1
|
Schou KB, Mandacaru S, Tahir M, Tom N, Nilsson AS, Andersen JS, Tiberti M, Papaleo E, Bartek J. Exploring the structural landscape of DNA maintenance proteins. Nat Commun 2024; 15:7748. [PMID: 39237506 PMCID: PMC11377751 DOI: 10.1038/s41467-024-49983-7] [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: 05/27/2023] [Accepted: 06/25/2024] [Indexed: 09/07/2024] Open
Abstract
Evolutionary annotation of genome maintenance (GM) proteins has conventionally been established by remote relationships within protein sequence databases. However, often no significant relationship can be established. Highly sensitive approaches to attain remote homologies based on iterative profile-to-profile methods have been developed. Still, these methods have not been systematically applied in the evolutionary annotation of GM proteins. Here, by applying profile-to-profile models, we systematically survey the repertoire of GM proteins from bacteria to man. We identify multiple GM protein candidates and annotate domains in numerous established GM proteins, among other PARP, OB-fold, Macro, TUDOR, SAP, BRCT, KU, MYB (SANT), and nuclease domains. We experimentally validate OB-fold and MIS18 (Yippee) domains in SPIDR and FAM72 protein families, respectively. Our results indicate that, surprisingly, despite the immense interest and long-term research efforts, the repertoire of genome stability caretakers is still not fully appreciated.
Collapse
Affiliation(s)
- Kenneth Bødkter Schou
- Genome Integrity, Danish Cancer Institute, Danish Cancer Society, Strandboulevarden 49, 2100, Copenhagen, Denmark.
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Laboratory, Karolinska Institute, Solna, 171 77, Sweden.
| | - Samuel Mandacaru
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Muhammad Tahir
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Nikola Tom
- Lipidomics Core Facility, Danish Cancer Institute (DCI), DK-2100, Copenhagen, Denmark
| | - Ann-Sofie Nilsson
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Laboratory, Karolinska Institute, Solna, 171 77, Sweden
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Jiri Bartek
- Genome Integrity, Danish Cancer Institute, Danish Cancer Society, Strandboulevarden 49, 2100, Copenhagen, Denmark.
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Laboratory, Karolinska Institute, Solna, 171 77, Sweden.
| |
Collapse
|
2
|
Ramesh J, Gopalakrishnan RM, Nguyen THA, Lai SK, Li HY, Kim PS, Kutzner A, Inoue N, Heese K. Deciphering the molecular landscape of the FAM72 gene family: Implications for stem cell biology and cancer. Neurochem Int 2024; 180:105853. [PMID: 39236808 DOI: 10.1016/j.neuint.2024.105853] [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: 06/27/2024] [Revised: 08/29/2024] [Accepted: 09/02/2024] [Indexed: 09/07/2024]
Abstract
Family with sequence similarity 72 (FAM72) is a protein-coding gene family located on chromosome 1 in humans, uniquely featuring four paralogs: FAM72A, FAM72B, FAM72C, and FAM72D. While FAM72's presence as a gene pair with the SLIT-ROBO Rho GTPase-activating protein 2 (SRGAP2) is intriguing, its functional roles, particularly in neural stem cells, remain incompletely understood. This review explores the distinct characteristics of FAM72, shedding light on its expression patterns, potential roles in cell cycle regulation, stem cell renewal and implications in neurogenesis and tumorigenesis.
Collapse
Affiliation(s)
- Janani Ramesh
- Department of Medical Biochemistry, Dr ALM Postgraduate Institute of Biomedical Sciences, University of Madras, Chennai, Tamil Nadu, 600-113, India.
| | - Raja Mohan Gopalakrishnan
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, Tamil Nadu, 600-025, India.
| | - Tuan Hoang Anh Nguyen
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea.
| | - Soak-Kuan Lai
- School of Biological Sciences, College of Science, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637-551, Singapore.
| | - Hoi-Yeung Li
- School of Biological Sciences, College of Science, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637-551, Singapore.
| | - Pok-Son Kim
- Department of Information Security, Cryptology, and Mathematics, Kookmin University, Seoul, 136-702, Republic of Korea.
| | - Arne Kutzner
- Department of Information Systems, College of Computer Science, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea.
| | - Noriko Inoue
- Osaka University Institute for Sports and Global Health, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea.
| |
Collapse
|
3
|
Barbulescu P, Chana CK, Wong MK, Ben Makhlouf I, Bruce JP, Feng Y, Keszei AFA, Wong C, Mohamad-Ramshan R, McGary LC, Kashem MA, Ceccarelli DF, Orlicky S, Fang Y, Kuang H, Mazhab-Jafari M, Pezo RC, Bhagwat AS, Pugh TJ, Gingras AC, Sicheri F, Martin A. FAM72A degrades UNG2 through the GID/CTLH complex to promote mutagenic repair during antibody maturation. Nat Commun 2024; 15:7541. [PMID: 39215025 PMCID: PMC11364545 DOI: 10.1038/s41467-024-52009-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 08/23/2024] [Indexed: 09/04/2024] Open
Abstract
A diverse antibody repertoire is essential for humoral immunity. Antibody diversification requires the introduction of deoxyuridine (dU) mutations within immunoglobulin genes to initiate somatic hypermutation (SHM) and class switch recombination (CSR). dUs are normally recognized and excised by the base excision repair (BER) protein uracil-DNA glycosylase 2 (UNG2). However, FAM72A downregulates UNG2 permitting dUs to persist and trigger SHM and CSR. How FAM72A promotes UNG2 degradation is unknown. Here, we show that FAM72A recruits a C-terminal to LisH (CTLH) E3 ligase complex to target UNG2 for proteasomal degradation. Deficiency in CTLH complex components result in elevated UNG2 and reduced SHM and CSR. Cryo-EM structural analysis reveals FAM72A directly binds to MKLN1 within the CTLH complex to recruit and ubiquitinate UNG2. Our study further suggests that FAM72A hijacks the CTLH complex to promote mutagenesis in cancer. These findings show that FAM72A is an E3 ligase substrate adaptor critical for humoral immunity and cancer development.
Collapse
Affiliation(s)
- Philip Barbulescu
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Chetan K Chana
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Matthew K Wong
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Ines Ben Makhlouf
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jeffrey P Bruce
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Yuqing Feng
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Alexander F A Keszei
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Cassandra Wong
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | | | - Laura C McGary
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - Mohammad A Kashem
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Derek F Ceccarelli
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Stephen Orlicky
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Yifei Fang
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Huihui Kuang
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY, USA
| | - Mohammad Mazhab-Jafari
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | | | - Ashok S Bhagwat
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Frank Sicheri
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Alberto Martin
- Department of Immunology, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
4
|
Mu Y, Chen Z, Plummer JB, Zelazowska MA, Dong Q, Krug LT, McBride KM. UNG-RPA interaction governs the choice between high-fidelity and mutagenic uracil repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591927. [PMID: 38746347 PMCID: PMC11092621 DOI: 10.1101/2024.04.30.591927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Mammalian Uracil DNA glycosylase (UNG) removes uracils and initiates high-fidelity base excision repair to maintain genomic stability. During B cell development, activation-induced cytidine deaminase (AID) creates uracils that UNG processes in an error-prone fashion to accomplish immunoglobulin (Ig) somatic hypermutation (SHM) or class switch recombination (CSR). The mechanism that governs high-fidelity versus mutagenic uracil repair is not understood. The B cell tropic gammaherpesvirus (GHV) encodes a functional homolog of UNG that can process AID induced genomic uracils. GHVUNG does not support hypermutation, suggesting intrinsic properties of UNG influence repair outcome. Noting the structural divergence between the UNGs, we define the RPA interacting motif as the determinant of mutation outcome. UNG or RPA mutants unable to interact with each other, only support high-fidelity repair. In B cells, transversions at the Ig variable region are abated while CSR is supported. Thus UNG-RPA governs the generation of mutations and has implications for locus specific mutagenesis in B cells and deamination associated mutational signatures in cancer.
Collapse
|
5
|
Fousek-Schuller VJ, Borgstahl GEO. The Intriguing Mystery of RPA Phosphorylation in DNA Double-Strand Break Repair. Genes (Basel) 2024; 15:167. [PMID: 38397158 PMCID: PMC10888239 DOI: 10.3390/genes15020167] [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: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Human Replication Protein A (RPA) was historically discovered as one of the six components needed to reconstitute simian virus 40 DNA replication from purified components. RPA is now known to be involved in all DNA metabolism pathways that involve single-stranded DNA (ssDNA). Heterotrimeric RPA comprises several domains connected by flexible linkers and is heavily regulated by post-translational modifications (PTMs). The structure of RPA has been challenging to obtain. Various structural methods have been applied, but a complete understanding of RPA's flexible structure, its function, and how it is regulated by PTMs has yet to be obtained. This review will summarize recent literature concerning how RPA is phosphorylated in the cell cycle, the structural analysis of RPA, DNA and protein interactions involving RPA, and how PTMs regulate RPA activity and complex formation in double-strand break repair. There are many holes in our understanding of this research area. We will conclude with perspectives for future research on how RPA PTMs control double-strand break repair in the cell cycle.
Collapse
Affiliation(s)
| | - Gloria E. O. Borgstahl
- Eppley Institute for Research in Cancer & Allied Diseases, UNMC, Omaha, NE 68198-6805, USA
| |
Collapse
|