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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.
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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.
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Yan S, Vaziri C. An introduction for the special issue on environmental health and genome integrity. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:660-663. [PMID: 32683747 PMCID: PMC7442621 DOI: 10.1002/em.22400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 05/23/2023]
Abstract
Environmental exposures and genome maintenance mechanisms that respond to environmentally-induced genotoxicity have a profound impact on human health. Eight review articles in this Special Issue (SI) titled "Environmental Health and Genome Integrity" describe emerging new mechanisms by which distinct forms of environmentally-induced DNA damage are remediated, and explain how DNA repair pathway choices impact genome integrity and disease propensity. Here, we provide an introduction to reviews from this SI. Our expanding knowledge of how genotoxic exposures impact the genome will allow us to better predict, prevent and treat environmentally-induced human diseases such as cancer and neurodegenerative disorders.
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Affiliation(s)
- Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
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