DOCSLIB.ORG

Targeting the Ubiquitin-Proteasome System for Cancer Therapeutics by Small-Molecule Inhibitors

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Targeting the Ubiquitin-Proteasome System for Cancer Therapeutics by Small-Molecule Inhibitors cancers Review Targeting the Ubiquitin-Proteasome System for Cancer Therapeutics by Small-Molecule Inhibitors Gabriel LaPlante 1 and Wei Zhang 1,2,* 1 Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, ON N1G2W1, Canada; [email protected] 2 CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, MaRS Centre West Tower, 661 University Avenue, Toronto, ON M5G1M1, Canada * Correspondence: [email protected] Simple Summary: The ubiquitin-proteasome system regulates multiple facets of protein homeostasis to modulate signal transduction in numerous biological processes. Not surprisingly, dysregulation of this delicately balanced system is frequently observed in cancer progression. In the past two decades, researchers in both academia and industry have made significant progress in developing small-molecule inhibitors targeting various components in the ubiquitin-proteasome system for cancer therapy. Here, we aim to provide a comprehensive summary of these efforts. Additionally, we overview the advancements of targeted protein degradation, a recently emerging drug discovery concept in cancer therapy. Abstract: The ubiquitin-proteasome system (UPS) is a critical regulator of cellular protein levels and activity. It is, therefore, not surprising that its dysregulation is implicated in numerous human diseases, including many types of cancer. Moreover, since cancer cells exhibit increased rates of protein turnover, their heightened dependence on the UPS makes it an attractive target for inhibition Citation: LaPlante, G.; Zhang, W. via targeted therapeutics. Indeed, the clinical application of proteasome inhibitors in treatment Targeting the Ubiquitin-Proteasome System for Cancer Therapeutics by of multiple myeloma has been very successful, stimulating the development of small-molecule Small-Molecule Inhibitors. Cancers inhibitors targeting other UPS components. On the other hand, while the discovery of potent and 2021, 13, 3079. https://doi.org/ selective chemical compounds can be both challenging and time consuming, the area of targeted 10.3390/cancers13123079 protein degradation through utilization of the UPS machinery has seen promising developments in recent years. The repertoire of proteolysis-targeting chimeras (PROTACs), which employ E3 ligases Academic Editors: Alberto Inga and for the degradation of cancer-related proteins via the proteasome, continues to grow. In this review, Lucília Saraiva we will provide a thorough overview of small-molecule UPS inhibitors and highlight advancements in the development of targeted protein degradation strategies for cancer therapeutics. Received: 27 May 2021 Accepted: 17 June 2021 Keywords: ubiquitin (Ub); ubiquitin-proteasome system (UPS); cancer; small-molecule; proteolysis- Published: 20 June 2021 targeting chimera (PROTAC); E3 ligase; deubiquitinase (DUB) Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- 1. Introduction iations. The ubiquitin-proteasome system (UPS) is vital for protein homeostasis and is im- plicated in many cellular processes, including DNA repair [1], endocytic trafficking [2], and the immune response [3]. The wide range of activities regulated by the UPS stems from the remarkable specificity and diversity of signal transduction events enabled by Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. the process of ubiquitination. Ubiquitination is a post-translational protein modification This article is an open access article involving the covalent attachment of ubiquitin (Ub), a highly conserved 76-amino acid distributed under the terms and polypeptide, to a substrate via the coordinated activities of a Ub-activating enzyme (E1), a conditions of the Creative Commons Ub-conjugating enzyme (E2), and a Ub ligase (E3) (Figure1)[ 4–6]. In the presence of ATP, Attribution (CC BY) license (https:// Ub is activated by E1 before being delivered to the E2 enzyme, and this is followed by its creativecommons.org/licenses/by/ eventual transfer to the substrate proteins, catalyzed by a E3 ligase [5,7]. Most commonly, 4.0/). Ub is reversibly conjugated either at a lysine (K) residue or an N-terminal amino acid Cancers 2021, 13, 3079. https://doi.org/10.3390/cancers13123079 https://www.mdpi.com/journal/cancers Cancers 2021, 13, x FOR PEER REVIEW 2 of 44 Cancers 2021, 13, 3079 2 of 43 Ub is reversibly conjugated either at a lysine (K) residue or an N-terminal amino acid and andcan canbe attached be attached as a single as a single polypeptide polypeptide (mono-ubiquitination) (mono-ubiquitination) or a polymer or a polymer of at least of four at least(poly-ubiquitination) four (poly-ubiquitination) [4,7–10]. Ub [4,7 itself–10]. cont Ub itselfains seven contains lysines, seven any lysines, of which any ofcan which be an canattachment be an attachment site for the site next for molecule the next moleculein a poly-Ub in achain. poly-Ub Additional chain. Additional layers of complexity layers of complexityarise by post-translational arise by post-translational modifications modifications and the addition and the additionof Ub-like of Ub-likemolecules, molecules, such as suchNEDD8, as NEDD8, to Ub chains to Ub [11]. chains The [11 resulting]. The resulting diverse diversepossibilities possibilities of mixed, of branched, mixed, branched, or mod- orified modified chains chainsprovides provides the basis the for basis the for functional the functional diversity diversity of Ub ofsignaling. Ub signaling. FigureFigure 1. 1.Overview Overview of of the the ubiquitin-proteasome ubiquitin-proteasome system system (UPS). (UPS). The The E1, E2,E1, E3E2, enzyme E3 enzyme cascade cascade results re- sults in the ubiquitination of a protein substrate. HECT and RBR-type E3 ligases perform a two-step in the ubiquitination of a protein substrate. HECT and RBR-type E3 ligases perform a two-step ubiquitination, whereas RING E3s perform direct Ub transfer. K48-linked poly-ubiquitination re- ubiquitination, whereas RING E3s perform direct Ub transfer. K48-linked poly-ubiquitination results sults in proteasomal degradation, whereby the 19S proteasomal subunit removes Ub moieties prior into proteasomal the substrate’s degradation, proteolytic wherebydegradation the by 19S the proteasomal 26S subunit. subunit DUBs can removes rescue Ub substrate moieties expression prior to theor substrate’salter cell signaling proteolytic by degradationremoving Ub by moieties. the 26S subunit.Ub, ubiquitin; DUBs canHECT, rescue Homologous substrate expression to E6-AP car- or alterboxyl cell terminus; signaling RBR, by removing RING-betw Ubeen-RING; moieties. Ub, RING, ubiquitin; really HECT,interesting Homologous new gene; to DUB, E6-AP deubiquiti- carboxyl terminus;nase. RBR, RING-between-RING; RING, really interesting new gene; DUB, deubiquitinase. TheThe eventual eventual fatefate ofof a a ubiquitinated ubiquitinated proteinprotein dependsdepends onon thethe naturenature ofof thethe UbUb chain.chain. TheThe most most well-studied well-studied linkage linkage is theis the K48-linked K48-linked polyubiquitination, polyubiquitination, which which generally generally targets tar- proteinsgets proteins for proteasomal for proteasomal degradation degradation [6]. The [6]. 26SThe proteasome 26S proteasome is a large is a large protein protein complex com- consistingplex consisting of the of 20S the catalytic20S catalytic core core and and 19S 19S regulatory regulatory subunit(s) subunit(s) [12 [12].]. The The 19S 19S subunit subunit cleavescleaves thethe Ub Ub moiety moiety from from the the protein protein substrate substrate and and threads threads the the unfolded unfolded protein protein into into thethe catalytic catalytic core, core, where where the the substrate substrate is is degraded degraded via via chymotrypsin-like, chymotrypsin-like, trypsin-like, trypsin-like, and and Cancers 2021, 13, 3079 3 of 43 caspase-like proteolysis activities [10,12,13]. The second-best understood linkage, K63, has important non-proteolytic roles, including functions in protein trafficking [2,14] and the DNA damage response pathways [1]. Importantly, K48 chains can also be involved in non- proteolytic functions, while K63 chains, conversely, have known proteolytic functions [7]. The other five lysine linkages (K6, K11, K27, K29, and K33) are less well-studied, although this topic has recently been comprehensively reviewed [15]. Briefly, K6-linked poly-Ub chains have been shown to be involved in autophagy and the DNA damage response; K11 chains are implicated in cell cycle regulation and proteasomal degradation or stabilization; K27 chains are important actors in the innate immune response; K29 chains are involved in cell signaling, with potentially protective roles in neurodegenerative diseases; and K33 chains have purported roles in cell signaling and protein trafficking. The diverse arsenal of Ub signals implies that Ub-interacting proteins must possess some means of deciphering the code, and indeed, the eukaryotic genome contains an array of Ub binding domains (UBDs) that can confer linkage specificity to a Ub receptor [16]. While many UBDs are promiscuous on their own, the structural environment created between the UBD and its surrounding domains, whether on the same protein or adjacent proteins within a complex, can confer remarkable selectivity [7]. While the specific mechanism of ubiquitination can vary, the process is generally catalyzed by the E1!E2!E3 signaling
Load more

Recommended publications
  • Kinetic Analysis of Human DNA Ligase III by Justin R. Mcnally A
    Kinetic Analysis of Human DNA Ligase III by Justin R. McNally A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Biological Chemistry) in the University of Michigan 2019 Doctoral Committee: Associate Professor Patrick J. O’Brien, Chair Associate Professor Bruce A. Palfey Associate Professor JoAnn M. Sekiguchi Associate Professor Raymond C. Trievel Professor Thomas E. Wilson Justin R. McNally [email protected] ORCID iD: 0000-0003-2694-2410 © Justin R. McNally 2019 Table of Contents List of Tables iii List of Figures iv Abstract vii Chapter 1 Introduction to the human DNA ligases 1 Chapter 2 Kinetic Analyses of Single-Strand Break Repair by Human DNA Ligase III Isoforms Reveal Biochemical Differences from DNA Ligase I 20 Chapter 3 The LIG3 N-terminus, in its entirety, contributes to single-strand DNA break ligation 56 Chapter 4 Comparative end-joining by human DNA ligases I and III 82 Chapter 5 A real-time DNA ligase assay suitable for high throughput screening 113 Chapter 6 Conclusions and Future Directions 137 ii List of Tables Table 2.1: Comparison of kinetic parameters for multiple turnover ligation by human DNA ligases 31 Table 2.2: Comparison of single-turnover parameters of LIG3β and LIG1 34 Table 3.1: Comparison of LIG3β N-terminal mutant kinetic parameters 67 Table 4.1: Rate constants for sequential ligation by LIG3β 95 Table 5.1: Comparison of multiple turnover kinetic parameters determined by real-time fluorescence assay and reported values 129 iii List of Figures Figure
    [Show full text]
  • Tricarboxylic Acid Cycle Metabolites As Mediators of DNA Methylation Reprogramming in Bovine Preimplantation Embryos
    Supplementary Materials Tricarboxylic Acid Cycle Metabolites as Mediators of DNA Methylation Reprogramming in Bovine Preimplantation Embryos Figure S1. (A) Total number of cells in fast (FBL) and slow (SBL) blastocysts; (B) Fluorescence intensity for 5-methylcytosine and 5-hydroxymethylcytosine of fast and slow blastocysts of cells from Trophoectoderm (TE) or inner cell mass (ICM). Fluorescence intensity for 5-methylcytosine of cells from the ICM or TE in blastocysts cultured with (C) dimethyl-succinate or (D) dimethyl-α- ketoglutarate. Statistical significance is identified by different letters. Figure S2. Experimental design. Table S1. Selected genes related to metabolism and epigenetic mechanisms from RNA-Seq analysis of bovine blastocysts (slow vs. fast). Genes in blue represent upregulation in slow blastocysts, genes in red represent upregulation in fast blastocysts. log2FoldCh Gene p-value p-Adj ange PDHB −1.425 0.000 0.000 MDH1 −1.206 0.000 0.000 APEX1 −1.193 0.000 0.000 OGDHL −3.417 0.000 0.002 PGK1 −0.942 0.000 0.002 GLS2 1.493 0.000 0.002 AICDA 1.171 0.001 0.005 ACO2 0.693 0.002 0.011 CS −0.660 0.002 0.011 SLC25A1 1.181 0.007 0.032 IDH3A −0.728 0.008 0.035 GSS 1.039 0.013 0.053 TET3 0.662 0.026 0.093 GLUD1 −0.450 0.032 0.108 SDHD −0.619 0.049 0.143 FH −0.547 0.054 0.149 OGDH 0.316 0.133 0.287 ACO1 −0.364 0.141 0.297 SDHC −0.335 0.149 0.311 LIG3 0.338 0.165 0.334 SUCLG −0.332 0.174 0.349 SDHA 0.297 0.210 0.396 SUCLA2 −0.324 0.248 0.439 DNMT1 0.266 0.279 0.486 IDH3B1 −0.269 0.296 0.503 SDHB −0.213 0.339 0.544 DNMT3B 0.181 0.386 0.598 APOBEC1 0.629 0.386 0.598 TDG 0.427 0.398 0.611 IDH3G 0.237 0.468 0.675 NEIL2 0.509 0.572 0.720 IDH2 0.298 0.571 0.720 DNMT3L 1.306 0.590 0.722 GLS 0.120 0.706 0.821 XRCC1 0.108 0.793 0.887 TET1 −0.028 0.879 0.919 DNMT3A 0.029 0.893 0.920 MBD4 −0.056 0.885 0.920 PDHX 0.033 0.890 0.920 SMUG1 0.053 0.936 0.954 TET2 −0.002 0.991 0.991 Table S2.
    [Show full text]
  • Kinase-Dead ATM Protein Is Highly Oncogenic and Can Be Preferentially Targeted by Topo
    1 Kinase-dead ATM protein is highly oncogenic and can be preferentially targeted by Topo- 2 isomerase I inhibitors 3 4 Kenta Yamamoto1,2, Jiguang Wang3, Lisa Sprinzen1,2, Jun Xu5, Christopher J. Haddock6, Chen 5 Li1, Brian J. Lee1, Denis G. Loredan1, Wenxia Jiang1, Alessandro Vindigni6, Dong Wang5, Raul 6 Rabadan3 and Shan Zha1,4 7 8 1 Institute for Cancer Genetics, Department of Pathology and Cell Biology, College of Physicians 9 and Surgeons, Columbia University, New York City, NY 10032 10 2 Pathobiology and Molecular Medicine Graduate Program, Department of Pathology and Cell 11 Biology, Columbia University, New York City, NY 10032 12 3 Department of Biomedical Informatics and Department of Systems Biology, College of 13 Physicians & Surgeons, Columbia University, New York City, NY 10032 14 4 Division of Pediatric Oncology, Hematology and Stem Cell Transplantation, Department of 15 Pediatrics, College of Physicians & Surgeons, Columbia University, New York City, NY 10032 16 5 Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 17 La Jolla, CA 92093 18 6 Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University 19 School of Medicine, St. Louis, MO 63104 20 21 Short Title: Topo1 inhibitors target ATM mutated cancers 22 Key Words: ATM, missense mutations, Topo I inhibitors 23 24 Address Correspondence to: Shan Zha at [email protected] 25 26 1 27 ABSTRACT 28 Missense mutations in ATM kinase, a master regulator of DNA damage responses, are 29 found in many cancers, but their impact on ATM function and implications for cancer therapy are 30 largely unknown.
    [Show full text]
  • Error-Prone DNA Repair As Cancer's Achilles' Heel
    cancers Review Alternative Non-Homologous End-Joining: Error-Prone DNA Repair as Cancer’s Achilles’ Heel Daniele Caracciolo, Caterina Riillo , Maria Teresa Di Martino , Pierosandro Tagliaferri and Pierfrancesco Tassone * Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, 88100 Catanzaro, Italy; [email protected] (D.C.); [email protected] (C.R.); [email protected] (M.T.D.M.); [email protected] (P.T.) * Correspondence: [email protected] Simple Summary: Cancer onset and progression lead to a high rate of DNA damage, due to replicative and metabolic stress. To survive in this dangerous condition, cancer cells switch the DNA repair machinery from faithful systems to error-prone pathways, strongly increasing the mutational rate that, in turn, supports the disease progression and drug resistance. Although DNA repair de-regulation boosts genomic instability, it represents, at the same time, a critical cancer vulnerability that can be exploited for synthetic lethality-based therapeutic intervention. We here discuss the role of the error-prone DNA repair, named Alternative Non-Homologous End Joining (Alt-NHEJ), as inducer of genomic instability and as a potential therapeutic target. We portray different strategies to drug Alt-NHEJ and discuss future challenges for selecting patients who could benefit from Alt-NHEJ inhibition, with the aim of precision oncology. Abstract: Error-prone DNA repair pathways promote genomic instability which leads to the onset of cancer hallmarks by progressive genetic aberrations in tumor cells. The molecular mechanisms which Citation: Caracciolo, D.; Riillo, C.; Di foster this process remain mostly undefined, and breakthrough advancements are eagerly awaited. Martino, M.T.; Tagliaferri, P.; Tassone, In this context, the alternative non-homologous end joining (Alt-NHEJ) pathway is considered P.
    [Show full text]
  • DNA Strand Break Repair and Neurodegeneration
    DNA strand break repair and neurodegeneration. Article (Accepted Version) Rulten, Stuart L and Caldecott, Keith W (2013) DNA strand break repair and neurodegeneration. DNA repair, 12 (8). pp. 558-567. ISSN 1568-7856 This version is available from Sussex Research Online: http://sro.sussex.ac.uk/id/eprint/47369/ This document is made available in accordance with publisher policies and may differ from the published version or from the version of record. If you wish to cite this item you are advised to consult the publisher’s version. Please see the URL above for details on accessing the published version. Copyright and reuse: Sussex Research Online is a digital repository of the research output of the University. Copyright and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable, the material made available in SRO has been checked for eligibility before being made available. Copies of full text items generally can be reproduced, displayed or performed and given to third parties in any format or medium for personal research or study, educational, or not-for-profit purposes without prior permission or charge, provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. http://sro.sussex.ac.uk DNA Strand Break Repair and Neurodegeneration Stuart L. Rulten and Keith W. Caldecott Genome Damage and Stability Centre, Science Park Road, Falmer, Brighton, BN1 9RQ, UK Correspondence: Stuart L.
    [Show full text]
  • D:\My Documents\Wordperfect
    ANNEX F DNA repair and mutagenesis CONTENTS Page INTRODUCTION..................................................... 2 I. DNADAMAGEANDREPAIR...................................... 2 A. THEROLEOFDNAREPAIRGENESINCELLFUNCTION .......... 2 B. TYPESOFDAMAGEANDPATHWAYSOFREPAIR ............... 3 C. SUMMARY................................................. 8 II. REPAIRPROCESSESANDRADIOSENSITIVITY ...................... 9 A. RADIOSENSITIVITYINMAMMALIANCELLSANDHUMANS...... 9 1. The identification of radiosensitive cell lines and disorders ......... 9 2. Mechanisms of enhanced sensitivity in human disorders .......... 11 3. Analysis of genes determining radiosensitivity .................. 12 4. Summary ............................................. 17 B. RELATIONSHIP BETWEEN REPAIR AND OTHERCELLREGULATORYPROCESSES...................... 18 1. Radiosensitivity and defective recombination in the immune system: non-homologousendjoiningofDNAdouble-strandbreaks........ 18 2. Radiosensitivity and the cell cycle ........................... 21 3. Apoptosis:analternativetorepair?.......................... 23 4. Summary.............................................. 25 III. HUMAN RADIATION RESPONSES ................................. 26 A. CONTRIBUTION OF MUTANT GENES TOHUMANRADIOSENSITIVITY ............................. 26 B. INFLUENCEOFREPAIRONRADIATIONRESPONSES............ 29 C. SUMMARY................................................ 32 IV. MECHANISMSOFRADIATIONMUTAGENESIS ..................... 33 A. MUTATIONASAREPAIR-RELATEDRESPONSE................ 33 B. THESPECTRUMOFRADIATION-INDUCEDMUTATIONS........
    [Show full text]
  • Rational Design of Human DNA Ligase Inhibitors That Target Cellular DNA Replication and Repair
    Research Article Rational Design of Human DNA Ligase Inhibitors that Target Cellular DNA Replication and Repair Xi Chen,1 Shijun Zhong,3 Xiao Zhu,3 Barbara Dziegielewska,1 Tom Ellenberger,4 Gerald M. Wilson,2 Alexander D. MacKerell, Jr.,3 and Alan E. Tomkinson1 1Radiation Oncology Research Laboratory and Marlene and Stewart Greenebaum Cancer Center, 2Department of Biochemistry and Molecular Biology, School of Medicine, 3Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland; and 4Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri Abstract exert their cytotoxic effects by damaging DNA. Unfortunately, these Based on the crystal structure of human DNA ligase I agents also kill normal cells, thereby limiting their utility. There is complexed with nicked DNA, computer-aided drug design growing interest in the identification of DNA repair inhibitors that was used to identify compounds in a database of 1.5 million will enhance the cytotoxicity of DNA-damaging agents because commercially available low molecular weight chemicals that combinations of DNA-damaging agents and DNA repair inhibitors were predicted to bind to a DNA-binding pocket within the have the potential to concomitantly increase the killing of cancer DNA-binding domain of DNA ligase I, thereby inhibiting DNA cells and reduce damage to normal tissues and cells if either the joining. Ten of 192 candidates specifically inhibited purified damaging agent or the inhibitor could be selectively delivered to human DNA ligase I. Notably, a subset of these compounds the cancer cells (1). Because DNA ligation is required during replication and is the was also active against the other human DNA ligases.
    [Show full text]
  • Mechanism of Hepatitis B Virus Cccdna Formation
    viruses Review Mechanism of Hepatitis B Virus cccDNA Formation Lei Wei and Alexander Ploss * 110 Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-609-258-7128 Abstract: Hepatitis B virus (HBV) remains a major medical problem affecting at least 257 million chronically infected patients who are at risk of developing serious, frequently fatal liver diseases. HBV is a small, partially double-stranded DNA virus that goes through an intricate replication cycle in its native cellular environment: human hepatocytes. A critical step in the viral life-cycle is the conversion of relaxed circular DNA (rcDNA) into covalently closed circular DNA (cccDNA), the latter being the major template for HBV gene transcription. For this conversion, HBV relies on multiple host factors, as enzymes capable of catalyzing the relevant reactions are not encoded in the viral genome. Combinations of genetic and biochemical approaches have produced findings that provide a more holistic picture of the complex mechanism of HBV cccDNA formation. Here, we review some of these studies that have helped to provide a comprehensive picture of rcDNA to cccDNA conversion. Mechanistic insights into this critical step for HBV persistence hold the key for devising new therapies that will lead not only to viral suppression but to a cure. Keywords: hepatitis B virus; HBV; viral replication; cccDNA biogenesis; rcDNA; DNA repair Citation: Wei, L.; Ploss, A. 1. Overview of HBV Life Cycle and cccDNA Biogenesis Mechanism of Hepatitis B Virus cccDNA Formation. Viruses 2021, 13, The hepatotropic HBV belongs to the Hepadnaviridae family and is a blood-borne 1463.
    [Show full text]
  • Polymerase Is a Robust Terminal Transferase That Oscillates Between
    RESEARCH ARTICLE Polymerase is a robust terminal transferase that oscillates between three different mechanisms during end-joining Tatiana Kent1,2, Pedro A Mateos-Gomez3,4, Agnel Sfeir3,4, Richard T Pomerantz1,2* 1Fels Institute for Cancer Research, Temple University Lewis Katz School of Medicine, Philadelphia, United States; 2Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, United States; 3Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, United States; 4Department of Cell Biology, New York University School of Medicine, New York, United States Abstract DNA polymerase q (Polq) promotes insertion mutations during alternative end-joining (alt-EJ) by an unknown mechanism. Here, we discover that mammalian Polq transfers nucleotides to the 3’ terminus of DNA during alt-EJ in vitro and in vivo by oscillating between three different modes of terminal transferase activity: non-templated extension, templated extension in cis, and templated extension in trans. This switching mechanism requires manganese as a co-factor for Polq template-independent activity and allows for random combinations of templated and non- templated nucleotide insertions. We further find that Polq terminal transferase activity is most efficient on DNA containing 3’ overhangs, is facilitated by an insertion loop and conserved residues that hold the 3’ primer terminus, and is surprisingly more proficient than terminal deoxynucleotidyl transferase. In summary, this report identifies an unprecedented switching mechanism used by Polq to generate genetic diversity during alt-EJ and characterizes Polq as among the most proficient terminal transferases known. DOI: 10.7554/eLife.13740.001 *For correspondence: richard.
    [Show full text]
  • Human RAP 1 Specifically Protects Telomeres of Senescent Cells from DNA Damage Liudmyla Lototska, Jia-Xing Yue, M.J
    Human RAP 1 specifically protects telomeres of senescent cells from DNA damage Liudmyla Lototska, Jia-xing Yue, M.J. Giraud-Panis, Zhou Songyang, Nicola Royle, Gianni Liti, Jing Ye, Eric Gilson, Aaron Mendez-bermudez To cite this version: Liudmyla Lototska, Jia-xing Yue, M.J. Giraud-Panis, Zhou Songyang, Nicola Royle, et al.. Human RAP 1 specifically protects telomeres of senescent cells from DNA damage. EMBO Reports, EMBO Press, 2020, 21 (4), 10.15252/embr.201949076. hal-03013736 HAL Id: hal-03013736 https://hal.archives-ouvertes.fr/hal-03013736 Submitted on 23 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Report Human RAP1 specifically protects telomeres of senescent cells from DNA damage Liudmyla Lototska1,2,†, Jia-Xing Yue2,‡, Jing Li2,‡, Marie-Josèphe Giraud-Panis2, Zhou Songyang3,4,5, Nicola J Royle6 , Gianni Liti2, Jing Ye1,* , Eric Gilson1,2,7,** & Aaron Mendez-Bermudez1,2,#,*** Abstract overhang. Over the course of evolution, mammalian telomeres invented the shelterin complex, a very elegant way to protect chro- Repressor/activator protein 1 (RAP1) is a highly evolutionarily mosome extremities from various DNA damaging insults, including conserved protein found at telomeres.
    [Show full text]
  • Ligase 1 Is a Predictor of Platinum Resistance and Its Blockade Is Synthetically Lethal In
    Ligase 1 is a predictor of platinum resistance and its blockade is synthetically lethal in XRCC1 deficient epithelial ovarian cancers Reem Ali1*, Muslim Alabdullah1,2*, Mashael Algethami1**, Adel Alblihy1,3**, Islam Miligy2, Ahmed Shoqafi1, Katia A. Mesquita1, Tarek Abdel-Fatah4, Stephen YT Chan4, Pei Wen Chiang5, Nigel P Mongan6,7, Emad A Rakha2, Alan E Tomkinson8, Srinivasan Madhusudan1,3*** 1 Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham NG7 3RD, UK. 2 Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham NG51PB, UK. 3 Medical Center, King Fahad Security College (KFSC), Riyadh 11461, Saudi Arabia. 4 Department of Oncology, Nottingham University Hospitals, City Hospital Campus, Nottingham NG5 1PB, UK. 5 Department of Obstetrics & Gynaecology, Queens Medical Centre, Nottingham University Hospitals, Nottingham NG7 2UH, UK. 6 Faculty of Medicine and Health Sciences, Centre for Cancer Sciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire LE12 5RD, UK 7 Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10065, USA 8 Department of Internal Medicine, Division of Molecular Medicine, Health Sciences Center, The University of New Mexico, Albuquerque, NM 87102, USA. * = Joint first authors, ** = Joint second authors Running title: LIG1 targeting in ovarian cancers Declarations of interest: none Word count: 3459 Figure: 5 Table:1 *** Corresponding author: Professor Srinivasan
    [Show full text]
  • Alternative Okazaki Fragment Ligation Pathway by DNA Ligase III
    Genes 2015, 6, 385-398; doi:10.3390/genes6020385 OPEN ACCESS genes ISSN 2073-4425 www.mdpi.com/journal/genes Review Alternative Okazaki Fragment Ligation Pathway by DNA Ligase III Hiroshi Arakawa 1,* and George Iliakis 2 1 IFOM-FIRC Institute of Molecular Oncology Foundation, IFOM-IEO Campus, Via Adamello 16, Milano 20139, Italy 2 Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, Essen 45122, Germany; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +39-2-574303306; Fax: +39-2-574303231. Academic Editor: Peter Frank Received: 31 March 2015 / Accepted: 18 June 2015 / Published: 23 June 2015 Abstract: Higher eukaryotes have three types of DNA ligases: DNA ligase 1 (Lig1), DNA ligase 3 (Lig3) and DNA ligase 4 (Lig4). While Lig1 and Lig4 are present in all eukaryotes from yeast to human, Lig3 appears sporadically in evolution and is uniformly present only in vertebrates. In the classical, textbook view, Lig1 catalyzes Okazaki-fragment ligation at the DNA replication fork and the ligation steps of long-patch base-excision repair (BER), homologous recombination repair (HRR) and nucleotide excision repair (NER). Lig4 is responsible for DNA ligation at DNA double strand breaks (DSBs) by the classical, DNA-PKcs-dependent pathway of non-homologous end joining (C-NHEJ). Lig3 is implicated in a short-patch base excision repair (BER) pathway, in single strand break repair in the nucleus, and in all ligation requirements of the DNA metabolism in mitochondria. In this scenario, Lig1 and Lig4 feature as the major DNA ligases serving the most essential ligation needs of the cell, while Lig3 serves in the cell nucleus only minor repair roles.
    [Show full text]