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Harami GM, Pálinkás J, Kovács ZJ, Jezsó B, Tárnok K, Harami-Papp H, Hegedüs J, Mahmudova L, Kucsma N, Tóth S, Szakács G, Kovács M. Redox-dependent condensation and cytoplasmic granulation by human ssDNA-binding protein-1 delineate roles in oxidative stress response. iScience 2024; 27:110788. [PMID: 39286502 PMCID: PMC11403420 DOI: 10.1016/j.isci.2024.110788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/06/2024] [Accepted: 08/19/2024] [Indexed: 09/19/2024] Open
Abstract
Human single-stranded DNA binding protein 1 (hSSB1/NABP2/OBFC2B) plays central roles in DNA repair. Here, we show that purified hSSB1 undergoes redox-dependent liquid-liquid phase separation (LLPS) in the presence of single-stranded DNA or RNA, features that are distinct from those of LLPS by bacterial SSB. hSSB1 nucleoprotein droplets form under physiological ionic conditions in response to treatment modeling cellular oxidative stress. hSSB1's intrinsically disordered region is indispensable for LLPS, whereas all three cysteine residues of the oligonucleotide/oligosaccharide-binding fold are necessary to maintain redox-sensitive droplet formation. Proteins interacting with hSSB1 show selective enrichment inside hSSB1 droplets, suggesting tight content control and recruitment functions for the condensates. While these features appear instrumental for genome repair, we detected cytoplasmic hSSB1 condensates in various cell lines colocalizing with stress granules upon oxidative stress, implying extranuclear function in cellular stress response. Our results suggest condensation-linked roles for hSSB1, linking genome repair and cytoplasmic defense.
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Affiliation(s)
- Gábor M Harami
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, 1117 Budapest, Hungary
| | - János Pálinkás
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, 1117 Budapest, Hungary
| | - Zoltán J Kovács
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, 1117 Budapest, Hungary
- HUN-REN-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, 1117 Budapest, Hungary
| | - Bálint Jezsó
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, 1117 Budapest, Hungary
| | - Krisztián Tárnok
- Department of Physiology and Neurobiology, Eötvös Loránd University, Pázmány P. s. 1/c, 1117 Budapest, Hungary
| | - Hajnalka Harami-Papp
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, 1117 Budapest, Hungary
| | - József Hegedüs
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, 1117 Budapest, Hungary
| | - Lamiya Mahmudova
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, 1117 Budapest, Hungary
| | - Nóra Kucsma
- HUN-REN Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, 1117 Budapest, Hungary
| | - Szilárd Tóth
- HUN-REN Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, 1117 Budapest, Hungary
| | - Gergely Szakács
- HUN-REN Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, 1117 Budapest, Hungary
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090 Wien, Austria
| | - Mihály Kovács
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, 1117 Budapest, Hungary
- HUN-REN-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, 1117 Budapest, Hungary
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Kovács ZJ, Harami GM, Pálinkás J, Kuljanishvili N, Hegedüs J, Harami‐Papp H, Mahmudova L, Khamisi L, Szakács G, Kovács M. DNA-dependent phase separation by human SSB2 (NABP1/OBFC2A) protein points to adaptations to eukaryotic genome repair processes. Protein Sci 2024; 33:e4959. [PMID: 38511671 PMCID: PMC10955726 DOI: 10.1002/pro.4959] [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: 10/19/2023] [Revised: 02/04/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Abstract
Single-stranded DNA binding proteins (SSBs) are ubiquitous across all domains of life and play essential roles via stabilizing and protecting single-stranded (ss) DNA as well as organizing multiprotein complexes during DNA replication, recombination, and repair. Two mammalian SSB paralogs (hSSB1 and hSSB2 in humans) were recently identified and shown to be involved in various genome maintenance processes. Following our recent discovery of the liquid-liquid phase separation (LLPS) propensity of Escherichia coli (Ec) SSB, here we show that hSSB2 also forms LLPS condensates under physiologically relevant ionic conditions. Similar to that seen for EcSSB, we demonstrate the essential contribution of hSSB2's C-terminal intrinsically disordered region (IDR) to condensate formation, and the selective enrichment of various genome metabolic proteins in hSSB2 condensates. However, in contrast to EcSSB-driven LLPS that is inhibited by ssDNA binding, hSSB2 phase separation requires single-stranded nucleic acid binding, and is especially facilitated by ssDNA. Our results reveal an evolutionarily conserved role for SSB-mediated LLPS in the spatiotemporal organization of genome maintenance complexes. At the same time, differential LLPS features of EcSSB and hSSB2 point to functional adaptations to prokaryotic versus eukaryotic genome metabolic contexts.
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Affiliation(s)
- Zoltán J. Kovács
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
- HUN‐REN–ELTE Motor Pharmacology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Gábor M. Harami
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - János Pálinkás
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Natalie Kuljanishvili
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - József Hegedüs
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Hajnalka Harami‐Papp
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Lamiya Mahmudova
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Lana Khamisi
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Gergely Szakács
- HUN‐REN Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Academy of SciencesBudapestHungary
- Center for Cancer ResearchMedical University of ViennaWienAustria
| | - Mihály Kovács
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
- HUN‐REN–ELTE Motor Pharmacology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
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Tan K, Tse-Dinh YC. Variation of Structure and Cellular Functions of Type IA Topoisomerases across the Tree of Life. Cells 2024; 13:553. [PMID: 38534397 DOI: 10.3390/cells13060553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/12/2024] [Accepted: 03/19/2024] [Indexed: 03/28/2024] Open
Abstract
Topoisomerases regulate the topological state of cellular genomes to prevent impediments to vital cellular processes, including replication and transcription from suboptimal supercoiling of double-stranded DNA, and to untangle topological barriers generated as replication or recombination intermediates. The subfamily of type IA topoisomerases are the only topoisomerases that can alter the interlinking of both DNA and RNA. In this article, we provide a review of the mechanisms by which four highly conserved N-terminal protein domains fold into a toroidal structure, enabling cleavage and religation of a single strand of DNA or RNA. We also explore how these conserved domains can be combined with numerous non-conserved protein sequences located in the C-terminal domains to form a diverse range of type IA topoisomerases in Archaea, Bacteria, and Eukarya. There is at least one type IA topoisomerase present in nearly every free-living organism. The variation in C-terminal domain sequences and interacting partners such as helicases enable type IA topoisomerases to conduct important cellular functions that require the passage of nucleic acids through the break of a single-strand DNA or RNA that is held by the conserved N-terminal toroidal domains. In addition, this review will exam a range of human genetic disorders that have been linked to the malfunction of type IA topoisomerase.
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Affiliation(s)
- Kemin Tan
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, IL 60439, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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Hu J, Crickard JB. All who wander are not lost: the search for homology during homologous recombination. Biochem Soc Trans 2024; 52:367-377. [PMID: 38323621 PMCID: PMC10903458 DOI: 10.1042/bst20230705] [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: 11/17/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 02/08/2024]
Abstract
Homologous recombination (HR) is a template-based DNA double-strand break repair pathway that functions to maintain genomic integrity. A vital component of the HR reaction is the identification of template DNA to be used during repair. This occurs through a mechanism known as the homology search. The homology search occurs in two steps: a collision step in which two pieces of DNA are forced to collide and a selection step that results in homologous pairing between matching DNA sequences. Selection of a homologous template is facilitated by recombinases of the RecA/Rad51 family of proteins in cooperation with helicases, translocases, and topoisomerases that determine the overall fidelity of the match. This menagerie of molecular machines acts to regulate critical intermediates during the homology search. These intermediates include recombinase filaments that probe for short stretches of homology and early strand invasion intermediates in the form of displacement loops (D-loops) that stabilize paired DNA. Here, we will discuss recent advances in understanding how these specific intermediates are regulated on the molecular level during the HR reaction. We will also discuss how the stability of these intermediates influences the ultimate outcomes of the HR reaction. Finally, we will discuss recent physiological models developed to explain how the homology search protects the genome.
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Affiliation(s)
- Jingyi Hu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, U.S.A
| | - J Brooks Crickard
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, U.S.A
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Saha LK, Saha S, Yang X, Huang SYN, Sun Y, Jo U, Pommier Y. Replication-associated formation and repair of human topoisomerase IIIα cleavage complexes. Nat Commun 2023; 14:1925. [PMID: 37024461 PMCID: PMC10079683 DOI: 10.1038/s41467-023-37498-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023] Open
Abstract
Topoisomerase IIIα (TOP3A) belongs to the conserved Type IA family of DNA topoisomerases. Here we report that human TOP3A is associated with DNA replication forks and that a "self-trapping" TOP3A mutant (TOP3A-R364W) generates cellular TOP3A DNA cleavage complexes (TOP3Accs). We show that trapped TOP3Accs that interfere with replication, induce DNA damage and genome instability. To elucidate how TOP3Accs are repaired, we explored the role of Spartan (SPRTN), the metalloprotease associated with DNA replication, which digests proteins forming DNA-protein crosslinks (DPCs). We find that SPRTN-deficient cells show elevated TOP3Accs, whereas overexpression of SPRTN lowers cellular TOP3Accs. SPRTN is deubiquitinated and epistatic with TDP2 in response to TOP3Accs. In addition, we found that MRE11 can excise TOP3Accs, and that cell cycle determines the preference for the SPRTN-TDP2 vs. the ATM-MRE11 pathways, in S vs. G2, respectively. Our study highlights the prevalence of TOP3Accs repair mechanisms to ensure normal DNA replication.
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Affiliation(s)
- Liton Kumar Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Xi Yang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yilun Sun
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Ukhyun Jo
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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Faria J, Briggs EM, Black JA, McCulloch R. Emergence and adaptation of the cellular machinery directing antigenic variation in the African trypanosome. Curr Opin Microbiol 2022; 70:102209. [PMID: 36215868 DOI: 10.1016/j.mib.2022.102209] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/30/2022] [Accepted: 09/04/2022] [Indexed: 01/25/2023]
Abstract
Survival of the African trypanosome within its mammalian hosts, and hence transmission between hosts, relies upon antigenic variation, where stochastic changes in the composition of their protective variant-surface glycoprotein (VSG) coat thwart effective removal of the pathogen by adaptive immunity. Antigenic variation has evolved remarkable mechanistic complexity in Trypanosoma brucei, with switching of the VSG coat executed by either transcriptional or recombination reactions. In the former, a single T. brucei cell selectively transcribes one telomeric VSG transcription site, termed the expression site (ES), from a pool of around 15. Silencing of the active ES and activation of one previously silent ES can lead to a co-ordinated VSG coat switch. Outside the ESs, the T. brucei genome contains an enormous archive of silent VSG genes and pseudogenes, which can be recombined into the ES to execute a coat switch. Most such recombination involves gene conversion, including copying of a complete VSG and more complex reactions where novel 'mosaic' VSGs are formed as patchworks of sequences from several silent (pseudo)genes. Understanding of the cellular machinery that directs transcriptional and recombination VSG switching is growing rapidly and the emerging picture is of the use of proteins, complexes and pathways that are not limited to trypanosomes, but are shared across the wider grouping of kinetoplastids and beyond, suggesting co-option of widely used, core cellular reactions. We will review what is known about the machinery of antigenic variation and discuss if there remains the possibility of trypanosome adaptations, or even trypanosome-specific machineries, that might offer opportunities to impair this crucial parasite-survival process.
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Affiliation(s)
- Joana Faria
- York Biomedical Research Institute, Department of Biology, University of York, United Kingdom.
| | - Emma M Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom; Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, United Kingdom
| | - Jennifer A Black
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, United Kingdom
| | - Richard McCulloch
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, United Kingdom.
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Xie C, Wang W, Tu C, Meng L, Lu G, Lin G, Lu LY, Tan YQ. OUP accepted manuscript. Hum Reprod Update 2022; 28:763-797. [PMID: 35613017 DOI: 10.1093/humupd/dmac024] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/18/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Chunbo Xie
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Weili Wang
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Chaofeng Tu
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Lanlan Meng
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Guangxiu Lu
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Ge Lin
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Lin-Yu Lu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yue-Qiu Tan
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
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