Acquisition of meiotic DNA repair regulators maintain genome stability in glioblastoma

AbstractCRISPR-Cas pathways provide prokaryotes with acquired “immunity” against foreign genetic elements, including phages and plasmids. Although many of the proteins associated with CRISPR-Cas mechanisms are characterized, some requisite enzymes remain elusive. Genetic studies have implicated host DNA polymerases in some CRISPR-Cas systems but CRISPR-specific replicases have not yet been discovered. We have identified and characterised a family of CRISPR-Associated Primase-Polymerases (CAPPs) in a range of prokaryotes that are operonically associated with Cas1 and Cas2. CAPPs belong to the Primase-Polymerase (Prim-Pol) superfamily of replicases that operate in various DNA repair and replication pathways that maintain genome stability. Here, we characterise the DNA synthesis activities of bacterial CAPP homologues from Type IIIA and IIIB CRISPR-Cas systems and establish that they possess a range of replicase activities including DNA priming, polymerisation and strand-displacement. We demonstrate that CAPPs operonically-associated partners, Cas1 and Cas2, form a complex that possesses spacer integration activity. We show that CAPPs physically associate with the Cas proteins to form bespoke CRISPR-Cas complexes. Finally, we propose how CAPPs activities, in conjunction with their partners, may function to undertake key roles in CRISPR-Cas adaptation.

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Overview of DNA Repair inTrypanosoma cruzi, Trypanosoma brucei,andLeishmania major

Journal of Nucleic Acids ◽

10.4061/2010/840768 ◽

2010 ◽

Vol 2010 ◽

pp. 1-14 ◽

Cited By ~ 40

Author(s):

Danielle Gomes Passos-Silva ◽

Matheus Andrade Rajão ◽

Pedro Henrique Nascimento de Aguiar ◽

João Pedro Vieira-da-Rocha ◽

Carlos Renato Machado ◽

...

Keyword(s):

Dna Repair ◽

Trypanosoma Brucei ◽

Genome Stability ◽

Leishmania Major ◽

Experimental Studies ◽

Life Cycles ◽

Dna Lesions ◽

Cellular Mechanisms ◽

Environmental Agents ◽

Maintain Genome Stability

A wide variety of DNA lesions arise due to environmental agents, normal cellular metabolism, or intrinsic weaknesses in the chemical bonds of DNA. Diverse cellular mechanisms have evolved to maintain genome stability, including mechanisms to repair damaged DNA, to avoid the incorporation of modified nucleotides, and to tolerate lesions (translesion synthesis). Studies of the mechanisms related to DNA metabolism in trypanosomatids have been very limited. Together with recent experimental studies, the genome sequencing ofTrypanosoma brucei, Trypanosoma cruzi,andLeishmania major, three related pathogens with different life cycles and disease pathology, has revealed interesting features of the DNA repair mechanism in these protozoan parasites, which will be reviewed here.

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Polynucleotide kinase–phosphatase enables neurogenesis via multiple DNA repair pathways to maintain genome stability

The EMBO Journal ◽

10.15252/embj.201591363 ◽

2015 ◽

Vol 34 (19) ◽

pp. 2465-2480 ◽

Cited By ~ 30

Author(s):

Mikio Shimada ◽

Lavinia C Dumitrache ◽

Helen R Russell ◽

Peter J McKinnon

Keyword(s):

Dna Repair ◽

Genome Stability ◽

Polynucleotide Kinase ◽

Repair Pathways ◽

Maintain Genome Stability

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Abstract B44: Acquisition of meiotic DNA repair regulators maintain genome stability in glioblastoma

10.1158/1538-7445.brain15-b44 ◽

2015 ◽

Author(s):

Maricruz Rivera ◽

Qiulian Wu ◽

Petra Hamerlik ◽

Anita Hjelmeland ◽

Shideng Bao ◽

...

Keyword(s):

Dna Repair ◽

Genome Stability ◽

Maintain Genome Stability

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CRISPR-Cas immunity, DNA repair and genome stability

Bioscience Reports ◽

10.1042/bsr20180457 ◽

2018 ◽

Vol 38 (5) ◽

Cited By ~ 12

Author(s):

Andrew Cubbon ◽

Ivana Ivancic-Bace ◽

Edward L. Bolt

Keyword(s):

Dna Repair ◽

Genome Editing ◽

Genome Stability ◽

Short Review ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

Dna Repair Enzymes ◽

Strand Breaks ◽

Repair Enzymes ◽

Maintain Genome Stability

Co-opting of CRISPR-Cas ‘Interference’ reactions for editing the genomes of eukaryotic and prokaryotic cells has highlighted crucial support roles for DNA repair systems that strive to maintain genome stability. As front-runners in genome editing that targets DNA, the class 2 CRISPR-Cas enzymes Cas9 and Cas12a rely on repair of DNA double-strand breaks (DDSBs) by host DNA repair enzymes, using mechanisms that vary in how well they are understood. Data are emerging about the identities of DNA repair enzymes that support genome editing in human cells. At the same time, it is becoming apparent that CRISPR-Cas systems functioning in their native environment, bacteria or archaea, also need DNA repair enzymes. In this short review, we survey how DNA repair and CRISPR-Cas systems are intertwined. We consider how understanding DNA repair and CRISPR-Cas interference reactions in nature might help improve the efficacy of genome editing procedures that utilise homologous or analogous systems in human and other cells.

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SUMO-Targeted Ubiquitin Ligases and Their Functions in Maintaining Genome Stability

International Journal of Molecular Sciences ◽

10.3390/ijms22105391 ◽

2021 ◽

Vol 22 (10) ◽

pp. 5391

Author(s):

Ya-Chu Chang ◽

Marissa K. Oram ◽

Anja-Katrin Bielinsky

Keyword(s):

Dna Repair ◽

Genome Stability ◽

Molecular Mechanisms ◽

Ubiquitin Ligases ◽

Genotoxic Stress ◽

E3 Ubiquitin Ligases ◽

Sumo Proteases ◽

Stalled Replication Forks ◽

Spatiotemporal Control ◽

Maintain Genome Stability

Small ubiquitin-like modifier (SUMO)-targeted E3 ubiquitin ligases (STUbLs) are specialized enzymes that recognize SUMOylated proteins and attach ubiquitin to them. They therefore connect the cellular SUMOylation and ubiquitination circuits. STUbLs participate in diverse molecular processes that span cell cycle regulated events, including DNA repair, replication, mitosis, and transcription. They operate during unperturbed conditions and in response to challenges, such as genotoxic stress. These E3 ubiquitin ligases modify their target substrates by catalyzing ubiquitin chains that form different linkages, resulting in proteolytic or non-proteolytic outcomes. Often, STUbLs function in compartmentalized environments, such as the nuclear envelope or kinetochore, and actively aid in nuclear relocalization of damaged DNA and stalled replication forks to promote DNA repair or fork restart. Furthermore, STUbLs reside in the same vicinity as SUMO proteases and deubiquitinases (DUBs), providing spatiotemporal control of their targets. In this review, we focus on the molecular mechanisms by which STUbLs help to maintain genome stability across different species.

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Exploiting DNA Endonucleases to Advance Mechanisms of DNA Repair

Biology ◽

10.3390/biology10060530 ◽

2021 ◽

Vol 10 (6) ◽

pp. 530

Author(s):

Marlo K. Thompson ◽

Robert W. Sobol ◽

Aishwarya Prakash

Keyword(s):

Dna Repair ◽

Mammalian Cells ◽

Genome Stability ◽

Gene Editing ◽

Adaptive Immune System ◽

Zinc Finger Nucleases ◽

Specific Gene ◽

Target Sequence ◽

Transcription Activator ◽

Low Cytotoxicity

The earliest methods of genome editing, such as zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALENs), utilize customizable DNA-binding motifs to target the genome at specific loci. While these approaches provided sequence-specific gene-editing capacity, the laborious process of designing and synthesizing recombinant nucleases to recognize a specific target sequence, combined with limited target choices and poor editing efficiency, ultimately minimized the broad utility of these systems. The discovery of clustered regularly interspaced short palindromic repeat sequences (CRISPR) in Escherichia coli dates to 1987, yet it was another 20 years before CRISPR and the CRISPR-associated (Cas) proteins were identified as part of the microbial adaptive immune system, by targeting phage DNA, to fight bacteriophage reinfection. By 2013, CRISPR/Cas9 systems had been engineered to allow gene editing in mammalian cells. The ease of design, low cytotoxicity, and increased efficiency have made CRISPR/Cas9 and its related systems the designer nucleases of choice for many. In this review, we discuss the various CRISPR systems and their broad utility in genome manipulation. We will explore how CRISPR-controlled modifications have advanced our understanding of the mechanisms of genome stability, using the modulation of DNA repair genes as examples.

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NME3 Regulates Mitochondria to Reduce ROS-Mediated Genome Instability

International Journal of Molecular Sciences ◽

10.3390/ijms21145048 ◽

2020 ◽

Vol 21 (14) ◽

pp. 5048

Author(s):

Chih-Wei Chen ◽

Ning Tsao ◽

Wei Zhang ◽

Zee-Fen Chang

Keyword(s):

Oxidative Stress ◽

Dna Repair ◽

Genome Stability ◽

Nuclear Dna ◽

Genome Instability ◽

Mitochondrial Fission ◽

Nucleoside Diphosphate Kinase ◽

Mitochondrial Fusion ◽

Mitochondrial Outer Membrane ◽

Mitochondrial Oxidative Stress

NME3 is a member of the nucleoside diphosphate kinase (NDPK) family that binds to the mitochondrial outer membrane to stimulate mitochondrial fusion. In this study, we showed that NME3 knockdown delayed DNA repair without reducing the cellular levels of nucleotide triphosphates. Further analyses revealed that NME3 knockdown increased fragmentation of mitochondria, which in turn led to mitochondrial oxidative stress-mediated DNA single-strand breaks (SSBs) in nuclear DNA. Re-expression of wild-type NME3 or inhibition of mitochondrial fission markedly reduced SSBs and facilitated DNA repair in NME3 knockdown cells, while expression of N-terminal deleted mutant defective in mitochondrial binding had no rescue effect. We further showed that disruption of mitochondrial fusion by knockdown of NME4 or MFN1 also caused mitochondrial oxidative stress-mediated genome instability. In conclusion, the contribution of NME3 to redox-regulated genome stability lies in its function in mitochondrial fusion.

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Recent Advances in Understanding Werner Syndrome

F1000Research ◽

10.12688/f1000research.12110.1 ◽

2017 ◽

Vol 6 ◽

pp. 1779 ◽

Cited By ~ 36

Author(s):

Raghavendra A. Shamanna ◽

Deborah L. Croteau ◽

Jong-Hyuk Lee ◽

Vilhelm A. Bohr

Keyword(s):

Dna Repair ◽

Stem Cell ◽

Genome Stability ◽

Werner Syndrome ◽

Genetic Disorder ◽

Accelerated Aging ◽

Nutrient Sensing ◽

Telomere Maintenance ◽

Telomere Attrition ◽

Recent Advances

Aging, the universal phenomenon, affects human health and is the primary risk factor for major disease pathologies. Progeroid diseases, which mimic aging at an accelerated rate, have provided cues in understanding the hallmarks of aging. Mutations in DNA repair genes as well as in telomerase subunits are known to cause progeroid syndromes. Werner syndrome (WS), which is characterized by accelerated aging, is an autosomal-recessive genetic disorder. Hallmarks that define the aging process include genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulation of nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and altered intercellular communication. WS recapitulates these hallmarks of aging and shows increased incidence and early onset of specific cancers. Genome integrity and stability ensure the normal functioning of the cell and are mainly guarded by the DNA repair machinery and telomeres. WRN, being a RecQ helicase, protects genome stability by regulating DNA repair pathways and telomeres. Recent advances in WS research have elucidated WRN’s role in DNA repair pathway choice regulation, telomere maintenance, resolution of complex DNA structures, epigenetic regulation, and stem cell maintenance.

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The Role of Posttranslational Modifications in DNA Repair

BioMed Research International ◽

10.1155/2020/7493902 ◽

2020 ◽

Vol 2020 ◽

pp. 1-13

Author(s):

Miaomiao Bai ◽

Dongdong Ti ◽

Qian Mei ◽

Jiejie Liu ◽

Xin Yan ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Protein Interactions ◽

Posttranslational Modifications ◽

Genome Stability ◽

Protein Localization ◽

Complex Structure ◽

Protein Protein Interactions ◽

Regulate Protein

The human body is a complex structure of cells, which are exposed to many types of stress. Cells must utilize various mechanisms to protect their DNA from damage caused by metabolic and external sources to maintain genomic integrity and homeostasis and to prevent the development of cancer. DNA damage inevitably occurs regardless of physiological or abnormal conditions. In response to DNA damage, signaling pathways are activated to repair the damaged DNA or to induce cell apoptosis. During the process, posttranslational modifications (PTMs) can be used to modulate enzymatic activities and regulate protein stability, protein localization, and protein-protein interactions. Thus, PTMs in DNA repair should be studied. In this review, we will focus on the current understanding of the phosphorylation, poly(ADP-ribosyl)ation, ubiquitination, SUMOylation, acetylation, and methylation of six typical PTMs and summarize PTMs of the key proteins in DNA repair, providing important insight into the role of PTMs in the maintenance of genome stability and contributing to reveal new and selective therapeutic approaches to target cancers.

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