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Sridalla K, Woodhouse MV, Hu J, Scheer J, Ferlez B, Crickard JB. The translocation activity of Rad54 reduces crossover outcomes during homologous recombination. Nucleic Acids Res 2024; 52:7031-7048. [PMID: 38828785 PMCID: PMC11229335 DOI: 10.1093/nar/gkae474] [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: 01/29/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 06/05/2024] Open
Abstract
Homologous recombination (HR) is a template-based DNA double-strand break repair pathway that requires the selection of an appropriate DNA sequence to facilitate repair. Selection occurs during a homology search that must be executed rapidly and with high fidelity. Failure to efficiently perform the homology search can result in complex intermediates that generate genomic rearrangements, a hallmark of human cancers. Rad54 is an ATP dependent DNA motor protein that functions during the homology search by regulating the recombinase Rad51. How this regulation reduces genomic exchanges is currently unknown. To better understand how Rad54 can reduce these outcomes, we evaluated several amino acid mutations in Rad54 that were identified in the COSMIC database. COSMIC is a collection of amino acid mutations identified in human cancers. These substitutions led to reduced Rad54 function and the discovery of a conserved motif in Rad54. Through genetic, biochemical and single-molecule approaches, we show that disruption of this motif leads to failure in stabilizing early strand invasion intermediates, causing increased crossovers between homologous chromosomes. Our study also suggests that the translocation rate of Rad54 is a determinant in balancing genetic exchange. The latch domain's conservation implies an interaction likely fundamental to eukaryotic biology.
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Affiliation(s)
- Krishay Sridalla
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Mitchell V Woodhouse
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jingyi Hu
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jessica Scheer
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Bryan Ferlez
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - J Brooks Crickard
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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2
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Shumega AR, Pavlov YI, Chirinskaite AV, Rubel AA, Inge-Vechtomov SG, Stepchenkova EI. CRISPR/Cas9 as a Mutagenic Factor. Int J Mol Sci 2024; 25:823. [PMID: 38255897 PMCID: PMC10815272 DOI: 10.3390/ijms25020823] [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: 11/15/2023] [Revised: 12/23/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
The discovery of the CRISPR/Cas9 microbial adaptive immune system has revolutionized the field of genetics, by greatly enhancing the capacity for genome editing. CRISPR/Cas9-based editing starts with DNA breaks (or other lesions) predominantly at target sites and, unfortunately, at off-target genome sites. DNA repair systems differing in accuracy participate in establishing desired genetic changes but also introduce unwanted mutations, that may lead to hereditary, oncological, and other diseases. New approaches to alleviate the risks associated with genome editing include attenuating the off-target activity of editing complex through the use of modified forms of Cas9 nuclease and single guide RNA (sgRNA), improving delivery methods for sgRNA/Cas9 complex, and directing DNA lesions caused by the sgRNA/Cas9 to non-mutagenic repair pathways. Here, we have described CRISPR/Cas9 as a new powerful mutagenic factor, discussed its mutagenic properties, and reviewed factors influencing the mutagenic activity of CRISPR/Cas9.
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Affiliation(s)
- Andrey R. Shumega
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.R.S.); (S.G.I.-V.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Departments of Biochemistry and Molecular Biology, Pathology and Microbiology, Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Angelina V. Chirinskaite
- Center of Transgenesis and Genome Editing, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia;
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Sergey G. Inge-Vechtomov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.R.S.); (S.G.I.-V.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.R.S.); (S.G.I.-V.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
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3
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Kim DV, Diatlova EA, Zharkov TD, Melentyev VS, Yudkina AV, Endutkin AV, Zharkov DO. Back-Up Base Excision DNA Repair in Human Cells Deficient in the Major AP Endonuclease, APE1. Int J Mol Sci 2023; 25:64. [PMID: 38203235 PMCID: PMC10778768 DOI: 10.3390/ijms25010064] [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: 11/15/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Apurinic/apyrimidinic (AP) sites are abundant DNA lesions generated both by spontaneous base loss and as intermediates of base excision DNA repair. In human cells, they are normally repaired by an essential AP endonuclease, APE1, encoded by the APEX1 gene. Other enzymes can cleave AP sites by either hydrolysis or β-elimination in vitro, but it is not clear whether they provide the second line of defense in living cells. Here, we studied AP site repairs in APEX1 knockout derivatives of HEK293FT cells using a reporter system based on transcriptional mutagenesis in the enhanced green fluorescent protein gene. Despite an apparent lack of AP site-processing activity in vitro, the cells efficiently repaired the tetrahydrofuran AP site analog resistant to β-elimination. This ability persisted even when the second AP endonuclease homolog, APE2, was also knocked out. Moreover, APEX1 null cells were able to repair uracil, a DNA lesion that is removed via the formation of an AP site. If AP site hydrolysis was chemically blocked, the uracil repair required the presence of NTHL1, an enzyme that catalyzes β-elimination. Our results suggest that human cells possess at least two back-up AP site repair pathways, one of which is NTHL1-dependent.
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Affiliation(s)
- Daria V. Kim
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Evgeniia A. Diatlova
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
| | - Timofey D. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
| | - Vasily S. Melentyev
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Anna V. Yudkina
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Anton V. Endutkin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
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Mishra N, Srivastava R. Bacterial worth in genotoxicity assessment studies. J Microbiol Methods 2023; 215:106860. [PMID: 38008307 DOI: 10.1016/j.mimet.2023.106860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/18/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
Bacterial-based genotoxicity test systems play a significant role in the detection and evaluation of genotoxicity in vitro and have gained importance due to attributes like wide applicability, speed, high sensitivity, good reproducibility, and simplicity. The Salmonella microsomal mutagenicity assay was created by Ames and colleagues at the beginning of the 1970s, and it was based on the fundamental notion that in auxotrophic bacterial strains with inhibited growth, a mutant gene would revert to its original state on exposure to genotoxicants. This is the most successful and widely used in vitro genotoxicity test. Later, a number of additional test systems that incorporated DNA repair mechanisms including the bacterial SOS response were created. Genetic engineering has further provided significant advancement in these test systems with the development of highly sophisticated bacterial tester strains with significantly increased sensitivity to evaluate the chemical nature of hazardous substances and pollutants. These bacterial bioassays render an opportunity to detect the defined effects of compounds at the molecular level. In this review, all the aspects related to the bacterial system in genotoxicity assessment have been summarized and their role is elaborated concerning real-time requirements and future perspectives.
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Affiliation(s)
- Nidhi Mishra
- Department of Zoology, University of Lucknow, Lucknow, U.P. 226007, India.
| | - Rashmi Srivastava
- Department of Zoology, Babasaheb Bhimrao Ambedkar University, Lucknow, U.P. 226025, India
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5
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Hu J, Ferlez B, Dau J, Crickard JB. Rad53 regulates the lifetime of Rdh54 at homologous recombination intermediates. Nucleic Acids Res 2023; 51:11688-11705. [PMID: 37850655 PMCID: PMC10681728 DOI: 10.1093/nar/gkad848] [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: 05/22/2023] [Revised: 09/12/2023] [Accepted: 09/21/2023] [Indexed: 10/19/2023] Open
Abstract
Rdh54 is a conserved DNA translocase that participates in homologous recombination (HR), DNA checkpoint adaptation, and chromosome segregation. Saccharomyces cerevisiae Rdh54 is a known target of the Mec1/Rad53 signaling axis, which globally protects genome integrity during DNA metabolism. While phosphorylation of DNA repair proteins by Mec1/Rad53 is critical for HR progression little is known about how specific post translational modifications alter HR reactions. Phosphorylation of Rdh54 is linked to protection of genomic integrity but the consequences of modification remain poorly understood. Here, we demonstrate that phosphorylation of the Rdh54 C-terminus by the effector kinase Rad53 regulates Rdh54 clustering activity as revealed by single molecule imaging. This stems from phosphorylation dependent and independent interactions between Rdh54 and Rad53. Genetic assays reveal that loss of phosphorylation leads to phenotypic changes resulting in loss-of-heterozygosity (LOH) outcomes. Our data highlight Rad53 as a key regulator of HR intermediates through activation and attenuation of Rdh54 motor function.
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Affiliation(s)
- Jingyi Hu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Bryan Ferlez
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jennifer Dau
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - J Brooks Crickard
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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Saroha B, Kumar A, Bhan V, Singh S, Tumba K, Singh P, Bahadur I. Interaction of heavy metals in Drosophila melanogaster larvae: Fourier transform infrared spectroscopy and single-cell electrophoresis study. J Biomol Struct Dyn 2023; 41:8810-8823. [PMID: 36411739 DOI: 10.1080/07391102.2022.2137587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/13/2022] [Indexed: 11/23/2022]
Abstract
The present study evaluates the Murraya Koenigii (CuLE) and Tinospora Crispa (TiSE) antimutagenic effect and the impact of industrial soil and solid waste leachate on Drosophila larvae. Larvae were exposed to leachate prepared at different pH (7, 4.93, 2.88) and treated with TiSE and CuLE at different concentration (4 g/L and 6 g/L) mixed with standard Drosophila medium. Emphasis was given to the binding interaction of heavy metals with proteins in Drosophila. The change in structure and molecular composition in Drosophila by leachate containing heavy metals induced toxicity has been studied by using Fourier transform infrared (FTIR) spectroscopy. Results from the study demonstrated that CuLE/TiSE administration restored the level of oxidative stress as evidenced by an enhanced antioxidant system and a decrease in lipid peroxidation and protein oxidation. The amide I and amide II bands spectral shifting revealed the binding interaction. The shift in the peak of PO2- asymmetric stretching might be due to compositional changes in nucleic acids. Single-cell electrophoresis was performed to detect the DNA damage which also proved to be ameliorated by administration of CuLE/TiSE. The result concludes that CuLE/TiSE may have great potential in the protection of Drosophila larvae from leachate induced oxidative stress through antioxidant and antimutagenic mechanisms this might help to cope with environmental toxicants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- B Saroha
- Department of Biotechnology, University Institute of Engineering and Technology, MDU, Rohtak, India
| | - A Kumar
- Department of Chemistry, SGRR (PG) College, Dehradun, India
| | - V Bhan
- Department of Biotechnology, University Institute of Engineering and Technology, MDU, Rohtak, India
| | - S Singh
- Thermodynamics-Materials-Separations Research Group, Department of Chemical Engineering, Mangosuthu University of Technology, Durban, uMlazi, South Africa
| | - K Tumba
- Thermodynamics-Materials-Separations Research Group, Department of Chemical Engineering, Mangosuthu University of Technology, Durban, uMlazi, South Africa
| | - P Singh
- Department of Chemistry, Atma Ram Sanatan Dharma (ARSD) College, University of Delhi, New Delhi, India
| | - I Bahadur
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, North-West University (Mafikeng Campus), Mmabatho, South Africa
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Qi L, Zhu YX, Wang YK, Tang XX, Li KJ, He M, Sui Y, Wang PM, Zheng DQ, Zhang K. Nonlethal Furfural Exposure Causes Genomic Alterations and Adaptability Evolution in Saccharomyces cerevisiae. Microbiol Spectr 2023; 11:e0121623. [PMID: 37395645 PMCID: PMC10434202 DOI: 10.1128/spectrum.01216-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/09/2023] [Indexed: 07/04/2023] Open
Abstract
Furfural is a major inhibitor found in lignocellulosic hydrolysate, a promising feedstock for the biofermentation industry. In this study, we aimed to investigate the potential impact of this furan-derived chemical on yeast genome integrity and phenotypic evolution by using genetic screening systems and high-throughput analyses. Our results showed that the rates of aneuploidy, chromosomal rearrangements (including large deletions and duplications), and loss of heterozygosity (LOH) increased by 50-fold, 23-fold, and 4-fold, respectively, when yeast cells were cultured in medium containing a nonlethal dose of furfural (0.6 g/L). We observed significantly different ratios of genetic events between untreated and furfural-exposed cells, indicating that furfural exposure induced a unique pattern of genomic instability. Furfural exposure also increased the proportion of CG-to-TA and CG-to-AT base substitutions among point mutations, which was correlated with DNA oxidative damage. Interestingly, although monosomy of chromosomes often results in the slower growth of yeast under spontaneous conditions, we found that monosomic chromosome IX contributed to the enhanced furfural tolerance. Additionally, terminal LOH events on the right arm of chromosome IV, which led to homozygosity of the SSD1 allele, were associated with furfural resistance. This study sheds light on the mechanisms underlying the influence of furfural on yeast genome integrity and adaptability evolution. IMPORTANCE Industrial microorganisms are often exposed to multiple environmental stressors and inhibitors during their application. This study demonstrates that nonlethal concentrations of furfural in the culture medium can significantly induce genome instability in the yeast Saccharomyces cerevisiae. Notably, furfural-exposed yeast cells displayed frequent chromosome aberrations, indicating the potent teratogenicity of this inhibitor. We identified specific genomic alterations, including monosomic chromosome IX and loss of heterozygosity of the right arm of chromosome IV, that confer furfural tolerance to a diploid S. cerevisiae strain. These findings enhance our understanding of how microorganisms evolve and adapt to stressful environments and offer insights for developing strategies to improve their performance in industrial applications.
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Affiliation(s)
- Lei Qi
- Donghai Laboratory, Zhoushan, China
- Ocean College, Zhejiang University, Zhoushan, China
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | | | - Ye-Ke Wang
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | | | - Ke-Jing Li
- Ocean College, Zhejiang University, Zhoushan, China
| | - Min He
- Ocean College, Zhejiang University, Zhoushan, China
| | - Yang Sui
- Donghai Laboratory, Zhoushan, China
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Pin-Mei Wang
- Donghai Laboratory, Zhoushan, China
- Ocean College, Zhejiang University, Zhoushan, China
| | - Dao-Qiong Zheng
- Donghai Laboratory, Zhoushan, China
- Ocean College, Zhejiang University, Zhoushan, China
| | - Ke Zhang
- College of Life Science, Zhejiang University, Hangzhou, China
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Deacetylation induced nuclear condensation of HP1γ promotes multiple myeloma drug resistance. Nat Commun 2023; 14:1290. [PMID: 36894562 PMCID: PMC9998874 DOI: 10.1038/s41467-023-37013-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/24/2023] [Indexed: 03/11/2023] Open
Abstract
Acquired chemoresistance to proteasome inhibitors is a major obstacle in managing multiple myeloma but key regulators and underlying mechanisms still remain to be explored. We find that high level of HP1γ is associated with low acetylation modification in the bortezomib-resistant myeloma cells using SILAC-based acetyl-proteomics assay, and higher HP1γ level is positively correlated with poorer outcomes in the clinic. Mechanistically, elevated HDAC1 in the bortezomib-resistant myeloma cells deacetylates HP1γ at lysine 5 and consequently alleviates the ubiquitin-mediated protein degradation, as well as the aberrant DNA repair capacity. HP1γ interacts with the MDC1 to induce DNA repair, and simultaneously the deacetylation modification and the interaction with MDC1 enhance the nuclear condensation of HP1γ protein and the chromatin accessibility of its target genes governing sensitivity to proteasome inhibitors, such as CD40, FOS and JUN. Thus, targeting HP1γ stability by using HDAC1 inhibitor re-sensitizes bortezomib-resistant myeloma cells to proteasome inhibitors treatment in vitro and in vivo. Our findings elucidate a previously unrecognized role of HP1γ in inducing drug resistance to proteasome inhibitors of myeloma cells and suggest that targeting HP1γ may be efficacious for overcoming drug resistance in refractory or relapsed multiple myeloma patients.
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A Natural Fungal Gene Drive Enacts Killing via DNA Disruption. mBio 2023; 14:e0317322. [PMID: 36537809 PMCID: PMC9972908 DOI: 10.1128/mbio.03173-22] [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] [Indexed: 12/24/2022] Open
Abstract
Fungal spore killers are a class of selfish genetic elements that positively bias their own inheritance by killing non-inheriting gametes following meiosis. As killing takes place specifically within the developing fungal ascus, a tissue which is experimentally difficult to isolate, our understanding of the mechanisms underlying spore killers are limited. In particular, how these loci kill other spores within the fungal ascus is largely unknown. Here, we overcome these experimental barriers by developing model systems in 2 evolutionary distant organisms, Escherichia coli (bacterium) and Saccharomyces cerevisiae (yeast), similar to previous approaches taken to examine the wtf spore killers. Using these systems, we show that the Podospora anserina spore killer protein SPOK1 enacts killing through targeting DNA. IMPORTANCE Natural gene drives have shaped the genomes of many eukaryotes and recently have been considered for applications to control undesirable species. In fungi, these loci are called spore killers. Despite their importance in evolutionary processes and possible applications, our understanding of how they enact killing is limited. We show that the spore killer protein Spok1, which has homologues throughout the fungal tree of life, acts via DNA disruption. Spok1 is only the second spore killer locus in which the cellular target of killing has been identified and is the first known to target DNA. We also show that the DNA disrupting activity of Spok1 is functional in both bacteria and yeast suggesting a highly conserved mode of action.
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Moise AC, Kay JE, Engelward BP. Transgenic mice harboring direct repeat substrates reveal key underlying causes of homologous recombination in vivo. DNA Repair (Amst) 2022; 120:103419. [DOI: 10.1016/j.dnarep.2022.103419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 12/01/2022]
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Pan-cancer analysis of co-occurring mutations in RAD52 and the BRCA1-BRCA2-PALB2 axis in human cancers. PLoS One 2022; 17:e0273736. [PMID: 36107942 PMCID: PMC9477347 DOI: 10.1371/journal.pone.0273736] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
In human cells homologous recombination (HR) is critical for repair of DNA double strand breaks (DSBs) and rescue of stalled or collapsed replication forks. HR is facilitated by RAD51 which is loaded onto DNA by either BRCA2-BRCA1-PALB2 or RAD52. In human culture cells, double-knockdowns of RAD52 and genes in the BRCA1-BRCA2-PALB2 axis are lethal. Mutations in BRCA2, BRCA1 or PALB2 significantly impairs error free HR as RAD51 loading relies on RAD52 which is not as proficient as BRCA2-BRCA1-PALB2. RAD52 also facilitates Single Strand Annealing (SSA) that produces intra-chromosomal deletions. Some RAD52 mutations that affect the SSA function or decrease RAD52 association with DNA can suppress certain BRCA2 associated phenotypes in breast cancers. In this report we did a pan-cancer analysis using data reported on the Catalogue of Somatic Mutations in Cancers (COSMIC) to identify double mutants between RAD52 and BRCA1, BRCA2 or PALB2 that occur in cancer cells. We find that co-occurring mutations are likely in certain cancer tissues but not others. However, all mutations occur in a heterozygous state. Further, using computational and machine learning tools we identified only a handful of pathogenic or driver mutations predicted to significantly affect the function of the proteins. This supports previous findings that co-inactivation of RAD52 with any members of the BRCA2-BRCA1-PALB2 axis is lethal. Molecular modeling also revealed that pathogenic RAD52 mutations co-occurring with mutations in BRCA2-BRCA1-PALB2 axis are either expected to attenuate its SSA function or its interaction with DNA. This study extends previous breast cancer findings to other cancer types and shows that co-occurring mutations likely destabilize HR by similar mechanisms as in breast cancers.
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12
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Keymakh M, Dau J, Hu J, Ferlez B, Lisby M, Crickard JB. Rdh54 stabilizes Rad51 at displacement loop intermediates to regulate genetic exchange between chromosomes. PLoS Genet 2022; 18:e1010412. [PMID: 36099310 PMCID: PMC9506641 DOI: 10.1371/journal.pgen.1010412] [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: 05/31/2022] [Revised: 09/23/2022] [Accepted: 09/04/2022] [Indexed: 11/20/2022] Open
Abstract
Homologous recombination (HR) is a double-strand break DNA repair pathway that preserves chromosome structure. To repair damaged DNA, HR uses an intact donor DNA sequence located elsewhere in the genome. After the double-strand break is repaired, DNA sequence information can be transferred between donor and recipient DNA molecules through different mechanisms, including DNA crossovers that form between homologous chromosomes. Regulation of DNA sequence transfer is an important step in effectively completing HR and maintaining genome integrity. For example, mitotic exchange of information between homologous chromosomes can result in loss-of-heterozygosity (LOH), and in higher eukaryotes, the development of cancer. The DNA motor protein Rdh54 is a highly conserved DNA translocase that functions during HR. Several existing phenotypes in rdh54Δ strains suggest that Rdh54 may regulate effective exchange of DNA during HR. In our current study, we used a combination of biochemical and genetic techniques to dissect the role of Rdh54 on the exchange of genetic information during DNA repair. Our data indicate that RDH54 regulates DNA strand exchange by stabilizing Rad51 at an early HR intermediate called the displacement loop (D-loop). Rdh54 acts in opposition to Rad51 removal by the DNA motor protein Rad54. Furthermore, we find that expression of a catalytically inactivate allele of Rdh54, rdh54K318R, favors non-crossover outcomes. From these results, we propose a model for how Rdh54 may kinetically regulate strand exchange during homologous recombination. Homologous recombination is an important pathway in repairing DNA double strand breaks. For the purposes of this study, HR can be divided into two stages. The first is a DNA repair stage in which the broken DNA molecule is fixed. In the second stage, information can move from one DNA molecule to another. Enzymes that use the power of ATP hydrolysis to move along dsDNA aid in regulating both stages of HR. In this work we focused on the understudied DNA motor protein Rdh54. We combined genetic and biochemical approaches to show that Rdh54 regulates HR by stabilizing the recombinase protein Rad51 at early HR intermediates.
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Affiliation(s)
- Margaret Keymakh
- Deparment of Molecular Biology and Genetics, Cornell University Ithaca, Ithaca, New York, United States of America
| | - Jennifer Dau
- Deparment of Molecular Biology and Genetics, Cornell University Ithaca, Ithaca, New York, United States of America
| | - Jingyi Hu
- Deparment of Molecular Biology and Genetics, Cornell University Ithaca, Ithaca, New York, United States of America
| | - Bryan Ferlez
- Deparment of Molecular Biology and Genetics, Cornell University Ithaca, Ithaca, New York, United States of America
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - J. Brooks Crickard
- Deparment of Molecular Biology and Genetics, Cornell University Ithaca, Ithaca, New York, United States of America
- * E-mail:
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13
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Toft CJ, Sorenson AE, Schaeffer PM. Rise of the terminator protein tus: A versatile tool in the biotechnologist's toolbox. Anal Chim Acta 2022; 1213:339946. [DOI: 10.1016/j.aca.2022.339946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 02/07/2023]
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14
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Nickens DG, Bochman ML. Genetic and biochemical interactions of yeast DNA helicases. Methods 2022; 204:234-240. [PMID: 35483549 DOI: 10.1016/j.ymeth.2022.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 12/13/2022] Open
Abstract
DNA helicases function in many types of nucleic acid transactions, and as such, they are vital for genome integrity. Although they are often considered individually, work from many groups demonstrates that these enzymes often genetically and biochemically interact in vivo. Here, we highlight methods to interrogate such interactions among the PIF1 (Pif1 and Rrm3) and RecQ (Hrq1 and Sgs1) family helicases in Saccharomyces cerevisiae. The interactions among these enzymes were investigated in vivo using deletion and inactivation alleles with a gross-chromosomal rearrangement (GCR) assay. Further, wild-type and inactive recombinant proteins were used to determine the effects of the helicases on telomerase activity in vitro. We found that synergistic increases in GCR rates often occur in double vs. single mutants, suggesting that the helicases function in distinct genome integrity pathways. Further, the recombinant helicases can function together in vitro to modulate telomerase activity. Overall, the data suggest that the interactions among the members of these DNA helicase families are multipartite and argue for a comprehensive systems biology approach to fully elucidate the physiological interplay between these enzymes.
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Affiliation(s)
- David G Nickens
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405 USA
| | - Matthew L Bochman
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405 USA.
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15
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Khan SR, Kuzminov A. Thymine-starvation-induced chromosomal fragmentation is not required for thymineless death in Escherichia coli. Mol Microbiol 2022; 117:1138-1155. [PMID: 35324030 DOI: 10.1111/mmi.14897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 11/29/2022]
Abstract
Thymine or thymidine starvation induces robust chromosomal fragmentation in E. coli thyA deoCABD mutants, and is proposed to be the cause of thymineless death (TLD). However, fragmentation kinetics challenges the idea that fragmentation causes TLD, by peaking before the onset of TLD and disappearing by the time TLD accelerates. Quantity and kinetics of fragmentation also stays unchanged in hyper-TLD-exhibiting recBCD mutant, making its faster and deeper TLD independent of fragmentation as well. Elimination of fragmentation without affecting cellular metabolism did not abolish TLD in the thyA mutant, but reduced early TLD in the thyA recBCD mutant, suggesting replication-dependent, but undetectable by pulsed field gel, double-strand breaks contributed to TLD. Chromosomal fragmentation, but not TLD, was eliminated in both the thyA and thyA recBCD mutants harboring deoCABD operon. Expression of a single gene, deoA, encoding thymidine phosphorylase, was sufficient to abolish fragmentation, suggesting thymidine-to-thymine interconversion during T-starvation being a key factor. Overall, this study reveals that chromosomal fragmentation, a direct consequence of T-starvation, is either dispensable or redundant for the overall TLD pathology, including hyper-TLD in the recBCD mutant. Replication forks, unlike chromosomal fragmentation, may provide minor contribution to TLD, but only in the repair-deficient thyA deoCABD recBCD mutant.
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Affiliation(s)
- Sharik R Khan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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16
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Pang T, Zhang X. Technical Evaluation of Commercial Sperm DFI Quality Control Products in SCSA Testing. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:9552123. [PMID: 35281543 PMCID: PMC8916875 DOI: 10.1155/2022/9552123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/08/2022] [Accepted: 01/31/2022] [Indexed: 11/25/2022]
Abstract
With the increase in population and the advancement of medicine, people even more hope that their offspring will be healthier. DNA fragmentation rate is currently one of the more common indicators for evaluating sperm fertility and predicting the outcome of pregnancy. In order to evaluate the technical performance and application value of commercial sperm DFI (DNA fragmentation index) quality control products in the flow cytometry sperm chromatin structure analysis (SCSA), this paper uses flow cytometry to test commercial sperm DFI quality control products (Celula) and laboratory routine self-made DFI quality control products. In this paper, the quality control of new commercial sperm DFI and laboratory-made quality control were compared and tested for 30 consecutive days. And this paper monitors the response of commercial quality control products to the interference of key reagent parameters. This paper compares the stability of the test results of two quality control products and their sensitivity to the interference of key performance parameters of the detection reagent. Experimental results show that commercial sperm DFI quality control products can simulate sperm DNA damage to achieve accurate detection of DNA integrity. The stability of commercial sperm DFI quality control (CV = 2.47%) is better than that of laboratory-made quality control (CV = 11.22%). The new commercial sperm DFI quality control product can sensitively detect changes in the concentration of acidified solution and staining solution at the same time. It can effectively control the quality of detection reagents and experimental procedures. The new commercial sperm DFI quality control product can effectively control sperm DNA integrity testing. It can be used as an external quality control product for quality control of test results to ensure that more accurate test results are provided to the clinic.
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Affiliation(s)
- Tao Pang
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou 510600, Guangdong, China
| | - Xinzong Zhang
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou 510600, Guangdong, China
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17
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Shademan B, Nourazarian A, Hajazimian S, Isazadeh A, Biray Avci C, Oskouee MA. CRISPR Technology in Gene-Editing-Based Detection and Treatment of SARS-CoV-2. Front Mol Biosci 2022; 8:772788. [PMID: 35087864 PMCID: PMC8787289 DOI: 10.3389/fmolb.2021.772788] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/21/2021] [Indexed: 01/08/2023] Open
Abstract
Outbreak and rapid spread of coronavirus disease (COVID-19) caused by coronavirus acute respiratory syndrome (SARS-CoV-2) caused severe acute respiratory syndrome (SARS-CoV-2) that started in Wuhan, and has become a global problem because of the high rate of human-to-human transmission and severe respiratory infections. Because of high prevalence of SARS-CoV-2, which threatens many people worldwide, rapid diagnosis and simple treatment are needed. Genome editing is a nucleic acid-based approach to altering the genome by artificially changes in genetic information and induce irreversible changes in the function of target gene. Clustered, regularly interspaced short palindromic repeats (CRISPR/Cas) could be a practical and straightforward approach to this disease. CRISPR/Cas system contains Cas protein, which is controlled by a small RNA molecule to create a double-stranded DNA gap. Evidence suggested that CRISPR/Cas was also usable for diagnosis and treatment of SARS-CoV-2 infection. In this review study, we discoursed on application of CRISPR technology in detection and treatment of SARS-CoV-2 infection. Another aspect of this study was to introduce potential future problems in use of CRISPR/Cas technology.
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Affiliation(s)
- Behrouz Shademan
- Department of Medical Biology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Alireza Nourazarian
- Department of Basic Medical Sciences, Khoy University of Medical Sciences, Khoy, Iran
| | - Saba Hajazimian
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Isazadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Cigir Biray Avci
- Department of Medical Biology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Mahin Ahangar Oskouee
- Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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18
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Uncovering bleomycin-induced genomic alterations and underlying mechanisms in yeast. Appl Environ Microbiol 2021; 88:e0170321. [PMID: 34731050 DOI: 10.1128/aem.01703-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bleomycin (BLM) is a widely used chemotherapeutic drug. BLM-treated cells showed an elevated rate of mutations, but the underlying mechanisms remained unclear. In this study, the global genomic alterations in BLM-treated cells were explored in the yeast Saccharomyces cerevisiae. Using genetic assay and whole-genome sequencing, we found that the mutation rate could be greatly elevated in S. cerevisiae cells that underwent ZeocinTM (a BLM member) treatment. One-base deletion and T to G substitution at the 5'-GT-3' motif was the most striking signature of ZeocinTM-induced mutations. This was mainly the result of translesion DNA synthesis involving Rev1 and polymerase ζ. ZeocinTM treatment led to the frequent loss of heterozygosity and chromosomal rearrangements in the diploid strains. The breakpoints of recombination events were significantly associated with certain chromosomal elements. Lastly, we identified multiple genomic alterations that contributed to BLM resistance in the ZeocinTM-treated mutants. Overall, this study provides new insights into the genotoxicity and evolutional effects of BLM. Importance Bleomycin is an antitumor antibiotic that can mutate genomic DNA. Using yeast models in combination with genome sequencing, the mutational signatures of ZeocinTM (a member of the bleomycin family) are disclosed. Translesion-synthesis polymerases are crucial for the viability of ZeocinTM-treated yeast cells at the sacrifice of a higher mutation rate. We also confirmed that multiple genomic alterations were associated with the improved resistance to ZeocinTM, providing novel insights into how bleomycin resistance is developed in cells.
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19
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Berzsenyi I, Pantazi V, Borsos BN, Pankotai T. Systematic overview on the most widespread techniques for inducing and visualizing the DNA double-strand breaks. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108397. [PMID: 34893162 DOI: 10.1016/j.mrrev.2021.108397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
Abstract
DNA double-strand breaks (DSBs) are one of the most frequent causes of initiating cancerous malformations, therefore, to reduce the risk, cells have developed sophisticated DNA repair mechanisms. These pathways ensure proper cellular function and genome integrity. However, any alteration or malfunction during DNA repair can influence cellular homeostasis, as improper recognition of the DNA damage or dysregulation of the repair process can lead to genome instability. Several powerful methods have been established to extend our current knowledge in the field of DNA repair. For this reason, in this review, we focus on the methods used to study DSB repair, and we summarize the advantages and disadvantages of the most commonly used techniques currently available for the site-specific induction of DSBs and the subsequent tracking of the repair processes in human cells. We highlight methods that are suitable for site-specific DSB induction (by restriction endonucleases, CRISPR-mediated DSB induction and laser microirradiation) as well as approaches [e.g., fluorescence-, confocal- and super-resolution microscopy, chromatin immunoprecipitation (ChIP), DSB-labeling and sequencing techniques] to visualize and follow the kinetics of DSB repair.
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Affiliation(s)
- Ivett Berzsenyi
- Institute of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, 1 Állomás Street H-6725, Szeged, Hungary.
| | - Vasiliki Pantazi
- Institute of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, 1 Állomás Street H-6725, Szeged, Hungary.
| | - Barbara N Borsos
- Institute of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, 1 Állomás Street H-6725, Szeged, Hungary.
| | - Tibor Pankotai
- Institute of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, 1 Állomás Street H-6725, Szeged, Hungary.
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20
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Agashe P, Kuzminov A. Catalase inhibition by nitric oxide potentiates hydrogen peroxide to trigger catastrophic chromosome fragmentation in Escherichia coli. Genetics 2021; 218:6214516. [PMID: 34027548 DOI: 10.1093/genetics/iyab057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/02/2021] [Indexed: 01/01/2023] Open
Abstract
Hydrogen peroxide (H2O2, HP) is a universal toxin that organisms deploy to kill competing or invading cells. Bactericidal action of H2O2 presents several questions. First, the lethal H2O2 concentrations in bacterial cultures are 1000x higher than, for example, those calculated for the phagosome. Second, H2O2-alone kills bacteria in cultures either by mode-one, via iron-mediated chromosomal damage, or by mode-two, via unknown targets, but the killing mode in phagosomes is unclear. Third, phagosomal H2O2 toxicity is enhanced by production of nitric oxide (NO), but in vitro studies disagree: some show NO synergy with H2O2 antimicrobial action, others instead report alleviation. To investigate this "NO paradox," we treated Escherichia coli with various concentrations of H2O2-alone or H2O2+NO, measuring survival and chromosome stability. We found that all NO concentrations make sublethal H2O2 treatments highly lethal, via triggering catastrophic chromosome fragmentation (mode-one killing). Yet, NO-alone is not lethal, potentiating H2O2 toxicity by blocking H2O2 scavenging in cultures. Catalases represent obvious targets of NO inhibition, and catalase-deficient mutants are indeed killed equally by H2O2-alone or H2O2+NO treatments, also showing similar levels of chromosome fragmentation. Interestingly, iron chelation blocks chromosome fragmentation in catalase-deficient mutants without blocking H2O2-alone lethality, indicating mode-two killing. In fact, mode-two killing of WT cells by much higher H2O2 concentrations is transiently alleviated by NO, reproducing the "NO paradox." We conclude that NO potentiates H2O2 toxicity by promoting mode-one killing (via catastrophic chromosome fragmentation) by otherwise static low H2O2 concentrations, while transiently suppressing mode-two killing by immediately lethal high H2O2 concentrations.
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Affiliation(s)
- Pooja Agashe
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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21
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Miné-Hattab J, Heltberg M, Villemeur M, Guedj C, Mora T, Walczak AM, Dahan M, Taddei A. Single molecule microscopy reveals key physical features of repair foci in living cells. eLife 2021; 10:60577. [PMID: 33543712 PMCID: PMC7924958 DOI: 10.7554/elife.60577] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/26/2021] [Indexed: 12/20/2022] Open
Abstract
In response to double strand breaks (DSB), repair proteins accumulate at damaged sites, forming membrane-less sub-compartments or foci. Here we explored the physical nature of these foci, using single molecule microscopy in living cells. Rad52, the functional homolog of BRCA2 in yeast, accumulates at DSB sites and diffuses ~6 times faster within repair foci than the focus itself, exhibiting confined motion. The Rad52 confinement radius coincides with the focus size: foci resulting from 2 DSBs are twice larger in volume that the ones induced by a unique DSB and the Rad52 confinement radius scales accordingly. In contrast, molecules of the single strand binding protein Rfa1 follow anomalous diffusion similar to the focus itself or damaged chromatin. We conclude that while most Rfa1 molecules are bound to the ssDNA, Rad52 molecules are free to explore the entire focus reflecting the existence of a liquid droplet around damaged DNA.
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Affiliation(s)
- Judith Miné-Hattab
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
| | - Mathias Heltberg
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France.,Laboratoire de Physique de l'Ecole Normale Supérieure, PSL University, CNRS, Sorbonne Université , Université de Paris, Paris, France
| | - Marie Villemeur
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
| | - Chloé Guedj
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
| | - Thierry Mora
- Laboratoire de Physique de l'Ecole Normale Supérieure, PSL University, CNRS, Sorbonne Université , Université de Paris, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique de l'Ecole Normale Supérieure, PSL University, CNRS, Sorbonne Université , Université de Paris, Paris, France
| | - Maxime Dahan
- Institut Curie, PSL University, Sorbonne Université, CNRS, Physico Chimie Curie, Paris, France
| | - Angela Taddei
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France.,Cogitamus Laboratory, Paris, France
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22
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Meschichi A, Rosa S. Visualizing and Measuring Single Locus Dynamics in Arabidopsis thaliana. Methods Mol Biol 2021; 2200:213-224. [PMID: 33175380 DOI: 10.1007/978-1-0716-0880-7_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In eukaryotes, DNA is packed into an incredibly complex structure called chromatin. Although chromatin was often considered as a static entity, it is now clear that chromatin proteins and the chromatin fiber itself are in fact very dynamic. For instance, the packaging of the DNA into the nucleus requires an extraordinary degree of compaction but this should be achieved without compromising the accessibility to the transcription machinery and other nuclear processes. Approaches such as gene tagging have been established for living cells in order to detect, track, and analyze the mobility of single loci. In this chapter, we provide an experimental protocol for performing locus tracking in Arabidopsis thaliana roots and for characterizing locus mobility behavior via a Mean Square Displacement analysis.
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Affiliation(s)
- Anis Meschichi
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Stefanie Rosa
- Swedish University of Agricultural Sciences, Uppsala, Sweden.
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23
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Abstract
DNA break lesions pose a serious threat to the integrity of the genome. Eukaryotic cells can repair these lesions using the homologous recombination pathway that guides the repair reaction by using a homologous DNA template. The budding yeast Saccharomyces cerevisiae is an excellent model system with which to study this repair mechanism and the resulting patterns of genomic change resulting from it. In this chapter, we describe an approach that utilizes whole-genome sequencing data to support the analysis of tracts of loss-of-heterozygosity (LOH) that can arise from mitotic recombination in the context of the entire diploid yeast genome. The workflow and the discussion in this chapter are intended to enable classically trained molecular biologists and geneticists with limited experience in computational methods to conceptually understand and execute the steps of genome-wide LOH analysis as well as to adapt and apply them to their own specific studies and experimental models.
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Affiliation(s)
- Lydia R Heasley
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Nadia M V Sampaio
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, USA
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, USA.
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24
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Waisertreiger I, Barlow J. Fragile site instability: measuring more than breaks. Oncoscience 2020; 7:60-67. [PMID: 33195735 PMCID: PMC7640903 DOI: 10.18632/oncoscience.513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/17/2020] [Indexed: 12/23/2022] Open
Abstract
Genome instability is not only a hallmark of cancer, it is necessary for its initiation and evolution, and naturally accumulates as cells age. Replication stress is a potent source of genome instability found in many tumor types [1]. Chromosomal fragile sites are genomic loci highly prone to DNA damage specifically from replication stress and are frequently mutated in cancer [2-4]2-4]. While tracking the origin of individual mutations has proved challenging, measuring DNA damage and repair at endogenous sites can offer key insights into understanding the etiology of cancer. In the past 15 years, the causal link between replication stress, oncogene activation, and tumor initiation and evolution has become increasingly clear [1, 5-9]. Replication-associated damage accumulates at early stages of tumorigenesis and may promote further transformation. Studying the causes and consequences of fragile site instability can offer a window into the earliest stages of carcinogenesis [10-13]. In particular, fragile site studies will help us understand the molecular underpinnings influencing the frequency of DNA breakage, successful repair processes suppressing genome instability, and unsuccessful repair leading to mutations and chromosome rearrangements. Of these, measuring successful repair is the most challenging as it leaves little evidence behind.
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Affiliation(s)
- Irina Waisertreiger
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
| | - Jacqueline Barlow
- Department of Microbiology and Molecular Genetics & Genome Center, University of California, Davis, CA, USA
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25
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Systemic and rapid restructuring of the genome: a new perspective on punctuated equilibrium. Curr Genet 2020; 67:57-63. [PMID: 33159552 DOI: 10.1007/s00294-020-01119-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/17/2022]
Abstract
The rates and patterns by which cells acquire mutations profoundly shape their evolutionary trajectories and phenotypic potential. Conventional models maintain that mutations are acquired independently of one another over many successive generations. Yet, recent evidence suggests that cells can also experience mutagenic processes that drive rapid genome evolution. One such process manifests as punctuated bursts of genomic instability, in which multiple new mutations are acquired simultaneously during transient episodes of genomic instability. This mutational mode is reminiscent of the theory of punctuated equilibrium, proposed by Stephen Jay Gould and Niles Eldredge in 1972 to explain the burst-like appearance of new species in the fossil record. In this review, we survey the dominant and emerging theories of eukaryotic genome evolution with a particular focus on the growing body of work that substantiates the existence and importance of punctuated bursts of genomic instability. In addition, we summarize and discuss two recent studies from our own group, the results of which indicate that punctuated bursts systemic genomic instability (SGI) can rapidly reconfigure the structure of the diploid genome of Saccharomyces cerevisiae.
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26
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Andreychuk YV, Zadorsky SP, Zhuk AS, Stepchenkova EI, Inge-Vechtomov SG. Relationship between Type I and Type II Template Processes: Amyloids and Genome Stability. Mol Biol 2020. [DOI: 10.1134/s0026893320050027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Cheblal A, Challa K, Seeber A, Shimada K, Yoshida H, Ferreira HC, Amitai A, Gasser SM. DNA Damage-Induced Nucleosome Depletion Enhances Homology Search Independently of Local Break Movement. Mol Cell 2020; 80:311-326.e4. [PMID: 32970994 DOI: 10.1016/j.molcel.2020.09.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 01/02/2023]
Abstract
To determine whether double-strand break (DSB) mobility enhances the physical search for an ectopic template during homology-directed repair (HDR), we tested the effects of factors that control chromatin dynamics, including cohesin loading and kinetochore anchoring. The former but not the latter is altered in response to DSBs. Loss of the nonhistone high-mobility group protein Nhp6 reduces histone occupancy and increases chromatin movement, decompaction, and ectopic HDR. The loss of nucleosome remodeler INO80-C did the opposite. To see whether enhanced HDR depends on DSB mobility or the global chromatin response, we tested the ubiquitin ligase mutant uls1Δ, which selectively impairs local but not global movement in response to a DSB. Strand invasion occurs in uls1Δ cells with wild-type kinetics, arguing that global histone depletion rather than DSB movement is rate limiting for HDR. Impaired break movement in uls1Δ correlates with elevated MRX and cohesin loading, despite normal resection and checkpoint activation.
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Affiliation(s)
- Anaïs Cheblal
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, 4056 Basel, Switzerland
| | - Kiran Challa
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Present address: Center for Advanced Imaging, Northwest Building, 52 Oxford St, Suite 147, Harvard University, Cambridge, MA 02138, USA
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Haruka Yoshida
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Helder C Ferreira
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Assaf Amitai
- Department of Chemical Engineering, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, 4056 Basel, Switzerland.
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28
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Intrachromosomal Recombination in Yeast. Methods Mol Biol 2020. [PMID: 32840781 DOI: 10.1007/978-1-0716-0644-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Spontaneous and induced mitotic recombinations are driven by lesions such as single-strand nicks and gaps and double-strand breaks in the genome. For regions of the genome that are not repetitive, spontaneous recombination rates are too low to be detected by simple screening and require reporters where a recombination product can be selected. This chapter describes commonly used types of reporters where a gene is duplicated as direct repeats and both copies are mutated with different mutations, rendering the cell defective for the gene and auxotrophic for the gene product. Recombination between the two defective copies can result in a wild-type gene and a prototrophic phenotype for the cell. Methods to use these types of reporters to determine recombination rates between the two gene copies are described, and their use in monitoring both increased and decreased recombinations is discussed.
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29
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A scalable CRISPR/Cas9-based fluorescent reporter assay to study DNA double-strand break repair choice. Nat Commun 2020; 11:4077. [PMID: 32796846 PMCID: PMC7429917 DOI: 10.1038/s41467-020-17962-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 07/23/2020] [Indexed: 02/07/2023] Open
Abstract
Double-strand breaks (DSBs) are the most toxic type of DNA lesions. Cells repair these lesions using either end protection- or end resection-coupled mechanisms. To study DSB repair choice, we present the Color Assay Tracing-Repair (CAT-R) to simultaneously quantify DSB repair via end protection and end resection pathways. CAT-R introduces DSBs using CRISPR/Cas9 in a tandem fluorescent reporter, whose repair distinguishes small insertions/deletions from large deletions. We demonstrate CAT-R applications in chemical and genetic screens. First, we evaluate 21 compounds currently in clinical trials which target the DNA damage response. Second, we examine how 417 factors involved in DNA damage response influence the choice between end protection and end resection. Finally, we show that impairing nucleotide excision repair favors error-free repair, providing an alternative way for improving CRISPR/Cas9-based knock-ins. CAT-R is a high-throughput, versatile assay to assess DSB repair choice, which facilitates comprehensive studies of DNA repair and drug efficiency testing. Cells employ different repair pathways to repair DNA double strand breaks. Here, the authors develop a CRISPR/Cas9-dependent method to study choices in DNA repair called the Color Assay Tracing-Repair (CAT-R) which simultaneously measure outcomes of DSB repair via end-protection and end-resection pathways.
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DNA damage response signaling pathways and targets for radiotherapy sensitization in cancer. Signal Transduct Target Ther 2020; 5:60. [PMID: 32355263 PMCID: PMC7192953 DOI: 10.1038/s41392-020-0150-x] [Citation(s) in RCA: 464] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/20/2020] [Accepted: 03/16/2020] [Indexed: 12/19/2022] Open
Abstract
Radiotherapy is one of the most common countermeasures for treating a wide range of tumors. However, the radioresistance of cancer cells is still a major limitation for radiotherapy applications. Efforts are continuously ongoing to explore sensitizing targets and develop radiosensitizers for improving the outcomes of radiotherapy. DNA double-strand breaks are the most lethal lesions induced by ionizing radiation and can trigger a series of cellular DNA damage responses (DDRs), including those helping cells recover from radiation injuries, such as the activation of DNA damage sensing and early transduction pathways, cell cycle arrest, and DNA repair. Obviously, these protective DDRs confer tumor radioresistance. Targeting DDR signaling pathways has become an attractive strategy for overcoming tumor radioresistance, and some important advances and breakthroughs have already been achieved in recent years. On the basis of comprehensively reviewing the DDR signal pathways, we provide an update on the novel and promising druggable targets emerging from DDR pathways that can be exploited for radiosensitization. We further discuss recent advances identified from preclinical studies, current clinical trials, and clinical application of chemical inhibitors targeting key DDR proteins, including DNA-PKcs (DNA-dependent protein kinase, catalytic subunit), ATM/ATR (ataxia–telangiectasia mutated and Rad3-related), the MRN (MRE11-RAD50-NBS1) complex, the PARP (poly[ADP-ribose] polymerase) family, MDC1, Wee1, LIG4 (ligase IV), CDK1, BRCA1 (BRCA1 C terminal), CHK1, and HIF-1 (hypoxia-inducible factor-1). Challenges for ionizing radiation-induced signal transduction and targeted therapy are also discussed based on recent achievements in the biological field of radiotherapy.
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McLaughlin MC, Blotevogel J, Watson RA, Schell B, Blewett TA, Folkerts EJ, Goss GG, Truong L, Tanguay RL, Argueso JL, Borch T. Mutagenicity assessment downstream of oil and gas produced water discharges intended for agricultural beneficial reuse. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 715:136944. [PMID: 32014773 PMCID: PMC7243347 DOI: 10.1016/j.scitotenv.2020.136944] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 05/08/2023]
Abstract
Produced water is the largest waste stream associated with oil and gas operations. This complex fluid contains petroleum hydrocarbons, heavy metals, salts, naturally occurring radioactive materials and any remaining chemical additives. In the United States, west of the 98th meridian, the federal National Pollutant Discharge Elimination System (NPDES) exemption allows release of produced water for agricultural beneficial reuse. The goal of this study was to quantify mutagenicity of a produced water NPDES release and discharge stream. We used four mutation assays in budding yeast cells that provide rate estimates for copy number variation (CNV) duplications and deletions, as well as forward and reversion point mutations. Higher mutation rates were observed at the discharge and decreased with distance downstream, which correlated with the concentrations of known carcinogens detected in the stream (e.g., benzene, radium), described in a companion study. Mutation rate increases were most prominent for CNV duplications and were higher than mutations observed in mixtures of known toxic compounds. Additionally, the samples were evaluated for acute toxicity in Daphnia magna and developmental toxicity in zebrafish. Acute toxicity was minimal, and no developmental toxicity was observed. This study illustrates that chemical analysis alone (McLaughlin et al., 2020) is insufficient for characterizing the risk of produced water NPDES releases and that a thorough evaluation of chronic toxicity is necessary to fully assess produced water for beneficial reuse.
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Affiliation(s)
- Molly C McLaughlin
- Department of Civil and Environmental Engineering, Colorado State University, 1320 Campus Delivery, Fort Collins, CO 80523, USA
| | - Jens Blotevogel
- Department of Civil and Environmental Engineering, Colorado State University, 1320 Campus Delivery, Fort Collins, CO 80523, USA.
| | - Ruth A Watson
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, United States
| | - Baylee Schell
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, United States; Department of Chemistry, Colorado State University, 1872 Campus Delivery, Fort Collins, CO 80523, USA
| | - Tamzin A Blewett
- Department of Biological Sciences, University of Alberta, Alberta T6G 2R3, Canada
| | - Erik J Folkerts
- Department of Biological Sciences, University of Alberta, Alberta T6G 2R3, Canada
| | - Greg G Goss
- Department of Biological Sciences, University of Alberta, Alberta T6G 2R3, Canada; National Institute for Nanotechnology, Edmonton, Alberta T6G 2M9, Canada
| | - Lisa Truong
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Robyn L Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, United States.
| | - Thomas Borch
- Department of Civil and Environmental Engineering, Colorado State University, 1320 Campus Delivery, Fort Collins, CO 80523, USA; Department of Chemistry, Colorado State University, 1872 Campus Delivery, Fort Collins, CO 80523, USA; Department of Soil and Crop Sciences, Colorado State University, 1170 Campus Delivery, Fort Collins, CO 80523, USA.
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32
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Detection of DNA Double-Strand Breaks by Pulsed-Field Gel Electrophoresis of Circular Bacterial Chromosomes. Methods Mol Biol 2020. [PMID: 31989522 DOI: 10.1007/978-1-0716-0323-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Double-strand breakage of DNA is a process central to life and death in DNA-coded organisms. Its sensitive and quantitative detection is realized by pulsed-field gel electrophoresis of a huge (Mb) circular chromosome. A single double-strand break at one of its millions of potential sites will make it linear and release it from branches of an agarose jungle. Then the huge fragments will move according to their size. We developed this method to analyze formation of DNA double-strand breaks and their processing in E. coli. Here we detail our protocol taking the example of chromosome breaks caused by action of a restriction enzyme in vivo. It is important to prevent formation of irrelevant double-strand breaks.
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Schizosaccharomyces pombe Assays to Study Mitotic Recombination Outcomes. Genes (Basel) 2020; 11:genes11010079. [PMID: 31936815 PMCID: PMC7016768 DOI: 10.3390/genes11010079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 01/16/2023] Open
Abstract
The fission yeast—Schizosaccharomyces pombe—has emerged as a powerful tractable system for studying DNA damage repair. Over the last few decades, several powerful in vivo genetic assays have been developed to study outcomes of mitotic recombination, the major repair mechanism of DNA double strand breaks and stalled or collapsed DNA replication forks. These assays have significantly increased our understanding of the molecular mechanisms underlying the DNA damage response pathways. Here, we review the assays that have been developed in fission yeast to study mitotic recombination.
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Ramos-Pérez C, Dominska M, Anaissi-Afonso L, Cazorla-Rivero S, Quevedo O, Lorenzo-Castrillejo I, Petes TD, Machín F. Cytological and genetic consequences for the progeny of a mitotic catastrophe provoked by Topoisomerase II deficiency. Aging (Albany NY) 2019; 11:11686-11721. [PMID: 31812950 PMCID: PMC6932922 DOI: 10.18632/aging.102573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/24/2019] [Indexed: 02/07/2023]
Abstract
Topoisomerase II (Top2) removes topological linkages between replicated chromosomes. Top2 inhibition leads to mitotic catastrophe (MC) when cells unsuccessfully try to split their genetic material between the two daughter cells. Herein, we have characterized the fate of these daughter cells in the budding yeast. Clonogenic and microcolony experiments, in combination with vital and apoptotic stains, showed that 75% of daughter cells become senescent in the short term; they are unable to divide but remain alive. Decline in cell vitality then occurred, yet slowly, uncoordinatedly when comparing pairs of daughters, and independently of the cell death mediator Mca1/Yca1. Furthermore, we showed that senescence can be modulated by ploidy, suggesting that gross chromosome imbalances during segregation may account for this phenotype. Indeed, we found that diploid long-term survivors of the MC are prone to genomic imbalances such as trisomies, uniparental disomies and terminal loss of heterozygosity (LOH), the latter affecting the longest chromosome arms.
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Affiliation(s)
- Cristina Ramos-Pérez
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Tenerife, Spain.,Present address: BenchSci Analytics Inc., Toronto, Canada
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Laura Anaissi-Afonso
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Tenerife, Spain
| | - Sara Cazorla-Rivero
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Tenerife, Spain
| | - Oliver Quevedo
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Present address: Genomic Integrity Unit, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Isabel Lorenzo-Castrillejo
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Félix Machín
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Tenerife, Spain.,Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
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Yan Z, Xue C, Kumar S, Crickard JB, Yu Y, Wang W, Pham N, Li Y, Niu H, Sung P, Greene EC, Ira G. Rad52 Restrains Resection at DNA Double-Strand Break Ends in Yeast. Mol Cell 2019; 76:699-711.e6. [PMID: 31542296 DOI: 10.1016/j.molcel.2019.08.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/26/2019] [Accepted: 08/20/2019] [Indexed: 12/29/2022]
Abstract
Rad52 is a key factor for homologous recombination (HR) in yeast. Rad52 helps assemble Rad51-ssDNA nucleoprotein filaments that catalyze DNA strand exchange, and it mediates single-strand DNA annealing. We find that Rad52 has an even earlier function in HR in restricting DNA double-stranded break ends resection that generates 3' single-stranded DNA (ssDNA) tails. In fission yeast, Exo1 is the primary resection nuclease, with the helicase Rqh1 playing a minor role. We demonstrate that the choice of two extensive resection pathways is regulated by Rad52. In rad52 cells, the resection rate increases from ∼3-5 kb/h up to ∼10-20 kb/h in an Rqh1-dependent manner, while Exo1 becomes dispensable. Budding yeast Rad52 similarly inhibits Sgs1-dependent resection. Single-molecule analysis with purified budding yeast proteins shows that Rad52 competes with Sgs1 for DNA end binding and inhibits Sgs1 translocation along DNA. These results identify a role for Rad52 in limiting ssDNA generated by end resection.
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Affiliation(s)
- Zhenxin Yan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chaoyou Xue
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Sandeep Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - J Brooks Crickard
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Yang Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weibin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nhung Pham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuxi Li
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA.
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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36
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Pannunzio NR, Lieber MR. Constitutively active Artemis nuclease recognizes structures containing single-stranded DNA configurations. DNA Repair (Amst) 2019; 83:102676. [PMID: 31377101 DOI: 10.1016/j.dnarep.2019.102676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 01/03/2023]
Abstract
The Artemis nuclease recognizes and endonucleolytically cleaves at single-stranded to double-stranded DNA (ss/dsDNA) boundaries. It is also a key enzyme in the non-homologous end joining (NHEJ) DNA double-strand break repair pathway. Previously, a truncated form, Artemis-413, was developed that is constitutively active both in vitro and in vivo. Here, we use this constitutively active form of Artemis to detect DNA structures with ss/dsDNA boundaries that arise under topological stress. Topoisomerases prevent abnormal levels of torsional stress through modulation of positive and negative supercoiling. We show that overexpression of Artemis-413 in yeast cells carrying genetic mutations that ablate topoisomerase activity have an increased frequency of DNA double-strand breaks (DSBs). Based on the biochemical activity of Artemis, this suggests an increase in ss/dsDNA-containing structures upon increased torsional stress, with DSBs arising due to Artemis cutting at these ss/dsDNA structures. Camptothecin targets topoisomerase IB (Top1), and cells treated with camptothecin show increased DSBs. We find that expression of Artemis-413 in camptothecin-treated cells leads to a reduction in DSBs, the opposite of what we find with topoisomerase genetic mutations. This contrast between outcomes not only confirms that topoisomerase mutation and topoisomerase poisoning have distinct effects on cells, but also demonstrates the usefulness of Artemis-413 to study changes in DNA structure.
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Affiliation(s)
- Nicholas R Pannunzio
- Department of Pathology, Keck School of Medicine of University of Southern California, Los Angeles, CA, 90089, USA; Norris Comprehensive Cancer Center, Keck School of Medicine of University of Southern California, Los Angeles, CA, 90089, USA.
| | - Michael R Lieber
- Department of Pathology, Keck School of Medicine of University of Southern California, Los Angeles, CA, 90089, USA; Norris Comprehensive Cancer Center, Keck School of Medicine of University of Southern California, Los Angeles, CA, 90089, USA; Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089, USA.
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37
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Xia J, Mei Q, Rosenberg SM. Tools To Live By: Bacterial DNA Structures Illuminate Cancer. Trends Genet 2019; 35:383-395. [PMID: 30962000 DOI: 10.1016/j.tig.2019.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/27/2019] [Accepted: 03/01/2019] [Indexed: 12/27/2022]
Abstract
Holliday junctions (HJs) are DNA intermediates in homology-directed DNA repair and replication stalling, but until recently were undetectable in living cells. We review how an engineered protein that traps and labels HJs in Escherichia coli illuminates the biology of DNA and cancer. HJ chromatin immunoprecipitation with deep sequencing (ChIP-seq) analysis showed the directionality of double-strand break (DSB) repair in the E. coli genome. Quantification of HJs as fluorescent foci in live cells revealed that the commonest spontaneous problem repaired via HJs is replication-dependent single-stranded DNA gaps, not DSBs. Focus quantification also indicates that RecQ DNA helicase plays dual roles in promoting repair HJs and preventing replication-stall HJs in an E. coli model of RAD51-overexpressing (most) cancers. Moreover, cancer transcriptomes imply that most cancers suffer frequent fork stalls that are reduced by the HJ removers EME1 and GEN1, as well as by the human RecQ orthologs BLM and RECQL4-surprising potential procancer roles for these known cancer-preventing proteins.
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Affiliation(s)
- Jun Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qian Mei
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77030, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77030, USA.
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38
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Miné-Hattab J, Taddei A. Physical principles and functional consequences of nuclear compartmentalization in budding yeast. Curr Opin Cell Biol 2019; 58:105-113. [PMID: 30928833 DOI: 10.1016/j.ceb.2019.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/28/2019] [Accepted: 02/20/2019] [Indexed: 12/19/2022]
Abstract
One striking feature of eukaryotic nuclei is the existence of discrete regions, in which specific factors concentrate while others are excluded, thus forming microenvironments with different molecular compositions and biological functions. These domains are often referred to as subcompartments even though they are not membrane enclosed. Despite their functional importance the physical nature of these structures remains largely unknown. Here, we describe how the Saccharomyces cerevisiae nucleus is compartmentalized and discuss possible physical models underlying the formation and maintenance of chromatin associated subcompartments. Focusing on three particular examples, the nucleolus, silencing foci, and repair foci, we discuss the biological implications of these different models as well as possible approaches to challenge them in living cells.
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Affiliation(s)
- Judith Miné-Hattab
- Institut Curi-PSL Research University, CNRS, Sorbonne Université, UMR3664, F-75005, Paris, France
| | - Angela Taddei
- Institut Curi-PSL Research University, CNRS, Sorbonne Université, UMR3664, F-75005, Paris, France.
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