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Acharya A, Bret H, Huang JW, Mütze M, Göse M, Kissling VM, Seidel R, Ciccia A, Guérois R, Cejka P. Mechanism of DNA unwinding by MCM8-9 in complex with HROB. Nat Commun 2024; 15:3584. [PMID: 38678026 PMCID: PMC11055865 DOI: 10.1038/s41467-024-47936-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 04/15/2024] [Indexed: 04/29/2024] Open
Abstract
HROB promotes the MCM8-9 helicase in DNA damage response. To understand how HROB activates MCM8-9, we defined their interaction interface. We showed that HROB makes important yet transient contacts with both MCM8 and MCM9, and binds the MCM8-9 heterodimer with the highest affinity. MCM8-9-HROB prefer branched DNA structures, and display low DNA unwinding processivity. MCM8-9 unwinds DNA as a hexamer that assembles from dimers on DNA in the presence of ATP. The hexamer involves two repeating protein-protein interfaces between the alternating MCM8 and MCM9 subunits. One of these interfaces is quite stable and forms an obligate heterodimer across which HROB binds. The other interface is labile and mediates hexamer assembly, independently of HROB. The ATPase site formed at the labile interface contributes disproportionally more to DNA unwinding than that at the stable interface. Here, we show that HROB promotes DNA unwinding downstream of MCM8-9 loading and ring formation on ssDNA.
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Affiliation(s)
- Ananya Acharya
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, 6500, Switzerland
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, 8093, Switzerland
| | - Hélène Bret
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jen-Wei Huang
- Department of Genetics and Development, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Martin Mütze
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, 04103, Germany
| | - Martin Göse
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, 04103, Germany
| | - Vera Maria Kissling
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, 8093, Switzerland
- Particles-Biology Interactions Laboratory, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), St. Gallen, 9014, Switzerland
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, 04103, Germany
| | - Alberto Ciccia
- Department of Genetics and Development, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Raphaël Guérois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, 6500, Switzerland.
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, 8093, Switzerland.
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2
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McKinzey DR, Li C, Gao Y, Trakselis MA. Activity, substrate preference and structure of the HsMCM8/9 helicase. Nucleic Acids Res 2023; 51:7330-7341. [PMID: 37309874 PMCID: PMC10415141 DOI: 10.1093/nar/gkad508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 06/14/2023] Open
Abstract
The minichromosomal maintenance proteins, MCM8 and MCM9, are more recent evolutionary additions to the MCM family, only cooccurring in selected higher eukaryotes. Mutations in these genes are directly linked to ovarian insufficiency, infertility, and several cancers. MCM8/9 appears to have ancillary roles in fork progression and recombination of broken replication forks. However, the biochemical activity, specificities and structures have not been adequately illustrated, making mechanistic determination difficult. Here, we show that human MCM8/9 (HsMCM8/9) is an ATP dependent DNA helicase that unwinds fork DNA substrates with a 3'-5' polarity. High affinity ssDNA binding occurs in the presence of nucleoside triphosphates, while ATP hydrolysis weakens the interaction with DNA. The cryo-EM structure of the HsMCM8/9 heterohexamer was solved at 4.3 Å revealing a trimer of heterodimer configuration with two types of interfacial AAA+ nucleotide binding sites that become more organized upon binding ADP. Local refinements of the N or C-terminal domains (NTD or CTD) improved the resolution to 3.9 or 4.1 Å, respectively, and shows a large displacement in the CTD. Changes in AAA+ CTD upon nucleotide binding and a large swing between the NTD and CTD likely implies that MCM8/9 utilizes a sequential subunit translocation mechanism for DNA unwinding.
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Affiliation(s)
- David R McKinzey
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA
| | - Chuxuan Li
- Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Yang Gao
- Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA
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3
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Acharya A, Bret H, Huang JW, Mütze M, Göse M, Kissling V, Seidel R, Ciccia A, Guérois R, Cejka P. Mechanism of DNA unwinding by hexameric MCM8-9 in complex with HROB. RESEARCH SQUARE 2023:rs.3.rs-3054483. [PMID: 37461676 PMCID: PMC10350107 DOI: 10.21203/rs.3.rs-3054483/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
The human MCM8-9 helicase functions in concert with HROB in the context of homologous recombination, but its precise function is unknown. To gain insights into how HROB regulates MCM8-9, we first used molecular modeling and biochemistry to define their interaction interface. We show that HROB makes important contacts with both MCM8 and MCM9 subunits, which directly promotes its DNA-dependent ATPase and helicase activities. MCM8-9-HROB preferentially binds and unwinds branched DNA structures, and single-molecule experiments reveal a low DNA unwinding processivity. MCM8-9 unwinds DNA as a hexameric complex that assembles from dimers on DNA in the presence of ATP, which is prerequisite for its helicase function. The hexamer formation thus involves two repeating protein-protein interfaces forming between the alternating MCM8 and MCM9 subunits. One of these interfaces is rather stable and forms an obligate heterodimer, while the other interface is labile and mediates the assembly of the hexamer on DNA, independently of HROB. The ATPase site composed of the subunits forming the labile interface disproportionally contributes to DNA unwinding. HROB does not affect the MCM8-9 ring formation, but promotes DNA unwinding downstream by possibly coordinating ATP hydrolysis with structural transitions accompanying translocation of MCM8-9 on DNA.
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Affiliation(s)
- Ananya Acharya
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, 6500, Switzerland
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, 8093, Switzerland
| | - Hélène Bret
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l’Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, 91190, France
| | - Jen-Wei Huang
- Department of Genetics and Development, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Martin Mütze
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, 04103, Germany
| | - Martin Göse
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, 04103, Germany
| | - Vera Kissling
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, 8093, Switzerland
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, 04103, Germany
| | - Alberto Ciccia
- Department of Genetics and Development, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Raphaël Guérois
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l’Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, 91190, France
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, 6500, Switzerland
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, 8093, Switzerland
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4
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Acharya A, Bret H, Huang JW, Mütze M, Göse M, Kissling V, Seidel R, Ciccia A, Guérois R, Cejka P. Mechanism of DNA unwinding by hexameric MCM8-9 in complex with HROB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544631. [PMID: 37398313 PMCID: PMC10312610 DOI: 10.1101/2023.06.12.544631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The human MCM8-9 helicase functions in concert with HROB in the context of homologous recombination, but its precise function is unknown. To gain insights into how HROB regulates MCM8-9, we first used molecular modeling and biochemistry to define their interaction interface. We show that HROB makes important contacts with both MCM8 and MCM9 subunits, which directly promotes its DNA-dependent ATPase and helicase activities. MCM8-9-HROB preferentially binds and unwinds branched DNA structures, and single-molecule experiments reveal a low DNA unwinding processivity. MCM8-9 unwinds DNA as a hexameric complex that assembles from dimers on DNA in the presence of ATP, which is prerequisite for its helicase function. The hexamer formation thus involves two repeating protein-protein interfaces forming between the alternating MCM8 and MCM9 subunits. One of these interfaces is rather stable and forms an obligate heterodimer, while the other interface is labile and mediates the assembly of the hexamer on DNA, independently of HROB. The ATPase site composed of the subunits forming the labile interface disproportionally contributes to DNA unwinding. HROB does not affect the MCM8-9 ring formation, but promotes DNA unwinding downstream by possibly coordinating ATP hydrolysis with structural transitions accompanying translocation of MCM8-9 on DNA.
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5
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Emmenecker C, Mézard C, Kumar R. Repair of DNA double-strand breaks in plant meiosis: role of eukaryotic RecA recombinases and their modulators. PLANT REPRODUCTION 2023; 36:17-41. [PMID: 35641832 DOI: 10.1007/s00497-022-00443-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Homologous recombination during meiosis is crucial for the DNA double-strand breaks (DSBs) repair that promotes the balanced segregation of homologous chromosomes and enhances genetic variation. In most eukaryotes, two recombinases RAD51 and DMC1 form nucleoprotein filaments on single-stranded DNA generated at DSB sites and play a central role in the meiotic DSB repair and genome stability. These nucleoprotein filaments perform homology search and DNA strand exchange to initiate repair using homologous template-directed sequences located elsewhere in the genome. Multiple factors can regulate the assembly, stability, and disassembly of RAD51 and DMC1 nucleoprotein filaments. In this review, we summarize the current understanding of the meiotic functions of RAD51 and DMC1 and the role of their positive and negative modulators. We discuss the current models and regulators of homology searches and strand exchange conserved during plant meiosis. Manipulation of these repair factors during plant meiosis also holds a great potential to accelerate plant breeding for crop improvements and productivity.
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Affiliation(s)
- Côme Emmenecker
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
- University of Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Christine Mézard
- Institut Jean-Pierre Bourgin (IJPB), CNRS, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France.
| | - Rajeev Kumar
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France.
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6
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Yuan J, Lan H, Huang D, Guo X, Liu C, Liu S, Zhang P, Cheng Y, Xiao S. Multi-Omics Analysis of MCM2 as a Promising Biomarker in Pan-Cancer. Front Cell Dev Biol 2022; 10:852135. [PMID: 35693940 PMCID: PMC9174984 DOI: 10.3389/fcell.2022.852135] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/29/2022] [Indexed: 11/30/2022] Open
Abstract
Minichromosome maintenance 2 (MCM2) is a member of the minichromosomal maintenance family of proteins that mainly regulates DNA replication and the cell cycle and is involved in regulating cancer cell proliferation in various cancers. Previous studies have reported that MCM2 plays a pivotal role in cell proliferation and cancer development. However, few articles have systematically reported the pathogenic roles of MCM2 across cancers. Therefore, the present pan-cancer study was conducted. Various computational tools were used to investigate the MCM2 expression level, genetic mutation rate, and regulating mechanism, immune infiltration, tumor diagnosis and prognosis, therapeutic response and drug sensitivity of various cancers. The expression and function of MCM2 were examined by Western blotting and CCK-8 assays. MCM2 was significantly upregulated in almost all cancers and cancer subtypes in The Cancer Genome Atlas and was closely associated with tumor mutation burden, tumor stage, and immune therapy response. Upregulation of MCM2 expression may be correlated with a high level of alterations rate. MCM2 expression was associated with the infiltration of various immune cells and molecules and markedly associated with a poor prognosis. Western blotting and CCK-8 assays revealed that MCM2 expression was significantly upregulated in melanoma cell lines. Our results also suggested that MCM2 promotes cell proliferation in vitro by activating cell proliferation pathways such as the Akt signaling pathways. This study explored the oncogenic role of MCM2 across cancers, provided data on the underlying mechanisms of these cancers for further research and demonstrated that MCM2 may be a promising target for cancer immunotherapy.
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Affiliation(s)
- Jing Yuan
- Department of Gynecology and Obstetrics, Third Xiangya Hospital, Central South University, Changsha, China
| | - Hua Lan
- Department of Gynecology and Obstetrics, Third Xiangya Hospital, Central South University, Changsha, China
| | - Dongqing Huang
- Department of Gynecology and Obstetrics, Third Xiangya Hospital, Central South University, Changsha, China
- Department of Gynecology, The Second Hospital of Zhuzhou, Zhuzhou, China
| | - Xiaohui Guo
- Department of Gynecology and Obstetrics, Third Xiangya Hospital, Central South University, Changsha, China
| | - Chu Liu
- Department of Gynecology and Obstetrics, Third Xiangya Hospital, Central South University, Changsha, China
| | - Shuping Liu
- Department of Rehabilitation, Changsha Central Hospital of University of South China, Changsha, China
| | - Peng Zhang
- Graduate Collaborative Training Base of the Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Yan Cheng
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yan Cheng, ; Songshu Xiao,
| | - Songshu Xiao
- Department of Gynecology and Obstetrics, Third Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yan Cheng, ; Songshu Xiao,
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7
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Lakhera S, Rana M, Devlal K, Celik I, Yadav R. A comprehensive exploration of pharmacological properties, bioactivities and inhibitory potentiality of luteolin from Tridax procumbens as anticancer drug by in-silico approach. Struct Chem 2022; 33:703-719. [PMID: 35106037 PMCID: PMC8795348 DOI: 10.1007/s11224-022-01882-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/13/2022] [Indexed: 11/25/2022]
Abstract
Tridax procumbens is a flowering plant of the Asteraceae family with a wide range of medicinal uses like anti-inflammatory, anti-diabetic, anti-microbial, immunomodulatory, etc. This study aimed to investigate the anti-cancerous activity of human lung cancer for targeting luteolin, a phytochemical of Tridax procumbens. The computational study has been done for studying the structural properties of luteolin. The drug-likeness of the molecule has been predicted by virtual screening of ADMET properties. The molecular docking technique of the in-silico method is performed to check the complex formation between protein and ligand. The reactivity and stability of the molecule are investigated with the help of molecular dynamics (MD) simulations. In the present work, we have tried to establish a strong candidature of any of the phytochemical of Tridax Procumbens as an inhibitor against human lung cancer.
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Affiliation(s)
- Shradha Lakhera
- Department of Physics, School of Sciences, Uttarakhand Open University, Haldwani, 263139 Uttarakhand India
| | - Meenakshi Rana
- Department of Physics, School of Sciences, Uttarakhand Open University, Haldwani, 263139 Uttarakhand India
| | - Kamal Devlal
- Department of Physics, School of Sciences, Uttarakhand Open University, Haldwani, 263139 Uttarakhand India
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, 38039 Turkey
| | - Rohitash Yadav
- All India Institute of Medical Sciences, Rishikesh, 249203 Uttarakhand India
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8
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Hoffman RA, MacAlpine HK, MacAlpine DM. Disruption of origin chromatin structure by helicase activation in the absence of DNA replication. Genes Dev 2021; 35:1339-1355. [PMID: 34556529 PMCID: PMC8494203 DOI: 10.1101/gad.348517.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022]
Abstract
Prior to initiation of DNA replication, the eukaryotic helicase, Mcm2-7, must be activated to unwind DNA at replication start sites in early S phase. To study helicase activation within origin chromatin, we constructed a conditional mutant of the polymerase α subunit Cdc17 (or Pol1) to prevent priming and block replication. Recovery of these cells at permissive conditions resulted in the generation of unreplicated gaps at origins, likely due to helicase activation prior to replication initiation. We used micrococcal nuclease (MNase)-based chromatin occupancy profiling under restrictive conditions to study chromatin dynamics associated with helicase activation. Helicase activation in the absence of DNA replication resulted in the disruption and disorganization of chromatin, which extends up to 1 kb from early, efficient replication origins. The CMG holohelicase complex also moves the same distance out from the origin, producing single-stranded DNA that activates the intra-S-phase checkpoint. Loss of the checkpoint did not regulate the progression and stalling of the CMG complex but rather resulted in the disruption of chromatin at both early and late origins. Finally, we found that the local sequence context regulates helicase progression in the absence of DNA replication, suggesting that the helicase is intrinsically less processive when uncoupled from replication.
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Affiliation(s)
- Rachel A Hoffman
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Heather K MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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9
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The Alterations and Potential Roles of MCMs in Breast Cancer. JOURNAL OF ONCOLOGY 2021; 2021:7928937. [PMID: 34475953 PMCID: PMC8407980 DOI: 10.1155/2021/7928937] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/07/2021] [Accepted: 08/04/2021] [Indexed: 12/11/2022]
Abstract
The minichromosome maintenance (MCM) protein family plays a key role in eukaryotic DNA replication and has been confirmed to be associated with the occurrence and progression of many tumors. However, the expression levels, functions, and prognostic values of MCMs in breast cancer (BC) have not been clearly and systematically explained. In this article, we studied the transcriptional levels of MCMs in BC based on the Oncomine database. Kaplan-Meier plotter was used to analyze prognostic value of MCMs in human BC patients. Furthermore, we constructed a MCM coexpression gene network and performed functional annotation analysis through DAVID to reveal the functions of MCMs and coexpressed genes. The data showed that the expression of MCM2–8 and MCM10 but not MCM1 and MCM9 was upregulated in BC. Kaplan-Meier plotter analysis revealed that high transcriptional levels of MCM2, MCM4–7, and MCM10 were significantly related to low relapse-free survival (RFS) in BC patients. In contrast, high levels of MCM1 and MCM9 predicted high RFS for BC patients. This study suggests that MCM2, MCM4–7, and MCM10 possess great potential to be valuable prognostic biomarkers for BC and that MCM1 and MCM9 may serve as potential treatment targets for BC patients.
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Maya-Maldonado K, Cime-Castillo J, Maya-Lucas O, Argotte-Ramos R, Rodríguez MC, Lanz-Mendoza H. Transcriptome analysis uncover differential regulation in cell cycle, immunity, and metabolism in Anopheles albimanus during immune priming with Plasmodium berghei. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 120:104046. [PMID: 33600838 DOI: 10.1016/j.dci.2021.104046] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
In invertebrates, "immunological priming" is considered as the ability to acquire a protective (adaptive) immune response against a pathogen due to previous exposure to the same organism. To date, the mechanism by which this type of adaptive immune response originates in insects is not well understood. In the Anopheles albimanus - Plasmodium berghei model, a DNA synthesis that probably indicates an endoreplication process during priming induction has been evidenced. This work aimed to know the transcriptomic profile in the midguts of An. albimanus after priming induction. Our analysis indicates the participation of regulatory elements of the cell cycle in the immunological priming and points out the importance of the cell cycle regulation in the mosquito midgut.
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Affiliation(s)
- Krystal Maya-Maldonado
- Centro de Investigaciones sobre Enfermedades Infecciosas. Instituto Nacional de Salud Pública, Av. Universidad 655, CP. 62100, Cuernavaca, Morelos, Mexico
| | - Jorge Cime-Castillo
- Centro de Investigaciones sobre Enfermedades Infecciosas. Instituto Nacional de Salud Pública, Av. Universidad 655, CP. 62100, Cuernavaca, Morelos, Mexico
| | - Otoniel Maya-Lucas
- Novo Nordisk Foundation Center for Basic Metabolic Research. University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark
| | - Rocio Argotte-Ramos
- Centro de Investigaciones sobre Enfermedades Infecciosas. Instituto Nacional de Salud Pública, Av. Universidad 655, CP. 62100, Cuernavaca, Morelos, Mexico
| | - Maria Carmen Rodríguez
- Centro de Investigaciones sobre Enfermedades Infecciosas. Instituto Nacional de Salud Pública, Av. Universidad 655, CP. 62100, Cuernavaca, Morelos, Mexico
| | - Humberto Lanz-Mendoza
- Centro de Investigaciones sobre Enfermedades Infecciosas. Instituto Nacional de Salud Pública, Av. Universidad 655, CP. 62100, Cuernavaca, Morelos, Mexico.
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11
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Motifs of the C-terminal domain of MCM9 direct localization to sites of mitomycin-C damage for RAD51 recruitment. J Biol Chem 2021; 296:100355. [PMID: 33539926 PMCID: PMC7949153 DOI: 10.1016/j.jbc.2021.100355] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 01/28/2021] [Indexed: 11/20/2022] Open
Abstract
The MCM8/9 complex is implicated in aiding fork progression and facilitating homologous recombination (HR) in response to several DNA damage agents. MCM9 itself is an outlier within the MCM family containing a long C-terminal extension (CTE) comprising 42% of the total length, but with no known functional components and high predicted disorder. In this report, we identify and characterize two unique motifs within the primarily unstructured CTE that are required for localization of MCM8/9 to sites of mitomycin C (MMC)-induced DNA damage. First, an unconventional “bipartite-like” nuclear localization (NLS) motif consisting of two positively charged amino acid stretches separated by a long intervening sequence is required for the nuclear import of both MCM8 and MCM9. Second, a variant of the BRC motif (BRCv) similar to that found in other HR helicases is necessary for localization to sites of MMC damage. The MCM9-BRCv directly interacts with and recruits RAD51 downstream to MMC-induced damage to aid in DNA repair. Patient lymphocytes devoid of functional MCM9 and discrete MCM9 knockout cells have a significantly impaired ability to form RAD51 foci after MMC treatment. Therefore, the disordered CTE in MCM9 is functionally important in promoting MCM8/9 activity and in recruiting downstream interactors; thus, requiring full-length MCM9 for proper DNA repair.
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12
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Comparative genomic analysis reveals evolutionary and structural attributes of MCM gene family in Arabidopsis thaliana and Oryza sativa. J Biotechnol 2020; 327:117-132. [PMID: 33373625 DOI: 10.1016/j.jbiotec.2020.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/16/2020] [Accepted: 12/17/2020] [Indexed: 11/20/2022]
Abstract
The mini-chromosome maintenance (MCM) family, a large and functionally diverse protein family belonging to the AAA+ superfamily, is essential for DNA replication in all eukaryotic organisms. The MCM 2-7 form a hetero-hexameric complex which serves as licensing factor necessary to ensure the proper genomic DNA replication during the S phase of cell cycle. MCM 8-10 are also associated with the DNA replication process though their roles are particularly unclear. In this study, we report an extensive in silico analysis of MCM gene family (MCM 2-10) in Arabidopsis and rice. Comparative analysis of genomic distribution across eukaryotes revealed conservation of core MCMs 2-7 while MCMs 8-10 are absent in some taxa. Domain architecture analysis underlined MCM 2-10 subfamily specific features. Phylogenetic analyses clustered MCMs into 9 clades as per their subfamily. Duplication events are prominent in plant MCM family, however no duplications are observed in Arabidopsis and rice MCMs. Synteny analysis among Arabidopsis thaliana, Oryza sativa, Glycine max and Zea mays MCMs demonstrated orthologous relationships and duplication events. Further, estimation of synonymous and non-synonymous substitution rates illustrated evolution of MCM family under strong constraints. Expression profiling using available microarray data and qRT-PCR revealed differential expression under various stress conditions, hinting at their potential use to develop stress resilient crops. Homology modeling of Arabidopsis and rice MCM 2-7 and detailed comparison with yeast MCMs identified conservation of eukaryotic specific insertions and extensions as compared to archeal MCMs. Protein-protein interaction analysis revealed an extensive network of putative interacting partners mainly involved in DNA replication and repair. The present study provides novel insights into the MCM family in Arabidopsis and rice and identifies unique features, thus opening new perspectives for further targeted analyses.
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13
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MCM family in gastrointestinal cancer and other malignancies: From functional characterization to clinical implication. Biochim Biophys Acta Rev Cancer 2020; 1874:188415. [PMID: 32822825 DOI: 10.1016/j.bbcan.2020.188415] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/15/2020] [Accepted: 08/15/2020] [Indexed: 02/07/2023]
Abstract
Despite the recent advances in cancer research and treatment, gastrointestinal (GI) cancers remain the most common deadly disease worldwide. The aberrant DNA replication serves as a major source of genomic instability and enhances cell proliferation that contributes to tumor initiation and progression. Minichromosome maintenance family (MCMs) is a well-recognized group of proteins responsible for DNA synthesis. Recent studies suggested that dysregulated MCMs lead to tumor initiation, progression, and chemoresistance via modulating cell cycle and DNA replication stress. Their underlying mechanisms in various cancer types have been gradually identified. Furthermore, multiple studies have investigated the association between MCMs expression and clinicopathological features of cancer patients, implying that MCMs might serve as prominent prognostic biomarkers for GI cancers. This review summarizes the current knowledge on the oncogenic role of MCM proteins and highlights their clinical implications in various malignancies, especially in GI cancers. Targeting MCMs might shed light on the potential for identifying novel therapeutic strategies.
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14
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Huang JW, Acharya A, Taglialatela A, Nambiar TS, Cuella-Martin R, Leuzzi G, Hayward SB, Joseph SA, Brunette GJ, Anand R, Soni RK, Clark NL, Bernstein KA, Cejka P, Ciccia A. MCM8IP activates the MCM8-9 helicase to promote DNA synthesis and homologous recombination upon DNA damage. Nat Commun 2020; 11:2948. [PMID: 32528060 PMCID: PMC7290032 DOI: 10.1038/s41467-020-16718-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 05/19/2020] [Indexed: 02/06/2023] Open
Abstract
Homologous recombination (HR) mediates the error-free repair of DNA double-strand breaks to maintain genomic stability. Here we characterize C17orf53/MCM8IP, an OB-fold containing protein that binds ssDNA, as a DNA repair factor involved in HR. MCM8IP-deficient cells exhibit HR defects, especially in long-tract gene conversion, occurring downstream of RAD51 loading, consistent with a role for MCM8IP in HR-dependent DNA synthesis. Moreover, loss of MCM8IP confers cellular sensitivity to crosslinking agents and PARP inhibition. Importantly, we report that MCM8IP directly associates with MCM8-9, a helicase complex mutated in primary ovarian insufficiency, and RPA1. We additionally show that the interactions of MCM8IP with MCM8-9 and RPA facilitate HR and promote replication fork progression and cellular viability in response to treatment with crosslinking agents. Mechanistically, MCM8IP stimulates the helicase activity of MCM8-9. Collectively, our work identifies MCM8IP as a key regulator of MCM8-9-dependent DNA synthesis during DNA recombination and replication.
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Affiliation(s)
- Jen-Wei Huang
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Ananya Acharya
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Tarun S Nambiar
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Raquel Cuella-Martin
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Samuel B Hayward
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Sarah A Joseph
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Gregory J Brunette
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Roopesh Anand
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Nathan L Clark
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Kara A Bernstein
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
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15
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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16
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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17
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Butenko A, Opperdoes FR, Flegontova O, Horák A, Hampl V, Keeling P, Gawryluk RMR, Tikhonenkov D, Flegontov P, Lukeš J. Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids. BMC Biol 2020; 18:23. [PMID: 32122335 PMCID: PMC7052976 DOI: 10.1186/s12915-020-0754-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background The Euglenozoa are a protist group with an especially rich history of evolutionary diversity. They include diplonemids, representing arguably the most species-rich clade of marine planktonic eukaryotes; trypanosomatids, which are notorious parasites of medical and veterinary importance; and free-living euglenids. These different lifestyles, and particularly the transition from free-living to parasitic, likely require different metabolic capabilities. We carried out a comparative genomic analysis across euglenozoan diversity to see how changing repertoires of enzymes and structural features correspond to major changes in lifestyles. Results We find a gradual loss of genes encoding enzymes in the evolution of kinetoplastids, rather than a sudden decrease in metabolic capabilities corresponding to the origin of parasitism, while diplonemids and euglenids maintain more metabolic versatility. Distinctive characteristics of molecular machines such as kinetochores and the pre-replication complex that were previously considered specific to parasitic kinetoplastids were also identified in their free-living relatives. Therefore, we argue that they represent an ancestral rather than a derived state, as thought until the present. We also found evidence of ancient redundancy in systems such as NADPH-dependent thiol-redox. Only the genus Euglena possesses the combination of trypanothione-, glutathione-, and thioredoxin-based systems supposedly present in the euglenozoan common ancestor, while other representatives of the phylum have lost one or two of these systems. Lastly, we identified convergent losses of specific metabolic capabilities between free-living kinetoplastids and ciliates. Although this observation requires further examination, it suggests that certain eukaryotic lineages are predisposed to such convergent losses of key enzymes or whole pathways. Conclusions The loss of metabolic capabilities might not be associated with the switch to parasitic lifestyle in kinetoplastids, and the presence of a highly divergent (or unconventional) kinetochore machinery might not be restricted to this protist group. The data derived from the transcriptomes of free-living early branching prokinetoplastids suggests that the pre-replication complex of Trypanosomatidae is a highly divergent version of the conventional machinery. Our findings shed light on trends in the evolution of metabolism in protists in general and open multiple avenues for future research.
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Affiliation(s)
- Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fred R Opperdoes
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Vladimír Hampl
- Faculty of Science, Charles University, Biocev, Vestec, Czech Republic
| | - Patrick Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Denis Tikhonenkov
- Department of Botany, University of British Columbia, Vancouver, Canada.,Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of Ostrava, Ostrava, Czech Republic. .,Present address: Department of Genetics, Harvard Medical School, Boston, USA.
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
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18
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Fumasoni M, Murray AW. The evolutionary plasticity of chromosome metabolism allows adaptation to constitutive DNA replication stress. eLife 2020; 9:e51963. [PMID: 32043971 PMCID: PMC7069727 DOI: 10.7554/elife.51963] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/11/2020] [Indexed: 01/22/2023] Open
Abstract
Many biological features are conserved and thus considered to be resistant to evolutionary change. While rapid genetic adaptation following the removal of conserved genes has been observed, we often lack a mechanistic understanding of how adaptation happens. We used the budding yeast, Saccharomyces cerevisiae, to investigate the evolutionary plasticity of chromosome metabolism, a network of evolutionary conserved modules. We experimentally evolved cells constitutively experiencing DNA replication stress caused by the absence of Ctf4, a protein that coordinates the enzymatic activities at replication forks. Parallel populations adapted to replication stress, over 1000 generations, by acquiring multiple, concerted mutations. These mutations altered conserved features of two chromosome metabolism modules, DNA replication and sister chromatid cohesion, and inactivated a third, the DNA damage checkpoint. The selected mutations define a functionally reproducible evolutionary trajectory. We suggest that the evolutionary plasticity of chromosome metabolism has implications for genome evolution in natural populations and cancer.
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Affiliation(s)
- Marco Fumasoni
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
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19
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Hustedt N, Saito Y, Zimmermann M, Álvarez-Quilón A, Setiaputra D, Adam S, McEwan A, Yuan JY, Olivieri M, Zhao Y, Kanemaki MT, Jurisicova A, Durocher D. Control of homologous recombination by the HROB-MCM8-MCM9 pathway. Genes Dev 2019; 33:1397-1415. [PMID: 31467087 PMCID: PMC6771392 DOI: 10.1101/gad.329508.119] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/08/2019] [Indexed: 12/17/2022]
Abstract
In this study, Hustedt et al. use CRISPR-based genetic screens to build a clear picture of the postsynaptic steps of homologous recombination in mammalian cells. They report the identification of C17orf53/HROB, a factor required for cell survival after exposure to a variety of replication stress-inducing genotoxins and for the resolution but not formation of Rad51 foci. DNA repair by homologous recombination (HR) is essential for genomic integrity, tumor suppression, and the formation of gametes. HR uses DNA synthesis to repair lesions such as DNA double-strand breaks and stalled DNA replication forks, but despite having a good understanding of the steps leading to homology search and strand invasion, we know much less of the mechanisms that establish recombination-associated DNA polymerization. Here, we report that C17orf53/HROB is an OB-fold-containing factor involved in HR that acts by recruiting the MCM8–MCM9 helicase to sites of DNA damage to promote DNA synthesis. Mice with targeted mutations in Hrob are infertile due to depletion of germ cells and display phenotypes consistent with a prophase I meiotic arrest. The HROB–MCM8–MCM9 pathway acts redundantly with the HELQ helicase, and cells lacking both HROB and HELQ have severely impaired HR, suggesting that they underpin two major routes for the completion of HR downstream from RAD51. The function of HROB in HR is reminiscent of that of gp59, which acts as the replicative helicase loader during bacteriophage T4 recombination-dependent DNA replication. We therefore propose that the loading of MCM8–MCM9 by HROB may similarly be a key step in the establishment of mammalian recombination-associated DNA synthesis.
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Affiliation(s)
- Nicole Hustedt
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Yuichiro Saito
- Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Michal Zimmermann
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | | | - Dheva Setiaputra
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Salomé Adam
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Andrea McEwan
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Jing Yi Yuan
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Michele Olivieri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Yichao Zhao
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Andrea Jurisicova
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario M5G 0D8, Canada
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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20
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Griffin WC, Trakselis MA. The MCM8/9 complex: A recent recruit to the roster of helicases involved in genome maintenance. DNA Repair (Amst) 2019; 76:1-10. [PMID: 30743181 DOI: 10.1016/j.dnarep.2019.02.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/03/2019] [Indexed: 12/11/2022]
Abstract
There are several DNA helicases involved in seemingly overlapping aspects of homologous and homoeologous recombination. Mutations of many of these helicases are directly implicated in genetic diseases including cancer, rapid aging, and infertility. MCM8/9 are recent additions to the catalog of helicases involved in recombination, and so far, the evidence is sparse, making assignment of function difficult. Mutations in MCM8/9 correlate principally with primary ovarian failure/insufficiency (POF/POI) and infertility indicating a meiotic defect. However, they also act when replication forks collapse/break shuttling products into mitotic recombination and several mutations are found in various somatic cancers. This review puts MCM8/9 in context with other replication and recombination helicases to narrow down its genomic maintenance role. We discuss the known structure/function relationship, the mutational spectrum, and dissect the available cellular and organismal data to better define its role in recombination.
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Affiliation(s)
- Wezley C Griffin
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798, USA.
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21
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Neves H, Kwok HF. In sickness and in health: The many roles of the minichromosome maintenance proteins. Biochim Biophys Acta Rev Cancer 2017; 1868:295-308. [DOI: 10.1016/j.bbcan.2017.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/29/2017] [Accepted: 06/01/2017] [Indexed: 01/09/2023]
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22
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Mehdi MZ, Nagi AH, Naseem N. MCM - 2 and Ki - 67 as proliferation markers in renal cell carcinoma: A quantitative and semi - quantitative analysis. Int Braz J Urol 2017; 42:1121-1128. [PMID: 27532114 PMCID: PMC5117967 DOI: 10.1590/s1677-5538.ibju.2015.0388] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 02/12/2016] [Indexed: 11/30/2022] Open
Abstract
Introduction/Background: Fuhrman nuclear grade is the most important histological parameter to predict prognosis in a patient of renal cell carcinoma (RCC). However, it suffers from inter-observer and intra-observer variation giving rise to need of a parameter that not only correlates with nuclear grade but is also objective and reproducible. Proliferation is the measure of aggressiveness of a tumour and it is strongly correlated with Fuhrman nuclear grade, clinical survival and recurrence in RCC. Ki-67 is conventionally used to assess proliferation. Mini-chromosome maintenance 2 (MCM-2) is a lesser known marker of proliferation and identifies a greater proliferation faction. This study was designed to assess the prognostic significance of MCM-2 by comparing it with Fuhrman nuclear grade and Ki-67. Material and Methods: n=50 cases of various ages, stages, histological subtypes and grades of RCC were selected for this study. Immunohistochemical staining using Ki-67(MIB-1, Mouse monoclonal antibody, Dako) and MCM-2 (Mouse monoclonal antibody, Thermo) was performed on the paraffin embedded blocks in the department of Morbid anatomy and Histopathology, University of Health Sciences, Lahore. Labeling indices (LI) were determined by two pathologists independently using quantitative and semi-quantitative analysis. Statistical analysis was carried out using SPSS 20.0. Kruskall-Wallis test was used to determine a correlation of proliferation markers with grade, and Pearson's correlate was used to determine correlation between the two proliferation markers. Results: Labeling index of MCM-2 (median=24.29%) was found to be much higher than Ki-67(median=13.05%). Both markers were significantly related with grade (p=0.00; Kruskall-Wallis test). LI of MCM-2 was found to correlate significantly with LI of Ki-67(r=0.0934;p=0.01 with Pearson's correlate). Results of semi-quantitative analysis correlated well with quantitative analysis. Conclusion: Both Ki-67 and MCM-2 are markers of proliferation which are closely linked to grade. Therefore, they can act as surrogate markers for grade in a manner that is more objective and reproducible.
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Affiliation(s)
- Muhammad Zain Mehdi
- Department of Pathology, University of Health Sciences, Lahore, Punjab, Pakistan
| | - Abdul Hanan Nagi
- Department of Morbid anatomy and Histopathology, University of Health Sciences, Lahore, Punjab, Pakistan
| | - Nadia Naseem
- Department of Morbid anatomy and Histopathology, University of Health Sciences, Lahore, Punjab, Pakistan
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23
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Natsume T, Nishimura K, Minocherhomji S, Bhowmick R, Hickson ID, Kanemaki MT. Acute inactivation of the replicative helicase in human cells triggers MCM8-9-dependent DNA synthesis. Genes Dev 2017; 31:816-829. [PMID: 28487407 PMCID: PMC5435893 DOI: 10.1101/gad.297663.117] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/10/2017] [Indexed: 01/15/2023]
Abstract
DNA replication fork progression can be disrupted at difficult to replicate loci in the human genome, which has the potential to challenge chromosome integrity. This replication fork disruption can lead to the dissociation of the replisome and the formation of DNA damage. To model the events stemming from replisome dissociation during DNA replication perturbation, we used a degron-based system for inducible proteolysis of a subunit of the replicative helicase. We show that MCM2-depleted cells activate a DNA damage response pathway and generate replication-associated DNA double-strand breaks (DSBs). Remarkably, these cells maintain some DNA synthesis in the absence of MCM2, and this requires the MCM8-9 complex, a paralog of the MCM2-7 replicative helicase. We show that MCM8-9 functions in a homologous recombination-based pathway downstream from RAD51, which is promoted by DSB induction. This RAD51/MCM8-9 axis is distinct from the recently described RAD52-dependent DNA synthesis pathway that operates in early mitosis at common fragile sites. We propose that stalled replication forks can be restarted in S phase via homologous recombination using MCM8-9 as an alternative replicative helicase.
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Affiliation(s)
- Toyoaki Natsume
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Kohei Nishimura
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka 411-8540, Japan
| | - Sheroy Minocherhomji
- Center for Chromosome Stability.,Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, 2200 Copenhagen N, Denmark
| | - Rahul Bhowmick
- Center for Chromosome Stability.,Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, 2200 Copenhagen N, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability.,Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, 2200 Copenhagen N, Denmark
| | - Masato T Kanemaki
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
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24
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Ren R, Sun Y, Zhao Y, Geiser D, Ma H, Zhou X. Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes. Genome Biol Evol 2016; 8:2683-701. [PMID: 27604879 PMCID: PMC5631032 DOI: 10.1093/gbe/evw196] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A comprehensive and reliable eukaryotic tree of life is important for many aspects of biological studies from comparative developmental and physiological analyses to translational medicine and agriculture. Both gene-rich and taxon-rich approaches are effective strategies to improve phylogenetic accuracy and are greatly facilitated by marker genes that are universally distributed, well conserved, and orthologous among divergent eukaryotes. In this article, we report the identification of 943 low-copy eukaryotic genes and we show that many of these genes are promising tools in resolving eukaryotic phylogenies, despite the challenges of determining deep eukaryotic relationships. As a case study, we demonstrate that smaller subsets of ∼20 and 52 genes could resolve controversial relationships among widely divergent taxa and provide strong support for deep relationships such as the monophyly and branching order of several eukaryotic supergroups. In addition, the use of these genes resulted in fungal phylogenies that are congruent with previous phylogenomic studies that used much larger datasets, and successfully resolved several difficult relationships (e.g., forming a highly supported clade with Microsporidia, Mitosporidium and Rozella sister to other fungi). We propose that these genes are excellent for both gene-rich and taxon-rich analyses and can be applied at multiple taxonomic levels and facilitate a more complete understanding of the eukaryotic tree of life.
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Affiliation(s)
- Ren Ren
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, China
| | - Yazhou Sun
- Department of Biology, Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Intercollege Graduate Program in Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University
| | - Yue Zhao
- Intercollege Graduate Program in Cell and Developmental Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University
| | - David Geiser
- Department of Plant Pathology, The Pennsylvania State University
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, China
| | - Xiaofan Zhou
- Department of Biology, Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Intercollege Graduate Program in Cell and Developmental Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University Present address: Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235
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Perez-Arnaiz P, Bruck I, Kaplan DL. Mcm10 coordinates the timely assembly and activation of the replication fork helicase. Nucleic Acids Res 2015; 44:315-29. [PMID: 26582917 PMCID: PMC4705653 DOI: 10.1093/nar/gkv1260] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/02/2015] [Indexed: 11/12/2022] Open
Abstract
Mcm10 is an essential replication factor that is required for DNA replication in eukaryotes. Two key steps in the initiation of DNA replication are the assembly and activation of Cdc45–Mcm2–7-GINS (CMG) replicative helicase. However, it is not known what coordinates helicase assembly with helicase activation. We show in this manuscript, using purified proteins from budding yeast, that Mcm10 directly interacts with the Mcm2–7 complex and Cdc45. In fact, Mcm10 recruits Cdc45 to Mcm2–7 complex in vitro. To study the role of Mcm10 in more detail in vivo we used an auxin inducible degron in which Mcm10 is degraded upon addition of auxin. We show in this manuscript that Mcm10 is required for the timely recruitment of Cdc45 and GINS recruitment to the Mcm2–7 complex in vivo during early S phase. We also found that Mcm10 stimulates Mcm2 phosphorylation by DDK in vivo and in vitro. These findings indicate that Mcm10 plays a critical role in coupling replicative helicase assembly with helicase activation. Mcm10 is first involved in the recruitment of Cdc45 to the Mcm2–7 complex. After Cdc45–Mcm2–7 complex assembly, Mcm10 promotes origin melting by stimulating DDK phosphorylation of Mcm2, which thereby leads to GINS attachment to Mcm2–7.
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Affiliation(s)
- Patricia Perez-Arnaiz
- Florida State University College of Medicine, Department of Biomedical Sciences, Tallahassee, FL 32306, USA
| | - Irina Bruck
- Florida State University College of Medicine, Department of Biomedical Sciences, Tallahassee, FL 32306, USA
| | - Daniel L Kaplan
- Florida State University College of Medicine, Department of Biomedical Sciences, Tallahassee, FL 32306, USA
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Plasmodium P-Type Cyclin CYC3 Modulates Endomitotic Growth during Oocyst Development in Mosquitoes. PLoS Pathog 2015; 11:e1005273. [PMID: 26565797 PMCID: PMC4643991 DOI: 10.1371/journal.ppat.1005273] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/21/2015] [Indexed: 11/20/2022] Open
Abstract
Cell-cycle progression and cell division in eukaryotes are governed in part by the cyclin family and their regulation of cyclin-dependent kinases (CDKs). Cyclins are very well characterised in model systems such as yeast and human cells, but surprisingly little is known about their number and role in Plasmodium, the unicellular protozoan parasite that causes malaria. Malaria parasite cell division and proliferation differs from that of many eukaryotes. During its life cycle it undergoes two types of mitosis: endomitosis in asexual stages and an extremely rapid mitotic process during male gametogenesis. Both schizogony (producing merozoites) in host liver and red blood cells, and sporogony (producing sporozoites) in the mosquito vector, are endomitotic with repeated nuclear replication, without chromosome condensation, before cell division. The role of specific cyclins during Plasmodium cell proliferation was unknown. We show here that the Plasmodium genome contains only three cyclin genes, representing an unusual repertoire of cyclin classes. Expression and reverse genetic analyses of the single Plant (P)-type cyclin, CYC3, in the rodent malaria parasite, Plasmodium berghei, revealed a cytoplasmic and nuclear location of the GFP-tagged protein throughout the lifecycle. Deletion of cyc3 resulted in defects in size, number and growth of oocysts, with abnormalities in budding and sporozoite formation. Furthermore, global transcript analysis of the cyc3-deleted and wild type parasites at gametocyte and ookinete stages identified differentially expressed genes required for signalling, invasion and oocyst development. Collectively these data suggest that cyc3 modulates oocyst endomitotic development in Plasmodium berghei. The malaria parasite is a single-celled organism that multiplies asexually in a non-canonical way in both vertebrate host and mosquito vector. In the mosquito midgut, atypical cell division occurs in oocysts, where repeated nuclear division (endomitosis) precedes cell division, which then gives rise to many sporozoites in a process known as sporogony. The molecular mechanisms controlling this process are poorly understood. In many model organisms including mouse and yeast cells the cell cycle is regulated by members of the cyclin protein family, but the role of this family in the malaria parasite is unknown. Here, we show that there are only three cyclin genes and investigate the function of the single P-type cyclin (CYC3) in the rodent malaria parasite, Plasmodium berghei. We show that CYC3 has a cytoplasmic and nuclear localisation throughout most of the parasite lifecycle and by gene deletion we demonstrate that CYC3 is important for normal oocyst development, maturation and sporozoite formation. Moreover, we show that deletion of cyc3 affects the transcription of genes required for cell signalling and oocyst development. The data suggest that CYC3 modulates asexual multiplication in oocysts and plays a vital role in parasite development in the mosquito.
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27
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Luo Y, Schimenti JC. MCM9 deficiency delays primordial germ cell proliferation independent of the ATM pathway. Genesis 2015; 53:678-84. [DOI: 10.1002/dvg.22901] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/14/2015] [Accepted: 09/17/2015] [Indexed: 02/02/2023]
Affiliation(s)
- Yunhai Luo
- Department of Biomedical Sciences; Cornell University; Ithaca New York
| | - John C. Schimenti
- Department of Biomedical Sciences; Cornell University; Ithaca New York
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28
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Reubens MC, Biller MD, Bedsole SE, Hopkins LT, Ables ET, Christensen TW. Mcm10 is required for oogenesis and early embryogenesis in Drosophila. Mech Dev 2015; 138 Pt 3:291-9. [PMID: 26369283 DOI: 10.1016/j.mod.2015.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/27/2015] [Accepted: 09/08/2015] [Indexed: 01/05/2023]
Abstract
Efficient replication of the genome and the establishment of endogenous chromatin states are processes that are essential to eukaryotic life. It is well documented that Mcm10 is intimately linked to both of these important biological processes; therefore, it is not surprising that Mcm10 is commonly misregulated in many human cancers. Most of the research regarding the biological roles of Mcm10 has been performed in single-cell or cell-free in-vitro systems. Though these systems are informative, they are unable to provide information on the cell-specific function of Mcm10 in the context of the tissue and organ systems that comprise multicellular eukaryotes. We therefore sought to identify the potential biological functions of Mcm10 in the context of a complex multicellular organism by continuing our analysis in Drosophila using three novel hypomorphic alleles. Observation of embryonic nuclear morphology and quantification of embryo hatch rates reveal that maternal loading of Mcm10 is required for embryonic nuclear stability, and suggest a role for Mcm10 post zygotic transition. Contrary to the essential nature of Mcm10 depicted in the literature, it does not appear to be required for adult viability in Drosophila if embryonic requirements are met. Although not required for adult somatic viability, analysis of fecundity and ovarian morphology in mutant females suggest that Mcm10 plays a role in maintenance of the female germline. Taken together, our results demonstrate critical roles for Mcm10 during early embryogenesis, and mark the first data linking Mcm10 to female specific reproduction in multicellular eukaryotes.
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Affiliation(s)
- Michael C Reubens
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| | - Megan D Biller
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| | - Sidney E Bedsole
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| | - Lucas T Hopkins
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| | - Elizabeth T Ables
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
| | - Tim W Christensen
- Department of Biology, East Carolina University, Greenville, NC 27878, USA.
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29
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Traver S, Coulombe P, Peiffer I, Hutchins J, Kitzmann M, Latreille D, Méchali M. MCM9 Is Required for Mammalian DNA Mismatch Repair. Mol Cell 2015; 59:831-9. [DOI: 10.1016/j.molcel.2015.07.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/23/2015] [Accepted: 07/15/2015] [Indexed: 10/23/2022]
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30
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Tiengwe C, Marques CA, McCulloch R. Nuclear DNA replication initiation in kinetoplastid parasites: new insights into an ancient process. Trends Parasitol 2013; 30:27-36. [PMID: 24287149 DOI: 10.1016/j.pt.2013.10.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 10/28/2013] [Accepted: 10/30/2013] [Indexed: 12/23/2022]
Abstract
Nuclear DNA replication is, arguably, the central cellular process in eukaryotes, because it drives propagation of life and intersects with many other genome reactions. Perhaps surprisingly, our understanding of nuclear DNA replication in kinetoplastids was limited until a clutch of studies emerged recently, revealing new insight into both the machinery and genome-wide coordination of the reaction. Here, we discuss how these studies suggest that the earliest acting components of the kinetoplastid nuclear DNA replication machinery - the factors that demarcate sites of the replication initiation, termed origins - are diverged from model eukaryotes. In addition, we discuss how origin usage and replication dynamics relate to the highly unusual organisation of transcription in the genome of Trypanosoma brucei.
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Affiliation(s)
- Calvin Tiengwe
- The University of Glasgow, Wellcome Trust Centre for Molecular Parasitology and Institute of Infection, Immunity and Inflammation, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK; The Johns Hopkins University School of Medicine, Department of Cell Biology, Baltimore, MD, USA
| | - Catarina A Marques
- The University of Glasgow, Wellcome Trust Centre for Molecular Parasitology and Institute of Infection, Immunity and Inflammation, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Richard McCulloch
- The University of Glasgow, Wellcome Trust Centre for Molecular Parasitology and Institute of Infection, Immunity and Inflammation, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK.
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31
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Kanemaki MT. The dimeric Mcm8-9 complex of Xenopus laevis likely has a conserved function for resistance to DNA damage. Cell Cycle 2013; 12:1338-9. [PMID: 23588076 PMCID: PMC3674061 DOI: 10.4161/cc.24670] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Masato T Kanemaki
- Center for Frontier Research, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan.
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32
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Gambus A, Blow JJ. Mcm8 and Mcm9 form a dimeric complex in Xenopus laevis egg extract that is not essential for DNA replication initiation. Cell Cycle 2013; 12:1225-32. [PMID: 23518502 PMCID: PMC3674087 DOI: 10.4161/cc.24310] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 03/12/2013] [Accepted: 03/14/2013] [Indexed: 11/22/2022] Open
Abstract
Hexameric complexes of the six related Mcm2-7 proteins form the core of the replicative helicase. Two other proteins, Mcm8 and Mcm9, with significant homology to Mcm2-7 were first shown to play distinct roles during DNA replication in Xenopus laevis egg extract. Recent work has revealed that Mcm8 and 9 form a complex that plays a role during homologous recombination in human, chicken and mouse cells. We have therefore re-examined the behavior of the Xenopus homologs of these proteins. We show that Mcm8 and Mcm9 form a dimeric complex in Xenopus egg extract. They both associate with chromatin at later stages of DNA replication, and this association is stimulated by DNA damage, suggesting that their function is analogous to the one described in higher eukaryotes. In contrast to previous reports, we do not find Mcm9 essential for loading of Mcm2-7 complex onto chromatin during origin licensing nor detect its interaction with Cdt1 origin licensing factor. Altogether, we conclude that the role Mcm8 and Mcm9 play in Xenopus egg extract is not different from recent findings in higher eukaryotes, consistent with an evolutionary conservation of their function.
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Affiliation(s)
- Agnieszka Gambus
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, UK.
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33
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Jeffries EP, Denq WI, Bartko JC, Trakselis MA. Identification, quantification, and evolutionary analysis of a novel isoform of MCM9. Gene 2013; 519:41-9. [DOI: 10.1016/j.gene.2013.01.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Revised: 01/25/2013] [Accepted: 01/28/2013] [Indexed: 12/29/2022]
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34
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Structure and evolutionary origins of the CMG complex. Chromosoma 2013; 122:47-53. [PMID: 23412083 DOI: 10.1007/s00412-013-0397-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 01/24/2013] [Accepted: 01/25/2013] [Indexed: 01/20/2023]
Abstract
The CMG (Cdc45-MCM-GINS) complex is the eukaryotic replicative helicase, the enzyme that unwinds double-stranded DNA at replication forks. All three components of the CMG complex are essential for its function, but only in the case of MCM, the molecular motor that harnesses the energy of ATP hydrolysis to catalyse strand separation, is that function clear. Here, we review current knowledge of the three-dimensional structure of the CMG complex and its components and highlight recent advances in our understanding of its evolutionary origins.
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35
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The MCM8-MCM9 complex promotes RAD51 recruitment at DNA damage sites to facilitate homologous recombination. Mol Cell Biol 2013; 33:1632-44. [PMID: 23401855 DOI: 10.1128/mcb.01503-12] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The minichromosome maintenance protein homologs MCM8 and MCM9 have previously been implicated in DNA replication elongation and prereplication complex (pre-RC) formation, respectively. We found that MCM8 and MCM9 physically associate with each other and that MCM8 is required for the stability of MCM9 protein in mammalian cells. Depletion of MCM8 or MCM9 in human cancer cells or the loss of function MCM9 mutation in mouse embryo fibroblasts sensitizes cells to the DNA interstrand cross-linking (ICL) agent cisplatin. Consistent with a role in the repair of ICLs by homologous recombination (HR), knockdown of MCM8 or MCM9 significantly reduces HR repair efficiency. Chromatin immunoprecipitation analysis using human DR-GFP cells or Xenopus egg extract demonstrated that MCM8 and MCM9 proteins are rapidly recruited to DNA damage sites and promote RAD51 recruitment. Thus, these two metazoan-specific MCM homologs are new components of HR and may represent novel targets for treating cancer in combination with DNA cross-linking agents.
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36
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Abstract
The MCM proteins are best known for their role in DNA replication, MCM2-7 forming the replicative helicase. Now, two reports in this issue of Molecular Cell, Nishimura et al. (2012) and Lutzmann et al. (2012) show the less well understood MCM8 and MCM9 to be crucial for effective homologous recombination.
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37
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Crismani W, Portemer V, Froger N, Chelysheva L, Horlow C, Vrielynck N, Mercier R. MCM8 is required for a pathway of meiotic double-strand break repair independent of DMC1 in Arabidopsis thaliana. PLoS Genet 2013; 9:e1003165. [PMID: 23300481 PMCID: PMC3536722 DOI: 10.1371/journal.pgen.1003165] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 10/28/2012] [Indexed: 11/25/2022] Open
Abstract
Mini-chromosome maintenance (MCM) 2–9 proteins are related helicases. The first six, MCM2–7, are essential for DNA replication in all eukaryotes. In contrast, MCM8 is not always conserved in eukaryotes but is present in Arabidopsis thaliana. MCM8 is required for 95% of meiotic crossovers (COs) in Drosophila and is essential for meiosis completion in mouse, prompting us to study this gene in Arabidopsis meiosis. Three allelic Atmcm8 mutants showed a limited level of chromosome fragmentation at meiosis. This defect was dependent on programmed meiotic double-strand break (DSB) formation, revealing a role for AtMCM8 in meiotic DSB repair. In contrast, CO formation was not affected, as shown both genetically and cytologically. The Atmcm8 DSB repair defect was greatly amplified in the absence of the DMC1 recombinase or in mutants affected in DMC1 dynamics (sds, asy1). The Atmcm8 fragmentation defect was also amplified in plants heterozygous for a mutation in either recombinase, DMC1 or RAD51. Finally, in the context of absence of homologous chromosomes (i.e. haploid), mutation of AtMCM8 also provoked a low level of chromosome fragmentation. This fragmentation was amplified by the absence of DMC1 showing that both MCM8 and DMC1 can promote repair on the sister chromatid in Arabidopsis haploids. Altogether, this establishes a role for AtMCM8 in meiotic DSB repair, in parallel to DMC1. We propose that MCM8 is involved with RAD51 in a backup pathway that repairs meiotic DSB without giving CO when the major pathway, which relies on DMC1, fails. Species that reproduce sexually have two copies of each chromosome, inherited from their father and mother. During a special cell division called meiosis, these two chromosomes are mixed by homologous recombination to give genetically unique chromosomes that will be transmitted to the next generation. This recombination process is initiated by DNA breaks that must be repaired efficiently to maintain fertility. Using the model plant Arabidopsis thaliana we revealed here that the gene AtMCM8 is required to repair a subset of these DNA breaks. However MCM8 appears to not be required for recombination with the homologous chromosome. Instead MCM8 appears to be involved in a safety system that operates to repair DNA breaks that have not been used for homologous recombination. Interestingly the equivalent gene also has an essential meiotic function in the fly and the mouse. However the three species require MCM8 for different aspects of meiosis.
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Affiliation(s)
- Wayne Crismani
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Virginie Portemer
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Nicole Froger
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Liudmila Chelysheva
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Christine Horlow
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Nathalie Vrielynck
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Raphaël Mercier
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
- * E-mail:
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38
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Kohl KP, Jones CD, Sekelsky J. Evolution of an MCM complex in flies that promotes meiotic crossovers by blocking BLM helicase. Science 2012; 338:1363-5. [PMID: 23224558 DOI: 10.1126/science.1228190] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Generation of meiotic crossovers in many eukaryotes requires the elimination of anti-crossover activities by using the Msh4-Msh5 heterodimer to block helicases. Msh4 and Msh5 have been lost from the flies Drosophila and Glossina, but we identified a complex of minichromosome maintenance (MCM) proteins that functionally replace Msh4-Msh5. We found that REC, an ortholog of MCM8 that evolved under strong positive selection in flies, interacts with MEI-217 and MEI-218, which arose from a previously undescribed metazoan-specific MCM protein. Meiotic crossovers were reduced in Drosophila rec, mei-217, and mei-218 mutants; however, removal of the Bloom syndrome helicase (BLM) ortholog restored crossovers. Thus, MCMs were co-opted into a novel complex that replaced the meiotic pro-crossover function of Msh4-Msh5 in flies.
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Affiliation(s)
- Kathryn P Kohl
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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39
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Shen Z, Prasanth SG. Emerging players in the initiation of eukaryotic DNA replication. Cell Div 2012; 7:22. [PMID: 23075259 PMCID: PMC3520825 DOI: 10.1186/1747-1028-7-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 10/12/2012] [Indexed: 12/23/2022] Open
Abstract
Faithful duplication of the genome in eukaryotes requires ordered assembly of a multi-protein complex called the pre-replicative complex (pre-RC) prior to S phase; transition to the pre-initiation complex (pre-IC) at the beginning of DNA replication; coordinated progression of the replisome during S phase; and well-controlled regulation of replication licensing to prevent re-replication. These events are achieved by the formation of distinct protein complexes that form in a cell cycle-dependent manner. Several components of the pre-RC and pre-IC are highly conserved across all examined eukaryotic species. Many of these proteins, in addition to their bona fide roles in DNA replication are also required for other cell cycle events including heterochromatin organization, chromosome segregation and centrosome biology. As the complexity of the genome increases dramatically from yeast to human, additional proteins have been identified in higher eukaryotes that dictate replication initiation, progression and licensing. In this review, we discuss the newly discovered components and their roles in cell cycle progression.
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Affiliation(s)
- Zhen Shen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S, Goodwin Avenue, Urbana, IL 61801, USA.
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40
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Lutzmann M, Grey C, Traver S, Ganier O, Maya-Mendoza A, Ranisavljevic N, Bernex F, Nishiyama A, Montel N, Gavois E, Forichon L, de Massy B, Méchali M. MCM8- and MCM9-deficient mice reveal gametogenesis defects and genome instability due to impaired homologous recombination. Mol Cell 2012; 47:523-34. [PMID: 22771120 DOI: 10.1016/j.molcel.2012.05.048] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 03/21/2012] [Accepted: 05/31/2012] [Indexed: 10/28/2022]
Abstract
We generated knockout mice for MCM8 and MCM9 and show that deficiency for these genes impairs homologous recombination (HR)-mediated DNA repair during gametogenesis and somatic cells cycles. MCM8(-/-) mice are sterile because spermatocytes are blocked in meiotic prophase I, and females have only arrested primary follicles and frequently develop ovarian tumors. MCM9(-/-) females also are sterile as ovaries are completely devoid of oocytes. In contrast, MCM9(-/-) testes produce spermatozoa, albeit in much reduced quantity. Mcm8(-/-) and Mcm9(-/-) embryonic fibroblasts show growth defects and chromosomal damage and cannot overcome a transient inhibition of replication fork progression. In these cells, chromatin recruitment of HR factors like Rad51 and RPA is impaired and HR strongly reduced. We further demonstrate that MCM8 and MCM9 form a complex and that they coregulate their stability. Our work uncovers essential functions of MCM8 and MCM9 in HR-mediated DSB repair during gametogenesis, replication fork maintenance, and DNA repair.
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Affiliation(s)
- Malik Lutzmann
- DNA Replication and Genome Dynamics, Institute of Human Genetics, CNRS, 141 Rue de la Cardonille, 34396 Montpellier, Cedex 5, France
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41
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Nishimura K, Ishiai M, Horikawa K, Fukagawa T, Takata M, Takisawa H, Kanemaki MT. Mcm8 and Mcm9 form a complex that functions in homologous recombination repair induced by DNA interstrand crosslinks. Mol Cell 2012; 47:511-22. [PMID: 22771115 DOI: 10.1016/j.molcel.2012.05.047] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 05/14/2012] [Accepted: 05/31/2012] [Indexed: 01/09/2023]
Abstract
DNA interstrand crosslinks (ICLs) are highly toxic lesions that stall the replication fork to initiate the repair process during the S phase of vertebrates. Proteins involved in Fanconi anemia (FA), nucleotide excision repair (NER), and translesion synthesis (TS) collaboratively lead to homologous recombination (HR) repair. However, it is not understood how ICL-induced HR repair is carried out and completed. Here, we showed that the replicative helicase-related Mcm family of proteins, Mcm8 and Mcm9, forms a complex required for HR repair induced by ICLs. Chicken DT40 cells lacking MCM8 or MCM9 are viable but highly sensitive to ICL-inducing agents, and exhibit more chromosome aberrations in the presence of mitomycin C compared with wild-type cells. During ICL repair, Mcm8 and Mcm9 form nuclear foci that partly colocalize with Rad51. Mcm8-9 works downstream of the FA and BRCA2/Rad51 pathways, and is required for HR that promotes sister chromatid exchanges, probably as a hexameric ATPase/helicase.
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Affiliation(s)
- Kohei Nishimura
- Center for Frontier Research, National Institute of Genetics, Research Organization of Information and Systems, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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Fokkens L, Hogeweg P, Snel B. Gene duplications contribute to the overrepresentation of interactions between proteins of a similar age. BMC Evol Biol 2012; 12:99. [PMID: 22732003 PMCID: PMC3457867 DOI: 10.1186/1471-2148-12-99] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 06/07/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The study of biological networks and how they have evolved is fundamental to our understanding of the cell. By investigating how proteins of different ages are connected in the protein interaction network, one can infer how that network has expanded in evolution, without the need for explicit reconstruction of ancestral networks. Studies that implement this approach show that proteins are often connected to proteins of a similar age, suggesting a simultaneous emergence of interacting proteins. There are several theories explaining this phenomenon, but despite the importance of gene duplication in genome evolution, none consider protein family dynamics as a contributing factor. RESULTS In an S. cerevisiae protein interaction network we investigate to what extent edges that arise from duplication events contribute to the observed tendency to interact with proteins of a similar age. We find that part of this tendency is explained by interactions between paralogs. Age is usually defined on the level of protein families, rather than individual proteins, hence paralogs have the same age. The major contribution however, is from interaction partners that are shared between paralogs. These interactions have most likely been conserved after a duplication event. To investigate to what extent a nearly neutral process of network growth can explain these results, we adjust a well-studied network growth model to incorporate protein families. Our model shows that the number of edges between paralogs can be amplified by subsequent duplication events, thus explaining the overrepresentation of interparalog edges in the data. The fact that interaction partners shared by paralogs are often of the same age as the paralogs does not arise naturally from our model and needs further investigation. CONCLUSION We amend previous theories that explain why proteins of a similar age prefer to interact by demonstrating that this observation can be partially explained by gene duplication events. There is an ongoing debate on whether the protein interaction network is predominantly shaped by duplication and subfunctionalization or whether network rewiring is most important. Our analyses of S. cerevisiae protein interaction networks demonstrate that duplications have influenced at least one property of the protein interaction network: how proteins of different ages are connected.
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Affiliation(s)
- Like Fokkens
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
| | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
- Netherlands Consortium for Systems Biology (NCSB), c/o NISB Bureau, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
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Mcm10 associates with the loaded DNA helicase at replication origins and defines a novel step in its activation. EMBO J 2012; 31:2195-206. [PMID: 22433841 DOI: 10.1038/emboj.2012.69] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 02/28/2012] [Indexed: 12/13/2022] Open
Abstract
Mcm10 is essential for chromosome replication in eukaryotic cells and was previously thought to link the Mcm2-7 DNA helicase at replication forks to DNA polymerase alpha. Here, we show that yeast Mcm10 interacts preferentially with the fraction of the Mcm2-7 helicase that is loaded in an inactive form at origins of DNA replication, suggesting a role for Mcm10 during the initiation of chromosome replication, but Mcm10 is not a stable component of the replisome subsequently. Studies with budding yeast and human cells indicated that Mcm10 chaperones the catalytic subunit of polymerase alpha and preserves its stability. We used a novel degron allele to inactivate Mcm10 efficiently and this blocked the initiation of chromosome replication without causing degradation of DNA polymerase alpha. Strikingly, the other essential helicase subunits Cdc45 and GINS were still recruited to Mcm2-7 when cells entered S-phase without Mcm10, but origin unwinding was blocked. These findings indicate that Mcm10 is required for a novel step during activation of the Cdc45-MCM-GINS helicase at DNA replication origins.
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Tiengwe C, Marcello L, Farr H, Gadelha C, Burchmore R, Barry JD, Bell SD, McCulloch R. Identification of ORC1/CDC6-interacting factors in Trypanosoma brucei reveals critical features of origin recognition complex architecture. PLoS One 2012; 7:e32674. [PMID: 22412905 PMCID: PMC3297607 DOI: 10.1371/journal.pone.0032674] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 02/02/2012] [Indexed: 12/13/2022] Open
Abstract
DNA Replication initiates by formation of a pre-replication complex on sequences termed origins. In eukaryotes, the pre-replication complex is composed of the Origin Recognition Complex (ORC), Cdc6 and the MCM replicative helicase in conjunction with Cdt1. Eukaryotic ORC is considered to be composed of six subunits, named Orc1–6, and monomeric Cdc6 is closely related in sequence to Orc1. However, ORC has been little explored in protists, and only a single ORC protein, related to both Orc1 and Cdc6, has been shown to act in DNA replication in Trypanosoma brucei. Here we identify three highly diverged putative T. brucei ORC components that interact with ORC1/CDC6 and contribute to cell division. Two of these factors are so diverged that we cannot determine if they are eukaryotic ORC subunit orthologues, or are parasite-specific replication factors. The other we show to be a highly diverged Orc4 orthologue, demonstrating that this is one of the most widely conserved ORC subunits in protists and revealing it to be a key element of eukaryotic ORC architecture. Additionally, we have examined interactions amongst the T. brucei MCM subunits and show that this has the conventional eukaryotic heterohexameric structure, suggesting that divergence in the T. brucei replication machinery is limited to the earliest steps in origin licensing.
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Affiliation(s)
- Calvin Tiengwe
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Lucio Marcello
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Helen Farr
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Catarina Gadelha
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Richard Burchmore
- Sir Henry Wellcome Functional Genomics Facility, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - J. David Barry
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Stephen D. Bell
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Richard McCulloch
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
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Aves SJ, Liu Y, Richards TA. Evolutionary diversification of eukaryotic DNA replication machinery. Subcell Biochem 2012; 62:19-35. [PMID: 22918578 DOI: 10.1007/978-94-007-4572-8_2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
DNA replication research to date has focused on model organisms such as the vertebrate Xenopus laevis and the yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. However, animals and fungi both belong to the Opisthokonta, one of about six eukaryotic phylogenetic 'supergroups', and therefore represent only a fraction of eukaryotic diversity. To explore evolutionary diversification of the eukaryotic DNA replication machinery a bioinformatic approach was used to investigate the presence or absence of yeast/animal replisome components in other eukaryotic taxa. A comparative genomic survey was undertaken of 59 DNA replication proteins in a diverse range of 36 eukaryotes from all six supergroups. Twenty-three proteins including Mcm2-7, Cdc45, RPA1, primase, some DNA polymerase subunits, RFC1-5, PCNA and Fen1 are present in all species examined. A further 20 proteins are present in all six eukaryotic supergroups, although not necessarily in every species: with the exception of RNase H2B and the fork protection complex component Timeless/Tof1, all of these are members of anciently derived paralogous families such as ORC, MCM, GINS or RPA. Together these form a set of 43 proteins that must have been present in the last common eukaryotic ancestor (LCEA). This minimal LCEA replisome is significantly more complex than the related replisome in Archaea, indicating evolutionary events including duplications of DNA replication genes in the LCEA lineage which parallel the early evolution of other complex eukaryotic cellular features.
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Affiliation(s)
- Stephen J Aves
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK,
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Abstract
In eukaryotes, the Mcm2-7 complex forms the core of the replicative helicase - the molecular motor that uses ATP binding and hydrolysis to fuel the unwinding of double-stranded DNA at the replication fork. Although it is a toroidal hexameric helicase superficially resembling better-studied homohexameric helicases from prokaryotes and viruses, Mcm2-7 is the only known helicase formed from six unique and essential subunits. Recent biochemical and structural analyses of both Mcm2-7 and a higher-order complex containing additional activator proteins (the CMG complex) shed light on the reason behind this unique subunit assembly: whereas only a limited number of specific ATPase active sites are needed for DNA unwinding, one particular ATPase active site has evolved to form a reversible discontinuity (gate) in the toroidal complex. The activation of Mcm2-7 helicase during S-phase requires physical association of the accessory proteins Cdc45 and GINS; structural data suggest that these accessory factors activate DNA unwinding through closure of the Mcm2-7 gate. Moreover, studies capitalizing on advances in the biochemical reconstitution of eukaryotic DNA replication demonstrate that Mcm2-7 loads onto origins during initiation as a double hexamer, yet does not act as a double-stranded DNA pump during elongation.
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Affiliation(s)
- Sriram Vijayraghavan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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Li JJ, Schnick J, Hayles J, MacNeill SA. Purification and functional inactivation of the fission yeast MCM(MCM-BP) complex. FEBS Lett 2011; 585:3850-5. [PMID: 22036784 DOI: 10.1016/j.febslet.2011.10.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 10/09/2011] [Accepted: 10/14/2011] [Indexed: 12/31/2022]
Abstract
The MCM (mini-chromosome maintenance) complex is the core of the eukaryotic replicative helicase and comprises six proteins, Mcm2-Mcm7. In humans, a variant form of the complex has Mcm2 replaced by the MCM-BP protein. Recent results suggest that a similar complex exists in fission yeast with an essential role in DNA replication and cell cycle progression. Here, we describe the purification and subunit composition of the fission yeast MCM(Mcb1) complex. Using newly generated temperature-sensitive alleles, we show that loss of MCM(Mcb1) function leads to accumulation of DNA damage, checkpoint activation and cell cycle arrest, and provide evidence for a role for MCM(Mcb1) in meiosis.
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Affiliation(s)
- Juan-juan Li
- Cancer Research UK London Research Institute, London, UK
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Abstract
The cytoskeleton is a system of intracellular filaments crucial for cell shape, division, and function in all three domains of life. The simple cytoskeletons of prokaryotes show surprising plasticity in composition, with none of the core filament-forming proteins conserved in all lineages. In contrast, eukaryotic cytoskeletal function has been hugely elaborated by the addition of accessory proteins and extensive gene duplication and specialization. Much of this complexity evolved before the last common ancestor of eukaryotes. The distribution of cytoskeletal filaments puts constraints on the likely prokaryotic line that made this leap of eukaryogenesis.
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Affiliation(s)
- Bill Wickstead
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, England, UK.
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Minichromosome maintenance helicase paralog MCM9 is dispensible for DNA replication but functions in germ-line stem cells and tumor suppression. Proc Natl Acad Sci U S A 2011; 108:17702-7. [PMID: 21987787 DOI: 10.1073/pnas.1113524108] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Effective DNA replication is critical to the health and reproductive success of organisms. The six MCM2-7 proteins, which form the replicative helicase, are essential for high-fidelity replication of the genome. Many eukaryotes have a divergent paralog, MCM9, that was reported to be essential for loading MCM2-7 onto replication origins in the Xenopus oocyte extract system. To address the in vivo role of mammalian MCM9, we created and analyzed the phenotypes of mice with various mutations in Mcm9 and an intronic DNA replication-related gene Asf1a. Ablation of Mcm9 was compatible with cell proliferation and mouse viability, showing that it is nonessential for MCM2-7 loading or DNA replication. Mcm9 mutants underwent p53-independent embryonic germ-cell depletion in both sexes, with males also exhibiting defective spermatogonial stem-cell renewal. MCM9-deficient cells had elevated genomic instability and defective cell cycle reentry following replication stress, and mutant animals were prone to sex-specific cancers, most notably hepatocellular carcinoma in males. The phenotypes of mutant mice and cells suggest that MCM9 evolved a specialized but nonessential role in DNA replication or replication-linked quality-control mechanisms that are especially important for germ-line stem cells, and also for tumor suppression and genome maintenance in the soma.
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50
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Bryant JA, Aves SJ. Initiation of DNA replication: functional and evolutionary aspects. ANNALS OF BOTANY 2011; 107:1119-26. [PMID: 21508040 PMCID: PMC3091809 DOI: 10.1093/aob/mcr075] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND The initiation of DNA replication is a very important and highly regulated step in the cell division cycle. It is of interest to compare different groups of eukaryotic organisms (a) to identify the essential molecular events that occur in all eukaryotes, (b) to start to identify higher-level regulatory mechanisms that are specific to particular groups and (c) to gain insights into the evolution of initiation mechanisms. SCOPE This review features a wide-ranging literature survey covering replication origins, origin recognition and usage, modification of origin usage (especially in response to plant hormones), assembly of the pre-replication complex, loading of the replisome, genomics, and the likely origin of these mechanisms and proteins in Archaea. CONCLUSIONS In all eukaryotes, chromatin is organized for DNA replication as multiple replicons. In each replicon, replication is initiated at an origin. With the exception of those in budding yeast, replication origins, including the only one to be isolated so far from a plant, do not appear to embody a specific sequence; rather, they are AT-rich, with short tracts of locally bent DNA. The proteins involved in initiation are remarkably similar across the range of eukaryotes. Nevertheless, their activity may be modified by plant-specific mechanisms, including regulation by plant hormones. The molecular features of initiation are seen in a much simpler form in the Archaea. In particular, where eukaryotes possess a number of closely related proteins that form 'hetero-complexes' (such as the origin recognition complex and the MCM complex), archaeans typically possess one type of protein (e.g. one MCM) that forms a homo-complex. This suggests that several eukaryotic initiation proteins have evolved from archaeal ancestors by gene duplication and divergence.
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Affiliation(s)
- John A Bryant
- Biosciences, College of Life and Environmental Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK.
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