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Feliciello I, Ljubić S, Đermić E, Ivanković S, Zahradka D, Đermić D. Single-strand DNA-binding protein suppresses illegitimate recombination in Escherichia coli, acting in synergy with RecQ helicase. Sci Rep 2024; 14:20476. [PMID: 39227621 DOI: 10.1038/s41598-024-70817-5] [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: 06/06/2024] [Accepted: 08/21/2024] [Indexed: 09/05/2024] Open
Abstract
Single-strand DNA-binding proteins SSB/RPA are ubiquitous and essential proteins that bind ssDNA in bacteria/eukaryotes and coordinate DNA metabolic processes such as replication, repair, and recombination. SSB protects ssDNA from degradation by nucleases, while also facilitating/regulating the activity of multiple partner proteins involved in DNA processes. Using Spi- assay, which detects aberrantly excised λ prophage from the E. coli chromosome as a measure of illegitimate recombination (IR) occurrence, we have shown that SSB inhibits IR in several DSB resection pathways. The conditional ssb-1 mutation produced a higher IR increase at the nonpermissive temperature than the recQ inactivation. A double ssb-1 recQ mutant had an even higher level of IR, while showing reduced homologous recombination (HR). Remarkably, the ssb gene overexpression complemented recQ deficiency in suppressing IR, indicating that the SSB function is epistatic to RecQ. Overproduced truncated SSBΔC8 protein, which binds to ssDNA, but does not interact with partner proteins, only partially complemented recQ and ssb-1 mutations, while causing an IR increase in otherwise wild-type bacteria, suggesting that ssDNA binding of SSB is required but not sufficient for effective IR inhibition, which rather entails interaction with RecQ and likely some other protein(s). Our results depict SSB as the main genome caretaker in E. coli, which facilitates HR while inhibiting IR. In enabling high-fidelity DSB repair under physiological conditions SSB is assisted by RecQ helicase, whose activity it controls. Conversely, an excess of SSB renders RecQ redundant for IR suppression.
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Affiliation(s)
- Isidoro Feliciello
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Napoli, Italy
| | - Sven Ljubić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10 000, Zagreb, Croatia
| | - Edyta Đermić
- Division of Phytomedicine, Department of Plant Pathology, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
| | - Siniša Ivanković
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Davor Zahradka
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10 000, Zagreb, Croatia
| | - Damir Đermić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10 000, Zagreb, Croatia.
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2
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Dennen MS, Kockler ZW, Roberts SA, Burkholder AB, Klimczak LJ, Gordenin DA. Hypomorphic mutation in the large subunit of replication protein A affects mutagenesis by human APOBEC cytidine deaminases in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601081. [PMID: 38979205 PMCID: PMC11230362 DOI: 10.1101/2024.06.27.601081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Human APOBEC single-strand (ss) specific DNA and RNA cytidine deaminases change cytosines to uracils and function in antiviral innate immunity, RNA editing, and can cause hypermutation in chromosomes. The resulting uracils can be directly replicated, resulting in C to T mutations, or uracil-DNA glycosylase can convert the uracils to abasic (AP) sites which are then fixed as C to T or C to G mutations by translesion DNA polymerases. We noticed that in yeast and in human cancers, contributions of C to T and C to G mutations depends on the origin of ssDNA mutagenized by APOBECs. Since ssDNA in eukaryotic genomes readily binds to replication protein A (RPA) we asked if RPA could affect APOBEC-induced mutation spectrum in yeast. For that purpose, we expressed human APOBECs in the wild-type yeast and in strains carrying a hypomorph mutation rfa1-t33 in the large RPA subunit. We confirmed that the rfa1-t33 allele can facilitate mutagenesis by APOBECs. We also found that the rfa1-t33 mutation changed the ratio of APOBEC3A-induced T to C and T to G mutations in replicating yeast to resemble a ratio observed in long-persistent ssDNA in yeast and in cancers. We present the data suggesting that RPA may shield APOBEC formed uracils in ssDNA from Ung1, thereby facilitating C to T mutagenesis through the accurate copying of uracils by replicative DNA polymerases. Unexpectedly, we also found that for uracils shielded from Ung1 by wild-type RPA the mutagenic outcome is reduced in the presence of translesion DNA polymerase zeta.
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Affiliation(s)
- Matthew S. Dennen
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC 27709
| | - Zachary W. Kockler
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC 27709
| | - Steven A. Roberts
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405
| | - Adam B. Burkholder
- Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC, 27709, USA
| | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Durham, NC, 27709
| | - Dmitry A. Gordenin
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC 27709
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Cho JE, Shaltz S, Yakovleva L, Shuman S, Jinks-Robertson S. Deletions initiated by the vaccinia virus TopIB protein in yeast. DNA Repair (Amst) 2024; 137:103664. [PMID: 38484460 PMCID: PMC10994728 DOI: 10.1016/j.dnarep.2024.103664] [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: 10/06/2023] [Revised: 02/14/2024] [Accepted: 03/01/2024] [Indexed: 04/06/2024]
Abstract
The type IB topoisomerase of budding yeast (yTop1) generates small deletions in tandem repeats through a sequential cleavage mechanism and larger deletions with random endpoints through the nonhomologous end-joining (NHEJ) pathway. Vaccinia virus Top1 (vTop1) is a minimized version of the eukaryal TopIB enzymes and uniquely has a strong consensus cleavage sequence: the pentanucleotide (T/C)CCTTp↓. To define the relationship between the position of TopIB cleavage and mutagenic outcomes, we expressed vTop1 in yeast top1Δ strains containing reporter constructs with a single CCCTT site, tandem CCCTT sites, or CCCTT sites separated by 42 bp. vTop1 cleavage at a single CCCTT site was associated with small, NHEJ-dependent deletions. As observed with yTop1, vTop1 generated 5-bp deletions at tandem CCCTT sites. In contrast to yTop1-initiated deletions, however, 5-bp deletions associated with vTop1 expression were not affected by the level of ribonucleotides in genomic DNA. vTop1 expression was associated with a 47-bp deletion when CCCTT sites were separated by 42 bp. Unlike yTop1-initiated large deletions, the vTop1-mediated 47-bp deletion did not require NHEJ, consistent with a model in which re-ligation of enzyme-associated double-strand breaks is catalyzed by vTop1.
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Affiliation(s)
- Jang Eun Cho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Samantha Shaltz
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lyudmila Yakovleva
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
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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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Fan J, Dhingra N, Yang T, Yang V, Zhao X. Srs2 binding to PCNA and its sumoylation contribute to RPA antagonism during the DNA damage response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587206. [PMID: 38586001 PMCID: PMC10996639 DOI: 10.1101/2024.03.28.587206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Activation of the DNA damage checkpoint upon genotoxin treatment induces a multitude of cellular changes, such as cell cycle arrest, to cope with genome stress. After prolonged genotoxin treatment, the checkpoint can be downregulated to allow cell cycle and growth resumption. In yeast, downregulation of the DNA damage checkpoint requires the Srs2 DNA helicase, which removes the ssDNA binding complex RPA and the associated Mec1 checkpoint kinase from DNA, thus dampening Mec1 activation. However, it is unclear whether the 'anti-checkpoint' role of Srs2 is temporally and spatially regulated to both allow timely checkpoint termination and to prevent superfluous RPA removal. Here we address this question by examining regulatory elements of Srs2, including its phosphorylation, sumoylation, and protein-interaction sites. Our genetic analyses and checkpoint level assessment suggest that the RPA countering role of Srs2 is promoted by Srs2 binding to PCNA, which is known to recruit Srs2 to subsets of ssDNA regions. RPA antagonism is further fostered by Srs2 sumoylation, which we found depends on the Srs2-PCNA interaction. Srs2 sumoylation is additionally reliant on Mec1 and peaks after Mec1 activity reaches maximal levels. Collectively, our data provide evidence for a two-step model wherein checkpoint downregulation is facilitated by PCNA-mediated Srs2 recruitment to ssDNA-RPA filaments and the subsequent Srs2 sumoylation stimulated upon Mec1 hyperactivation. We propose that this mechanism allows Mec1 hyperactivation to trigger checkpoint recovery.
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Affiliation(s)
- Jiayi Fan
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Nalini Dhingra
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Tammy Yang
- City University of New York Hunter College, New York, NY 10065
| | - Vicki Yang
- City University of New York Hunter College, New York, NY 10065
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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Yu Y, Wang X, Fox J, Li Q, Yu Y, Hastings PJ, Chen K, Ira G. RPA and Rad27 limit templated and inverted insertions at DNA breaks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583931. [PMID: 38496432 PMCID: PMC10942419 DOI: 10.1101/2024.03.07.583931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Formation of templated insertions at DNA double-strand breaks (DSBs) is very common in cancer cells. The mechanisms and enzymes regulating these events are largely unknown. Here, we investigated templated insertions in yeast at DSBs using amplicon sequencing across a repaired locus. We document very short (most ∼5-34 bp), templated inverted duplications at DSBs. They are generated through a foldback mechanism that utilizes microhomologies adjacent to the DSB. Enzymatic requirements suggest a hybrid mechanism wherein one end requires Polδ-mediated synthesis while the other end is captured by nonhomologous end joining (NHEJ). This process is exacerbated in mutants with low levels or mutated RPA ( rtt105 Δ; rfa1 -t33) or extensive resection mutant ( sgs1 Δ exo1 Δ). Templated insertions from various distant genomic locations also increase in these mutants as well as in rad27 Δ and originate from fragile regions of the genome. Among complex insertions, common events are insertions of two sequences, originating from the same locus and with inverted orientation. We propose that these inversions are also formed by microhomology-mediated template switching. Taken together, we propose that a shortage of RPA typical in cancer cells is one possible factor stimulating the formation of templated insertions.
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Nasheuer HP, Meaney AM, Hulshoff T, Thiele I, Onwubiko NO. Replication Protein A, the Main Eukaryotic Single-Stranded DNA Binding Protein, a Focal Point in Cellular DNA Metabolism. Int J Mol Sci 2024; 25:588. [PMID: 38203759 PMCID: PMC10779431 DOI: 10.3390/ijms25010588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Replication protein A (RPA) is a heterotrimeric protein complex and the main single-stranded DNA (ssDNA)-binding protein in eukaryotes. RPA has key functions in most of the DNA-associated metabolic pathways and DNA damage signalling. Its high affinity for ssDNA helps to stabilise ssDNA structures and protect the DNA sequence from nuclease attacks. RPA consists of multiple DNA-binding domains which are oligonucleotide/oligosaccharide-binding (OB)-folds that are responsible for DNA binding and interactions with proteins. These RPA-ssDNA and RPA-protein interactions are crucial for DNA replication, DNA repair, DNA damage signalling, and the conservation of the genetic information of cells. Proteins such as ATR use RPA to locate to regions of DNA damage for DNA damage signalling. The recruitment of nucleases and DNA exchange factors to sites of double-strand breaks are also an important RPA function to ensure effective DNA recombination to correct these DNA lesions. Due to its high affinity to ssDNA, RPA's removal from ssDNA is of central importance to allow these metabolic pathways to proceed, and processes to exchange RPA against downstream factors are established in all eukaryotes. These faceted and multi-layered functions of RPA as well as its role in a variety of human diseases will be discussed.
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Affiliation(s)
- Heinz Peter Nasheuer
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland
| | - Anna Marie Meaney
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland
| | - Timothy Hulshoff
- Molecular Systems Physiology Group, School of Biological and Chemical Sciences, University of Galway, H91 TK33 Galway, Ireland
| | - Ines Thiele
- Molecular Systems Physiology Group, School of Biological and Chemical Sciences, University of Galway, H91 TK33 Galway, Ireland
| | - Nichodemus O. Onwubiko
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland
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Al-Zain AM, Nester MR, Ahmed I, Symington LS. Double-strand breaks induce inverted duplication chromosome rearrangements by a DNA polymerase δ-dependent mechanism. Nat Commun 2023; 14:7020. [PMID: 37919272 PMCID: PMC10622511 DOI: 10.1038/s41467-023-42640-5] [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: 01/24/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023] Open
Abstract
Inverted duplications, also known as foldback inversions, are commonly observed in cancers and are the major class of chromosome rearrangement recovered from yeast cells lacking Mre11 nuclease activity. Foldback priming at DNA double-strand breaks (DSBs) is one mechanism proposed for the generation of inverted duplications. However, the other pathway steps have not been fully elucidated. Here, we show that a DSB induced near natural inverted repeats drives high frequency inverted duplication in Sae2 and Mre11-deficient cells. We find that DNA polymerase δ proof-reading activity, but not Rad1 nuclease, trims the heterologous flaps formed after foldback annealing. Additionally, Pol32 is required for the generation of inverted duplications, suggesting that Pol δ catalyzes fill-in synthesis primed from the foldback to create a hairpin-capped chromosome that is subsequently replicated to form a dicentric inversion chromosome. Finally, we show that stabilization of the dicentric chromosome after breakage involves telomere capture by non-reciprocal translocation mediated by repeat sequences or by deletion of one centromere.
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Affiliation(s)
- Amr M Al-Zain
- Program in Biological Sciences, Columbia University, New York, NY, 10027, USA
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Mattie R Nester
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Iffat Ahmed
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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9
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Dueva R, Krieger LM, Li F, Luo D, Xiao H, Stuschke M, Metzen E, Iliakis G. Chemical Inhibition of RPA by HAMNO Alters Cell Cycle Dynamics by Impeding DNA Replication and G2-to-M Transition but Has Little Effect on the Radiation-Induced DNA Damage Response. Int J Mol Sci 2023; 24:14941. [PMID: 37834389 PMCID: PMC10573259 DOI: 10.3390/ijms241914941] [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: 09/01/2023] [Revised: 09/28/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
Replication protein A (RPA) is the major single-stranded DNA (ssDNA) binding protein that is essential for DNA replication and processing of DNA double-strand breaks (DSBs) by homology-directed repair pathways. Recently, small molecule inhibitors have been developed targeting the RPA70 subunit and preventing RPA interactions with ssDNA and various DNA repair proteins. The rationale of this development is the potential utility of such compounds as cancer therapeutics, owing to their ability to inhibit DNA replication that sustains tumor growth. Among these compounds, (1Z)-1-[(2-hydroxyanilino) methylidene] naphthalen-2-one (HAMNO) has been more extensively studied and its efficacy against tumor growth was shown to arise from the associated DNA replication stress. Here, we study the effects of HAMNO on cells exposed to ionizing radiation (IR), focusing on the effects on the DNA damage response and the processing of DSBs and explore its potential as a radiosensitizer. We show that HAMNO by itself slows down the progression of cells through the cell cycle by dramatically decreasing DNA synthesis. Notably, HAMNO also attenuates the progression of G2-phase cells into mitosis by a mechanism that remains to be elucidated. Furthermore, HAMNO increases the fraction of chromatin-bound RPA in S-phase but not in G2-phase cells and suppresses DSB repair by homologous recombination. Despite these marked effects on the cell cycle and the DNA damage response, radiosensitization could neither be detected in exponentially growing cultures, nor in cultures enriched in G2-phase cells. Our results complement existing data on RPA inhibitors, specifically HAMNO, and suggest that their antitumor activity by replication stress induction may not extend to radiosensitization. However, it may render cells more vulnerable to other forms of DNA damaging agents through synthetically lethal interactions, which requires further investigation.
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Affiliation(s)
- Rositsa Dueva
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (L.M.K.); (F.L.); (D.L.); (H.X.)
- Institute of Physiology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Lisa Marie Krieger
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (L.M.K.); (F.L.); (D.L.); (H.X.)
- Division of Experimental Radiation Biology, Department of Radiotherapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Fanghua Li
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (L.M.K.); (F.L.); (D.L.); (H.X.)
- West German Proton Therapy Centre Essen (WPE), 45147 Essen, Germany
| | - Daxian Luo
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (L.M.K.); (F.L.); (D.L.); (H.X.)
- Division of Experimental Radiation Biology, Department of Radiotherapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Huaping Xiao
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (L.M.K.); (F.L.); (D.L.); (H.X.)
- Division of Experimental Radiation Biology, Department of Radiotherapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Martin Stuschke
- Division of Experimental Radiation Biology, Department of Radiotherapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Eric Metzen
- Institute of Physiology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - George Iliakis
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (L.M.K.); (F.L.); (D.L.); (H.X.)
- Division of Experimental Radiation Biology, Department of Radiotherapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
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10
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Shaltz S, Jinks-Robertson S. Genetic control of the error-prone repair of a chromosomal double-strand break with 5' overhangs in yeast. Genetics 2023; 225:iyad122. [PMID: 37418686 PMCID: PMC10471200 DOI: 10.1093/genetics/iyad122] [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: 05/03/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023] Open
Abstract
A targeted double-strand break introduced into the genome of Saccharomyces cerevisiae is repaired by the relatively error-prone nonhomologous end joining (NHEJ) pathway when homologous recombination is not an option. A zinc finger nuclease cleavage site was inserted out-of-frame into the LYS2 locus of a haploid yeast strain to study the genetic control of NHEJ when the ends contain 5' overhangs. Repair events that destroyed the cleavage site were identified either as Lys+ colonies on selective medium or as surviving colonies on rich medium. Junction sequences in Lys+ events solely reflected NHEJ and were influenced by the nuclease activity of Mre11 as well as by the presence/absence of the NHEJ-specific polymerase Pol4 and the translesion-synthesis DNA polymerases Pol ζ and Pol η. Although most NHEJ events were dependent on Pol4, a 29-bp deletion with endpoints in 3-bp repeats was an exception. The Pol4-independent deletion required translesion synthesis polymerases as well as the exonuclease activity of the replicative Pol δ DNA polymerase. Survivors were equally split between NHEJ events and 1.2 or 11.7 kb deletions that reflected microhomology-mediated end joining (MMEJ). MMEJ events required the processive resection activity of Exo1/Sgs1, but there unexpectedly was no dependence on the Rad1-Rad10 endonuclease for the removal of presumptive 3' tails. Finally, NHEJ was more efficient in nongrowing than in growing cells and was most efficient in G0 cells. These studies provide novel insights into the flexibility and complexity of error-prone DSB repair in yeast.
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Affiliation(s)
- Samantha Shaltz
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
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11
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Miller JM, Prange S, Ji H, Rau AR, Khodaverdian VY, Li X, Patel A, Butova N, Lutter A, Chung H, Merigliano C, Rawal CC, Hanscom T, McVey M, Chiolo I. Alternative end-joining results in smaller deletions in heterochromatin relative to euchromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.03.531058. [PMID: 37645729 PMCID: PMC10461932 DOI: 10.1101/2023.03.03.531058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Pericentromeric heterochromatin is highly enriched for repetitive sequences prone to aberrant recombination. Previous studies showed that homologous recombination (HR) repair is uniquely regulated in this domain to enable 'safe' repair while preventing aberrant recombination. In Drosophila cells, DNA double-strand breaks (DSBs) relocalize to the nuclear periphery through nuclear actin-driven directed motions before recruiting the strand invasion protein Rad51 and completing HR repair. End-joining (EJ) repair also occurs with high frequency in heterochromatin of fly tissues, but how alternative EJ (alt-EJ) pathways operate in heterochromatin remains largely uncharacterized. Here, we induce DSBs in single euchromatic and heterochromatic sites using a new system that combines the DR- white reporter and I-SceI expression in spermatogonia of flies. Using this approach, we detect higher frequency of HR repair in heterochromatin, relative to euchromatin. Further, sequencing of mutagenic repair junctions reveals the preferential use of different EJ pathways across distinct euchromatic and heterochromatic sites. Interestingly, synthesis-dependent microhomology-mediated end joining (SD-MMEJ) appears differentially regulated in the two domains, with a preferential use of motifs close to the cut site in heterochromatin relative to euchromatin, resulting in smaller deletions. Together, these studies establish a new approach to study repair outcomes in fly tissues, and support the conclusion that heterochromatin uses more HR and less mutagenic EJ repair relative to euchromatin.
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12
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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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13
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Ding J, Li X, Shen J, Zhao Y, Zhong S, Lai L, Niu H, Qi Z. ssDNA accessibility of Rad51 is regulated by orchestrating multiple RPA dynamics. Nat Commun 2023; 14:3864. [PMID: 37391417 PMCID: PMC10313831 DOI: 10.1038/s41467-023-39579-y] [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: 11/23/2022] [Accepted: 06/20/2023] [Indexed: 07/02/2023] Open
Abstract
The eukaryotic single-stranded DNA (ssDNA)-binding protein Replication Protein A (RPA) plays a crucial role in various DNA metabolic pathways, including DNA replication and repair, by dynamically associating with ssDNA. While the binding of a single RPA molecule to ssDNA has been thoroughly studied, the accessibility of ssDNA is largely governed by the bimolecular behavior of RPA, the biophysical nature of which remains unclear. In this study, we develop a three-step low-complexity ssDNA Curtains method, which, when combined with biochemical assays and a Markov chain model in non-equilibrium physics, allow us to decipher the dynamics of multiple RPA binding to long ssDNA. Interestingly, our results suggest that Rad52, the mediator protein, can modulate the ssDNA accessibility of Rad51, which is nucleated on RPA coated ssDNA through dynamic ssDNA exposure between neighboring RPA molecules. We find that this process is controlled by the shifting between the protection mode and action mode of RPA ssDNA binding, where tighter RPA spacing and lower ssDNA accessibility are favored under RPA protection mode, which can be facilitated by the Rfa2 WH domain and inhibited by Rad52 RPA interaction.
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Affiliation(s)
- Jiawei Ding
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiangting Li
- Department of Computational Medicine, University of California, Los Angeles, CA, USA
| | - Jiangchuan Shen
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Yiling Zhao
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Shuchen Zhong
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Luhua Lai
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA.
| | - Zhi Qi
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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14
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Gan X, Zhang Y, Jiang D, Shi J, Zhao H, Xie C, Wang Y, Xu J, Zhang X, Cai G, Wang H, Huang J, Chen X. Proper RPA acetylation promotes accurate DNA replication and repair. Nucleic Acids Res 2023; 51:5565-5583. [PMID: 37140030 PMCID: PMC10287905 DOI: 10.1093/nar/gkad291] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/05/2023] Open
Abstract
The single-stranded DNA (ssDNA) binding protein complex RPA plays a critical role in promoting DNA replication and multiple DNA repair pathways. However, how RPA is regulated to achieve its functions precisely in these processes remains elusive. Here, we found that proper acetylation and deacetylation of RPA are required to regulate RPA function in promoting high-fidelity DNA replication and repair. We show that yeast RPA is acetylated on multiple conserved lysines by the acetyltransferase NuA4 upon DNA damage. Mimicking constitutive RPA acetylation or blocking its acetylation causes spontaneous mutations with the signature of micro-homology-mediated large deletions or insertions. In parallel, improper RPA acetylation/deacetylation impairs DNA double-strand break (DSB) repair by the accurate gene conversion or break-induced replication while increasing the error-prone repair by single-strand annealing or alternative end joining. Mechanistically, we show that proper acetylation and deacetylation of RPA ensure its normal nuclear localization and ssDNA binding ability. Importantly, mutation of the equivalent residues in human RPA1 also impairs RPA binding on ssDNA, leading to attenuated RAD51 loading and homologous recombination repair. Thus, timely RPA acetylation and deacetylation likely represent a conserved mechanism promoting high-fidelity replication and repair while discriminating the error-prone repair mechanisms in eukaryotes.
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Affiliation(s)
- Xiaoli Gan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Yueyue Zhang
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Donghao Jiang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Jingyao Shi
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Han Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Chengyu Xie
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Yanyan Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Jingyan Xu
- Department of Hematology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Gang Cai
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jun Huang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
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15
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Barone D, Iannuzzi CA, Forte IM, Ragosta MC, Cuomo M, Dell’Aquila M, Altieri A, Caporaso A, Camerlingo R, Rigano MM, Monti DM, Barone A, Imbimbo P, Frusciante L, Monda M, D’Angelo M, De Laurentiis M, Giordano A, Alfano L. The hydrophilic extract from a new tomato genotype (named DHO) kills cancer cell lines through the modulation of the DNA damage response induced by Campthotecin treatment. Front Oncol 2023; 13:1117262. [PMID: 37409248 PMCID: PMC10318356 DOI: 10.3389/fonc.2023.1117262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/13/2023] [Indexed: 07/07/2023] Open
Abstract
Introduction DNA double-strand breaks are the most toxic lesions repaired through the non-homologous and joining (NHEJ) or the homologous recombination (HR), which is dependent on the generation of single-strand tails, by the DNA end resection mechanism. The resolution of the HR intermediates leads to error-free repair (Gene Conversion) or the mutagenic pathways (Single Strand Annealing and Alternative End-Joining); the regulation of processes leading to the resolution of the HR intermediates is not fully understood. Methods Here, we used a hydrophilic extract of a new tomato genotype (named DHO) in order to modulate the Camptothecin (CPT) DNA damage response. Results We demonstrated increased phosphorylation of Replication Protein A 32 Serine 4/8 (RPA32 S4/8) protein in HeLa cells treated with the CPT in combination with DHO extract with respect to CPT alone. Moreover, we pointed out a change in HR intermediates resolution from Gene Conversion to Single Strand Annealing through the modified DNA repair protein RAD52 homolog (RAD52), DNA excision repair protein ERCC-1 (ERCC1) chromatin loading in response to DHO extract, and CPT co-treatment, with respect to the vehicle. Finally, we showed an increased sensitivity of HeLa cell lines to DHO extract and CPT co-treatment suggesting a possible mechanism for increasing the efficiency of cancer therapy. Discussion We described the potential role of DHO extract in the modulation of DNA repair, in response to Camptothecin treatment (CPT), favoring an increased sensitivity of HeLa cell lines to topoisomerase inhibitor therapy.
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Affiliation(s)
- Daniela Barone
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Carmelina Antonella Iannuzzi
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Iris Maria Forte
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Maria Carmen Ragosta
- Department of Medicine, Surgery and Neuroscience, University of Siena and Istituto Toscana Tumori (ITT), Siena, Italy
| | - Maria Cuomo
- Department of Medicine, Surgery and Neuroscience, University of Siena and Istituto Toscana Tumori (ITT), Siena, Italy
| | - Milena Dell’Aquila
- Department of Medicine, Surgery and Neuroscience, University of Siena and Istituto Toscana Tumori (ITT), Siena, Italy
| | - Angela Altieri
- Department of Medicine, Surgery and Neuroscience, University of Siena and Istituto Toscana Tumori (ITT), Siena, Italy
| | - Antonella Caporaso
- Department of Medicine, Surgery and Neuroscience, University of Siena and Istituto Toscana Tumori (ITT), Siena, Italy
| | - Rosa Camerlingo
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Maria Manuela Rigano
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Daria Maria Monti
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Amalia Barone
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Paola Imbimbo
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Marcellino Monda
- Unit of Dietetics and Sports Medicine, Department of Experimental Medicine, Section of Human Physiology, Università degli Studi della Campania “Luigi Vanvitelli”, Naples, Italy
| | - Margherita D’Angelo
- Unit of Dietetics and Sports Medicine, Department of Experimental Medicine, Section of Human Physiology, Università degli Studi della Campania “Luigi Vanvitelli”, Naples, Italy
| | - Michelino De Laurentiis
- Department of Breast and Thoracic Oncology, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Antonio Giordano
- Department of Medicine, Surgery and Neuroscience, University of Siena and Istituto Toscana Tumori (ITT), Siena, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, United States
| | - Luigi Alfano
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
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16
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Shaltz S, Jinks-Robertson S. Genetic control of the error-prone repair of a chromosomal double-strand break with 5' overhangs in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539391. [PMID: 37205473 PMCID: PMC10187297 DOI: 10.1101/2023.05.04.539391] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A targeted double-strand break introduced into the genome of Saccharomyces cerevisiae is repaired by the relatively error-prone nonhomologous-end joining (NHEJ) pathway when homologous recombination is not an option. A ZFN cleavage site was inserted out-of-frame into the LYS2 locus of a haploid yeast strain to study the genetic control of NHEJ when the ends contain 5' overhangs. Repair events that destroyed the cleavage site were identified either as Lys + colonies on selective medium or as surviving colonies on rich medium. Junction sequences in Lys + events solely reflected NHEJ and were influenced by the nuclease activity of Mre11 as well as by the presence/absence of the NHEJ-specific polymerase Pol4 and the translesion-synthesis DNA polymerases Pol σ and Pol 11. Although most NHEJ events were dependent on Pol4, a 29-bp deletion with endpoints in 3-bp repeats was an exception. The Pol4-independent deletion required TLS polymerases as well as the exonuclease activity of the replicative Pol DNA polymerase. Survivors were equally split between NHEJ events and 1 kb or 11 kb deletions that reflected microhomology-mediated end joining (MMEJ). MMEJ events required the processive resection activity of Exo1/Sgs1, but there unexpectedly was no dependence on the Rad1-Rad10 endonuclease for the removal of presumptive 3' tails. Finally, NHEJ was more efficient in non-growing than in growing cells and was most efficient in G0 cells. These studies provide novel insight into the flexibility and complexity of error-prone DSB repair in yeast.
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Affiliation(s)
- Samantha Shaltz
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710
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17
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Multifaceted Nature of DNA Polymerase θ. Int J Mol Sci 2023; 24:ijms24043619. [PMID: 36835031 PMCID: PMC9962433 DOI: 10.3390/ijms24043619] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 02/15/2023] Open
Abstract
DNA polymerase θ belongs to the A family of DNA polymerases and plays a key role in DNA repair and damage tolerance, including double-strand break repair and DNA translesion synthesis. Pol θ is often overexpressed in cancer cells and promotes their resistance to chemotherapeutic agents. In this review, we discuss unique biochemical properties and structural features of Pol θ, its multiple roles in protection of genome stability and the potential of Pol θ as a target for cancer treatment.
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18
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Al-Zain A, Nester MR, Symington LS. Double-strand breaks induce inverted duplication chromosome rearrangements by a DNA polymerase δ and Rad51-dependent mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.24.525421. [PMID: 36747747 PMCID: PMC9900772 DOI: 10.1101/2023.01.24.525421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Inverted duplications, also known as foldback inversions, are commonly observed in cancers and are the major class of chromosome rearrangement recovered from yeast cells lacking Mre11 nuclease. Foldback priming at naturally occurring inverted repeats is one mechanism proposed for the generation of inverted duplications. However, the initiating lesion for these events and the mechanism by which they form has not been fully elucidated. Here, we show that a DNA double-strand break (DSB) induced near natural short, inverted repeats drives high frequency inverted duplication in Sae2 and Mre11-deficient cells. We find that DNA polymerase δ proof-reading activity acts non-redundantly with Rad1 nuclease to remove heterologous tails formed during foldback annealing. Additionally, Pol32 is required for the generation of inverted duplications, suggesting that Pol δ catalyzes fill-in synthesis primed from the foldback to create a hairpin-capped chromosome that is subsequently replicated to form a dicentric isochromosome. Stabilization of the dicentric chromosome after breakage involves telomere capture by non-reciprocal translocation mediated by repeat sequences and requires Rad51.
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19
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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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20
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Jiang Y. Contribution of Microhomology to Genome Instability: Connection between DNA Repair and Replication Stress. Int J Mol Sci 2022; 23:12937. [PMID: 36361724 PMCID: PMC9657218 DOI: 10.3390/ijms232112937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/23/2022] [Accepted: 10/23/2022] [Indexed: 11/23/2023] Open
Abstract
Microhomology-mediated end joining (MMEJ) is a highly mutagenic pathway to repair double-strand breaks (DSBs). MMEJ was thought to be a backup pathway of homologous recombination (HR) and canonical nonhomologous end joining (C-NHEJ). However, it attracts more attention in cancer research due to its special function of microhomology in many different aspects of cancer. In particular, it is initiated with DNA end resection and upregulated in homologous recombination-deficient cancers. In this review, I summarize the following: (1) the recent findings and contributions of MMEJ to genome instability, including phenotypes relevant to MMEJ; (2) the interaction between MMEJ and other DNA repair pathways; (3) the proposed mechanistic model of MMEJ in DNA DSB repair and a new connection with microhomology-mediated break-induced replication (MMBIR); and (4) the potential clinical application by targeting MMEJ based on synthetic lethality for cancer therapy.
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Affiliation(s)
- Yuning Jiang
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22903, USA
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21
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Kuppa S, Deveryshetty J, Chadda R, Mattice JR, Pokhrel N, Kaushik V, Patterson A, Dhingra N, Pangeni S, Sadauskas MK, Shiekh S, Balci H, Ha T, Zhao X, Bothner B, Antony E. Rtt105 regulates RPA function by configurationally stapling the flexible domains. Nat Commun 2022; 13:5152. [PMID: 36056028 PMCID: PMC9440123 DOI: 10.1038/s41467-022-32860-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/18/2022] [Indexed: 11/23/2022] Open
Abstract
Replication Protein A (RPA) is a heterotrimeric complex that binds to single-stranded DNA (ssDNA) and recruits over three dozen RPA-interacting proteins to coordinate multiple aspects of DNA metabolism including DNA replication, repair, and recombination. Rtt105 is a molecular chaperone that regulates nuclear localization of RPA. Here, we show that Rtt105 binds to multiple DNA binding and protein-interaction domains of RPA and configurationally staples the complex. In the absence of ssDNA, Rtt105 inhibits RPA binding to Rad52, thus preventing spurious binding to RPA-interacting proteins. When ssDNA is available, Rtt105 promotes formation of high-density RPA nucleoprotein filaments and dissociates during this process. Free Rtt105 further stabilizes the RPA-ssDNA filaments by inhibiting the facilitated exchange activity of RPA. Collectively, our data suggest that Rtt105 sequesters free RPA in the nucleus to prevent untimely binding to RPA-interacting proteins, while stabilizing RPA-ssDNA filaments at DNA lesion sites. The single stranded DNA binding protein RPA coordinates DNA metabolism using multiple protein and DNA interaction domains. Here, the authors show that the chaperone-like protein Rtt105 staples RPA domains to prevent untimely protein interactions.
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Affiliation(s)
- Sahiti Kuppa
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Jaigeeth Deveryshetty
- 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
| | - Jenna R Mattice
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Nilisha Pokhrel
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53201, USA.,Laronde Bio, Cambridge, MA, USA
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Nalini Dhingra
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sushil Pangeni
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Marisa K Sadauskas
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, 21205, USA.,Howard Hughes Medical Institute, Baltimore, MD, 21205, USA
| | - Xiaolan Zhao
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA. .,Department of Biological Sciences, Marquette University, Milwaukee, WI, 53201, USA.
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22
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Chen BR, Sleckman BP. The regulation of DNA end resection by chromatin response to DNA double strand breaks. Front Cell Dev Biol 2022; 10:932633. [PMID: 35912102 PMCID: PMC9335370 DOI: 10.3389/fcell.2022.932633] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/29/2022] [Indexed: 11/18/2022] Open
Abstract
DNA double-strand breaks (DSBs) constantly arise upon exposure to genotoxic agents and during physiological processes. The timely repair of DSBs is important for not only the completion of the cellular functions involving DSBs as intermediates, but also the maintenance of genome stability. There are two major pathways dedicated to DSB repair: homologous recombination (HR) and non-homologous end joining (NHEJ). The decision of deploying HR or NHEJ to repair DSBs largely depends on the structures of broken DNA ends. DNA ends resected to generate extensive single-strand DNA (ssDNA) overhangs are repaired by HR, while those remaining blunt or minimally processed can be repaired by NHEJ. As the generation and repair of DSB occurs within the context of chromatin, the resection of broken DNA ends is also profoundly affected by the state of chromatin flanking DSBs. Here we review how DNA end resection can be regulated by histone modifications, chromatin remodeling, and the presence of ssDNA structure through altering the accessibility to chromatin and the activity of pro- and anti-resection proteins.
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Affiliation(s)
- Bo-Ruei Chen
- Division of Hematology and Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
- *Correspondence: Bo-Ruei Chen,
| | - Barry P. Sleckman
- Division of Hematology and Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
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23
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Danforth JM, Provencher L, Goodarzi AA. Chromatin and the Cellular Response to Particle Radiation-Induced Oxidative and Clustered DNA Damage. Front Cell Dev Biol 2022; 10:910440. [PMID: 35912116 PMCID: PMC9326100 DOI: 10.3389/fcell.2022.910440] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/21/2022] [Indexed: 12/03/2022] Open
Abstract
Exposure to environmental ionizing radiation is prevalent, with greatest lifetime doses typically from high Linear Energy Transfer (high-LET) alpha particles via the radioactive decay of radon gas in indoor air. Particle radiation is highly genotoxic, inducing DNA damage including oxidative base lesions and DNA double strand breaks. Due to the ionization density of high-LET radiation, the consequent damage is highly clustered wherein ≥2 distinct DNA lesions occur within 1–2 helical turns of one another. These multiply-damaged sites are difficult for eukaryotic cells to resolve either quickly or accurately, resulting in the persistence of DNA damage and/or the accumulation of mutations at a greater rate per absorbed dose, relative to lower LET radiation types. The proximity of the same and different types of DNA lesions to one another is challenging for DNA repair processes, with diverse pathways often confounding or interplaying with one another in complex ways. In this context, understanding the state of the higher order chromatin compaction and arrangements is essential, as it influences the density of damage produced by high-LET radiation and regulates the recruitment and activity of DNA repair factors. This review will summarize the latest research exploring the processes by which clustered DNA damage sites are induced, detected, and repaired in the context of chromatin.
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24
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Huang J, Cook DE. The contribution of DNA repair pathways to genome editing and evolution in filamentous pathogens. FEMS Microbiol Rev 2022; 46:6638986. [PMID: 35810003 PMCID: PMC9779921 DOI: 10.1093/femsre/fuac035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 01/09/2023] Open
Abstract
DNA double-strand breaks require repair or risk corrupting the language of life. To ensure genome integrity and viability, multiple DNA double-strand break repair pathways function in eukaryotes. Two such repair pathways, canonical non-homologous end joining and homologous recombination, have been extensively studied, while other pathways such as microhomology-mediated end joint and single-strand annealing, once thought to serve as back-ups, now appear to play a fundamental role in DNA repair. Here, we review the molecular details and hierarchy of these four DNA repair pathways, and where possible, a comparison for what is known between animal and fungal models. We address the factors contributing to break repair pathway choice, and aim to explore our understanding and knowledge gaps regarding mechanisms and regulation in filamentous pathogens. We additionally discuss how DNA double-strand break repair pathways influence genome engineering results, including unexpected mutation outcomes. Finally, we review the concept of biased genome evolution in filamentous pathogens, and provide a model, termed Biased Variation, that links DNA double-strand break repair pathways with properties of genome evolution. Despite our extensive knowledge for this universal process, there remain many unanswered questions, for which the answers may improve genome engineering and our understanding of genome evolution.
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Affiliation(s)
- Jun Huang
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Throckmorton Hall, Manhattan, KS 66506, United States
| | - David E Cook
- Corresponding author: 1712 Claflin Road, 4004 Throckmorton Hall, Manhattan, KS 66502, United States. E-mail:
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25
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Müller B, Serafin F, Laucke LL, Rheinhard W, Wimmer T, Stieger K. Characterization of Double-Strand Break Repair Protein Ku80 Location Within the Murine Retina. Invest Ophthalmol Vis Sci 2022; 63:22. [PMID: 35737378 PMCID: PMC9233284 DOI: 10.1167/iovs.63.6.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To characterize the spatial distribution of the DNA-double strand break-repair protein Ku80 in the murine retina. Even though robust data exist on the complexity of DNA repair mechanisms in dividing cells in vitro, almost nothing is known about it in post-mitotic neurons or photoreceptors (PRs). This knowledge is an important prerequisite for in vivo therapeutic approaches by genome editing in retina and PRs. Recently, it was shown that mouse rod PRs are incapable of repairing double-strand breaks induced by radiation. Material and Methods Retinae from wild-type, rd10, and RPGR-KI mouse lines were obtained and stained with antibodies against Ku80, and cellular markers CtBP2, beta-Dystropglycan, Lamin B, and peanut agglutinin. Organotypic explant cultures were generated and maintained for up to 10 days. Laser microdissection was performed to obtain photoreceptor nuclei, and Ku80 expression was compared to whole retina by real-time PCR (RT-PCR). Results Strong Ku80 immunoreactivity was observed in rod but not cone photoreceptor terminals localized in the outer plexiform layer of the retina in all three mouse lines. During retinal explant culture, we observed that Ku80-positive globules translocate into the heterochromatin region of nuclei in the outer nuclear layer (ONL). By quantitative PCR, we showed upregulation of relative Ku80 expression in the ONL during wild-type retinal explant culture. Discussion The unexpected localization of Ku80 to murine rod terminals indicates another tissue-specific modification to the canonical DNA repair mechanisms and warrants further investigation.
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Affiliation(s)
- Brigitte Müller
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Franziska Serafin
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Leonie Luise Laucke
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Wilhelm Rheinhard
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Tobias Wimmer
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Knut Stieger
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
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26
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Bai W, Zhao B, Gu M, Dong J. Alternative end-joining in BCR gene rearrangements and translocations. Acta Biochim Biophys Sin (Shanghai) 2022; 54:782-795. [PMID: 35593472 PMCID: PMC9828324 DOI: 10.3724/abbs.2022051] [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] [Indexed: 12/18/2022] Open
Abstract
Programmed DNA double-strand breaks (DSBs) occur during antigen receptor gene recombination, namely V(D)J recombination in developing B lymphocytes and class switch recombination (CSR) in mature B cells. Repair of these DSBs by classical end-joining (c-NHEJ) enables the generation of diverse BCR repertoires for efficient humoral immunity. Deletion of or mutation in c-NHEJ genes in mice and humans confer various degrees of primary immune deficiency and predisposition to lymphoid malignancies that often harbor oncogenic chromosomal translocations. In the absence of c-NHEJ, alternative end-joining (A-EJ) catalyzes robust CSR and to a much lesser extent, V(D)J recombination, but the mechanisms of A-EJ are only poorly defined. In this review, we introduce recent advances in the understanding of A-EJ in the context of V(D)J recombination and CSR with emphases on DSB end processing, DNA polymerases and ligases, and discuss the implications of A-EJ to lymphoid development and chromosomal translocations.
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Affiliation(s)
- Wanyu Bai
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China
| | - Bo Zhao
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China
| | - Mingyu Gu
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China
| | - Junchao Dong
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China,Correspondence address. Tel: +86-20-87330571; E-mail:
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27
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Al-Soodani AT, Wu X, Kelp NC, Brown AJ, Roberts SA, Her C. hMSH5 Regulates NHEJ and Averts Excessive Nucleotide Alterations at Repair Joints. Genes (Basel) 2022; 13:genes13040673. [PMID: 35456479 PMCID: PMC9026759 DOI: 10.3390/genes13040673] [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: 03/11/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 02/05/2023] Open
Abstract
Inappropriate repair of DNA double-strand breaks (DSBs) leads to genomic instability, cell death, or malignant transformation. Cells minimize these detrimental effects by selectively activating suitable DSB repair pathways in accordance with their underlying cellular context. Here, we report that hMSH5 down-regulates NHEJ and restricts the extent of DSB end processing before rejoining, thereby reducing “excessive” deletions and insertions at repair joints. RNAi-mediated knockdown of hMSH5 led to large nucleotide deletions and longer insertions at the repair joints, while at the same time reducing the average length of microhomology (MH) at repair joints. Conversely, hMSH5 overexpression reduced end-joining activity and increased RPA foci formation (i.e., more stable ssDNA at DSB ends). Furthermore, silencing of hMSH5 delayed 53BP1 chromatin spreading, leading to increased end resection at DSB ends.
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28
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Schaub JM, Soniat MM, Finkelstein IJ. Polymerase theta-helicase promotes end joining by stripping single-stranded DNA-binding proteins and bridging DNA ends. Nucleic Acids Res 2022; 50:3911-3921. [PMID: 35357490 PMCID: PMC9023281 DOI: 10.1093/nar/gkac119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 01/20/2022] [Accepted: 03/29/2022] [Indexed: 01/20/2023] Open
Abstract
Homologous recombination-deficient cancers rely on DNA polymerase Theta (Polθ)-Mediated End Joining (TMEJ), an alternative double-strand break repair pathway. Polθ is the only vertebrate polymerase that encodes an N-terminal superfamily 2 (SF2) helicase domain, but the role of this helicase domain in TMEJ remains unclear. Using single-molecule imaging, we demonstrate that Polθ-helicase (Polθ-h) is a highly processive single-stranded DNA (ssDNA) motor protein that can efficiently strip Replication Protein A (RPA) from ssDNA. Polθ-h also has a limited capacity for disassembling RAD51 filaments but is not processive on double-stranded DNA. Polθ-h can bridge two non-complementary DNA strands in trans. PARylation of Polθ-h by PARP-1 resolves these DNA bridges. We conclude that Polθ-h removes RPA and RAD51 filaments and mediates bridging of DNA overhangs to aid in polymerization by the Polθ polymerase domain.
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Affiliation(s)
- Jeffrey M Schaub
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Michael M Soniat
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
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29
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Ramsden DA, Carvajal-Garcia J, Gupta GP. Mechanism, cellular functions and cancer roles of polymerase-theta-mediated DNA end joining. Nat Rev Mol Cell Biol 2022; 23:125-140. [PMID: 34522048 DOI: 10.1038/s41580-021-00405-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2021] [Indexed: 02/08/2023]
Abstract
Cellular pathways that repair chromosomal double-strand breaks (DSBs) have pivotal roles in cell growth, development and cancer. These DSB repair pathways have been the target of intensive investigation, but one pathway - alternative end joining (a-EJ) - has long resisted elucidation. In this Review, we highlight recent progress in our understanding of a-EJ, especially the assignment of DNA polymerase theta (Polθ) as the predominant mediator of a-EJ in most eukaryotes, and discuss a potential molecular mechanism by which Polθ-mediated end joining (TMEJ) occurs. We address possible cellular functions of TMEJ in resolving DSBs that are refractory to repair by non-homologous end joining (NHEJ), DSBs generated following replication fork collapse and DSBs present owing to stalling of repair by homologous recombination. We also discuss how these context-dependent cellular roles explain how TMEJ can both protect against and cause genome instability, and the emerging potential of Polθ as a therapeutic target in cancer.
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Affiliation(s)
- Dale A Ramsden
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Juan Carvajal-Garcia
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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30
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Finelli R, Moreira BP, Alves MG, Agarwal A. Unraveling the Molecular Impact of Sperm DNA Damage on Human Reproduction. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1358:77-113. [DOI: 10.1007/978-3-030-89340-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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So A, Dardillac E, Muhammad A, Chailleux C, Sesma-Sanz L, Ragu S, Le Cam E, Canitrot Y, Masson J, Dupaigne P, Lopez BS, Guirouilh-Barbat J. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2651-2666. [PMID: 35137208 PMCID: PMC8934640 DOI: 10.1093/nar/gkac073] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 01/18/2022] [Accepted: 01/25/2022] [Indexed: 11/23/2022] Open
Abstract
Selection of the appropriate DNA double-strand break (DSB) repair pathway is decisive for genetic stability. It is proposed to act according to two steps: 1-canonical nonhomologous end-joining (C-NHEJ) versus resection that generates single-stranded DNA (ssDNA) stretches; 2-on ssDNA, gene conversion (GC) versus nonconservative single-strand annealing (SSA) or alternative end-joining (A-EJ). Here, we addressed the mechanisms by which RAD51 regulates this second step, preventing nonconservative repair in human cells. Silencing RAD51 or BRCA2 stimulated both SSA and A-EJ, but not C-NHEJ, validating the two-step model. Three different RAD51 dominant-negative forms (DN-RAD51s) repressed GC and stimulated SSA/A-EJ. However, a fourth DN-RAD51 repressed SSA/A-EJ, although it efficiently represses GC. In living cells, the three DN-RAD51s that stimulate SSA/A-EJ failed to load efficiently onto damaged chromatin and inhibited the binding of endogenous RAD51, while the fourth DN-RAD51, which inhibits SSA/A-EJ, efficiently loads on damaged chromatin. Therefore, the binding of RAD51 to DNA, rather than its ability to promote GC, is required for SSA/A-EJ inhibition by RAD51. We showed that RAD51 did not limit resection of endonuclease-induced DSBs, but prevented spontaneous and RAD52-induced annealing of complementary ssDNA in vitro. Therefore, RAD51 controls the selection of the DSB repair pathway, protecting genome integrity from nonconservative DSB repair through ssDNA occupancy, independently of the promotion of CG.
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Affiliation(s)
- Ayeong So
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, France
- CNRS UMR 8200, Gustave-Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Elodie Dardillac
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, France
- CNRS UMR 8200, Gustave-Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Ali Muhammad
- Genome Maintenance and Molecular Microscopy UMR 9019 CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
| | | | - Laura Sesma-Sanz
- Genome Stability Laboratory, CHU de Québec Research Center (Oncology Division), Quebec City, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Sandrine Ragu
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, France
- CNRS UMR 8200, Gustave-Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Eric Le Cam
- Genome Maintenance and Molecular Microscopy UMR 9019 CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
| | - Yvan Canitrot
- CBI, CNRS UMR5088, LBCMCP, Toulouse University, Toulouse, France
| | - Jean Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center (Oncology Division), Quebec City, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Pauline Dupaigne
- Genome Maintenance and Molecular Microscopy UMR 9019 CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
| | - Bernard S Lopez
- To whom correspondence should be addressed. Tel: +33 1 53 73 27 40;
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32
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Tsuboi Y, Sakuma T, Yamamoto T, Horiuchi H, Takahashi F, Igarashi K, Hagihara H, Takimura Y. OUP accepted manuscript. FEMS Microbiol Lett 2022; 369:6524178. [PMID: 35137045 PMCID: PMC8863565 DOI: 10.1093/femsle/fnac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/11/2021] [Accepted: 02/04/2022] [Indexed: 12/02/2022] Open
Abstract
The Mucorales fungal genus Rhizopus is used for the industrial production of organic acids, enzymes and fermented foods. The metabolic engineering efficiency of Rhizopus could be improved using gene manipulation; however, exogenous DNA rarely integrates into the host genome. Consequently, a genetic tool for Mucorales fungi needs to be developed. Recently, programmable nucleases that generate DNA double-strand breaks (DSBs) at specific genomic loci have been used for genome editing in various organisms. In this study, we examined gene disruption in Rhizopus oryzae using transcription activator-like effector nucleases (TALENs), with and without exonuclease overexpression. TALENs with an overexpressing exonuclease induced DSBs, followed by target site deletions. Although DSBs are repaired mainly by nonhomologous end joining in most organisms, our results suggested that in R. oryzae microhomology-mediated end joining was the major DSB repair system. Our gene manipulation method using TALENs coupled with exonuclease overexpression contributes to basic scientific knowledge and the metabolic engineering of Rhizopus.
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Affiliation(s)
- Yuichi Tsuboi
- Corresponding author: Biological Science Laboratories, KAO Corporation, 1334 Minato, Wakayama, Wakayama 640-8580, Japan. Tel: +81-70-3297-1291; Fax: +81-73-426-5027; E-mail:
| | | | - Takashi Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Fumikazu Takahashi
- Biological Science Laboratories, KAO Corporation, 1334 Minato, Wakayama, Wakayama 640-8580, Japan
| | - Kazuaki Igarashi
- Biological Science Laboratories, KAO Corporation, 1334 Minato, Wakayama, Wakayama 640-8580, Japan
| | - Hiroshi Hagihara
- Biological Science Laboratories, KAO Corporation, 1334 Minato, Wakayama, Wakayama 640-8580, Japan
| | - Yasushi Takimura
- Biological Science Laboratories, KAO Corporation, 1334 Minato, Wakayama, Wakayama 640-8580, Japan
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33
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Kong M, Greene EC. Mechanistic Insights From Single-Molecule Studies of Repair of Double Strand Breaks. Front Cell Dev Biol 2021; 9:745311. [PMID: 34869333 PMCID: PMC8636147 DOI: 10.3389/fcell.2021.745311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/28/2021] [Indexed: 01/01/2023] Open
Abstract
DNA double strand breaks (DSBs) are among some of the most deleterious forms of DNA damage. Left unrepaired, they are detrimental to genome stability, leading to high risk of cancer. Two major mechanisms are responsible for the repair of DSBs, homologous recombination (HR) and nonhomologous end joining (NHEJ). The complex nature of both pathways, involving a myriad of protein factors functioning in a highly coordinated manner at distinct stages of repair, lend themselves to detailed mechanistic studies using the latest single-molecule techniques. In avoiding ensemble averaging effects inherent to traditional biochemical or genetic methods, single-molecule studies have painted an increasingly detailed picture for every step of the DSB repair processes.
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Affiliation(s)
| | - Eric C. Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, United States
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Llorens-Agost M, Ensminger M, Le HP, Gawai A, Liu J, Cruz-García A, Bhetawal S, Wood RD, Heyer WD, Löbrich M. POLθ-mediated end joining is restricted by RAD52 and BRCA2 until the onset of mitosis. Nat Cell Biol 2021; 23:1095-1104. [PMID: 34616022 PMCID: PMC8675436 DOI: 10.1038/s41556-021-00764-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/30/2021] [Indexed: 01/25/2023]
Abstract
BRCA2-mutant cells are defective in homologous recombination, making them vulnerable to the inactivation of other pathways for the repair of DNA double-strand breaks (DSBs). This concept can be clinically exploited but is currently limited due to insufficient knowledge about how DSBs are repaired in the absence of BRCA2. We show that DNA polymerase θ (POLθ)-mediated end joining (TMEJ) repairs DSBs arising during the S phase in BRCA2-deficient cells only after the onset of the ensuing mitosis. This process is regulated by RAD52, whose loss causes the premature usage of TMEJ and the formation of chromosomal fusions. Purified RAD52 and BRCA2 proteins both block the DNA polymerase function of POLθ, suggesting a mechanism explaining their synthetic lethal relationships. We propose that the delay of TMEJ until mitosis ensures the conversion of originally one-ended DSBs into two-ended DSBs. Mitotic chromatin condensation might further serve to juxtapose correct break ends and limit chromosomal fusions.
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Affiliation(s)
- Marta Llorens-Agost
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Michael Ensminger
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Hang Phuong Le
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Anugrah Gawai
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Jie Liu
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Andrés Cruz-García
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Sarita Bhetawal
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Markus Löbrich
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany.
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Peng H, Zhang S, Peng Y, Zhu S, Zhao X, Zhao X, Yang S, Liu G, Dong Y, Gan X, Li Q, Zhang X, Pei H, Chen X. Yeast Bromodomain Factor 1 and Its Human Homolog TAF1 Play Conserved Roles in Promoting Homologous Recombination. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100753. [PMID: 34056863 PMCID: PMC8336524 DOI: 10.1002/advs.202100753] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/27/2021] [Indexed: 05/12/2023]
Abstract
Histone acetylation is a key histone post-translational modification that shapes chromatin structure, dynamics, and function. Bromodomain (BRD) proteins, the readers of acetyl-lysines, are located in the center of the histone acetylation-signaling network. How they regulate DNA repair and genome stability remains poorly understood. Here, a conserved function of the yeast Bromodomain Factor 1 (Bdf1) and its human counterpart TAF1 is reported in promoting DNA double-stranded break repair by homologous recombination (HR). Depletion of either yeast BDF1 or human TAF1, or disruption of their BRDs impairs DNA end resection, Replication Protein A (RPA) and Rad51 loading, and HR repair, causing genome instability and hypersensitivity to DNA damage. Mechanistically, it is shown that Bdf1 preferentially binds the DNA damage-induced histone H4 acetylation (H4Ac) via the BRD motifs, leading to its chromatin recruitment. Meanwhile, Bdf1 physically interacts with RPA, and this interaction facilitates RPA loading in the chromatin context and the subsequent HR repair. Similarly, TAF1 also interacts with H4Ac or RPA. Thus, Bdf1 and TAF1 appear to share a conserved mechanism in linking the HR repair to chromatin acetylation in preserving genome integrity.
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Affiliation(s)
- Haoyang Peng
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Simin Zhang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Yihan Peng
- Department of Biochemistry and Molecular MedicineGeorge Washington University School of Medicine and Health ScienceWashingtonDC20037USA
| | - Shuangyi Zhu
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Xin Zhao
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Xiaocong Zhao
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Shuangshuang Yang
- State Key Laboratory of Protein and Plant Gene ResearchSchool of Life Sciences and Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
| | - Guangxue Liu
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Yang Dong
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Xiaoli Gan
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene ResearchSchool of Life Sciences and Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Huadong Pei
- Department of Biochemistry and Molecular MedicineGeorge Washington University School of Medicine and Health ScienceWashingtonDC20037USA
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
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36
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DNA end resection during homologous recombination. Curr Opin Genet Dev 2021; 71:99-105. [PMID: 34329854 DOI: 10.1016/j.gde.2021.07.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/15/2022]
Abstract
Exposure to environmental mutagens but also cell-endogenous processes can create DNA double-strand breaks (DSBs) in a cell's genome. DSBs need to be repaired accurately and timely to ensure genomic integrity and cell survival. One major DSB repair mechanism, called homologous recombination, relies on the nucleolytic degradation of the 5'-terminated strands in a process termed end resection. Here, we review new insights into end resection with a focus on the mechanistic interplay of the nucleases, helicases, and accessory factors involved.
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37
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Chen XS, Pomerantz RT. DNA Polymerase θ: A Cancer Drug Target with Reverse Transcriptase Activity. Genes (Basel) 2021; 12:1146. [PMID: 34440316 PMCID: PMC8391894 DOI: 10.3390/genes12081146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
The emergence of precision medicine from the development of Poly (ADP-ribose) polymerase (PARP) inhibitors that preferentially kill cells defective in homologous recombination has sparked wide interest in identifying and characterizing additional DNA repair enzymes that are synthetic lethal with HR factors. DNA polymerase theta (Polθ) is a validated anti-cancer drug target that is synthetic lethal with HR factors and other DNA repair proteins and confers cellular resistance to various genotoxic cancer therapies. Since its initial characterization as a helicase-polymerase fusion protein in 2003, many exciting and unexpected activities of Polθ in microhomology-mediated end-joining (MMEJ) and translesion synthesis (TLS) have been discovered. Here, we provide a short review of Polθ's DNA repair activities and its potential as a drug target and highlight a recent report that reveals Polθ as a naturally occurring reverse transcriptase (RT) in mammalian cells.
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Affiliation(s)
- Xiaojiang S. Chen
- Molecular and Computational Biology, USC Dornsife Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA;
| | - Richard T. Pomerantz
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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Al-Zain AM, Symington LS. The dark side of homology-directed repair. DNA Repair (Amst) 2021; 106:103181. [PMID: 34311272 DOI: 10.1016/j.dnarep.2021.103181] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/16/2021] [Accepted: 07/16/2021] [Indexed: 10/20/2022]
Abstract
DNA double strand breaks (DSB) are cytotoxic lesions that can lead to genome rearrangements and genomic instability, which are hallmarks of cancer. The two main DSB repair pathways are non-homologous end joining and homologous recombination (HR). While HR is generally highly accurate, it has the potential for rearrangements that occur directly or through intermediates generated during the repair process. Whole genome sequencing of cancers has revealed numerous types of structural rearrangement signatures that are often indicative of repair mediated by sequence homology. However, it can be challenging to delineate repair mechanisms from sequence analysis of rearrangement end products from cancer genomes, or even model systems, because the same rearrangements can be generated by different pathways. Here, we review homology-directed repair pathways and their consequences. Exploring those pathways can lead to a greater understanding of rearrangements that occur in cancer cells.
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Affiliation(s)
- Amr M Al-Zain
- Program in Biological Sciences, Columbia University, New York, NY, 10027, United States; Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, United States
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, United States; Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, 10032, United States.
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Ray U, Raghavan SC. Understanding the DNA double-strand break repair and its therapeutic implications. DNA Repair (Amst) 2021; 106:103177. [PMID: 34325086 DOI: 10.1016/j.dnarep.2021.103177] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/25/2021] [Accepted: 07/07/2021] [Indexed: 10/20/2022]
Abstract
Repair of DNA double-strand breaks (DSBs) and its regulation are tightly integrated inside cells. Homologous recombination, nonhomologous end joining and microhomology mediated end joining are three major DSB repair pathways in mammalian cells. Targeting proteins associated with these repair pathways using small molecule inhibitors can prove effective in tumors, especially those with deregulated repair. Sensitization of cancer to current age therapy including radio and chemotherapy, using small molecule inhibitors is promising and warrant further development. Although several are under clinical trial, till date no repair inhibitor is approved for commercial use in cancer patients, with the exception of PARP inhibitors targeting single-strand break repair. Based on molecular profiling of repair proteins, better prognostic and therapeutic output can be achieved in patients. In the present review, we highlight the different mechanisms of DSB repair, chromatin dynamics to provide repair accessibility and modulation of inhibitors in association with molecular profiling and current gold standard treatment modalities for cancer.
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Affiliation(s)
- Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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40
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Cheng X, Côté V, Côté J. NuA4 and SAGA acetyltransferase complexes cooperate for repair of DNA breaks by homologous recombination. PLoS Genet 2021; 17:e1009459. [PMID: 34228704 PMCID: PMC8284799 DOI: 10.1371/journal.pgen.1009459] [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: 02/27/2021] [Revised: 07/16/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022] Open
Abstract
Chromatin modifying complexes play important yet not fully defined roles in DNA repair processes. The essential NuA4 histone acetyltransferase (HAT) complex is recruited to double-strand break (DSB) sites and spreads along with DNA end resection. As predicted, NuA4 acetylates surrounding nucleosomes upon DSB induction and defects in its activity correlate with altered DNA end resection and Rad51 recombinase recruitment. Importantly, we show that NuA4 is also recruited to the donor sequence during recombination along with increased H4 acetylation, indicating a direct role during strand invasion/D-loop formation after resection. We found that NuA4 cooperates locally with another HAT, the SAGA complex, during DSB repair as their combined action is essential for DNA end resection to occur. This cooperation of NuA4 and SAGA is required for recruitment of ATP-dependent chromatin remodelers, targeted acetylation of repair factors and homologous recombination. Our work reveals a multifaceted and conserved cooperation mechanism between acetyltransferase complexes to allow repair of DNA breaks by homologous recombination. DNA double-strand breaks (DSBs) are among the most dangerous types of DNA lesions as they can produce genomic instability that leads to cancer and genetic diseases. It is therefore crucial to understand the precise molecular mechanisms used by cells to detect and repair this type of damages. Homologous recombination using sister chromatid as template is the most accurate pathway to repair these breaks but has to occur within the context of the DNA compacted structure in chromosomes. Here, we show that two enzymes, NuA4 and SAGA, that acetylate the structural components of chromosomes in the vicinity of the DNA breaks are together essential for recombination-mediated repair to occur. We found that they are recruited at an early step after damage detection and their action allows subsequent remodeling of local structural organisation by other enzymes, providing DNA access to the recombination machinery. These results highlight the cooperation of enzymes for a same goal, providing robustness in the repair process as only the loss of both leads to major defects.
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Affiliation(s)
- Xue Cheng
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Canada
| | - Valérie Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Canada
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41
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Xue C, Greene EC. DNA Repair Pathway Choices in CRISPR-Cas9-Mediated Genome Editing. Trends Genet 2021; 37:639-656. [PMID: 33896583 PMCID: PMC8187289 DOI: 10.1016/j.tig.2021.02.008] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/14/2022]
Abstract
Many clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-based genome editing technologies take advantage of Cas nucleases to induce DNA double-strand breaks (DSBs) at desired locations within a genome. Further processing of the DSBs by the cellular DSB repair machinery is then necessary to introduce desired mutations, sequence insertions, or gene deletions. Thus, the accuracy and efficiency of genome editing are influenced by the cellular DSB repair pathways. DSBs are themselves highly genotoxic lesions and as such cells have evolved multiple mechanisms for their repair. These repair pathways include homologous recombination (HR), classical nonhomologous end joining (cNHEJ), microhomology-mediated end joining (MMEJ) and single-strand annealing (SSA). In this review, we briefly highlight CRISPR-Cas9 and then describe the mechanisms of DSB repair. Finally, we summarize recent findings of factors that can influence the choice of DNA repair pathway in response to Cas9-induced DSBs.
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Affiliation(s)
- Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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42
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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: 9] [Impact Index Per Article: 3.0] [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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43
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Wronska AK, van den Broek M, Perli T, de Hulster E, Pronk JT, Daran JM. Engineering oxygen-independent biotin biosynthesis in Saccharomyces cerevisiae. Metab Eng 2021; 67:88-103. [PMID: 34052444 DOI: 10.1016/j.ymben.2021.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/17/2021] [Accepted: 05/23/2021] [Indexed: 01/10/2023]
Abstract
An oxygen requirement for de novo biotin synthesis in Saccharomyces cerevisiae precludes the application of biotin-prototrophic strains in anoxic processes that use biotin-free media. To overcome this issue, this study explores introduction of the oxygen-independent Escherichia coli biotin-biosynthesis pathway in S. cerevisiae. Implementation of this pathway required expression of seven E. coli genes involved in fatty-acid synthesis and three E. coli genes essential for the formation of a pimelate thioester, key precursor of biotin synthesis. A yeast strain expressing these genes readily grew in biotin-free medium, irrespective of the presence of oxygen. However, the engineered strain exhibited specific growth rates 25% lower in biotin-free media than in biotin-supplemented media. Following adaptive laboratory evolution in anoxic cultures, evolved cell lines that no longer showed this growth difference in controlled bioreactors, were characterized by genome sequencing and proteome analyses. The evolved isolates exhibited a whole-genome duplication accompanied with an alteration in the relative gene dosages of biosynthetic pathway genes. These alterations resulted in a reduced abundance of the enzymes catalyzing the first three steps of the E. coli biotin pathway. The evolved pathway configuration was reverse engineered in the diploid industrial S. cerevisiae strain Ethanol Red. The resulting strain grew at nearly the same rate in biotin-supplemented and biotin-free media non-controlled batches performed in an anaerobic chamber. This study established an unique genetic engineering strategy to enable biotin-independent anoxic growth of S. cerevisiae and demonstrated its portability in industrial strain backgrounds.
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Affiliation(s)
- Anna K Wronska
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
| | - Thomas Perli
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
| | - Erik de Hulster
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
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44
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Ghosh D, Raghavan SC. Nonhomologous end joining: new accessory factors fine tune the machinery. Trends Genet 2021; 37:582-599. [PMID: 33785198 DOI: 10.1016/j.tig.2021.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 01/08/2023]
Abstract
Nonhomologous DNA end joining (NHEJ) is one of the major DNA double-strand break (DSB) repair pathways in eukaryotes. The well-known critical proteins involved in NHEJ include Ku70/80, DNA-PKcs, Artemis, DNA pol λ/μ, DNA ligase IV-XRCC4, and XLF. Recent studies have added a number of new proteins to the NHEJ repertoire namely paralog of XRCC4 and XLF (PAXX), modulator of retroviral infection (MRI)/ cell cycle regulator of NHEJ (CYREN), transactivation response DNA-binding protein (TARDBP) of 43 kDa (TDP-43), intermediate filament family orphan (IFFO1), ERCC excision repair 6 like 2 (ERCC6L2), and RNase H2. PAXX acts as a stabilizing factor for the main NHEJ components. MRI/CYREN seems to play a dual role stimulating NHEJ in the G1 phase of the cell cycle, while inhibiting the pathway in the S and G2 phases. TDP-43 can recruit the ligase IV-XRCC4 complex to the DSB sites and stimulate ligation in neuronal cells. RNase H2 excises out the ribonucleotides inserted during repair by DNA polymerase μ/TdT. This review provides a brief glimpse into how these new partners were discovered and their contribution to the mechanism and regulation of NHEJ.
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Affiliation(s)
- Dipayan Ghosh
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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45
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Nelson CB, Alturki TM, Luxton JJ, Taylor LE, Maranon DG, Muraki K, Murnane JP, Bailey SM. Telomeric Double Strand Breaks in G1 Human Cells Facilitate Formation of 5' C-Rich Overhangs and Recruitment of TERRA. Front Genet 2021; 12:644803. [PMID: 33841503 PMCID: PMC8027502 DOI: 10.3389/fgene.2021.644803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/08/2021] [Indexed: 12/12/2022] Open
Abstract
Telomeres, repetitive nucleoprotein complexes that protect chromosomal termini and prevent them from activating inappropriate DNA damage responses (DDRs), shorten with cell division and thus with aging. Here, we characterized the human cellular response to targeted telomeric double-strand breaks (DSBs) in telomerase-positive and telomerase-independent alternative lengthening of telomere (ALT) cells, specifically in G1 phase. Telomeric DSBs in human G1 cells elicited early signatures of a DDR; however, localization of 53BP1, an important regulator of resection at broken ends, was not observed at telomeric break sites. Consistent with this finding and previously reported repression of classical non-homologous end-joining (c-NHEJ) at telomeres, evidence for c-NHEJ was also lacking. Likewise, no evidence of homologous recombination (HR)-dependent repair of telomeric DSBs in G1 was observed. Rather, and supportive of rapid truncation events, telomeric DSBs in G1 human cells facilitated formation of extensive tracks of resected 5′ C-rich telomeric single-stranded (ss)DNA, a previously proposed marker of the recombination-dependent ALT pathway. Indeed, induction of telomeric DSBs in human ALT cells resulted in significant increases in 5′ C-rich (ss)telomeric DNA in G1, which rather than RPA, was bound by the complementary telomeric RNA, TERRA, presumably to protect these exposed ends so that they persist into S/G2 for telomerase-mediated or HR-dependent elongation, while also circumventing conventional repair pathways. Results demonstrate the remarkable adaptability of telomeres, and thus they have important implications for persistent telomeric DNA damage in normal human G1/G0 cells (e.g., lymphocytes), as well as for therapeutically relevant targets to improve treatment of ALT-positive tumors.
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Affiliation(s)
- Christopher B Nelson
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, United States
| | - Taghreed M Alturki
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, United States
| | - Jared J Luxton
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, United States
| | - Lynn E Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - David G Maranon
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Keiko Muraki
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - John P Murnane
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, United States
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46
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Svetec Miklenić M, Svetec IK. Palindromes in DNA-A Risk for Genome Stability and Implications in Cancer. Int J Mol Sci 2021; 22:2840. [PMID: 33799581 PMCID: PMC7999016 DOI: 10.3390/ijms22062840] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
A palindrome in DNA consists of two closely spaced or adjacent inverted repeats. Certain palindromes have important biological functions as parts of various cis-acting elements and protein binding sites. However, many palindromes are known as fragile sites in the genome, sites prone to chromosome breakage which can lead to various genetic rearrangements or even cell death. The ability of certain palindromes to initiate genetic recombination lies in their ability to form secondary structures in DNA which can cause replication stalling and double-strand breaks. Given their recombinogenic nature, it is not surprising that palindromes in the human genome are involved in genetic rearrangements in cancer cells as well as other known recurrent translocations and deletions associated with certain syndromes in humans. Here, we bring an overview of current understanding and knowledge on molecular mechanisms of palindrome recombinogenicity and discuss possible implications of DNA palindromes in carcinogenesis. Furthermore, we overview the data on known palindromic sequences in the human genome and efforts to estimate their number and distribution, as well as underlying mechanisms of genetic rearrangements specific palindromic sequences cause.
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Affiliation(s)
| | - Ivan Krešimir Svetec
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia;
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Charifi F, Churikov D, Eckert-Boulet N, Minguet C, Jourquin F, Hardy J, Lisby M, Simon MN, Géli V. Rad52 SUMOylation functions as a molecular switch that determines a balance between the Rad51- and Rad59-dependent survivors. iScience 2021; 24:102231. [PMID: 33748714 PMCID: PMC7966982 DOI: 10.1016/j.isci.2021.102231] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/01/2021] [Accepted: 02/22/2021] [Indexed: 12/21/2022] Open
Abstract
Functional telomeres in yeast lacking telomerase can be restored by rare Rad51- or Rad59-dependent recombination events that lead to type I and type II survivors, respectively. We previously proposed that polySUMOylation of proteins and the SUMO-targeted ubiquitin ligase Slx5-Slx8 are key factors in type II recombination. Here, we show that SUMOylation of Rad52 favors the formation of type I survivors. Conversely, preventing Rad52 SUMOylation partially bypasses the requirement of Slx5-Slx8 for type II recombination. We further report that SUMO-dependent proteasomal degradation favors type II recombination. Finally, inactivation of Rad59, but not Rad51, impairs the relocation of eroded telomeres to the Nuclear Pore complexes (NPCs). We propose that Rad59 cooperates with non-SUMOylated Rad52 to promote type II recombination at NPCs, resulting in the emergence of more robust survivors akin to ALT cancer cells. Finally, neither Rad59 nor Rad51 is required by itself for the survival of established type II survivors.
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Affiliation(s)
- Ferose Charifi
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes, Marseille, 13009, France
| | - Dmitri Churikov
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes, Marseille, 13009, France
| | | | - Christopher Minguet
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes, Marseille, 13009, France
| | - Frédéric Jourquin
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes, Marseille, 13009, France
| | - Julien Hardy
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes, Marseille, 13009, France
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Marie-Noëlle Simon
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes, Marseille, 13009, France
| | - Vincent Géli
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes, Marseille, 13009, France
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The Srs2 helicase dampens DNA damage checkpoint by recycling RPA from chromatin. Proc Natl Acad Sci U S A 2021; 118:2020185118. [PMID: 33602817 DOI: 10.1073/pnas.2020185118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The DNA damage checkpoint induces many cellular changes to cope with genotoxic stress. However, persistent checkpoint signaling can be detrimental to growth partly due to blockage of cell cycle resumption. Checkpoint dampening is essential to counter such harmful effects, but its mechanisms remain to be understood. Here, we show that the DNA helicase Srs2 removes a key checkpoint sensor complex, RPA, from chromatin to down-regulate checkpoint signaling in budding yeast. The Srs2 and RPA antagonism is supported by their numerous suppressive genetic interactions. Importantly, moderate reduction of RPA binding to single-strand DNA (ssDNA) rescues hypercheckpoint signaling caused by the loss of Srs2 or its helicase activity. This rescue correlates with a reduction in the accumulated RPA and the associated checkpoint kinase on chromatin in srs2 mutants. Moreover, our data suggest that Srs2 regulation of RPA is separable from its roles in recombinational repair and critically contributes to genotoxin resistance. We conclude that dampening checkpoint by Srs2-mediated RPA recycling from chromatin aids cellular survival of genotoxic stress and has potential implications in other types of DNA transactions.
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Single-Strand Annealing in Cancer. Int J Mol Sci 2021; 22:ijms22042167. [PMID: 33671579 PMCID: PMC7926775 DOI: 10.3390/ijms22042167] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/23/2022] Open
Abstract
DNA double-strand breaks (DSBs) are among the most serious forms of DNA damage. In humans, DSBs are repaired mainly by non-homologous end joining (NHEJ) and homologous recombination repair (HRR). Single-strand annealing (SSA), another DSB repair system, uses homologous repeats flanking a DSB to join DNA ends and is error-prone, as it removes DNA fragments between repeats along with one repeat. Many DNA deletions observed in cancer cells display homology at breakpoint junctions, suggesting the involvement of SSA. When multiple DSBs occur in different chromosomes, SSA may result in chromosomal translocations, essential in the pathogenesis of many cancers. Inhibition of RAD52 (RAD52 Homolog, DNA Repair Protein), the master regulator of SSA, results in decreased proliferation of BRCA1/2 (BRCA1/2 DNA Repair Associated)-deficient cells, occurring in many hereditary breast and ovarian cancer cases. Therefore, RAD52 may be targeted in synthetic lethality in cancer. SSA may modulate the response to platinum-based anticancer drugs and radiation. SSA may increase the efficacy of the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 (CRISPR associated 9) genome editing and reduce its off-target effect. Several basic problems associated with SSA, including its evolutionary role, interplay with HRR and NHEJ and should be addressed to better understand its role in cancer pathogenesis and therapy.
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Van Vu T, Thi Hai Doan D, Kim J, Sung YW, Thi Tran M, Song YJ, Das S, Kim J. CRISPR/Cas-based precision genome editing via microhomology-mediated end joining. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:230-239. [PMID: 33047464 PMCID: PMC7868975 DOI: 10.1111/pbi.13490] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/11/2020] [Accepted: 10/03/2020] [Indexed: 05/05/2023]
Abstract
Gene editing and/or allele introgression with absolute precision and control appear to be the ultimate goals of genetic engineering. Precision genome editing in plants has been developed through various approaches, including oligonucleotide-directed mutagenesis (ODM), base editing, prime editing and especially homologous recombination (HR)-based gene targeting. With the advent of CRISPR/Cas for the targeted generation of DNA breaks (single-stranded breaks (SSBs) or double-stranded breaks (DSBs)), a substantial advancement in HR-mediated precise editing frequencies has been achieved. Nonetheless, further research needs to be performed for commercially viable applications of precise genome editing; hence, an alternative innovative method for genome editing may be required. Within this scope, we summarize recent progress regarding precision genome editing mediated by microhomology-mediated end joining (MMEJ) and discuss their potential applications in crop improvement.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
- National Key Laboratory for Plant Cell BiotechnologyAgricultural Genetics InstituteKm 02, Pham Van Dong RoadCo Nhue 1, Bac Tu Liem, Hanoi11917Vietnam
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Young Jong Song
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Swati Das
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Jae‐Yean Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
- Division of Life ScienceGyeongsang National University501 Jinju‐daeroJinju52828Republic of Korea
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