unclear. Using electron microscopy, we have determined the structure of the CMG in the presence of ATPγS and a DNA duplex bearing a 3' single-stranded tail. The structure shows that the MCM subunits of the CMG bind preferentially to single-stranded DNA, establishes the polarity by which DNA enters into the Mcm2-7 pore, and explains how Cdc45 helps prevent DNA from dissociating from the helicase. The Mcm2-7 subcomplex forms a cracked-ring, right-handed spiral when DNA and nucleotide are bound, revealing unexpected congruencies between the CMG and both bacterial DnaB helicases and the AAA+ motor of the eukaryotic proteasome. The existence of a subpopulation of dimeric CMGs establishes the subunit register of Mcm2-7 double hexamers and together with the spiral form highlights how Mcm2-7 transitions through different conformational and assembly states as it matures into a functional helicase.
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Affiliation(s)
- Alessandro Costa
- London Research Institute, Cancer Research UK, London, United Kingdom
| | - Ludovic Renault
- London Research Institute, Cancer Research UK, London, United Kingdom Department of Imaging, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Paolo Swuec
- London Research Institute, Cancer Research UK, London, United Kingdom
| | - Tatjana Petojevic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - James J Pesavento
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Ivar Ilves
- Institute of Technology, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Kirsty MacLellan-Gibson
- Department of Imaging, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Roland A Fleck
- Department of Imaging, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Michael R Botchan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States
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281
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Activation of the MCM helicase from the thermophilic archaeon, Thermoplasma acidophilum by interactions with GINS and Cdc6-2. Extremophiles 2014; 18:915-24. [PMID: 25107272 DOI: 10.1007/s00792-014-0673-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/06/2014] [Indexed: 01/25/2023]
Abstract
In DNA replication studies, the mechanism for regulation of the various steps from initiation to elongation is a crucial subject to understand cell cycle control. The eukaryotic minichromosome maintenance (MCM) protein complex is recruited to the replication origin by Cdc6 and Cdt1 to form the pre-replication complex, and participates in forming the CMG complex formation with Cdc45 and GINS to work as the active helicase. Intriguingly, Thermoplasma acidophilum, as well as many other archaea, has only one Gins protein homolog, contrary to the heterotetramer of the eukaryotic GINS made of four different proteins. The Gins51 protein reportedly forms a homotetramer (TaGINS) and physically interacts with TaMCM. In addition, TaCdc6-2, one of the two Cdc6/Orc1 homologs in T. acidophilum reportedly stimulates the ATPase and helicase activities of TaMCM in vitro. Here, we found a reaction condition, in which TaGINS stimulated the ATPase and helicase activities of TaMCM in a concentration dependent manner. Furthermore, the stimulation of the TaMCM helicase activity by TaGINS was enhanced by the addition of TaCdc6-2. A gel retardation assay revealed that TaMCM, TaGINS, and TaCdc6-2 form a complex on ssDNA. However, glutaraldehyde-crosslinking was necessary to detect the shifted band, indicating that the ternary complex of TaMCM-TaGINS-TaCdc6-2 is not stable in vitro. Immunoprecipitation experiment supported a weak interaction of these three proteins in vivo. Activation of the replicative helicase by a mechanism including a Cdc6-like protein suggests the divergent evolution after the division into Archaea and Eukarya.
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282
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Samel SA, Fernández-Cid A, Sun J, Riera A, Tognetti S, Herrera MC, Li H, Speck C. A unique DNA entry gate serves for regulated loading of the eukaryotic replicative helicase MCM2-7 onto DNA. Genes Dev 2014; 28:1653-66. [PMID: 25085418 PMCID: PMC4117941 DOI: 10.1101/gad.242404.114] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/25/2014] [Indexed: 01/24/2023]
Abstract
The regulated loading of the replicative helicase minichromosome maintenance proteins 2-7 (MCM2-7) onto replication origins is a prerequisite for replication fork establishment and genomic stability. Origin recognition complex (ORC), Cdc6, and Cdt1 assemble two MCM2-7 hexamers into one double hexamer around dsDNA. Although the MCM2-7 hexamer can adopt a ring shape with a gap between Mcm2 and Mcm5, it is unknown which Mcm interface functions as the DNA entry gate during regulated helicase loading. Here, we establish that the Saccharomyces cerevisiae MCM2-7 hexamer assumes a closed ring structure, suggesting that helicase loading requires active ring opening. Using a chemical biology approach, we show that ORC-Cdc6-Cdt1-dependent helicase loading occurs through a unique DNA entry gate comprised of the Mcm2 and Mcm5 subunits. Controlled inhibition of DNA insertion triggers ATPase-driven complex disassembly in vitro, while in vivo analysis establishes that Mcm2/Mcm5 gate opening is essential for both helicase loading onto chromatin and cell cycle progression. Importantly, we demonstrate that the MCM2-7 helicase becomes loaded onto DNA as a single hexamer during ORC/Cdc6/Cdt1/MCM2-7 complex formation prior to MCM2-7 double hexamer formation. Our study establishes the existence of a unique DNA entry gate for regulated helicase loading, revealing key mechanisms in helicase loading, which has important implications for helicase activation.
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Affiliation(s)
- Stefan A Samel
- DNA Replication Group, Institute of Clinical Science, Imperial College, London W12 0NN, United Kingdom
| | - Alejandra Fernández-Cid
- DNA Replication Group, Institute of Clinical Science, Imperial College, London W12 0NN, United Kingdom
| | - Jingchuan Sun
- Biosciences Department, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Alberto Riera
- DNA Replication Group, Institute of Clinical Science, Imperial College, London W12 0NN, United Kingdom
| | - Silvia Tognetti
- DNA Replication Group, Institute of Clinical Science, Imperial College, London W12 0NN, United Kingdom
| | - M Carmen Herrera
- DNA Replication Group, Institute of Clinical Science, Imperial College, London W12 0NN, United Kingdom
| | - Huilin Li
- Biosciences Department, Brookhaven National Laboratory, Upton, New York 11973, USA; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Christian Speck
- DNA Replication Group, Institute of Clinical Science, Imperial College, London W12 0NN, United Kingdom;
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283
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Georgescu RE, Langston L, Yao NY, Yurieva O, Zhang D, Finkelstein J, Agarwal T, O'Donnell ME. Mechanism of asymmetric polymerase assembly at the eukaryotic replication fork. Nat Struct Mol Biol 2014; 21:664-70. [PMID: 24997598 PMCID: PMC4482249 DOI: 10.1038/nsmb.2851] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 06/06/2014] [Indexed: 12/19/2022]
Abstract
Eukaryotes use distinct polymerases for leading- and lagging-strand replication, but how they target their respective strands is uncertain. We reconstituted Saccharomyces cerevisiae replication forks and found that CMG helicase selects polymerase (Pol) ɛ to the exclusion of Pol δ on the leading strand. Even if Pol δ assembles on the leading strand, Pol ɛ rapidly replaces it. Pol δ-PCNA is distributive with CMG, in contrast to its high stability on primed ssDNA. Hence CMG will not stabilize Pol δ, instead leaving the leading strand accessible for Pol ɛ and stabilizing Pol ɛ. Comparison of Pol ɛ and Pol δ on a lagging-strand model DNA reveals the opposite. Pol δ dominates over excess Pol ɛ on PCNA-primed ssDNA. Thus, PCNA strongly favors Pol δ over Pol ɛ on the lagging strand, but CMG over-rides and flips this balance in favor of Pol ɛ on the leading strand.
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Affiliation(s)
- Roxana E Georgescu
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, New York, USA
| | - Lance Langston
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, New York, USA
| | - Nina Y Yao
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, New York, USA
| | - Olga Yurieva
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, New York, USA
| | - Dan Zhang
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, New York, USA
| | - Jeff Finkelstein
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, New York, USA
| | - Tani Agarwal
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, New York, USA
| | - Mike E O'Donnell
- DNA Replication Laboratory, Howard Hughes Medical Institute, Rockefeller University, New York, New York, USA
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284
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Kang S, Warner MD, Bell SP. Multiple functions for Mcm2-7 ATPase motifs during replication initiation. Mol Cell 2014; 55:655-65. [PMID: 25087876 DOI: 10.1016/j.molcel.2014.06.033] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 05/29/2014] [Accepted: 06/26/2014] [Indexed: 11/26/2022]
Abstract
The Mcm2-7 replicative helicase is central to all steps of eukaryotic DNA replication. The hexameric ring of Mcm subunits forms six essential ATPases whose contributions to replication initiation remain unclear. Mcm2-7 complexes containing ATPase-motif mutations showed Mcm2-7 ATP binding and hydrolysis are required for helicase loading. Loading-defective Mcm2-7 mutant complexes were defective in initial Mcm2-7 recruitment or Cdt1 release. Comparison with Cdc6 ATPase mutants showed that Cdc6 ATP hydrolysis is not required for helicase loading but instead drives removal of Mcm2-7 complexes that cannot complete loading. A subset of Mcm2-7 ATPase-site mutants completed helicase loading but could not initiate replication. Individual mutants were defective in distinct events during helicase activation, including maintenance of DNA association, recruitment of the GINS helicase activator, and DNA unwinding. Consistent with its heterohexameric structure, our findings show that the six Mcm2-7 ATPase active sites are specialized for different functions during helicase loading and activation.
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Affiliation(s)
- Sukhyun Kang
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Megan D Warner
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stephen P Bell
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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285
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Maya-Mendoza A, Merchut-Maya JM, Bartkova J, Bartek J, Streuli CH, Jackson DA. Immortalised breast epithelia survive prolonged DNA replication stress and return to cycle from a senescent-like state. Cell Death Dis 2014; 5:e1351. [PMID: 25058425 PMCID: PMC4123104 DOI: 10.1038/cddis.2014.315] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/09/2014] [Accepted: 06/11/2014] [Indexed: 12/20/2022]
Abstract
Mammalian cells have mechanisms to counteract the effects of metabolic and exogenous stresses, many of that would be mutagenic if ignored. Damage arising during DNA replication is a major source of mutagenesis. The extent of damage dictates whether cells undergo transient cell cycle arrest and damage repair, senescence or apoptosis. Existing dogma defines these alternative fates as distinct choices. Here we show that immortalised breast epithelial cells are able to survive prolonged S phase arrest and subsequently re-enter cycle after many days of being in an arrested, senescence-like state. Prolonged cell cycle inhibition in fibroblasts induced DNA damage response and cell death. However, in immortalised breast epithelia, efficient S phase arrest minimised chromosome damage and protected sufficient chromatin-bound replication licensing complexes to allow cell cycle re-entry. We propose that our observation could have implications for the design of drug therapies for breast cancer.
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Affiliation(s)
- A Maya-Mendoza
- 1] Faculty of Life Sciences and Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Oxford Road, Manchester M13 9PT, UK [2] Genome Integrity Unit, Danish Cancer Society Research Centre, Copenhagen, Denmark
| | - J M Merchut-Maya
- Genome Integrity Unit, Danish Cancer Society Research Centre, Copenhagen, Denmark
| | - J Bartkova
- Genome Integrity Unit, Danish Cancer Society Research Centre, Copenhagen, Denmark
| | - J Bartek
- 1] Genome Integrity Unit, Danish Cancer Society Research Centre, Copenhagen, Denmark [2] Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, CZ-779 00 Olomouc, Czech Republic
| | - C H Streuli
- Faculty of Life Sciences and Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - D A Jackson
- Faculty of Life Sciences and Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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286
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Alver RC, Chadha GS, Blow JJ. The contribution of dormant origins to genome stability: from cell biology to human genetics. DNA Repair (Amst) 2014; 19:182-9. [PMID: 24767947 PMCID: PMC4065331 DOI: 10.1016/j.dnarep.2014.03.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The ability of a eukaryotic cell to precisely and accurately replicate its DNA is crucial to maintain genome stability. Here we describe our current understanding of the process by which origins are licensed for DNA replication and review recent work suggesting that fork stalling has exerted a strong selective pressure on the positioning of licensed origins. In light of this, we discuss the complex and disparate phenotypes observed in mouse models and humans patients that arise due to defects in replication licensing proteins.
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Affiliation(s)
- Robert C Alver
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Gaganmeet Singh Chadha
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - J Julian Blow
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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287
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Imaging analysis of cell cycle-dependent degradation of Cdt1 in mammalian cells. Methods Mol Biol 2014. [PMID: 24906323 DOI: 10.1007/978-1-4939-0888-2_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Numerous cell cycle-regulating proteins are controlled by protein degradation. Recent work shows that ubiquitination-dependent proteolysis plays an important role in once-per-cell cycle control of DNA replication. Cdt1 is a licensing factor essential for assembling the pre-replicative complex on replication origins. Cdt1 is present in G1 phase, but after S phase ubiquitin-mediated proteolysis maintains Cdt1 at low levels. This is important to prevent the re-replication of chromosomal DNA. The cell cycle-dependent degradation of Cdt1 can be monitored by dual staining of the cell nuclei with antibodies against Cdt1- and S/G2-phase marker proteins, such as cyclin A or geminin.
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288
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Bellelli R, Castellone MD, Guida T, Limongello R, Dathan NA, Merolla F, Cirafici AM, Affuso A, Masai H, Costanzo V, Grieco D, Fusco A, Santoro M, Carlomagno F. NCOA4 transcriptional coactivator inhibits activation of DNA replication origins. Mol Cell 2014; 55:123-37. [PMID: 24910095 DOI: 10.1016/j.molcel.2014.04.031] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 03/31/2014] [Accepted: 04/28/2014] [Indexed: 11/19/2022]
Abstract
NCOA4 is a transcriptional coactivator of nuclear hormone receptors that undergoes gene rearrangement in human cancer. By combining studies in Xenopus laevis egg extracts and mouse embryonic fibroblasts (MEFs), we show here that NCOA4 is a minichromosome maintenance 7 (MCM7)-interacting protein that is able to control DNA replication. Depletion-reconstitution experiments in Xenopus laevis egg extracts indicate that NCOA4 acts as an inhibitor of DNA replication origin activation by regulating CMG (CDC45/MCM2-7/GINS) helicase. NCOA4(-/-) MEFs display unscheduled origin activation and reduced interorigin distance; this results in replication stress, as shown by the presence of fork stalling, reduction of fork speed, and premature senescence. Together, our findings indicate that NCOA4 acts as a regulator of DNA replication origins that helps prevent inappropriate DNA synthesis and replication stress.
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Affiliation(s)
- Roberto Bellelli
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR/Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II," 80131 Naples, Italy
| | - Maria Domenica Castellone
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR/Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II," 80131 Naples, Italy
| | - Teresa Guida
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR/Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II," 80131 Naples, Italy
| | - Roberto Limongello
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR/Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II," 80131 Naples, Italy
| | | | - Francesco Merolla
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR/Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II," 80131 Naples, Italy
| | - Anna Maria Cirafici
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR/Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II," 80131 Naples, Italy
| | - Andrea Affuso
- Animal Model Facility, Biogem s.c.a.r.l., 83031 Ariano Irpino, Avellino, Italy
| | - Hisao Masai
- Tokyo Metropolitan Institute of Medical Sciences, 156-8506 Tokyo, Japan
| | - Vincenzo Costanzo
- London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms EN6 3LD, UK
| | - Domenico Grieco
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR/Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II," 80131 Naples, Italy
| | - Alfredo Fusco
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR/Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II," 80131 Naples, Italy
| | - Massimo Santoro
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR/Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II," 80131 Naples, Italy.
| | - Francesca Carlomagno
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR/Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II," 80131 Naples, Italy.
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289
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Henninger EE, Pursell ZF. DNA polymerase ε and its roles in genome stability. IUBMB Life 2014; 66:339-51. [PMID: 24861832 DOI: 10.1002/iub.1276] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 05/02/2014] [Indexed: 12/14/2022]
Abstract
DNA Polymerase Epsilon (Pol ε) is one of three DNA Polymerases (along with Pol δ and Pol α) required for nuclear DNA replication in eukaryotes. Pol ε is comprised of four subunits, the largest of which is encoded by the POLE gene and contains the catalytic polymerase and exonuclease activities. The 3'-5' exonuclease proofreading activity is able to correct DNA synthesis errors and helps protect against genome instability. Recent cancer genome sequencing efforts have shown that 3% of colorectal and 7% of endometrial cancers contain mutations within the exonuclease domain of POLE and are associated with significantly elevated levels of single nucleotide substitutions (15-500 per Mb) and microsatellite stability. POLE mutations have also been found in other tumor types, though at lower frequency, suggesting roles in tumorigenesis more broadly in different tissue types. In addition to its proofreading activity, Pol ε contributes to genome stability through multiple mechanisms that are discussed in this review.
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Affiliation(s)
- Erin E Henninger
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
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290
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Abstract
DNA replication must be tightly regulated to ensure that the genome is accurately duplicated during each cell cycle. When these regulatory mechanisms fail, replicative stress and DNA damage ensue. Activated oncogenes promote replicative stress, inducing a DNA damage response (DDR) early in tumorigenesis. Senescence or apoptosis result, forming a barrier against tumour progression. This may provide a selective pressure for acquisition of mutations in the DDR pathway during tumorigenesis. Despite its potential importance in early cancer development, the precise nature of oncogene-induced replicative stress remains poorly understood. Here, we review our current understanding of replication initiation and its regulation, describe mechanisms by which activated oncogenes might interfere with these processes and discuss how replicative stress might contribute to the genomic instability seen in cancers.
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Affiliation(s)
- Stephanie A Hills
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Herts, EN6 3LD, UK
| | - John F X Diffley
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Herts, EN6 3LD, UK.
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291
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Singh J. Role of DNA replication in establishment and propagation of epigenetic states of chromatin. Semin Cell Dev Biol 2014; 30:131-43. [PMID: 24794003 DOI: 10.1016/j.semcdb.2014.04.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
Abstract
DNA replication is the fundamental process of duplication of the genetic information that is vital for survival of all living cells. The basic mechanistic steps of replication initiation, elongation and termination are conserved among bacteria, lower eukaryotes, like yeast and metazoans. However, the details of the mechanisms are different. Furthermore, there is a close coordination between chromatin assembly pathways and various components of replication machinery whereby DNA replication is coupled to "chromatin replication" during cell cycle. Thereby, various epigenetic modifications associated with different states of gene expression in differentiated cells and the related chromatin structures are faithfully propagated during the cell division through tight coupling with the DNA replication machinery. Several examples are found in lower eukaryotes like budding yeast and fission yeast with close parallels in metazoans.
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Affiliation(s)
- Jagmohan Singh
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India.
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292
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Liu S, Chistol G, Hetherington CL, Tafoya S, Aathavan K, Schnitzbauer J, Grimes S, Jardine PJ, Bustamante C. A viral packaging motor varies its DNA rotation and step size to preserve subunit coordination as the capsid fills. Cell 2014; 157:702-713. [PMID: 24766813 PMCID: PMC4003460 DOI: 10.1016/j.cell.2014.02.034] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 01/05/2014] [Accepted: 02/15/2014] [Indexed: 11/18/2022]
Abstract
Multimeric, ring-shaped molecular motors rely on the coordinated action of their subunits to perform crucial biological functions. During these tasks, motors often change their operation in response to regulatory signals. Here, we investigate a viral packaging machine as it fills the capsid with DNA and encounters increasing internal pressure. We find that the motor rotates the DNA during packaging and that the rotation per base pair increases with filling. This change accompanies a reduction in the motor's step size. We propose that these adjustments preserve motor coordination by allowing one subunit to make periodic, specific, and regulatory contacts with the DNA. At high filling, we also observe the downregulation of the ATP-binding rate and the emergence of long-lived pauses, suggesting a throttling-down mechanism employed by the motor near the completion of packaging. This study illustrates how a biological motor adjusts its operation in response to changing conditions, while remaining highly coordinated.
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Affiliation(s)
- Shixin Liu
- Jason L. Choy Laboratory of Single Molecule Biophysics University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences University of California, Berkeley, CA 94720, USA
| | - Gheorghe Chistol
- Jason L. Choy Laboratory of Single Molecule Biophysics University of California, Berkeley, CA 94720, USA
- Department of Physics University of California, Berkeley, CA 94720, USA
| | - Craig L. Hetherington
- Jason L. Choy Laboratory of Single Molecule Biophysics University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences University of California, Berkeley, CA 94720, USA
- Department of Physics University of California, Berkeley, CA 94720, USA
| | - Sara Tafoya
- Jason L. Choy Laboratory of Single Molecule Biophysics University of California, Berkeley, CA 94720, USA
- Biophysics Graduate Group University of California, Berkeley, CA 94720, USA
| | - K. Aathavan
- Jason L. Choy Laboratory of Single Molecule Biophysics University of California, Berkeley, CA 94720, USA
- Biophysics Graduate Group University of California, Berkeley, CA 94720, USA
| | - Joerg Schnitzbauer
- Jason L. Choy Laboratory of Single Molecule Biophysics University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences University of California, Berkeley, CA 94720, USA
| | - Shelley Grimes
- Department of Diagnostic and Biological Sciences and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paul J. Jardine
- Department of Diagnostic and Biological Sciences and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Carlos Bustamante
- Jason L. Choy Laboratory of Single Molecule Biophysics University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences University of California, Berkeley, CA 94720, USA
- Department of Physics University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, Department of Chemistry, and Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Kavli Energy NanoSciences Institute at the University of California, Berkeley and the Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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293
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Ayuda-Durán P, Devesa F, Gomes F, Sequeira-Mendes J, Avila-Zarza C, Gómez M, Calzada A. The CDK regulators Cdh1 and Sic1 promote efficient usage of DNA replication origins to prevent chromosomal instability at a chromosome arm. Nucleic Acids Res 2014; 42:7057-68. [PMID: 24753426 PMCID: PMC4066753 DOI: 10.1093/nar/gku313] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Robustness and completion of DNA replication rely on redundant DNA replication origins. Reduced efficiency of origin licensing is proposed to contribute to chromosome instability in CDK-deregulated cell cycles, a frequent alteration in oncogenesis. However, the mechanism by which this instability occurs is largely unknown. Current models suggest that limited origin numbers would reduce fork density favouring chromosome rearrangements, but experimental support in CDK-deregulated cells is lacking. We have investigated the pattern of origin firing efficiency in budding yeast cells lacking the CDK regulators Cdh1 and Sic1. We show that each regulator is required for efficient origin activity, and that both cooperate non-redundantly. Notably, origins are differentially sensitive to CDK deregulation. Origin sensitivity is independent on normal origin efficiency, firing timing or chromosomal location. Interestingly, at a chromosome arm, there is a shortage of origin firing involving active and dormant origins, and the extent of shortage correlates with the severity of CDK deregulation and chromosome instability. We therefore propose that CDK deregulation in G1 phase compromises origin redundancy by decreasing the number of active and dormant origins, leading to origin shortage and increased chromosome instability.
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Affiliation(s)
- Pilar Ayuda-Durán
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología CNB-CSIC, Darwin 3, Madrid 28049, Spain
| | - Fernando Devesa
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología CNB-CSIC, Darwin 3, Madrid 28049, Spain
| | - Fábia Gomes
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología CNB-CSIC, Darwin 3, Madrid 28049, Spain
| | - Joana Sequeira-Mendes
- Centro de Biología Molecular Severo Ochoa CBMSO-CSIC/UAM, Nicolás Cabrera 1, Madrid 28049, Spain
| | | | - María Gómez
- Centro de Biología Molecular Severo Ochoa CBMSO-CSIC/UAM, Nicolás Cabrera 1, Madrid 28049, Spain
| | - Arturo Calzada
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología CNB-CSIC, Darwin 3, Madrid 28049, Spain
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294
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Myc induced replicative stress response: How to cope with it and exploit it. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:517-24. [PMID: 24735945 DOI: 10.1016/j.bbagrm.2014.04.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 11/21/2022]
Abstract
Myc is a cellular oncogene frequently deregulated in cancer that has the ability to stimulate cellular growth by promoting a number of proliferative and pro-survival pathways. Here we will focus on how Myc controls a number of diverse cellular processes that converge to ensure processivity and robustness of DNA synthesis, thus preventing the inherent replicative stress responses usually evoked by oncogenic lesions. While these processes provide cancer cells with a long-term proliferative advantage, they also represent cancer liabilities that can be exploited to devise innovative therapeutic approaches to target Myc overexpressing tumors. This article is part of a Special Issue entitled: Myc proteins in cell biology and pathology.
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295
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Leman AR, Noguchi E. The replication fork: understanding the eukaryotic replication machinery and the challenges to genome duplication. Genes (Basel) 2014; 4:1-32. [PMID: 23599899 PMCID: PMC3627427 DOI: 10.3390/genes4010001] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Eukaryotic cells must accurately and efficiently duplicate their genomes during each round of the cell cycle. Multiple linear chromosomes, an abundance of regulatory elements, and chromosome packaging are all challenges that the eukaryotic DNA replication machinery must successfully overcome. The replication machinery, the “replisome” complex, is composed of many specialized proteins with functions in supporting replication by DNA polymerases. Efficient replisome progression relies on tight coordination between the various factors of the replisome. Further, replisome progression must occur on less than ideal templates at various genomic loci. Here, we describe the functions of the major replisome components, as well as some of the obstacles to efficient DNA replication that the replisome confronts. Together, this review summarizes current understanding of the vastly complicated task of replicating eukaryotic DNA.
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Affiliation(s)
- Adam R. Leman
- Authors to whom correspondence should be addressed; E-Mails: (A.R.L.); (E.N.); Tel.: +1-215-762-4825 (E.N.); Fax: +1-215-762-4452 (E.N.)
| | - Eishi Noguchi
- Authors to whom correspondence should be addressed; E-Mails: (A.R.L.); (E.N.); Tel.: +1-215-762-4825 (E.N.); Fax: +1-215-762-4452 (E.N.)
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296
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Fu Y, Slaymaker IM, Wang J, Wang G, Chen XS. The 1.8-Å crystal structure of the N-terminal domain of an archaeal MCM as a right-handed filament. J Mol Biol 2014; 426:1512-23. [PMID: 24378617 DOI: 10.1016/j.jmb.2013.12.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/18/2013] [Accepted: 12/19/2013] [Indexed: 11/16/2022]
Abstract
Mini-chromosome maintenance (MCM) proteins are the replicative helicase necessary for DNA replication in both eukarya and archaea. Most of archaea only have one MCM gene. Here, we report a 1.8-Å crystal structure of the N-terminal MCM from the archaeon Thermoplasma acidophilum (tapMCM). In the structure, the MCM N-terminus forms a right-handed filament that contains six subunits in each turn, with a diameter of 25Å of the central channel opening. The inner surface is highly positively charged, indicating DNA binding. This filament structure with six subunits per turn may also suggests a potential role for an open-ring structure for hexameric MCM and dynamic conformational changes in initiation and elongation stages of DNA replication.
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Affiliation(s)
- Yang Fu
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ian M Slaymaker
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Junfeng Wang
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ganggang Wang
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA.
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297
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Froelich CA, Kang S, Epling LB, Bell SP, Enemark EJ. A conserved MCM single-stranded DNA binding element is essential for replication initiation. eLife 2014; 3:e01993. [PMID: 24692448 PMCID: PMC3970758 DOI: 10.7554/elife.01993] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The ring-shaped MCM helicase is essential to all phases of DNA replication. The complex loads at replication origins as an inactive double-hexamer encircling duplex DNA. Helicase activation converts this species to two active single hexamers that encircle single-stranded DNA (ssDNA). The molecular details of MCM DNA interactions during these events are unknown. We determined the crystal structure of the Pyrococcus furiosus MCM N-terminal domain hexamer bound to ssDNA and define a conserved MCM-ssDNA binding motif (MSSB). Intriguingly, ssDNA binds the MCM ring interior perpendicular to the central channel with defined polarity. In eukaryotes, the MSSB is conserved in several Mcm2-7 subunits, and MSSB mutant combinations in S. cerevisiae Mcm2-7 are not viable. Mutant Mcm2-7 complexes assemble and are recruited to replication origins, but are defective in helicase loading and activation. Our findings identify an important MCM-ssDNA interaction and suggest it functions during helicase activation to select the strand for translocation. DOI:http://dx.doi.org/10.7554/eLife.01993.001 When DNA was first recognised to be a double helix, it was clear that this structure could easily explain how DNA could be replicated. Each strand was made of bases—represented by the letters ‘A’, ‘C’, ‘G’ and ‘T’—and the two strands were held together by bonds between pairs of bases, one from each strand. Moreover, ‘A’ always paired with ‘T’, and ‘C’ always paired with ‘G’. Therefore, if the two strands were separated, each could be used as a template to guide the synthesis of a new complementary strand and thus create two copies of the original double-stranded molecule. One of the first steps in this replication process involves a ring-shaped complex of six proteins, called an MCM helicase, separating the two strands. To prepare for DNA replication, two MCM helicase rings wrap around the double-stranded DNA. Then, after the helicase has been activated, the bonds between the DNA base pairs break, and the two rings separate with one ring encircling each DNA strand. However, the details of the interactions between the helicase and the DNA during these events are not fully understood. Now Froelich, Kang et al. have solved the three-dimensional structure of an MCM helicase ring—taken from a microbe originally found at deep ocean vents—on its own and also when bound to a short piece of single-stranded DNA. The helicase ring becomes more oval when the DNA binds to it. Moreover, rather than passing straight through the ring, the DNA wraps part of the way around the inside of the ring. Specific amino acids—the building blocks of proteins—on the inside of the ring interact with the single-stranded DNA, and these amino acids are also found in MCM proteins in many other organisms. Furthermore, swapping these amino acids for different amino acids significantly reduced the ability of the ring to bind to single-stranded DNA, but its ability to bind to double-stranded DNA was only slightly affected. Engineering similar changes into the ring complexes of yeast cells was lethal, and the mutant complexes were less able to be loaded onto the DNA, or to be activated and separate the two strands ready for replication. These insights into how helicases are loaded onto double-stranded DNA, and select one DNA strand to encircle, have improved our understanding of how DNA replication is initiated: a process that is vital for living things. DOI:http://dx.doi.org/10.7554/eLife.01993.002
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Affiliation(s)
- Clifford A Froelich
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States
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298
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Zech J, Dalgaard JZ. Replisome components--post-translational modifications and their effects. Semin Cell Dev Biol 2014; 30:144-53. [PMID: 24685613 DOI: 10.1016/j.semcdb.2014.03.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 03/10/2014] [Accepted: 03/23/2014] [Indexed: 12/22/2022]
Abstract
The process of DNA replication is highly regulated, but at the same time very dynamic. Once S-phase is initiated and replication elongation is occurring, the cells are committed to complete replication in order to ensure genome stability and survival. Many pathways exist to resolve situations where normal replisome progression is not possible. It is becoming more and more evident that post-translational modifications of replisome components play a key role in regulating these pathways which ensure fork progression. Here we review the known modifications of the progressing replisome and how these modifications are thought to affect DNA replication in unperturbed and perturbed S-phases.
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Affiliation(s)
- Juergen Zech
- Warwick Medical School, University of Warwick, Gibbert Hill Campus, CV47AL Coventry, UK
| | - Jacob Zeuthen Dalgaard
- Warwick Medical School, University of Warwick, Gibbert Hill Campus, CV47AL Coventry, UK.
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299
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Diversity of the DNA replication system in the Archaea domain. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:675946. [PMID: 24790526 PMCID: PMC3984812 DOI: 10.1155/2014/675946] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 02/16/2014] [Indexed: 12/11/2022]
Abstract
The precise and timely duplication of the genome is essential for cellular life. It is achieved by DNA replication, a complex process that is conserved among the three domains of life. Even though the cellular structure of archaea closely resembles that of bacteria, the information processing machinery of archaea is evolutionarily more closely related to the eukaryotic system, especially for the proteins involved in the DNA replication process. While the general DNA replication mechanism is conserved among the different domains of life, modifications in functionality and in some of the specialized replication proteins are observed. Indeed, Archaea possess specific features unique to this domain. Moreover, even though the general pattern of the replicative system is the same in all archaea, a great deal of variation exists between specific groups.
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300
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On KF, Beuron F, Frith D, Snijders AP, Morris EP, Diffley JFX. Prereplicative complexes assembled in vitro support origin-dependent and independent DNA replication. EMBO J 2014; 33:605-20. [PMID: 24566989 PMCID: PMC3989654 DOI: 10.1002/embj.201387369] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 12/17/2013] [Accepted: 01/10/2014] [Indexed: 11/09/2022] Open
Abstract
Eukaryotic DNA replication initiates from multiple replication origins. To ensure each origin fires just once per cell cycle, initiation is divided into two biochemically discrete steps: the Mcm2-7 helicase is first loaded into prereplicative complexes (pre-RCs) as an inactive double hexamer by the origin recognition complex (ORC), Cdt1 and Cdc6; the helicase is then activated by a set of "firing factors." Here, we show that plasmids containing pre-RCs assembled with purified proteins support complete and semi-conservative replication in extracts from budding yeast cells overexpressing firing factors. Replication requires cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK). DDK phosphorylation of Mcm2-7 does not by itself promote separation of the double hexamer, but is required for the recruitment of firing factors and replisome components in the extract. Plasmid replication does not require a functional replication origin; however, in the presence of competitor DNA and limiting ORC concentrations, replication becomes origin-dependent in this system. These experiments indicate that Mcm2-7 double hexamers can be precursors of replication and provide insight into the nature of eukaryotic DNA replication origins.
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Affiliation(s)
- Kin Fan On
- Chromosome Replication Laboratory, Cancer Research UK London Research InstituteSouth Mimms, Herts, UK
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer ResearchLondon, UK
| | - David Frith
- Protein Analysis and Proteomics, Cancer Research UK London Research Institute, Clare Hall LaboratoriesSouth Mimms, Herts, UK
| | - Ambrosius P Snijders
- Protein Analysis and Proteomics, Cancer Research UK London Research Institute, Clare Hall LaboratoriesSouth Mimms, Herts, UK
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer ResearchLondon, UK
| | - John F X Diffley
- Chromosome Replication Laboratory, Cancer Research UK London Research InstituteSouth Mimms, Herts, UK
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