1
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Mre11-Rad50: the DNA end game. Biochem Soc Trans 2023; 51:527-538. [PMID: 36892213 DOI: 10.1042/bst20220754] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/09/2023] [Accepted: 02/17/2023] [Indexed: 03/10/2023]
Abstract
The Mre11-Rad50-(Nbs1/Xrs2) complex is an evolutionarily conserved factor for the repair of DNA double-strand breaks and other DNA termini in all kingdoms of life. It is an intricate DNA associated molecular machine that cuts, among other functions, a large variety of free and obstructed DNA termini for DNA repair by end joining or homologous recombination, yet leaves undamaged DNA intact. Recent years have brought progress in both the structural and functional analyses of Mre11-Rad50 orthologs, revealing mechanisms of DNA end recognition, endo/exonuclease activities, nuclease regulation and DNA scaffolding. Here, I review our current understanding and recent progress on the functional architecture Mre11-Rad50 and how this chromosome associated coiled-coil ABC ATPase acts as DNA topology specific endo-/exonuclease.
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2
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Rotheneder M, Stakyte K, van de Logt E, Bartho JD, Lammens K, Fan Y, Alt A, Kessler B, Jung C, Roos WP, Steigenberger B, Hopfner KP. Cryo-EM structure of the Mre11-Rad50-Nbs1 complex reveals the molecular mechanism of scaffolding functions. Mol Cell 2023; 83:167-185.e9. [PMID: 36577401 DOI: 10.1016/j.molcel.2022.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/14/2022] [Accepted: 12/03/2022] [Indexed: 12/28/2022]
Abstract
The DNA double-strand break repair complex Mre11-Rad50-Nbs1 (MRN) detects and nucleolytically processes DNA ends, activates the ATM kinase, and tethers DNA at break sites. How MRN can act both as nuclease and scaffold protein is not well understood. The cryo-EM structure of MRN from Chaetomium thermophilum reveals a 2:2:1 complex with a single Nbs1 wrapping around the autoinhibited Mre11 nuclease dimer. MRN has two DNA-binding modes, one ATP-dependent mode for loading onto DNA ends and one ATP-independent mode through Mre11's C terminus, suggesting how it may interact with DSBs and intact DNA. MRNs two 60-nm-long coiled-coil domains form a linear rod structure, the apex of which is assembled by the two joined zinc-hook motifs. Apices from two MRN complexes can further dimerize, forming 120-nm spanning MRN-MRN structures. Our results illustrate the architecture of MRN and suggest how it mechanistically integrates catalytic and tethering functions.
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Affiliation(s)
- Matthias Rotheneder
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Kristina Stakyte
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Erik van de Logt
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Joseph D Bartho
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Katja Lammens
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Yilan Fan
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Aaron Alt
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Brigitte Kessler
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Christophe Jung
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Wynand P Roos
- Institute for Toxicology, Johannes-Gutenberg-Universität, Mainz, Germany
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany.
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3
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Zhao B, He D, Gao S, Zhang Y, Wang L. Hypothetical protein FoDbp40 influences the growth and virulence of Fusarium oxysporum by regulating the expression of isocitrate lyase. Front Microbiol 2022; 13:1050637. [DOI: 10.3389/fmicb.2022.1050637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/04/2022] [Indexed: 11/29/2022] Open
Abstract
Fungal growth is closely related to virulence. Finding the key genes and pathways that regulate growth can help elucidate the regulatory mechanisms of fungal growth and virulence in efforts to locate new drug targets. Fusarium oxysporum is an important plant pathogen and human opportunistic pathogen that has research value in agricultural and medicinal fields. A mutant of F. oxysporum with reduced growth was obtained by Agrobacterium tumefaciens-mediated transformation, the transferred DNA (T-DNA) interrupted gene in this mutant coded a hypothetical protein that we named FoDbp40. FoDbp40 has an unknown function, but we chose to explore its possible functions as it may play a role in fungal growth regulatory mechanisms. Results showed that F. oxysporum growth and virulence decreased after FoDbp40 deletion. FOXG_05529 (NCBI Gene ID, isocitrate lyase, ICL) was identified as a key gene that involved in the reduced growth of this mutant. Deletion of FoDbp40 results in a decrease of more than 80% in ICL expression and activity, succinate level, and energy level, plus a decrease in phosphorylated mammalian target of rapamycin level and an increase in phosphorylated 5′-adenosine monophosphate activated protein kinase level. In summary, our study found that the FoDbp40 regulates the expression of ICL at a transcriptional level and affects energy levels and downstream related pathways, thereby regulating the growth and virulence of F. oxysporum.
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4
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Review on the applications of atomic force microscopy imaging in proteins. Micron 2022; 159:103293. [DOI: 10.1016/j.micron.2022.103293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/22/2022] [Accepted: 05/06/2022] [Indexed: 11/19/2022]
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5
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Mojumdar A, Adam N, Cobb JA. Nej1 interacts with Sae2 at DNA double-stranded breaks to inhibit DNA resection. J Biol Chem 2022; 298:101937. [PMID: 35429499 PMCID: PMC9117546 DOI: 10.1016/j.jbc.2022.101937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
The two major pathways of DNA double-strand break repair, nonhomologous end-joining and homologous recombination, are highly conserved from yeast to mammals. The regulation of 5′-DNA resection controls repair pathway choice and influences repair outcomes. Nej1 was first identified as a canonical NHEJ factor involved in stimulating the ligation of broken DNA ends, and more recently, it was shown to participate in DNA end-bridging and in the inhibition of 5′-resection mediated by the nuclease/helicase complex Dna2–Sgs1. Here, we show that Nej1 interacts with Sae2 to impact DSB repair in three ways. First, we show that Nej1 inhibits interaction of Sae2 with the Mre11–Rad50–Xrs2 complex and Sae2 localization to DSBs. Second, we found that Nej1 inhibits Sae2-dependent recruitment of Dna2 independently of Sgs1. Third, we determined that NEJ1 and SAE2 showed an epistatic relationship for end-bridging, an event that restrains broken DNA ends and reduces the frequency of genomic deletions from developing at the break site. Finally, we demonstrate that deletion of NEJ1 suppressed the synthetic lethality of sae2Δ sgs1Δ mutants, and that triple mutant viability was dependent on Dna2 nuclease activity. Taken together, these findings provide mechanistic insight to how Nej1 functionality inhibits the initiation of DNA resection, a role that is distinct from its involvement in end-joining repair at DSBs.
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Affiliation(s)
- Aditya Mojumdar
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine; University of Calgary; 3330 Hospital Drive N.W., Calgary, AB T2N 4N1, Canada
| | - Nancy Adam
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine; University of Calgary; 3330 Hospital Drive N.W., Calgary, AB T2N 4N1, Canada
| | - Jennifer A Cobb
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine; University of Calgary; 3330 Hospital Drive N.W., Calgary, AB T2N 4N1, Canada.
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6
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Frock RL, Sadeghi C, Meng J, Wang JL. DNA End Joining: G0-ing to the Core. Biomolecules 2021; 11:biom11101487. [PMID: 34680120 PMCID: PMC8533500 DOI: 10.3390/biom11101487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/28/2022] Open
Abstract
Humans have evolved a series of DNA double-strand break (DSB) repair pathways to efficiently and accurately rejoin nascently formed pairs of double-stranded DNA ends (DSEs). In G0/G1-phase cells, non-homologous end joining (NHEJ) and alternative end joining (A-EJ) operate to support covalent rejoining of DSEs. While NHEJ is predominantly utilized and collaborates extensively with the DNA damage response (DDR) to support pairing of DSEs, much less is known about A-EJ collaboration with DDR factors when NHEJ is absent. Non-cycling lymphocyte progenitor cells use NHEJ to complete V(D)J recombination of antigen receptor genes, initiated by the RAG1/2 endonuclease which holds its pair of targeted DSBs in a synapse until each specified pair of DSEs is handed off to the NHEJ DSB sensor complex, Ku. Similar to designer endonuclease DSBs, the absence of Ku allows for A-EJ to access RAG1/2 DSEs but with random pairing to complete their repair. Here, we describe recent insights into the major phases of DSB end joining, with an emphasis on synapsis and tethering mechanisms, and bring together new and old concepts of NHEJ vs. A-EJ and on RAG2-mediated repair pathway choice.
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7
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Interplay between Nucleoid-Associated Proteins and Transcription Factors in Controlling Specialized Metabolism in Streptomyces. mBio 2021; 12:e0107721. [PMID: 34311581 PMCID: PMC8406272 DOI: 10.1128/mbio.01077-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Lsr2 is a small nucleoid-associated protein found throughout the actinobacteria. Lsr2 functions similarly to the well-studied H-NS, in that it preferentially binds AT-rich sequences and represses gene expression. In Streptomyces venezuelae, Lsr2 represses the expression of many specialized metabolic clusters, including the chloramphenicol antibiotic biosynthetic gene cluster, and deleting lsr2 leads to significant upregulation of chloramphenicol cluster expression. We show here that Lsr2 likely exerts its repressive effects on the chloramphenicol cluster by polymerizing along the chromosome and by bridging sites within and adjacent to the chloramphenicol cluster. CmlR is a known activator of the chloramphenicol cluster, but expression of its associated gene is not upregulated in an lsr2 mutant strain. We demonstrate that CmlR is essential for chloramphenicol production, and further reveal that CmlR functions to “countersilence” Lsr2’s repressive effects by recruiting RNA polymerase and enhancing transcription, with RNA polymerase effectively clearing bound Lsr2 from the chloramphenicol cluster DNA. Our results provide insight into the interplay between opposing regulatory proteins that govern antibiotic production in S. venezuelae, which could be exploited to maximize the production of bioactive natural products in other systems.
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8
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Morton CR, Rzechorzek NJ, Maman JD, Kuramochi M, Sekiguchi H, Rambo R, Sasaki YC, Davies OR, Pellegrini L. Structural basis for the coiled-coil architecture of human CtIP. Open Biol 2021; 11:210060. [PMID: 34129781 PMCID: PMC8205527 DOI: 10.1098/rsob.210060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The DNA repair factor CtIP has a critical function in double-strand break (DSB) repair by homologous recombination, promoting the assembly of the repair apparatus at DNA ends and participating in DNA-end resection. However, the molecular mechanisms of CtIP function in DSB repair remain unclear. Here, we present an atomic model for the three-dimensional architecture of human CtIP, derived from a multi-disciplinary approach that includes X-ray crystallography, small-angle X-ray scattering (SAXS) and diffracted X-ray tracking (DXT). Our data show that CtIP adopts an extended dimer-of-dimers structure, in agreement with a role in bridging distant sites on chromosomal DNA during the recombinational repair. The zinc-binding motif in the CtIP N-terminus alters dynamically the coiled-coil structure, with functional implications for the long-range interactions of CtIP with DNA. Our results provide a structural basis for the three-dimensional arrangement of chains in the CtIP tetramer, a key aspect of CtIP function in DNA DSB repair.
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Affiliation(s)
- C R Morton
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - N J Rzechorzek
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - J D Maman
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - M Kuramochi
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Kashiwa, Japan
| | - H Sekiguchi
- Centre for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - R Rambo
- Diamond Light Source, Didcot, Oxfordshire OX11 0DE, UK
| | - Y C Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Kashiwa, Japan.,Centre for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - O R Davies
- Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - L Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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9
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A conserved Ctp1/CtIP C-terminal peptide stimulates Mre11 endonuclease activity. Proc Natl Acad Sci U S A 2021; 118:2016287118. [PMID: 33836577 DOI: 10.1073/pnas.2016287118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Mre11-Rad50-Nbs1 complex (MRN) is important for repairing DNA double-strand breaks (DSBs) by homologous recombination (HR). The endonuclease activity of MRN is critical for resecting 5'-ended DNA strands at DSB ends, producing 3'-ended single-strand DNA, a prerequisite for HR. This endonuclease activity is stimulated by Ctp1, the Schizosaccharomyces pombe homolog of human CtIP. Here, with purified proteins, we show that Ctp1 phosphorylation stimulates MRN endonuclease activity by inducing the association of Ctp1 with Nbs1. The highly conserved extreme C terminus of Ctp1 is indispensable for MRN activation. Importantly, a polypeptide composed of the conserved 15 amino acids at the C terminus of Ctp1 (CT15) is sufficient to stimulate Mre11 endonuclease activity. Furthermore, the CT15 equivalent from CtIP can stimulate human MRE11 endonuclease activity, arguing for the generality of this stimulatory mechanism. Thus, we propose that Nbs1-mediated recruitment of CT15 plays a pivotal role in the activation of the Mre11 endonuclease by Ctp1/CtIP.
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10
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Kuster A, Mozaffari NL, Wilkinson OJ, Wojtaszek JL, Zurfluh C, Przetocka S, Zyla D, von Aesch C, Dillingham MS, Williams RS, Sartori AA. A stapled peptide mimetic of the CtIP tetramerization motif interferes with double-strand break repair and replication fork protection. SCIENCE ADVANCES 2021; 7:7/8/eabc6381. [PMID: 33608267 PMCID: PMC7895427 DOI: 10.1126/sciadv.abc6381] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Cancer cells display high levels of DNA damage and replication stress, vulnerabilities that could be exploited by drugs targeting DNA repair proteins. Human CtIP promotes homology-mediated repair of DNA double-strand breaks (DSBs) and protects stalled replication forks from nucleolytic degradation, thus representing an attractive candidate for targeted cancer therapy. Here, we establish a peptide mimetic of the CtIP tetramerization motif that inhibits CtIP activity. The hydrocarbon-stapled peptide encompassing amino acid residues 18 to 28 of CtIP (SP18-28) stably binds to CtIP tetramers in vitro and facilitates their aggregation into higher-order structures. Efficient intracellular uptake of SP18-28 abrogates CtIP localization to damaged chromatin, impairs DSB repair, and triggers extensive fork degradation. Moreover, prolonged SP18-28 treatment causes hypersensitivity to DNA-damaging agents and selectively reduces the viability of BRCA1-mutated cancer cell lines. Together, our data provide a basis for the future development of CtIP-targeting compounds with the potential to treat patients with cancer.
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Affiliation(s)
- Anika Kuster
- Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Nour L Mozaffari
- Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Oliver J Wilkinson
- School of Biochemistry, University of Bristol, University Walk, Clifton BS8 1TD, Bristol, UK
| | - Jessica L Wojtaszek
- Structural Cell Biology Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, U.S. National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Christina Zurfluh
- Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Sara Przetocka
- Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Dawid Zyla
- Institute of Molecular Biology and Biophysics, ETH-Zürich, Otto-Stern-Weg 5, CH-8093 Zürich, Switzerland
| | - Christine von Aesch
- Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Mark S Dillingham
- School of Biochemistry, University of Bristol, University Walk, Clifton BS8 1TD, Bristol, UK
| | - R Scott Williams
- Structural Cell Biology Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, U.S. National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
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Gaullier G, Roberts G, Muthurajan UM, Bowerman S, Rudolph J, Mahadevan J, Jha A, Rae PS, Luger K. Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1. PLoS One 2020; 15:e0240932. [PMID: 33141820 PMCID: PMC7608914 DOI: 10.1371/journal.pone.0240932] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/05/2020] [Indexed: 12/19/2022] Open
Abstract
Poly(ADP-ribose) Polymerase 2 (PARP2) is one of three DNA-dependent PARPs involved in the detection of DNA damage. Upon binding to DNA double-strand breaks, PARP2 uses nicotinamide adenine dinucleotide to synthesize poly(ADP-ribose) (PAR) onto itself and other proteins, including histones. PAR chains in turn promote the DNA damage response by recruiting downstream repair factors. These early steps of DNA damage signaling are relevant for understanding how genome integrity is maintained and how their failure leads to genome instability or cancer. There is no structural information on DNA double-strand break detection in the context of chromatin. Here we present a cryo-EM structure of two nucleosomes bridged by human PARP2 and confirm that PARP2 bridges DNA ends in the context of nucleosomes bearing short linker DNA. We demonstrate that the conformation of PARP2 bound to damaged chromatin provides a binding platform for the regulatory protein Histone PARylation Factor 1 (HPF1), and that the resulting HPF1•PARP2•nucleosome complex is enzymatically active. Our results contribute to a structural view of the early steps of the DNA damage response in chromatin.
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Affiliation(s)
- Guillaume Gaullier
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, United States of America
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, United States of America
| | - Genevieve Roberts
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, United States of America
| | - Uma M. Muthurajan
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, United States of America
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, United States of America
| | - Samuel Bowerman
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, United States of America
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, United States of America
| | - Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, United States of America
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, United States of America
| | - Jyothi Mahadevan
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, United States of America
| | - Asmita Jha
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, United States of America
| | - Purushka S. Rae
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, United States of America
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, United States of America
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, United States of America
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12
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Mozaffari NL, Pagliarulo F, Sartori AA. Human CtIP: A 'double agent' in DNA repair and tumorigenesis. Semin Cell Dev Biol 2020; 113:47-56. [PMID: 32950401 DOI: 10.1016/j.semcdb.2020.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/20/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022]
Abstract
Human CtIP was originally identified as an interactor of the retinoblastoma protein and BRCA1, two bona fide tumour suppressors frequently mutated in cancer. CtIP is renowned for its role in the resection of DNA double-strand breaks (DSBs) during homologous recombination, a largely error-free DNA repair pathway crucial in maintaining genome integrity. However, CtIP-dependent DNA end resection is equally accountable for alternative end-joining, a mutagenic DSB repair mechanism implicated in oncogenic chromosomal translocations. In addition, CtIP contributes to transcriptional regulation of G1/S transition, DNA damage checkpoint signalling, and replication fork protection pathways. In this review, we present a perspective on the current state of knowledge regarding the tumour-suppressive and oncogenic properties of CtIP and provide an overview of their relevance for cancer development, progression, and therapy.
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Affiliation(s)
- Nour L Mozaffari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Fabio Pagliarulo
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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13
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Abstract
The DNA of our cells is constantly exposed to various types of damaging agents. One of the most critical types of damage is when both strands of the DNA break, and thus such breaks need to be efficiently repaired. It is known that CtIP promotes nucleases in DNA break repair. Here we show that CtIP can also hold the two DNA strands together in solution when DNA is free to move, using novel methodology that allows the monitoring of thousands of single DNA molecules in nanofabricated devices. DNA bridging likely facilitates the enzymatic repair steps and identifies novel CtIP functions that are crucial for repairing broken DNA. The early steps of DNA double-strand break (DSB) repair in human cells involve the MRE11-RAD50-NBS1 (MRN) complex and its cofactor, phosphorylated CtIP. The roles of these proteins in nucleolytic DSB resection are well characterized, but their role in bridging the DNA ends for efficient and correct repair is much less explored. Here we study the binding of phosphorylated CtIP, which promotes the endonuclease activity of MRN, to single long (∼50 kb) DNA molecules using nanofluidic channels and compare it to the yeast homolog Sae2. CtIP bridges DNA in a manner that depends on the oligomeric state of the protein, and truncated mutants demonstrate that the bridging depends on CtIP regions distinct from those that stimulate the nuclease activity of MRN. Sae2 is a much smaller protein than CtIP, and its bridging is significantly less efficient. Our results demonstrate that the nuclease cofactor and structural functions of CtIP may depend on the same protein population, which may be crucial for CtIP functions in both homologous recombination and microhomology-mediated end-joining.
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14
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Ceppi I, Howard SM, Kasaciunaite K, Pinto C, Anand R, Seidel R, Cejka P. CtIP promotes the motor activity of DNA2 to accelerate long-range DNA end resection. Proc Natl Acad Sci U S A 2020; 117:8859-8869. [PMID: 32241893 PMCID: PMC7183222 DOI: 10.1073/pnas.2001165117] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
To repair a DNA double-strand break by homologous recombination, 5'-terminated DNA strands must first be resected to reveal 3'-overhangs. This process is initiated by a short-range resection catalyzed by MRE11-RAD50-NBS1 (MRN) stimulated by CtIP, which is followed by a long-range step involving EXO1 or DNA2 nuclease. DNA2 is a bifunctional enzyme that contains both single-stranded DNA (ssDNA)-specific nuclease and motor activities. Upon DNA unwinding by Bloom (BLM) or Werner (WRN) helicase, RPA directs the DNA2 nuclease to degrade the 5'-strand. RPA bound to ssDNA also represents a barrier, explaining the need for the motor activity of DNA2 to displace RPA prior to resection. Using ensemble and single-molecule biochemistry, we show that CtIP also dramatically stimulates the adenosine 5'-triphosphate (ATP) hydrolysis-driven motor activity of DNA2 involved in the long-range resection step. This activation in turn strongly promotes the degradation of RPA-coated ssDNA by DNA2. Accordingly, the stimulatory effect of CtIP is only observed with wild-type DNA2, but not the helicase-deficient variant. Similarly to the function of CtIP to promote MRN, also the DNA2 stimulatory effect is facilitated by CtIP phosphorylation. The domain of CtIP required to promote DNA2 is located in the central region lacking in lower eukaryotes and is fully separable from domains involved in the stimulation of MRN. These results establish how CtIP couples both MRE11-dependent short-range and DNA2-dependent long-range resection and define the involvement of the motor activity of DNA2 in this process. Our data might help explain the less severe resection defects of MRE11 nuclease-deficient cells compared to those lacking CtIP.
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Affiliation(s)
- Ilaria Ceppi
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, 6500, Switzerland
- Institute of Biochemistry, Department of Biology, ETH, Zürich, 8093, Switzerland
| | - Sean M Howard
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, 6500, Switzerland
| | - Kristina Kasaciunaite
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, 04103, Germany
| | - Cosimo Pinto
- Institute of Molecular Cancer Research, University of Zürich, Zürich, 8057, Switzerland
| | - Roopesh Anand
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, 6500, Switzerland
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, 04103, Germany
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, 6500, Switzerland;
- Institute of Biochemistry, Department of Biology, ETH, Zürich, 8093, Switzerland
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Mohapatra S, Mishra SS, Bhalla P, Thatoi H. Engineering grass biomass for sustainable and enhanced bioethanol production. PLANTA 2019; 250:395-412. [PMID: 31236698 DOI: 10.1007/s00425-019-03218-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 06/18/2019] [Indexed: 06/09/2023]
Abstract
Bioethanol from lignocellulosic biomass is a promising step for the future energy requirements. Grass is a potential lignocellulosic biomass which can be utilised for biorefinery-based bioethanol production. Grass biomass is a suitable feedstock for bioethanol production due to its all the year around production, requirement of less fertile land and noninterference with food system. However, the processes involved, i.e. pretreatment, enzymatic hydrolysis and fermentation for bioethanol production from grass biomass, are both time consuming and costly. Developing the grass biomass in planta for enhanced bioethanol production is a promising step for maximum utilisation of this valuable feedstock and, thus, is the focus of the present review. Modern breeding techniques and transgenic processes are attractive methods which can be utilised for development of the feedstock. However, the outcomes are not always predictable and the time period required for obtaining a robust variety is generation dependent. Sophisticated genome editing technologies such as synthetic genetic circuits (SGC) or clustered regularly interspaced short palindromic repeats (CRISPR) systems are advantageous for induction of desired traits/heritable mutations in a foreseeable genome location in the 1st mutant generation. Although, its application in grass biomass for bioethanol is limited, these sophisticated techniques are anticipated to exhibit more flexibility in engineering the expression pattern for qualitative and qualitative traits. Nevertheless, the fundamentals rendered by the genetics of the transgenic crops will remain the basis of such developments for obtaining biorefinery-based bioethanol concepts from grass biomass. Grasses which are abundant and widespread in nature epitomise attractive lignocellulosic feedstocks for bioethanol production. The complexity offered by the grass cell wall in terms of lignin recalcitrance and its binding to polysaccharides forms a barricade for its commercialization as a biofuel feedstock. Inspired by the possibilities for rewiring the genetic makeup of grass biomass for reduced lignin and lignin-polysaccharide linkages along with increase in carbohydrates, innovative approaches for in planta modifications are forging ahead. In this review, we highlight the progress made in the field of transgenic grasses for bioethanol production and focus our understanding on improvements of simple breeding techniques and post-harvest techniques for development in shortening of lignin-carbohydrate and carbohydrate-carbohydrate linkages. Further, we discuss about the designer lignins which are aimed for qualitable lignins and also emphasise on remodelling of polysaccharides and mixed-linkage glucans for enhancing carbohydrate content and in planta saccharification efficiency. As a final point, we discuss the role of synthetic genetic circuits and CRISPR systems in targeted improvement of cell wall components without compromising the plant growth and health. It is anticipated that this review can provide a rational approach towards a better understanding of application of in planta genetic engineering aspects for designing synthetic genetic circuits which can promote grass feedstocks for biorefinery-based bioethanol concepts.
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Affiliation(s)
- Sonali Mohapatra
- Department of Biotechnology, College of Engineering and Technology, Biju Patnaik University of Technology, Bhubaneswar, 751003, India.
| | - Suruchee Samparana Mishra
- Department of Biotechnology, College of Engineering and Technology, Biju Patnaik University of Technology, Bhubaneswar, 751003, India
| | - Prerna Bhalla
- Bhupat and Jyoti Mehta School of Biosciences Building, Indian Institute of Technology Madras, Chennai, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, North Orissa University, Sriram Chandra Vihar, Takatpur, Baripada, 757003, Odisha, India
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16
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Cejka P. Seeing is believing: DNA zipping promotes DNA repair. J Biol Chem 2019; 294:3321-3322. [PMID: 30824572 DOI: 10.1074/jbc.h119.007814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA double-strand break repair by homologous recombination is initiated by the Ctp1 protein together with the Mre11-Rad50-Nbs1 nuclease complex in Schizosaccharomyces pombe, but the mechanism by which Ctp1 promotes this process has remained unknown. Andres et al. now use atomic force microscopy to image Ctp1-DNA complexes, demonstrating a striking capacity of Ctp1 filaments to bridge DNA molecules. This unanticipated role of Ctp1 might help explain how the processing of DNA ends is coordinated to facilitate DNA break repair.
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Affiliation(s)
- Petr Cejka
- From the Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona, 6500, Switzerland and Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, 8093, Switzerland
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