1
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Yuan B, Bi C, Tian Y, Wang J, Jin Y, Alsayegh K, Tehseen M, Yi G, Zhou X, Shao Y, Romero FV, Fischle W, Izpisua Belmonte JC, Hamdan S, Huang Y, Li M. Modulation of the microhomology-mediated end joining pathway suppresses large deletions and enhances homology-directed repair following CRISPR-Cas9-induced DNA breaks. BMC Biol 2024; 22:101. [PMID: 38685010 PMCID: PMC11059712 DOI: 10.1186/s12915-024-01896-z] [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: 06/12/2023] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND CRISPR-Cas9 genome editing often induces unintended, large genomic rearrangements, posing potential safety risks. However, there are no methods for mitigating these risks. RESULTS Using long-read individual-molecule sequencing (IDMseq), we found the microhomology-mediated end joining (MMEJ) DNA repair pathway plays a predominant role in Cas9-induced large deletions (LDs). We targeted MMEJ-associated genes genetically and/or pharmacologically and analyzed Cas9-induced LDs at multiple gene loci using flow cytometry and long-read sequencing. Reducing POLQ levels or activity significantly decreases LDs, while depleting or overexpressing RPA increases or reduces LD frequency, respectively. Interestingly, small-molecule inhibition of POLQ and delivery of recombinant RPA proteins also dramatically promote homology-directed repair (HDR) at multiple disease-relevant gene loci in human pluripotent stem cells and hematopoietic progenitor cells. CONCLUSIONS Our findings reveal the contrasting roles of RPA and POLQ in Cas9-induced LD and HDR, suggesting new strategies for safer and more precise genome editing.
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Affiliation(s)
- Baolei Yuan
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Chongwei Bi
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Yeteng Tian
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Jincheng Wang
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, College of Chemistry, College of Engineering, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yiqing Jin
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Khaled Alsayegh
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Present address: King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Jeddah, Saudi Arabia
| | - Muhammad Tehseen
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Gang Yi
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Xuan Zhou
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | | | - Fernanda Vargas Romero
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Wolfgang Fischle
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Juan Carlos Izpisua Belmonte
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Altos Labs, Inc, San Diego, CA, 92121, USA
| | - Samir Hamdan
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, College of Chemistry, College of Engineering, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, China
| | - Mo Li
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
- Bioengineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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2
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Pytko KG, Dannenberg RL, Eckert KA, Hedglin M. Replication of [AT/TA] 25 Microsatellite Sequences by Human DNA Polymerase δ Holoenzymes Is Dependent on dNTP and RPA Levels. Biochemistry 2024; 63:969-983. [PMID: 38623046 DOI: 10.1021/acs.biochem.4c00006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Fragile sites are unstable genomic regions that are prone to breakage during stressed DNA replication. Several common fragile sites (CFS) contain A+T-rich regions including perfect [AT/TA] microsatellite repeats that may collapse into hairpins when in single-stranded DNA (ssDNA) form and coincide with chromosomal hotspots for breakage and rearrangements. While many factors contribute to CFS instability, evidence exists for replication stalling within [AT/TA] microsatellite repeats. Currently, it is unknown how stress causes replication stalling within [AT/TA] microsatellite repeats. To investigate this, we utilized FRET to characterize the structures of [AT/TA]25 sequences and also reconstituted lagging strand replication to characterize the progression of pol δ holoenzymes through A+T-rich sequences. The results indicate that [AT/TA]25 sequences adopt hairpins that are unwound by the major ssDNA-binding complex, RPA, and the progression of pol δ holoenzymes through A+T-rich sequences saturated with RPA is dependent on the template sequence and dNTP concentration. Importantly, the effects of RPA on the replication of [AT/TA]25 sequences are dependent on dNTP concentration, whereas the effects of RPA on the replication of A+T-rich, nonstructure-forming sequences are independent of dNTP concentration. Collectively, these results reveal complexities in lagging strand replication and provide novel insights into how [AT/TA] microsatellite repeats contribute to genome instability.
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Affiliation(s)
- Kara G Pytko
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Rachel L Dannenberg
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Kristin A Eckert
- Department of Pathology and Laboratory Medicine, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, United States
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
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3
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Granger SL, Sharma R, Kaushik V, Razzaghi M, Honda M, Gaur P, Bhat DS, Labenz SM, Heinen JE, Williams BA, Tabei SMA, Wlodarski MW, Antony E, Spies M. Human hnRNPA1 reorganizes telomere-bound Replication Protein A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.09.540056. [PMID: 37214874 PMCID: PMC10197631 DOI: 10.1101/2023.05.09.540056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Human replication protein A (RPA) is a heterotrimeric ssDNA binding protein responsible for many aspects of cellular DNA metabolism. Dynamic interactions of the four RPA DNA binding domains (DBDs) with DNA control replacement of RPA by downstream proteins in various cellular metabolic pathways. RPA plays several important functions at telomeres where it binds to and melts telomeric G-quadruplexes, non-canonical DNA structures formed at the G-rich telomeric ssDNA overhangs. Here, we combine single-molecule total internal reflection fluorescence microscopy (smTIRFM) and mass photometry (MP) with biophysical and biochemical analyses to demonstrate that heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) specifically remodels RPA bound to telomeric ssDNA by dampening the RPA configurational dynamics and forming a ternary complex. Uniquely, among hnRNPA1 target RNAs, telomeric repeat-containing RNA (TERRA) is selectively capable of releasing hnRNPA1 from the RPA-telomeric DNA complex. We speculate that this telomere specific RPA-DNA-hnRNPA1 complex is an important structure in telomere protection. One Sentence Summary At the single-stranded ends of human telomeres, the heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) binds to and modulates conformational dynamics of the ssDNA binding protein RPA forming a ternary complex which is controlled by telomeric repeat-containing RNA (TERRA).
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4
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Yang SF, Nelson CB, Wells JK, Fernando M, Lu R, Allen JAM, Malloy L, Lamm N, Murphy VJ, Mackay JP, Deans AJ, Cesare AJ, Sobinoff AP, Pickett HA. ZNF827 is a single-stranded DNA binding protein that regulates the ATR-CHK1 DNA damage response pathway. Nat Commun 2024; 15:2210. [PMID: 38472229 PMCID: PMC10933417 DOI: 10.1038/s41467-024-46578-0] [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: 06/15/2022] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
The ATR-CHK1 DNA damage response pathway becomes activated by the exposure of RPA-coated single-stranded DNA (ssDNA) that forms as an intermediate during DNA damage and repair, and as a part of the replication stress response. Here, we identify ZNF827 as a component of the ATR-CHK1 kinase pathway. We demonstrate that ZNF827 is a ssDNA binding protein that associates with RPA through concurrent binding to ssDNA intermediates. These interactions are dependent on two clusters of C2H2 zinc finger motifs within ZNF827. We find that ZNF827 accumulates at stalled forks and DNA damage sites, where it activates ATR and promotes the engagement of homologous recombination-mediated DNA repair. Additionally, we demonstrate that ZNF827 depletion inhibits replication initiation and sensitizes cancer cells to the topoisomerase inhibitor topotecan, revealing ZNF827 as a therapeutic target within the DNA damage response pathway.
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Affiliation(s)
- Sile F Yang
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Christopher B Nelson
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Jadon K Wells
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Madushan Fernando
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Robert Lu
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Lisa Malloy
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Noa Lamm
- Nuclear Dynamics Group, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Vincent J Murphy
- Genome Stability Unit, St Vincent's Institute, Fitzroy, VIC, 3065, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Andrew J Deans
- Genome Stability Unit, St Vincent's Institute, Fitzroy, VIC, 3065, Australia
- Department of Medicine (St Vincent's), University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia.
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5
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Zheng F, Yao NY, Georgescu RE, Li H, O’Donnell ME. Structure of the PCNA unloader Elg1-RFC. SCIENCE ADVANCES 2024; 10:eadl1739. [PMID: 38427736 PMCID: PMC10906927 DOI: 10.1126/sciadv.adl1739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
During DNA replication, the proliferating cell nuclear antigen (PCNA) clamps are loaded onto primed sites for each Okazaki fragment synthesis by the AAA+ heteropentamer replication factor C (RFC). PCNA encircling duplex DNA is quite stable and is removed from DNA by the dedicated clamp unloader Elg1-RFC. Here, we show the cryo-EM structure of Elg1-RFC in various states with PCNA. The structures reveal essential features of Elg1-RFC that explain how it is dedicated to PCNA unloading. Specifically, Elg1 contains two external loops that block opening of the Elg1-RFC complex for DNA binding, and an "Elg1 plug" domain that fills the central DNA binding chamber, thereby reinforcing the exclusive PCNA unloading activity of Elg1-RFC. Elg1-RFC was capable of unloading PCNA using non-hydrolyzable AMP-PNP. Both RFC and Elg1-RFC could remove PCNA from covalently closed circular DNA, indicating that PCNA unloading occurs by a mechanism that is distinct from PCNA loading. Implications for the PCNA unloading mechanism are discussed.
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Affiliation(s)
- Fengwei Zheng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Nina Y. Yao
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, NY, New York, USA
| | - Roxana E. Georgescu
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, NY, New York, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Michael E. O’Donnell
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, NY, New York, USA
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6
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Kumar N, Taneja A, Ghosh M, Rothweiler U, Sundaresan N, Singh M. Harmonin homology domain-mediated interaction of RTEL1 helicase with RPA and DNA provides insights into its recruitment to DNA repair sites. Nucleic Acids Res 2024; 52:1450-1470. [PMID: 38153196 PMCID: PMC10853778 DOI: 10.1093/nar/gkad1208] [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: 11/03/2022] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023] Open
Abstract
The regulator of telomere elongation helicase 1 (RTEL1) plays roles in telomere DNA maintenance, DNA repair, and genome stability by dismantling D-loops and unwinding G-quadruplex structures. RTEL1 comprises a helicase domain, two tandem harmonin homology domains 1&2 (HHD1 and HHD2), and a Zn2+-binding RING domain. In vitro D-loop disassembly by RTEL1 is enhanced in the presence of replication protein A (RPA). However, the mechanism of RTEL1 recruitment at non-telomeric D-loops remains unknown. In this study, we have unravelled a direct physical interaction between RTEL1 and RPA. Under DNA damage conditions, we showed that RTEL1 and RPA colocalise in the cell. Coimmunoprecipitation showed that RTEL1 and RPA interact, and the deletion of HHDs of RTEL1 significantly reduced this interaction. NMR chemical shift perturbations (CSPs) showed that RPA uses its 32C domain to interact with the HHD2 of RTEL1. Interestingly, HHD2 also interacted with DNA in the in vitro experiments. HHD2 structure was determined using X-ray crystallography, and NMR CSPs mapping revealed that both RPA 32C and DNA competitively bind to HHD2 on an overlapping surface. These results establish novel roles of accessory HHDs in RTEL1's functions and provide mechanistic insights into the RPA-mediated recruitment of RTEL1 to DNA repair sites.
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Affiliation(s)
- Niranjan Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Arushi Taneja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Meenakshi Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Ulli Rothweiler
- The Norwegian Structural Biology Centre, Department of Chemistry, The Arctic University of Norway, N-9037, Tromsø, Norway
| | | | - Mahavir Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India
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7
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Isik E, Shukla K, Pospisilova M, König C, Andrs M, Rao S, Rosano V, Dobrovolna J, Krejci L, Janscak P. MutSβ-MutLβ-FANCJ axis mediates the restart of DNA replication after fork stalling at cotranscriptional G4/R-loops. SCIENCE ADVANCES 2024; 10:eadk2685. [PMID: 38324687 PMCID: PMC10849593 DOI: 10.1126/sciadv.adk2685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024]
Abstract
Transcription-replication conflicts (TRCs) induce formation of cotranscriptional RNA:DNA hybrids (R-loops) stabilized by G-quadruplexes (G4s) on the displaced DNA strand, which can cause fork stalling. Although it is known that these stalled forks can resume DNA synthesis in a process initiated by MUS81 endonuclease, how TRC-associated G4/R-loops are removed to allow fork passage remains unclear. Here, we identify the mismatch repair protein MutSβ, an MLH1-PMS1 heterodimer termed MutLβ, and the G4-resolving helicase FANCJ as factors that are required for MUS81-initiated restart of DNA replication at TRC sites in human cells. This DNA repair process depends on the G4-binding activity of MutSβ, the helicase activity of FANCJ, and the binding of FANCJ to MLH1. Furthermore, we show that MutSβ, MutLβ, and MLH1-FANCJ interaction mediate FANCJ recruitment to G4s. These data suggest that MutSβ, MutLβ, and FANCJ act in conjunction to eliminate G4/R-loops at TRC sites, allowing replication restart.
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Affiliation(s)
- Esin Isik
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kaustubh Shukla
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 143 00 Prague, Czech Republic
| | - Michaela Pospisilova
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A7, Brno 62500, Czech Republic
- International Clinical Research Center, St Anne's University Hospital, Pekarska 53, Brno 656 91, Czech Republic
| | - Christiane König
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Andrs
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Satyajeet Rao
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Vinicio Rosano
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jana Dobrovolna
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 143 00 Prague, Czech Republic
| | - Lumir Krejci
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A7, Brno 62500, Czech Republic
- International Clinical Research Center, St Anne's University Hospital, Pekarska 53, Brno 656 91, Czech Republic
| | - Pavel Janscak
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 143 00 Prague, Czech Republic
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8
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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.
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Affiliation(s)
| | - Gloria E. O. Borgstahl
- Eppley Institute for Research in Cancer & Allied Diseases, UNMC, Omaha, NE 68198-6805, USA
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9
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Maltseva EA, Vasil’eva IA, Moor NA, Kim DV, Dyrkheeva NS, Kutuzov MM, Vokhtantsev IP, Kulishova LM, Zharkov DO, Lavrik OI. Cas9 is mostly orthogonal to human systems of DNA break sensing and repair. PLoS One 2023; 18:e0294683. [PMID: 38019812 PMCID: PMC10686484 DOI: 10.1371/journal.pone.0294683] [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: 06/28/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
CRISPR/Cas9 system is а powerful gene editing tool based on the RNA-guided cleavage of target DNA. The Cas9 activity can be modulated by proteins involved in DNA damage signalling and repair due to their interaction with double- and single-strand breaks (DSB and SSB, respectively) generated by wild-type Cas9 or Cas9 nickases. Here we address the interplay between Streptococcus pyogenes Cas9 and key DNA repair factors, including poly(ADP-ribose) polymerase 1 (SSB/DSB sensor), its closest homolog poly(ADP-ribose) polymerase 2, Ku antigen (DSB sensor), DNA ligase I (SSB sensor), replication protein A (DNA duplex destabilizer), and Y-box binding protein 1 (RNA/DNA binding protein). None of those significantly affected Cas9 activity, while Cas9 efficiently shielded DSBs and SSBs from their sensors. Poly(ADP-ribosyl)ation of Cas9 detected for poly(ADP-ribose) polymerase 2 had no apparent effect on the activity. In cellulo, Cas9-dependent gene editing was independent of poly(ADP-ribose) polymerase 1. Thus, Cas9 can be regarded as an enzyme mostly orthogonal to the natural regulation of human systems of DNA break sensing and repair.
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Affiliation(s)
| | - Inna A. Vasil’eva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Nina A. Moor
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Daria V. Kim
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | - Mikhail M. Kutuzov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Ivan P. Vokhtantsev
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Lilya M. Kulishova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Olga I. Lavrik
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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10
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Honda M, Razzaghi M, Gaur P, Malacaria E, Di Biagi L, Aiello FA, Paintsil EA, Stanfield A, Deppe BJ, Gakhar L, Schnicker NJ, Spies MA, Pichierri P, Spies M. Human RAD52 double-ring remodels replication forks restricting fork reversal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.566657. [PMID: 38014173 PMCID: PMC10680749 DOI: 10.1101/2023.11.14.566657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Human RAD52 1,2 is a multifunctional DNA repair protein involved in several cellular events that support genome stability including protection of stalled DNA replication forks from excessive degradation 3-7 . In its gatekeeper role, RAD52 binds to and stabilizes stalled replication forks during replication stress protecting them from reversal by SMARCAL1 5 . The structural and molecular mechanism of the RAD52-mediated fork protection remains elusive. Here, using P1 nuclease sensitivity, biochemical and single-molecule analyses we show that RAD52 dynamically remodels replication forks through its strand exchange activity. The presence of the ssDNA binding protein RPA at the fork modulates the kinetics of the strand exchange without impeding the reaction outcome. Mass photometry and single-particle cryo-electron microscopy show that the replication fork promotes a unique nucleoprotein structure containing head-to-head arrangement of two undecameric RAD52 rings with an extended positively charged surface that accommodates all three arms of the replication fork. We propose that the formation and continuity of this surface is important for the strand exchange reaction and for competition with SMARCAL1.
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11
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Pytko KG, Dannenberg RL, Eckert KA, Hedglin M. Replication of [AT/TA] 25 microsatellite sequences by human DNA polymerase δ holoenzymes is dependent on dNTP and RPA levels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566133. [PMID: 37986888 PMCID: PMC10659299 DOI: 10.1101/2023.11.07.566133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Difficult-to-Replicate Sequences (DiToRS) are natural impediments in the human genome that inhibit DNA replication under endogenous replication. Some of the most widely-studied DiToRS are A+T-rich, high "flexibility regions," including long stretches of perfect [AT/TA] microsatellite repeats that have the potential to collapse into hairpin structures when in single-stranded DNA (ssDNA) form and are sites of recurrent structural variation and double-stranded DNA (dsDNA) breaks. Currently, it is unclear how these flexibility regions impact DNA replication, greatly limiting our fundamental understanding of human genome stability. To investigate replication through flexibility regions, we utilized FRET to characterize the effects of the major ssDNA-binding complex, RPA, on the structure of perfect [AT/TA]25 microsatellite repeats and also re-constituted human lagging strand replication to quantitatively characterize initial encounters of pol δ holoenzymes with A+T-rich DNA template sequences. The results indicate that [AT/TA]25 sequences adopt hairpin structures that are unwound by RPA and pol δ holoenzymes support dNTP incorporation through the [AT/TA]25 sequences as well as an A+T-rich, non-structure forming sequence. Furthermore, the extent of dNTP incorporation is dependent on the sequence of the DNA template and the concentration of dNTPs. Importantly, the effects of RPA on the replication of [AT/TA]25 sequences are dependent on the concentration of dNTPs, whereas the effects of RPA on the replication of an A+T-rich, non-structure forming sequence are independent of dNTP concentration. Collectively, these results reveal complexities in lagging strand replication and provide novel insights into how flexibility regions contribute to genome instability.
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Affiliation(s)
- Kara G. Pytko
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Rachel L. Dannenberg
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Kristin A. Eckert
- Department of Pathology and Laboratory Medicine, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
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12
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Gall-Duncan T, Luo J, Jurkovic CM, Fischer LA, Fujita K, Deshmukh AL, Harding RJ, Tran S, Mehkary M, Li V, Leib DE, Chen R, Tanaka H, Mason AG, Lévesque D, Khan M, Razzaghi M, Prasolava T, Lanni S, Sato N, Caron MC, Panigrahi GB, Wang P, Lau R, Castel AL, Masson JY, Tippett L, Turner C, Spies M, La Spada AR, Campos EI, Curtis MA, Boisvert FM, Faull RLM, Davidson BL, Nakamori M, Okazawa H, Wold MS, Pearson CE. Antagonistic roles of canonical and Alternative-RPA in disease-associated tandem CAG repeat instability. Cell 2023; 186:4898-4919.e25. [PMID: 37827155 DOI: 10.1016/j.cell.2023.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 06/30/2023] [Accepted: 09/09/2023] [Indexed: 10/14/2023]
Abstract
Expansions of repeat DNA tracts cause >70 diseases, and ongoing expansions in brains exacerbate disease. During expansion mutations, single-stranded DNAs (ssDNAs) form slipped-DNAs. We find the ssDNA-binding complexes canonical replication protein A (RPA1, RPA2, and RPA3) and Alternative-RPA (RPA1, RPA3, and primate-specific RPA4) are upregulated in Huntington disease and spinocerebellar ataxia type 1 (SCA1) patient brains. Protein interactomes of RPA and Alt-RPA reveal unique and shared partners, including modifiers of CAG instability and disease presentation. RPA enhances in vitro melting, FAN1 excision, and repair of slipped-CAGs and protects against CAG expansions in human cells. RPA overexpression in SCA1 mouse brains ablates expansions, coincident with decreased ATXN1 aggregation, reduced brain DNA damage, improved neuron morphology, and rescued motor phenotypes. In contrast, Alt-RPA inhibits melting, FAN1 excision, and repair of slipped-CAGs and promotes CAG expansions. These findings suggest a functional interplay between the two RPAs where Alt-RPA may antagonistically offset RPA's suppression of disease-associated repeat expansions, which may extend to other DNA processes.
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Affiliation(s)
- Terence Gall-Duncan
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jennifer Luo
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Laura A Fischer
- Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kyota Fujita
- Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Amit L Deshmukh
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rachel J Harding
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Stephanie Tran
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mustafa Mehkary
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Vanessa Li
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - David E Leib
- Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Ran Chen
- Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hikari Tanaka
- Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Amanda G Mason
- Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Dominique Lévesque
- Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Mahreen Khan
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mortezaali Razzaghi
- Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Tanya Prasolava
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stella Lanni
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Nozomu Sato
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marie-Christine Caron
- CHU de Québec-Université Laval, Oncology Division, Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec, QC, Canada
| | - Gagan B Panigrahi
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Peixiang Wang
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rachel Lau
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Jean-Yves Masson
- CHU de Québec-Université Laval, Oncology Division, Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec, QC, Canada
| | - Lynette Tippett
- School of Psychology, University of Auckland, Auckland, New Zealand; University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Clinton Turner
- Anatomical Pathology, LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - Maria Spies
- Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Albert R La Spada
- Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, University of California, Irvine School of Medicine, Irvine, CA, USA; Neurobiology & Behavior, University of California, Irvine, Irvine, CA, USA; Center for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA
| | - Eric I Campos
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Maurice A Curtis
- University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand; Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | | | - Richard L M Faull
- University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand; Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | - Beverly L Davidson
- Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Masayuki Nakamori
- Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hitoshi Okazawa
- Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Marc S Wold
- Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Christopher E Pearson
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.
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13
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Papageorgiou AC, Pospisilova M, Cibulka J, Ashraf R, Waudby CA, Kadeřávek P, Maroz V, Kubicek K, Prokop Z, Krejci L, Tripsianes K. Recognition and coacervation of G-quadruplexes by a multifunctional disordered region in RECQ4 helicase. Nat Commun 2023; 14:6751. [PMID: 37875529 PMCID: PMC10598209 DOI: 10.1038/s41467-023-42503-z] [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: 02/09/2022] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
Biomolecular polyelectrolyte complexes can be formed between oppositely charged intrinsically disordered regions (IDRs) of proteins or between IDRs and nucleic acids. Highly charged IDRs are abundant in the nucleus, yet few have been functionally characterized. Here, we show that a positively charged IDR within the human ATP-dependent DNA helicase Q4 (RECQ4) forms coacervates with G-quadruplexes (G4s). We describe a three-step model of charge-driven coacervation by integrating equilibrium and kinetic binding data in a global numerical model. The oppositely charged IDR and G4 molecules form a complex in the solution that follows a rapid nucleation-growth mechanism leading to a dynamic equilibrium between dilute and condensed phases. We also discover a physical interaction with Replication Protein A (RPA) and demonstrate that the IDR can switch between the two extremes of the structural continuum of complexes. The structural, kinetic, and thermodynamic profile of its interactions revealed a dynamic disordered complex with nucleic acids and a static ordered complex with RPA protein. The two mutually exclusive binding modes suggest a regulatory role for the IDR in RECQ4 function by enabling molecular handoffs. Our study extends the functional repertoire of IDRs and demonstrates a role of polyelectrolyte complexes involved in G4 binding.
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Affiliation(s)
- Anna C Papageorgiou
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michaela Pospisilova
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jakub Cibulka
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Raghib Ashraf
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Pavel Kadeřávek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Volha Maroz
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Karel Kubicek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic
| | - Lumir Krejci
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic.
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14
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Kang Y, Han YG, Khim KW, Choi WG, Ju MK, Park K, Shin KJ, Chae YC, Choi JH, Kim H, Lee JY. Alteration of replication protein A binding mode on single-stranded DNA by NSMF potentiates RPA phosphorylation by ATR kinase. Nucleic Acids Res 2023; 51:7936-7950. [PMID: 37378431 PMCID: PMC10450186 DOI: 10.1093/nar/gkad543] [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: 12/03/2022] [Revised: 06/07/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Replication protein A (RPA), a eukaryotic single-stranded DNA (ssDNA) binding protein, dynamically interacts with ssDNA in different binding modes and plays essential roles in DNA metabolism such as replication, repair, and recombination. RPA accumulation on ssDNA due to replication stress triggers the DNA damage response (DDR) by activating the ataxia telangiectasia and RAD3-related (ATR) kinase, which phosphorylates itself and downstream DDR factors, including RPA. We recently reported that the N-methyl-D-aspartate receptor synaptonuclear signaling and neuronal migration factor (NSMF), a neuronal protein associated with Kallmann syndrome, promotes RPA32 phosphorylation via ATR upon replication stress. However, how NSMF enhances ATR-mediated RPA32 phosphorylation remains elusive. Here, we demonstrate that NSMF colocalizes and physically interacts with RPA at DNA damage sites in vivo and in vitro. Using purified RPA and NSMF in biochemical and single-molecule assays, we find that NSMF selectively displaces RPA in the more weakly bound 8- and 20-nucleotide binding modes from ssDNA, allowing the retention of more stable RPA molecules in the 30-nt binding mode. The 30-nt binding mode of RPA enhances RPA32 phosphorylation by ATR, and phosphorylated RPA becomes stabilized on ssDNA. Our findings provide new mechanistic insight into how NSMF facilitates the role of RPA in the ATR pathway.
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Affiliation(s)
- Yujin Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ye Gi Han
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Keon Woo Khim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Woo Gyun Choi
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Min Kyung Ju
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kibeom Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kyeong Jin Shin
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Young Chan Chae
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jang Hyun Choi
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Institute of Basic Science Center for Genomic Integrity, Ulsan 44919, Republic of Korea
| | - Hongtae Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Institute of Basic Science Center for Genomic Integrity, Ulsan 44919, Republic of Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Institute of Basic Science Center for Genomic Integrity, Ulsan 44919, Republic of Korea
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15
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Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H. Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification on biology. Cell Rep 2023; 42:112694. [PMID: 37392384 PMCID: PMC10529453 DOI: 10.1016/j.celrep.2023.112694] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/01/2023] [Accepted: 06/09/2023] [Indexed: 07/03/2023] Open
Abstract
Rad24-RFC (replication factor C) loads the 9-1-1 checkpoint clamp onto the recessed 5' ends by binding a 5' DNA at an external surface site and threading the 3' single-stranded DNA (ssDNA) into 9-1-1. We find here that Rad24-RFC loads 9-1-1 onto DNA gaps in preference to a recessed 5' end, thus presumably leaving 9-1-1 on duplex 3' ss/double-stranded DNA (dsDNA) after Rad24-RFC ejects from DNA. We captured five Rad24-RFC-9-1-1 loading intermediates using a 10-nt gap DNA. We also determined the structure of Rad24-RFC-9-1-1 using a 5-nt gap DNA. The structures reveal that Rad24-RFC is unable to melt DNA ends and that a Rad24 loop limits the dsDNA length in the chamber. These observations explain Rad24-RFC's preference for a preexisting gap of over 5-nt ssDNA and suggest a direct role of the 9-1-1 in gap repair with various TLS (trans-lesion synthesis) polymerases in addition to signaling the ATR kinase.
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Affiliation(s)
- Fengwei Zheng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Roxana E Georgescu
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA
| | - Nina Y Yao
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA
| | - Michael E O'Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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16
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Hoitsma NM, Norris J, Khoang TH, Kaushik V, Chadda R, Antony E, Hedglin M, Freudenthal BD. Mechanistic insight into AP-endonuclease 1 cleavage of abasic sites at stalled replication fork mimics. Nucleic Acids Res 2023; 51:6738-6753. [PMID: 37264933 PMCID: PMC10359615 DOI: 10.1093/nar/gkad481] [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: 11/07/2022] [Revised: 05/13/2023] [Accepted: 05/31/2023] [Indexed: 06/03/2023] Open
Abstract
Many types of damage, including abasic sites, block replicative DNA polymerases causing replication fork uncoupling and generating ssDNA. AP-Endonuclease 1 (APE1) has been shown to cleave abasic sites in ssDNA. Importantly, APE1 cleavage of ssDNA at a replication fork has significant biological implications by generating double strand breaks that could collapse the replication fork. Despite this, the molecular basis and efficiency of APE1 processing abasic sites at replication forks remain elusive. Here, we investigate APE1 cleavage of abasic substrates that mimic APE1 interactions at stalled replication forks or gaps. We determine that APE1 has robust activity on these substrates, like dsDNA, and report rates for cleavage and product release. X-ray structures visualize the APE1 active site, highlighting an analogous mechanism is used to process ssDNA substrates as canonical APE1 activity on dsDNA. However, mutational analysis reveals R177 to be uniquely critical for the APE1 ssDNA cleavage mechanism. Additionally, we investigate the interplay between APE1 and Replication Protein A (RPA), the major ssDNA-binding protein at replication forks, revealing that APE1 can cleave an abasic site while RPA is still bound to the DNA. Together, this work provides molecular level insights into abasic ssDNA processing by APE1, including the presence of RPA.
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Affiliation(s)
- Nicole M Hoitsma
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jessica Norris
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Thu H Khoang
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Rahul Chadda
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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17
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Mukherjee A, Hossain Z, Erben E, Ma S, Choi JY, Kim HS. Identification of a small-molecule inhibitor that selectively blocks DNA-binding by Trypanosoma brucei replication protein A1. Nat Commun 2023; 14:4390. [PMID: 37474515 PMCID: PMC10359466 DOI: 10.1038/s41467-023-39839-x] [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: 10/12/2022] [Accepted: 06/30/2023] [Indexed: 07/22/2023] Open
Abstract
Replication Protein A (RPA) is a broadly conserved complex comprised of the RPA1, 2 and 3 subunits. RPA protects the exposed single-stranded DNA (ssDNA) during DNA replication and repair. Using structural modeling, we discover an inhibitor, JC-229, that targets RPA1 in Trypanosoma brucei, the causative parasite of African trypanosomiasis. The inhibitor is highly toxic to T. brucei cells, while mildly toxic to human cells. JC-229 treatment mimics the effects of TbRPA1 depletion, including DNA replication inhibition and DNA damage accumulation. In-vitro ssDNA-binding assays demonstrate that JC-229 inhibits the activity of TbRPA1, but not the human ortholog. Indeed, despite the high sequence identity with T. cruzi and Leishmania RPA1, JC-229 only impacts the ssDNA-binding activity of TbRPA1. Site-directed mutagenesis confirms that the DNA-Binding Domain A (DBD-A) in TbRPA1 contains a JC-229 binding pocket. Residue Serine 105 determines specific binding and inhibition of TbRPA1 but not T. cruzi and Leishmania RPA1. Our data suggest a path toward developing and testing highly specific inhibitors for the treatment of African trypanosomiasis.
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Affiliation(s)
- Aditi Mukherjee
- Public Health Research Institute, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA
| | - Zakir Hossain
- Department of Chemistry and Biochemistry, Queens College, New York, NY, 11367, USA
| | - Esteban Erben
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Provincia de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín, Provincia de Buenos Aires, Argentina
| | - Shuai Ma
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Jun Yong Choi
- Department of Chemistry and Biochemistry, Queens College, New York, NY, 11367, USA.
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| | - Hee-Sook Kim
- Public Health Research Institute, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA.
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA.
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18
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Nieminuszczy J, Martin PR, Broderick R, Krwawicz J, Kanellou A, Mocanu C, Bousgouni V, Smith C, Wen KK, Woodward B, Bakal C, Shackley F, Aguilera A, Stewart G, Vyas Y, Niedzwiedz W. Actin nucleators safeguard replication forks by limiting nascent strand degradation. Nucleic Acids Res 2023; 51:6337-6354. [PMID: 37224534 PMCID: PMC10325910 DOI: 10.1093/nar/gkad369] [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: 10/13/2022] [Revised: 04/17/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023] Open
Abstract
Accurate genome replication is essential for all life and a key mechanism of disease prevention, underpinned by the ability of cells to respond to replicative stress (RS) and protect replication forks. These responses rely on the formation of Replication Protein A (RPA)-single stranded (ss) DNA complexes, yet this process remains largely uncharacterized. Here, we establish that actin nucleation-promoting factors (NPFs) associate with replication forks, promote efficient DNA replication and facilitate association of RPA with ssDNA at sites of RS. Accordingly, their loss leads to deprotection of ssDNA at perturbed forks, impaired ATR activation, global replication defects and fork collapse. Supplying an excess of RPA restores RPA foci formation and fork protection, suggesting a chaperoning role for actin nucleators (ANs) (i.e. Arp2/3, DIAPH1) and NPFs (i.e, WASp, N-WASp) in regulating RPA availability upon RS. We also discover that β-actin interacts with RPA directly in vitro, and in vivo a hyper-depolymerizing β-actin mutant displays a heightened association with RPA and the same dysfunctional replication phenotypes as loss of ANs/NPFs, which contrasts with the phenotype of a hyper-polymerizing β-actin mutant. Thus, we identify components of actin polymerization pathways that are essential for preventing ectopic nucleolytic degradation of perturbed forks by modulating RPA activity.
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Affiliation(s)
- Jadwiga Nieminuszczy
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Peter R Martin
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Ronan Broderick
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Joanna Krwawicz
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Alexandra Kanellou
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Camelia Mocanu
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Vicky Bousgouni
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Charlotte Smith
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Kuo-Kuang Wen
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, Penn State College of Medicine, Penn State Health Children's Hospital, Hershey, PA 17033, USA
| | - Beth L Woodward
- Genome Stability and Human Disease Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Chris Bakal
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Fiona Shackley
- Paediatric Immunology, Allergy and Infectious Diseases, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Grant S Stewart
- Genome Stability and Human Disease Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Yatin M Vyas
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, Penn State College of Medicine, Penn State Health Children's Hospital, Hershey, PA 17033, USA
| | - Wojciech Niedzwiedz
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
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19
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Bhat D, Malacaria E, Biagi L, Razzaghi M, Honda M, Hobbs K, Hengel S, Pichierri P, Spies M, Spies M. Therapeutic disruption of RAD52-ssDNA complexation via novel drug-like inhibitors. NAR Cancer 2023; 5:zcad018. [PMID: 37139244 PMCID: PMC10150327 DOI: 10.1093/narcan/zcad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/09/2023] [Accepted: 04/14/2023] [Indexed: 05/05/2023] Open
Abstract
RAD52 protein is a coveted target for anticancer drug discovery. Similar to poly-ADP-ribose polymerase (PARP) inhibitors, pharmacological inhibition of RAD52 is synthetically lethal with defects in genome caretakers BRCA1 and BRCA2 (∼25% of breast and ovarian cancers). Emerging structure activity relationships for RAD52 are complex, making it challenging to transform previously identified disruptors of the RAD52-ssDNA interaction into drug-like leads using traditional medicinal chemistry approaches. Using pharmacophoric informatics on the RAD52 complexation by epigallocatechin (EGC), and the Enamine in silico REAL database, we identified six distinct chemical scaffolds that occupy the same physical space on RAD52 as EGC. All six were RAD52 inhibitors (IC50 ∼23-1200 μM) with two of the compounds (Z56 and Z99) selectively killing BRCA-mutant cells and inhibiting cellular activities of RAD52 at micromolar inhibitor concentrations. While Z56 had no effect on the ssDNA-binding protein RPA and was toxic to BRCA-mutant cells only, Z99 inhibited both proteins and displayed toxicity towards BRCA-complemented cells. Optimization of the Z99 scaffold resulted in a set of more powerful and selective inhibitors (IC50 ∼1.3-8 μM), which were only toxic to BRCA-mutant cells. RAD52 complexation by Z56, Z99 and its more specific derivatives provide a roadmap for next generation of cancer therapeutics.
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Affiliation(s)
- Divya S Bhat
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - Eva Malacaria
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Ludovica Di Biagi
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Mortezaali Razzaghi
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - Masayoshi Honda
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - Kathryn F Hobbs
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, Iowa City, IA 52242, USA
| | - Sarah R Hengel
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - Pietro Pichierri
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - M Ashley Spies
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, Iowa City, IA 52242, USA
- Naturis Informatika LLC, 401 Mullin Ave., Iowa City, IA 52246, USA
| | - Maria Spies
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
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20
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Greenwood SN, Kulkarni RS, Mikhail M, Weiser BP. Replication Protein A Enhances Kinetics of Uracil DNA Glycosylase on ssDNA and Across DNA Junctions: Explored with a DNA Repair Complex Produced with SpyCatcher/SpyTag Ligation. Chembiochem 2023; 24:e202200765. [PMID: 36883884 PMCID: PMC10267839 DOI: 10.1002/cbic.202200765] [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: 12/22/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/09/2023]
Abstract
DNA repair proteins participate in extensive protein-protein interactions that promote the formation of DNA repair complexes. To understand how complex formation affects protein function during base excision repair, we used SpyCatcher/SpyTag ligation to produce a covalent complex between human uracil DNA glycosylase (UNG2) and replication protein A (RPA). Our covalent "RPA-Spy-UNG2" complex could identify and excise uracil bases in duplex areas next to ssDNA-dsDNA junctions slightly faster than the wild-type proteins, but this was highly dependent on DNA structure, as the turnover of the RPA-Spy-UNG2 complex slowed at DNA junctions where RPA tightly engaged long ssDNA sections. Conversely, the enzymes preferred uracil sites in ssDNA where RPA strongly enhanced uracil excision by UNG2 regardless of ssDNA length. Finally, RPA was found to promote UNG2 excision of two uracil sites positioned across a ssDNA-dsDNA junction, and dissociation of UNG2 from RPA enhanced this process. Our approach of ligating together RPA and UNG2 to reveal how complex formation affects enzyme function could be applied to examine other assemblies of DNA repair proteins.
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Affiliation(s)
- Sharon N Greenwood
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Rashmi S Kulkarni
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Michel Mikhail
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
- Department of Internal Medicine, Newark Beth Israel Medical Center, Newark, NJ 07112, USA
| | - Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
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21
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Wang X, Zhang S, Zhang Z, Mazloum NA, Lee EYC, Lee MYW. The DHX9 helicase interacts with human DNA polymerase δ4 and stimulates its activity in D-loop extension synthesis. DNA Repair (Amst) 2023; 128:103513. [PMID: 37285751 DOI: 10.1016/j.dnarep.2023.103513] [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: 03/08/2023] [Revised: 04/28/2023] [Accepted: 05/11/2023] [Indexed: 06/09/2023]
Abstract
The extension of the invading strand within a displacement loop (D-loop) is a key step in homology directed repair (HDR) of doubled stranded DNA breaks. The primary goal of these studies was to test the hypotheses that 1) D-loop extension by human DNA polymerase δ4 (Pol δ4) is facilitated by DHX9, a 3' to 5' motor helicase, which acts to unwind the leading edge of the D-loop, and 2) the recruitment of DHX9 is mediated by direct protein-protein interactions between DHX9 and Pol δ4 and/or PCNA. DNA synthesis by Pol δ4 was analyzed in a reconstitution assay by the extension of a 93mer oligonucleotide inserted into a plasmid to form a D-loop. Product formation by Pol δ4 was monitored by incorporation of [α-32P]dNTPs into the 93mer primer followed by denaturing gel electrophoresis. The results showed that DHX9 strongly stimulated Pol δ4 mediated D-loop extension. Direct interactions of DHX9 with PCNA, the p125 and the p12 subunits of Pol δ4 were demonstrated by pull-down assays with purified proteins. These data support the hypothesis that DHX9 helicase is recruited by Pol δ4/PCNA to facilitate D-loop synthesis in HDR, and is a participant in cellular HDR. The involvement of DHX9 in HDR represents an important addition to its multiple cellular roles. Such helicase-polymerase interactions may represent an important aspect of the mechanisms involved in D-loop primer extension synthesis in HDR.
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Affiliation(s)
- Xiaoxiao Wang
- Department of Biochemistry and Molecular Biology, New York Medical College, 15 Dana Road, Valhalla, NY 10595, USA
| | - Sufang Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, 15 Dana Road, Valhalla, NY 10595, USA
| | - Zhongtao Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, 15 Dana Road, Valhalla, NY 10595, USA
| | - Nayef A Mazloum
- Department of Biochemistry and Molecular Biology, New York Medical College, 15 Dana Road, Valhalla, NY 10595, USA
| | - Ernest Y C Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, 15 Dana Road, Valhalla, NY 10595, USA
| | - Marietta Y W Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, 15 Dana Road, Valhalla, NY 10595, USA.
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22
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Norris JL, Rogers LO, Pytko KG, Dannenberg RL, Perreault S, Kaushik V, Kuppa S, Antony E, Hedglin M. Interplay of macromolecular interactions during assembly of human DNA polymerase δ holoenzymes and initiation of DNA synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539896. [PMID: 37215012 PMCID: PMC10197535 DOI: 10.1101/2023.05.09.539896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In humans, DNA polymerase δ (Pol δ) holoenzymes, comprised of Pol δ and the processivity sliding clamp, proliferating cell nuclear antigen (PCNA), carry out DNA synthesis during lagging strand DNA replication, initiation of leading strand DNA replication, and the major DNA damage repair and tolerance pathways. Pol δ holoenzymes are assembled at primer/template (P/T) junctions and initiate DNA synthesis in a coordinated process involving the major single strand DNA-binding protein complex, replication protein A (RPA), the processivity sliding clamp loader, replication factor C (RFC), PCNA, and Pol δ. Each of these factors interact uniquely with a P/T junction and most directly engage one another. Currently, the interplay between these macromolecular interactions is largely unknown. In the present study, novel Förster Resonance Energy Transfer (FRET) assays reveal that dynamic interactions of RPA with a P/T junction during assembly of a Pol δ holoenzyme and initiation of DNA synthesis maintain RPA at a P/T junction and accommodate RFC, PCNA, and Pol δ, maximizing the efficiency of each process. Collectively, these studies significantly advance our understanding of human DNA replication and DNA repair.
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Affiliation(s)
- Jessica L. Norris
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Lindsey O. Rogers
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Kara G. Pytko
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Rachel L. Dannenberg
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Samuel Perreault
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Vikas Kaushik
- The Saint Louis University School of Medicine, Department of Biochemistry and Molecular Biology, St. Louis MO, 63104
| | - Sahiti Kuppa
- The Saint Louis University School of Medicine, Department of Biochemistry and Molecular Biology, St. Louis MO, 63104
| | - Edwin Antony
- The Saint Louis University School of Medicine, Department of Biochemistry and Molecular Biology, St. Louis MO, 63104
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
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23
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Zheng F, Georgescu RE, Yao NY, O’Donnell ME, Li H. Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539266. [PMID: 37205533 PMCID: PMC10187155 DOI: 10.1101/2023.05.03.539266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Recent structural studies show the Rad24-RFC loads the 9-1-1 checkpoint clamp onto a recessed 5' end by binding the 5' DNA on Rad24 at an external surface site and threading the 3' ssDNA into the well-established internal chamber and into 9-1-1. We find here that Rad24-RFC loads 9-1-1 onto DNA gaps in preference to a recessed 5' DNA end, thus presumably leaving 9-1-1 on a 3' ss/ds DNA after Rad24-RFC ejects from the 5' gap end and may explain reports of 9-1-1 directly functioning in DNA repair with various TLS polymerases, in addition to signaling the ATR kinase. To gain a deeper understanding of 9-1-1 loading at gaps we report high-resolution structures of Rad24-RFC during loading of 9-1-1 onto 10-nt and 5-nt gapped DNAs. At a 10-nt gap we captured five Rad24-RFC-9-1-1 loading intermediates in which the 9-1-1 DNA entry gate varies from fully open to fully closed around DNA using ATPγS, supporting the emerging view that ATP hydrolysis is not needed for clamp opening/closing, but instead for dissociation of the loader from the clamp encircling DNA. The structure of Rad24-RFC-9-1-1 at a 5-nt gap shows a 180° axially rotated 3'-dsDNA which orients the template strand to bridge the 3'- and 5'- junctions with a minimum 5-nt ssDNA. The structures reveal a unique loop on Rad24 that limits the length of dsDNA in the inner chamber, and inability to melt DNA ends unlike RFC, thereby explaining Rad24-RFC's preference for a preexisting ssDNA gap and suggesting a direct role in gap repair in addition to its checkpoint role.
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Affiliation(s)
- Fengwei Zheng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Roxana E. Georgescu
- DNA Replication Laboratory, The Rockefeller University, New York, New York, USA
| | - Nina Y. Yao
- DNA Replication Laboratory, The Rockefeller University, New York, New York, USA
| | - Michael E. O’Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
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24
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Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W. Lesion recognition by XPC, TFIIH and XPA in DNA excision repair. Nature 2023; 617:170-175. [PMID: 37076618 PMCID: PMC10416759 DOI: 10.1038/s41586-023-05959-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 03/15/2023] [Indexed: 04/21/2023]
Abstract
Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts1. After initial recognition by XPC in global genome repair or a stalled RNA polymerase in transcription-coupled repair, damaged DNA is transferred to the seven-subunit TFIIH core complex (Core7) for verification and dual incisions by the XPF and XPG nucleases2. Structures capturing lesion recognition by the yeast XPC homologue Rad4 and TFIIH in transcription initiation or DNA repair have been separately reported3-7. How two different lesion recognition pathways converge and how the XPB and XPD helicases of Core7 move the DNA lesion for verification are unclear. Here we report on structures revealing DNA lesion recognition by human XPC and DNA lesion hand-off from XPC to Core7 and XPA. XPA, which binds between XPB and XPD, kinks the DNA duplex and shifts XPC and the DNA lesion by nearly a helical turn relative to Core7. The DNA lesion is thus positioned outside of Core7, as would occur with RNA polymerase. XPB and XPD, which track the lesion-containing strand but translocate DNA in opposite directions, push and pull the lesion-containing strand into XPD for verification.
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Affiliation(s)
- Jinseok Kim
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Chia-Lung Li
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Xuemin Chen
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
- School of Life Sciences, Anhui University, Hefei, China
| | - Yanxiang Cui
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Filip M Golebiowski
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
- Roche Polska, Warsaw, Poland
| | - Huaibin Wang
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Fumio Hanaoka
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan
| | - Kaoru Sugasawa
- Biosignal Research Center and Graduate School of Science, Kobe University, Kobe, Japan.
| | - Wei Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA.
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25
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Njeri C, Pepenella S, Battapadi T, Bambara RA, Balakrishnan L. DNA Polymerase Delta Exhibits Altered Catalytic Properties on Lysine Acetylation. Genes (Basel) 2023; 14:genes14040774. [PMID: 37107532 PMCID: PMC10137900 DOI: 10.3390/genes14040774] [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: 01/11/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
DNA polymerase delta is the primary polymerase that is involved in undamaged nuclear lagging strand DNA replication. Our mass-spectroscopic analysis has revealed that the human DNA polymerase δ is acetylated on subunits p125, p68, and p12. Using substrates that simulate Okazaki fragment intermediates, we studied alterations in the catalytic properties of acetylated polymerase and compared it to the unmodified form. The current data show that the acetylated form of human pol δ displays a higher polymerization activity compared to the unmodified form of the enzyme. Additionally, acetylation enhances the ability of the polymerase to resolve complex structures such as G-quadruplexes and other secondary structures that might be present on the template strand. More importantly, the ability of pol δ to displace a downstream DNA fragment is enhanced upon acetylation. Our current results suggest that acetylation has a profound effect on the activity of pol δ and supports the hypothesis that acetylation may promote higher-fidelity DNA replication.
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Affiliation(s)
- Catherine Njeri
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Sharon Pepenella
- Department of Microbiology and Immunology, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Tripthi Battapadi
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Robert A Bambara
- Department of Microbiology and Immunology, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Lata Balakrishnan
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
- Indiana University Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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26
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Phase separation properties of RPA combine high-affinity ssDNA binding with dynamic condensate functions at telomeres. Nat Struct Mol Biol 2023; 30:451-462. [PMID: 36894693 PMCID: PMC10113159 DOI: 10.1038/s41594-023-00932-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 01/27/2023] [Indexed: 03/11/2023]
Abstract
RPA has been shown to protect single-stranded DNA (ssDNA) intermediates from instability and breakage. RPA binds ssDNA with sub-nanomolar affinity, yet dynamic turnover is required for downstream ssDNA transactions. How ultrahigh-affinity binding and dynamic turnover are achieved simultaneously is not well understood. Here we reveal that RPA has a strong propensity to assemble into dynamic condensates. In solution, purified RPA phase separates into liquid droplets with fusion and surface wetting behavior. Phase separation is stimulated by sub-stoichiometric amounts of ssDNA, but not RNA or double-stranded DNA, and ssDNA gets selectively enriched in RPA condensates. We find the RPA2 subunit required for condensation and multi-site phosphorylation of the RPA2 N-terminal intrinsically disordered region to regulate RPA self-interaction. Functionally, quantitative proximity proteomics links RPA condensation to telomere clustering and integrity in cancer cells. Collectively, our results suggest that RPA-coated ssDNA is contained in dynamic RPA condensates whose properties are important for genome organization and stability.
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27
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Nieminuszczy J, Martin PR, Broderick R, Krwawicz J, Kanellou A, Mocanu C, Bousgouni V, Smith C, Wen KK, Woodward BL, Bakal C, Shackley F, Aguilera A, Stewart GS, Vyas YM, Niedzwiedz W. Actin nucleators safeguard replication forks by limiting nascent strand degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523639. [PMID: 36711944 PMCID: PMC9882250 DOI: 10.1101/2023.01.12.523639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Accurate genome replication is essential for all life and a key mechanism of disease prevention, underpinned by the ability of cells to respond to replicative stress (RS) and protect replication forks. These responses rely on the formation of Replication Protein A (RPA)-single stranded (ss) DNA complexes, yet this process remains largely uncharacterized. Here we establish that actin nucleation-promoting factors (NPFs) associate with replication forks, promote efficient DNA replication and facilitate association of RPA with ssDNA at sites of RS. Accordingly, their loss leads to deprotection of ssDNA at perturbed forks, impaired ATR activation, global replication defects and fork collapse. Supplying an excess of RPA restores RPA foci formation and fork protection, suggesting a chaperoning role for actin nucleators (ANs) (i.e., Arp2/3, DIAPH1) and NPFs (i.e, WASp, N-WASp) in regulating RPA availability upon RS. We also discover that β-actin interacts with RPA directly in vitro , and in vivo a hyper-depolymerizing β-actin mutant displays a heightened association with RPA and the same dysfunctional replication phenotypes as loss of ANs/NPFs, which contrasts with the phenotype of a hyper-polymerizing β-actin mutant. Thus, we identify components of actin polymerization pathways that are essential for preventing ectopic nucleolytic degradation of perturbed forks by modulating RPA activity.
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Affiliation(s)
| | - Peter R. Martin
- Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Ronan Broderick
- Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Joanna Krwawicz
- Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | | | - Camelia Mocanu
- Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Vicky Bousgouni
- Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Charlotte Smith
- Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Kuo-Kuang Wen
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, PennState College of Medicine, PennState Health Children’s Hospital, Hershey, Pennsylvania 17033, USA
| | - Beth L. Woodward
- Genome Stability and Human Disease Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Chris Bakal
- Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Fiona Shackley
- Paediatric Immunology, Allergy and Infectious Diseases, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK
| | - Andres Aguilera
- Centro Andaluz de Biologia Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Grant S. Stewart
- Genome Stability and Human Disease Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Yatin M. Vyas
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, PennState College of Medicine, PennState Health Children’s Hospital, Hershey, Pennsylvania 17033, USA
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28
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Shin S, Hyun K, Lee J, Joo D, Kulikowicz T, Bohr V, Kim J, Hohng S. Werner syndrome protein works as a dimer for unwinding and replication fork regression. Nucleic Acids Res 2022; 51:337-348. [PMID: 36583333 PMCID: PMC9841404 DOI: 10.1093/nar/gkac1200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 11/28/2022] [Accepted: 12/05/2022] [Indexed: 12/31/2022] Open
Abstract
The determination of the oligomeric state of functional enzymes is essential for the mechanistic understanding of their catalytic activities. RecQ helicases have diverse biochemical activities, but it is still unclear how their activities are related to their oligomeric states. We use single-molecule multi-color fluorescence imaging to determine the oligomeric states of Werner syndrome protein (WRN) during its unwinding and replication fork regression activities. We reveal that WRN binds to a forked DNA as a dimer, and unwinds it without any change of its oligomeric state. In contrast, WRN binds to a replication fork as a tetramer, and is dimerized during activation of replication fork regression. By selectively inhibiting the helicase activity of WRN on specific strands, we reveal how the active dimers of WRN distinctly use the energy of ATP hydrolysis for repetitive unwinding and replication fork regression.
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Affiliation(s)
| | | | - Jinwoo Lee
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Seoul, Republic of Korea
| | - Dongwon Joo
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Seoul, Republic of Korea
| | - Tomasz Kulikowicz
- Section on DNA repair, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Vilhelm A Bohr
- Section on DNA repair, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Sungchul Hohng
- To whom correspondence should be addressed. Tel: +82 2 880 6593;
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29
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Hodson C, van Twest S, Dylewska M, O'Rourke JJ, Tan W, Murphy VJ, Walia M, Abbouche L, Nieminuszczy J, Dunn E, Bythell-Douglas R, Heierhorst J, Niedzwiedz W, Deans AJ. Branchpoint translocation by fork remodelers as a general mechanism of R-loop removal. Cell Rep 2022; 41:111749. [PMID: 36476850 DOI: 10.1016/j.celrep.2022.111749] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/05/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Co-transcriptional R loops arise from stalling of RNA polymerase, leading to the formation of stable DNA:RNA hybrids. Unresolved R loops promote genome instability but are counteracted by helicases and nucleases. Here, we show that branchpoint translocases are a third class of R-loop-displacing enzyme in vitro. In cells, deficiency in the Fanconi-anemia-associated branchpoint translocase FANCM causes R-loop accumulation, particularly after treatment with DNA:RNA-hybrid-stabilizing agents. This correlates with FANCM localization at R-loop-prone regions of the genome. Moreover, other branchpoint translocases associated with human disease, such as SMARCAL1 and ZRANB3, and those from lower organisms can also remove R loops in vitro. Branchpoint translocases are more potent than helicases in resolving R loops, indicating their evolutionary important role in R-loop suppression. In human cells, FANCM, SMARCAL1, and ZRANB3 depletion causes additive effects on R-loop accumulation and DNA damage. Our work reveals a mechanistic basis for R-loop displacement that is linked to genome stability.
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Affiliation(s)
- Charlotte Hodson
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Sylvie van Twest
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | | | - Julienne J O'Rourke
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Winnie Tan
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Vincent J Murphy
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Mannu Walia
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Lara Abbouche
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | | | - Elyse Dunn
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Rohan Bythell-Douglas
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Jörg Heierhorst
- Department of Medicine (St Vincent's Health), University of Melbourne, Fitzroy, VIC 3065, Australia; Molecular Genetics Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | | | - Andrew J Deans
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine (St Vincent's Health), University of Melbourne, Fitzroy, VIC 3065, Australia.
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30
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Dannenberg RL, Cardina JA, Pytko KG, Hedglin M. Tracking of progressing human DNA polymerase δ holoenzymes reveals distributions of DNA lesion bypass activities. Nucleic Acids Res 2022; 50:9893-9908. [PMID: 36107777 PMCID: PMC9508823 DOI: 10.1093/nar/gkac745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/10/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
During DNA replication, DNA lesions in lagging strand templates are initially encountered by DNA polymerase δ (pol δ) holoenzymes comprised of pol δ and the PCNA processivity sliding clamp. These encounters are thought to stall replication of an afflicted template before the lesion, activating DNA damage tolerance (DDT) pathways that replicate the lesion and adjacent DNA sequence, allowing pol δ to resume. However, qualitative studies observed that human pol δ can replicate various DNA lesions, albeit with unknown proficiencies, which raises issues regarding the role of DDT in replicating DNA lesions. To address these issues, we re-constituted human lagging strand replication to quantitatively characterize initial encounters of pol δ holoenzymes with DNA lesions. The results indicate pol δ holoenzymes support dNTP incorporation opposite and beyond multiple lesions and the extent of these activities depends on the lesion and pol δ proofreading. Furthermore, after encountering a given DNA lesion, subsequent dissociation of pol δ is distributed around the lesion and a portion does not dissociate. The distributions of these events are dependent on the lesion and pol δ proofreading. Collectively, these results reveal complexity and heterogeneity in the replication of lagging strand DNA lesions, significantly advancing our understanding of human DDT.
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Affiliation(s)
- Rachel L Dannenberg
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Joseph A Cardina
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kara G Pytko
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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31
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Halder S, Sanchez A, Ranjha L, Reginato G, Ceppi I, Acharya A, Anand R, Cejka P. Double-stranded DNA binding function of RAD51 in DNA protection and its regulation by BRCA2. Mol Cell 2022; 82:3553-3565.e5. [PMID: 36070766 DOI: 10.1016/j.molcel.2022.08.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/16/2022] [Accepted: 08/10/2022] [Indexed: 11/26/2022]
Abstract
RAD51 and the breast cancer suppressor BRCA2 have critical functions in DNA double-strand (dsDNA) break repair by homologous recombination and the protection of newly replicated DNA from nucleolytic degradation. The recombination function of RAD51 requires its binding to single-stranded DNA (ssDNA), whereas binding to dsDNA is inhibitory. Using reconstituted MRE11-, EXO1-, and DNA2-dependent nuclease reactions, we show that the protective function of RAD51 unexpectedly depends on its binding to dsDNA. The BRC4 repeat of BRCA2 abrogates RAD51 binding to dsDNA and accordingly impairs the function of RAD51 in protection. The BRCA2 C-terminal RAD51-binding segment (TR2) acts in a dominant manner to overcome the effect of BRC4. Mechanistically, TR2 stabilizes RAD51 binding to dsDNA, even in the presence of BRC4, promoting DNA protection. Our data suggest that RAD51's dsDNA-binding capacity may have evolved together with its function in replication fork protection and provide a mechanistic basis for the DNA-protection function of BRCA2.
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Affiliation(s)
- Swagata Halder
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Aurore Sanchez
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Lepakshi Ranjha
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Giordano Reginato
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland
| | - Ilaria Ceppi
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland
| | - Ananya Acharya
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland
| | - Roopesh Anand
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland.
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32
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Shaw AE, Kairamkonda S, Ghodke H, Schauer GD. Biochemical and single-molecule techniques to study accessory helicase resolution of R-loop proteins at stalled replication forks. Methods Enzymol 2022; 673:191-225. [PMID: 35965008 DOI: 10.1016/bs.mie.2022.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
R-loop proteins present a stable and robust blockade to the progression of a DNA replication fork during S-phase. The consequences of this block can include mutagenesis and other irreversible chromosomal catastrophes, causing genomic instability and disease. As such, further investigation into the molecular mechanisms underlying R-loop protein resolution is warranted. The critical role of non-replicative accessory helicases in R-loop protein resolution has increasingly come into light in recent years. Such helicases include the Pif1-family, monomeric helicases that have been studied in many different contexts and that have been ascribed to a multitude of separable protective functions in the cell. In this chapter, we present protocols to study R-loop protein resolution by Pif1 helicase at stalled replication forks using purified proteins, both at the biochemical and single-molecule level. Our system uses recombinant proteins expressed in Saccharomyces cerevisiae but could apply to practically any organism of interest due to the high interspecies homology of the proteins involved in DNA replication. The methods we outline are extensible to many systems and should be applicable to studying R-loop clearance by any Superfamily (SF) 1B helicase. These techniques will further enable mechanistic research on these critical but understudied components of the genomic maintenance program.
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Affiliation(s)
- Alisa E Shaw
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Sreeya Kairamkonda
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Harshad Ghodke
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW, Australia
| | - Grant D Schauer
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States.
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33
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Zheng F, Georgescu RE, Yao NY, Li H, O'Donnell ME. Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair. eLife 2022; 11:77469. [PMID: 35829698 PMCID: PMC9293004 DOI: 10.7554/elife.77469] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/06/2022] [Indexed: 12/27/2022] Open
Abstract
RFC uses ATP to assemble PCNA onto primed sites for replicative DNA polymerases d and e. The RFC pentamer forms a central chamber that binds 3' ss/ds DNA junctions to load PCNA onto DNA during replication. We show here five structures that identify a 2nd DNA binding site in RFC that binds a 5' duplex. This 5' DNA site is located between the N-terminal BRCT domain and AAA+ module of the large Rfc1 subunit. Our structures reveal ideal binding to a 7-nt gap, which includes 2 bp unwound by the clamp loader. Biochemical studies show enhanced binding to 5 and 10 nt gaps, consistent with the structural results. Because both 3' and 5' ends are present at a ssDNA gap, we propose that the 5' site facilitates RFC's PCNA loading activity at a DNA damage-induced gap to recruit gap-filling polymerases. These findings are consistent with genetic studies showing that base excision repair of gaps greater than 1 base requires PCNA and involves the 5' DNA binding domain of Rfc1. We further observe that a 5' end facilitates PCNA loading at an RPA coated 30-nt gap, suggesting a potential role of the RFC 5'-DNA site in lagging strand DNA synthesis.
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Affiliation(s)
- Fengwei Zheng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, United States
| | - Roxana E Georgescu
- DNA Replication Laboratory, Rockefeller University, New York, United States
| | - Nina Y Yao
- DNA Replication Laboratory, Rockefeller University, New York, United States
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, United States
| | - Michael E O'Donnell
- Howard Hughes Medical Institute, Rockefeller University, New York, United States
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34
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WASp modulates RPA function on single-stranded DNA in response to replication stress and DNA damage. Nat Commun 2022; 13:3743. [PMID: 35768435 PMCID: PMC9243104 DOI: 10.1038/s41467-022-31415-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 06/08/2022] [Indexed: 02/07/2023] Open
Abstract
Perturbation in the replication-stress response (RSR) and DNA-damage response (DDR) causes genomic instability. Genomic instability occurs in Wiskott-Aldrich syndrome (WAS), a primary immunodeficiency disorder, yet the mechanism remains largely uncharacterized. Replication protein A (RPA), a single-strand DNA (ssDNA) binding protein, has key roles in the RSR and DDR. Here we show that human WAS-protein (WASp) modulates RPA functions at perturbed replication forks (RFs). Following genotoxic insult, WASp accumulates at RFs, associates with RPA, and promotes RPA:ssDNA complexation. WASp deficiency in human lymphocytes destabilizes RPA:ssDNA-complexes, impairs accumulation of RPA, ATR, ETAA1, and TOPBP1 at genotoxin-perturbed RFs, decreases CHK1 activation, and provokes global RF dysfunction. las17 (yeast WAS-homolog)-deficient S. cerevisiae also show decreased ScRPA accumulation at perturbed RFs, impaired DNA recombination, and increased frequency of DNA double-strand break (DSB)-induced single-strand annealing (SSA). Consequently, WASp (or Las17)-deficient cells show increased frequency of DSBs upon genotoxic insult. Our study reveals an evolutionarily conserved, essential role of WASp in the DNA stress-resolution pathway, such that WASp deficiency provokes RPA dysfunction-coupled genomic instability. Cancer develops in Wiskott-Aldrich syndrome (WAS). Here the authors identify a role for WAS-protein (WASp) in the DNA stress-resolution pathway by promoting the function of Replication Protein A at replication forks after DNA damage.
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35
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Baris Y, Taylor MRG, Aria V, Yeeles JTP. Fast and efficient DNA replication with purified human proteins. Nature 2022; 606:204-210. [PMID: 35585232 PMCID: PMC7613936 DOI: 10.1038/s41586-022-04759-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/13/2022] [Indexed: 12/16/2022]
Abstract
Chromosome replication is performed by a complex and intricate ensemble of proteins termed the replisome, where the DNA polymerases Polδ and Polε, DNA polymerase α-primase (Polα) and accessory proteins including AND-1, CLASPIN and TIMELESS-TIPIN (respectively known as Ctf4, Mrc1 and Tof1-Csm3 in Saccharomyces cerevisiae) are organized around the CDC45-MCM-GINS (CMG) replicative helicase1-7. Because a functional human replisome has not been reconstituted from purified proteins, how these factors contribute to human DNA replication and whether additional proteins are required for optimal DNA synthesis are poorly understood. Here we report the biochemical reconstitution of human replisomes that perform fast and efficient DNA replication using 11 purified human replication factors made from 43 polypeptides. Polε, but not Polδ, is crucial for optimal leading-strand synthesis. Unexpectedly, Polε-mediated leading-strand replication is highly dependent on the sliding-clamp processivity factor PCNA and the alternative clamp loader complex CTF18-RFC. We show how CLASPIN and TIMELESS-TIPIN contribute to replisome progression and demonstrate that, in contrast to the budding yeast replisome8, AND-1 directly augments leading-strand replication. Moreover, although AND-1 binds to Polα9,10, the interaction is dispensable for lagging-strand replication, indicating that Polα is functionally recruited via an AND-1-independent mechanism for priming in the human replisome. Collectively, our work reveals how the human replisome achieves fast and efficient leading-strand and lagging-strand DNA replication, and provides a powerful system for future studies of the human replisome and its interactions with other DNA metabolic processes.
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36
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Gao B, Zheng YT, Su AM, Sun B, Xi XG, Hou XM. Remodeling the conformational dynamics of I-motif DNA by helicases in ATP-independent mode at acidic environment. iScience 2022; 25:103575. [PMID: 34988409 PMCID: PMC8704484 DOI: 10.1016/j.isci.2021.103575] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/09/2021] [Accepted: 12/03/2021] [Indexed: 01/18/2023] Open
Abstract
I-motifs are noncanonical four-stranded DNA structures formed by C-rich sequences at acidic environment with critical biofunctions. The particular pH sensitivity has inspired the development of i-motifs as pH sensors and DNA motors in nanotechnology. However, the folding and regulation mechanisms of i-motifs remain elusive. Here, using single-molecule FRET, we first show that i-motifs are more dynamic than G4s. Impressively, i-motifs display a high diversity of six folding species with slow interconversion. Further results indicate that i-motifs can be linearized by Replication protein A. More importantly, we identified a number of helicases with high specificity to i-motifs at low pH. All these helicases directly act on and efficiently resolve i-motifs into intermediates independent of ATP, although they poorly unwind G4 or duplex at low pH. Owing to the extreme sensitivity to helicases and no need for ATP, i-motif may be applied as a probe for helicase sensing both in vitro and in vivo.
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Affiliation(s)
- Bo Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Ya-Ting Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Ai-Min Su
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, China
- LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Gif-sur-Yvette, France
| | - Xi-Miao Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Corresponding author
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37
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Brown AL, Collins CD, Thompson S, Coxon M, Mertz TM, Roberts SA. Single-stranded DNA binding proteins influence APOBEC3A substrate preference. Sci Rep 2021; 11:21008. [PMID: 34697369 PMCID: PMC8546098 DOI: 10.1038/s41598-021-00435-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/11/2021] [Indexed: 11/09/2022] Open
Abstract
The cytidine deaminase, APOBEC3A (A3A), is a prominent source of mutations in multiple cancer types. These APOBEC-signature mutations are non-uniformly distributed across cancer genomes, associating with single-stranded (ss) DNA formed during DNA replication and hairpin-forming sequences. The biochemical and cellular factors that influence these specificities are unclear. We measured A3A's cytidine deaminase activity in vitro on substrates that model potential sources of ssDNA in the cell and found that A3A is more active on hairpins containing 4 nt ssDNA loops compared to hairpins with larger loops, bubble structures, replication fork mimics, ssDNA gaps, or linear DNA. Despite pre-bent ssDNAs being expected to fit better in the A3A active site, we determined A3A favors a 4 nt hairpin substrate only 2- to fivefold over linear ssDNA substrates. Addition of whole cell lysates or purified RPA to cytidine deaminase assays more severely reduced A3A activity on linear ssDNA (45 nt) compared to hairpin substrates. These results indicate that the large enrichment of A3A-driven mutations in hairpin-forming sequences in tumor genomes is likely driven in part by other proteins that preferentially bind longer ssDNA regions, which limit A3A's access. Furthermore, A3A activity is reduced at ssDNA associated with a stalled T7 RNA polymerase, suggesting that potential protein occlusion by RNA polymerase also limits A3A activity. These results help explain the small transcriptional strand bias for APOBEC mutation signatures in cancer genomes and the general targeting of hairpin-forming sequences in the lagging strand template during DNA replication.
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Affiliation(s)
- Amber L Brown
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Christopher D Collins
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Secily Thompson
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Margo Coxon
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Tony M Mertz
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Steven A Roberts
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA.
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38
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Rtt105 promotes high-fidelity DNA replication and repair by regulating the single-stranded DNA-binding factor RPA. Proc Natl Acad Sci U S A 2021; 118:2106393118. [PMID: 34140406 DOI: 10.1073/pnas.2106393118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Single-stranded DNA (ssDNA) covered with the heterotrimeric Replication Protein A (RPA) complex is a central intermediate of DNA replication and repair. How RPA is regulated to ensure the fidelity of DNA replication and repair remains poorly understood. Yeast Rtt105 is an RPA-interacting protein required for RPA nuclear import and efficient ssDNA binding. Here, we describe an important role of Rtt105 in high-fidelity DNA replication and recombination and demonstrate that these functions of Rtt105 primarily depend on its regulation of RPA. The deletion of RTT105 causes elevated spontaneous DNA mutations with large duplications or deletions mediated by microhomologies. Rtt105 is recruited to DNA double-stranded break (DSB) ends where it promotes RPA assembly and homologous recombination repair by gene conversion or break-induced replication. In contrast, Rtt105 attenuates DSB repair by the mutagenic single-strand annealing or alternative end joining pathway. Thus, Rtt105-mediated regulation of RPA promotes high-fidelity replication and recombination while suppressing repair by deleterious pathways. Finally, we show that the human RPA-interacting protein hRIP-α, a putative functional homolog of Rtt105, also stimulates RPA assembly on ssDNA, suggesting the conservation of an Rtt105-mediated mechanism.
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39
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Wang YR, Guo TT, Zheng YT, Lai CW, Sun B, Xi XG, Hou XM. Replication protein A plays multifaceted roles complementary to specialized helicases in processing G-quadruplex DNA. iScience 2021; 24:102493. [PMID: 34113828 PMCID: PMC8169993 DOI: 10.1016/j.isci.2021.102493] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/28/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
G-quadruplexes (G4s) are non-canonical DNA structures with critical roles in DNA metabolisms. To resolve those structures that can cause replication fork stalling and genomic instability, single-stranded DNA-binding proteins and helicases are required. Here, we characterized the interplay between RPA and helicases on G4s using single-molecule FRET. We first discovered that human RPA efficiently prevents G4 formation by preempting ssDNA before its folding. RPA also differentially interacts with the folded G4s. However, helicases such as human BLM and yeast Pif1 have different G4 preferences from RPA mainly based on loop lengths. More importantly, both RPA and these helicases are required for the stable G4 unfolding, as RPA promotes helicase-mediated repetitive unfolding into durative linear state. Furthermore, BLM can traverse G4 obstacles temporarily disrupted by RPA and continue to unwind downstream duplex. We finally proposed the mechanisms underlying above functions of RPA in preventing, resolving, and assisting helicases to eliminate G4s. RPA efficiently prevents G4 formation by preempting ssDNA before its folding Loop length may direct folded G4s to different unfolding way by RPA and helicases RPA promotes helicase-mediated repetitive G4 unfolding into durative linear state RPA assists BLM to overcome G4 obstacle and continue to unwind downstream duplex
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Affiliation(s)
- Yi-Ran Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ting-Ting Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ya-Ting Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chang-Wei Lai
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.,LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Gif-sur-Yvette, France
| | - Xi-Miao Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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40
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Kavli B, Iveland TS, Buchinger E, Hagen L, Liabakk NB, Aas PA, Obermann TS, Aachmann FL, Slupphaug G. RPA2 winged-helix domain facilitates UNG-mediated removal of uracil from ssDNA; implications for repair of mutagenic uracil at the replication fork. Nucleic Acids Res 2021; 49:3948-3966. [PMID: 33784377 PMCID: PMC8053108 DOI: 10.1093/nar/gkab195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 01/14/2023] Open
Abstract
Uracil occurs at replication forks via misincorporation of deoxyuridine monophosphate (dUMP) or via deamination of existing cytosines, which occurs 2-3 orders of magnitude faster in ssDNA than in dsDNA and is 100% miscoding. Tethering of UNG2 to proliferating cell nuclear antigen (PCNA) allows rapid post-replicative removal of misincorporated uracil, but potential 'pre-replicative' removal of deaminated cytosines in ssDNA has been questioned since this could mediate mutagenic translesion synthesis and induction of double-strand breaks. Here, we demonstrate that uracil-DNA glycosylase (UNG), but not SMUG1 efficiently excises uracil from replication protein A (RPA)-coated ssDNA and that this depends on functional interaction between the flexible winged-helix (WH) domain of RPA2 and the N-terminal RPA-binding helix in UNG. This functional interaction is promoted by mono-ubiquitination and diminished by cell-cycle regulated phosphorylations on UNG. Six other human proteins bind the RPA2-WH domain, all of which are involved in DNA repair and replication fork remodelling. Based on this and the recent discovery of the AP site crosslinking protein HMCES, we propose an integrated model in which templated repair of uracil and potentially other mutagenic base lesions in ssDNA at the replication fork, is orchestrated by RPA. The UNG:RPA2-WH interaction may also play a role in adaptive immunity by promoting efficient excision of AID-induced uracils in transcribed immunoglobulin loci.
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Affiliation(s)
- Bodil Kavli
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Tobias S Iveland
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Cancer Clinic, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Edith Buchinger
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N-7034 Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway.,PROMEC Proteomics and Modomics Experimental Core at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Nina B Liabakk
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Per A Aas
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Tobias S Obermann
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Finn L Aachmann
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N-7034 Trondheim, Norway
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway.,PROMEC Proteomics and Modomics Experimental Core at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
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41
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Jenkins T, Northall SJ, Ptchelkine D, Lever R, Cubbon A, Betts H, Taresco V, Cooper CDO, McHugh PJ, Soultanas P, Bolt EL. The HelQ human DNA repair helicase utilizes a PWI-like domain for DNA loading through interaction with RPA, triggering DNA unwinding by the HelQ helicase core. NAR Cancer 2021; 3:zcaa043. [PMID: 34316696 PMCID: PMC8210318 DOI: 10.1093/narcan/zcaa043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/30/2020] [Accepted: 12/16/2020] [Indexed: 01/04/2023] Open
Abstract
Genome instability is a characteristic enabling factor for carcinogenesis. HelQ helicase is a component of human DNA maintenance systems that prevent or reverse genome instability arising during DNA replication. Here, we provide details of the molecular mechanisms that underpin HelQ function-its recruitment onto ssDNA through interaction with replication protein A (RPA), and subsequent translocation of HelQ along ssDNA. We describe for the first time a functional role for the non-catalytic N-terminal region of HelQ, by identifying and characterizing its PWI-like domain. We present evidence that this domain of HelQ mediates interaction with RPA that orchestrates loading of the helicase domains onto ssDNA. Once HelQ is loaded onto the ssDNA, ATP-Mg2+ binding in the catalytic site activates the helicase core and triggers translocation along ssDNA as a dimer. Furthermore, we identify HelQ-ssDNA interactions that are critical for the translocation mechanism. Our data are novel and detailed insights into the mechanisms of HelQ function relevant for understanding how human cells avoid genome instability provoking cancers, and also how cells can gain resistance to treatments that rely on DNA crosslinking agents.
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Affiliation(s)
- Tabitha Jenkins
- School of Life Sciences, The University of Nottingham, NG7 2UH, Nottingham, UK
| | - Sarah J Northall
- School of Life Sciences, The University of Nottingham, NG7 2UH, Nottingham, UK
| | | | - Rebecca Lever
- School of Life Sciences, The University of Nottingham, NG7 2UH, Nottingham, UK
| | - Andrew Cubbon
- School of Life Sciences, The University of Nottingham, NG7 2UH, Nottingham, UK
| | - Hannah Betts
- School of Chemistry, The University of Nottingham, NG7 2RD, Nottingham, UK
| | - Vincenzo Taresco
- School of Pharmacy, The University of Nottingham, NG7 2RD, Nottingham, UK
| | - Christopher D O Cooper
- Department of Biological and Geographical Sciences, School of Applied Sciences, The University of Huddersfield, HD1 3DH, Huddersfield, UK
| | - Peter J McHugh
- MRC Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, OX3 9DS, Oxford, UK
| | - Panos Soultanas
- School of Chemistry, The University of Nottingham, NG7 2RD, Nottingham, UK
| | - Edward L Bolt
- School of Life Sciences, The University of Nottingham, NG7 2UH, Nottingham, UK
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42
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Abstract
The homologous recombination (HR) pathway maintains genomic integrity by repairing DNA double-strand breaks (DSBs), single-strand DNA gaps, and collapsed replication forks. The process of HR involves strand invasion, homology search, and DNA strand exchange between paired DNA molecules. HR is critical for the high-fidelity repair of DNA DSBs in mitotic cells and for the exchange of genetic information during meiosis. Here we describe a DNA strand exchange reaction in vitro utilizing purified proteins and defined DNA substrates to measure the strand invasion and pairing activities of the human RAD51 protein. We further discuss how this reaction can be catalytically stimulated by the mediator protein BRCA2.
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Affiliation(s)
- Sudipta Lahiri
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - Ryan B Jensen
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA.
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43
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Matsumoto Y, Brooks RC, Sverzhinsky A, Pascal JM, Tomkinson AE. Dynamic DNA-bound PCNA complexes co-ordinate Okazaki fragment synthesis, processing and ligation. J Mol Biol 2020; 432:166698. [PMID: 33157085 DOI: 10.1016/j.jmb.2020.10.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 10/07/2020] [Accepted: 10/27/2020] [Indexed: 11/28/2022]
Abstract
More than a million Okazaki fragments are synthesized, processed and joined during replication of the human genome. After synthesis of an RNA-DNA oligonucleotide by DNA polymerase α holoenzyme, proliferating cell nuclear antigen (PCNA), a homotrimeric DNA sliding clamp and polymerase processivity factor, is loaded onto the primer-template junction by replication factor C (RFC). Although PCNA interacts with the enzymes DNA polymerase δ (Pol δ), flap endonuclease 1 (FEN1) and DNA ligase I (LigI) that complete Okazaki fragment processing and joining, it is not known how the activities of these enzymes are coordinated. Here we describe a novel interaction between Pol δ and LigI that is critical for Okazaki fragment joining in vitro. Both LigI and FEN1 associate with PCNA-Pol δ during gap-filling synthesis, suggesting that gap-filling synthesis is carried out by a complex of PCNA, Pol δ, FEN1 and LigI. Following ligation, PCNA and LigI remain on the DNA, indicating that Pol δ and FEN1 dissociate during 5' end processing and that LigI engages PCNA at the DNA nick generated by FEN1 and Pol δ. Thus, dynamic PCNA complexes coordinate Okazaki fragment synthesis and processing with PCNA and LigI forming a terminal structure of two linked protein rings encircling the ligated DNA.
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Affiliation(s)
- Yoshihiro Matsumoto
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, United States
| | - Rhys C Brooks
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, United States
| | - Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Alan E Tomkinson
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, United States.
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44
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Schauer GD, Spenkelink LM, Lewis JS, Yurieva O, Mueller SH, van Oijen AM, O'Donnell ME. Replisome bypass of a protein-based R-loop block by Pif1. Proc Natl Acad Sci U S A 2020; 117:30354-30361. [PMID: 33199603 PMCID: PMC7720201 DOI: 10.1073/pnas.2020189117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Efficient and faithful replication of the genome is essential to maintain genome stability. Replication is carried out by a multiprotein complex called the replisome, which encounters numerous obstacles to its progression. Failure to bypass these obstacles results in genome instability and may facilitate errors leading to disease. Cells use accessory helicases that help the replisome bypass difficult barriers. All eukaryotes contain the accessory helicase Pif1, which tracks in a 5'-3' direction on single-stranded DNA and plays a role in genome maintenance processes. Here, we reveal a previously unknown role for Pif1 in replication barrier bypass. We use an in vitro reconstituted Saccharomyces cerevisiae replisome to demonstrate that Pif1 enables the replisome to bypass an inactive (i.e., dead) Cas9 (dCas9) R-loop barrier. Interestingly, dCas9 R-loops targeted to either strand are bypassed with similar efficiency. Furthermore, we employed a single-molecule fluorescence visualization technique to show that Pif1 facilitates this bypass by enabling the simultaneous removal of the dCas9 protein and the R-loop. We propose that Pif1 is a general displacement helicase for replication bypass of both R-loops and protein blocks.
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Affiliation(s)
- Grant D Schauer
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523;
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Jacob S Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Olga Yurieva
- HHMI, Rockefeller University, New York, NY 10065
- Laboratory of DNA Replication, Rockefeller University, New York, NY 10065
| | - Stefan H Mueller
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia;
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Michael E O'Donnell
- HHMI, Rockefeller University, New York, NY 10065;
- Laboratory of DNA Replication, Rockefeller University, New York, NY 10065
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45
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Bezalel-Buch R, Cheun YK, Roy U, Schärer OD, Burgers PM. Bypass of DNA interstrand crosslinks by a Rev1-DNA polymerase ζ complex. Nucleic Acids Res 2020; 48:8461-8473. [PMID: 32633759 PMCID: PMC7470978 DOI: 10.1093/nar/gkaa580] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/18/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022] Open
Abstract
DNA polymerase ζ (Pol ζ) and Rev1 are essential for the repair of DNA interstrand crosslink (ICL) damage. We have used yeast DNA polymerases η, ζ and Rev1 to study translesion synthesis (TLS) past a nitrogen mustard-based interstrand crosslink (ICL) with an 8-atom linker between the crosslinked bases. The Rev1-Pol ζ complex was most efficient in complete bypass synthesis, by 2-3 fold, compared to Pol ζ alone or Pol η. Rev1 protein, but not its catalytic activity, was required for efficient TLS. A dCMP residue was faithfully inserted across the ICL-G by Pol η, Pol ζ, and Rev1-Pol ζ. Rev1-Pol ζ, and particularly Pol ζ alone showed a tendency to stall before the ICL, whereas Pol η stalled just after insertion across the ICL. The stalling of Pol η directly past the ICL is attributed to its autoinhibitory activity, caused by elongation of the short ICL-unhooked oligonucleotide (a six-mer in our study) by Pol η providing a barrier to further elongation of the correct primer. No stalling by Rev1-Pol ζ directly past the ICL was observed, suggesting that the proposed function of Pol ζ as an extender DNA polymerase is also required for ICL repair.
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Affiliation(s)
- Rachel Bezalel-Buch
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Young K Cheun
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Upasana Roy
- Department of Chemistry, Stony Brook University, Stony Book, NY 11794, USA.,Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA
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46
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Zhang H, Schaub JM, Finkelstein IJ. RADX condenses single-stranded DNA to antagonize RAD51 loading. Nucleic Acids Res 2020; 48:7834-7843. [PMID: 32621611 PMCID: PMC7430644 DOI: 10.1093/nar/gkaa559] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 12/31/2022] Open
Abstract
RADX is a mammalian single-stranded DNA-binding protein that stabilizes telomeres and stalled replication forks. Cellular biology studies have shown that the balance between RADX and Replication Protein A (RPA) is critical for DNA replication integrity. RADX is also a negative regulator of RAD51-mediated homologous recombination at stalled forks. However, the mechanism of RADX acting on DNA and its interactions with RPA and RAD51 are enigmatic. Using single-molecule imaging of the key proteins in vitro, we reveal that RADX condenses ssDNA filaments, even when the ssDNA is coated with RPA at physiological protein ratios. RADX compacts RPA-coated ssDNA filaments via higher-order assemblies that can capture ssDNA in trans. Furthermore, RADX blocks RPA displacement by RAD51 and prevents RAD51 loading on ssDNA. Our results indicate that RADX is an ssDNA condensation protein that inhibits RAD51 filament formation and may antagonize other ssDNA-binding proteins on RPA-coated ssDNA.
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Affiliation(s)
- Hongshan Zhang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.,Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
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47
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Sparks MA, Burgers PM, Galletto R. Pif1, RPA, and FEN1 modulate the ability of DNA polymerase δ to overcome protein barriers during DNA synthesis. J Biol Chem 2020; 295:15883-15891. [PMID: 32913126 DOI: 10.1074/jbc.ra120.015699] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/09/2020] [Indexed: 01/20/2023] Open
Abstract
Successful DNA replication requires carefully regulated mechanisms to overcome numerous obstacles that naturally occur throughout chromosomal DNA. Scattered across the genome are tightly bound proteins, such as transcription factors and nucleosomes, that are necessary for cell function, but that also have the potential to impede timely DNA replication. Using biochemically reconstituted systems, we show that two transcription factors, yeast Reb1 and Tbf1, and a tightly positioned nucleosome, are strong blocks to the strand displacement DNA synthesis activity of DNA polymerase δ. Although the block imparted by Tbf1 can be overcome by the DNA-binding activity of the single-stranded DNA-binding protein RPA, efficient DNA replication through either a Reb1 or a nucleosome block occurs only in the presence of the 5'-3' DNA helicase Pif1. The Pif1-dependent stimulation of DNA synthesis across strong protein barriers may be beneficial during break-induced replication where barriers are expected to pose a problem to efficient DNA bubble migration. However, in the context of lagging strand DNA synthesis, the efficient disruption of a nucleosome barrier by Pif1 could lead to the futile re-replication of newly synthetized DNA. In the presence of FEN1 endonuclease, the major driver of nick translation during lagging strand replication, Pif1-dependent stimulation of DNA synthesis through a nucleosome or Reb1 barrier is prevented. By cleaving the short 5' tails generated during strand displacement, FEN1 eliminates the entry point for Pif1. We propose that this activity would protect the cell from potential DNA re-replication caused by unwarranted Pif1 interference during lagging strand replication.
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Affiliation(s)
- Melanie A Sparks
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri USA
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri USA.
| | - Roberto Galletto
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri USA.
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48
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Mazina OM, Somarowthu S, Kadyrova LY, Baranovskiy AG, Tahirov TH, Kadyrov FA, Mazin AV. Replication protein A binds RNA and promotes R-loop formation. J Biol Chem 2020; 295:14203-14213. [PMID: 32796030 DOI: 10.1074/jbc.ra120.013812] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 08/10/2020] [Indexed: 12/15/2022] Open
Abstract
Replication protein A (RPA), a major eukaryotic ssDNA-binding protein, is essential for all metabolic processes that involve ssDNA, including DNA replication, repair, and damage signaling. To perform its functions, RPA binds ssDNA tightly. In contrast, it was presumed that RPA binds RNA weakly. However, recent data suggest that RPA may play a role in RNA metabolism. RPA stimulates RNA-templated DNA repair in vitro and associates in vivo with R-loops, the three-stranded structures consisting of an RNA-DNA hybrid and the displaced ssDNA strand. R-loops are common in the genomes of pro- and eukaryotes, including humans, and may play an important role in transcription-coupled homologous recombination and DNA replication restart. However, the mechanism of R-loop formation remains unknown. Here, we investigated the RNA-binding properties of human RPA and its possible role in R-loop formation. Using gel-retardation and RNA/DNA competition assays, we found that RPA binds RNA with an unexpectedly high affinity (KD ≈ 100 pm). Furthermore, RPA, by forming a complex with RNA, can promote R-loop formation with homologous dsDNA. In reconstitution experiments, we showed that human DNA polymerases can utilize RPA-generated R-loops for initiation of DNA synthesis, mimicking the process of replication restart in vivo These results demonstrate that RPA binds RNA with high affinity, supporting the role of this protein in RNA metabolism and suggesting a mechanism of genome maintenance that depends on RPA-mediated DNA replication restart.
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Affiliation(s)
- Olga M Mazina
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Srinivas Somarowthu
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Lyudmila Y Kadyrova
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois, USA
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Farid A Kadyrov
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois, USA
| | - Alexander V Mazin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
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49
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Onwubiko NO, Borst A, Diaz SA, Passkowski K, Scheffel F, Tessmer I, Nasheuer HP. SV40 T antigen interactions with ssDNA and replication protein A: a regulatory role of T antigen monomers in lagging strand DNA replication. Nucleic Acids Res 2020; 48:3657-3677. [PMID: 32128579 PMCID: PMC7144908 DOI: 10.1093/nar/gkaa138] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/14/2020] [Accepted: 02/26/2020] [Indexed: 01/08/2023] Open
Abstract
DNA replication is a central process in all living organisms. Polyomavirus DNA replication serves as a model system for eukaryotic DNA replication and has considerably contributed to our understanding of basic replication mechanisms. However, the details of the involved processes are still unclear, in particular regarding lagging strand synthesis. To delineate the complex mechanism of coordination of various cellular proteins binding simultaneously or consecutively to DNA to initiate replication, we investigated single-stranded DNA (ssDNA) interactions by the SV40 large T antigen (Tag). Using single molecule imaging by atomic force microscopy (AFM) combined with biochemical and spectroscopic analyses we reveal independent activity of monomeric and oligomeric Tag in high affinity binding to ssDNA. Depending on ssDNA length, we obtain dissociation constants for Tag-ssDNA interactions (KD values of 10–30 nM) that are in the same order of magnitude as ssDNA binding by human replication protein A (RPA). Furthermore, we observe the formation of RPA-Tag-ssDNA complexes containing hexameric as well as monomeric Tag forms. Importantly, our data clearly show stimulation of primase function in lagging strand Okazaki fragment synthesis by monomeric Tag whereas hexameric Tag inhibits the reaction, redefining DNA replication initiation on the lagging strand.
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Affiliation(s)
- Nichodemus O Onwubiko
- Biochemistry, School of Natural Sciences, Center for Chromosome Biology, Biomedical SciencesBuilding, NUI Galway, New Castle Road, Galway, Ireland
| | - Angela Borst
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Suraya A Diaz
- Biochemistry, School of Natural Sciences, Center for Chromosome Biology, Biomedical SciencesBuilding, NUI Galway, New Castle Road, Galway, Ireland
| | - Katharina Passkowski
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Felicia Scheffel
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Heinz P Nasheuer
- Biochemistry, School of Natural Sciences, Center for Chromosome Biology, Biomedical SciencesBuilding, NUI Galway, New Castle Road, Galway, Ireland
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50
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Mariotti L, Wild S, Brunoldi G, Piceni A, Ceppi I, Kummer S, Lutz RE, Cejka P, Gari K. The iron-sulphur cluster in human DNA2 is required for all biochemical activities of DNA2. Commun Biol 2020; 3:322. [PMID: 32576938 PMCID: PMC7311471 DOI: 10.1038/s42003-020-1048-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 06/03/2020] [Indexed: 11/25/2022] Open
Abstract
The nuclease/helicase DNA2 plays important roles in DNA replication, repair and processing of stalled replication forks. DNA2 contains an iron-sulphur (FeS) cluster, conserved in eukaryotes and in a related bacterial nuclease. FeS clusters in DNA maintenance proteins are required for structural integrity and/or act as redox-sensors. Here, we demonstrate that loss of the FeS cluster affects binding of human DNA2 to specific DNA substrates, likely through a conformational change that distorts the central DNA binding tunnel. Moreover, we show that the FeS cluster is required for DNA2’s nuclease, helicase and ATPase activities. Our data also establish that oxidation of DNA2 impairs DNA binding in vitro, an effect that is reversible upon reduction. Unexpectedly, though, this redox-regulation is independent of the presence of the FeS cluster. Together, our study establishes an important structural role for the FeS cluster in human DNA2 and discovers a redox-regulatory mechanism to control DNA binding. Mariotti et al. show that the iron-sulphur cluster in human DNA2 is required for its nuclease, helicase and ATPase activities. This study highlights the structural importance of the iron-sulphur cluster in human DNA2 and presents a separate redox-regulatory mechanism that controls DNA binding.
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Affiliation(s)
- Laura Mariotti
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland.
| | - Sebastian Wild
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland
| | - Giulia Brunoldi
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland
| | - Alessandra Piceni
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland
| | - Ilaria Ceppi
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6500, Bellinzona, Switzerland.,Department of Biology, Institute of Biochemistry, ETH Zurich, 8092, Zurich, Switzerland
| | - Sandra Kummer
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland
| | - Richard E Lutz
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6500, Bellinzona, Switzerland.,Department of Biology, Institute of Biochemistry, ETH Zurich, 8092, Zurich, Switzerland
| | - Kerstin Gari
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland.
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