1
|
Yang R, Hunker O, Wise M, Bleichert F. Multiple pathways for licensing human replication origins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588796. [PMID: 38645015 PMCID: PMC11030351 DOI: 10.1101/2024.04.10.588796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The loading of replicative helicases constitutes an obligatory step in the assembly of DNA replication machineries. In eukaryotes, the MCM2-7 replicative helicase motor is deposited onto DNA by the origin recognition complex (ORC) and co-loader proteins as a head-to-head MCM double hexamer to license replication origins. Although extensively studied in the budding yeast model system, the mechanisms of origin licensing in higher eukaryotes remain poorly defined. Here, we use biochemical reconstitution and electron microscopy (EM) to reconstruct the human MCM loading pathway. Unexpectedly, we find that, unlike in yeast, ORC's Orc6 subunit is not essential for human MCM loading but can enhance loading efficiency. EM analyses identify several intermediates en route to MCM double hexamer formation in the presence and absence of Orc6, including an abundant DNA-loaded, closed-ring single MCM hexamer intermediate that can mature into a head-to-head double hexamer through different pathways. In an Orc6-facilitated pathway, ORC and a second MCM2-7 hexamer are recruited to the dimerization interface of the first hexamer through an MCM-ORC intermediate that is architecturally distinct from an analogous intermediate in yeast. In an alternative, Orc6-independent pathway, MCM double hexamer formation proceeds through dimerization of two independently loaded single MCM2-7 hexamers, promoted by a propensity of human MCM2-7 hexamers to dimerize without the help of other loading factors. This redundancy in human MCM loading pathways likely provides resilience against replication stress under cellular conditions by ensuring that enough origins are licensed for efficient DNA replication. Additionally, the biochemical reconstitution of human origin licensing paves the way to address many outstanding questions regarding DNA replication initiation and replication-coupled events in higher eukaryotes in the future.
Collapse
Affiliation(s)
| | | | - Marleigh Wise
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Franziska Bleichert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| |
Collapse
|
2
|
Nasheuer HP, Meaney AM. Starting DNA Synthesis: Initiation Processes during the Replication of Chromosomal DNA in Humans. Genes (Basel) 2024; 15:360. [PMID: 38540419 PMCID: PMC10969946 DOI: 10.3390/genes15030360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 06/14/2024] Open
Abstract
The initiation reactions of DNA synthesis are central processes during human chromosomal DNA replication. They are separated into two main processes: the initiation events at replication origins, the start of the leading strand synthesis for each replicon, and the numerous initiation events taking place during lagging strand DNA synthesis. In addition, a third mechanism is the re-initiation of DNA synthesis after replication fork stalling, which takes place when DNA lesions hinder the progression of DNA synthesis. The initiation of leading strand synthesis at replication origins is regulated at multiple levels, from the origin recognition to the assembly and activation of replicative helicase, the Cdc45-MCM2-7-GINS (CMG) complex. In addition, the multiple interactions of the CMG complex with the eukaryotic replicative DNA polymerases, DNA polymerase α-primase, DNA polymerase δ and ε, at replication forks play pivotal roles in the mechanism of the initiation reactions of leading and lagging strand DNA synthesis. These interactions are also important for the initiation of signalling at unperturbed and stalled replication forks, "replication stress" events, via ATR (ATM-Rad 3-related protein kinase). These processes are essential for the accurate transfer of the cells' genetic information to their daughters. Thus, failures and dysfunctions in these processes give rise to genome instability causing genetic diseases, including cancer. In their influential review "Hallmarks of Cancer: New Dimensions", Hanahan and Weinberg (2022) therefore call genome instability a fundamental function in the development process of cancer cells. In recent years, the understanding of the initiation processes and mechanisms of human DNA replication has made substantial progress at all levels, which will be discussed in the review.
Collapse
Affiliation(s)
- Heinz Peter Nasheuer
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland;
| | | |
Collapse
|
3
|
Ahmad H, Chetlangia N, Prasanth SG. Chromatin's Influence on Pre-Replication Complex Assembly and Function. BIOLOGY 2024; 13:152. [PMID: 38534422 DOI: 10.3390/biology13030152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024]
Abstract
In all eukaryotes, the initiation of DNA replication requires a stepwise assembly of factors onto the origins of DNA replication. This is pioneered by the Origin Recognition Complex, which recruits Cdc6. Together, they bring Cdt1, which shepherds MCM2-7 to form the OCCM complex. Sequentially, a second Cdt1-bound hexamer of MCM2-7 is recruited by ORC-Cdc6 to form an MCM double hexamer, which forms a part of the pre-RC. Although the mechanism of ORC binding to DNA varies across eukaryotes, how ORC is recruited to replication origins in human cells remains an area of intense investigation. This review discusses how the chromatin environment influences pre-RC assembly, function, and, eventually, origin activity.
Collapse
Affiliation(s)
- Hina Ahmad
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Neha Chetlangia
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
4
|
Orc6 is a component of the replication fork and enables efficient mismatch repair. Proc Natl Acad Sci U S A 2022; 119:e2121406119. [PMID: 35622890 DOI: 10.1073/pnas.2121406119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Significance Origin recognition complex (ORC) is required for the initiation of DNA replication. Unlike other ORC components, the role of human Orc6 in replication remains to be resolved. We identified an unexpected role for hOrc6, which is to promote S-phase progression after prereplication complex assembly and DNA damage response. Orc6 localizes at the replication fork, is an accessory factor of the mismatch repair complex, and plays a fundamental role in genome surveillance during S phase.
Collapse
|
5
|
Schmidt JM, Yang R, Kumar A, Hunker O, Seebacher J, Bleichert F. A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6. Nat Commun 2022; 13:1059. [PMID: 35217664 PMCID: PMC8881611 DOI: 10.1038/s41467-022-28695-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/04/2022] [Indexed: 11/10/2022] Open
Abstract
The coordinated action of multiple replicative helicase loading factors is needed for the licensing of replication origins prior to DNA replication. Binding of the Origin Recognition Complex (ORC) to DNA initiates the ATP-dependent recruitment of Cdc6, Cdt1 and Mcm2-7 loading, but the structural details for timely ATPase site regulation and for how loading can be impeded by inhibitory signals, such as cyclin-dependent kinase phosphorylation, are unknown. Using cryo-electron microscopy, we have determined several structures of S. cerevisiae ORC·DNA·Cdc6 intermediates at 2.5-2.7 Å resolution. These structures reveal distinct ring conformations of the initiator·co-loader assembly and inactive ATPase site configurations for ORC and Cdc6. The Orc6 N-terminal domain laterally engages the ORC·Cdc6 ring in a manner that is incompatible with productive Mcm2-7 docking, while deletion of this Orc6 region alleviates the CDK-mediated inhibition of Mcm7 recruitment. Our findings support a model in which Orc6 promotes the assembly of an autoinhibited ORC·DNA·Cdc6 intermediate to block origin licensing in response to CDK phosphorylation and to avert DNA re-replication.
Collapse
Affiliation(s)
- Jan Marten Schmidt
- Friedrich Miescher Institute for Biomedical Research, Basel, 4058, Switzerland
- University of Basel, Basel, 4051, Switzerland
- Novartis Institutes for Biomedical Research, Basel, 4033, Switzerland
| | - Ran Yang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Ashish Kumar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Olivia Hunker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jan Seebacher
- Friedrich Miescher Institute for Biomedical Research, Basel, 4058, Switzerland
| | - Franziska Bleichert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
| |
Collapse
|
6
|
Abstract
DNA replication in eukaryotic cells initiates from large numbers of sites called replication origins. Initiation of replication from these origins must be tightly controlled to ensure the entire genome is precisely duplicated in each cell cycle. This is accomplished through the regulation of the first two steps in replication: loading and activation of the replicative DNA helicase. Here we describe what is known about the mechanism and regulation of these two reactions from a genetic, biochemical, and structural perspective, focusing on recent progress using proteins from budding yeast. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London, UK;
| | - John F X Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, London, UK;
| |
Collapse
|
7
|
Tu Q, Feng W, Chen Z, Li Q, Zhao Y, Chen J, Jiang P, Xue X, Zhang L, Zhao KN. Characterization of Episomal Replication of Bovine Papillomavirus Type 1 DNA in Long-Term Virion-Infected Saccharomyces Cerevisiae Culture. Virol Sin 2021; 36:1492-1502. [PMID: 34460066 PMCID: PMC8692549 DOI: 10.1007/s12250-021-00439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/21/2021] [Indexed: 11/29/2022] Open
Abstract
We have previously reported that bovine papillomavirus type 1 (BPV-1) DNA can replicate its genome and produce infectious virus-like particles in short term virion-infected S. cerevisiae (budding yeast) cultures (Zhao and Frazer 2002, Journal of Virology, 76:3359–64 and 76:12265–73). Here, we report the episomal replications of BPV-1 DNA in long term virion-infected S. cerevisiae culture up to 108 days. Episomal replications of the BPV-1 DNA could be divided into three patterns at three stages, early active replication (day 3–16), middle weak replication (day 23–34/45) and late stable replication (day 45–82). Two-dimensional gel electrophoresis analysis and Southern blot hybridization have revealed further that multiple replication intermediates of BPV-1 DNA including linear form, stranded DNA, monomers and higher oligomers were detected in the virion-infected yeast cells over the time course. Higher oligomers shown as covalently closed circular DNAs (cccDNAs) are the most important replication intermediates that serve as the main nuclear transcription template for producing all viral RNAs in the viral life cycle. In this study, the cccDNAs were generated at the early active replication stage with the highest frequencies and then at late stable replication, but they appeared to be suppressed at the middle weak replication. Our data provided a novel insight that BPV-1 genomic DNA could replicate episomally for the long period and produce the key replication intermediates cccDNAs in S. cerevisiae system.
Collapse
Affiliation(s)
- Quanmei Tu
- Department of Obstetrics and Gynaecology, The Second Affiliated Hospital and Yuyin Children Hospital of Wenzhou Medical University, Wenzhou, 325035, China
| | - Weixu Feng
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Zhuo Chen
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Qijia Li
- Department of Obstetrics and Gynaecology, The Second Affiliated Hospital and Yuyin Children Hospital of Wenzhou Medical University, Wenzhou, 325035, China.,Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yu Zhao
- Department of Obstetrics and Gynaecology, The Second Affiliated Hospital and Yuyin Children Hospital of Wenzhou Medical University, Wenzhou, 325035, China
| | - Jun Chen
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Pengfei Jiang
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Xiangyang Xue
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Lifang Zhang
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
| | - Kong-Nan Zhao
- Department of Obstetrics and Gynaecology, The Second Affiliated Hospital and Yuyin Children Hospital of Wenzhou Medical University, Wenzhou, 325035, China. .,Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, China. .,Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, St Lucia, 4067, Australia.
| |
Collapse
|
8
|
The structure of ORC-Cdc6 on an origin DNA reveals the mechanism of ORC activation by the replication initiator Cdc6. Nat Commun 2021; 12:3883. [PMID: 34162887 PMCID: PMC8222357 DOI: 10.1038/s41467-021-24199-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 06/07/2021] [Indexed: 01/31/2023] Open
Abstract
The Origin Recognition Complex (ORC) binds to sites in chromosomes to specify the location of origins of DNA replication. The S. cerevisiae ORC binds to specific DNA sequences throughout the cell cycle but becomes active only when it binds to the replication initiator Cdc6. It has been unclear at the molecular level how Cdc6 activates ORC, converting it to an active recruiter of the Mcm2-7 hexamer, the core of the replicative helicase. Here we report the cryo-EM structure at 3.3 Å resolution of the yeast ORC–Cdc6 bound to an 85-bp ARS1 origin DNA. The structure reveals that Cdc6 contributes to origin DNA recognition via its winged helix domain (WHD) and its initiator-specific motif. Cdc6 binding rearranges a short α-helix in the Orc1 AAA+ domain and the Orc2 WHD, leading to the activation of the Cdc6 ATPase and the formation of the three sites for the recruitment of Mcm2-7, none of which are present in ORC alone. The results illuminate the molecular mechanism of a critical biochemical step in the licensing of eukaryotic replication origins. Eukaryotic DNA replication is mediated by many proteins which are tightly regulated for an efficient firing of replication at each cell cycle. Here the authors report a cryo-EM structure of the yeast ORC–Cdc6 bound to an 85-bp ARS1 origin DNA revealing additional insights into how Cdc6 contributes to origin DNA recognition.
Collapse
|
9
|
Chou HC, Bhalla K, Demerdesh OE, Klingbeil O, Hanington K, Aganezov S, Andrews P, Alsudani H, Chang K, Vakoc CR, Schatz MC, McCombie WR, Stillman B. The human origin recognition complex is essential for pre-RC assembly, mitosis, and maintenance of nuclear structure. eLife 2021; 10:61797. [PMID: 33522487 PMCID: PMC7877914 DOI: 10.7554/elife.61797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/30/2021] [Indexed: 12/23/2022] Open
Abstract
The origin recognition complex (ORC) cooperates with CDC6, MCM2-7, and CDT1 to form pre-RC complexes at origins of DNA replication. Here, using tiling-sgRNA CRISPR screens, we report that each subunit of ORC and CDC6 is essential in human cells. Using an auxin-inducible degradation system, we created stable cell lines capable of ablating ORC2 rapidly, revealing multiple cell division cycle phenotypes. The primary defects in the absence of ORC2 were cells encountering difficulty in initiating DNA replication or progressing through the cell division cycle due to reduced MCM2-7 loading onto chromatin in G1 phase. The nuclei of ORC2-deficient cells were also large, with decompacted heterochromatin. Some ORC2-deficient cells that completed DNA replication entered into, but never exited mitosis. ORC1 knockout cells also demonstrated extremely slow cell proliferation and abnormal cell and nuclear morphology. Thus, ORC proteins and CDC6 are indispensable for normal cellular proliferation and contribute to nuclear organization.
Collapse
Affiliation(s)
- Hsiang-Chen Chou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States.,Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, United States
| | - Kuhulika Bhalla
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | | | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | | | - Sergey Aganezov
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, United States
| | - Peter Andrews
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Habeeb Alsudani
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Kenneth Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | | | - Michael C Schatz
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, United States
| | | | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| |
Collapse
|
10
|
Prospect of reprogramming replication licensing for cancer drug development. Biomed Pharmacother 2021; 136:111190. [PMID: 33497909 DOI: 10.1016/j.biopha.2020.111190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/15/2020] [Accepted: 12/26/2020] [Indexed: 12/15/2022] Open
Abstract
Eukaryotic chromosomal DNA replication is preceded by replication licensing which involves the identification of the origin of replication by origin recognition complex (ORC). The ORC loads pre-replication complexes (pre-RCs) through a series of tightly regulated mechanisms where the ORC interacts with Cdc6 to recruit cdt1-MCM2-7 complexes to the origin of replication. In eukaryotes, adherence to regulatory mechanisms of the replication program is required to ensure that all daughter cells carry the exact copy of genetic material as the parent cell. Failure of which leads to the development of genome instability syndromes like cancer, diabetes, etc. In an event of such occurrence, preventing cells from carrying the defaulted genetic material and passing it to other cells hinges on the regulation of chromosomal DNA replication. Thus, understanding the mechanisms underpinning chromosomal DNA replication and particularly replication licensing can expose druggable enzymes, effector molecules, and secondary messengers that can be targeted for diagnosis and therapeutic purposes. Effectively drugging these molecular markers to reprogram pre-replication events can be used to control the fate of chromosomal DNA replication for the treatment of genome instability disorders and in this case, cancer. This review discusses available knowledge of replication licensing in the contest of molecular drug discovery for the treatment of cancer.
Collapse
|
11
|
Shibata E, Dutta A. A human cancer cell line initiates DNA replication normally in the absence of ORC5 and ORC2 proteins. J Biol Chem 2020; 295:16949-16959. [PMID: 32989049 PMCID: PMC7863895 DOI: 10.1074/jbc.ra120.015450] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/23/2020] [Indexed: 01/03/2023] Open
Abstract
The origin recognition complex (ORC), composed of six subunits, ORC1-6, binds to origins of replication as a ring-shaped heterohexameric ATPase that is believed to be essential to recruit and load MCM2-7, the minichromosome maintenance protein complex, around DNA and initiate DNA replication. We previously reported the creation of viable cancer cell lines that lacked detectable ORC1 or ORC2 protein without a reduction in the number of origins firing. Here, using CRISPR-Cas9-mediated mutations, we report that human HCT116 colon cancer cells also survive when ORC5 protein expression is abolished via a mutation in the initiator ATG of the ORC5 gene. Even if an internal methionine is used to produce an undetectable, N terminally deleted ORC5, the protein would lack 80% of the AAA+ ATPase domain, including the Walker A motif. The ORC5-depleted cells show normal chromatin binding of MCM2-7 and initiate replication from a similar number of origins as WT cells. In addition, we introduced a second mutation in ORC2 in the ORC5 mutant cells, rendering both ORC5 and ORC2 proteins undetectable in the same cells and destabilizing the ORC1, ORC3, and ORC4 proteins. Yet the double mutant cells grow, recruit MCM2-7 normally to chromatin, and initiate DNA replication with normal number of origins. Thus, in these selected cancer cells, either a crippled ORC lacking ORC2 and ORC5 and present at minimal levels on the chromatin can recruit and load enough MCM2-7 to initiate DNA replication, or human cell lines can sometimes recruit MCM2-7 to origins independent of ORC.
Collapse
Affiliation(s)
- Etsuko Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA.
| |
Collapse
|
12
|
Balasov M, Akhmetova K, Chesnokov I. Humanized Drosophila Model of the Meier-Gorlin Syndrome Reveals Conserved and Divergent Features of the Orc6 Protein. Genetics 2020; 216:995-1007. [PMID: 33037049 PMCID: PMC7768257 DOI: 10.1534/genetics.120.303698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/06/2020] [Indexed: 11/18/2022] Open
Abstract
Meier-Gorlin syndrome (MGS) is a rare, autosomal recessive disorder characterized by microtia, primordial dwarfism, small ears, and skeletal abnormalities. Patients with MGS often carry mutations in genes encoding the subunits of the Origin Recognition Complex (ORC), components of the prereplicative complex and replication machinery. Orc6 is an important component of ORC and has functions in both DNA replication and cytokinesis. A mutation in the conserved C-terminal motif of Orc6 associated with MGS impedes the interaction of Orc6 with core ORC. Recently, a new mutation in Orc6 was also identified; however, it is localized in the N-terminal domain of the protein. To study the functions of Orc6, we used the human gene to rescue the orc6 deletion in Drosophila Using this "humanized" Orc6-based Drosophila model of MGS, we discovered that unlike the previous Y225S MGS mutation in Orc6, the K23E substitution in the N-terminal TFIIB-like domain of Orc6 disrupts the protein ability to bind DNA. Our studies revealed the importance of evolutionarily conserved and variable domains of Orc6 protein, and allowed the studies of human protein functions and the analysis of the critical amino acids in live animal heterologous system, as well as provided novel insights into the mechanisms underlying MGS pathology.
Collapse
Affiliation(s)
- Maxim Balasov
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Alabama 35294
| | - Katarina Akhmetova
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Alabama 35294
| | - Igor Chesnokov
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Alabama 35294
| |
Collapse
|
13
|
Xu N, You Y, Liu C, Balasov M, Lun LT, Geng Y, Fung CP, Miao H, Tian H, Choy TT, Shi X, Fan Z, Zhou B, Akhmetova K, Din RU, Yang H, Hao Q, Qian P, Chesnokov I, Zhu G. Structural basis of DNA replication origin recognition by human Orc6 protein binding with DNA. Nucleic Acids Res 2020; 48:11146-11161. [PMID: 32986843 PMCID: PMC7641730 DOI: 10.1093/nar/gkaa751] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 08/18/2020] [Accepted: 09/19/2020] [Indexed: 01/08/2023] Open
Abstract
The six-subunit origin recognition complex (ORC), a DNA replication initiator, defines the localization of the origins of replication in eukaryotes. The Orc6 subunit is the smallest and the least conserved among ORC subunits. It is required for DNA replication and essential for viability in all species. Orc6 in metazoans carries a structural homology with transcription factor TFIIB and can bind DNA on its own. Here, we report a solution structure of the full-length human Orc6 (HsOrc6) alone and in a complex with DNA. We further showed that human Orc6 is composed of three independent domains: N-terminal, middle and C-terminal (HsOrc6-N, HsOrc6-M and HsOrc6-C). We also identified a distinct DNA-binding domain of human Orc6, named as HsOrc6-DBD. The detailed analysis of the structure revealed novel amino acid clusters important for the interaction with DNA. Alterations of these amino acids abolish DNA-binding ability of Orc6 and result in reduced levels of DNA replication. We propose that Orc6 is a DNA-binding subunit of human/metazoan ORC and may play roles in targeting, positioning and assembling the functional ORC at the origins.
Collapse
Affiliation(s)
- Naining Xu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
- Department of Oral and Maxillofacial Surgery, Peking University ShenzhenHospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Yingying You
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
- Department of Oncology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Changdong Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Maxim Balasov
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Lee Tung Lun
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Yanyan Geng
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Chun Po Fung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Haitao Miao
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Honglei Tian
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - To To Choy
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Xiao Shi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Zhuming Fan
- School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong SAR, 00000, China
| | - Bo Zhou
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Katarina Akhmetova
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Rahman Ud Din
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Hongyu Yang
- Department of Oral and Maxillofacial Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University, Shenzhen, 518036, China
| | - Quan Hao
- School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong SAR, 00000, China
| | - Peiyuan Qian
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Igor Chesnokov
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| |
Collapse
|
14
|
Jaremko MJ, On KF, Thomas DR, Stillman B, Joshua-Tor L. The dynamic nature of the human origin recognition complex revealed through five cryoEM structures. eLife 2020; 9:e58622. [PMID: 32808929 PMCID: PMC7467728 DOI: 10.7554/elife.58622] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022] Open
Abstract
Genome replication is initiated from specific origin sites established by dynamic events. The Origin Recognition Complex (ORC) is necessary for orchestrating the initiation process by binding to origin DNA, recruiting CDC6, and assembling the MCM replicative helicase on DNA. Here we report five cryoEM structures of the human ORC (HsORC) that illustrate the native flexibility of the complex. The absence of ORC1 revealed a compact, stable complex of ORC2-5. Introduction of ORC1 opens the complex into several dynamic conformations. Two structures revealed dynamic movements of the ORC1 AAA+ and ORC2 winged-helix domains that likely impact DNA incorporation into the ORC core. Additional twist and pinch motions were observed in an open ORC conformation revealing a hinge at the ORC5·ORC3 interface that may facilitate ORC binding to DNA. Finally, a structure of ORC was determined with endogenous DNA bound in the core revealing important differences between human and yeast origin recognition.
Collapse
Affiliation(s)
- Matt J Jaremko
- W. M. Keck Structural Biology LaboratoryNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
- Cold Spring Harbor LaboratoryNew YorkUnited States
| | - Kin Fan On
- W. M. Keck Structural Biology LaboratoryNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
- Cold Spring Harbor LaboratoryNew YorkUnited States
| | - Dennis R Thomas
- W. M. Keck Structural Biology LaboratoryNew YorkUnited States
- Cold Spring Harbor LaboratoryNew YorkUnited States
| | | | - Leemor Joshua-Tor
- W. M. Keck Structural Biology LaboratoryNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
- Cold Spring Harbor LaboratoryNew YorkUnited States
| |
Collapse
|
15
|
Wu R, Amin A, Wang Z, Huang Y, Man-Hei Cheung M, Yu Z, Yang W, Liang C. The interaction networks of the budding yeast and human DNA replication-initiation proteins. Cell Cycle 2019; 18:723-741. [PMID: 30890025 DOI: 10.1080/15384101.2019.1586509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
DNA replication is a stringently regulated cellular process. In proliferating cells, DNA replication-initiation proteins (RIPs) are sequentially loaded onto replication origins during the M-to-G1 transition to form the pre-replicative complex (pre-RC), a process known as replication licensing. Subsequently, additional RIPs are recruited to form the pre-initiation complex (pre-IC). RIPs and their regulators ensure that chromosomal DNA is replicated exactly once per cell cycle. Origin recognition complex (ORC) binds to, and marks replication origins throughout the cell cycle and recruits other RIPs including Noc3p, Ipi1-3p, Cdt1p, Cdc6p and Mcm2-7p to form the pre-RC. The detailed mechanisms and regulation of the pre-RC and its exact architecture still remain unclear. In this study, pairwise protein-protein interactions among 23 budding yeast and 16 human RIPs were systematically and comprehensively examined by yeast two-hybrid analysis. This study tested 470 pairs of yeast and 196 pairs of human RIPs, from which 113 and 96 positive interactions, respectively, were identified. While many of these interactions were previously reported, some were novel, including various ORC and MCM subunit interactions, ORC self-interactions, and the interactions of IPI3 and NOC3 with several pre-RC and pre-IC proteins. Ten of the novel interactions were further confirmed by co-immunoprecipitation assays. Furthermore, we identified the conserved interaction networks between the yeast and human RIPs. This study provides a foundation and framework for further understanding the architectures, interactions and functions of the yeast and human pre-RC and pre-IC.
Collapse
Affiliation(s)
- Rentian Wu
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,b Guangzhou HKUST Fok Ying Tung Research Institute , Guangzhou , China
| | - Aftab Amin
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,b Guangzhou HKUST Fok Ying Tung Research Institute , Guangzhou , China.,c School of Chinese Medicine , Hong Kong Baptist University , Guangzhou , China
| | - Ziyi Wang
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China
| | - Yining Huang
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China
| | - Marco Man-Hei Cheung
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,b Guangzhou HKUST Fok Ying Tung Research Institute , Guangzhou , China
| | - Zhiling Yu
- c School of Chinese Medicine , Hong Kong Baptist University , Guangzhou , China
| | - Wei Yang
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,d Guangdong Lewwin Pharmaceutical Research Institute Co., Ltd , Hong Kong , China
| | - Chun Liang
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,b Guangzhou HKUST Fok Ying Tung Research Institute , Guangzhou , China.,e ntelgen Limited , Hong Kong-Guangzhou-Foshan , China
| |
Collapse
|
16
|
Popova VV, Brechalov AV, Georgieva SG, Kopytova DV. Nonreplicative functions of the origin recognition complex. Nucleus 2018; 9:460-473. [PMID: 30196754 PMCID: PMC6244734 DOI: 10.1080/19491034.2018.1516484] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/04/2018] [Accepted: 08/16/2018] [Indexed: 12/14/2022] Open
Abstract
Origin recognition complex (ORC), a heteromeric six-subunit complex, is the central component of the eukaryotic pre-replication complex. Recent data from yeast, frogs, flies and mammals present compelling evidence that ORC and its individual subunits have nonreplicative functions as well. The majority of these functions, such as heterochromatin formation, chromosome condensation, and segregation are dependent on ORC-DNA interactions. Furthermore, ORC is involved in the control of cell division via its participation in centrosome duplication and cytokinesis. Recent findings have also demonstrated a direct interaction between ORC and mRNPs and highlighted an essential role of ORC in mRNA nuclear export. Along with the growth of evolutionary complexity of organisms, ORC complex functions become more elaborate and new functions of the ORC sub-complexes and individual subunits have emerged.
Collapse
Affiliation(s)
- Varvara V. Popova
- Department of Transcription Regulation and Chromatin Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander V. Brechalov
- Department of Transcription Regulation and Chromatin Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sofia G. Georgieva
- Department of Transcription Regulation and Chromatin Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Daria V. Kopytova
- Department of Transcription Regulation and Chromatin Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
17
|
Nguyen H, James NG, Nguyen L, Nguyen TP, Vuong C, Ortega MA, Jameson DM, Ward WS. Higher Order Oligomerization of the Licensing ORC4 Protein Is Required for Polar Body Extrusion in Murine Meiosis. J Cell Biochem 2017; 118:2941-2949. [PMID: 28230328 DOI: 10.1002/jcb.25949] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 02/22/2017] [Indexed: 01/01/2023]
Abstract
We have previously shown that the DNA replication licensing factor ORC4 forms a cage around the chromosomes that are extruded in both polar bodies during murine oogenesis, but not around the chromosomes that are retained in the oocyte or around the sperm chromatin. We termed this structure the ORC4 cage. Here, we tested whether the formation of the ORC4 cage is necessary for polar body extrusion (PBE). We first experimentally forced oocytes to extrude sperm chromatin as a pseudo-polar body and found that under these conditions the sperm chromatin did become enclosed in an ORC4 cage. Next, we attempted to prevent the formation of the ORC4 cage by injecting peptides that contained sequences of different domains of the ORC4 protein into metaphase II (MII) oocytes just before the cage normally forms. Our rationale was that the ORC4 peptides would block protein-protein interactions required for cage formation. Two out of six tested peptides prevented the ORC4 cage formation and simultaneously inhibited PBE, resulting in the formation of two pronuclei (2 PN) that were retained in the oocyte. Together, these data demonstrate that ORC4 oligomerization is required to form the ORC4 cage and that it is required for PBE. J. Cell. Biochem. 118: 2941-2949, 2017. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Hieu Nguyen
- Department of Anatomy, Biochemistry and Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Nicholas G James
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu
| | - Lynn Nguyen
- Department of Anatomy, Biochemistry and Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Thien P Nguyen
- Department of Anatomy, Biochemistry and Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Cindy Vuong
- Department of Anatomy, Biochemistry and Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Michael A Ortega
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
| | - David M Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu
| | - W Steven Ward
- Department of Anatomy, Biochemistry and Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii.,Department of Obstetrics, Gynecology and Women's Health, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii
| |
Collapse
|
18
|
Tocilj A, On KF, Yuan Z, Sun J, Elkayam E, Li H, Stillman B, Joshua-Tor L. Structure of the active form of human origin recognition complex and its ATPase motor module. eLife 2017; 6. [PMID: 28112645 PMCID: PMC5291709 DOI: 10.7554/elife.20818] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/15/2017] [Indexed: 12/21/2022] Open
Abstract
Binding of the Origin Recognition Complex (ORC) to origins of replication marks the first step in the initiation of replication of the genome in all eukaryotic cells. Here, we report the structure of the active form of human ORC determined by X-ray crystallography and cryo-electron microscopy. The complex is composed of an ORC1/4/5 motor module lobe in an organization reminiscent of the DNA polymerase clamp loader complexes. A second lobe contains the ORC2/3 subunits. The complex is organized as a double-layered shallow corkscrew, with the AAA+ and AAA+-like domains forming one layer, and the winged-helix domains (WHDs) forming a top layer. CDC6 fits easily between ORC1 and ORC2, completing the ring and the DNA-binding channel, forming an additional ATP hydrolysis site. Analysis of the ATPase activity of the complex provides a basis for understanding ORC activity as well as molecular defects observed in Meier-Gorlin Syndrome mutations. DOI:http://dx.doi.org/10.7554/eLife.20818.001
Collapse
Affiliation(s)
- Ante Tocilj
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, United States.,Howard Hughes Medical Institute, Cold Spring Harbor, New York, United States.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Kin Fan On
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, United States.,Howard Hughes Medical Institute, Cold Spring Harbor, New York, United States.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Zuanning Yuan
- Biology Department, Brookhaven National Laboratory, New York, United States.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Jingchuan Sun
- Biology Department, Brookhaven National Laboratory, New York, United States
| | - Elad Elkayam
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, United States.,Howard Hughes Medical Institute, Cold Spring Harbor, New York, United States.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Huilin Li
- Biology Department, Brookhaven National Laboratory, New York, United States.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Leemor Joshua-Tor
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, United States.,Howard Hughes Medical Institute, Cold Spring Harbor, New York, United States.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| |
Collapse
|
19
|
Parker MW, Botchan MR, Berger JM. Mechanisms and regulation of DNA replication initiation in eukaryotes. Crit Rev Biochem Mol Biol 2017; 52:107-144. [PMID: 28094588 DOI: 10.1080/10409238.2016.1274717] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cellular DNA replication is initiated through the action of multiprotein complexes that recognize replication start sites in the chromosome (termed origins) and facilitate duplex DNA melting within these regions. In a typical cell cycle, initiation occurs only once per origin and each round of replication is tightly coupled to cell division. To avoid aberrant origin firing and re-replication, eukaryotes tightly regulate two events in the initiation process: loading of the replicative helicase, MCM2-7, onto chromatin by the origin recognition complex (ORC), and subsequent activation of the helicase by its incorporation into a complex known as the CMG. Recent work has begun to reveal the details of an orchestrated and sequential exchange of initiation factors on DNA that give rise to a replication-competent complex, the replisome. Here, we review the molecular mechanisms that underpin eukaryotic DNA replication initiation - from selecting replication start sites to replicative helicase loading and activation - and describe how these events are often distinctly regulated across different eukaryotic model organisms.
Collapse
Affiliation(s)
- Matthew W Parker
- a Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Michael R Botchan
- b Department of Molecular and Cell Biology , University of California Berkeley , Berkeley , CA , USA
| | - James M Berger
- a Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| |
Collapse
|
20
|
Kopytova D, Popova V, Kurshakova M, Shidlovskii Y, Nabirochkina E, Brechalov A, Georgiev G, Georgieva S. ORC interacts with THSC/TREX-2 and its subunits promote Nxf1 association with mRNP and mRNA export in Drosophila. Nucleic Acids Res 2016; 44:4920-33. [PMID: 27016737 PMCID: PMC4889942 DOI: 10.1093/nar/gkw192] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 03/11/2016] [Indexed: 12/20/2022] Open
Abstract
The origin recognition complex (ORC) of eukaryotes associates with the replication origins and initiates the pre-replication complex assembly. In the literature, there are several reports of interaction of ORC with different RNAs. Here, we demonstrate for the first time a direct interaction of ORC with the THSC/TREX-2 mRNA nuclear export complex. The THSC/TREX-2 was purified from the Drosophila embryonic extract and found to bind with a fraction of the ORC. This interaction occurred via several subunits and was essential for Drosophila viability. Also, ORC was associated with mRNP, which was facilitated by TREX-2. ORC subunits interacted with the Nxf1 receptor mediating the bulk mRNA export. The knockdown of Orc5 led to a drop in the Nxf1 association with mRNP, while Orc3 knockdown increased the level of mRNP-bound Nxf1. The knockdown of Orc5, Orc3 and several other ORC subunits led to an accumulation of mRNA in the nucleus, suggesting that ORC participates in the regulation of the mRNP export.
Collapse
Affiliation(s)
- Daria Kopytova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Varvara Popova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria Kurshakova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Yulii Shidlovskii
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Elena Nabirochkina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Alexander Brechalov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Georgii Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Sofia Georgieva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| |
Collapse
|
21
|
Siena LA, Ortiz JPA, Calderini O, Paolocci F, Cáceres ME, Kaushal P, Grisan S, Pessino SC, Pupilli F. An apomixis-linked ORC3-like pseudogene is associated with silencing of its functional homolog in apomictic Paspalum simplex. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1965-78. [PMID: 26842983 DOI: 10.1093/jxb/erw018] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Apomixis in plants consists of asexual reproduction by seeds. Here we characterized at structural and functional levels an apomixis-linked sequence of Paspalum simplex homologous to subunit 3 of the ORIGIN RECOGNITION COMPLEX (ORC3). ORC is a multiprotein complex which controls DNA replication and cell differentiation in eukaryotes. Three PsORC3 copies were identified, each one characterized by a specific expression profile. Of these, PsORC3a, specific for apomictic genotypes, is a pseudogene that was poorly and constitutively expressed in all developmental stages of apomictic flowers, whereas PsORC3b, the putative functional gene in sexual flowers, showed a precise time-related regulation. Sense transcripts of PsORC3 were expressed in the female cell lineage of both apomictic and sexual reproductive phenotypes, and in aposporous initials. Although strong expression was detected in sexual early endosperm, no expression was present in the apomictic endosperm. Antisense PsORC3 transcripts were revealed exclusively in apomictic germ cell lineages. Defective orc3 mutants of rice and Arabidopsis showed normal female gametophytes although the embryo and endosperm were arrested at early phases of development. We hypothesize that PsORC3a is associated with the down-regulation of its functional homolog and with the development of apomictic endosperm which deviates from the canonical 2(maternal):1(paternal) genome ratio.
Collapse
Affiliation(s)
- Lorena A Siena
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, (S2125ZAA) Zavalla, Argentina Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, (S2125ZAA) Zavalla, Argentina
| | - Juan Pablo A Ortiz
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, (S2125ZAA) Zavalla, Argentina Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, (S2125ZAA) Zavalla, Argentina
| | - Ornella Calderini
- Istituto di Bioscienze e Biorisorse (IBBR-CNR), via della Madonna alta 130, I-06128 Perugia, Italy
| | - Francesco Paolocci
- Istituto di Bioscienze e Biorisorse (IBBR-CNR), via della Madonna alta 130, I-06128 Perugia, Italy
| | - Maria E Cáceres
- Istituto di Bioscienze e Biorisorse (IBBR-CNR), via della Madonna alta 130, I-06128 Perugia, Italy
| | - Pankaj Kaushal
- Istituto di Bioscienze e Biorisorse (IBBR-CNR), via della Madonna alta 130, I-06128 Perugia, Italy
| | - Simone Grisan
- Istituto di Bioscienze e Biorisorse (IBBR-CNR), via della Madonna alta 130, I-06128 Perugia, Italy
| | - Silvina C Pessino
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, (S2125ZAA) Zavalla, Argentina Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, (S2125ZAA) Zavalla, Argentina
| | - Fulvio Pupilli
- Istituto di Bioscienze e Biorisorse (IBBR-CNR), via della Madonna alta 130, I-06128 Perugia, Italy
| |
Collapse
|
22
|
Nguyen H, Ortega MA, Ko M, Marh J, Ward WS. ORC4 surrounds extruded chromatin in female meiosis. J Cell Biochem 2015; 116:778-86. [PMID: 25502171 DOI: 10.1002/jcb.25033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 12/09/2014] [Indexed: 12/19/2022]
Abstract
Six proteins, ORC1-6, make up the origin recognition complex (ORC) that initiates licensing of DNA replication origins. We have previously reported that subunit ORC2 is localized between the separating maternal chromosomes at anaphase II just after fertilization and is present in zygotic pronuclei at G1. Here, we found that ORC1, 3, and 5 all localize between the chromosomes at anaphase II, but could not be detected in zygotic G1. ORC6 localized to the periphery of the nucleoli at all zygotic stages. We identified an unexpected potential role for ORC4 in polar body formation. We found that in both female meiotic divisions, ORC4 surrounds the set of chromosomes, as a sphere-like structure, that will eventually be discarded in the polar bodies, but not the chromosomes that segregate into the oocyte. None of the other five ORC proteins are involved in this structure. In Zygotic G1, ORC4 surrounds the nuclei of the polar bodies, but was not detectable in the pronuclei. When the zygote entered mitosis ORC4 was only detected in the polar body. However, ORC4 appeared on both sets of separating chromosomes at telophase. At this point, the ORC4 that was in the polar body also migrated into the nuclei, suggesting that ORC4 or an associated protein is modified during the first embryonic cell cycle to allow it to bind DNA. Our results suggest that ORC4 may help identify the chromosomes that are destined to be expelled in the polar body, and may play a role in polar body extrusion. ORC4 surrounds the chromatin that will be extruded in the polar body in both female meiotic divisions, then makes a transition from the cytoplasm to the chromosomes at zygotic anaphase, suggesting multiple roles for this replication licensing protein.
Collapse
Affiliation(s)
- Hieu Nguyen
- Institute for Biogenesis Research Department of Anatomy, Biochemistry & Physiology, and the Department of Obstetrics and Gynecology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii
| | | | | | | | | |
Collapse
|
23
|
Giri S, Chakraborty A, Sathyan KM, Prasanth KV, Prasanth SG. Orc5 induces large-scale chromatin decondensation in a GCN5-dependent manner. J Cell Sci 2015; 129:417-29. [PMID: 26644179 DOI: 10.1242/jcs.178889] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/27/2015] [Indexed: 12/11/2022] Open
Abstract
In eukaryotes, origin recognition complex (ORC) proteins establish the pre-replicative complex (preRC) at the origins, and this is essential for the initiation of DNA replication. Open chromatin structures regulate the efficiency of preRC formation and replication initiation. However, the molecular mechanisms that control chromatin structure, and how the preRC components establish themselves on the chromatin remain to be understood. In human cells, the ORC is a highly dynamic complex with many separate functions attributed to sub-complexes or individual subunits of the ORC, including heterochromatin organization, telomere and centromere function, centrosome duplication and cytokinesis. We demonstrate that human Orc5, unlike other ORC subunits, when ectopically tethered to a chromatin locus, induces large-scale chromatin decondensation, predominantly during G1 phase of the cell cycle. Orc5 associates with the H3 histone acetyl transferase GCN5 (also known as KAT2A), and this association enhances the chromatin-opening function of Orc5. In the absence of Orc5, histone H3 acetylation is decreased at the origins. We propose that the ability of Orc5 to induce chromatin unfolding during G1 allows the establishment of the preRC at the origins.
Collapse
Affiliation(s)
- Sumanprava Giri
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Arindam Chakraborty
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Kizhakke M Sathyan
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| |
Collapse
|
24
|
Wiśniewski JR, Duś-Szachniewicz K, Ostasiewicz P, Ziółkowski P, Rakus D, Mann M. Absolute Proteome Analysis of Colorectal Mucosa, Adenoma, and Cancer Reveals Drastic Changes in Fatty Acid Metabolism and Plasma Membrane Transporters. J Proteome Res 2015; 14:4005-18. [PMID: 26245529 DOI: 10.1021/acs.jproteome.5b00523] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Colorectal cancer is a leading cause of cancer-related death. It develops from normal enterocytes, through a benign adenoma stage, into the cancer and finally into the metastatic form. We previously compared the proteomes of normal colorectal enterocytes, cancer and nodal metastasis to a depth of 8100 proteins and found extensive quantitative remodeling between normal and cancer tissues but not cancer and metastasis (Wiśniewski et al. PMID 22968445). Here we utilize advances in the proteomic workflow to perform an in depth analysis of the normal tissue (N), the adenoma (A), and the cancer (C). Absolute proteomics of 10 000 proteins per patient from microdissected formalin-fixed and paraffin-embedded clinical material established a quantitative protein repository of the disease. Between N and A, 23% of all proteins changed significantly, 17.8% from A to C and 21.6% from N to C. Together with principal component analysis of the patient groups, this suggests that N, A, and C are equidistant but not on one developmental line. Our proteomics approach allowed us to assess changes in varied cell size, the composition of different subcellular components, and alterations in basic biological processes including the energy metabolism, plasma membrane transport, DNA replication, and transcription. This revealed several-fold higher concentrations of enzymes in fatty acid metabolism in C compared with N, and unexpectedly, the same held true of plasma membrane transporters.
Collapse
Affiliation(s)
- Jacek R Wiśniewski
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Kamila Duś-Szachniewicz
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany.,Department of Pathology, Wrocław Medical University , 50-368 Wrocław, Poland
| | - Paweł Ostasiewicz
- Department of Pathology, Wrocław Medical University , 50-368 Wrocław, Poland
| | - Piotr Ziółkowski
- Department of Pathology, Wrocław Medical University , 50-368 Wrocław, Poland
| | - Dariusz Rakus
- Department of Animal Molecular Physiology, Wroclaw University , 50-205 Wrocław, Poland
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| |
Collapse
|
25
|
Balasov M, Akhmetova K, Chesnokov I. Drosophila model of Meier-Gorlin syndrome based on the mutation in a conserved C-Terminal domain of Orc6. Am J Med Genet A 2015; 167A:2533-40. [PMID: 26139588 DOI: 10.1002/ajmg.a.37214] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/05/2015] [Indexed: 11/09/2022]
Abstract
Meier-Gorlin syndrome (MGS) is an autosomal recessive disorder characterized by microtia, primordial dwarfism, small ears, and skeletal abnormalities. Patients with MGS often carry mutations in the genes encoding the components of the pre-replicative complex such as Origin Recognition Complex (ORC) subunits Orc1, Orc4, Orc6, and helicase loaders Cdt1 and Cdc6. Orc6 is an important component of ORC and has functions in both DNA replication and cytokinesis. Mutation in conserved C-terminal motif of Orc6 associated with MGS impedes the interaction of Orc6 with core ORC. In order to study the effects of MGS mutation in an animal model system we introduced MGS mutation in Orc6 and established Drosophila model of MGS. Mutant flies die at third instar larval stage with abnormal chromosomes and DNA replication defects. The lethality can be rescued by elevated expression of mutant Orc6 protein. Rescued MGS flies are unable to fly and display multiple planar cell polarity defects. © 2015 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Maxim Balasov
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama
| | - Katarina Akhmetova
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama.,The Federal Research Center Institute of Cytology and Genetics, Prospekt Lavrentyeva 10, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Igor Chesnokov
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama
| |
Collapse
|
26
|
Sequeira-Mendes J, Gutierrez C. Links between genome replication and chromatin landscapes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:38-51. [PMID: 25847096 DOI: 10.1111/tpj.12847] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/27/2015] [Accepted: 04/01/2015] [Indexed: 05/07/2023]
Abstract
Post-embryonic organogenesis in plants requires the continuous production of cells in the organ primordia, their expansion and a coordinated exit to differentiation. Genome replication is one of the most important processes that occur during the cell cycle, as the maintenance of genomic integrity is of primary relevance for development. As it is chromatin that must be duplicated, a strict coordination occurs between DNA replication, the deposition of new histones, and the introduction of histone modifications and variants. In turn, the chromatin landscape affects several stages during genome replication. Thus, chromatin accessibility is crucial for the initial stages and to specify the location of DNA replication origins with different chromatin signatures. The chromatin landscape also determines the timing of activation during the S phase. Genome replication must occur fully, but only once during each cell cycle. The re-replication avoidance mechanisms rely primarily on restricting the availability of certain replication factors; however, the presence of specific histone modifications are also revealed as contributing to the mechanisms that avoid re-replication, in particular for heterochromatin replication. We provide here an update of genome replication mostly focused on data from Arabidopsis, and the advances that genomic approaches are likely to provide in the coming years. The data available, both in plants and animals, point to the relevance of the chromatin landscape in genome replication, and require a critical evaluation of the existing views about the nature of replication origins, the mechanisms of origin specification and the relevance of epigenetic modifications for genome replication.
Collapse
Affiliation(s)
- Joana Sequeira-Mendes
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| |
Collapse
|
27
|
Kara N, Hossain M, Prasanth SG, Stillman B. Orc1 Binding to Mitotic Chromosomes Precedes Spatial Patterning during G1 Phase and Assembly of the Origin Recognition Complex in Human Cells. J Biol Chem 2015; 290:12355-69. [PMID: 25784553 DOI: 10.1074/jbc.m114.625012] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Indexed: 12/21/2022] Open
Abstract
Replication of eukaryotic chromosomes occurs once every cell division cycle in normal cells and is a tightly controlled process that ensures complete genome duplication. The origin recognition complex (ORC) plays a key role during the initiation of DNA replication. In human cells, the level of Orc1, the largest subunit of ORC, is regulated during the cell division cycle, and thus ORC is a dynamic complex. Upon S phase entry, Orc1 is ubiquitinated and targeted for destruction, with subsequent dissociation of ORC from chromosomes. Time lapse and live cell images of human cells expressing fluorescently tagged Orc1 show that Orc1 re-localizes to condensing chromatin during early mitosis and then displays different nuclear localization patterns at different times during G1 phase, remaining associated with late replicating regions of the genome in late G1 phase. The initial binding of Orc1 to mitotic chromosomes requires C-terminal amino acid sequences that are similar to mitotic chromosome-binding sequences in the transcriptional pioneer protein FOXA1. Depletion of Orc1 causes concomitant loss of the mini-chromosome maintenance (Mcm2-7) helicase proteins on chromatin. The data suggest that Orc1 acts as a nucleating center for ORC assembly and then pre-replication complex assembly by binding to mitotic chromosomes, followed by gradual removal from chromatin during the G1 phase.
Collapse
Affiliation(s)
- Nihan Kara
- From the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, the Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11779, and
| | - Manzar Hossain
- From the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Supriya G Prasanth
- From the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, the Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois 61801
| | - Bruce Stillman
- From the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724,
| |
Collapse
|
28
|
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.
Collapse
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.
| |
Collapse
|
29
|
Wang Z, Zhong M, Fu M, Dou T, Bian Z. Evidence of positive selection at codon sites localized in the C-terminal peptide of ORC6. Biotechnol Lett 2014; 36:251-6. [DOI: 10.1007/s10529-013-1371-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/30/2013] [Indexed: 11/29/2022]
|
30
|
Desvoyes B, Fernández-Marcos M, Sequeira-Mendes J, Otero S, Vergara Z, Gutierrez C. Looking at plant cell cycle from the chromatin window. FRONTIERS IN PLANT SCIENCE 2014; 5:369. [PMID: 25120553 PMCID: PMC4110626 DOI: 10.3389/fpls.2014.00369] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/11/2014] [Indexed: 05/03/2023]
Abstract
The cell cycle is defined by a series of complex events, finely coordinated through hormonal, developmental and environmental signals, which occur in a unidirectional manner and end up in producing two daughter cells. Accumulating evidence reveals that chromatin is not a static entity throughout the cell cycle. In fact, there are many changes that include nucleosome remodeling, histone modifications, deposition and exchange, among others. Interestingly, it is possible to correlate the occurrence of several of these chromatin-related events with specific processes necessary for cell cycle progression, e.g., licensing of DNA replication origins, the E2F-dependent transcriptional wave in G1, the activation of replication origins in S-phase, the G2-specific transcription of genes required for mitosis or the chromatin packaging occurring in mitosis. Therefore, an emerging view is that chromatin dynamics must be considered as an intrinsic part of cell cycle regulation. In this article, we review the main features of several key chromatin events that occur at defined times throughout the cell cycle and discuss whether they are actually controlling the transit through specific cell cycle stages.
Collapse
Affiliation(s)
| | | | | | | | | | - Crisanto Gutierrez
- *Correspondence: Crisanto Gutierrez, Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas, Universidad Autónoma de Madrid, Nicolas Cabrera 1, Cantoblanco, Madrid 28049, Spain e-mail:
| |
Collapse
|
31
|
Bleichert F, Balasov M, Chesnokov I, Nogales E, Botchan MR, Berger JM. A Meier-Gorlin syndrome mutation in a conserved C-terminal helix of Orc6 impedes origin recognition complex formation. eLife 2013; 2:e00882. [PMID: 24137536 PMCID: PMC3791464 DOI: 10.7554/elife.00882] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 09/05/2013] [Indexed: 02/06/2023] Open
Abstract
In eukaryotes, DNA replication requires the origin recognition complex (ORC), a six-subunit assembly that promotes replisome formation on chromosomal origins. Despite extant homology between certain subunits, the degree of structural and organizational overlap between budding yeast and metazoan ORC has been unclear. Using 3D electron microscopy, we determined the subunit organization of metazoan ORC, revealing that it adopts a global architecture very similar to the budding yeast complex. Bioinformatic analysis extends this conservation to Orc6, a subunit of somewhat enigmatic function. Unexpectedly, a mutation in the Orc6 C-terminus linked to Meier-Gorlin syndrome, a dwarfism disorder, impedes proper recruitment of Orc6 into ORC; biochemical studies reveal that this region of Orc6 associates with a previously uncharacterized domain of Orc3 and is required for ORC function and MCM2-7 loading in vivo. Together, our results suggest that Meier-Gorlin syndrome mutations in Orc6 impair the formation of ORC hexamers, interfering with appropriate ORC functions. DOI:http://dx.doi.org/10.7554/eLife.00882.001.
Collapse
Affiliation(s)
- Franziska Bleichert
- Miller Institute for Basic Research in Science, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Maxim Balasov
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, United States
| | - Igor Chesnokov
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, United States
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Michael R Botchan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - James M Berger
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| |
Collapse
|
32
|
Chen X, Liu G, Leffak M. Activation of a human chromosomal replication origin by protein tethering. Nucleic Acids Res 2013; 41:6460-74. [PMID: 23658226 PMCID: PMC3711443 DOI: 10.1093/nar/gkt368] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The specification of mammalian chromosomal replication origins is incompletely understood. To analyze the assembly and activation of prereplicative complexes (pre-RCs), we tested the effects of tethered binding of chromatin acetyltransferases and replication proteins on chromosomal c-myc origin deletion mutants containing a GAL4-binding cassette. GAL4DBD (DNA binding domain) fusions with Orc2, Cdt1, E2F1 or HBO1 coordinated the recruitment of the Mcm7 helicase subunit, the DNA unwinding element (DUE)-binding protein DUE-B and the minichromosome maintenance (MCM) helicase activator Cdc45 to the replicator, and restored origin activity. In contrast, replication protein binding and origin activity were not stimulated by fusion protein binding in the absence of flanking c-myc DNA. Substitution of the GAL4-binding site for the c-myc replicator DUE allowed Orc2 and Mcm7 binding, but eliminated origin activity, indicating that the DUE is essential for pre-RC activation. Additionally, tethering of DUE-B was not sufficient to recruit Cdc45 or activate pre-RCs formed in the absence of a DUE. These results show directly in a chromosomal background that chromatin acetylation, Orc2 or Cdt1 suffice to recruit all downstream replication initiation activities to a prospective origin, and that chromosomal origin activity requires singular DNA sequences.
Collapse
Affiliation(s)
- Xiaomi Chen
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | | | | |
Collapse
|
33
|
Ortega MA, Marh J, Alarcon VB, Ward WS. Unique pattern of ORC2 and MCM7 localization during DNA replication licensing in the mouse zygote. Biol Reprod 2012; 87:62. [PMID: 22674395 DOI: 10.1095/biolreprod.112.101774] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
In eukaryotes, DNA synthesis is preceded by licensing of replication origins. We examined the subcellular localization of two licensing proteins, ORC2 and MCM7, in the mouse zygotes and two-cell embryos. In somatic cells ORC2 remains bound to DNA replication origins throughout the cell cycle, while MCM7 is one of the last proteins to bind to the licensing complex. We found that MCM7 but not ORC2 was bound to DNA in metaphase II oocytes and remained associated with the DNA until S-phase. Shortly after fertilization, ORC2 was detectable at the metaphase II spindle poles and then between the separating chromosomes. Neither protein was present in the sperm cell at fertilization. As the sperm head decondensed, MCM7 was bound to DNA, but no ORC2 was seen. By 4 h after fertilization, both pronuclei contained DNA bound ORC2 and MCM7. As expected, during S-phase of the first zygotic cell cycle, MCM7 was released from the DNA, but ORC2 remained bound. During zygotic mitosis, ORC2 again localized first to the spindle poles, then to the area between the separating chromosomes. ORC2 then formed a ring around the developing two-cell nuclei before entering the nucleus. Only soluble MCM7 was present in the G2 pronuclei, but by zygotic metaphase it was bound to DNA, again apparently before ORC2. In G1 of the two-cell stage, both nuclei had salt-resistant ORC2 and MCM7. These data suggest that licensing follows a unique pattern in the early zygote that differs from what has been described for other mammalian cells that have been studied.
Collapse
Affiliation(s)
- Michael A Ortega
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry & Physiology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
| | | | | | | |
Collapse
|
34
|
Uno S, You Z, Masai H. Purification of replication factors using insect and mammalian cell expression systems. Methods 2012; 57:214-21. [PMID: 22800621 DOI: 10.1016/j.ymeth.2012.06.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/12/2012] [Accepted: 06/25/2012] [Indexed: 10/28/2022] Open
Abstract
Purification of factors for DNA replication in an amount sufficient for detailed biochemical characterization is essential to elucidating its mechanisms. Insect cell expression systems are commonly used for purification of the factors proven to be difficult to deal with in bacteria. We describe first the detailed protocols for purification of mammalian Mcm complexes including the Mcm2/3/4/5/6/7 heterohexamer expressed in insect cells. We then describe a convenient and economical system in which large-sized proteins and multi-factor complexes can be transiently overexpressed in human 293T cells and be rapidly purified in a large quantity. We describe various expression vectors and detailed methods for transfection and purification of various replication factors which have been difficult to obtain in a sufficient amount in other systems. Availability of efficient methods to overproduce and purify the proteins that have been challenging would facilitate the enzymatic analyses of the processes of DNA replication.
Collapse
Affiliation(s)
- Shuji Uno
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | | | | |
Collapse
|
35
|
Sun J, Kawakami H, Zech J, Speck C, Stillman B, Li H. Cdc6-induced conformational changes in ORC bound to origin DNA revealed by cryo-electron microscopy. Structure 2012; 20:534-44. [PMID: 22405012 DOI: 10.1016/j.str.2012.01.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 01/16/2012] [Accepted: 01/17/2012] [Indexed: 01/21/2023]
Abstract
The eukaryotic origin recognition complex (ORC) interacts with and remodels origins of DNA replication prior to initiation in S phase. Here, we report a single-particle cryo-EM-derived structure of the supramolecular assembly comprising Saccharomyces cerevisiae ORC, the replication initiation factor Cdc6, and double-stranded ARS1 origin DNA in the presence of ATPγS. The six subunits of ORC are arranged as Orc1:Orc4:Orc5:Orc2:Orc3, with Orc6 binding to Orc2. Cdc6 binding changes the conformation of ORC, in particular reorienting the Orc1 N-terminal BAH domain. Segmentation of the 3D map of ORC-Cdc6 on DNA and docking with the crystal structure of the homologous archaeal Orc1/Cdc6 protein suggest an origin DNA binding model in which the DNA tracks along the interior surface of the crescent-like ORC. Thus, ORC bends and wraps the DNA. This model is consistent with the observation that binding of a single Cdc6 extends the ORC footprint on origin DNA from both ends.
Collapse
Affiliation(s)
- Jingchuan Sun
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | | | | | | | | |
Collapse
|
36
|
Dynamic association of ORCA with prereplicative complex components regulates DNA replication initiation. Mol Cell Biol 2012; 32:3107-20. [PMID: 22645314 DOI: 10.1128/mcb.00362-12] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In eukaryotes, initiation of DNA replication requires the assembly of a multiprotein prereplicative complex (pre-RC) at the origins. We recently reported that a WD repeat-containing protein, origin recognition complex (ORC)-associated (ORCA/LRWD1), plays a crucial role in stabilizing ORC to chromatin. Here, we find that ORCA is required for the G(1)-to-S-phase transition in human cells. In addition to binding to ORC, ORCA associates with Cdt1 and its inhibitor, geminin. Single-molecule pulldown experiments demonstrate that each molecule of ORCA can bind to one molecule of ORC, one molecule of Cdt1, and two molecules of geminin. Further, ORCA directly interacts with the N terminus of Orc2, and the stability of ORCA is dependent on its association with Orc2. ORCA associates with Orc2 throughout the cell cycle, with Cdt1 during mitosis and G(1), and with geminin in post-G(1) cells. Overexpression of geminin results in the loss of interaction between ORCA and Cdt1, suggesting that increased levels of geminin in post-G(1) cells titrate Cdt1 away from ORCA. We propose that the dynamic association of ORCA with pre-RC components modulates the assembly of its interacting partners on chromatin and facilitates DNA replication initiation.
Collapse
|
37
|
Lee KY, Bang SW, Yoon SW, Lee SH, Yoon JB, Hwang DS. Phosphorylation of ORC2 protein dissociates origin recognition complex from chromatin and replication origins. J Biol Chem 2012; 287:11891-8. [PMID: 22334659 DOI: 10.1074/jbc.m111.338467] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
During the late M to the G(1) phase of the cell cycle, the origin recognition complex (ORC) binds to the replication origin, leading to the assembly of the prereplicative complex for subsequent initiation of eukaryotic chromosome replication. We found that the cell cycle-dependent phosphorylation of human ORC2, one of the six subunits of ORC, dissociates ORC2, -3, -4, and -5 (ORC2-5) subunits from chromatin and replication origins. Phosphorylation at Thr-116 and Thr-226 of ORC2 occurs by cyclin-dependent kinase during the S phase and is maintained until the M phase. Phosphorylation of ORC2 at Thr-116 and Thr-226 dissociated the ORC2-5 from chromatin. Consistent with this, the phosphomimetic ORC2 protein exhibited defective binding to replication origins as well as to chromatin, whereas the phosphodefective protein persisted in binding throughout the cell cycle. These results suggest that the phosphorylation of ORC2 dissociates ORC from chromatin and replication origins and inhibits binding of ORC to newly replicated DNA.
Collapse
Affiliation(s)
- Kyung Yong Lee
- Department of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | | | | | | | | | | |
Collapse
|
38
|
Abstract
The origin recognition complex (ORC) was first discovered in the baker's yeast in 1992. Identification of ORC opened up a path for subsequent molecular level investigations on how eukaryotic cells initiate and control genome duplication each cell cycle. Twenty years after the first biochemical isolation, ORC is now taking on a three-dimensional shape, although a very blurry shape at the moment, thanks to the recent electron microscopy and image reconstruction efforts. In this chapter, we outline the current biochemical knowledge about ORC from several eukaryotic systems, with emphasis on the most recent structural and biochemical studies. Despite many species-specific properties, an emerging consensus is that ORC is an ATP-dependent machine that recruits other key proteins to form pre-replicative complexes (pre-RCs) at many origins of DNA replication, enabling the subsequent initiation of DNA replication in S phase.
Collapse
Affiliation(s)
- Huilin Li
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA, And, Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA, , Tel: 631-344-2931, Fax: 631-344-3407
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, , Tel: 516-367-8383
| |
Collapse
|
39
|
Kong BW, Lee JY, Bottje WG, Lassiter K, Lee J, Foster DN. Genome-wide differential gene expression in immortalized DF-1 chicken embryo fibroblast cell line. BMC Genomics 2011; 12:571. [PMID: 22111699 PMCID: PMC3258366 DOI: 10.1186/1471-2164-12-571] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 11/23/2011] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND When compared to primary chicken embryo fibroblast (CEF) cells, the immortal DF-1 CEF line exhibits enhanced growth rates and susceptibility to oxidative stress. Although genes responsible for cell cycle regulation and antioxidant functions have been identified, the genome-wide transcription profile of immortal DF-1 CEF cells has not been previously reported. Global gene expression in primary CEF and DF-1 cells was performed using a 4X44K chicken oligo microarray. RESULTS A total of 3876 differentially expressed genes were identified with a 2 fold level cutoff that included 1706 up-regulated and 2170 down-regulated genes in DF-1 cells. Network and functional analyses using Ingenuity Pathways Analysis (IPA, Ingenuity® Systems, http://www.ingenuity.com) revealed that 902 of 3876 differentially expressed genes were classified into a number of functional groups including cellular growth and proliferation, cell cycle, cellular movement, cancer, genetic disorders, and cell death. Also, the top 5 gene networks with intermolecular connections were identified. Bioinformatic analyses suggested that DF-1 cells were characterized by enhanced molecular mechanisms for cell cycle progression and proliferation, suppressing cell death pathways, altered cellular morphogenesis, and accelerated capacity for molecule transport. Key molecules for these functions include E2F1, BRCA1, SRC, CASP3, and the peroxidases. CONCLUSIONS The global gene expression profiles provide insight into the cellular mechanisms that regulate the unique characteristics observed in immortal DF-1 CEF cells.
Collapse
Affiliation(s)
- Byung-Whi Kong
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | | | | | | | | | | |
Collapse
|
40
|
Thomae AW, Baltin J, Pich D, Deutsch MJ, Ravasz M, Zeller K, Gossen M, Hammerschmidt W, Schepers A. Different roles of the human Orc6 protein in the replication initiation process. Cell Mol Life Sci 2011; 68:3741-56. [PMID: 21461783 PMCID: PMC11114885 DOI: 10.1007/s00018-011-0675-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 02/25/2011] [Accepted: 03/17/2011] [Indexed: 01/05/2023]
Abstract
In eukaryotes, binding of the six-subunit origin recognition complex (ORC) to DNA provides an interactive platform for the sequential assembly of pre-replicative complexes. This process licenses replication origins competent for the subsequent initiation step. Here, we analyze the contribution of human Orc6, the smallest subunit of ORC, to DNA binding and pre-replicative complex formation. We show that Orc6 not only interacts with Orc1-Orc5 but also with the initiation factor Cdc6. Biochemical and imaging experiments reveal that this interaction is required for licensing DNA replication competent. Furthermore, we demonstrate that Orc6 contributes to the interaction of ORC with the chaperone protein HMGA1a (high mobility group protein A1a). Binding of human ORC to replication origins is not specified at the level of DNA sequence and the functional organization of origins is poorly understood. We have identified HMGA1a as one factor that might direct ORC to AT-rich heterochromatic regions. The systematic analysis of the interaction between ORC and HMGA1a revealed that Orc6 interacts with the acidic C-terminus of HMGA1a and also with its AT-hooks. Both domains support autonomous replication if targeted to DNA templates. As such, Orc6 functions at different stages of the replication initiation process. Orc6 can interact with ORC chaperone proteins such as HMGA1a to facilitate chromatin binding of ORC and is also an essential factor for pre-RC formation.
Collapse
Affiliation(s)
- Andreas W. Thomae
- Department of Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistr. 25, 81377 Munich, Germany
- Adolf-Butenandt-Institut, Ludwig-Maximilians-University, Schillerstraße 44, 80336 Munich, Germany
| | - Jens Baltin
- Department of Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistr. 25, 81377 Munich, Germany
| | - Dagmar Pich
- Department of Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistr. 25, 81377 Munich, Germany
| | - Manuel J. Deutsch
- Department of Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistr. 25, 81377 Munich, Germany
| | - Máté Ravasz
- Department of Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistr. 25, 81377 Munich, Germany
| | - Krisztina Zeller
- Department of Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistr. 25, 81377 Munich, Germany
| | - Manfred Gossen
- Berlin-Brandenburg Center for Regenerative Therapies, Charité, BCRT, Campus Virchow-Klinikum, Föhrer Straße 15, 13353 Berlin, Germany
| | - Wolfgang Hammerschmidt
- Department of Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistr. 25, 81377 Munich, Germany
| | - Aloys Schepers
- Department of Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistr. 25, 81377 Munich, Germany
| |
Collapse
|
41
|
Sharma A, Kar A, Kaur M, Ranade SM, Sankaran A, Misra S, Rawat K, Saxena S. Specific replication factors are targeted by different genotoxic agents to inhibit replication. IUBMB Life 2011; 62:764-75. [PMID: 20945455 DOI: 10.1002/iub.380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
When mammalian cells experience DNA damaging stress, they block DNA replication to avoid erroneous replication of the damaged template. The cells that are unable to respond to DNA damage continue faulty DNA replication that results in incorporation of genomic lesions. To understand the regulation of replication machinery during stress, systemic studies have been carried out but they have been restricted to the evaluation of the mRNA levels and therefore have not been able to identify post-transcriptional changes, vital for immediate blocking of the progressing DNA replication. We have recently discovered that an essential replication factor is downregulated by radiation stress. In this study, we have carried out a systematic evaluation of protein levels of entire replication apparatus after different types of DNA damage. We report that, independent of the status of p53 and retinoblastoma protein, mammalian cells choose targets that are essential for prereplication, preinitiation, and elongation phases of replication. We imposed different kinds of stress to discern whether similar or unique responses are invoked, and we propose a model for inhibition of replication machinery in which mammalian cells target specific essential replication factors based on the experienced stress.
Collapse
Affiliation(s)
- Aparna Sharma
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Ghosh S, Vassilev AP, Zhang J, Zhao Y, DePamphilis ML. Assembly of the human origin recognition complex occurs through independent nuclear localization of its components. J Biol Chem 2011; 286:23831-41. [PMID: 21555516 DOI: 10.1074/jbc.m110.215988] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Initiation of eukaryotic genome duplication begins when a six-subunit origin recognition complex (ORC) binds to DNA. However, the mechanism by which this occurs in vivo and the roles played by individual subunits appear to differ significantly among organisms. Previous studies identified a soluble human ORC(2-5) complex in the nucleus, an ORC(1-5) complex bound to chromatin, and an Orc6 protein that binds weakly, if at all, to other ORC subunits. Here we show that stable ORC(1-6) complexes also can be purified from human cell extracts and that Orc6 and Orc1 each contain a single nuclear localization signal that is essential for nuclear localization but not for ORC assembly. The Orc6 nuclear localization signal, which is essential for Orc6 function, is facilitated by phosphorylation at its cyclin-dependent kinase consensus site and by association with Kpna6/1, nuclear transport proteins that did not co-purify with other ORC subunits. These and other results support a model in which Orc6, Orc1, and ORC(2-5) are transported independently to the nucleus where they can either assemble into ORC(1-6) or function individually.
Collapse
Affiliation(s)
- Soma Ghosh
- NICHD, National Institutes of Health, Bethesda, Maryland 20892-2753, USA
| | | | | | | | | |
Collapse
|
43
|
Structural analysis of human Orc6 protein reveals a homology with transcription factor TFIIB. Proc Natl Acad Sci U S A 2011; 108:7373-8. [PMID: 21502537 DOI: 10.1073/pnas.1013676108] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Origin Recognition Complex (ORC) is a six-subunit protein important for the initiation of DNA replication in eukaryotic cells. Orc6 is the smallest and the least conserved among ORC subunits. It is required for the DNA replication but also has a function in cytokinesis in metazoan species, however, the mechanisms of Orc6 action in these processes are not clear. Here we report a structure of the middle domain of human Orc6. This domain has an overall fold similar to the corresponding helical domain of transcription factor TFIIB. Based on these findings, a model of Orc6 binding to DNA is produced. We have identified amino acids of Orc6 which are directly involved in DNA binding. Alterations of these amino acids abolish DNA binding ability of Orc6 and also result in reduced levels of DNA replication in vitro and in cultured cells. Our data indicate that Orc6 is one of the DNA binding subunits of ORC in metazoan species. We propose that Orc6 may participate in positioning of ORC at the origins of DNA replication similar to the role of TFIIB in positioning transcription preinitiation complex at the promoter.
Collapse
|
44
|
Lubelsky Y, Sasaki T, Kuipers MA, Lucas I, Le Beau MM, Carignon S, Debatisse M, Prinz JA, Dennis JH, Gilbert DM. Pre-replication complex proteins assemble at regions of low nucleosome occupancy within the Chinese hamster dihydrofolate reductase initiation zone. Nucleic Acids Res 2010; 39:3141-55. [PMID: 21148149 PMCID: PMC3082903 DOI: 10.1093/nar/gkq1276] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genome-scale mapping of pre-replication complex proteins has not been reported in mammalian cells. Poor enrichment of these proteins at specific sites may be due to dispersed binding, poor epitope availability or cell cycle stage-specific binding. Here, we have mapped sites of biotin-tagged ORC and MCM protein binding in G1-synchronized populations of Chinese hamster cells harboring amplified copies of the dihydrofolate reductase (DHFR) locus, using avidin-affinity purification of biotinylated chromatin followed by high-density microarray analysis across the DHFR locus. We have identified several sites of significant enrichment for both complexes distributed throughout the previously identified initiation zone. Analysis of the frequency of initiations across stretched DNA fibers from the DHFR locus confirmed a broad zone of de-localized initiation activity surrounding the sites of ORC and MCM enrichment. Mapping positions of mononucleosomal DNA empirically and computing nucleosome-positioning information in silico revealed that ORC and MCM map to regions of low measured and predicted nucleosome occupancy. Our results demonstrate that specific sites of ORC and MCM enrichment can be detected within a mammalian intitiation zone, and suggest that initiation zones may be regions of generally low nucleosome occupancy where flexible nucleosome positioning permits flexible pre-RC assembly sites.
Collapse
Affiliation(s)
- Yoav Lubelsky
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Mendoza-Maldonado R, Paolinelli R, Galbiati L, Giadrossi S, Giacca M. Interaction of the retinoblastoma protein with Orc1 and its recruitment to human origins of DNA replication. PLoS One 2010; 5:e13720. [PMID: 21085491 PMCID: PMC2976706 DOI: 10.1371/journal.pone.0013720] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 10/05/2010] [Indexed: 02/02/2023] Open
Abstract
Background The retinoblastoma protein (Rb) is a crucial regulator of cell cycle progression by binding with E2F transcription factor and repressing the expression of a variety of genes required for the G1-S phase transition. Methodology/Principal Findings Here we show that Rb and E2F1 directly participate in the control of initiation of DNA replication in human HeLa, U2OS and T98G cells by specifically binding to origins of DNA replication in a cell cycle regulated manner. We show that, both in vitro and inside the cells, the largest subunit of the origin recognition complex (Orc1) specifically binds hypo-phosphorylated Rb and that this interaction is competitive with the binding of Rb to E2F1. The displacement of Rb-bound Orc1 by E2F1 at origins of DNA replication marks the progression of the G1 phase of the cell cycle toward the G1-S border. Conclusions/Significance The participation of Rb and E2F1 in the formation of the multiprotein complex that binds origins of DNA replication in mammalian cells appears to represent an effective mechanism to couple the expression of genes required for cell cycle progression to the activation of DNA replication.
Collapse
Affiliation(s)
- Ramiro Mendoza-Maldonado
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | | | - Laura Galbiati
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Sara Giadrossi
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Mauro Giacca
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- Department of Biomedicine, University of Trieste, Faculty of Medicine, Trieste, Italy
- * E-mail:
| |
Collapse
|
46
|
Álamo MMD, Sánchez-Gorostiaga A, Serrano AM, Prieto A, Cuéllar J, Martín-Benito J, Valpuesta JM, Giraldo R. Structural analysis of the interactions between hsp70 chaperones and the yeast DNA replication protein Orc4p. J Mol Biol 2010; 403:24-39. [PMID: 20732327 DOI: 10.1016/j.jmb.2010.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 07/29/2010] [Accepted: 08/11/2010] [Indexed: 12/11/2022]
Abstract
Hsp70 chaperones, besides their role in assisting protein folding, are key modulators of protein disaggregation, being consistently found as components of most macromolecular assemblies isolated in proteome-wide affinity purifications. A wealth of structural information has been recently acquired on Hsp70s complexed with Hsp40 and NEF co-factors and with small hydrophobic target peptides. However, knowledge of how Hsp70s recognize large protein substrates is still limited. Earlier, we reported that homologue Hsp70 chaperones (DnaK in Escherichia coli and Ssa1-4p/Ssb1-2p in Saccharomyces cerevisiae) bind strongly, both in vitro and in vivo, to the AAA+ domain in the Orc4p subunit of yeast origin recognition complex (ORC). ScORC is the paradigm for eukaryotic DNA replication initiators and consists of six distinct protein subunits (ScOrc1p-ScOrc 6p). Here, we report that a hydrophobic sequence (IL(4)) in the initiator specific motif (ISM) in Orc4p is the main target for DnaK/Hsp70. The three-dimensional electron microscopy reconstruction of a stable Orc4p(2)-DnaK complex suggests that the C-terminal substrate-binding domain in the chaperone clamps the AAA+ IL(4) motif in one Orc4p molecule, with the substrate-binding domain lid subdomain wedging apart the other Orc4p subunit. Pairwise co-expression in E. coli shows that Orc4p interacts with Orc1/2/5p. Mutation of IL(4) selectively disrupts Orc4p interaction with Orc2p. Allelic substitution of ORC4 by mutants in each residue of IL(4) results in lethal (I184A) or thermosensitive (L185A and L186A) initiation-defective phenotypes in vivo. The interplay between Hsp70 chaperones and the Orc4p-IL(4) motif might have an adaptor role in the sequential, stoichiometric assembly of ScORC subunits.
Collapse
Affiliation(s)
- María Moreno-Del Álamo
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas - CSIC, C/ Ramiro de Maeztu, 9, E-28040 Madrid, Spain
| | - Alicia Sánchez-Gorostiaga
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas - CSIC, C/ Ramiro de Maeztu, 9, E-28040 Madrid, Spain
| | - Ana M Serrano
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas - CSIC, C/ Ramiro de Maeztu, 9, E-28040 Madrid, Spain
| | - Alicia Prieto
- Department of Environmental Biology, Centro de Investigaciones Biológicas - CSIC, C/ Ramiro de Maeztu, 9, E-28040 Madrid, Spain
| | - Jorge Cuéllar
- Department of Macromolecular Structures, Centro Nacional de Biotecnología - CSIC, C/ Darwin, 3, E-28049 Madrid, Spain
| | - Jaime Martín-Benito
- Department of Macromolecular Structures, Centro Nacional de Biotecnología - CSIC, C/ Darwin, 3, E-28049 Madrid, Spain
| | - José M Valpuesta
- Department of Macromolecular Structures, Centro Nacional de Biotecnología - CSIC, C/ Darwin, 3, E-28049 Madrid, Spain
| | - Rafael Giraldo
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas - CSIC, C/ Ramiro de Maeztu, 9, E-28040 Madrid, Spain.
| |
Collapse
|
47
|
Human origin recognition complex is essential for HP1 binding to chromatin and heterochromatin organization. Proc Natl Acad Sci U S A 2010; 107:15093-8. [PMID: 20689044 DOI: 10.1073/pnas.1009945107] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The origin recognition complex (ORC) is a DNA replication initiator protein also known to be involved in diverse cellular functions including gene silencing, sister chromatid cohesion, telomere biology, heterochromatin localization, centromere and centrosome activity, and cytokinesis. We show that, in human cells, multiple ORC subunits associate with hetereochromatin protein 1 (HP1) alpha- and HP1beta-containing heterochromatic foci. Fluorescent bleaching studies indicate that multiple subcomplexes of ORC exist at heterochromatin, with Orc1 stably associating with heterochromatin in G1 phase, whereas other ORC subunits have transient interactions throughout the cell-division cycle. Both Orc1 and Orc3 directly bind to HP1alpha, and two domains of Orc3, a coiled-coil domain and a mod-interacting region domain, can independently bind to HP1alpha; however, both are essential for in vivo localization of Orc3 to heterochromatic foci. Direct binding of both Orc1 and Orc3 to HP1 suggests that, after the degradation of Orc1 at the G1/S boundary, Orc3 facilitates assembly of ORC/HP1 proteins to chromatin. Although depletion of Orc2 and Orc3 subunits by siRNA caused loss of HP1alpha association to heterochromatin, loss of Orc1 and Orc5 caused aberrant HP1alpha distribution only to pericentric heterochromatin-surrounding nucleoli. Depletion of HP1alpha from human cells also shows loss of Orc2 binding to heterochromatin, suggesting that ORC and HP1 proteins are mutually required for each other to bind to heterochromatin. Similar to HP1alpha-depleted cells, Orc2 and Orc3 siRNA-treated cells also show loss of compaction at satellite repeats, suggesting that ORC together with HP1 proteins may be involved in organizing higher-order chromatin structure and centromere function.
Collapse
|
48
|
Abstract
The origin recognition complex (ORC) is a 6-subunit complex required for the initiation of DNA replication in eukaryotic organisms. ORC is also involved in other cell functions. The smallest Drosophila ORC subunit, Orc6, is important for both DNA replication and cytokinesis. To study the role of Orc6 in vivo, the orc6 gene was deleted by imprecise excision of P element. Lethal alleles of orc6 are defective in DNA replication and also show abnormal chromosome condensation and segregation. The analysis of cells containing the orc6 deletion revealed that they arrest in both the G(1) and mitotic stages of the cell cycle. Orc6 deletion can be rescued to viability by a full-length Orc6 transgene. The expression of mutant transgenes of Orc6 with deleted or mutated C-terminal domain results in a release of mutant cells from G(1) arrest and restoration of DNA replication, indicating that the DNA replication function of Orc6 is associated with its N-terminal domain. However, these mutant cells accumulate at mitosis, suggesting that the C-terminal domain of Orc6 is important for the passage through the M phase. In a cross-species complementation experiment, the expression of human Orc6 in Drosophila Orc6 mutant cells rescued DNA replication, suggesting that this function of the protein is conserved among metazoans.
Collapse
|
49
|
Gautier VW, Gu L, O'Donoghue N, Pennington S, Sheehy N, Hall WW. In vitro nuclear interactome of the HIV-1 Tat protein. Retrovirology 2009; 6:47. [PMID: 19454010 PMCID: PMC2702331 DOI: 10.1186/1742-4690-6-47] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 05/19/2009] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND One facet of the complexity underlying the biology of HIV-1 resides not only in its limited number of viral proteins, but in the extensive repertoire of cellular proteins they interact with and their higher-order assembly. HIV-1 encodes the regulatory protein Tat (86-101aa), which is essential for HIV-1 replication and primarily orchestrates HIV-1 provirus transcriptional regulation. Previous studies have demonstrated that Tat function is highly dependent on specific interactions with a range of cellular proteins. However they can only partially account for the intricate molecular mechanisms underlying the dynamics of proviral gene expression. To obtain a comprehensive nuclear interaction map of Tat in T-cells, we have designed a proteomic strategy based on affinity chromatography coupled with mass spectrometry. RESULTS Our approach resulted in the identification of a total of 183 candidates as Tat nuclear partners, 90% of which have not been previously characterised. Subsequently we applied in silico analysis, to validate and characterise our dataset which revealed that the Tat nuclear interactome exhibits unique signature(s). First, motif composition analysis highlighted that our dataset is enriched for domains mediating protein, RNA and DNA interactions, and helicase and ATPase activities. Secondly, functional classification and network reconstruction clearly depicted Tat as a polyvalent protein adaptor and positioned Tat at the nexus of a densely interconnected interaction network involved in a range of biological processes which included gene expression regulation, RNA biogenesis, chromatin structure, chromosome organisation, DNA replication and nuclear architecture. CONCLUSION We have completed the in vitro Tat nuclear interactome and have highlighted its modular network properties and particularly those involved in the coordination of gene expression by Tat. Ultimately, the highly specialised set of molecular interactions identified will provide a framework to further advance our understanding of the mechanisms of HIV-1 proviral gene silencing and activation.
Collapse
Affiliation(s)
- Virginie W Gautier
- UCD-Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin (UCD), Belfield, Dublin 4, Ireland.
| | | | | | | | | | | |
Collapse
|
50
|
Kato JI. Regulatory Network of the Initiation of Chromosomal Replication inEscherichia coli. Crit Rev Biochem Mol Biol 2008; 40:331-42. [PMID: 16338685 DOI: 10.1080/10409230500366090] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The bacterial chromosome is replicated once during the division cycle, a process ensured by the tight regulation of initiation at oriC. In prokaryotes, the initiator protein DnaA plays an essential role at the initiation step, and feedback control is critical in regulating initiation. Three systems have been identified that exert feedback control in Escherichia coli, all of which are necessary for tight strict regulation of the initiation step. In particular, the ATP-dependent control of DnaA activity is essential. A missing link in initiator activity regulation has been identified, facilitating analysis of the reaction mechanism. Furthermore, key components of this regulatory network have also been described. Because the eukaryotic initiator complex, ORC, is also regulated by ATP, the bacterial system provides an important model for understanding initiation in eukaryotes. This review summarizes recent studies on the regulation of initiator activity.
Collapse
Affiliation(s)
- Jun-ichi Kato
- Department of Biology, Graduate School of Science, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo, Japan
| |
Collapse
|