International Journal of Molecular Sciences

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19 pages, 4681 KiB

Open AccessArticle

New 5-Hydroxycoumarin-Based Tyrosyl-DNA Phosphodiesterase I Inhibitors Sensitize Tumor Cell Line to Topotecan

by Tatyana M. Khomenko, Alexandra L. Zakharenko, Tatyana E. Kornienko, Arina A. Chepanova, Nadezhda S. Dyrkheeva, Anastasia O. Artemova, Dina V. Korchagina, Chigozie Achara, Anthony Curtis, Jóhannes Reynisson, Konstantin P. Volcho, Nariman F. Salakhutdinov and Olga I. Lavrik

Int. J. Mol. Sci. 2023, 24(11), 9155; https://doi.org/10.3390/ijms24119155 - 23 May 2023

Cited by 2 | Viewed by 1319

Abstract

Tyrosyl-DNA-phosphodiesterase 1 (TDP1) is an important enzyme in the DNA repair system. The ability of the enzyme to repair DNA damage induced by a topoisomerase 1 poison such as the anticancer drug topotecan makes TDP1 a promising target for complex antitumor therapy. In [...] Read more.

Tyrosyl-DNA-phosphodiesterase 1 (TDP1) is an important enzyme in the DNA repair system. The ability of the enzyme to repair DNA damage induced by a topoisomerase 1 poison such as the anticancer drug topotecan makes TDP1 a promising target for complex antitumor therapy. In this work, a set of new 5-hydroxycoumarin derivatives containing monoterpene moieties was synthesized. It was shown that most of the conjugates synthesized demonstrated high inhibitory properties against TDP1 with an IC₅₀ in low micromolar or nanomolar ranges. Geraniol derivative 33a was the most potent inhibitor with IC₅₀ 130 nM. Docking the ligands to TDP1 predicted a good fit with the catalytic pocket blocking access to it. The conjugates used in non-toxic concentration increased cytotoxicity of topotecan against HeLa cancer cell line but not against conditionally normal HEK 293A cells. Thus, a new structural series of TDP1 inhibitors, which are able to sensitize cancer cells to the topotecan cytotoxic effect has been discovered. Full article

(This article belongs to the Special Issue Nuclear Genome Stability: DNA Replication and DNA Repair)

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13 pages, 2269 KiB

Open AccessArticle

Effects of Defective Unloading and Recycling of PCNA Revealed by the Analysis of ELG1 Mutants

by Ziv Itzkovich, Karan Choudhary, Matan Arbel and Martin Kupiec

Int. J. Mol. Sci. 2023, 24(2), 1568; https://doi.org/10.3390/ijms24021568 - 13 Jan 2023

Cited by 2 | Viewed by 2194

Abstract

Timely and complete replication of the genome is essential for life. The PCNA ring plays an essential role in DNA replication and repair by contributing to the processivity of DNA polymerases and by recruiting proteins that act in DNA replication-associated processes. The ELG1 [...] Read more.

Timely and complete replication of the genome is essential for life. The PCNA ring plays an essential role in DNA replication and repair by contributing to the processivity of DNA polymerases and by recruiting proteins that act in DNA replication-associated processes. The ELG1 gene encodes a protein that works, together with the Rfc2-5 subunits (shared by the replication factor C complex), to unload PCNA from chromatin. While ELG1 is not essential for life, deletion of the gene has strong consequences for the stability of the genome, and elg1 mutants exhibit sensitivity to DNA damaging agents, defects in genomic silencing, high mutation rates, and other striking phenotypes. Here, we sought to understand whether all the roles attributed to Elg1 in genome stability maintenance are due to its effects on PCNA unloading, or whether they are due to additional functions of the protein. By using a battery of mutants that affect PCNA accumulation at various degrees, we show that all the phenotypes measured correlate with the amount of PCNA left at the chromatin. Our results thus demonstrate the importance of Elg1 and of PCNA unloading in promoting proper chromatin structure and in maintaining a stable genome. Full article

(This article belongs to the Special Issue Nuclear Genome Stability: DNA Replication and DNA Repair)

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24 pages, 3519 KiB

Open AccessArticle

Integration Host Factor Binds DNA Holliday Junctions

by Shawn H. Lin, Dacheng Zhao, Vivian Deng, Veronica K. Birdsall, Suzanne Ho, Olga Buzovetsky, Candice M. Etson and Ishita Mukerji

Int. J. Mol. Sci. 2023, 24(1), 580; https://doi.org/10.3390/ijms24010580 - 29 Dec 2022

Cited by 3 | Viewed by 1998

Abstract

Integration host factor (IHF) is a nucleoid-associated protein involved in DNA packaging, integration of viral DNA and recombination. IHF binds with nanomolar affinity to duplex DNA containing a 13 bp consensus sequence, inducing a bend of ~160° upon binding. We determined that IHF [...] Read more.

Integration host factor (IHF) is a nucleoid-associated protein involved in DNA packaging, integration of viral DNA and recombination. IHF binds with nanomolar affinity to duplex DNA containing a 13 bp consensus sequence, inducing a bend of ~160° upon binding. We determined that IHF binds to DNA Four-way or Holliday junctions (HJ) with high affinity regardless of the presence of the consensus sequence, signifying a structure-based mechanism of recognition. Junctions, important intermediates in DNA repair and homologous recombination, are dynamic and can adopt either an open or stacked conformation, where the open conformation facilitates branch migration and strand exchange. Using ensemble and single molecule Förster resonance energy transfer (FRET) methods, we investigated IHF-induced changes in the population distribution of junction conformations and determined that IHF binding shifts the population to the open conformation. Further analysis of smFRET dynamics revealed that even in the presence of protein, the junctions remain dynamic as fast transitions are observed for the protein-bound open state. Protein binding alters junction conformational dynamics, as cross correlation analyses reveal the protein slows the transition rate at 1 mM Mg²⁺ but accelerates the transition rate at 10 mM Mg²⁺. Stopped flow kinetic experiments provide evidence for two binding steps, a rapid, initial binding step followed by a slower step potentially associated with a conformational change. These measurements also confirm that the protein remains bound to the junction during the conformer transitions and further suggest that the protein forms a partially dissociated state that allows junction arms to be dynamic. These findings, which demonstrate that IHF binds HJs with high affinity and stabilizes junctions in the open conformation, suggest that IHF may play multiple roles in the processes of integration and recombination in addition to stabilizing bacterial biofilms. Full article

(This article belongs to the Special Issue Nuclear Genome Stability: DNA Replication and DNA Repair)

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20 pages, 3061 KiB

Open AccessArticle

Transcriptional Profiling of the Candida albicans Response to the DNA Damage Agent Methyl Methanesulfonate

by Yuting Feng, Yan Zhang, Jie Li, Raha Parvizi Omran, Malcolm Whiteway and Jinrong Feng

Int. J. Mol. Sci. 2022, 23(14), 7555; https://doi.org/10.3390/ijms23147555 - 7 Jul 2022

Cited by 3 | Viewed by 2292

Abstract

The infection of a mammalian host by the pathogenic fungus Candida albicans involves fungal resistance to reactive oxygen species (ROS)—induced DNA damage stress generated by the defending macrophages or neutrophils. Thus, the DNA damage response in C. albicans may contribute to its pathogenicity. [...] Read more.

The infection of a mammalian host by the pathogenic fungus Candida albicans involves fungal resistance to reactive oxygen species (ROS)—induced DNA damage stress generated by the defending macrophages or neutrophils. Thus, the DNA damage response in C. albicans may contribute to its pathogenicity. Uncovering the transcriptional changes triggered by the DNA damage—inducing agent MMS in many model organisms has enhanced the understanding of their DNA damage response processes. However, the transcriptional regulation triggered by MMS remains unclear in C. albicans. Here, we explored the global transcription profile in response to MMS in C. albicans and identified 306 defined genes whose transcription was significantly affected by MMS. Only a few MMS-responsive genes, such as MGT1, DDR48, MAG1, and RAD7, showed potential roles in DNA repair. GO term analysis revealed that a large number of induced genes were involved in antioxidation responses, and some downregulated genes were involved in nucleosome packing and IMP biosynthesis. Nevertheless, phenotypic assays revealed that MMS-induced antioxidation gene CAP1 and glutathione metabolism genes GST2 and GST3 showed no direct roles in MMS resistance. Furthermore, the altered transcription of several MMS—responsive genes exhibited RAD53—related regulation. Intriguingly, the transcription profile in response to MMS in C. albicans shared a limited similarity with the pattern in S. cerevisiae, including COX17, PRI2, and MGT1. Overall, C. albicans cells exhibit global transcriptional changes to the DNA damage agent MMS; these findings improve our understanding of this pathogen’s DNA damage response pathways. Full article

(This article belongs to the Special Issue Nuclear Genome Stability: DNA Replication and DNA Repair)

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19 pages, 47511 KiB

Open AccessArticle

A Non-Cell-Autonomous Mode of DNA Damage Response in Soma of Caenorhabditis elegans

by Zhangyu Dai, Wenjing Zhang, Mengke Shang, Huangqi Tang, Lijun Wu, Yuejin Wu, Ting Wang and Po Bian

Int. J. Mol. Sci. 2022, 23(14), 7544; https://doi.org/10.3390/ijms23147544 - 7 Jul 2022

Cited by 1 | Viewed by 1835

Abstract

Life has evolved a mechanism called DNA damage response (DDR) to sense, signal and remove/repair DNA damage, and its deficiency and dysfunction usually lead to genomic instability and development of cancer. The signaling mode of the DDR has been believed to be of [...] Read more.

Life has evolved a mechanism called DNA damage response (DDR) to sense, signal and remove/repair DNA damage, and its deficiency and dysfunction usually lead to genomic instability and development of cancer. The signaling mode of the DDR has been believed to be of cell-autonomy. However, the paradigm is being shifted with in-depth research into model organism Caenorhabditis elegans. Here, we mainly investigate the effect of DDR activation on the radiosensitivity of vulva of C. elegans, and first found that the vulval radiosensitivity is mainly regulated by somatic DDR, rather than the DDR of germline. Subsequently, the worm lines with pharynx-specific rescue of DDR were constructed, and it is shown that the 9-1-1-ATR and MRN-ATM cascades in pharynx restore approximately 90% and 70% of vulval radiosensitivity, respectively, through distantly regulating the NHEJ repair of vulval cells. The results suggest that the signaling cascade of DDR might also operate in a non-cell autonomous mode. To further explore the underlying regulatory mechanisms, the cpr-4 mutated gene is introduced into the DDR-rescued worms, and CPR-4, a cysteine protease cathepsin B, is confirmed to mediate the inter-tissue and inter-individual regulation of DDR as a signaling molecule downstream of 9-1-1-ATR. Our findings throw some light on the regulation of DNA repair in soma of C. elegans, and might also provide new cues for cancer prevention and treatment. Full article

(This article belongs to the Special Issue Nuclear Genome Stability: DNA Replication and DNA Repair)

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Review

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29 pages, 2110 KiB

Open AccessReview

Base Excision Repair: Mechanisms and Impact in Biology, Disease, and Medicine

by Dhara Gohil, Altaf H. Sarker and Rabindra Roy

Int. J. Mol. Sci. 2023, 24(18), 14186; https://doi.org/10.3390/ijms241814186 - 16 Sep 2023

Cited by 8 | Viewed by 3664

Abstract

Base excision repair (BER) corrects forms of oxidative, deamination, alkylation, and abasic single-base damage that appear to have minimal effects on the helix. Since its discovery in 1974, the field has grown in several facets: mechanisms, biology and physiology, understanding deficiencies and human [...] Read more.

Base excision repair (BER) corrects forms of oxidative, deamination, alkylation, and abasic single-base damage that appear to have minimal effects on the helix. Since its discovery in 1974, the field has grown in several facets: mechanisms, biology and physiology, understanding deficiencies and human disease, and using BER genes as potential inhibitory targets to develop therapeutics. Within its segregation of short nucleotide (SN-) and long patch (LP-), there are currently six known global mechanisms, with emerging work in transcription- and replication-associated BER. Knockouts (KOs) of BER genes in mouse models showed that single glycosylase knockout had minimal phenotypic impact, but the effects were clearly seen in double knockouts. However, KOs of downstream enzymes showed critical impact on the health and survival of mice. BER gene deficiency contributes to cancer, inflammation, aging, and neurodegenerative disorders. Medicinal targets are being developed for single or combinatorial therapies, but only PARP and APE1 have yet to reach the clinical stage. Full article

(This article belongs to the Special Issue Nuclear Genome Stability: DNA Replication and DNA Repair)

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15 pages, 615 KiB

Open AccessReview

The Cellular Response to Complex DNA Damage Induced by Ionising Radiation

by Beth Wilkinson, Mark A. Hill and Jason L. Parsons

Int. J. Mol. Sci. 2023, 24(5), 4920; https://doi.org/10.3390/ijms24054920 - 3 Mar 2023

Cited by 15 | Viewed by 2795

Abstract

Radiotherapy (ionising radiation; IR) is utilised in the treatment of ~50% of all human cancers, and where the therapeutic effect is largely achieved through DNA damage induction. In particular, complex DNA damage (CDD) containing two or more lesions within one to two helical [...] Read more.

Radiotherapy (ionising radiation; IR) is utilised in the treatment of ~50% of all human cancers, and where the therapeutic effect is largely achieved through DNA damage induction. In particular, complex DNA damage (CDD) containing two or more lesions within one to two helical turns of the DNA is a signature of IR and contributes significantly to the cell killing effects due to the difficult nature of its repair by the cellular DNA repair machinery. The levels and complexity of CDD increase with increasing ionisation density (linear energy transfer, LET) of the IR, such that photon (X-ray) radiotherapy is deemed low-LET whereas some particle ions (such as carbon ions) are high-LET radiotherapy. Despite this knowledge, there are challenges in the detection and quantitative measurement of IR-induced CDD in cells and tissues. Furthermore, there are biological uncertainties with the specific DNA repair proteins and pathways, including components of DNA single and double strand break mechanisms, that are engaged in CDD repair, which very much depends on the radiation type and associated LET. However, there are promising signs that advancements are being made in these areas and which will enhance our understanding of the cellular response to CDD induced by IR. There is also evidence that targeting CDD repair, particularly through inhibitors against selected DNA repair enzymes, can exacerbate the impact of higher LET, which could be explored further in a translational context. Full article

(This article belongs to the Special Issue Nuclear Genome Stability: DNA Replication and DNA Repair)

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14 pages, 2080 KiB

Open AccessReview

DNA Holliday Junction: History, Regulation and Bioactivity

by Qinqin Song, Yuemiao Hu, Anqi Yin, Hongbo Wang and Qikun Yin

Int. J. Mol. Sci. 2022, 23(17), 9730; https://doi.org/10.3390/ijms23179730 - 27 Aug 2022

Cited by 12 | Viewed by 4925

Abstract

DNA Holliday junction (HJ) is a four-way stranded DNA intermediate that formed in replication fork regression, homology-dependent repair and mitosis, performing a significant role in genomic stability. Failure to remove HJ can induce an acceptable replication fork stalling and DNA damage in normal [...] Read more.

DNA Holliday junction (HJ) is a four-way stranded DNA intermediate that formed in replication fork regression, homology-dependent repair and mitosis, performing a significant role in genomic stability. Failure to remove HJ can induce an acceptable replication fork stalling and DNA damage in normal cells, leading to a serious chromosomal aberration and even cell death in HJ nuclease-deficient tumor cells. Thus, HJ is becoming an attractive target in cancer therapy. However, the development of HJ-targeting ligand faces great challenges because of flexile cavities on the center of HJs. This review introduces the discovery history of HJ, elucidates the formation and dissociation procedures of HJ in corresponding bio-events, emphasizes the importance of prompt HJ-removing in genome stability, and summarizes recent advances in HJ-based ligand discovery. Our review indicate that target HJ is a promising approach in oncotherapy. Full article

(This article belongs to the Special Issue Nuclear Genome Stability: DNA Replication and DNA Repair)

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18 pages, 2928 KiB

Open AccessReview

The Role of the TSK/TONSL-H3.1 Pathway in Maintaining Genome Stability in Multicellular Eukaryotes

by Yi-Chun Huang, Wenxin Yuan and Yannick Jacob

Int. J. Mol. Sci. 2022, 23(16), 9029; https://doi.org/10.3390/ijms23169029 - 12 Aug 2022

Cited by 4 | Viewed by 2151

Abstract

Replication-dependent histone H3.1 and replication-independent histone H3.3 are nearly identical proteins in most multicellular eukaryotes. The N-terminal tails of these H3 variants, where the majority of histone post-translational modifications are made, typically differ by only one amino acid. Despite extensive sequence similarity with [...] Read more.

Replication-dependent histone H3.1 and replication-independent histone H3.3 are nearly identical proteins in most multicellular eukaryotes. The N-terminal tails of these H3 variants, where the majority of histone post-translational modifications are made, typically differ by only one amino acid. Despite extensive sequence similarity with H3.3, the H3.1 variant has been hypothesized to play unique roles in cells, as it is specifically expressed and inserted into chromatin during DNA replication. However, identifying a function that is unique to H3.1 during replication has remained elusive. In this review, we discuss recent findings regarding the involvement of the H3.1 variant in regulating the TSK/TONSL-mediated resolution of stalled or broken replication forks. Uncovering this new function for the H3.1 variant has been made possible by the identification of the first proteins containing domains that can selectively bind or modify the H3.1 variant. The functional characterization of H3-variant-specific readers and writers reveals another layer of chromatin-based information regulating transcription, DNA replication, and DNA repair. Full article

(This article belongs to the Special Issue Nuclear Genome Stability: DNA Replication and DNA Repair)

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