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Role of condensates in modulating DNA repair pathways and its implication for chemoresistance

DNA修复 DNA DNA损伤 细胞生物学 计算生物学 化学 生物 癌症研究 遗传学
作者
Giuseppe Dall'Agnese,Alessandra Dall’Agnese,Salman F. Banani,Marta Codrich,Matilde Clarissa Malfatti,Giulia Antoniali,Gianluca Tell
出处
期刊:Journal of Biological Chemistry [Elsevier]
卷期号:299 (6): 104800-104800 被引量:5
标识
DOI:10.1016/j.jbc.2023.104800
摘要

For cells, it is important to repair DNA damage, such as double-strand and single-strand DNA breaks, because unrepaired DNA can compromise genetic integrity, potentially leading to cell death or cancer. Cells have multiple DNA damage repair pathways that have been the subject of detailed genetic, biochemical, and structural studies. Recently, the scientific community has started to gain evidence that the repair of DNA double-strand breaks may occur within biomolecular condensates and that condensates may also contribute to DNA damage through concentrating genotoxic agents used to treat various cancers. Here, we summarize key features of biomolecular condensates and note where they have been implicated in the repair of DNA double-strand breaks. We also describe evidence suggesting that condensates may be involved in the repair of other types of DNA damage, including single-strand DNA breaks, nucleotide modifications (e.g., mismatch and oxidized bases), and bulky lesions, among others. Finally, we discuss old and new mysteries that could now be addressed considering the properties of condensates, including chemoresistance mechanisms. For cells, it is important to repair DNA damage, such as double-strand and single-strand DNA breaks, because unrepaired DNA can compromise genetic integrity, potentially leading to cell death or cancer. Cells have multiple DNA damage repair pathways that have been the subject of detailed genetic, biochemical, and structural studies. Recently, the scientific community has started to gain evidence that the repair of DNA double-strand breaks may occur within biomolecular condensates and that condensates may also contribute to DNA damage through concentrating genotoxic agents used to treat various cancers. Here, we summarize key features of biomolecular condensates and note where they have been implicated in the repair of DNA double-strand breaks. We also describe evidence suggesting that condensates may be involved in the repair of other types of DNA damage, including single-strand DNA breaks, nucleotide modifications (e.g., mismatch and oxidized bases), and bulky lesions, among others. Finally, we discuss old and new mysteries that could now be addressed considering the properties of condensates, including chemoresistance mechanisms. Chemical changes in DNA can be highly harmful to living organisms. DNA, like other molecules, can undergo multiple chemical reactions. These reactions can occur spontaneously or as a result of exposure to chemicals or radiation (1Lindahl T. Instability and decay of the primary structure of DNA.Nature. 1993; 362: 709-715Crossref PubMed Scopus (4388) Google Scholar). When these reactions result in altered DNA structure, including base excision and DNA breaks, DNA damage can block gene expression and replication negatively affecting cell homeostasis, function, and survival (2Alhmoud J.F. 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Considerations and challenges in studying liquid-liquid phase separation and biomolecular condensates.Cell. 2019; 176: 419-434Abstract Full Text Full Text PDF PubMed Scopus (1065) Google Scholar). Condensates may allow for fast adaptive responses to changes in the environment. They can buffer concentrations of proteins; concentrate proteins to activate biochemical reactions; or sequester proteins to inactivate biochemical reactions. Thanks to their specific viscoelastic properties, condensates could generate mechanical forces. Condensates may also act as filters, for example, the nucleopore condensates, which permit or deny the entry of molecules into the nucleus (30Su X. Ditlev J.A. Hui E. Xing W. Banjade S. Okrut J. et al.Phase separation of signaling molecules promotes T cell receptor signal transduction.Science. 2016; 352: 595-599Crossref PubMed Scopus (625) Google Scholar, 45Alberti S. Gladfelter A. Mittag T. 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LLPS can be described as a thermodynamically driven phenomenon consisting of de-mixing of a solution into two or more distinct liquid phases. In the 1940s, Flory and Huggins described the ability of polymers, such as proteins, to self-organize into discrete liquid-like droplets (49Flory P.J. Thermodynamics of high polymer solutions.J. Chem. Phys. 1941; 9: 423-432Crossref Scopus (1278) Google Scholar, 50Huggins M.L. Solutions of long chain compounds.J. Chem. Phys. 1941; 9: 440Crossref Google Scholar), and over the last 10 years, many different proteins essential for life have been shown to be able to form dense phases resembling liquid-like droplets (14Sabari B.R. Dall'Agnese A. Young R.A. Biomolecular condensates in the nucleus.Trends Biochem. Sci. 2020; 45: 961-977Abstract Full Text Full Text PDF PubMed Scopus (148) Google Scholar, 16Banani S.F. Lee H.O. Hyman A.A. Rosen M.K. Biomolecular condensates: organizers of cellular biochemistry.Nat. Rev. Mol. 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IDRs seem to preferentially form condensates with specific partners that show similar physicochemical characteristics and behavior, including charge–charge interactions and hydrophobic interactions (59Lyons H. Veettil R.T. Pradhan P. Fornero C. De La Cruz N. Ito K. et al.Functional partitioning of transcriptional regulators by patterned charge blocks.Cell. 2023; 186: 327-345.e328Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar). Considering the importance of protein–protein interactions for condensate formation, it is reasonable to think that it would be possible to artificially design molecules that will alter condensate formation for therapeutic purposes. Kameda and colleagues artificially designed small peptides that either promoted or impaired the formation of p53 condensates in vitro. This approach could also be taken to design peptide-therapeutics to alter condensate properties in cells (60Kamagata K. Ariefai M. Takahashi H. Hando A. Subekti D.R.G. 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Mismatch repair: from preserving genome
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