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Davis Z, Coyle K, Park MK, Oren T, Hartley T, Umphlett A, Monahan J, Light K, Hunter K, Choi YS. A Modular Biosensor Design for Quantitative Measurement of Free Nedd8. ACS Sens 2024; 9:4740-4747. [PMID: 39253816 PMCID: PMC11443517 DOI: 10.1021/acssensors.4c01130] [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: 05/12/2024] [Revised: 08/23/2024] [Accepted: 09/04/2024] [Indexed: 09/11/2024]
Abstract
The objective of our study was to develop a genetically encoded biosensor for quantification of Nedd8, a post-translational modifier that regulates cellular signals through conjugation to other proteins. Perturbations in the balance of free (i.e., unconjugated) and conjugated Nedd8 caused by defects in Nedd8 enzymes or cellular stress are implicated in various diseases. Despite the biological and biomedical importance of Nedd8 dynamics, no method exists for direct quantification of free Nedd8, hindering the study of Nedd8 and activities of its associated enzymes. Genetically encoded biosensors are established as tools to study other dynamic systems, but limitations of current biosensor design methods make them poorly suited for free Nedd8 quantification. We have developed a modular method to design genetically encoded biosensors that employs a target binding domain and two reporter domains positioned on opposite sides of the target binding site. Target quantification is based on competition between target binding and the interaction of the reporter domains. We applied our design strategy to free Nedd8 quantification by developing a selective binder for free Nedd8 and combining it with fluorescent or split nanoluciferase reporters. Our sensors produced quantifiable and specific signals for free Nedd8 and enabled real-time monitoring of deneddylation by DEN1 with a physiological substrate. Our sensor design will be useful for high-throughput screening for deneddylation inhibitors, which have potential in treatment of cancers such as acute lymphoblastic leukemia. The modular design strategy can be extended to develop genetically encoded quantitative biosensors for other proteins of interest.
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Affiliation(s)
- Zachary
Wyatt Davis
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
| | - Korbyn Coyle
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
| | - Min Kyung Park
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
| | - Tara Oren
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
| | - Teagen Hartley
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
| | - Alyssa Umphlett
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
| | - Jessilyn Monahan
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
| | - Kylie Light
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
| | - Kaylyn Hunter
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
| | - Yun-Seok Choi
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
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Li Y, Perez-Gil J, Lois LM, Varejão N, Reverter D. Broad-spectrum ubiquitin/ubiquitin-like deconjugation activity of the rhizobial effector NopD from Bradyrhizobium (sp. XS1150). Commun Biol 2024; 7:644. [PMID: 38802699 PMCID: PMC11130253 DOI: 10.1038/s42003-024-06344-w] [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: 01/25/2024] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
The post-translational modification of proteins by ubiquitin-like modifiers (UbLs), such as SUMO, ubiquitin, and Nedd8, regulates a vast array of cellular processes. Dedicated UbL deconjugating proteases families reverse these modifications. During bacterial infection, effector proteins, including deconjugating proteases, are released to disrupt host cell defenses and promote bacterial survival. NopD, an effector protein from rhizobia involved in legume nodule symbiosis, exhibits deSUMOylation activity and, unexpectedly, also deubiquitination and deNeddylation activities. Here, we present two crystal structures of Bradyrhizobium (sp. XS1150) NopD complexed with either Arabidopsis SUMO2 or ubiquitin at 1.50 Å and 1.94 Å resolution, respectively. Despite their low sequence similarity, SUMO and ubiquitin bind to a similar NopD interface, employing a unique loop insertion in the NopD sequence. In vitro binding and activity assays reveal specific residues that distinguish between deubiquitination and deSUMOylation. These unique multifaceted deconjugating activities against SUMO, ubiquitin, and Nedd8 exemplify an optimized bacterial protease that disrupts distinct UbL post-translational modifications during host cell infection.
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Affiliation(s)
- Ying Li
- Institut de Biotecnologia i de Biomedicina and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
- Qingdao University, 266071, Qingdao, China
| | - Jordi Perez-Gil
- Center for Research in Agricultural Genomics-CRAG, Edifici CRAG-Campus UAB, 08193, Bellaterra, Barcelona, Spain
- ARC Centre of Excellence in Synthetic Biology and Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - L Maria Lois
- Center for Research in Agricultural Genomics-CRAG, Edifici CRAG-Campus UAB, 08193, Bellaterra, Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Nathalia Varejão
- Institut de Biotecnologia i de Biomedicina and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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Liu D, Wu G, Wang S, Zheng X, Che X. Evaluating the Role of Neddylation Modifications in Kidney Renal Clear Cell Carcinoma: An Integrated Approach Using Bioinformatics, MLN4924 Dosing Experiments, and RNA Sequencing. Pharmaceuticals (Basel) 2024; 17:635. [PMID: 38794205 PMCID: PMC11125012 DOI: 10.3390/ph17050635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/07/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Neddylation, a post-translational modification process, plays a crucial role in various human neoplasms. However, its connection with kidney renal clear cell carcinoma (KIRC) remains under-researched. METHODS We validated the Gene Set Cancer Analysis Lite (GSCALite) platform against The Cancer Genome Atlas (TCGA) database, analyzing 33 cancer types and their link with 17 neddylation-related genes. This included examining copy number variations (CNVs), single nucleotide variations (SNVs), mRNA expression, cellular pathway involvement, and methylation. Using Gene Set Variation Analysis (GSVA), we categorized these genes into three clusters and examined their impact on KIRC patient prognosis, drug responses, immune infiltration, and oncogenic pathways. Afterward, our objective is to identify genes that exhibit overexpression in KIRC and are associated with an adverse prognosis. After pinpointing the specific target gene, we used the specific inhibitor MLN4924 to inhibit the neddylation pathway to conduct RNA sequencing and related in vitro experiments to verify and study the specificity and potential mechanisms related to the target. This approach is geared towards enhancing our understanding of the prognostic importance of neddylation modification in KIRC. RESULTS We identified significant CNV, SNV, and methylation events in neddylation-related genes across various cancers, with notably higher expression levels observed in KIRC. Cluster analysis revealed a potential trade-off in the interactions among neddylation-related genes, where both high and low levels of gene expression are linked to adverse prognoses. This association is particularly pronounced concerning lymph node involvement, T stage classification, and Fustat score. Simultaneously, our research discovered that PSMB10 exhibits overexpression in KIRC when compared to normal tissues, negatively impacting patient prognosis. Through RNA sequencing and in vitro assays, we confirmed that the inhibition of neddylation modification could play a role in the regulation of various signaling pathways, thereby influencing the prognosis of KIRC. Moreover, our results underscore PSMB10 as a viable target for therapeutic intervention in KIRC, opening up novel pathways for the development of targeted treatment strategies. CONCLUSION This study underscores the regulatory function and potential mechanism of neddylation modification on the phenotype of KIRC, identifying PSMB10 as a key regulatory target with a significant role in influencing the prognosis of KIRC.
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Affiliation(s)
- Dequan Liu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (D.L.); (G.W.); (S.W.)
| | - Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (D.L.); (G.W.); (S.W.)
| | - Shijin Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (D.L.); (G.W.); (S.W.)
| | - Xu Zheng
- Department of Cell Biology, College of Basic Medical Science, Dalian Medical University, Dalian 116011, China
| | - Xiangyu Che
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (D.L.); (G.W.); (S.W.)
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Gomez K, Allen HN, Duran P, Loya-Lopez S, Calderon-Rivera A, Moutal A, Tang C, Nelson TS, Perez-Miller S, Khanna R. Targeted transcriptional upregulation of SENP1 by CRISPR activation enhances deSUMOylation pathways to elicit antinociception in the spinal nerve ligation model of neuropathic pain. Pain 2024; 165:866-883. [PMID: 37862053 PMCID: PMC11389604 DOI: 10.1097/j.pain.0000000000003080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/04/2023] [Indexed: 10/21/2023]
Abstract
ABSTRACT The voltage-gated sodium channel Na V 1.7 is an essential component of human pain signaling. Changes in Na V 1.7 trafficking are considered critical in the development of neuropathic pain. SUMOylation of collapsin response mediator protein 2 (CRMP2) regulates the membrane trafficking and function of Na V 1.7. Enhanced CRMP2 SUMOylation in neuropathic pain correlates with increased Na V 1.7 activity. Pharmacological and genetic interventions that interfere with CRMP2 SUMOylation in rodents with neuropathic pain have been shown to reverse mechanical allodynia. Sentrin or SUMO-specific proteases (SENPs) are vital for balancing SUMOylation and deSUMOylation of substrates. Overexpression of SENP1 and/or SENP2 in CRMP2-expressing cells results in increased deSUMOylation and decreased membrane expression and currents of Na V 1.7. Although SENP1 is present in the spinal cord and dorsal root ganglia, its role in regulating Na V 1.7 function and pain is not known. We hypothesized that favoring SENP1 expression can enhance CRMP2 deSUMOylation to modulate Na V 1.7 channels. In this study, we used a clustered regularly interspaced short palindromic repeats activation (CRISPRa) SENP1 lentivirus to overexpress SENP1 in dorsal root ganglia neurons. We found that SENP1 lentivirus reduced CRMP2 SUMOylation, Na V 1.7-CRMP2 interaction, and Na V 1.7 membrane expression. SENP1 overexpression decreased Na V 1.7 currents through clathrin-mediated endocytosis, directly linked to CRMP2 deSUMOylation. Moreover, enhancing SENP1 expression did not affect the activity of TRPV1 channels or voltage-gated calcium and potassium channels. Intrathecal injection of CRISPRa SENP1 lentivirus reversed mechanical allodynia in male and female rats with spinal nerve injury. These results provide evidence that the pain-regulating effects of SENP1 overexpression involve, in part, the modulation of Na V 1.7 channels through the indirect mechanism of CRMP2 deSUMOylation.
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Affiliation(s)
- Kimberly Gomez
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY, United States
- NYU Pain Research Center, New York, NY, United States
| | - Heather N Allen
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY, United States
- NYU Pain Research Center, New York, NY, United States
| | - Paz Duran
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY, United States
- NYU Pain Research Center, New York, NY, United States
| | - Santiago Loya-Lopez
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY, United States
- NYU Pain Research Center, New York, NY, United States
| | - Aida Calderon-Rivera
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY, United States
- NYU Pain Research Center, New York, NY, United States
| | - Aubin Moutal
- School of Medicine, Department of Pharmacology and Physiology, Saint Louis University, Saint Louis, MO, United States
| | - Cheng Tang
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY, United States
- NYU Pain Research Center, New York, NY, United States
| | - Tyler S Nelson
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY, United States
- NYU Pain Research Center, New York, NY, United States
| | - Samantha Perez-Miller
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY, United States
- NYU Pain Research Center, New York, NY, United States
| | - Rajesh Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY, United States
- NYU Pain Research Center, New York, NY, United States
- Department of Neuroscience and Physiology and Neuroscience Institute, School of Medicine, New York University, New York, NY, United States
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5
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Campos Alonso M, Knobeloch KP. In the moonlight: non-catalytic functions of ubiquitin and ubiquitin-like proteases. Front Mol Biosci 2024; 11:1349509. [PMID: 38455765 PMCID: PMC10919355 DOI: 10.3389/fmolb.2024.1349509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 03/09/2024] Open
Abstract
Proteases that cleave ubiquitin or ubiquitin-like proteins (UBLs) are critical players in maintaining the homeostasis of the organism. Concordantly, their dysregulation has been directly linked to various diseases, including cancer, neurodegeneration, developmental aberrations, cardiac disorders and inflammation. Given their potential as novel therapeutic targets, it is essential to fully understand their mechanisms of action. Traditionally, observed effects resulting from deficiencies in deubiquitinases (DUBs) and UBL proteases have often been attributed to the misregulation of substrate modification by ubiquitin or UBLs. Therefore, much research has focused on understanding the catalytic activities of these proteins. However, this view has overlooked the possibility that DUBs and UBL proteases might also have significant non-catalytic functions, which are more prevalent than previously believed and urgently require further investigation. Moreover, multiple examples have shown that either selective loss of only the protease activity or complete absence of these proteins can have different functional and physiological consequences. Furthermore, DUBs and UBL proteases have been shown to often contain domains or binding motifs that not only modulate their catalytic activity but can also mediate entirely different functions. This review aims to shed light on the non-catalytic, moonlighting functions of DUBs and UBL proteases, which extend beyond the hydrolysis of ubiquitin and UBL chains and are just beginning to emerge.
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Affiliation(s)
- Marta Campos Alonso
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- CIBSS—Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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6
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Zhao Z, O’Dea R, Wendrich K, Kazi N, Gersch M. Native Semisynthesis of Isopeptide-Linked Substrates for Specificity Analysis of Deubiquitinases and Ubl Proteases. J Am Chem Soc 2023; 145:20801-20812. [PMID: 37712884 PMCID: PMC10540217 DOI: 10.1021/jacs.3c04062] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Indexed: 09/16/2023]
Abstract
Post-translational modifications with ubiquitin (Ub) and ubiquitin-like proteins (Ubls) are regulated by isopeptidases termed deubiquitinases (DUBs) and Ubl proteases. Here, we describe a mild chemical method for the preparation of fluorescence polarization substrates for these enzymes that is based on the activation of C-terminal Ub/Ubl hydrazides to acyl azides and their subsequent functionalization to isopeptides. The procedure is complemented by native purification routes and thus circumvents the previous need for desulfurization and refolding. Its broad applicability was demonstrated by the generation of fully cleavable substrates for Ub, SUMO1, SUMO2, NEDD8, ISG15, and Fubi. We employed these reagents for the investigation of substrate specificities of human UCHL3, USPL1, USP2, USP7, USP16, USP18, and USP36. Pronounced selectivity of USPL1 for SUMO2/3 over SUMO1 was observed, which we rationalize with crystal structures and biochemical assays, revealing a SUMO paralogue specificity mechanism distinct from SENP family deSUMOylases. Moreover, we investigated the recently identified Fubi proteases USP16 and USP36 and found both to act as bona fide deFubiylases, harboring catalytic activity against isopeptide-linked Fubi. Surprisingly, we also noticed the activity of both enzymes toward ISG15, previously not identified in chemoproteomics, which makes USP16 and USP36 the first human DUBs with specific isopeptidase activity toward three distinct modifiers. The methods described here for the preparation of isopeptide-linked, fully folded substrates will aid in the characterization of further DUBs/Ubl proteases. More broadly, our findings highlight possible limitations associated with fluorogenic substrates and Ubl activity-based probes and stress the importance of isopeptide-containing reagents for validating isopeptidase activities and quantifying substrate specificities.
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Affiliation(s)
- Zhou Zhao
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Rachel O’Dea
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Kim Wendrich
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Nafizul Kazi
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Malte Gersch
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
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7
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Roberts CG, Franklin TG, Pruneda JN. Ubiquitin-targeted bacterial effectors: rule breakers of the ubiquitin system. EMBO J 2023; 42:e114318. [PMID: 37555693 PMCID: PMC10505922 DOI: 10.15252/embj.2023114318] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
Regulation through post-translational ubiquitin signaling underlies a large portion of eukaryotic biology. This has not gone unnoticed by invading pathogens, many of which have evolved mechanisms to manipulate or subvert the host ubiquitin system. Bacteria are particularly adept at this and rely heavily upon ubiquitin-targeted virulence factors for invasion and replication. Despite lacking a conventional ubiquitin system of their own, many bacterial ubiquitin regulators loosely follow the structural and mechanistic rules established by eukaryotic ubiquitin machinery. Others completely break these rules and have evolved novel structural folds, exhibit distinct mechanisms of regulation, or catalyze foreign ubiquitin modifications. Studying these interactions can not only reveal important aspects of bacterial pathogenesis but also shed light on unexplored areas of ubiquitin signaling and regulation. In this review, we discuss the methods by which bacteria manipulate host ubiquitin and highlight aspects that follow or break the rules of ubiquitination.
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Affiliation(s)
- Cameron G Roberts
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Tyler G Franklin
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
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8
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Wei M, Duan P, Zhao S, Gou B, Wang Y, Yang N, Ma Y, Ma Z, Zhang G, Wei B. Genome-wide identification of RUB activating enzyme and conjugating enzyme gene families and their expression analysis under abiotic stresses in Capsicum annuum. PROTOPLASMA 2023; 260:821-837. [PMID: 36322293 DOI: 10.1007/s00709-022-01816-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
NEDD8/RUB, as a ubiquitin-like protein, participates in the post-translational modification of protein and requires unique E1, E2, and E3 enzymes to bind to its substrate. The RUB E1 activating enzyme and E2 conjugating enzyme play a significant role in the neddylation. However, it is unknown whether RUB E1 and E2 exist in pepper and what its function is. In this study, a total of three putative RUB E1 and five RUB E2 genes have been identified in the pepper genome. Subsequently, their physical and chemical properties, gene structure, conserved domains and motifs, phylogenetic relationship, and cis-acting elements were analyzed. The structure and conserved domain of RUB E1 and E2 are similar to that of Arabidopsis and tomato. The RUB E1 and E2 genes were randomly distributed on seven chromosomes, and there were two pairs of collinearity between pepper and Arabidopsis and eight pairs of collinearity between pepper and tomato. Phylogenetic analysis reveals that RUB E1 and E2 genes of pepper have a closer relationship with that of tomato, potato, and Nicotiana attenuate. The cis-elements of RUB E1 and E2 genes contained hormone response and stress response. RUB E1 and E2 genes were expressed in at least one tissue and CaRCE1.3 and CaRCE2.1 were exclusively expressed in flowers and anthers. Moreover, the expression of RUB E1 genes (CaECR1, CaAXR1.1, and CaAXR1.2) and RUB E2 genes (CaRCE1.1, CaRCE1.2, and CaRCE2.1) was increased to varying degrees under low-temperature, drought, salt, ABA, and IAA treatments, while CaRCE1.3 and CaRCE2.2 were down-regulated under low-temperature treatment. In addition, these genes were hardly expressed under MeJA treatment. In summary, this study provides a theoretical foundation to explore the role of RUB E1 and E2 in the response of plants to stress.
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Affiliation(s)
- Min Wei
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Panpan Duan
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Shufang Zhao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Bingdiao Gou
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Yongfu Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Nan Yang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Yan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Zhengbao Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Gaoyuan Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Bingqiang Wei
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China.
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9
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Kassouf T, Shrivastava R, Meszka I, Bailly A, Polanowska J, Trauchessec H, Mandrioli J, Carra S, Xirodimas DP. Targeting the NEDP1 enzyme to ameliorate ALS phenotypes through stress granule disassembly. SCIENCE ADVANCES 2023; 9:eabq7585. [PMID: 37000881 PMCID: PMC10065448 DOI: 10.1126/sciadv.abq7585] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
The elimination of aberrant inclusions is regarded as a therapeutic approach in neurodegeneration. In amyotrophic lateral sclerosis (ALS), mutations in proteins found within cytoplasmic condensates called stress granules (SGs) are linked to the formation of pathological SGs, aberrant protein inclusions, and neuronal toxicity. We found that inhibition of NEDP1, the enzyme that processes/deconjugates the ubiquitin-like molecule NEDD8, promotes the disassembly of physiological and pathological SGs. Reduction in poly(ADP-ribose) polymerase1 activity through hyper-NEDDylation is a key mechanism for the observed phenotype. These effects are related to improved cell survival in human cells, and in C. elegans, nedp1 deletion ameliorates ALS phenotypes related to animal motility. Our studies reveal NEDP1 as potential therapeutic target for ALS, correlated to the disassembly of pathological SGs.
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Affiliation(s)
| | | | - Igor Meszka
- CRBM, Univ. Montpellier, CNRS, Montpellier, France
| | | | | | | | - Jessica Mandrioli
- Neurology Unit, Azienda Ospedaliero Universitaria di Modena, 41126 Modena, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia,G. Campi 287, 41125 Modena, Italy
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia,G. Campi 287, 41125 Modena, Italy
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10
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Song JM, Kang M, Lee S, Kim J, Park S, Park DH, Lee S, Suh YH. Deneddylating enzyme SENP8 regulates neuronal development. J Neurochem 2023; 165:348-361. [PMID: 36847487 DOI: 10.1111/jnc.15797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 01/16/2023] [Accepted: 02/13/2023] [Indexed: 03/01/2023]
Abstract
Neddylation is a cellular process in which the neural precursor cell expressed, developmentally down-regulated 8 (NEDD8) is conjugated to the lysine residue of target proteins via serial enzymatic cascades. Recently, it has been demonstrated that neddylation is required for synaptic clustering of metabotropic glutamate receptor 7 (mGlu7) and postsynaptic density protein 95 (PSD-95), and the inhibition of neddylation impairs neurite outgrowth and excitatory synaptic maturation. Similar to the balanced role of deubiquitylating enzymes (DUBs) in the ubiquitination process, we hypothesized that deneddylating enzymes can regulate neuronal development by counteracting the process of neddylation. We find that the SUMO peptidase family member, NEDD8 specific (SENP8) acts as a key neuronal deneddylase targeting the global neuronal substrates in primary rat cultured neurons. We demonstrate that SENP8 expression levels are developmentally regulated, peaking around the first postnatal week and gradually diminishing in mature brain and neurons. We find that SENP8 negatively regulates neurite outgrowth through multiple pathways, including actin dynamics, Wnt/β-catenin signaling, and autophagic processes. Alterations in neurite outgrowth by SENP8 subsequently result in the impairment of excitatory synapse maturation. Our data indicate that SENP8 plays an essential role in neuronal development and is a promising therapeutic target for neurodevelopmental disorders.
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Affiliation(s)
- Jae-Man Song
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Minji Kang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Seungha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Jungho Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Sunha Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Da-Ha Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Sanghyeon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Young Ho Suh
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
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11
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Li Y, De Bolòs A, Amador V, Reverter D. Structural Basis for the SUMO2 Isoform Specificity of SENP7. J Mol Biol 2022; 434:167875. [PMID: 36334780 DOI: 10.1016/j.jmb.2022.167875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 10/25/2022] [Accepted: 10/29/2022] [Indexed: 11/07/2022]
Abstract
SUMO proteases or deSUMOylases regulate the lifetime of SUMO-conjugated targets in the cell by cleaving off the isopetidic bond between the substrate and the SUMO modifier, thus reversing the conjugation activity of the SUMO E3 ligases. In humans the deSUMOylating activity is mainly conducted by the SENP/ULP protease family, which is constituted of six members sharing a homologous catalytic globular domain. SENP6 and SENP7 are the most divergent members of the family and they show a unique SUMO2/3 isoform preference and a particular activity for dismantling polySUMO2 chains. Here, we present the crystal structure of the catalytic domain of human SENP7 bound to SUMO2, revealing structural key elements for the SUMO2 isoform specificity of SENP7. In particular, we describe the specific contacts between SUMO2 and a unique insertion in SENP7 (named Loop1) that is responsible for the SUMO2 isoform specificity. All the other interface contacts between SENP7 and SUMO2, including the SUMO2 C-terminal tail interaction, are conserved among members of the SENP/ULP family. Our data give insight into an evolutionary adaptation to restrict the deSUMOylating activity in SENP6 and SENP7 for the SUMO2/3 isoforms.
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Affiliation(s)
- Ying Li
- Institut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Anna De Bolòs
- Institut de Investigacions Biomèdiques Agustí Pi i Sunyer (IDIBABS), Barcelona 08036, Spain
| | - Virginia Amador
- Institut de Investigacions Biomèdiques Agustí Pi i Sunyer (IDIBABS), Barcelona 08036, Spain
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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12
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Gorka M, Magnussen HM, Kulathu Y. Chemical biology tools to study Deubiquitinases and Ubl proteases. Semin Cell Dev Biol 2022; 132:86-96. [PMID: 35216867 DOI: 10.1016/j.semcdb.2022.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 12/15/2022]
Abstract
The reversible attachment of ubiquitin (Ub) and ubiquitin like modifiers (Ubls) to proteins are crucial post-translational modifications (PTMs) for many cellular processes. Not only do cells possess hundreds of ligases to mediate substrate specific modification with Ub and Ubls, but they also have a repertoire of more than 100 dedicated enzymes for the specific removal of ubiquitin (Deubiquitinases or DUBs) and Ubl modifications (Ubl-specific proteases or ULPs). Over the past two decades, there has been significant progress in our understanding of how DUBs and ULPs function at a molecular level and many novel DUBs and ULPs, including several new DUB classes, have been identified. Here, the development of chemical tools that can bind and trap active DUBs has played a key role. Since the introduction of the first activity-based probe for DUBs in 1986, several innovations have led to the development of more sophisticated tools to study DUBs and ULPs. In this review we discuss how chemical biology has led to the development of activity-based probes and substrates that have been invaluable to the study of DUBs and ULPs. We summarise our currently available toolbox, highlight the main achievements and give an outlook of how these tools may be applied to gain a better understanding of the regulatory mechanisms of DUBs and ULPs.
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Affiliation(s)
- Magdalena Gorka
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Helge Magnus Magnussen
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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13
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Kim WD, Mathavarajah S, Huber RJ. The Cellular and Developmental Roles of Cullins, Neddylation, and the COP9 Signalosome in Dictyostelium discoideum. Front Physiol 2022; 13:827435. [PMID: 35586714 PMCID: PMC9108976 DOI: 10.3389/fphys.2022.827435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/03/2022] [Indexed: 12/02/2022] Open
Abstract
Cullins (CULs) are a core component of cullin-RING E3 ubiquitin ligases (CRLs), which regulate the degradation, function, and subcellular trafficking of proteins. CULs are post-translationally regulated through neddylation, a process that conjugates the ubiquitin-like modifier protein neural precursor cell expressed developmentally downregulated protein 8 (NEDD8) to target cullins, as well as non-cullin proteins. Counteracting neddylation is the deneddylase, COP9 signalosome (CSN), which removes NEDD8 from target proteins. Recent comparative genomics studies revealed that CRLs and the CSN are highly conserved in Amoebozoa. A well-studied representative of Amoebozoa, the social amoeba Dictyostelium discoideum, has been used for close to 100 years as a model organism for studying conserved cellular and developmental processes owing to its unique life cycle comprised of unicellular and multicellular phases. The organism is also recognized as an exceptional model system for studying cellular processes impacted by human diseases, including but not limited to, cancer and neurodegeneration. Recent work shows that the neddylation inhibitor, MLN4924 (Pevonedistat), inhibits growth and multicellular development in D. discoideum, which supports previous work that revealed the cullin interactome in D. discoideum and the roles of cullins and the CSN in regulating cellular and developmental processes during the D. discoideum life cycle. Here, we review the roles of cullins, neddylation, and the CSN in D. discoideum to guide future work on using this biomedical model system to further explore the evolutionarily conserved functions of cullins and neddylation.
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Affiliation(s)
- William D. Kim
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | | | - Robert J. Huber
- Department of Biology, Trent University, Peterborough, ON, Canada
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14
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Ruidiaz SF, Dreier JE, Hartmann-Petersen R, Kragelund BB. The disordered PCI-binding human proteins CSNAP and DSS1 have diverged in structure and function. Protein Sci 2021; 30:2069-2082. [PMID: 34272906 PMCID: PMC8442969 DOI: 10.1002/pro.4159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 12/30/2022]
Abstract
Intrinsically disordered proteins (IDPs) regularly constitute components of larger protein assemblies contributing to architectural stability. Two small, highly acidic IDPs have been linked to the so-called PCI complexes carrying PCI-domain subunits, including the proteasome lid and the COP9 signalosome. These two IDPs, DSS1 and CSNAP, have been proposed to have similar structural propensities and functions, but they display differences in their interactions and interactome sizes. Here we characterized the structural properties of human DSS1 and CSNAP at the residue level using NMR spectroscopy and probed their propensities to bind ubiquitin. We find that distinct structural features present in DSS1 are completely absent in CSNAP, and vice versa, with lack of relevant ubiquitin binding to CSNAP, suggesting the two proteins to have diverged in both structure and function. Our work additionally highlights that different local features of seemingly similar IDPs, even subtle sequence variance, may endow them with different functional traits. Such traits may underlie their potential to engage in multiple interactions thereby impacting their interactome sizes.
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Affiliation(s)
- Sarah F Ruidiaz
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Jesper E Dreier
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Rasmus Hartmann-Petersen
- REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
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15
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Zheng YC, Guo YJ, Wang B, Wang C, Mamun MAA, Gao Y, Liu HM. Targeting neddylation E2s: a novel therapeutic strategy in cancer. J Hematol Oncol 2021; 14:57. [PMID: 33827629 PMCID: PMC8028724 DOI: 10.1186/s13045-021-01070-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/29/2021] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin-conjugating enzyme E2 M (UBE2M) and ubiquitin-conjugating enzyme E2 F (UBE2F) are the two NEDD8-conjugating enzymes of the neddylation pathway that take part in posttranslational modification and change the activity of target proteins. The activity of E2 enzymes requires both a 26-residue N-terminal docking peptide and a conserved E2 catalytic core domain, which is the basis for the transfer of neural precursor cell-expressed developmentally downregulated 8 (NEDD8). By recruiting E3 ligases and targeting cullin and non-cullin substrates, UBE2M and UBE2F play diverse biological roles. Currently, there are several inhibitors that target the UBE2M-defective in cullin neddylation protein 1 (DCN1) interaction to treat cancer. As described above, this review provides insights into the mechanism of UBE2M and UBE2F and emphasizes these two E2 enzymes as appealing therapeutic targets for the treatment of cancers.
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Affiliation(s)
- Yi-Chao Zheng
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China
| | - Yan-Jia Guo
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China
| | - Bo Wang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China
| | - Chong Wang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - M A A Mamun
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China
| | - Ya Gao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China.
| | - Hong-Min Liu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China.
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16
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Chen DV, Suzuki T, Itoh Y, Maeda Y, Hirano J, Haga S, Zhang H, Ito D, Matsuura Y, Okamoto T. Deneddylation by SENP8 restricts hepatitis B virus propagation. Microbiol Immunol 2021; 65:125-135. [PMID: 33433029 DOI: 10.1111/1348-0421.12874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 12/15/2022]
Abstract
Proteins newly synthesized from messenger RNA undergo Posttranslational modifications (PTMs) such as phosphorylation, glycosylation, methylation, and ubiquitination. These PTMs have important roles in protein stability, localization, and conformation and have been reported to be involved in hepatitis B virus (HBV) propagation. Although ubiquitination plays an essential role in HBV life cycles, the involvement of ubiquitin-like proteins (UBLs) in HBV life cycles has been understudied. Through comprehensive gain- and loss-of-function screening of UBLs, we observed that neddylation, a PTM in which neural precursor cell, expressed developmentally downregulated 8 (NEDD8) is conjugated to substrate proteins, was required for efficient HBV propagation. We also found that overexpression of sentrin-specific protease 8 (SENP8), which cleaves conjugated NEDD8, suppressed HBV propagation. Further, the catalytic activity of SENP8 was required for the suppression of HBV propagation. These results indicated that the reduction of neddylation negatively regulated HBV propagation. In addition, we demonstrated that suppression of HBV propagation via SENP8 overexpression was independent of hepatitis B protein X (HBx) and HBV promoter activity. Therefore, our data suggested that neddylation plays an important role in the late stages of HBV life cycles.
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Affiliation(s)
- David Virya Chen
- Institute for Advanced Co-Creation Studies, Research, Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Tatsuya Suzuki
- Institute for Advanced Co-Creation Studies, Research, Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yumi Itoh
- Institute for Advanced Co-Creation Studies, Research, Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yusuke Maeda
- Department of Molecular Virology, Research, Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Junki Hirano
- Institute for Advanced Co-Creation Studies, Research, Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Saori Haga
- Institute for Advanced Co-Creation Studies, Research, Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - He Zhang
- Institute for Advanced Co-Creation Studies, Research, Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Daiki Ito
- Institute for Advanced Co-Creation Studies, Research, Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yoshiharu Matsuura
- Department of Molecular Virology, Research, Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research, Institute for Microbial Diseases, Osaka University, Suita, Japan
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17
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Characterization of Plasmodium falciparum NEDD8 and identification of cullins as its substrates. Sci Rep 2020; 10:20220. [PMID: 33214620 PMCID: PMC7677368 DOI: 10.1038/s41598-020-77001-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022] Open
Abstract
A variety of post-translational modifications of Plasmodium falciparum proteins, including phosphorylation and ubiquitination, are shown to have key regulatory roles during parasite development. NEDD8 is a ubiquitin-like modifier of cullin-RING E3 ubiquitin ligases, which regulates diverse cellular processes. Although neddylation is conserved in eukaryotes, it is yet to be characterized in Plasmodium and related apicomplexan parasites. We characterized P. falciparum NEDD8 (PfNEDD8) and identified cullins as its physiological substrates. PfNEDD8 is a 76 amino acid residue protein without the C-terminal tail, indicating that it can be readily conjugated. The wild type and mutant (Gly75Ala/Gly76Ala) PfNEDD8 were expressed in P. falciparum. Western blot of wild type PfNEDD8-expressing parasites indicated multiple high molecular weight conjugates, which were absent in the parasites expressing the mutant, indicating conjugation of NEDD8 through Gly76. Immunoprecipitation followed by mass spectrometry of wild type PfNEDD8-expressing parasites identified two putative cullins. Furthermore, we expressed PfNEDD8 in mutant S. cerevisiae strains that lacked endogenous NEDD8 (rub1Δ) or NEDD8 conjugating E2 enzyme (ubc12Δ). The PfNEDD8 immunoprecipitate also contained S. cerevisiae cullin cdc53, further substantiating cullins as physiological substrates of PfNEDD8. Our findings lay ground for investigation of specific roles and drug target potential of neddylation in malaria parasites.
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18
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Bailly AP, Perrin A, Serrano-Macia M, Maghames C, Leidecker O, Trauchessec H, Martinez-Chantar ML, Gartner A, Xirodimas DP. The Balance between Mono- and NEDD8-Chains Controlled by NEDP1 upon DNA Damage Is a Regulatory Module of the HSP70 ATPase Activity. Cell Rep 2020; 29:212-224.e8. [PMID: 31577950 PMCID: PMC6899524 DOI: 10.1016/j.celrep.2019.08.070] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/27/2019] [Accepted: 08/22/2019] [Indexed: 12/11/2022] Open
Abstract
Ubiquitin and ubiquitin-like chains are finely balanced by conjugating and de-conjugating enzymes. Alterations in this balance trigger the response to stress conditions and are often observed in pathologies. How such changes are detected is not well understood. We identify the HSP70 chaperone as a sensor of changes in the balance between mono- and poly-NEDDylation. Upon DNA damage, the induction of the de-NEDDylating enzyme NEDP1 restricts the formation of NEDD8 chains, mainly through lysines K11/K48. This promotes APAF1 oligomerization and apoptosis induction, a step that requires the HSP70 ATPase activity. HSP70 binds to NEDD8, and, in vitro, the conversion of NEDD8 chains into mono-NEDD8 stimulates HSP70 ATPase activity. This effect is independent of NEDD8 conjugation onto substrates. The study indicates that the NEDD8 cycle is a regulatory module of HSP70 function. These findings may be important in tumorigenesis, as we find decreased NEDP1 levels in hepatocellular carcinoma with concomitant accumulation of NEDD8 conjugates. Restriction of NEDD8 chains by NEDP1 is required for DNA damage-induced apoptosis The HSP70 chaperone is a sensor of the balance between mono- and NEDD8 chains Mono-NEDD8 stimulates HSP70 activity, which allows the formation of the apoptosome NEDP1 levels are downregulated in mouse hepatocellular carcinoma
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Affiliation(s)
- Aymeric P Bailly
- CRBM, CNRS, Univ. Montpellier, UMR5237, Montpellier 34090, Cedex 5, France.
| | - Aurelien Perrin
- CRBM, CNRS, Univ. Montpellier, UMR5237, Montpellier 34090, Cedex 5, France
| | - Marina Serrano-Macia
- Liver Disease Laboratory, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain
| | - Chantal Maghames
- CRBM, CNRS, Univ. Montpellier, UMR5237, Montpellier 34090, Cedex 5, France
| | - Orsolya Leidecker
- CRBM, CNRS, Univ. Montpellier, UMR5237, Montpellier 34090, Cedex 5, France
| | - Helene Trauchessec
- CRBM, CNRS, Univ. Montpellier, UMR5237, Montpellier 34090, Cedex 5, France
| | - M L Martinez-Chantar
- Liver Disease Laboratory, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain
| | - Anton Gartner
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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19
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Lin YL, Chung CL, Huang PJ, Chen CH, Fang SC. Revised annotation and extended characterizations of components of the Chlamydomonas reinhardtii SUMOylation system. PLANT DIRECT 2020; 4:e00266. [PMID: 33015534 PMCID: PMC7522501 DOI: 10.1002/pld3.266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 05/16/2023]
Abstract
Small ubiquitin-like modifier (SUMO) conjugation, or SUMOylation, is a reversible post-translational modification that is important for regulation of many cellular processes including cell division cycle in the eukaryotic kingdom. However, only a portion of the components of the Chlamydomonas SUMOylation system are known and their functions and regulation investigated. The present studies are aimed at extending discovery and characterization of new components and improving the annotation and nomenclature of all known proteins and genes involved in the system. Even though only one copy of the heterodimerized SUMO-activating enzyme, SAE1 and SAE2, was identified, the number of SUMO-conjugating enzymes (SCEs) and SUMO proteases/isopeptidase was expanded in Chlamydomonas. Using the reconstituted SUMOylation system, we showed that SCE1, SCE2, and SCE3 have SUMO-conjugating activity. In addition to SUMOylation, components required for other post-translational modifications such as NEDDylation, URMylation, and UFMylation, were confirmed to be present in Chlamydomonas. Our data also showed that besides isopeptidase activity, the SUMO protease domain of SUPPRESSOR OF MAT3 7/SENTRIN-SPECIFIC PROTEASE 1 (SMT7/SENP1) has endopeptidase activity that is capable of processing SUMO precursors. Moreover, the key cell cycle regulators of Chlamydomonas E2F1, DP1, CDKG1, CYCD2, and CYCD3 were SUMOylated in vitro, suggesting SUMOylation may be part of regulatory pathway modulating cell cycle regulators.
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Affiliation(s)
- Yen-Ling Lin
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
- Ph.D. Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung Taiwan
| | - Chin-Lin Chung
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
| | - Pin-Jui Huang
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
| | - Chun-Han Chen
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
| | - Su-Chiung Fang
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
- Ph.D. Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung Taiwan
- Institute of Tropical Plant Sciences and Microbiology National Cheng Kung University Tainan Taiwan
- National Cheng Kung University-Academia Sinica Graduate Program in Translational Agricultural Sciences Tainan Taiwan
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20
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Xiong X, Cui D, Bi Y, Sun Y, Zhao Y. Neddylation modification of ribosomal protein RPS27L or RPS27 by MDM2 or NEDP1 regulates cancer cell survival. FASEB J 2020; 34:13419-13429. [PMID: 32779270 DOI: 10.1096/fj.202000530rrr] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 11/11/2022]
Abstract
Neddylation plays a distinct role in stabilization of a subset of ribosomal proteins. Whether the family of ribosomal proteins S27 (RPS27 and RPS27-like) is subjected to neddylation regulation with associated biological consequence is totally unknown. Here, we report that both family members are subjected to neddylation by MDM2 E3 ubiquitin ligase, and deneddylation by NEDP1. Blockage of neddylation with MLN4924, a small molecule inhibitor of neddylation-activating enzyme, destabilizes RPS27L and RPS27 by shortening their protein half-lives. Biologically, knockdown of RPS27L and RPS27 sensitizes, whereas ectopic expression of RPS27L and RPS27 desensitizes cancer cells to MLN4924-induced apoptosis. Taken together, our study demonstrates that neddylation stabilizes RPS27L and RPS27 to confer the survival of cancer cells.
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Affiliation(s)
- Xiufang Xiong
- Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Danrui Cui
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Yanli Bi
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Yi Sun
- Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Yongchao Zhao
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, P. R. China
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21
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The COP9 Signalosome: A Multi-DUB Complex. Biomolecules 2020; 10:biom10071082. [PMID: 32708147 PMCID: PMC7407660 DOI: 10.3390/biom10071082] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/07/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023] Open
Abstract
The COP9 signalosome (CSN) is a signaling platform controlling the cellular ubiquitylation status. It determines the activity and remodeling of ~700 cullin-RING ubiquitin ligases (CRLs), which control more than 20% of all ubiquitylation events in cells and thereby influence virtually any cellular pathway. In addition, it is associated with deubiquitylating enzymes (DUBs) protecting CRLs from autoubiquitylation and rescuing ubiquitylated proteins from degradation. The coordination of ubiquitylation and deubiquitylation by the CSN is presumably important for fine-tuning the precise formation of defined ubiquitin chains. Considering its intrinsic DUB activity specific for deneddylation of CRLs and belonging to the JAMM family as well as its associated DUBs, the CSN represents a multi-DUB complex. Two CSN-associated DUBs, the ubiquitin-specific protease 15 (USP15) and USP48 are regulators in the NF-κB signaling pathway. USP15 protects CRL1β-TrCP responsible for IκBα ubiquitylation, whereas USP48 stabilizes the nuclear pool of the NF-κB transcription factor RelA upon TNF stimulation by counteracting CRL2SOCS1. Moreover, the CSN controls the neddylation status of cells by its intrinsic DUB activity and by destabilizing the associated deneddylation enzyme 1 (DEN1). Thus, the CSN is a master regulator at the intersection between ubiquitylation and neddylation.
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22
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Ibrahim AFM, Shen L, Tatham MH, Dickerson D, Prescott AR, Abidi N, Xirodimas DP, Hay RT. Antibody RING-Mediated Destruction of Endogenous Proteins. Mol Cell 2020; 79:155-166.e9. [PMID: 32454028 PMCID: PMC7332993 DOI: 10.1016/j.molcel.2020.04.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/20/2020] [Accepted: 04/27/2020] [Indexed: 01/05/2023]
Abstract
To understand gene function, the encoding DNA or mRNA transcript can be manipulated and the consequences observed. However, these approaches do not have a direct effect on the protein product of the gene, which is either permanently abrogated or depleted at a rate defined by the half-life of the protein. We therefore developed a single-component system that could induce the rapid degradation of the specific endogenous protein itself. A construct combining the RING domain of ubiquitin E3 ligase RNF4 with a protein-specific camelid nanobody mediates target destruction by the ubiquitin proteasome system, a process we describe as antibody RING-mediated destruction (ARMeD). The technique is highly specific because we observed no off-target protein destruction. Furthermore, bacterially produced nanobody-RING fusion proteins electroporated into cells induce degradation of target within minutes. With increasing availability of protein-specific nanobodies, this method will allow rapid and specific degradation of a wide range of endogenous proteins.
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Affiliation(s)
- Adel F M Ibrahim
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Linnan Shen
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Michael H Tatham
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - David Dickerson
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Alan R Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Naima Abidi
- Cell Biology Research Centre of Montpellier, CNRS, UMR 5237, Montpellier, France
| | - Dimitris P Xirodimas
- Cell Biology Research Centre of Montpellier, CNRS, UMR 5237, Montpellier, France
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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23
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Li G, Liu X, Yang M, Zhang G, Wang Z, Guo K, Gao Y, Jiao P, Sun J, Chen C, Wang H, Deng W, Xiao H, Li S, Wu H, Wang Y, Cao L, Jia Z, Shang L, Yang C, Guo Y, Rao Z. Crystal Structure of African Swine Fever Virus pS273R Protease and Implications for Inhibitor Design. J Virol 2020; 94:e02125-19. [PMID: 32075933 PMCID: PMC7199414 DOI: 10.1128/jvi.02125-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/11/2020] [Indexed: 01/21/2023] Open
Abstract
African swine fever (ASF) is a highly contagious hemorrhagic viral disease of domestic and wild pigs that is responsible for serious economic and production losses. It is caused by the African swine fever virus (ASFV), a large and complex icosahedral DNA virus of the Asfarviridae family. Currently, there is no effective treatment or approved vaccine against the ASFV. pS273R, a specific SUMO-1 cysteine protease, catalyzes the maturation of the pp220 and pp62 polyprotein precursors into core-shell proteins. Here, we present the crystal structure of the ASFV pS273R protease at a resolution of 2.3 Å. The overall structure of the pS273R protease is represented by two domains named the "core domain" and the N-terminal "arm domain." The "arm domain" contains the residues from M1 to N83, and the "core domain" contains the residues from N84 to A273. A structure analysis reveals that the "core domain" shares a high degree of structural similarity with chlamydial deubiquitinating enzyme, sentrin-specific protease, and adenovirus protease, while the "arm domain" is unique to ASFV. Further, experiments indicated that the "arm domain" plays an important role in maintaining the enzyme activity of ASFV pS273R. Moreover, based on the structural information of pS273R, we designed and synthesized several peptidomimetic aldehyde compounds at a submolar 50% inhibitory concentration, which paves the way for the design of inhibitors to target this severe pathogen.IMPORTANCE African swine fever virus, a large and complex icosahedral DNA virus, causes a deadly infection in domestic pigs. In addition to Africa and Europe, countries in Asia, including China, Vietnam, and Mongolia, were negatively affected by the hazards posed by ASFV outbreaks in 2018 and 2019, at which time more than 30 million pigs were culled. Until now, there has been no vaccine for protection against ASFV infection or effective treatments to cure ASF. Here, we solved the high-resolution crystal structure of the ASFV pS273R protease. The pS273R protease has a two-domain structure that distinguishes it from other members of the SUMO protease family, while the unique "arm domain" has been proven to be essential for its hydrolytic activity. Moreover, the peptidomimetic aldehyde compounds designed to target the substrate binding pocket exert prominent inhibitory effects and can thus be used in a potential lead for anti-ASFV drug development.
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Affiliation(s)
- Guobang Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Xiaoxia Liu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China
| | - Mengyuan Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Guangshun Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Zhengyang Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China
| | - Kun Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China
| | - Yuxue Gao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Peng Jiao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China
| | - Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Cheng Chen
- School of Life Sciences, Tianjin University, Tianjin, People's Republic of China
| | - Hao Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Weilong Deng
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Huihe Xiao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Sizheng Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Haoru Wu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Ying Wang
- Tianjin Crops Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, People's Republic of China
| | - Lin Cao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- College of Life Science, Nankai University, Tianjin, People's Republic of China
| | - Zihan Jia
- College of Life Science, Nankai University, Tianjin, People's Republic of China
- School of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, People's Republic of China
| | - Luqing Shang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Cheng Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China
- Frontiers Science Center for Cell Responses, Nankai University, Tianjin, People's Republic of China
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China
- College of Life Science, Nankai University, Tianjin, People's Republic of China
- Frontiers Science Center for Cell Responses, Nankai University, Tianjin, People's Republic of China
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24
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Hausman JM, Kenny S, Iyer S, Babar A, Qiu J, Fu J, Luo ZQ, Das C. The Two Deubiquitinating Enzymes from Chlamydia trachomatis Have Distinct Ubiquitin Recognition Properties. Biochemistry 2020; 59:1604-1617. [PMID: 32275137 PMCID: PMC7700883 DOI: 10.1021/acs.biochem.9b01107] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chlamydia trachomatis is the cause of several diseases such as sexually transmitted urogenital disease and ocular trachoma. The pathogen contains a small genome yet, upon infection, expresses two enzymes with deubiquitinating activity, termed ChlaDUB1 and ChlaDUB2, presumed to have redundant deubiquitinase (DUB) function because of the similarity of the primary structure of their catalytic domain. Previous studies have led to structural characterization of the enzymatic properties of ChlaDUB1; however, ChlaDUB2 has yet to be investigated thoroughly. In this study, we investigated the deubiquitinase properties of ChlaDUB2 and compared them to those of ChlaDUB1. This revealed a distinct difference in hydrolytic activity with regard to di- and polyubiquitin chains while showing similar ability to cleave a monoubiquitin-based substrate, ubiquitin aminomethylcoumarin (Ub-AMC). ChlaDUB2 was unable to cleave a diubiquitin substrate efficiently, whereas ChlaDUB1 could rapidly hydrolyze this substrate like a prototypical prokaryotic DUB, SdeA. With polyubiquitinated green fluorescent protein substrate (GFP-Ubn), whereas ChlaDUB1 efficiently disassembled the polyubiquitin chains into the monoubiquitin product, the deubiquitination activity of ChlaDUB2, while showing depletion of the substrate, did not produce appreciable levels of the monoubiquitin product. We report the structures of a catalytic construct of ChlaDUB2 and its complex with ubiquitin propargyl amide. These structures revealed differences in residues involved in substrate recognition between the two Chlamydia DUBs. On the basis of the structures, we conclude that the distal ubiquitin binding is equivalent between the two DUBs, consistent with the Ub-AMC activity result. Therefore, the difference in activity with longer ubiquitinated substrates may be due to the differential recognition of these substrates involving additional ubiquitin binding sites.
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Affiliation(s)
- John M. Hausman
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Sebastian Kenny
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Shalini Iyer
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Aditya Babar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jiazhang Qiu
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Xi’an Road 5333, Changchun, Jilin 130062, China
| | - Jiaqi Fu
- Department of Biology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhao-Qing Luo
- Department of Biology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States,Corresponding Author:
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25
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Zhou L, Jia L. Targeting Protein Neddylation for Cancer Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1217:297-315. [PMID: 31898235 DOI: 10.1007/978-981-15-1025-0_18] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Neddylation is a posttranslational modification that conjugates a ubiquitin-like protein NEDD8 to substrate proteins. The best-characterized substrates of neddylation are the cullin subunits of cullin-RING E3 ubiquitin ligase complexes (CRLs). CRLs as the largest family of E3 ubiquitin ligases control many important biological processes, including tumorigenesis, through promoting ubiquitylation and subsequent degradation of a variety of key regulatory proteins. The process of protein neddylation is overactivated in multiple types of human cancers, providing a sound rationale as an attractive anticancer therapeutic strategy, evidenced by the development of the NEDD8-activating enzyme (NAE) inhibitor MLN4924 (also known as pevonedistat). Recently, increasing evidence strongly indicates that neddylation inhibition by MLN4924 exerts anticancer effects mainly by triggering cell apoptosis, senescence, and autophagy and causing angiogenesis suppression, inflammatory responses, and chemo-/radiosensitization in a context-dependent manner. Here, we briefly summarize the latest progresses in this field, focusing on the preclinical studies to validate neddylation modification as a promising anticancer target.
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Affiliation(s)
- Lisha Zhou
- Department of Biochemistry, Medical College, Taizhou University, Taizhou, China.
| | - Lijun Jia
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
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26
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Karpiyevich M, Adjalley S, Mol M, Ascher DB, Mason B, van der Heden van Noort GJ, Laman H, Ovaa H, Lee MCS, Artavanis-Tsakonas K. Nedd8 hydrolysis by UCH proteases in Plasmodium parasites. PLoS Pathog 2019; 15:e1008086. [PMID: 31658303 PMCID: PMC6837540 DOI: 10.1371/journal.ppat.1008086] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/07/2019] [Accepted: 09/16/2019] [Indexed: 11/19/2022] Open
Abstract
Plasmodium parasites are the causative agents of malaria, a disease with wide public health repercussions. Increasing drug resistance and the absence of a vaccine make finding new chemotherapeutic strategies imperative. Components of the ubiquitin and ubiquitin-like pathways have garnered increased attention as novel targets given their necessity to parasite survival. Understanding how these pathways are regulated in Plasmodium and identifying differences to the host is paramount to selectively interfering with parasites. Here, we focus on Nedd8 modification in Plasmodium falciparum, given its central role to cell division and DNA repair, processes critical to Plasmodium parasites given their unusual cell cycle and requirement for refined repair mechanisms. By applying a functional chemical approach, we show that deNeddylation is controlled by a different set of enzymes in the parasite versus the human host. We elucidate the molecular determinants of the unusual dual ubiquitin/Nedd8 recognition by the essential PfUCH37 enzyme and, through parasite transgenics and drug assays, determine that only its ubiquitin activity is critical to parasite survival. Our experiments reveal interesting evolutionary differences in how neddylation is controlled in higher versus lower eukaryotes, and highlight the Nedd8 pathway as worthy of further exploration for therapeutic targeting in antimalarial drug design. Ubiquitin and ubiquitin-like post-translational modifications are evolutionarily conserved and involved in fundamental cellular processes essential to all eukaryotes. As such, enzymatic components of these pathways present attractive targets for therapeutic intervention for both chronic and communicable diseases. Nedd8 modification of cullin ubiquitin E3 ligases is critical to the viability of eukaryotic organisms and mediates cell cycle progression and DNA damage repair. Given the complex lifecycle and unusual replication mechanisms of the malaria parasite, one would expect neddylation to be of central importance to its survival, yet little is known about this pathway in Plasmodium. Here we present our findings on how Nedd8 removal is controlled in Plasmodium falciparum and how this pathway differs to that of its human host.
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Affiliation(s)
- Maryia Karpiyevich
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Sophie Adjalley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Marco Mol
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - David B. Ascher
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Melbourne, Melbourne, Australia
| | - Bethany Mason
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Heike Laman
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Marcus C. S. Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
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27
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Ambaye ND. Noncovalent structure of SENP1 in complex with SUMO2. Acta Crystallogr F Struct Biol Commun 2019; 75:332-339. [PMID: 31045562 PMCID: PMC6497105 DOI: 10.1107/s2053230x19004266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/28/2019] [Indexed: 02/02/2023] Open
Abstract
SUMOylation is a post-translational modification in which a small ubiquitin-like molecule (SUMO) is appended to substrate proteins and is known to influence myriads of biological processes. A delicate interplay between several families of SUMOylation proteins and their substrates ensures the proper level of SUMOylation required for normal cell function. Among the SUMO proteins, SUMO2 is known to form mono-SUMOylated proteins and engage in poly-SUMO chain formation, while sentrin-specific protease 1 (SENP1) is a key enzyme in regulating both events. Determination of the SENP1-SUMO2 interaction is therefore necessary to better understand SUMOylation. In this regard, the current paper reports the noncovalent structure of SENP1 in complex with SUMO2, which was refined to a resolution of 2.62 Å with R and Rfree values of 22.92% and 27.66%, respectively. The structure shows that SENP1-SUMO2 complex formation is driven largely by polar interactions and limited hydrophobic contacts. The essential C-terminal motif (QQTGG) of SUMO2 is stabilized by a number of specific bonding interactions that enable it to protrude into the catalytic triad of SENP1 and provide the arrangement necessary for maturation of SUMO and deSUMOylation activity. Overall, the structure shows a number of structural details that pinpoint the basis of SENP1-SUMO2 complex formation.
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Affiliation(s)
- Nigus D. Ambaye
- Department of Immune-Oncology, Beckman Research Institute, City of Hope National Medical Center, 1500 East Duarte Road, Duarte, CA 91010, USA
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28
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Keuss MJ, Hjerpe R, Hsia O, Gourlay R, Burchmore R, Trost M, Kurz T. Unanchored tri-NEDD8 inhibits PARP-1 to protect from oxidative stress-induced cell death. EMBO J 2019; 38:embj.2018100024. [PMID: 30804002 PMCID: PMC6418418 DOI: 10.15252/embj.2018100024] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 01/10/2019] [Accepted: 01/28/2019] [Indexed: 12/18/2022] Open
Abstract
NEDD8 is a ubiquitin‐like protein that activates cullin‐RING E3 ubiquitin ligases (CRLs). Here, we identify a novel role for NEDD8 in regulating the activity of poly(ADP‐ribose) polymerase 1 (PARP‐1) in response to oxidative stress. We show that treatment of cells with H2O2 results in the accumulation of NEDD8 chains, likely by directly inhibiting the deneddylase NEDP1. One chain type, an unanchored NEDD8 trimer, specifically bound to the second zinc finger domain of PARP‐1 and attenuated its activation. In cells in which Nedp1 is deleted, large amounts of tri‐NEDD8 constitutively form, resulting in inhibition of PARP‐1 and protection from PARP‐1‐dependent cell death. Surprisingly, these NEDD8 trimers are additionally acetylated, as shown by mass spectrometry analysis, and their binding to PARP‐1 is reduced by the overexpression of histone de‐acetylases, which rescues PARP‐1 activation. Our data suggest that trimeric, acetylated NEDD8 attenuates PARP‐1 activation after oxidative stress, likely to delay the initiation of PARP‐1‐dependent cell death.
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Affiliation(s)
- Matthew J Keuss
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, UK
| | - Roland Hjerpe
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, UK
| | - Oliver Hsia
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, UK
| | - Robert Gourlay
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dundee, UK
| | - Richard Burchmore
- Glasgow Polyomics, College of Veterinary, Medical and Life Sciences, University of Glasgow, Glasgow, UK
| | - Matthias Trost
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dundee, UK.,Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Thimo Kurz
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, UK
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29
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Castagnoli L, Mandaliti W, Nepravishta R, Valentini E, Mattioni A, Procopio R, Iannuccelli M, Polo S, Paci M, Cesareni G, Santonico E. Selectivity of the CUBAN domain in the recognition of ubiquitin and NEDD8. FEBS J 2019; 286:653-677. [PMID: 30659753 DOI: 10.1111/febs.14752] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/25/2018] [Accepted: 12/28/2018] [Indexed: 12/27/2022]
Abstract
Among the members of the ubiquitin-like (Ubl) protein family, neural precursor cell expressed developmentally down-regulated protein 8 (NEDD8) is the closest in sequence to ubiquitin (57% identity). The two modification mechanisms and their functions, however, are highly distinct and the two Ubls are not interchangeable. A complex network of interactions between modifying enzymes and adaptors, most of which are specific while others are promiscuous, ensures selectivity. Many domains that bind the ubiquitin hydrophobic patch also bind NEDD8 while no domain that specifically binds NEDD8 has yet been described. Here, we report an unbiased selection of domains that bind ubiquitin and/or NEDD8 and we characterize their specificity/promiscuity. Many ubiquitin-binding domains bind ubiquitin preferentially and, to a lesser extent, NEDD8. In a few cases, the affinity of these domains for NEDD8 can be increased by substituting the alanine at position 72 with arginine, as in ubiquitin. We have also identified a unique domain, mapping to the carboxyl end of the protein KHNYN, which has a stark preference for NEDD8. Given its ability to bind neddylated cullins, we have named this domain CUBAN (Cullin-Binding domain Associating with NEDD8). We present here the solution structure of the CUBAN domain both in the isolated form and in complex with NEDD8. The results contribute to the understanding of the discrimination mechanism between ubiquitin and the Ubl. They also provide new insights on the biological role of a ill-defined protein, whose function is hitherto only predicted.
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Affiliation(s)
| | - Walter Mandaliti
- Department of Chemical Sciences and Technologies, Tor Vergata University, Rome, Italy
| | - Ridvan Nepravishta
- Department of Chemical Sciences and Technologies, Tor Vergata University, Rome, Italy.,School of Pharmacy East Anglia, University of Norwich, UK
| | | | - Anna Mattioni
- Department of Biology, Tor Vergata University, Rome, Italy
| | - Radha Procopio
- Department of Biology, Tor Vergata University, Rome, Italy.,Institute of Molecular Bioimaging and Physiology, CNR, Catanzaro, Italy
| | | | - Simona Polo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy.,DIPO, Dipartimento di Oncologia ed Emato-oncologia, University of Milan, Italy
| | - Maurizio Paci
- Department of Chemical Sciences and Technologies, Tor Vergata University, Rome, Italy
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30
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Pruneda JN, Bastidas RJ, Bertsoulaki E, Swatek KN, Santhanam B, Clague MJ, Valdivia RH, Urbé S, Komander D. A Chlamydia effector combining deubiquitination and acetylation activities induces Golgi fragmentation. Nat Microbiol 2018; 3:1377-1384. [PMID: 30397340 DOI: 10.1038/s41564-018-0271-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/13/2018] [Indexed: 01/10/2023]
Abstract
Pathogenic bacteria are armed with potent effector proteins that subvert host signalling processes during infection1. The activities of bacterial effectors and their associated roles within the host cell are often poorly understood, particularly for Chlamydia trachomatis2, a World Health Organization designated neglected disease pathogen. We identify and explain remarkable dual Lys63-deubiquitinase (DUB) and Lys-acetyltransferase activities in the Chlamydia effector ChlaDUB1. Crystal structures capturing intermediate stages of each reaction reveal how the same catalytic centre of ChlaDUB1 can facilitate such distinct processes, and enable the generation of mutations that uncouple the two activities. Targeted Chlamydia mutant strains allow us to link the DUB activity of ChlaDUB1 and the related, dedicated DUB ChlaDUB2 to fragmentation of the host Golgi apparatus, a key process in Chlamydia infection for which effectors have remained elusive. Our work illustrates the incredible versatility of bacterial effector proteins, and provides important insights towards understanding Chlamydia pathogenesis.
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Affiliation(s)
- Jonathan N Pruneda
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Robert J Bastidas
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Erithelgi Bertsoulaki
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Kirby N Swatek
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Balaji Santhanam
- Division of Structural Studies, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Michael J Clague
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Sylvie Urbé
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - David Komander
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK.
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31
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Delgado TC, Barbier-Torres L, Zubiete-Franco I, Lopitz-Otsoa F, Varela-Rey M, Fernández-Ramos D, Martínez-Chantar ML. Neddylation, a novel paradigm in liver cancer. Transl Gastroenterol Hepatol 2018; 3:37. [PMID: 30050997 DOI: 10.21037/tgh.2018.06.05] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/19/2018] [Indexed: 12/16/2022] Open
Abstract
Liver cancer is the sixth most prevailing cancer worldwide. Hepatocellular carcinoma (HCC), the most common form of primary liver cancer, has a rather heterogeneous pathogenesis making it highly refractive to current therapeutic approaches. Hence, HCC patients have a poor and gloomy prognosis making liver cancer the second leading cause of global cancer-related deaths. On this basis, a more global mechanism, such as post-translational modifications (PTMs) of proteins, may provide a valuable therapeutic approach for HCC clinical management by simultaneously regulating multiple disrupted signaling pathways. In the last years, the ubiquitin-like molecule NEDD8 (Neural precursor cell-expressed developmentally downregulated-8) conjugation pathway, neddylation, was shown to be aberrant in HCC patients with a significant positive correlation found among global levels of neddylation and poorer prognosis. Even though the best-established role for NEDD8 is the activation of ubiquitin E3 ligase family of cullin-RING ligases, the putative role for other NEDD8 substrates has been explored in recent years leading to the identification of novel neddylation targets in HCC. Importantly, treatment with the small pharmacological inhibitor Pevonedistat (MLN4924) (Millennium Pharmaceuticals, Takeda Pharmaceutical), currently in clinical trials for the treatment of some types of leukemias and other advanced solid tumors, was shown to suppress the outgrowth of hepatoma cells and liver cancer in pre-clinical mouse models. Overall, considering that the neddylation inhibitor Pevonedistat was well-tolerated and displayed a significant antitumor effect in pre-clinical models, combinatory pharmacological treatment based on Pevonedistat are highly recommended to enter clinical trials targeting advanced HCC.
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Affiliation(s)
- Teresa Cardoso Delgado
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain
| | - Lúcia Barbier-Torres
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain.,Division of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Imanol Zubiete-Franco
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Fernando Lopitz-Otsoa
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain
| | - Marta Varela-Rey
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain
| | - David Fernández-Ramos
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain
| | - María-Luz Martínez-Chantar
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain
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32
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Kim KH, Ha BH, Kim EE. Structural basis for Ufm1 recognition by Uf
SP. FEBS Lett 2018; 592:263-273. [DOI: 10.1002/1873-3468.12951] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 12/06/2017] [Accepted: 12/10/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Kyung Hee Kim
- Biomedical Research Institute Korea Institute of Science and Technology Seoul Korea
| | - Byung Hak Ha
- Biomedical Research Institute Korea Institute of Science and Technology Seoul Korea
| | - Eunice EunKyeong Kim
- Biomedical Research Institute Korea Institute of Science and Technology Seoul Korea
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33
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Liu N, Chaudhry MT, Xie Z, Kreth J, Merritt J. Identification of New Degrons in Streptococcus mutans Reveals a Novel Strategy for Engineering Targeted, Controllable Proteolysis. Front Microbiol 2017; 8:2572. [PMID: 29312250 PMCID: PMC5742171 DOI: 10.3389/fmicb.2017.02572] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/11/2017] [Indexed: 12/20/2022] Open
Abstract
Recently, controllable, targeted proteolysis has emerged as one of the most promising new strategies to study essential genes and otherwise toxic mutations. One of the principal limitations preventing the wider adoption of this approach is due to the lack of easily identifiable species-specific degrons that can be used to trigger the degradation of target proteins. Here, we report new advancements in the targeted proteolysis concept by creating the first prokaryotic N-terminal targeted proteolysis system. We demonstrate how proteins from the LexA-like protein superfamily can be exploited as species-specific reservoirs of N- and/or C-degrons, which are easily identifiable due to their proximity to strictly conserved residues found among LexA-like proteins. Using the LexA-like regulator HdiR of Streptococcus mutans, we identified two separate N-degrons derived from HdiR that confer highly efficient constitutive proteolysis upon target proteins when added as N-terminal peptide tags. Both degrons mediate degradation via AAA+ family housekeeping proteases with one degron primarily targeting FtsH and the other targeting the ClpP-dependent proteases. To modulate degron activity, our approach incorporates a hybrid N-terminal protein tag consisting of the ubiquitin-like protein NEDD8 fused to an HdiR degron. The NEDD8 fusion inhibits degron function until the NEDD8-specific endopeptidase NEDP1 is heterologously expressed to expose the N-degron. By fusing the NEDD8-degron tag onto GFP, luciferase, and the pleiotropic regulator RNase J2, we demonstrate that the N-terminal proteolysis approach exhibits far superior performance compared to the classic transcriptional depletion approach and is similarly applicable for the study of highly toxic mutations.
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Affiliation(s)
- Nan Liu
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
| | | | - Zhoujie Xie
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
| | - Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health and Science University, Portland, OR, United States
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Wytynck P, Rougé P, Van Damme EJM. Genome-wide screening of Oryza sativa ssp. japonica and indica reveals a complex family of proteins with ribosome-inactivating protein domains. PHYTOCHEMISTRY 2017; 143:87-97. [PMID: 28797946 DOI: 10.1016/j.phytochem.2017.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/08/2017] [Accepted: 07/22/2017] [Indexed: 06/07/2023]
Abstract
Ribosome-inactivating proteins (RIPs) are cytotoxic enzymes capable of halting protein synthesis by irreversible modification of ribosomes. Although RIPs are widespread they are not ubiquitous in the plant kingdom. The physiological importance of RIPs is not fully elucidated, but evidence suggests a role in the protection of the plant against biotic and abiotic stresses. Searches in the rice genome revealed a large and highly complex family of proteins with a RIP domain. A comparative analysis retrieved 38 RIP sequences from the genome sequence of Oryza sativa subspecies japonica and 34 sequences from the subspecies indica. The RIP sequences are scattered over different chromosomes but are mostly found on the third chromosome. The phylogenetic tree revealed the pairwise clustering of RIPs from japonica and indica. Molecular modeling and sequence analysis yielded information on the catalytic site of the enzyme, and suggested that a large part of RIP domains probably possess N-glycosidase activity. Several RIPs are differentially expressed in plant tissues and in response to specific abiotic stresses. This study provides an overview of RIP motifs in rice and will help to understand their biological role(s) and evolutionary relationships.
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Affiliation(s)
- Pieter Wytynck
- Lab Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Pierre Rougé
- UMR152 PHARMA-DEV, Université de Toulouse, IRD, UPS, Chemin des Maraîchers 35, 31400, Toulouse, France
| | - Els J M Van Damme
- Lab Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium.
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35
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Sherwood RK, Roy CR. Autophagy Evasion and Endoplasmic Reticulum Subversion: The Yin and Yang of Legionella Intracellular Infection. Annu Rev Microbiol 2017; 70:413-33. [PMID: 27607556 DOI: 10.1146/annurev-micro-102215-095557] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The gram-negative bacterial pathogen Legionella pneumophila creates a novel organelle inside of eukaryotic host cells that supports intracellular replication. The L. pneumophila-containing vacuole evades fusion with lysosomes and interacts intimately with the host endoplasmic reticulum (ER). Although the natural hosts for L. pneumophila are free-living protozoa that reside in freshwater environments, the mechanisms that enable this pathogen to replicate intracellularly also function when mammalian macrophages phagocytose aerosolized bacteria, and infection of humans by L. pneumophila can result in a severe pneumonia called Legionnaires' disease. A bacterial type IVB secretion system called Dot/Icm is essential for intracellular replication of L. pneumophila. The Dot/Icm apparatus delivers over 300 different bacterial proteins into host cells during infection. These bacterial proteins have biochemical activities that target evolutionarily conserved host factors that control membrane transport processes, which results in the formation of the ER-derived vacuole that supports L. pneumophila replication. This review highlights research discoveries that have defined interactions between vacuoles containing L. pneumophila and the host ER. These studies reveal how L. pneumophila creates a vacuole that supports intracellular replication by subverting host proteins that control biogenesis and fusion of early secretory vesicles that exit the ER and host proteins that regulate the shape and dynamics of the ER. In addition to recruiting ER-derived membranes for biogenesis of the vacuole in which L. pneumophila replicates, these studies have revealed that this pathogen has a remarkable ability to interfere with the host's cellular process of autophagy, which is an ancient cell autonomous defense pathway that utilizes ER-derived membranes to target intracellular pathogens for destruction. Thus, this intracellular pathogen has evolved multiple mechanisms to control membrane transport processes that center on the involvement of the host ER.
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Affiliation(s)
- Racquel Kim Sherwood
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536;
| | - Craig R Roy
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536;
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36
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Shin YC, Chen JH, Chang SC. The molecular determinants for distinguishing between ubiquitin and NEDD8 by USP2. Sci Rep 2017; 7:2304. [PMID: 28536428 PMCID: PMC5442100 DOI: 10.1038/s41598-017-02322-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/18/2017] [Indexed: 12/23/2022] Open
Abstract
Ubiquitin (Ub) shares the highest sequence identity with neuronal-precursor-cell-expressed developmentally downregulated protein-8 (NEDD8) in the Ub-like protein family. However, different enzyme systems are precisely employed for targeting Ub and NEDD8 to specific substrates. The molecular determinants for distinguishing between Ub and NEDD8 by Ub-specific peptidases (USPs) remain poorly characterized. By replacing the non-conserved residues of Ub with their NEDD8 equivalents by mutagenesis, and vice versa, we observed that the Ub4K, Ub12E, and Ub14E mutants partially and the Ub4K/12E/14E/72A mutant completely prevented their hydrolysis by USP2. The NEDD84F and NEDD814T mutants were slightly hydrolyzed by USP2; however, the NEDD812T/14T/72R and NEDD84F/12T/14T/72R mutants were accessible for hydrolysis by USP2, suggesting that Ub and NEDD8 residues 4, 12, 14, and 72 serve as the molecular determinants for specific recognition by USP2. We also demonstrated that the level of inhibition caused by Ub mutants with multiple mutation sites was not purely additive when compared with the single mutation results. Furthermore, USP2 was determined to bind to the N-terminus of Ub to form a stable interaction, after which it binds with the C-terminus of Ub to ensure substrate specificity. The same results were also discovered when Ub, Ub4K/12E/14E/72A, NEDD8, and NEDD84F/12T/14T/72R were incubated with USP21.
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Affiliation(s)
- Yung-Cheng Shin
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Jou-Han Chen
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Shih-Chung Chang
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan. .,Center of Biotechnology, National Taiwan University, Taipei, Taiwan.
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37
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Coleman KE, Békés M, Chapman JR, Crist SB, Jones MJK, Ueberheide BM, Huang TT. SENP8 limits aberrant neddylation of NEDD8 pathway components to promote cullin-RING ubiquitin ligase function. eLife 2017; 6:e24325. [PMID: 28475037 PMCID: PMC5419743 DOI: 10.7554/elife.24325] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 04/19/2017] [Indexed: 01/02/2023] Open
Abstract
NEDD8 is a ubiquitin-like modifier most well-studied for its role in activating the largest family of ubiquitin E3 ligases, the cullin-RING ligases (CRLs). While many non-cullin neddylation substrates have been proposed over the years, validation of true NEDD8 targets has been challenging, as overexpression of exogenous NEDD8 can trigger NEDD8 conjugation through the ubiquitylation machinery. Here, we developed a deconjugation-resistant form of NEDD8 to stabilize the neddylated form of cullins and other non-cullin substrates. Using this strategy, we identified Ubc12, a NEDD8-specific E2 conjugating enzyme, as a substrate for auto-neddylation. Furthermore, we characterized SENP8/DEN1 as the protease that counteracts Ubc12 auto-neddylation, and observed aberrant neddylation of Ubc12 and other NEDD8 conjugation pathway components in SENP8-deficient cells. Importantly, loss of SENP8 function contributes to accumulation of CRL substrates and defective cell cycle progression. Thus, our study highlights the importance of SENP8 in maintaining proper neddylation levels for CRL-dependent proteostasis.
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Affiliation(s)
- Kate E Coleman
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - Miklós Békés
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - Jessica R Chapman
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University School of Medicine, New York, United States
| | - Sarah B Crist
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - Mathew JK Jones
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, Unites States
| | - Beatrix M Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University School of Medicine, New York, United States
| | - Tony T Huang
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
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38
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Yang A, Pantoom S, Wu YW. Elucidation of the anti-autophagy mechanism of the Legionella effector RavZ using semisynthetic LC3 proteins. eLife 2017; 6. [PMID: 28395732 PMCID: PMC5388539 DOI: 10.7554/elife.23905] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 03/15/2017] [Indexed: 12/13/2022] Open
Abstract
Autophagy is a conserved cellular process involved in the elimination of proteins and organelles. It is also used to combat infection with pathogenic microbes. The intracellular pathogen Legionella pneumophila manipulates autophagy by delivering the effector protein RavZ to deconjugate Atg8/LC3 proteins coupled to phosphatidylethanolamine (PE) on autophagosomal membranes. To understand how RavZ recognizes and deconjugates LC3-PE, we prepared semisynthetic LC3 proteins and elucidated the structures of the RavZ:LC3 interaction. Semisynthetic LC3 proteins allowed the analysis of structure-function relationships. RavZ extracts LC3-PE from the membrane before deconjugation. RavZ initially recognizes the LC3 molecule on membranes via its N-terminal LC3-interacting region (LIR) motif. The RavZ α3 helix is involved in extraction of the PE moiety and docking of the acyl chains into the lipid-binding site of RavZ that is related in structure to that of the phospholipid transfer protein Sec14. Thus, Legionella has evolved a novel mechanism to specifically evade host autophagy.
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Affiliation(s)
- Aimin Yang
- Institute of Chemical Biology and Precision Therapy, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.,Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.,Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Supansa Pantoom
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.,Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Yao-Wen Wu
- Institute of Chemical Biology and Precision Therapy, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.,Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.,Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
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39
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Li L, Cao Y, Wu H, Ye X, Zhu Z, Xing G, Shen C, Barik A, Zhang B, Xie X, Zhi W, Gan L, Su H, Xiong WC, Mei L. Enzymatic Activity of the Scaffold Protein Rapsyn for Synapse Formation. Neuron 2016; 92:1007-1019. [PMID: 27839998 DOI: 10.1016/j.neuron.2016.10.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 07/21/2016] [Accepted: 10/07/2016] [Indexed: 12/22/2022]
Abstract
Neurotransmission is ensured by a high concentration of neurotransmitter receptors at the postsynaptic membrane. This is mediated by scaffold proteins that bridge the receptors with cytoskeleton. One such protein is rapsyn (receptor-associated protein at synapse), which is essential for acetylcholine receptor (AChR) clustering and NMJ (neuromuscular junction) formation. We show that the RING domain of rapsyn contains E3 ligase activity. Mutation of the RING domain that abolishes the enzyme activity inhibits rapsyn- as well as agrin-induced AChR clustering in heterologous and muscle cells. Further biological and genetic studies support a working model where rapsyn, a classic scaffold protein, serves as an E3 ligase to induce AChR clustering and NMJ formation, possibly by regulation of AChR neddylation. This study identifies a previously unappreciated enzymatic function of rapsyn and a role of neddylation in synapse formation, and reveals a potential target of therapeutic intervention for relevant neurological disorders.
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Affiliation(s)
- Lei Li
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Yu Cao
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Haitao Wu
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Xinchun Ye
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Zhihui Zhu
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Guanglin Xing
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Chengyong Shen
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Arnab Barik
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Bin Zhang
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Xiaoling Xie
- Department of Ophthalmology, University of Rochester, Rochester, NY 14642, USA
| | - Wenbo Zhi
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Lin Gan
- Department of Ophthalmology, University of Rochester, Rochester, NY 14642, USA
| | - Huabo Su
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Wen-Cheng Xiong
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; Department of Neurology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; Charlie Norwood VA Medical Center, Augusta, GA 30912, USA
| | - Lin Mei
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; Department of Neurology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; Charlie Norwood VA Medical Center, Augusta, GA 30912, USA.
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40
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The Molecular Basis for Ubiquitin and Ubiquitin-like Specificities in Bacterial Effector Proteases. Mol Cell 2016; 63:261-276. [PMID: 27425412 PMCID: PMC4961225 DOI: 10.1016/j.molcel.2016.06.015] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/02/2016] [Accepted: 06/08/2016] [Indexed: 12/18/2022]
Abstract
Pathogenic bacteria rely on secreted effector proteins to manipulate host signaling pathways, often in creative ways. CE clan proteases, specific hydrolases for ubiquitin-like modifications (SUMO and NEDD8) in eukaryotes, reportedly serve as bacterial effector proteins with deSUMOylase, deubiquitinase, or, even, acetyltransferase activities. Here, we characterize bacterial CE protease activities, revealing K63-linkage-specific deubiquitinases in human pathogens, such as Salmonella, Escherichia, and Shigella, as well as ubiquitin/ubiquitin-like cross-reactive enzymes in Chlamydia, Rickettsia, and Xanthomonas. Five crystal structures, including ubiquitin/ubiquitin-like complexes, explain substrate specificities and redefine relationships across the CE clan. Importantly, this work identifies novel family members and provides key discoveries among previously reported effectors, such as the unexpected deubiquitinase activity in Xanthomonas XopD, contributed by an unstructured ubiquitin binding region. Furthermore, accessory domains regulate properties such as subcellular localization, as exemplified by a ubiquitin-binding domain in Salmonella Typhimurium SseL. Our work both highlights and explains the functional adaptations observed among diverse CE clan proteins. Bacterial CE proteases exhibit distinct ubiquitin/ubiquitin-like specificities Substrate specificity is acquired through variability in three common regions Structural and functional data redefine CE clan relationships across kingdoms CE effectors are fitted with accessory domains that modulate function
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41
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Abstract
Conjugation and deconjugation of ubiquitin and ubiquitin-like proteins (Ubls) to cellular proteins are highly regulated processes integral to cellular homeostasis. Most often, the C-termini of these small polypeptides are attached to lysine side chains of target proteins by an amide (isopeptide) linkage. Deubiquitinating enzymes (DUBs) and Ubl-specific proteases (ULPs) comprise a diverse group of proteases that recognize and remove ubiquitin and Ubls from their substrates. How DUBs and ULPs distinguish among different modifiers, or different polymeric forms of these modifiers, remains poorly understood. The specificity of ubiquitin/Ubl-deconjugating enzymes for particular substrates depends on multiple factors, ranging from the topography of specific substrate features, as in different polyubiquitin chain types, to structural elements unique to each enzyme. Here we summarize recent structural and biochemical studies that provide insights into mechanisms of substrate specificity among various DUBs and ULPs. We also discuss the unexpected specificities of non-eukaryotic proteases in these families.
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Affiliation(s)
- Judith A Ronau
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - John F Beckmann
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
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42
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Structural basis of substrate recognition by a bacterial deubiquitinase important for dynamics of phagosome ubiquitination. Proc Natl Acad Sci U S A 2015; 112:15090-5. [PMID: 26598703 DOI: 10.1073/pnas.1514568112] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Manipulation of the host's ubiquitin network is emerging as an important strategy for counteracting and repurposing the posttranslational modification machineries of the host by pathogens. Ubiquitin E3 ligases encoded by infectious agents are well known, as are a variety of viral deubiquitinases (DUBs). Bacterial DUBs have been discovered, but little is known about the structure and mechanism underlying their ubiquitin recognition. In this report, we found that members of the Legionella pneumophila SidE effector family harbor a DUB module important for ubiquitin dynamics on the bacterial phagosome. Structural analysis of this domain alone and in complex with ubiquitin vinyl methyl ester (Ub-VME) reveals unique molecular contacts used in ubiquitin recognition. Instead of relying on the Ile44 patch of ubiquitin, as commonly used in eukaryotic counterparts, the SdeADub module engages Gln40 of ubiquitin. The architecture of the active-site cleft presents an open arrangement with conformational plasticity, permitting deubiquitination of three of the most abundant polyubiquitin chains, with a distinct preference for Lys63 linkages. We have shown that this preference enables efficient removal of Lys63 linkages from the phagosomal surface. Remarkably, the structure reveals by far the most parsimonious use of molecular contacts to achieve deubiquitination, with less than 1,000 Å(2) of accessible surface area buried upon complex formation with ubiquitin. This type of molecular recognition appears to enable dual specificity toward ubiquitin and the ubiquitin-like modifier NEDD8.
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Louis M, Hofmann K, Broemer M. Evolutionary Loss of Activity in De-Ubiquitylating Enzymes of the OTU Family. PLoS One 2015; 10:e0143227. [PMID: 26588485 PMCID: PMC4654579 DOI: 10.1371/journal.pone.0143227] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/02/2015] [Indexed: 01/21/2023] Open
Abstract
Understanding function and specificity of de-ubiquitylating enzymes (DUBs) is a major goal of current research, since DUBs are key regulators of ubiquitylation events and have been shown to be mutated in human diseases. Most DUBs are cysteine proteases, relying on a catalytic triad of cysteine, histidine and aspartate to cleave the isopeptide bond between two ubiquitin units in a poly-ubiquitin chain. We have discovered that the two Drosophila melanogaster homologues of human OTUD4, CG3251 and Otu, contain a serine instead of a cysteine in the catalytic OTU (ovarian tumor) domain. DUBs that are serine proteases instead of cysteine- or metallo-proteases have not been described. In line with this, neither CG3251 nor Otu protein were active to cleave ubiquitin chains. Re-introduction of a cysteine in the catalytic center did not render the enzymes active, indicating that further critical features for ubiquitin binding or cleavage have been lost in these proteins. Sequence analysis of OTUD4 homologues from various other species showed that within this OTU subfamily, loss of the catalytic cysteine has occurred frequently in presumably independent events, as well as gene duplications or triplications, suggesting DUB-independent functions of OTUD4 proteins. Using an in vivo RNAi approach, we show that CG3251 might function in the regulation of Inhibitor of Apoptosis (IAP)-antagonist-induced apoptosis, presumably in a DUB-independent manner.
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Affiliation(s)
- Marcell Louis
- German Center for Neurodegenerative Diseases (DZNE), Bonn, c/o LiMeS, Carl-Troll-Str. 31, 53115, Bonn, Germany
| | - Kay Hofmann
- University of Cologne, Institute for Genetics, Zülpicher Str. 47a, 50674, Cologne, Germany
| | - Meike Broemer
- German Center for Neurodegenerative Diseases (DZNE), Bonn, c/o LiMeS, Carl-Troll-Str. 31, 53115, Bonn, Germany
- * E-mail:
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Horenkamp FA, Kauffman KJ, Kohler LJ, Sherwood RK, Krueger KP, Shteyn V, Roy CR, Melia TJ, Reinisch KM. The Legionella Anti-autophagy Effector RavZ Targets the Autophagosome via PI3P- and Curvature-Sensing Motifs. Dev Cell 2015; 34:569-76. [PMID: 26343456 DOI: 10.1016/j.devcel.2015.08.010] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/18/2015] [Accepted: 08/12/2015] [Indexed: 02/06/2023]
Abstract
Autophagy is a conserved membrane transport pathway used to destroy pathogenic microbes that access the cytosol of cells. The intracellular pathogen Legionella pneumophila interferes with autophagy by delivering an effector protein, RavZ, into the host cytosol. RavZ acts by cleaving membrane-conjugated Atg8/LC3 proteins from pre-autophagosomal structures. Its remarkable efficiency allows minute quantities of RavZ to block autophagy throughout the cell. To understand how RavZ targets pre-autophagosomes and specifically acts only on membrane-associated Atg8 proteins, we elucidated its structure. Revealed is a catalytic domain related in fold to Ulp family deubiquitinase-like enzymes and a C-terminal PI3P-binding module. RavZ targets the autophagosome via the PI3P-binding module and a catalytic domain helix, and it preferentially binds high-curvature membranes, intimating localization to highly curved domains in autophagosome intermediate membranes. RavZ-membrane interactions enhance substrate affinity, providing a mechanism for interfacial activation that also may be used by host autophagy proteins engaging only lipidated Atg8 proteins.
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Affiliation(s)
- Florian A Horenkamp
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Karlina J Kauffman
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lara J Kohler
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Racquel K Sherwood
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Kathryn P Krueger
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Vladimir Shteyn
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Craig R Roy
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Thomas J Melia
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Karin M Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.
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Abstract
NEDD8 (neural precursor cell expressed developmentally downregulated protein 8) is a ubiquitin-like protein that activates the largest ubiquitin E3 ligase family, the cullin-RING ligases. Many non-cullin neddylation targets have been proposed in recent years. However, overexpression of exogenous NEDD8 can trigger NEDD8 conjugation through the ubiquitylation machinery, which makes validating potential NEDD8 targets challenging. Here, we re-evaluate studies of non-cullin targets of NEDD8 in light of the current understanding of the neddylation pathway, and suggest criteria for identifying genuine neddylation substrates under homeostatic conditions. We describe the biological processes that might be regulated by non-cullin neddylation, and the utility of neddylation inhibitors for research and as potential therapies. Understanding the biological significance of non-cullin neddylation is an exciting research prospect primed to reveal fundamental insights.
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Mergner J, Heinzlmeir S, Kuster B, Schwechheimer C. DENEDDYLASE1 deconjugates NEDD8 from non-cullin protein substrates in Arabidopsis thaliana. THE PLANT CELL 2015; 27:741-53. [PMID: 25783028 PMCID: PMC4558671 DOI: 10.1105/tpc.114.135996] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/05/2015] [Accepted: 02/26/2015] [Indexed: 05/25/2023]
Abstract
The evolutionarily conserved 8-kD protein NEDD8 (NEURAL PRECURSOR CELL EXPRESSED, DEVELOPMENTALLY DOWN-REGULATED8) belongs to the family of ubiquitin-like modifiers. Like ubiquitin, NEDD8 is conjugated to and deconjugated from target proteins. Many targets and functions of ubiquitylation have been described; by contrast, few targets of NEDD8 have been identified. In plants as well as in non-plant organisms, the cullin subunits of cullin-RING E3 ligases are NEDD8 conjugates with a demonstrated functional role for the NEDD8 modification. The existence of other non-cullin NEDD8 targets has generally been questioned. NEDD8 is translated as a precursor protein and proteolytic processing exposes a C-terminal glycine required for NEDD8 conjugation. In animals and yeast, DENEDDYLASE1 (DEN1) processes NEDD8. Here, we show that mutants of a DEN1 homolog from Arabidopsis thaliana have no detectable defects in NEDD8 processing but do accumulate a broad range of NEDD8 conjugates; this provides direct evidence for the existence of non-cullin NEDD8 conjugates. We further identify AUXIN RESISTANT1 (AXR1), a subunit of the heterodimeric NEDD8 E1 activating enzyme, as a NEDD8-modified protein in den1 mutants and wild type and provide evidence that AXR1 function may be compromised in the absence of DEN1 activity. Thus, in plants, neddylation may serve as a regulatory mechanism for cullin and non-cullin proteins.
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Affiliation(s)
- Julia Mergner
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany Proteomics and Bioanalytics, Technische Universität München, 85354 Freising, Germany
| | - Stephanie Heinzlmeir
- Proteomics and Bioanalytics, Technische Universität München, 85354 Freising, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, Technische Universität München, 85354 Freising, Germany
| | - Claus Schwechheimer
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
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Abidi N, Xirodimas DP. Regulation of cancer-related pathways by protein NEDDylation and strategies for the use of NEDD8 inhibitors in the clinic. Endocr Relat Cancer 2015; 22:T55-70. [PMID: 25504797 DOI: 10.1530/erc-14-0315] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Post-translational modification of proteins with ubiquitin and ubiquitin-like molecules (UBLs) controls a vast if not every biological process in the cell. It is not surprising that deregulation in ubiquitin and UBL signalling has been implicated in the pathogenesis of many diseases and that these pathways are considered as major targets for therapeutic intervention. In this review, we summarise recent advances in our understanding of the role of the UBL neural precursor cell expressed developmentally downregulated-8 (NEDD8) in cancer-related processes and potential strategies for the use of NEDD8 inhibitors as chemotherapeutics.
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Affiliation(s)
- Naima Abidi
- Centre de Recherche de Biochimie MacromoléculaireUMR5235, 1919 Route de Mende, Montpellier 34293, France
| | - Dimitris P Xirodimas
- Centre de Recherche de Biochimie MacromoléculaireUMR5235, 1919 Route de Mende, Montpellier 34293, France
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Kandala S, Kim IM, Su H. Neddylation and deneddylation in cardiac biology. AMERICAN JOURNAL OF CARDIOVASCULAR DISEASE 2014; 4:140-158. [PMID: 25628956 PMCID: PMC4299693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 12/23/2014] [Indexed: 06/04/2023]
Abstract
Neddylation is a post-translational protein modification that conjugates a ubiquitin-like protein NEDD8 to target proteins. Similar to ubiquitination, neddylation is mediated by a cascade of three NEDD8 specific enzymes, an E1 activating enzyme, an E2 conjugating enzyme and one of the several E3 ligases. Neddylation is countered by the action of deneddylases via a process termed deneddylation. By altering the substrate's conformation, stability, subcellular localization or binding affinity to DNA or proteins, neddylation regulates diverse cellular processes including the ubiquitin-proteasome system-mediated protein degradation, protein transcription, cell signaling etc. Dysregulation of neddylation has been linked to cancer, neurodegenerative disorders, and more recently, cardiac disease. Here we comprehensively overview the biochemistry, the proteome and the biological function of neddylation. We also summarize the recent progress in revealing the physiological and pathological role of neddylation and deneddylation in the heart.
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Affiliation(s)
- Sridhar Kandala
- Vascular Biology Center, Medical College of Georgia, Georgia Regents UniversityAugusta, GA, USA
| | - Il-man Kim
- Vascular Biology Center, Medical College of Georgia, Georgia Regents UniversityAugusta, GA, USA
| | - Huabo Su
- Vascular Biology Center, Medical College of Georgia, Georgia Regents UniversityAugusta, GA, USA
- Department of Pharmacology and Toxicology, Medical College of Georgia, Georgia Regents UniversityAugusta, GA, USA
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Zhao Y, Morgan MA, Sun Y. Targeting Neddylation pathways to inactivate cullin-RING ligases for anticancer therapy. Antioxid Redox Signal 2014; 21:2383-400. [PMID: 24410571 PMCID: PMC4241876 DOI: 10.1089/ars.2013.5795] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 01/12/2014] [Indexed: 12/11/2022]
Abstract
SIGNIFICANCE Protein neddylation is catalyzed by an E1 NEDD8-activating enzyme (NAE), an E2 NEDD8-conjugating enzyme, and an E3 NEDD8 ligase. Known physiological substrates of neddylation are cullin family members. Cullin neddylation leads to activation of cullin-RING ligases (CRLs), the largest family of E3 ubiquitin ligases responsible for ubiquitylation and degradation of many key signaling/regulatory proteins. Thus, through modulating CRLs, neddylation regulates many biological processes, including cell cycle progression, signal transduction, and tumorigenesis. Given that NEDD8 is overexpressed and CRLs are abnormally activated in many human cancers, targeting protein neddylation, in general, and cullin neddylation, in particular, appears to be an attractive anticancer approach. RECENT ADVANCES MLN4924, a small molecule inhibitor of NAE, was discovered that inactivates CRLs and causes accumulation of CRL substrates to suppress tumor cell growth both in vitro and in vivo. Promising preclinical results advanced MLN4924 to several clinical trials for anticancer therapy. CRITICAL ISSUES In preclinical settings, MLN4924 effectively suppresses tumor cell growth by inducing apoptosis, senescence, and autophagy, and causes sensitization to chemoradiation therapies in a cellular context-dependent manner. Signal molecules that determine the cell fate upon MLN4924 treatment, however, remain elusive. Cancer cells develop MLN4924 resistance by selecting target mutations. FUTURE DIRECTIONS In the clinical side, several Phase 1b trials are under way to determine the safety and efficacy of MLN4924, acting alone or in combination with conventional chemotherapy, against human solid tumors. In the preclinical side, the efforts are being made to develop additional neddylation inhibitors by targeting NEDD8 E2s and E3s.
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Affiliation(s)
- Yongchao Zhao
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, University of Michigan , Ann Arbor, Michigan
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Friend SF, Deason-Towne F, Peterson LK, Berger AJ, Dragone LL. Regulation of T cell receptor complex-mediated signaling by ubiquitin and ubiquitin-like modifications. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL IMMUNOLOGY 2014; 3:107-123. [PMID: 25628960 PMCID: PMC4299764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 11/10/2014] [Indexed: 06/04/2023]
Abstract
Post-translational protein modifications are a dynamic method of regulating protein function in response to environmental signals. As with any cellular process, T cell receptor (TCR) complex-mediated signaling is highly regulated, since the strength and duration of TCR-generated signals governs T cell development and activation. While regulation of TCR complex-mediated signaling by phosphorylation has been well studied, regulation by ubiquitin and ubiquitin-like modifiers is still an emerging area of investigation. This review will examine how ubiquitin, E3 ubiquitin ligases, and other ubiquitin-like modifications such as SUMO and NEDD8 regulate TCR complex-mediated signaling.
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Affiliation(s)
- Samantha F Friend
- Department of Pediatrics, University of Colorado School of MedicineAurora, CO 80045, USA
- Integrated Department of Immunology, University of Colorado School of Medicine and National Jewish HealthDenver, CO 80206, USA
| | - Francina Deason-Towne
- Department of Pediatrics, University of Colorado School of MedicineAurora, CO 80045, USA
- Department of Biology, Regis UniversityDenver, CO 80221, USA
| | - Lisa K Peterson
- Department of Pediatrics, University of Colorado School of MedicineAurora, CO 80045, USA
- Integrated Department of Immunology, University of Colorado School of Medicine and National Jewish HealthDenver, CO 80206, USA
| | - Allison J Berger
- Takeda Pharmaceuticals International Co.Cambridge, MA 02139, USA
| | - Leonard L Dragone
- Department of Pediatrics, University of Colorado School of MedicineAurora, CO 80045, USA
- Integrated Department of Immunology, University of Colorado School of Medicine and National Jewish HealthDenver, CO 80206, USA
- Division of Rheumatology, Colorado Children’s HospitalAurora, CO 80045, USA
- Since completing this study, Dr. Dragone has joined Genentech, a member of the Roche group. GenentechSouth San Francisco, CA 94090, USA
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