1
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Torrado C, Ashton NW, D'Andrea AD, Yap TA. USP1 inhibition: A journey from target discovery to clinical translation. Pharmacol Ther 2025; 271:108865. [PMID: 40274197 DOI: 10.1016/j.pharmthera.2025.108865] [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: 01/23/2025] [Revised: 04/04/2025] [Accepted: 04/20/2025] [Indexed: 04/26/2025]
Abstract
Ubiquitin-specific protease 1 (USP1) is a deubiquitinating enzyme involved in the DNA damage response. Upon DNA damage, USP1 stabilizes replication forks by removing monoubiquitin from PCNA and FANCD2-FANCI, thereby catalyzing critical final steps in translesion synthesis and interstrand crosslink (ICL) repair. This function is particularly crucial in BRCA1 mutant cancers, where the homologous recombination pathway is compromised, leading tumors to rely on USP1 for effective repair. USP1 is also overexpressed in BRCA1 mutant cancers, as well as other tumor types. Preclinical studies have demonstrated that knockout of USP1 is synthetically lethal in tumors with biallelic BRCA1 mutations, and this relationship is enhanced by combination with PARP inhibitors. Newly developed USP1 inhibitors have confirmed this synthetic lethality in BRCA1-deficient tumor cells. Moreover, these drugs have the potential for resensitizing platinum-resistant tumors. Currently, potent and specific USP1 inhibitors are undergoing evaluation in phase I clinical trials. RO7623066 (KSQ-4279) reported an acceptable safety profile during a phase I dose escalation study, with anemia being the most common side effect, and demonstrated robust pharmacokinetic, pharmacodynamic, and clinical activity. Other USP1 inhibitors, including SIM0501, XL309-101, and HSK39775, are currently in early clinical development. In this review, we provide an overview of the molecular function of USP1 and its importance as a therapeutic target in oncology, before focusing on the current state of preclinical and clinical development of USP1 inhibitors.
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Affiliation(s)
- Carlos Torrado
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicholas W Ashton
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Timothy A Yap
- University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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2
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Mazloumi Aboukheili AM, Walden H. USP1 in regulation of DNA repair pathways. DNA Repair (Amst) 2025; 146:103807. [PMID: 39848025 DOI: 10.1016/j.dnarep.2025.103807] [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: 12/04/2023] [Revised: 12/20/2024] [Accepted: 01/07/2025] [Indexed: 01/25/2025]
Abstract
Ubiquitin-specific protease 1 (USP1) is the founding member of the family of cysteine proteases that catalyse hydrolysis of the isopeptide bond between ubiquitin and targets. USP1 is often overexpressed in various cancers, and expression levels correlate with poor prognosis. USP1 and its partner USP1-associated Factor 1 (UAF1) are required for deubiquitinating monoubiquitin signals in DNA interstrand crosslink repair, and in Translesion synthesis, among others, and both proteins are subject to multiple regulations themselves. This review covers recent findings on the mechanisms and functions of USP1 in DNA repair, its regulation, and its potential as a target for therapeutic intervention.
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Affiliation(s)
| | - Helen Walden
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, Scotland.
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3
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Varshavsky A. N-degron pathways. Proc Natl Acad Sci U S A 2024; 121:e2408697121. [PMID: 39264755 PMCID: PMC11441550 DOI: 10.1073/pnas.2408697121] [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] [Indexed: 09/14/2024] Open
Abstract
An N-degron is a degradation signal whose main determinant is a "destabilizing" N-terminal residue of a protein. Specific N-degrons, discovered in 1986, were the first identified degradation signals in short-lived intracellular proteins. These N-degrons are recognized by a ubiquitin-dependent proteolytic system called the Arg/N-degron pathway. Although bacteria lack the ubiquitin system, they also have N-degron pathways. Studies after 1986 have shown that all 20 amino acids of the genetic code can act, in specific sequence contexts, as destabilizing N-terminal residues. Eukaryotic proteins are targeted for the conditional or constitutive degradation by at least five N-degron systems that differ both functionally and mechanistically: the Arg/N-degron pathway, the Ac/N-degron pathway, the Pro/N-degron pathway, the fMet/N-degron pathway, and the newly named, in this perspective, GASTC/N-degron pathway (GASTC = Gly, Ala, Ser, Thr, Cys). I discuss these systems and the expanded terminology that now encompasses the entire gamut of known N-degron pathways.
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Affiliation(s)
- Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
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4
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Shimshon A, Dahan K, Israel-Gueta M, Olmayev-Yaakobov D, Timms RT, Bekturova A, Makaros Y, Elledge SJ, Koren I. Dipeptidyl peptidases and E3 ligases of N-degron pathways cooperate to regulate protein stability. J Cell Biol 2024; 223:e202311035. [PMID: 38874443 PMCID: PMC11178506 DOI: 10.1083/jcb.202311035] [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: 11/09/2023] [Revised: 03/21/2024] [Accepted: 04/30/2024] [Indexed: 06/15/2024] Open
Abstract
N-degrons are short sequences located at protein N-terminus that mediate the interaction of E3 ligases (E3s) with substrates to promote their proteolysis. It is well established that N-degrons can be exposed following protease cleavage to allow recognition by E3s. However, our knowledge regarding how proteases and E3s cooperate in protein quality control mechanisms remains minimal. Using a systematic approach to monitor the protein stability of an N-terminome library, we found that proline residue at the third N-terminal position (hereafter "P+3") promotes instability. Genetic perturbations identified the dipeptidyl peptidases DPP8 and DPP9 and the primary E3s of N-degron pathways, UBR proteins, as regulators of P+3 bearing substrate turnover. Interestingly, P+3 UBR substrates are significantly enriched for secretory proteins. We found that secretory proteins relying on a signal peptide (SP) for their targeting contain a "built-in" N-degron within their SP. This degron becomes exposed by DPP8/9 upon translocation failure to the designated compartments, thus enabling clearance of mislocalized proteins by UBRs to maintain proteostasis.
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Affiliation(s)
- Adi Shimshon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Karin Dahan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Mor Israel-Gueta
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Diana Olmayev-Yaakobov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Richard T. Timms
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Aizat Bekturova
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Yaara Makaros
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Stephen J. Elledge
- Department of Genetics, Harvard Medical School, Brigham and Women’s Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | - Itay Koren
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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5
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Kang JM, Park JS, Lee JS, Jang JY, Han BW. Structural study for substrate recognition of human N-terminal glutamine amidohydrolase 1 in the arginine N-degron pathway. Protein Sci 2024; 33:e5067. [PMID: 38864716 PMCID: PMC11168063 DOI: 10.1002/pro.5067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/12/2024] [Accepted: 05/19/2024] [Indexed: 06/13/2024]
Abstract
The N-degron pathway determines the half-life of proteins by selectively destabilizing the proteins bearing N-degrons. N-terminal glutamine amidohydrolase 1 (NTAQ1) plays an essential role in the arginine N-degron (Arg/N-degron) pathway as an initializing enzyme via the deamidation of the N-terminal (Nt) glutamine (Gln). However, the Nt-serine-bound conformation of hNTAQ1 according to the previously identified crystal structure suggests the possibility of other factors influencing the recognition of Nt residues by hNTAQ1. Hence, in the current study, we aimed to further elucidate the substrate recognition of hNTAQ1; specifically, we explored 12 different substrate-binding conformations of hNTAQ1 depending on the subsequent residue of Nt-Gln. Results revealed that hNTAQ1 primarily interacts with the protein Nt backbone, instead of the side chain, for substrate recognition. Here, we report that the Nt backbone of proteins appears to be a key component of hNTAQ1 function and is the main determinant of substrate recognition. Moreover, not all second residues from Nt-Gln, but rather distinctive and charged residues, appeared to aid in detecting substrate recognition. These new findings define the substrate-recognition process of hNTAQ1 and emphasize the importance of the subsequent Gln residue in the Nt-Gln degradation system. Our extensive structural and biochemical analyses provide insights into the substrate specificity of the N-degron pathway and shed light on the mechanism underlying hNTAQ1 substrate recognition. An improved understanding of the protein degradation machinery could aid in developing therapies to promote overall health through enhanced protein regulation, such as targeted protein therapies.
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Affiliation(s)
- Jin Mo Kang
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of PharmacySeoul National UniversitySeoulRepublic of Korea
| | - Joon Sung Park
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of PharmacySeoul National UniversitySeoulRepublic of Korea
| | - Jae Seok Lee
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of PharmacySeoul National UniversitySeoulRepublic of Korea
| | - Jun Young Jang
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of PharmacySeoul National UniversitySeoulRepublic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of PharmacySeoul National UniversitySeoulRepublic of Korea
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6
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Bolhuis DL, Emanuele MJ, Brown NG. Friend or foe? Reciprocal regulation between E3 ubiquitin ligases and deubiquitinases. Biochem Soc Trans 2024; 52:241-267. [PMID: 38414432 PMCID: PMC11349938 DOI: 10.1042/bst20230454] [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: 12/19/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/29/2024]
Abstract
Protein ubiquitination is a post-translational modification that entails the covalent attachment of the small protein ubiquitin (Ub), which acts as a signal to direct protein stability, localization, or interactions. The Ub code is written by a family of enzymes called E3 Ub ligases (∼600 members in humans), which can catalyze the transfer of either a single ubiquitin or the formation of a diverse array of polyubiquitin chains. This code can be edited or erased by a different set of enzymes termed deubiquitinases (DUBs; ∼100 members in humans). While enzymes from these distinct families have seemingly opposing activities, certain E3-DUB pairings can also synergize to regulate vital cellular processes like gene expression, autophagy, innate immunity, and cell proliferation. In this review, we highlight recent studies describing Ub ligase-DUB interactions and focus on their relationships.
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Affiliation(s)
- Derek L Bolhuis
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC, 27599
| | - Michael J Emanuele
- Department of Pharmacology and Lineberger Comprehensive Care Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC, 27599
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Care Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC, 27599
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7
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Huang H, Jones LH. Covalent drug discovery using sulfur(VI) fluoride exchange warheads. Expert Opin Drug Discov 2023:1-11. [PMID: 37243622 DOI: 10.1080/17460441.2023.2218642] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
Abstract
INTRODUCTION Covalent drug discovery has traditionally focused on targeting cysteine, but the amino acid is often absent in protein binding sites. This review makes the case to move beyond cysteine labeling using sulfur (VI) fluoride exchange (SuFEx) chemistry to expand the druggable proteome. AREAS COVERED Recent advances in SuFEx medicinal chemistry and chemical biology are described, which have enabled the development of covalent chemical probes that site-selectively engage amino acid residues (including tyrosine, lysine, histidine, serine, and threonine) in binding pockets. Areas covered include chemoproteomic mapping of the targetable proteome, structure-based design of covalent inhibitors and molecular glues, metabolic stability profiling, and synthetic methodologies that have expedited the delivery of SuFEx modulators. EXPERT OPINION Despite recent innovations in SuFEx medicinal chemistry, focused preclinical research is required to ensure the field moves from early chemical probe discovery to the delivery of transformational covalent drug candidates. The authors believe that covalent drug candidates designed to engage residues beyond cysteine using sulfonyl exchange warheads will likely enter clinical trials in the coming years.
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Affiliation(s)
- Huang Huang
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Lyn H Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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8
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Scott DC, King MT, Baek K, Gee CT, Kalathur R, Li J, Purser N, Nourse A, Chai SC, Vaithiyalingam S, Chen T, Lee RE, Elledge SJ, Kleiger G, Schulman BA. E3 ligase autoinhibition by C-degron mimicry maintains C-degron substrate fidelity. Mol Cell 2023; 83:770-786.e9. [PMID: 36805027 PMCID: PMC10080726 DOI: 10.1016/j.molcel.2023.01.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/19/2022] [Accepted: 01/18/2023] [Indexed: 02/18/2023]
Abstract
E3 ligase recruitment of proteins containing terminal destabilizing motifs (degrons) is emerging as a major form of regulation. How those E3s discriminate bona fide substrates from other proteins with terminal degron-like sequences remains unclear. Here, we report that human KLHDC2, a CRL2 substrate receptor targeting C-terminal Gly-Gly degrons, is regulated through interconversion between two assemblies. In the self-inactivated homotetramer, KLHDC2's C-terminal Gly-Ser motif mimics a degron and engages the substrate-binding domain of another protomer. True substrates capture the monomeric CRL2KLHDC2, driving E3 activation by neddylation and subsequent substrate ubiquitylation. Non-substrates such as NEDD8 bind KLHDC2 with high affinity, but its slow on rate prevents productive association with CRL2KLHDC2. Without substrate, neddylated CRL2KLHDC2 assemblies are deactivated via distinct mechanisms: the monomer by deneddylation and the tetramer by auto-ubiquitylation. Thus, substrate specificity is amplified by KLHDC2 self-assembly acting like a molecular timer, where only bona fide substrates may bind before E3 ligase inactivation.
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Affiliation(s)
- Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Moeko T King
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Clifford T Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ravi Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Protein Technologies Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Nicholas Purser
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Amanda Nourse
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Protein Technologies Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sivaraja Vaithiyalingam
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Protein Technologies Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen J Elledge
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
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9
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Chemical mimetics of the N-degron pathway alleviate systemic inflammation by activating mitophagy and immunometabolic remodeling. Exp Mol Med 2023; 55:333-346. [PMID: 36720915 PMCID: PMC9981610 DOI: 10.1038/s12276-023-00929-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/19/2022] [Accepted: 11/04/2022] [Indexed: 02/02/2023] Open
Abstract
The Arg/N-degron pathway, which is involved in the degradation of proteins bearing an N-terminal signal peptide, is connected to p62/SQSTM1-mediated autophagy. However, the impact of the molecular link between the N-degron and autophagy pathways is largely unknown in the context of systemic inflammation. Here, we show that chemical mimetics of the N-degron Nt-Arg pathway (p62 ligands) decreased mortality in sepsis and inhibited pathological inflammation by activating mitophagy and immunometabolic remodeling. The p62 ligands alleviated systemic inflammation in a mouse model of lipopolysaccharide (LPS)-induced septic shock and in the cecal ligation and puncture model of sepsis. In macrophages, the p62 ligand attenuated the production of proinflammatory cytokines and chemokines in response to various innate immune stimuli. Mechanistically, the p62 ligand augmented LPS-induced mitophagy and inhibited the production of mitochondrial reactive oxygen species in macrophages. The p62 ligand-mediated anti-inflammatory, antioxidative, and mitophagy-activating effects depended on p62. In parallel, the p62 ligand significantly downregulated the LPS-induced upregulation of aerobic glycolysis and lactate production. Together, our findings demonstrate that p62 ligands play a critical role in the regulation of inflammatory responses by orchestrating mitophagy and immunometabolic remodeling.
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10
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Crystal structure of the Ate1 arginyl-tRNA-protein transferase and arginylation of N-degron substrates. Proc Natl Acad Sci U S A 2022; 119:e2209597119. [PMID: 35878037 PMCID: PMC9351520 DOI: 10.1073/pnas.2209597119] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
N-degron pathways are proteolytic systems that target proteins bearing N-terminal (Nt) degradation signals (degrons) called N-degrons. Nt-Arg of a protein is among Nt-residues that can be recognized as destabilizing ones by the Arg/N-degron pathway. A proteolytic cleavage of a protein can generate Arg at the N terminus of a resulting C-terminal (Ct) fragment either directly or after Nt-arginylation of that Ct-fragment by the Ate1 arginyl-tRNA-protein transferase (R-transferase), which uses Arg-tRNAArg as a cosubstrate. Ate1 can Nt-arginylate Nt-Asp, Nt-Glu, and oxidized Nt-Cys* (Cys-sulfinate or Cys-sulfonate) of proteins or short peptides. Ate1 genes of fungi, animals, and plants have been cloned decades ago, but a three-dimensional structure of Ate1 remained unknown. A detailed mechanism of arginylation is unknown as well. We describe here the crystal structure of the Ate1 R-transferase from the budding yeast Kluyveromyces lactis. The 58-kDa R-transferase comprises two domains that recognize, together, an acidic Nt-residue of an acceptor substrate, the Arg residue of Arg-tRNAArg, and a 3'-proximal segment of the tRNAArg moiety. The enzyme's active site is located, at least in part, between the two domains. In vitro and in vivo arginylation assays with site-directed Ate1 mutants that were suggested by structural results yielded inferences about specific binding sites of Ate1. We also analyzed the inhibition of Nt-arginylation activity of Ate1 by hemin (Fe3+-heme), and found that hemin induced the previously undescribed disulfide-mediated oligomerization of Ate1. Together, these results advance the understanding of R-transferase and the Arg/N-degron pathway.
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11
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USP1-trapping lesions as a source of DNA replication stress and genomic instability. Nat Commun 2022; 13:1740. [PMID: 35365626 PMCID: PMC8975806 DOI: 10.1038/s41467-022-29369-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/08/2022] [Indexed: 12/16/2022] Open
Abstract
The deubiquitinase USP1 is a critical regulator of genome integrity through the deubiquitylation of Fanconi Anemia proteins and the DNA replication processivity factor, proliferating cell nuclear antigen (PCNA). Uniquely, following UV irradiation, USP1 self-inactivates through autocleavage, which enables its own degradation and in turn, upregulates PCNA monoubiquitylation. However, the functional role for this autocleavage event during physiological conditions remains elusive. Herein, we discover that cells harboring an autocleavage-defective USP1 mutant, while still able to robustly deubiquitylate PCNA, experience more replication fork-stalling and premature fork termination events. Using super-resolution microscopy and live-cell single-molecule tracking, we show that these defects are related to the inability of this USP1 mutant to be properly recycled from sites of active DNA synthesis, resulting in replication-associated lesions. Furthermore, we find that the removal of USP1 molecules from DNA is facilitated by the DNA-dependent metalloprotease Spartan to counteract the cytotoxicity caused by “USP1-trapping”. We propose a utility of USP1 inhibitors in cancer therapy based on their ability to induce USP1-trapping lesions and consequent replication stress and genomic instability in cancer cells, similar to how non-covalent DNA-protein crosslinks cause cytotoxicity by imposing steric hindrances upon proteins involved in DNA transactions. Here the authors provide mechanistic insights into how auto-cleavage of the USP1 deubiquitinase regulates DNA replication and genome stability. Implications for the targeting of USP1 activity via protein-DNA trapping in cancer therapy are discussed.
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12
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Sherpa D, Chrustowicz J, Schulman BA. How the ends signal the end: Regulation by E3 ubiquitin ligases recognizing protein termini. Mol Cell 2022; 82:1424-1438. [PMID: 35247307 PMCID: PMC9098119 DOI: 10.1016/j.molcel.2022.02.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/18/2022] [Accepted: 02/01/2022] [Indexed: 12/31/2022]
Abstract
Specificity of eukaryotic protein degradation is determined by E3 ubiquitin ligases and their selective binding to protein motifs, termed "degrons," in substrates for ubiquitin-mediated proteolysis. From the discovery of the first substrate degron and the corresponding E3 to a flurry of recent studies enabled by modern systems and structural methods, it is clear that many regulatory pathways depend on E3s recognizing protein termini. Here, we review the structural basis for recognition of protein termini by E3s and how this recognition underlies biological regulation. Diverse E3s evolved to harness a substrate's N and/or C terminus (and often adjacent residues as well) in a sequence-specific manner. Regulation is achieved through selective activation of E3s and also through generation of degrons at ribosomes or by posttranslational means. Collectively, many E3 interactions with protein N and C termini enable intricate control of protein quality and responses to cellular signals.
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Affiliation(s)
- Dawafuti Sherpa
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany
| | - Jakub Chrustowicz
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany.
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13
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Cruite JT, Dann GP, Che J, Donovan KA, Ferrao S, Ficarro SB, Fischer ES, Gray NS, Huerta F, Kong NR, Liu H, Marto JA, Metivier RJ, Nowak RP, Zerfas BL, Jones LH. Cereblon covalent modulation through structure-based design of histidine targeting chemical probes. RSC Chem Biol 2022; 3:1105-1110. [PMID: 36128501 PMCID: PMC9428674 DOI: 10.1039/d2cb00078d] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/08/2022] [Indexed: 01/01/2023] Open
Abstract
Synthetic re-engineering of a surface histidine residue on cereblon using sulfonyl exchange chemistry yielded potent irreversible modulators of the E3 ubiquitin ligase complex, including a molecular glue degrader of the novel neosubstrate NTAQ1.
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Affiliation(s)
- Justin T. Cruite
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Geoffrey P. Dann
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jianwei Che
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Katherine A. Donovan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Silas Ferrao
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott B. Ficarro
- Department of Cancer Biology, Department of Oncologic Pathology, and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eric S. Fischer
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA, USA
| | - Fidel Huerta
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nikki R. Kong
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Hu Liu
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jarrod A. Marto
- Department of Cancer Biology, Department of Oncologic Pathology, and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Radosław P. Nowak
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Breanna L. Zerfas
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Lyn H. Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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14
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Abstract
Post-translational modifications (PTMs) direct the assembly of protein complexes. In this context, proteolysis is a unique PTM because it is irreversible; the hydrolysis of the peptide backbone generates separate fragments bearing a new N and C terminus. Proteolysis can "re-wire" protein-protein interactions (PPIs) via the recruitment of end-binding proteins to new termini. In this review, we focus on the role of proteolysis in specifically creating complexes by recruiting E3 ubiquitin ligases to new N and C termini. These complexes potentiate proteolytic signaling by "erasing" proteolytic modifications. This activity tunes the duration and magnitude of protease signaling events. Recent work has shown that the stepwise process of proteolysis, end-binding by E3 ubiquitin ligases, and fragment turnover is associated with both the nascent N terminus (i.e., N-degron pathways) and the nascent C terminus (i.e., the C-degron pathways). Here, we discuss how these pathways might harmonize protease signaling with protein homeostasis (i.e., proteostasis).
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Affiliation(s)
- Matthew Ravalin
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Koli Basu
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Jason E. Gestwicki
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
- Institute for Neurodegenerative Diseases, University of California at San Francisco, San Francisco, CA, USA
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
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15
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Chrustowicz J, Sherpa D, Teyra J, Loke MS, Popowicz GM, Basquin J, Sattler M, Prabu JR, Sidhu SS, Schulman BA. Multifaceted N-Degron Recognition and Ubiquitylation by GID/CTLH E3 Ligases. J Mol Biol 2021; 434:167347. [PMID: 34767800 DOI: 10.1016/j.jmb.2021.167347] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022]
Abstract
N-degron E3 ubiquitin ligases recognize specific residues at the N-termini of substrates. Although molecular details of N-degron recognition are known for several E3 ligases, the range of N-terminal motifs that can bind a given E3 substrate binding domain remains unclear. Here, we discovered capacity of Gid4 and Gid10 substrate receptor subunits of yeast "GID"/human "CTLH" multiprotein E3 ligases to tightly bind a wide range of N-terminal residues whose recognition is determined in part by the downstream sequence context. Screening of phage displaying peptide libraries with exposed N-termini identified novel consensus motifs with non-Pro N-terminal residues binding Gid4 or Gid10 with high affinity. Structural data reveal that conformations of flexible loops in Gid4 and Gid10 complement sequences and folds of interacting peptides. Together with analysis of endogenous substrate degrons, the data show that degron identity, substrate domains harboring targeted lysines, and varying E3 ligase higher-order assemblies combinatorially determine efficiency of ubiquitylation and degradation.
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Affiliation(s)
- Jakub Chrustowicz
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. https://twitter.com/chrustowicz_j
| | - Dawafuti Sherpa
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. https://twitter.com/dawafutisherpa
| | - Joan Teyra
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Mun Siong Loke
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Grzegorz M Popowicz
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Germany
| | - Jerome Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Michael Sattler
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. https://twitter.com/rajanprabu
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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16
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Tying up loose ends: the N-degron and C-degron pathways of protein degradation. Biochem Soc Trans 2021; 48:1557-1567. [PMID: 32627813 PMCID: PMC7458402 DOI: 10.1042/bst20191094] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 12/13/2022]
Abstract
Selective protein degradation by the ubiquitin-proteasome system (UPS) is thought to be governed primarily by the recognition of specific motifs — degrons — present in substrate proteins. The ends of proteins — the N- and C-termini – have unique properties, and an important subset of protein–protein interactions involve the recognition of free termini. The first degrons to be discovered were located at the extreme N-terminus of proteins, a finding which initiated the study of the N-degron (formerly N-end rule) pathways, but only in the last few years has it emerged that a diverse set of C-degron pathways target analogous degron motifs located at the extreme C-terminus of proteins. In this minireview we summarise the N-degron and C-degron pathways currently known to operate in human cells, focussing primarily on those that have been discovered in recent years. In each case we describe the cellular machinery responsible for terminal degron recognition, and then consider some of the functional roles of terminal degron pathways. Altogether, a broad spectrum of E3 ubiquitin ligases mediate the recognition of a diverse array of terminal degron motifs; these degradative pathways have the potential to influence a wide variety of cellular functions.
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17
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Basar MA, Beck DB, Werner A. Deubiquitylases in developmental ubiquitin signaling and congenital diseases. Cell Death Differ 2021; 28:538-556. [PMID: 33335288 PMCID: PMC7862630 DOI: 10.1038/s41418-020-00697-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Metazoan development from a one-cell zygote to a fully formed organism requires complex cellular differentiation and communication pathways. To coordinate these processes, embryos frequently encode signaling information with the small protein modifier ubiquitin, which is typically attached to lysine residues within substrates. During ubiquitin signaling, a three-step enzymatic cascade modifies specific substrates with topologically unique ubiquitin modifications, which mediate changes in the substrate's stability, activity, localization, or interacting proteins. Ubiquitin signaling is critically regulated by deubiquitylases (DUBs), a class of ~100 human enzymes that oppose the conjugation of ubiquitin. DUBs control many essential cellular functions and various aspects of human physiology and development. Recent genetic studies have identified mutations in several DUBs that cause developmental disorders. Here we review principles controlling DUB activity and substrate recruitment that allow these enzymes to regulate ubiquitin signaling during development. We summarize key mechanisms of how DUBs control embryonic and postnatal differentiation processes, highlight developmental disorders that are caused by mutations in particular DUB members, and describe our current understanding of how these mutations disrupt development. Finally, we discuss how emerging tools from human disease genetics will enable the identification and study of novel congenital disease-causing DUBs.
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Affiliation(s)
- Mohammed A Basar
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David B Beck
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
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18
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Yeh CW, Huang WC, Hsu PH, Yeh KH, Wang LC, Hsu PWC, Lin HC, Chen YN, Chen SC, Yeang CH, Yen HCS. The C-degron pathway eliminates mislocalized proteins and products of deubiquitinating enzymes. EMBO J 2021; 40:e105846. [PMID: 33469951 PMCID: PMC8013793 DOI: 10.15252/embj.2020105846] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 01/22/2023] Open
Abstract
Protein termini are determinants of protein stability. Proteins bearing degradation signals, or degrons, at their amino‐ or carboxyl‐termini are eliminated by the N‐ or C‐degron pathways, respectively. We aimed to elucidate the function of C‐degron pathways and to unveil how normal proteomes are exempt from C‐degron pathway‐mediated destruction. Our data reveal that C‐degron pathways remove mislocalized cellular proteins and cleavage products of deubiquitinating enzymes. Furthermore, the C‐degron and N‐degron pathways cooperate in protein removal. Proteome analysis revealed a shortfall in normal proteins targeted by C‐degron pathways, but not of defective proteins, suggesting proteolysis‐based immunity as a constraint for protein evolution/selection. Our work highlights the importance of protein termini for protein quality surveillance, and the relationship between the functional proteome and protein degradation pathways.
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Affiliation(s)
- Chi-Wei Yeh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Wei-Chieh Huang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Pang-Hung Hsu
- Department of Life Science, Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Kun-Hai Yeh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Li-Chin Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | | | - Hsiu-Chuan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Yi-Ning Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Chuan Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chen-Hsiang Yeang
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.,Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Hsueh-Chi S Yen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
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19
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Vu TTM, Varshavsky A. The ATF3 Transcription Factor Is a Short-Lived Substrate of the Arg/N-Degron Pathway. Biochemistry 2020; 59:2796-2812. [PMID: 32692156 DOI: 10.1021/acs.biochem.0c00514] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Arg/N-degron pathway targets proteins for degradation by recognizing their specific N-terminal residues or, alternatively, their non-N-terminal degrons. In mammals, this pathway is mediated by the UBR1, UBR2, UBR4, and UBR5 E3 ubiquitin ligases, and by the p62 regulator of autophagy. UBR1 and UBR2 are sequelogous, functionally overlapping, and dominate the targeting of Arg/N-degron substrates in examined cell lines. We constructed, here, mouse strains in which the double mutant [UBR1-/- UBR2-/-] genotype can be induced conditionally, in adult mice. We also constructed human [UBR1-/- UBR2-/-] HEK293T cell lines that unconditionally lack UBR1/UBR2. ATF3 is a basic leucine zipper transcription factor that regulates hundreds of genes and can act as either a repressor or an activator of transcription. Using the above double-mutant mice and human cells, we found that the levels of endogenous, untagged ATF3 were significantly higher in both of these [UBR1-/- UBR2-/-] settings than in wild-type cells. We also show, through chase-degradation assays with [UBR1-/- UBR2-/-] and wild-type human cells, that the Arg/N-degron pathway mediates a large fraction of ATF3 degradation. Furthermore, we used split-ubiquitin and another protein interaction assay to detect the binding of ATF3 to both UBR1 and UBR2, in agreement with the UBR1/UBR2-mediated degradation of endogenous ATF3. Full-length 24 kDa ATF3 binds to ∼100 kDa fragments of 200 kDa UBR1 and UBR2 but does not bind (in the setting of interaction assays) to full-length UBR1/UBR2. These and other binding patterns, whose mechanics remain to be understood, may signify a conditional (regulated) degradation of ATF3 by the Arg/N-degron pathway.
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Affiliation(s)
- Tri T M Vu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
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20
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Dong C, Chen SJ, Melnykov A, Weirich S, Sun K, Jeltsch A, Varshavsky A, Min J. Recognition of nonproline N-terminal residues by the Pro/N-degron pathway. Proc Natl Acad Sci U S A 2020; 117:14158-14167. [PMID: 32513738 PMCID: PMC7322002 DOI: 10.1073/pnas.2007085117] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Eukaryotic N-degron pathways are proteolytic systems whose unifying feature is their ability to recognize proteins containing N-terminal (Nt) degradation signals called N-degrons, and to target these proteins for degradation by the 26S proteasome or autophagy. GID4, a subunit of the GID ubiquitin ligase, is the main recognition component of the proline (Pro)/N-degron pathway. GID4 targets proteins through their Nt-Pro residue or a Pro at position 2, in the presence of specific downstream sequence motifs. Here we show that human GID4 can also recognize hydrophobic Nt-residues other than Pro. One example is the sequence Nt-IGLW, bearing Nt-Ile. Nt-IGLW binds to wild-type human GID4 with a Kd of 16 μM, whereas the otherwise identical Nt-Pro-bearing sequence PGLW binds to GID4 more tightly, with a Kd of 1.9 μM. Despite this difference in affinities of GID4 for Nt-IGLW vs. Nt-PGLW, we found that the GID4-mediated Pro/N-degron pathway of the yeast Saccharomyces cerevisiae can target an Nt-IGLW-bearing protein for rapid degradation. We solved crystal structures of human GID4 bound to a peptide bearing Nt-Ile or Nt-Val. We also altered specific residues of human GID4 and measured the affinities of resulting mutant GID4s for Nt-IGLW and Nt-PGLW, thereby determining relative contributions of specific GID4 residues to the GID4-mediated recognition of Nt-Pro vs. Nt-residues other than Pro. These and related results advance the understanding of targeting by the Pro/N-degron pathway and greatly expand the substrate recognition range of the GID ubiquitin ligase in both human and yeast cells.
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Affiliation(s)
- Cheng Dong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070 Tianjin, People's Republic of China
| | - Shun-Jia Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | | | - Sara Weirich
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University Stuttgart, 70569 Stuttgart, Germany
| | - Kelly Sun
- Structural Genomics Consortium, Department of Physiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University Stuttgart, 70569 Stuttgart, Germany
| | - Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;
| | - Jinrong Min
- Structural Genomics Consortium, Department of Physiology, University of Toronto, Toronto, ON M5G 1L7, Canada;
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, 430079 Wuhan, People's Republic of China
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21
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Five enzymes of the Arg/N-degron pathway form a targeting complex: The concept of superchanneling. Proc Natl Acad Sci U S A 2020; 117:10778-10788. [PMID: 32366662 DOI: 10.1073/pnas.2003043117] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Arg/N-degron pathway targets proteins for degradation by recognizing their N-terminal (Nt) residues. If a substrate bears, for example, Nt-Asn, its targeting involves deamidation of Nt-Asn, arginylation of resulting Nt-Asp, binding of resulting (conjugated) Nt-Arg to the UBR1-RAD6 E3-E2 ubiquitin ligase, ligase-mediated synthesis of a substrate-linked polyubiquitin chain, its capture by the proteasome, and substrate's degradation. We discovered that the human Nt-Asn-specific Nt-amidase NTAN1, Nt-Gln-specific Nt-amidase NTAQ1, arginyltransferase ATE1, and the ubiquitin ligase UBR1-UBE2A/B (or UBR2-UBE2A/B) form a complex in which NTAN1 Nt-amidase binds to NTAQ1, ATE1, and UBR1/UBR2. In addition, NTAQ1 Nt-amidase and ATE1 arginyltransferase also bind to UBR1/UBR2. In the yeast Saccharomyces cerevisiae, the Nt-amidase, arginyltransferase, and the double-E3 ubiquitin ligase UBR1-RAD6/UFD4-UBC4/5 are shown to form an analogous targeting complex. These complexes may enable substrate channeling, in which a substrate bearing, for example, Nt-Asn, would be captured by a complex-bound Nt-amidase, followed by sequential Nt modifications of the substrate and its polyubiquitylation at an internal Lys residue without substrate's dissociation into the bulk solution. At least in yeast, the UBR1/UFD4 ubiquitin ligase interacts with the 26S proteasome, suggesting an even larger Arg/N-degron-targeting complex that contains the proteasome as well. In addition, specific features of protein-sized Arg/N-degron substrates, including their partly sequential and partly nonsequential enzymatic modifications, led us to a verifiable concept termed "superchanneling." In superchanneling, the synthesis of a substrate-linked poly-Ub chain can occur not only after a substrate's sequential Nt modifications, but also before them, through a skipping of either some or all of these modifications within a targeting complex.
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22
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Goldbraikh D, Neufeld D, Eid‐Mutlak Y, Lasry I, Gilda JE, Parnis A, Cohen S. USP1 deubiquitinates Akt to inhibit PI3K-Akt-FoxO signaling in muscle during prolonged starvation. EMBO Rep 2020; 21:e48791. [PMID: 32133736 PMCID: PMC7132338 DOI: 10.15252/embr.201948791] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 01/29/2020] [Accepted: 02/11/2020] [Indexed: 01/11/2023] Open
Abstract
PI3K-Akt-FoxO-mTOR signaling is the central pathway controlling growth and metabolism in all cells. Ubiquitination of the protein kinase Akt prior to its phosphorylation is required for PI3K-Akt activity. Here, we found that the deubiquitinating (DUB) enzyme USP1 removes K63-linked polyubiquitin chains on Akt to restrict PI3K-Akt-FoxO signaling in mouse muscle during prolonged starvation. DUB screening platform identified USP1 as a direct DUB for Akt, and USP1 depletion in mouse muscle increased Akt ubiquitination, PI3K-Akt-FoxO signaling, and glucose uptake during fasting. Co-immunoprecipitation and mass spectrometry identified disabled homolog-2 (Dab2), the tuberous sclerosis complex TSC1/TSC2, and PHLPP1 as USP1 bound proteins. During starvation, Dab2 is essential for Akt recruitment to USP1-TSC1-PHLPP1 complex, and for PI3K-Akt-FoxO inhibition. Surprisingly, USP1 limits TSC1 levels to sustain mTOR-mediated basal protein synthesis rates and maintain its own protein levels. We propose that Dab2 recruits Akt to USP1-TSC1-PHLPP1 complex to efficiently terminate the transmission of growth signals when cellular energy level is low.
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Affiliation(s)
- Dana Goldbraikh
- Faculty of BiologyTechnion Institute of TechnologyHaifaIsrael
| | | | - Yara Eid‐Mutlak
- Faculty of BiologyTechnion Institute of TechnologyHaifaIsrael
| | - Inbal Lasry
- Faculty of BiologyTechnion Institute of TechnologyHaifaIsrael
| | | | - Anna Parnis
- Faculty of BiologyTechnion Institute of TechnologyHaifaIsrael
| | - Shenhav Cohen
- Faculty of BiologyTechnion Institute of TechnologyHaifaIsrael
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23
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Timms RT, Zhang Z, Rhee DY, Harper JW, Koren I, Elledge SJ. A glycine-specific N-degron pathway mediates the quality control of protein N-myristoylation. Science 2020; 365:365/6448/eaaw4912. [PMID: 31273098 DOI: 10.1126/science.aaw4912] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/29/2019] [Accepted: 05/15/2019] [Indexed: 12/21/2022]
Abstract
The N-terminal residue influences protein stability through N-degron pathways. We used stability profiling of the human N-terminome to uncover multiple additional features of N-degron pathways. In addition to uncovering extended specificities of UBR E3 ligases, we characterized two related Cullin-RING E3 ligase complexes, Cul2ZYG11B and Cul2ZER1, that act redundantly to target N-terminal glycine. N-terminal glycine degrons are depleted at native N-termini but strongly enriched at caspase cleavage sites, suggesting roles for the substrate adaptors ZYG11B and ZER1 in protein degradation during apoptosis. Furthermore, ZYG11B and ZER1 were found to participate in the quality control of N-myristoylated proteins, in which N-terminal glycine degrons are conditionally exposed after a failure of N-myristoylation. Thus, an additional N-degron pathway specific for glycine regulates the stability of metazoan proteomes.
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Affiliation(s)
- Richard T Timms
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Zhiqian Zhang
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - David Y Rhee
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Itay Koren
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA. .,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA. .,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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24
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Park JS, Lee JY, Nguyen YTK, Kang NW, Oh EK, Jang DM, Kim HJ, Kim DD, Han BW. Structural Analyses on the Deamidation of N-Terminal Asn in the Human N-Degron Pathway. Biomolecules 2020; 10:biom10010163. [PMID: 31968674 PMCID: PMC7022378 DOI: 10.3390/biom10010163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/30/2019] [Accepted: 01/13/2020] [Indexed: 01/01/2023] Open
Abstract
The N-degron pathway is a proteolytic system in which a single N-terminal amino acid acts as a determinant of protein degradation. Especially, degradation signaling of N-terminal asparagine (Nt-Asn) in eukaryotes is initiated from its deamidation by N-terminal asparagine amidohydrolase 1 (NTAN1) into aspartate. Here, we have elucidated structural principles of deamidation by human NTAN1. NTAN1 adopts the characteristic scaffold of CNF1/YfiH-like cysteine hydrolases that features an α-β-β sandwich structure and a catalytic triad comprising Cys, His, and Ser. In vitro deamidation assays using model peptide substrates with varying lengths and sequences showed that NTAN1 prefers hydrophobic residues at the second-position. The structures of NTAN1-peptide complexes further revealed that the recognition of Nt-Asn is sufficiently organized to produce high specificity, and the side chain of the second-position residue is accommodated in a hydrophobic pocket adjacent to the active site of NTAN1. Collectively, our structural and biochemical analyses of the substrate specificity of NTAN1 contribute to understanding the structural basis of all three amidases in the eukaryotic N-degron pathway.
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Affiliation(s)
- Joon Sung Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Jae-Young Lee
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea;
| | - Yen Thi Kim Nguyen
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Nae-Won Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Eun Kyung Oh
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Dong Man Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Korea;
| | - Dae-Duk Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
- Correspondence: ; Tel.: +82-2-880-7899
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Chen SJ, Melnykov A, Varshavsky A. Evolution of Substrates and Components of the Pro/N-Degron Pathway. Biochemistry 2020; 59:582-593. [PMID: 31895557 DOI: 10.1021/acs.biochem.9b00953] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Gid4, a subunit of the ubiquitin ligase GID, is the recognition component of the Pro/N-degron pathway. Gid4 targets proteins in particular through their N-terminal (Nt) proline (Pro) residue. In Saccharomyces cerevisiae and other Saccharomyces yeasts, the gluconeogenic enzymes Fbp1, Icl1, and Mdh2 bear Nt-Pro and are conditionally destroyed by the Pro/N-degron pathway. However, in mammals and in many non-Saccharomyces yeasts, for example, in Kluyveromyces lactis, these enzymes lack Nt-Pro. We used K. lactis to explore evolution of the Pro/N-degron pathway. One question to be addressed was whether the presence of non-Pro Nt residues in K. lactis Fbp1, Icl1, and Mdh2 was accompanied, on evolutionary time scales (S. cerevisiae and K. lactis diverged ∼150 million years ago), by a changed specificity of the Gid4 N-recognin. We used yeast-based two-hybrid binding assays and protein-degradation assays to show that the non-Pro (Ala) Nt residue of K. lactis Fbp1 makes this enzyme long-lived in K. lactis. We also found that the replacement, through mutagenesis, of Nt-Ala and the next three residues of K. lactis Fbp1 with the four-residue Nt-PTLV sequence of S. cerevisiae Fbp1 sufficed to make the resulting "hybrid" Fbp1 a short-lived substrate of Gid4 in K. lactis. We consider a blend of quasi-neutral genetic drift and natural selection that can account for these and related results. To the best of our knowledge, this work is the first study of the ubiquitin system in K. lactis, including development of the first protein-degradation assay (based on the antibiotic blasticidin) suitable for use with this organism.
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Affiliation(s)
- Shun-Jia Chen
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - Artem Melnykov
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - Alexander Varshavsky
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
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Rageul J, Park JJ, Jo U, Weinheimer AS, Vu TTM, Kim H. Conditional degradation of SDE2 by the Arg/N-End rule pathway regulates stress response at replication forks. Nucleic Acids Res 2019; 47:3996-4010. [PMID: 30698750 PMCID: PMC6486553 DOI: 10.1093/nar/gkz054] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/24/2019] [Indexed: 12/14/2022] Open
Abstract
Multiple pathways counteract DNA replication stress to prevent genomic instability and tumorigenesis. The recently identified human SDE2 is a genome surveillance protein regulated by PCNA, a DNA clamp and processivity factor at replication forks. Here, we show that SDE2 cleavage after its ubiquitin-like domain generates Lys-SDE2Ct, the C-terminal SDE2 fragment bearing an N-terminal Lys residue. Lys-SDE2Ct constitutes a short-lived physiological substrate of the Arg/N-end rule proteolytic pathway, in which UBR1 and UBR2 ubiquitin ligases mediate the degradation. The Arg/N-end rule and VCP/p97UFD1-NPL4 segregase cooperate to promote phosphorylation-dependent, chromatin-associated Lys-SDE2Ct degradation upon UVC damage. Conversely, cells expressing the degradation-refractory K78V mutant, Val-SDE2Ct, fail to induce RPA phosphorylation and single-stranded DNA formation, leading to defects in PCNA-dependent DNA damage bypass and stalled fork recovery. Together, our study elucidates a previously unappreciated axis connecting the Arg/N-end rule and the p97-mediated proteolysis with the replication stress response, working together to preserve replication fork integrity.
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Affiliation(s)
- Julie Rageul
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jennifer J Park
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ukhyun Jo
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Alexandra S Weinheimer
- Biochemistry and Structural Biology graduate program, Stony Brook University, Stony Brook, NY 11794, USA
| | - Tri T M Vu
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA.,Stony Brook Cancer Center, Stony Brook School of Medicine, Stony Brook, NY 11794, USA
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Eldeeb MA, Fahlman RP, Ragheb MA, Esmaili M. Does N‐Terminal Protein Acetylation Lead to Protein Degradation? Bioessays 2019; 41:e1800167. [DOI: 10.1002/bies.201800167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 08/12/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Mohamed A. Eldeeb
- Department of Chemistry (Biochemistry Division)Faculty of ScienceCairo University Giza 12613 Egypt
- Department of Neurology and NeurosurgeryMontreal Neurological InstituteMcGill University Montreal Quebec H3A 2B4 Canada
| | - Richard P. Fahlman
- Department of BiochemistryUniversity of Alberta Edmonton Alberta T6G 2R3 Canada
| | - Mohamed A. Ragheb
- Department of Chemistry (Biochemistry Division)Faculty of ScienceCairo University Giza 12613 Egypt
| | - Mansoore Esmaili
- Department of BiochemistryUniversity of Alberta Edmonton Alberta T6G 2R3 Canada
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Abstract
Faithful duplication of the genome is critical for the survival of an organism and prevention of malignant transformation. Accurate replication of a large amount of genetic information in a timely manner is one of the most challenging cellular processes and is often perturbed by intrinsic and extrinsic barriers to DNA replication fork progression, a phenomenon referred to as DNA replication stress. Elevated DNA replication stress is a primary source of genomic instability and one of the key hallmarks of cancer. Therefore, targeting DNA replication stress is an emerging concept for cancer therapy. The replication machinery associated with PCNA and other regulatory factors coordinates the synthesis and repair of DNA strands at the replication fork. The dynamic interaction of replication protein complexes with DNA is essential for sensing and responding to various signaling events relevant to DNA replication and damage. Thus, the disruption of the spatiotemporal regulation of protein homeostasis at the replication fork impairs genome integrity, which often involves the deregulation of ubiquitin-mediated proteolytic signaling. Notably, emerging evidence has highlighted the role of the AAA+ATPase VCP/p97 in extracting ubiquitinated protein substrates from the chromatin and facilitating the turnover of genome surveillance factors during DNA replication and repair. Here, we review recent advances in our understanding of chromatin-associated degradation pathways at the replication fork and the implication of these findings for cancer therapy.
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Affiliation(s)
- Julie Rageul
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA
| | - Alexandra S Weinheimer
- Biochemistry and Structural Biology graduate program, Stony Brook University, New York 11794, USA
| | - Jennifer J Park
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA; Stony Brook Cancer Center, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, 11794, USA.
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Melnykov A, Chen SJ, Varshavsky A. Gid10 as an alternative N-recognin of the Pro/N-degron pathway. Proc Natl Acad Sci U S A 2019; 116:15914-15923. [PMID: 31337681 PMCID: PMC6689949 DOI: 10.1073/pnas.1908304116] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In eukaryotes, N-degron pathways (formerly "N-end rule pathways") comprise a set of proteolytic systems whose unifying feature is their ability to recognize proteins containing N-terminal degradation signals called N-degrons, thereby causing degradation of these proteins by the 26S proteasome or autophagy. Gid4, a subunit of the GID ubiquitin ligase in the yeast Saccharomyces cerevisiae, is the recognition component (N-recognin) of the GID-mediated Pro/N-degron pathway. Gid4 targets proteins by recognizing their N-terminal Pro residues or a Pro at position 2, in the presence of distinct adjoining sequence motifs. Under conditions of low or absent glucose, cells make it through gluconeogenesis. When S. cerevisiae grows on a nonfermentable carbon source, its gluconeogenic enzymes Fbp1, Icl1, Mdh2, and Pck1 are expressed and long-lived. Transition to a medium containing glucose inhibits the synthesis of these enzymes and induces their degradation by the Gid4-dependent Pro/N-degron pathway. While studying yeast Gid4, we identified a similar but uncharacterized yeast protein (YGR066C), which we named Gid10. A screen for N-terminal peptide sequences that can bind to Gid10 showed that substrate specificities of Gid10 and Gid4 overlap but are not identical. Gid10 is not expressed under usual (unstressful) growth conditions, but is induced upon starvation or osmotic stresses. Using protein binding analyses and degradation assays with substrates of GID, we show that Gid10 can function as a specific N-recognin of the Pro/N-degron pathway.
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Affiliation(s)
- Artem Melnykov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Shun-Jia Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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On the cause of sleep: Protein fragments, the concept of sentinels, and links to epilepsy. Proc Natl Acad Sci U S A 2019; 116:10773-10782. [PMID: 31085645 DOI: 10.1073/pnas.1904709116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The molecular-level cause of sleep is unknown. In 2012, we suggested that the cause of sleep stems from cumulative effects of numerous intracellular and extracellular protein fragments. According to the fragment generation (FG) hypothesis, protein fragments (which are continually produced through nonprocessive cleavages by intracellular, intramembrane, and extracellular proteases) can be beneficial but toxic as well, and some fragments are eliminated slowly during wakefulness. We consider the FG hypothesis and propose that, during wakefulness, the degradation of accumulating fragments is delayed within natural protein aggregates such as postsynaptic densities (PSDs) in excitatory synapses and in other dense protein meshworks, owing to an impeded diffusion of the ∼3,000-kDa 26S proteasome. We also propose that a major function of sleep involves a partial and reversible expansion of PSDs, allowing an accelerated destruction of PSD-localized fragments by the ubiquitin/proteasome system. Expansion of PSDs would alter electrochemistry of synapses, thereby contributing to a decreased neuronal firing during sleep. If so, the loss of consciousness, a feature of sleep, would be the consequence of molecular processes (expansions of protein meshworks) that are required for degradation of protein fragments. We consider the concept of FG sentinels, which signal to sleep-regulating circuits that the levels of fragments are going up. Also discussed is the possibility that protein fragments, which are known to be overproduced during an epileptic seizure, may contribute to postictal sleep and termination of seizures. These and related suggestions, described in the paper, are compatible with current evidence about sleep and lead to testable predictions.
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Abstract
This perspective is partly review and partly proposal. N-degrons and C-degrons are degradation signals whose main determinants are, respectively, the N-terminal and C-terminal residues of cellular proteins. N-degrons and C-degrons include, to varying extents, adjoining sequence motifs, and also internal lysine residues that function as polyubiquitylation sites. Discovered in 1986, N-degrons were the first degradation signals in short-lived proteins. A particularly large set of C-degrons was discovered in 2018. We describe multifunctional proteolytic systems that target N-degrons and C-degrons. We also propose to denote these systems as "N-degron pathways" and "C-degron pathways." The former notation replaces the earlier name "N-end rule pathways." The term "N-end rule" was introduced 33 years ago, when only some N-terminal residues were thought to be destabilizing. However, studies over the last three decades have shown that all 20 amino acids of the genetic code can act, in cognate sequence contexts, as destabilizing N-terminal residues. Advantages of the proposed terms include their brevity and semantic uniformity for N-degrons and C-degrons. In addition to being topologically analogous, N-degrons and C-degrons are related functionally. A proteolytic cleavage of a subunit in a multisubunit complex can create, at the same time, an N-degron (in a C-terminal fragment) and a spatially adjacent C-degron (in an N-terminal fragment). Consequently, both fragments of a subunit can be selectively destroyed through attacks by the N-degron and C-degron pathways.
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Lin HC, Yeh CW, Chen YF, Lee TT, Hsieh PY, Rusnac DV, Lin SY, Elledge SJ, Zheng N, Yen HCS. C-Terminal End-Directed Protein Elimination by CRL2 Ubiquitin Ligases. Mol Cell 2019; 70:602-613.e3. [PMID: 29775578 DOI: 10.1016/j.molcel.2018.04.006] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/12/2018] [Accepted: 04/05/2018] [Indexed: 12/31/2022]
Abstract
The proteolysis-assisted protein quality control system guards the proteome from potentially detrimental aberrant proteins. How miscellaneous defective proteins are specifically eliminated and which molecular characteristics direct them for removal are fundamental questions. We reveal a mechanism, DesCEND (destruction via C-end degrons), by which CRL2 ubiquitin ligase uses interchangeable substrate receptors to recognize the unusual C termini of abnormal proteins (i.e., C-end degrons). C-end degrons are mostly less than ten residues in length and comprise a few indispensable residues along with some rather degenerate ones. The C-terminal end position is essential for C-end degron function. Truncated selenoproteins generated by translation errors and the USP1 N-terminal fragment from post-translational cleavage are eliminated by DesCEND. DesCEND also targets full-length proteins with naturally occurring C-end degrons. The C-end degron in DesCEND echoes the N-end degron in the N-end rule pathway, highlighting the dominance of protein "ends" as indicators for protein elimination.
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Affiliation(s)
- Hsiu-Chuan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Chi-Wei Yeh
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yen-Fu Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ting-Ting Lee
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Pei-Yun Hsieh
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Domnita V Rusnac
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Sung-Ya Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Stephen J Elledge
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ning Zheng
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Hsueh-Chi S Yen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan.
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33
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Vicente J, Mendiondo GM, Pauwels J, Pastor V, Izquierdo Y, Naumann C, Movahedi M, Rooney D, Gibbs DJ, Smart K, Bachmair A, Gray JE, Dissmeyer N, Castresana C, Ray RV, Gevaert K, Holdsworth MJ. Distinct branches of the N-end rule pathway modulate the plant immune response. THE NEW PHYTOLOGIST 2019; 221:988-1000. [PMID: 30117535 DOI: 10.1111/nph.15387] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/11/2018] [Indexed: 05/24/2023]
Abstract
The N-end rule pathway is a highly conserved constituent of the ubiquitin proteasome system, yet little is known about its biological roles. Here we explored the role of the N-end rule pathway in the plant immune response. We investigated the genetic influences of components of the pathway and known protein substrates on physiological, biochemical and metabolic responses to pathogen infection. We show that the glutamine (Gln) deamidation and cysteine (Cys) oxidation branches are both components of the plant immune system, through the E3 ligase PROTEOLYSIS (PRT)6. In Arabidopsis thaliana Gln-specific amino-terminal (Nt)-amidase (NTAQ1) controls the expression of specific defence-response genes, activates the synthesis pathway for the phytoalexin camalexin and influences basal resistance to the hemibiotroph pathogen Pseudomonas syringae pv tomato (Pst). The Nt-Cys ETHYLENE RESPONSE FACTOR VII transcription factor substrates enhance pathogen-induced stomatal closure. Transgenic barley with reduced HvPRT6 expression showed enhanced resistance to Ps. japonica and Blumeria graminis f. sp. hordei, indicating a conserved role of the pathway. We propose that that separate branches of the N-end rule pathway act as distinct components of the plant immune response in flowering plants.
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Affiliation(s)
- Jorge Vicente
- School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | | | - Jarne Pauwels
- VIB-UGent Center for Medical Biotechnology, Albert Baertsoenkaai 3, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Ghent, Belgium
| | - Victoria Pastor
- Área de Fisiología Vegetal, Departamento de Ciencias Agrarias y del Medio Natural, Universitat Jaume I, Castellón, E-12071, Spain
| | - Yovanny Izquierdo
- Centro National de Biotecnología CSIC, C/Darwin, 3, Campus of Cantoblanco, E-28049, Madrid, Spain
| | - Christin Naumann
- Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, D-06120, Halle (Saale), Germany
- Science Campus Halle - Plant-Based Bioeconomy, 06120 Halle (Saale), Germany
| | - Mahsa Movahedi
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Daniel Rooney
- School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Daniel J Gibbs
- School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Katherine Smart
- SABMiller Plc, SABMiller House, Church Street West, Woking, GU21 6HS, UK
| | - Andreas Bachmair
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9, Vienna, A-1030, Austria
| | - Julie E Gray
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Nico Dissmeyer
- Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, D-06120, Halle (Saale), Germany
- Science Campus Halle - Plant-Based Bioeconomy, 06120 Halle (Saale), Germany
| | - Carmen Castresana
- Centro National de Biotecnología CSIC, C/Darwin, 3, Campus of Cantoblanco, E-28049, Madrid, Spain
| | - Rumiana V Ray
- School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Albert Baertsoenkaai 3, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Ghent, Belgium
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Regulating Apoptosis by Degradation: The N-End Rule-Mediated Regulation of Apoptotic Proteolytic Fragments in Mammalian Cells. Int J Mol Sci 2018; 19:ijms19113414. [PMID: 30384441 PMCID: PMC6274719 DOI: 10.3390/ijms19113414] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/24/2018] [Accepted: 10/27/2018] [Indexed: 12/13/2022] Open
Abstract
A pivotal hallmark of some cancer cells is the evasion of apoptotic cell death. Importantly, the initiation of apoptosis often results in the activation of caspases, which, in turn, culminates in the generation of proteolytically-activated protein fragments with potentially new or altered roles. Recent investigations have revealed that the activity of a significant number of the protease-generated, activated, pro-apoptotic protein fragments can be curbed via their selective degradation by the N-end rule degradation pathways. Of note, previous work revealed that several proteolytically-generated, pro-apoptotic fragments are unstable in cells, as their destabilizing N-termini target them for proteasomal degradation via the N-end rule degradation pathways. Remarkably, previous studies also showed that the proteolytically-generated anti-apoptotic Lyn kinase protein fragment is targeted for degradation by the UBR1/UBR2 E3 ubiquitin ligases of the N-end rule pathway in chronic myeloid leukemia cells. Crucially, the degradation of cleaved fragment of Lyn by the N-end rule counters imatinib resistance in these cells, implicating a possible linkage between the N-end rule degradation pathway and imatinib resistance. Herein, we highlight recent studies on the role of the N-end rule proteolytic pathways in regulating apoptosis in mammalian cells, and also discuss some possible future directions with respect to apoptotic proteolysis signaling.
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35
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Dissmeyer N, Rivas S, Graciet E. Life and death of proteins after protease cleavage: protein degradation by the N-end rule pathway. THE NEW PHYTOLOGIST 2018; 218:929-935. [PMID: 28581033 DOI: 10.1111/nph.14619] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
UNLABELLED Contents Summary 929 I. INTRODUCTION conservation and diversity of N-end rule pathways 929 II. Defensive functions of the N-end rule pathway in plants 930 III. Proteases and degradation by the N-end rule pathway 930 IV. New proteomics approaches for the identification of N-end rule substrates 932 V. Concluding remarks 932 Acknowledgements 934 References 934 SUMMARY: The N-end rule relates the stability of a protein to the identity of its N-terminal residue and some of its modifications. Since its discovery in the 1980s, the repertoire of N-terminal degradation signals has expanded, leading to a diversity of N-end rule pathways. Although some of these newly discovered N-end rule pathways remain largely unexplored in plants, recent discoveries have highlighted roles of N-end rule-mediated protein degradation in plant defense against pathogens and in cell proliferation during organ growth. Despite this progress, a bottleneck remains the proteome-wide identification of N-end rule substrates due to the prerequisite for endoproteolytic cleavage and technical limitations. Here, we discuss the recent diversification of N-end rule pathways and their newly discovered functions in plant defenses, stressing the role of proteases. We expect that novel proteomics techniques (N-terminomics) will be essential for substrate identification. We review these methods, their limitations and future developments.
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Affiliation(s)
- Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, Halle (Saale), D-06120, Germany
- ScienceCampus Halle - Plant-based Bioeconomy, Betty-Heimann-Strasse 3, Halle (Saale), D-06120, Germany
| | - Susana Rivas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, 31 326, France
| | - Emmanuelle Graciet
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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36
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Eldeeb MA, Leitao LCA, Fahlman RP. Emerging branches of the N-end rule pathways are revealing the sequence complexities of N-termini dependent protein degradation. Biochem Cell Biol 2017; 96:289-294. [PMID: 29253354 DOI: 10.1139/bcb-2017-0274] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The N-end rule links the identity of the N-terminal amino acid of a protein to its in vivo half-life, as some N-terminal residues confer metabolic instability to a protein via their recognition by the cellular machinery that targets them for degradation. Since its discovery, the N-end rule has generally been defined as set of rules of whether an N-terminal residue is stabilizing or not. However, recent studies are revealing that the N-terminal code of amino acids conferring protein instability is more complex than previously appreciated, as recent investigations are revealing that the identity of adjoining downstream residues can also influence the metabolic stability of N-end rule substrate. This is exemplified by the recent discovery of a new branch of N-end rule pathways that target proteins bearing N-terminal proline. In addition, recent investigations are demonstrating that the molecular machinery in N-termini dependent protein degradation may also target proteins for lysosomal degradation, in addition to proteasome-dependent degradation. Herein, we describe some of the recent advances in N-end rule pathways and discuss some of the implications regarding the emerging additional sequence requirements.
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Affiliation(s)
- Mohamed A Eldeeb
- a Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.,b Department of Chemistry, Faculty of Science, Cairo University, Giza, Cairo, Egypt
| | - Luana C A Leitao
- a Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Richard P Fahlman
- a Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.,c Department of Oncology, University of Alberta, Edmonton, AB T6G 2H7, Canada
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37
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Hedglin M, Benkovic SJ. Eukaryotic Translesion DNA Synthesis on the Leading and Lagging Strands: Unique Detours around the Same Obstacle. Chem Rev 2017; 117:7857-7877. [PMID: 28497687 PMCID: PMC5662946 DOI: 10.1021/acs.chemrev.7b00046] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
During S-phase, minor DNA damage may be overcome by DNA damage tolerance (DDT) pathways that bypass such obstacles, postponing repair of the offending damage to complete the cell cycle and maintain cell survival. In translesion DNA synthesis (TLS), specialized DNA polymerases replicate the damaged DNA, allowing stringent DNA synthesis by a replicative polymerase to resume beyond the offending damage. Dysregulation of this DDT pathway in human cells leads to increased mutation rates that may contribute to the onset of cancer. Furthermore, TLS affords human cancer cells the ability to counteract chemotherapeutic agents that elicit cell death by damaging DNA in actively replicating cells. Currently, it is unclear how this critical pathway unfolds, in particular, where and when TLS occurs on each template strand. Given the semidiscontinuous nature of DNA replication, it is likely that TLS on the leading and lagging strand templates is unique for each strand. Since the discovery of DDT in the late 1960s, most studies on TLS in eukaryotes have focused on DNA lesions resulting from ultraviolet (UV) radiation exposure. In this review, we revisit these and other related studies to dissect the step-by-step intricacies of this complex process, provide our current understanding of TLS on leading and lagging strand templates, and propose testable hypotheses to gain further insights.
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Affiliation(s)
- Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Stephen J. Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, U.S.A
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38
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Abstract
Ubiquitin E3 ligases control every aspect of eukaryotic biology by promoting protein ubiquitination and degradation. At the end of a three-enzyme cascade, ubiquitin ligases mediate the transfer of ubiquitin from an E2 ubiquitin-conjugating enzyme to specific substrate proteins. Early investigations of E3s of the RING (really interesting new gene) and HECT (homologous to the E6AP carboxyl terminus) types shed light on their enzymatic activities, general architectures, and substrate degron-binding modes. Recent studies have provided deeper mechanistic insights into their catalysis, activation, and regulation. In this review, we summarize the current progress in structure-function studies of ubiquitin ligases as well as exciting new discoveries of novel classes of E3s and diverse substrate recognition mechanisms. Our increased understanding of ubiquitin ligase function and regulation has provided the rationale for developing E3-targeting therapeutics for the treatment of human diseases.
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Affiliation(s)
- Ning Zheng
- Howard Hughes Medical Institute and Department of Pharmacology, University of Washington, Seattle, Washington 98195; ,
| | - Nitzan Shabek
- Howard Hughes Medical Institute and Department of Pharmacology, University of Washington, Seattle, Washington 98195; ,
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39
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Leznicki P, Kulathu Y. Mechanisms of regulation and diversification of deubiquitylating enzyme function. J Cell Sci 2017; 130:1997-2006. [PMID: 28476940 DOI: 10.1242/jcs.201855] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Deubiquitylating (or deubiquitinating) enzymes (DUBs) are proteases that reverse protein ubiquitylation and therefore modulate the outcome of this post-translational modification. DUBs regulate a variety of intracellular processes, including protein turnover, signalling pathways and the DNA damage response. They have also been linked to a number of human diseases, such as cancer, and inflammatory and neurodegenerative disorders. Although we are beginning to better appreciate the role of DUBs in basic cell biology and their importance for human health, there are still many unknowns. Central among these is the conundrum of how the small number of ∼100 DUBs encoded in the human genome is capable of regulating the thousands of ubiquitin modification sites detected in human cells. This Commentary addresses the biological mechanisms employed to modulate and expand the functions of DUBs, and sets directions for future research aimed at elucidating the details of these fascinating processes.This article is part of a Minifocus on Ubiquitin Regulation and Function. For further reading, please see related articles: 'Exploitation of the host cell ubiquitin machinery by microbial effector proteins' by Yi-Han Lin and Matthias P. Machner (J. Cell Sci.130, 1985-1996). 'Cell scientist to watch - Mads Gyrd-Hansen' (J. Cell Sci.130, 1981-1983).
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Affiliation(s)
- Pawel Leznicki
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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40
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Domitrovic T, Fausto AK, Silva TDF, Romanel E, Vaslin MFS. Plant arginyltransferases (ATEs). Genet Mol Biol 2017; 40:253-260. [PMID: 28199445 PMCID: PMC5452128 DOI: 10.1590/1678-4685-gmb-2016-0084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/16/2016] [Indexed: 12/03/2022] Open
Abstract
Regulation of protein stability and/or degradation of misfolded and damaged proteins are essential cellular processes. A part of this regulation is mediated by the so-called N-end rule proteolytic pathway, which, in concert with the ubiquitin proteasome system (UPS), drives protein degradation depending on the N-terminal amino acid sequence. One important enzyme involved in this process is arginyl-t-RNA transferase, known as ATE. This enzyme acts post-translationally by introducing an arginine residue at the N-terminus of specific protein targets to signal degradation via the UPS. However, the function of ATEs has only recently begun to be revealed. Nonetheless, the few studies to date investigating ATE activity in plants points to the great importance of the ATE/N-end rule pathway in regulating plant signaling. Plant development, seed germination, leaf morphology and responses to gas signaling in plants are among the processes affected by the ATE/N-end rule pathway. In this review, we present some of the known biological functions of plant ATE proteins, highlighting the need for more in-depth studies on this intriguing pathway.
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Affiliation(s)
- Tatiana Domitrovic
- Laboratório de Virologia Molecular Vegetal, Departamento de Virologia IMPPG, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Anna K Fausto
- Laboratório de Virologia Molecular Vegetal, Departamento de Virologia IMPPG, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Tatiane da F Silva
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP, Brazil
| | - Elisson Romanel
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP, Brazil
| | - Maite F S Vaslin
- Laboratório de Virologia Molecular Vegetal, Departamento de Virologia IMPPG, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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41
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Tan JL, Ward L, Truscott KN, Dougan DA. The N‐end rule adaptor protein ClpS from
Plasmodium falciparum
exhibits broad substrate specificity. FEBS Lett 2016; 590:3397-3406. [DOI: 10.1002/1873-3468.12382] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/25/2016] [Accepted: 08/28/2016] [Indexed: 01/11/2023]
Affiliation(s)
- Ju Lin Tan
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne Australia
| | - Linda Ward
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne Australia
| | - Kaye N. Truscott
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne Australia
| | - David A. Dougan
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne Australia
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42
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Wadas B, Piatkov KI, Brower CS, Varshavsky A. Analyzing N-terminal Arginylation through the Use of Peptide Arrays and Degradation Assays. J Biol Chem 2016; 291:20976-20992. [PMID: 27510035 DOI: 10.1074/jbc.m116.747956] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 01/29/2023] Open
Abstract
Nα-terminal arginylation (Nt-arginylation) of proteins is mediated by the Ate1 arginyltransferase (R-transferase), a component of the Arg/N-end rule pathway. This proteolytic system recognizes proteins containing N-terminal degradation signals called N-degrons, polyubiquitylates these proteins, and thereby causes their degradation by the proteasome. The definitively identified ("canonical") residues that are Nt-arginylated by R-transferase are N-terminal Asp, Glu, and (oxidized) Cys. Over the last decade, several publications have suggested (i) that Ate1 can also arginylate non-canonical N-terminal residues; (ii) that Ate1 is capable of arginylating not only α-amino groups of N-terminal residues but also γ-carboxyl groups of internal (non-N-terminal) Asp and Glu; and (iii) that some isoforms of Ate1 are specific for substrates bearing N-terminal Cys residues. In the present study, we employed arrays of immobilized 11-residue peptides and pulse-chase assays to examine the substrate specificity of mouse R-transferase. We show that amino acid sequences immediately downstream of a substrate's canonical (Nt-arginylatable) N-terminal residue, particularly a residue at position 2, can affect the rate of Nt-arginylation by R-transferase and thereby the rate of degradation of a substrate protein. We also show that the four major isoforms of mouse R-transferase have similar Nt-arginylation specificities in vitro, contrary to the claim about the specificity of some Ate1 isoforms for N-terminal Cys. In addition, we found no evidence for a significant activity of the Ate1 R-transferase toward previously invoked non-canonical N-terminal or internal amino acid residues. Together, our results raise technical concerns about earlier studies that invoked non-canonical arginylation specificities of Ate1.
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Affiliation(s)
- Brandon Wadas
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Konstantin I Piatkov
- the Center for Biotechnology and Biomedicine, Skolkovo Institute of Science and Technology, Moscow 143026, Russia, and
| | | | - Alexander Varshavsky
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125,
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43
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McClurg UL, Robson CN. Deubiquitinating enzymes as oncotargets. Oncotarget 2016; 6:9657-68. [PMID: 25962961 PMCID: PMC4496387 DOI: 10.18632/oncotarget.3922] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 04/08/2015] [Indexed: 12/19/2022] Open
Abstract
Carcinogenesis is a complex process tightly regulated at multiple levels by post-translational modifications. Epigenetics plays a major role in cancer development, all stable changes to the gene expression process that are not a result of a direct change in the DNA code are described as epigenetics. Epigenetic processes are regulated by post-translational modifications including ubiquitination which can directly affect either histones or transcription factors or may target their co-factors and interacting partners exerting an indirect effect. Deubiquitination of these target proteins is equally important and alterations in this pathway can also lead to cancer development, progression and metastasis. Only the correct, unaltered balance between ubiquitination and deubiquitination ensures healthy cellular homeostasis. In this review we focus on the role of deubiquitinating (DUB) enzymes in various aspects of epigenetics including the regulation of transcription factors, histone modifications, DNA damage repair pathways and cell cycle regulation. We discuss the impact of those processes on tumourigenesis and potential therapeutic applications of DUBs for cancer treatment.
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Affiliation(s)
- Urszula L McClurg
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Craig N Robson
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
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44
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Piatkov KI, Vu TTM, Hwang CS, Varshavsky A. Formyl-methionine as a degradation signal at the N-termini of bacterial proteins. MICROBIAL CELL (GRAZ, AUSTRIA) 2016; 2:376-393. [PMID: 26866044 PMCID: PMC4745127 DOI: 10.15698/mic2015.10.231] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 08/17/2015] [Indexed: 02/04/2023]
Abstract
In bacteria, all nascent proteins bear the pretranslationally formed N-terminal formyl-methionine (fMet) residue. The fMet residue is cotranslationally deformylated by a ribosome-associated deformylase. The formylation of N-terminal Met in bacterial proteins is not strictly essential for either translation or cell viability. Moreover, protein synthesis by the cytosolic ribosomes of eukaryotes does not involve the formylation of N-terminal Met. What, then, is the main biological function of this metabolically costly, transient, and not strictly essential modification of N-terminal Met, and why has Met formylation not been eliminated during bacterial evolution? One possibility is that the similarity of the formyl and acetyl groups, their identical locations in N-terminally formylated (Nt-formylated) and Nt-acetylated proteins, and the recently discovered proteolytic function of Nt-acetylation in eukaryotes might also signify a proteolytic role of Nt-formylation in bacteria. We addressed this hypothesis about fMet-based degradation signals, termed fMet/N-degrons, using specific E. coli mutants, pulse-chase degradation assays, and protein reporters whose deformylation was altered, through site-directed mutagenesis, to be either rapid or relatively slow. Our findings strongly suggest that the formylated N-terminal fMet can act as a degradation signal, largely a cotranslational one. One likely function of fMet/N-degrons is the control of protein quality. In bacteria, the rate of polypeptide chain elongation is nearly an order of magnitude higher than in eukaryotes. We suggest that the faster emergence of nascent proteins from bacterial ribosomes is one mechanistic and evolutionary reason for the pretranslational design of bacterial fMet/N-degrons, in contrast to the cotranslational design of analogous Ac/N-degrons in eukaryotes.
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Affiliation(s)
- Konstantin I. Piatkov
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
- Center for Biotechnology and Biomedicine, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Tri T. M. Vu
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 790-784, South Korea
| | - Alexander Varshavsky
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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45
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Liu YJ, Liu C, Chang Z, Wadas B, Brower CS, Song ZH, Xu ZL, Shang YL, Liu WX, Wang LN, Dong W, Varshavsky A, Hu RG, Li W. Degradation of the Separase-cleaved Rec8, a Meiotic Cohesin Subunit, by the N-end Rule Pathway. J Biol Chem 2016; 291:7426-38. [PMID: 26858254 DOI: 10.1074/jbc.m116.714964] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Indexed: 02/05/2023] Open
Abstract
The Ate1 arginyltransferase (R-transferase) is a component of the N-end rule pathway, which recognizes proteins containing N-terminal degradation signals called N-degrons, polyubiquitylates these proteins, and thereby causes their degradation by the proteasome. Ate1 arginylates N-terminal Asp, Glu, or (oxidized) Cys. The resulting N-terminal Arg is recognized by ubiquitin ligases of the N-end rule pathway. In the yeastSaccharomyces cerevisiae, the separase-mediated cleavage of the Scc1/Rad21/Mcd1 cohesin subunit generates a C-terminal fragment that bears N-terminal Arg and is destroyed by the N-end rule pathway without a requirement for arginylation. In contrast, the separase-mediated cleavage of Rec8, the mammalian meiotic cohesin subunit, yields a fragment bearing N-terminal Glu, a substrate of the Ate1 R-transferase. Here we constructed and used a germ cell-confinedAte1(-/-)mouse strain to analyze the separase-generated C-terminal fragment of Rec8. We show that this fragment is a short-lived N-end rule substrate, that its degradation requires N-terminal arginylation, and that maleAte1(-/-)mice are nearly infertile, due to massive apoptotic death ofAte1(-/-)spermatocytes during the metaphase of meiosis I. These effects ofAte1ablation are inferred to be caused, at least in part, by the failure to destroy the C-terminal fragment of Rec8 in the absence of N-terminal arginylation.
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Affiliation(s)
- Yu-Jiao Liu
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China, the College of Marine Life, Ocean University of China, Qingdao 266003, China, and
| | - Chao Liu
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China, the University of the Chinese Academy of Sciences, Beijing 100049, China
| | - ZeNan Chang
- the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Brandon Wadas
- the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Christopher S Brower
- the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, the Department of Biology, Texas Woman's University, Denton, Texas 76204
| | - Zhen-Hua Song
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China, the University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi-Liang Xu
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China, the University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Liang Shang
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China, the University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Xiao Liu
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li-Na Wang
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China, the University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wen Dong
- the College of Marine Life, Ocean University of China, Qingdao 266003, China, and
| | - Alexander Varshavsky
- the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125,
| | - Rong-Gui Hu
- the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wei Li
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China,
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46
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Kim M, Kim JM. The role of USP1 autocleavage in DNA interstrand crosslink repair. FEBS Lett 2016; 590:340-8. [DOI: 10.1002/1873-3468.12060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 12/22/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Mira Kim
- Department of Pharmacology; Medical Research Center for Gene Regulation; Chonnam National University Medical School; Gwangju Korea
| | - Jung Min Kim
- Department of Pharmacology; Medical Research Center for Gene Regulation; Chonnam National University Medical School; Gwangju Korea
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47
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Abstract
Both proteolytic and nonproteolytic functions of ubiquitination are essential regulatory mechanisms for promoting DNA repair and the DNA damage response in mammalian cells. Deubiquitinating enzymes (DUBs) have emerged as key players in the maintenance of genome stability. In this minireview, we discuss the recent findings on human DUBs that participate in genome maintenance, with a focus on the role of DUBs in the modulation of DNA repair and DNA damage signaling.
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Abstract
Fanconi anemia (FA) is a rare recessive genetic disease characterized by congenital abnormalities, bone marrow failure and heightened cancer susceptibility in early adulthood. FA is caused by biallelic germ-line mutation of any one of 16 genes. While several functions for the FA proteins have been ascribed, the prevailing hypothesis is that the FA proteins function cooperatively in the FA-BRCA pathway to repair damaged DNA. A pivotal step in the activation of the FA-BRCA pathway is the monoubiquitination of the FANCD2 and FANCI proteins. Despite their importance for DNA repair, the domain structure, regulation, and function of FANCD2 and FANCI remain poorly understood. In this review, we provide an overview of our current understanding of FANCD2 and FANCI, with an emphasis on their posttranslational modification and common and unique functions.
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Key Words
- AML , acute myeloid leukemia
- APC/C, anaphase-promoting complex/cyclosome
- APH, aphidicolin
- ARM, armadillo repeat domain
- AT, ataxia-telangiectasia
- ATM, ataxia-telangiectasia mutated
- ATR, ATM and Rad3-related
- BAC, bacterial-artificial-chromosome
- BS, Bloom syndrome
- CUE, coupling of ubiquitin conjugation to endoplasmic reticulum degradation
- ChIP-seq, CHIP sequencing
- CtBP, C-terminal binding protein
- CtIP, CtBP-interacting protein
- DNA interstrand crosslink repair
- DNA repair
- EPS15, epidermal growth factor receptor pathway substrate 15
- FA, Fanconi anemia
- FAN1, FANCD2-associated nuclease1
- FANCD2
- FANCI
- FISH, fluorescence in situ hybridization
- Fanconi anemia
- HECT, homologous to E6-AP Carboxy Terminus
- HJ, Holliday junction
- HR, homologous recombination
- MCM2-MCM7, minichromosome maintenance 2–7
- MEFs, mouse embryonic fibroblasts
- MMC, mitomycin C
- MRN, MRE11/RAD50/NBS1
- NLS, nuclear localization signal
- PCNA, proliferating cell nuclear antigen
- PIKK, phosphatidylinositol-3-OH-kinase-like family of protein kinases
- PIP-box, PCNA-interacting protein motif
- POL κ, DNA polymerase κ
- RACE, rapid amplification of cDNA ends
- RING, really interesting new gene
- RTK, receptor tyrosine kinase
- SCF, Skp1/Cullin/F-box protein complex
- SCKL1, seckel syndrome
- SILAC, stable isotope labeling with amino acids in cell culture
- SLD1/SLD2, SUMO-like domains
- SLIM, SUMO-like domain interacting motif
- TIP60, 60 kDa Tat-interactive protein
- TLS, Translesion DNA synthesis
- UAF1, USP1-associated factor 1
- UBD, ubiquitin-binding domain
- UBZ, ubiquitin-binding zinc finger
- UFB, ultra-fine DNA bridges
- UIM, ubiquitin-interacting motif
- ULD, ubiquitin-like domain
- USP1, ubiquitin-specific protease 1
- VRR-nuc, virus-type replication repair nuclease
- iPOND, isolation of proteins on nascent DNA
- ubiquitin
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Affiliation(s)
- Rebecca A Boisvert
- a Department of Cell and Molecular Biology ; University of Rhode Island ; Kingston , RI USA
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Park SE, Kim JM, Seok OH, Cho H, Wadas B, Kim SY, Varshavsky A, Hwang CS. Control of mammalian G protein signaling by N-terminal acetylation and the N-end rule pathway. Science 2015; 347:1249-1252. [PMID: 25766235 PMCID: PMC4748709 DOI: 10.1126/science.aaa3844] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Rgs2, a regulator of G proteins, lowers blood pressure by decreasing signaling through Gαq. Human patients expressing Met-Leu-Rgs2 (ML-Rgs2) or Met-Arg-Rgs2 (MR-Rgs2) are hypertensive relative to people expressing wild-type Met-Gln-Rgs2 (MQ-Rgs2). We found that wild-type MQ-Rgs2 and its mutant, MR-Rgs2, were destroyed by the Ac/N-end rule pathway, which recognizes N(α)-terminally acetylated (Nt-acetylated) proteins. The shortest-lived mutant, ML-Rgs2, was targeted by both the Ac/N-end rule and Arg/N-end rule pathways. The latter pathway recognizes unacetylated N-terminal residues. Thus, the Nt-acetylated Ac-MX-Rgs2 (X = Arg, Gln, Leu) proteins are specific substrates of the mammalian Ac/N-end rule pathway. Furthermore, the Ac/N-degron of Ac-MQ-Rgs2 was conditional, and Teb4, an endoplasmic reticulum (ER) membrane-embedded ubiquitin ligase, was able to regulate G protein signaling by targeting Ac-MX-Rgs2 proteins for degradation through their N(α)-terminal acetyl group.
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Affiliation(s)
- Sang-Eun Park
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Jeong-Mok Kim
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Ok-Hee Seok
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Hanna Cho
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Brandon Wadas
- Division of Biology and Biological Engineering, California Institute
of Technology, Pasadena, CA 91125, USA
| | - Seon-Young Kim
- Medical Genomics Research Center, KRIBB, Daejeon, South Korea
- Department of Functional Genomics, University of Science and
Technology, Daejeon, South Korea
| | - Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute
of Technology, Pasadena, CA 91125, USA
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang, Gyeongbuk 790-784, South Korea
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50
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Eldeeb MA, Fahlman RP. The anti-apoptotic form of tyrosine kinase Lyn that is generated by proteolysis is degraded by the N-end rule pathway. Oncotarget 2015; 5:2714-22. [PMID: 24798867 PMCID: PMC4058039 DOI: 10.18632/oncotarget.1931] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The activation of apoptotic pathways results in the caspase cleavage of the Lyn tyrosine kinase to generate the N-terminal truncated LynΔN. This LynΔN fragment has been demonstrated to exert negative feedback on imatinib induced apoptosis in chronic myelogenous leukemia (CML) K562 cells. Our investigations focus on LynΔN stability and how reduced stability reduces imatinib resistance. As the proteolytical generated LynΔN has a leucine as an N-terminal amino acid, we hypothesized that LynΔN would be degraded by the N-end rule pathway. We demonstrated that LynΔN is unstable and that its stability is dependent on the identity of its N-terminus. Additionally we established that LynΔN degradation could be inhibited by either inhibiting the proteasome or knocking down the UBR1 and UBR2 ubiquitin E3 ligases. Importantly, we also demonstrate that LynΔN degradation by the N-end rule counters the imatinib resistance of K562 cells provided by LynΔN expression. Together our data suggest a possible mechanism for the N-end rule pathway having a link to imatinib resistance in CML. With LynΔN being an N-end rule substrate, it provides the first example that this pathway can also provide a pro-apoptotic function as previous reports have currently only demonstrated anti-apoptotic roles for the N-end rule pathway.
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Affiliation(s)
- Mohamed A Eldeeb
- Department of Biochemistry, University of Alberta, Edmonton Alberta Canada
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