1
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Hara K, Tatsukawa K, Nagata K, Iida N, Hishiki A, Ohashi E, Hashimoto H. Structural basis for intra- and intermolecular interactions on RAD9 subunit of 9-1-1 checkpoint clamp implies functional 9-1-1 regulation by RHINO. J Biol Chem 2024; 300:105751. [PMID: 38354779 PMCID: PMC10937111 DOI: 10.1016/j.jbc.2024.105751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
Eukaryotic DNA clamp is a trimeric protein featuring a toroidal ring structure that binds DNA on the inside of the ring and multiple proteins involved in DNA transactions on the outside. Eukaryotes have two types of DNA clamps: the replication clamp PCNA and the checkpoint clamp RAD9-RAD1-HUS1 (9-1-1). 9-1-1 activates the ATR-CHK1 pathway in DNA damage checkpoint, regulating cell cycle progression. Structure of 9-1-1 consists of two moieties: a hetero-trimeric ring formed by PCNA-like domains of three subunits and an intrinsically disordered C-terminal region of the RAD9 subunit, called RAD9 C-tail. The RAD9 C-tail interacts with the 9-1-1 ring and disrupts the interaction between 9-1-1 and DNA, suggesting a negative regulatory role for this intramolecular interaction. In contrast, RHINO, a 9-1-1 binding protein, interacts with both RAD1 and RAD9 subunits, positively regulating checkpoint activation by 9-1-1. This study presents a biochemical and structural analysis of intra- and inter-molecular interactions on the 9-1-1 ring. Biochemical analysis indicates that RAD9 C-tail binds to the hydrophobic pocket on the PCNA-like domain of RAD9, implying that the pocket is involved in multiple protein-protein interactions. The crystal structure of the 9-1-1 ring in complex with a RHINO peptide reveals that RHINO binds to the hydrophobic pocket of RAD9, shedding light on the RAD9-binding motif. Additionally, the study proposes a structural model of the 9-1-1-RHINO quaternary complex. Together, these findings provide functional insights into the intra- and inter-molecular interactions on the front side of RAD9, elucidating the roles of RAD9 C-tail and RHINO in checkpoint activation.
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Affiliation(s)
- Kodai Hara
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kensuke Tatsukawa
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Kiho Nagata
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Nao Iida
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Asami Hishiki
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Eiji Ohashi
- Faculty of Science, Department of Biology, Kyushu University, Fukuoka, Japan; Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Hiroshi Hashimoto
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.
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2
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Fukumoto Y, Hoshino T, Nakayama Y, Ogra Y. The C-terminal tail of Rad17, iVERGE, binds the 9‒1‒1 complex independently of AAA+ ATPase domains to provide another clamp-loader interface. DNA Repair (Amst) 2023; 130:103567. [PMID: 37713925 DOI: 10.1016/j.dnarep.2023.103567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/17/2023] [Accepted: 09/03/2023] [Indexed: 09/17/2023]
Abstract
The ATR pathway plays a crucial role in maintaining genome integrity as the major DNA damage checkpoint. It also attracts attention as a therapeutic target in cancer treatment. The Rad17-RFC2-5 complex loads the Rad9-Hus1-Rad1 (9-1-1) DNA clamp complex onto damaged chromatin to activate the ATR pathway. We previously reported that phosphorylation of a polyanionic C-terminal tail of human Rad17, iVERGE, is essential for the interaction between Rad17 and the 9-1-1 complex. However, the molecular mechanism has remained unclear. Here, we show that iVERGE directly interacts with the Hus1 subunit of the 9-1-1 complex through Rad17-S667 phosphorylation independently of the AAA+ ATPase domains. An exogenous iVERGE peptide interacted with the 9-1-1 complex in vivo. The binding conformation of the iVERGE peptide was analyzed by de novo modeling with docking simulation, simulated annealing-molecular dynamics simulation, and the fragment molecular orbital method. The in silico analyses predicted the association of the iVERGE peptide with the hydrophobic and basic patches on the Hus1 protein, and the corresponding Hus1 mutants were deficient in the interaction with the iVERGE peptide in vivo. The iVERGE peptide occupied the same position as the C-terminus of Saccharomyces cerevisiae RAD24 on MEC3. The interaction energy calculation suggested that the Rad17 KYxxL motif and the iVERGE peptide are the primary and secondary interaction surfaces between the Rad17-RFC2-5 and 9-1-1 complexes. Our data reveal a novel molecular interface, iVERGE, between the Rad17-RFC2-5 and 9-1-1 complexes in vertebrates and implicate that Rad17 utilizes two distinct molecular interfaces to regulate the 9-1-1 complex.
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Affiliation(s)
- Yasunori Fukumoto
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan.
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
| | - Yuji Nakayama
- Department of Biochemistry & Molecular Biology, Kyoto Pharmaceutical University, Kyoto 607-8414, Japan
| | - Yasumitsu Ogra
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
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3
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Hara K, Hishiki A, Hoshino T, Nagata K, Iida N, Sawada Y, Ohashi E, Hashimoto H. The 9-1-1 DNA clamp subunit RAD1 forms specific interactions with clamp loader RAD17, revealing functional implications for binding-protein RHINO. J Biol Chem 2023; 299:103061. [PMID: 36841485 PMCID: PMC10060742 DOI: 10.1016/j.jbc.2023.103061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023] Open
Abstract
The RAD9-RAD1-HUS1 complex (9-1-1) is a eukaryotic DNA clamp with a crucial role at checkpoints for DNA damage. The ring-like structure of 9-1-1 is opened for loading onto 5' recessed DNA by the clamp loader RAD17 RFC-like complex (RAD17-RLC), in which the RAD17 subunit is responsible for specificity to 9-1-1. Loading of 9-1-1 is required for activation of the ATR-CHK1 checkpoint pathway and the activation is stimulated by a 9-1-1 interacting protein, RHINO, which interacts with 9-1-1 via a recently identified RAD1-binding motif. This discovery led to the hypothesis that other interacting proteins may contain a RAD1-binding motif as well. Here, we show that vertebrate RAD17 proteins also have a putative RAD1-binding motif in their N-terminal regions, and we report the crystal structure of human 9-1-1 bound to a human RAD17 peptide incorporating the motif at 2.1 Å resolution. Our structure confirms that the N-terminal region of RAD17 binds to the RAD1 subunit of 9-1-1 via specific interactions. Furthermore, we show that the RAD1-binding motif of RHINO disturbs the interaction of the N-terminal region of RAD17 with 9-1-1. Our results provide deeper understanding of how RAD17-RLC specifically recognizes 9-1-1 and imply that RHINO has a functional role in 9-1-1 loading/unloading and checkpoint activation.
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Affiliation(s)
- Kodai Hara
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Asami Hishiki
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Takako Hoshino
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kiho Nagata
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Nao Iida
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yukimasa Sawada
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Eiji Ohashi
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Hiroshi Hashimoto
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.
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4
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Hashimoto H, Hara K, Hishiki A. Structural basis for molecular interactions on the eukaryotic DNA sliding clamps PCNA and RAD9-RAD1-HUS1. J Biochem 2022; 172:189-196. [PMID: 35731009 DOI: 10.1093/jb/mvac053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/13/2022] [Indexed: 11/14/2022] Open
Abstract
DNA sliding clamps are widely conserved in all living organisms and play crucial roles in DNA replication and repair. Each DNA sliding clamp is a doughnut-shaped protein with a quaternary structure that encircles the DNA strand and recruits various factors involved in DNA replication and repair, thereby stimulating their biological functions. Eukaryotes have two types of DNA sliding clamp, proliferating cell nuclear antigen (PCNA) and RAD9-RAD1-HUS1 (9-1-1). The homo-trimer PCNA physically interacts with multiple proteins containing a PIP-box and/or APIM. The two motifs bind to PCNA by a similar mechanism; in addition, the bound PCNA structure is similar, implying a universality of PCNA interactions. In contrast to PCNA, 9-1-1 is a hetero-trimer composed of RAD9, RAD1, and HUS1 subunits. Although 9-1-1 forms a trimeric ring structure similar to PCNA, the C-terminal extension of the RAD9 is intrinsically unstructured. Based on the structural similarity between PCNA and 9-1-1, the mechanism underlying the interaction of 9-1-1 with its partners was thought to be analogous to that of PCNA. Unexpectedly, however, the recent structure of the 9-1-1 ring bound to a partner has revealed a novel interaction distinct from that of PCNA, potentially providing a new principle for molecular interactions on DNA sliding clamps.
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Affiliation(s)
- Hiroshi Hashimoto
- School of Pharmaceutical Science, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Kodai Hara
- School of Pharmaceutical Science, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Asami Hishiki
- School of Pharmaceutical Science, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
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Day M, Oliver AW, Pearl LH. Phosphorylation-dependent assembly of DNA damage response systems and the central roles of TOPBP1. DNA Repair (Amst) 2021; 108:103232. [PMID: 34678589 PMCID: PMC8651625 DOI: 10.1016/j.dnarep.2021.103232] [Citation(s) in RCA: 16] [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: 06/30/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 11/11/2022]
Abstract
The cellular response to DNA damage (DDR) that causes replication collapse and/or DNA double strand breaks, is characterised by a massive change in the post-translational modifications (PTM) of hundreds of proteins involved in the detection and repair of DNA damage, and the communication of the state of damage to the cellular systems that regulate replication and cell division. A substantial proportion of these PTMs involve targeted phosphorylation, which among other effects, promotes the formation of multiprotein complexes through the specific binding of phosphorylated motifs on one protein, by specialised domains on other proteins. Understanding the nature of these phosphorylation mediated interactions allows definition of the pathways and networks that coordinate the DDR, and helps identify new targets for therapeutic intervention that may be of benefit in the treatment of cancer, where DDR plays a key role. In this review we summarise the present understanding of how phosphorylated motifs are recognised by BRCT domains, which occur in many DDR proteins. We particularly focus on TOPBP1 - a multi-BRCT domain scaffold protein with essential roles in replication and the repair and signalling of DNA damage.
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Affiliation(s)
- Matthew Day
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK; Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW1E 6BT, UK.
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6
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Nakamura T, Okabe K, Hirayama S, Chirifu M, Ikemizu S, Morioka H, Nakabeppu Y, Yamagata Y. Structure of the mammalian adenine DNA glycosylase MUTYH: insights into the base excision repair pathway and cancer. Nucleic Acids Res 2021; 49:7154-7163. [PMID: 34142156 PMCID: PMC8266592 DOI: 10.1093/nar/gkab492] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/17/2021] [Accepted: 05/22/2021] [Indexed: 11/17/2022] Open
Abstract
Mammalian MutY homologue (MUTYH) is an adenine DNA glycosylase that excises adenine inserted opposite 8-oxoguanine (8-oxoG). The inherited variations in human MUTYH gene are known to cause MUTYH-associated polyposis (MAP), which is associated with colorectal cancer. MUTYH is involved in base excision repair (BER) with proliferating cell nuclear antigen (PCNA) in DNA replication, which is unique and critical for effective mutation-avoidance. It is also reported that MUTYH has a Zn-binding motif in a unique interdomain connector (IDC) region, which interacts with Rad9–Rad1–Hus1 complex (9–1–1) in DNA damage response, and with apurinic/apyrimidinic endonuclease 1 (APE1) in BER. However, the structural basis for the BER pathway by MUTYH and its interacting proteins is unclear. Here, we determined the crystal structures of complexes between mouse MUTYH and DNA, and between the C-terminal domain of mouse MUTYH and human PCNA. The structures elucidated the repair mechanism for the A:8-oxoG mispair including DNA replication-coupled repair process involving MUTYH and PCNA. The Zn-binding motif was revealed to comprise one histidine and three cysteine residues. The IDC, including the Zn-binding motif, is exposed on the MUTYH surface, suggesting its interaction modes with 9–1–1 and APE1, respectively. The structure of MUTYH explains how MAP mutations perturb MUTYH function.
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan.,Priority Organization for Innovation and Excellence, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Kohtaro Okabe
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Shogo Hirayama
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Mami Chirifu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Shinji Ikemizu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Hiroshi Morioka
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan.,Shokei University and Shokei University Junior College, 2-6-78, Kuhonji, Chuo-ku, Kumamoto, 862-8678 Kumamoto, Japan
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7
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Barger CJ, Chee L, Albahrani M, Munoz-Trujillo C, Boghean L, Branick C, Odunsi K, Drapkin R, Zou L, Karpf AR. Co-regulation and function of FOXM1/ RHNO1 bidirectional genes in cancer. eLife 2021; 10:e55070. [PMID: 33890574 PMCID: PMC8104967 DOI: 10.7554/elife.55070] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
The FOXM1 transcription factor is an oncoprotein and a top biomarker of poor prognosis in human cancer. Overexpression and activation of FOXM1 is frequent in high-grade serous carcinoma (HGSC), the most common and lethal form of human ovarian cancer, and is linked to copy number gains at chromosome 12p13.33. We show that FOXM1 is co-amplified and co-expressed with RHNO1, a gene involved in the ATR-Chk1 signaling pathway that functions in the DNA replication stress response. We demonstrate that FOXM1 and RHNO1 are head-to-head (i.e., bidirectional) genes (BDG) regulated by a bidirectional promoter (BDP) (named F/R-BDP). FOXM1 and RHNO1 each promote oncogenic phenotypes in HGSC cells, including clonogenic growth, DNA homologous recombination repair, and poly-ADP ribosylase inhibitor resistance. FOXM1 and RHNO1 are one of the first examples of oncogenic BDG, and therapeutic targeting of FOXM1/RHNO1 BDG is a potential therapeutic approach for ovarian and other cancers.
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MESH Headings
- Ataxia Telangiectasia Mutated Proteins/genetics
- Ataxia Telangiectasia Mutated Proteins/metabolism
- Carboplatin/pharmacology
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Line, Tumor
- Cell Proliferation
- Checkpoint Kinase 1/genetics
- Checkpoint Kinase 1/metabolism
- Databases, Genetic
- Drug Resistance, Neoplasm
- Female
- Forkhead Box Protein M1/genetics
- Forkhead Box Protein M1/metabolism
- Gene Expression Regulation, Neoplastic
- Humans
- Neoplasms, Cystic, Mucinous, and Serous/drug therapy
- Neoplasms, Cystic, Mucinous, and Serous/genetics
- Neoplasms, Cystic, Mucinous, and Serous/metabolism
- Neoplasms, Cystic, Mucinous, and Serous/pathology
- Ovarian Neoplasms/drug therapy
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/pathology
- Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
- Promoter Regions, Genetic
- Recombinational DNA Repair
- Signal Transduction
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Affiliation(s)
- Carter J Barger
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Linda Chee
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Mustafa Albahrani
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Catalina Munoz-Trujillo
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Lidia Boghean
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Connor Branick
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Kunle Odunsi
- Departments of Gynecologic Oncology, Immunology, and Center for Immunotherapy, Roswell Park Comprehensive Cancer CenterBuffaloUnited States
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, University of Pennsylvania Perelman School of MedicinePhiladelphiaUnited States
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical SchoolCharlestownUnited States
| | - Adam R Karpf
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
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