151
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Hochstrasser M. Preface. Methods Enzymol 2019; 618:xvii-xix. [DOI: 10.1016/s0076-6879(19)30079-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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152
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Bramasole L, Sinha A, Gurevich S, Radzinski M, Klein Y, Panat N, Gefen E, Rinaldi T, Jimenez-Morales D, Johnson J, Krogan NJ, Reis N, Reichmann D, Glickman MH, Pick E. Proteasome lid bridges mitochondrial stress with Cdc53/Cullin1 NEDDylation status. Redox Biol 2019; 20:533-543. [PMID: 30508698 PMCID: PMC6279957 DOI: 10.1016/j.redox.2018.11.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/11/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023] Open
Abstract
Cycles of Cdc53/Cullin1 rubylation (a.k.a NEDDylation) protect ubiquitin-E3 SCF (Skp1-Cullin1-F-box protein) complexes from self-destruction and play an important role in mediating the ubiquitination of key protein substrates involved in cell cycle progression, development, and survival. Cul1 rubylation is balanced by the COP9 signalosome (CSN), a multi-subunit derubylase that shows 1:1 paralogy to the 26S proteasome lid. The turnover of SCF substrates and their relevance to various diseases is well studied, yet, the extent by which environmental perturbations influence Cul1 rubylation/derubylation cycles per se is still unclear. In this study, we show that the level of cellular oxidation serves as a molecular switch, determining Cullin1 rubylation/derubylation ratio. We describe a mutant of the proteasome lid subunit, Rpn11 that exhibits accumulated levels of Cullin1-Rub1 conjugates, a characteristic phenotype of csn mutants. By dissecting between distinct phenotypes of rpn11 mutants, proteasome and mitochondria dysfunction, we were able to recognize the high reactive oxygen species (ROS) production during the transition of cells into mitochondrial respiration, as a checkpoint of Cullin1 rubylation in a reversible manner. Thus, the study adds the rubylation cascade to the list of cellular pathways regulated by redox homeostasis.
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Affiliation(s)
- L Bramasole
- Department of Human Biology, The Faculty of Natural Sciences, University of Haifa, Haifa 3190500, Israel; Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - A Sinha
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - S Gurevich
- Department of Biology, Technion-Israel Institute of Technology, 3200000 Haifa, Israel
| | - M Radzinski
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 9190400, Israel
| | - Y Klein
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - N Panat
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - E Gefen
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - T Rinaldi
- Department of Biology and Biotechnology, University of Rome ''La Sapienza'', Rome 00185, Italy
| | - D Jimenez-Morales
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - J Johnson
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - N J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - N Reis
- Department of Biology, Technion-Israel Institute of Technology, 3200000 Haifa, Israel
| | - D Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 9190400, Israel
| | - M H Glickman
- Department of Biology, Technion-Israel Institute of Technology, 3200000 Haifa, Israel
| | - E Pick
- Department of Human Biology, The Faculty of Natural Sciences, University of Haifa, Haifa 3190500, Israel; Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel.
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153
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Abstract
Protein (poly-)ubiquitination is a posttranslational modification that plays a key role in almost all cellular processes. It involves the installment of either single ubiquitin (Ub) moieties or one of eight different polyUb linkage types, each giving a distinct cellular outcome. Deubiquitinating enzymes (DUBs) reverse Ub signaling by disassembly of one or multiple poly-Ub chain types and their malfunction is often associated with human disease. The Ub system displays significant crosstalk with structurally homologous ubiquitin-like proteins (Ubls), including SUMO, Nedd8, and ISG15. This can be seen with the existence of heterogeneous chains made from Ub-Ubl mixtures as well as the proteolytic cross reactivity displayed by several DUBs toward other Ubl systems. In addition, numerous pathogens have been found to encode Ub(l)-ligases and deconjugating enzymes in order to facilitate infection and fight the host immune response. Studying the activity of DUBs and Ubl-specific proteases, both human as well as pathogen-derived, gives fundamental insights into their physiological roles. Activity-based probes (ABPs) have proven to be valuable tools to achieve this, as they report on enzyme activities by making a (often irreversible) covalent complex, rather than on their relative abundance. In this chapter, we explain the potential of ABPs to assess substrate preferences, structural features, and activity of Ub and Ubl deconjugating enzymes. We further demonstrate the practical use of ABPs to (1) characterize the activity of viral proteases toward Ub and Ubls and (2) to gain more insight in the structural determinants of substrate preference of DUBs.
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154
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Chicooree N, Griffiths JR. A Combined Chemical Derivatization/Mass Spectrometric Method for the Enhanced Detection and Relative Quantification of Protein Ubiquitination. Methods Mol Biol 2019; 1977:17-24. [PMID: 30980319 DOI: 10.1007/978-1-4939-9232-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Mass spectrometry (MS) is a sensitive analytical technique with wide application across the sciences including for the detection of peptides and proteins in biological analysis. Ubiquitinated (Ub) proteins are typically analyzed by proteolytic digestion and subsequent chromatographic separation followed by MS detection of the resulting isopeptides. Here we describe a novel method which enables enhanced detection of this important posttranslational modification (PTM) by use of a simple chemical labeling strategy prior to Data-Independent Acquisition (DIA) using a SWATH-based acquisition approach on a suitable Quadrupole-Time-Of-Flight (Q-TOF) mass spectrometer.
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155
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Philippsen GS, DeMarco R. Impact of transposable elements in the architecture of genes of the human parasite Schistosoma mansoni. Mol Biochem Parasitol 2018; 228:27-31. [PMID: 30597185 DOI: 10.1016/j.molbiopara.2018.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 12/06/2018] [Accepted: 12/27/2018] [Indexed: 01/26/2023]
Abstract
The parasites belonging to the genus Schistosoma are agents of schistosomiasis, a disease estimated as affecting 235 million people in the world. To better understand the structure of Schistosoma mansoni genome, transposable elements (TEs) distribution and impact on gene structures were investigated. Our analyses indicated a differential distribution of TEs throughout the gene structure. Introns located at the 5' end of the genes are less prone to display TEs and introns lacking TEs tend to be shorter. Therefore, this could be one of the factors explaining previous data showing that S. mansoni displays shorter introns near the 5' end of the genes. Identification of six genes harboring TEs in their coding region suggests a positive contribution for the evolution of proteome repertory of S. mansoni. Taken together, our data suggest significant contributions of TEs to the architecture of genes from S. mansoni.
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Affiliation(s)
- Gisele S Philippsen
- Universidade Federal do Paraná, Jandaia do Sul, Dr. Maximiano street, n. 426, Paraná, Brazil.
| | - Ricardo DeMarco
- Departamento de Física e Ciência Interdisciplinar, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
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156
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Han HG, Moon HW, Jeon YJ. ISG15 in cancer: Beyond ubiquitin-like protein. Cancer Lett 2018; 438:52-62. [DOI: 10.1016/j.canlet.2018.09.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 09/06/2018] [Indexed: 01/08/2023]
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157
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Ye X, Zhang Y, Qiu C, Corke H, Sui Z. Extraction and characterization of starch granule-associated proteins from rice that affect in vitro starch digestibility. Food Chem 2018; 276:754-760. [PMID: 30409658 DOI: 10.1016/j.foodchem.2018.10.042] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 10/06/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
Abstract
Starch granule-associated proteins (SGAPs) including granule-surface proteins and granule-channel proteins in waxy, low- and high-amylose rice starch were extracted and identified. The in vitro digestibility of starch was investigated before and after the extraction of granule-channel proteins or total SGAPs. The results showed that 10 types of major differentially expressed proteins (DEPs) including 14-3-3-like protein and ribosomal protein were found among starches. In addition, the lack of only granule-channel proteins or total SGAPs led to significant and different changes in the levels of rapidly digestible starch, slowly digestible starch and resistant starch. Possible mechanisms are related to the accessibility of amylase into starch granules and structural properties of SGAPs. This study provides more information about DEPs in rice starch with different amylose content and supports further study on the relationship between SGAPs and in vitro starch digestibility.
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Affiliation(s)
- Xiaoting Ye
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; International Institute for Professional Education, Shanghai University of Finance and Economics, Shanghai 200083, China
| | - Yu Zhang
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen Qiu
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Harold Corke
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Zhongquan Sui
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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158
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Mehrtash AB, Hochstrasser M. Ubiquitin-dependent protein degradation at the endoplasmic reticulum and nuclear envelope. Semin Cell Dev Biol 2018; 93:111-124. [PMID: 30278225 DOI: 10.1016/j.semcdb.2018.09.013] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 01/01/2023]
Abstract
Numerous nascent proteins undergo folding and maturation within the luminal and membrane compartments of the endoplasmic reticulum (ER). Despite the presence of various factors in the ER that promote protein folding, many proteins fail to properly fold and assemble and are subsequently degraded. Regulatory proteins in the ER also undergo degradation in a way that is responsive to stimuli or the changing needs of the cell. As in most cellular compartments, the ubiquitin-proteasome system (UPS) is responsible for the majority of the degradation at the ER-in a process termed ER-associated degradation (ERAD). Autophagic processes utilizing ubiquitin-like protein-conjugating systems also play roles in protein degradation at the ER. The ER is continuous with the nuclear envelope (NE), which consists of the outer nuclear membrane (ONM) and inner nuclear membrane (INM). While ERAD is known also to occur at the NE, only some of the ERAD ubiquitin-ligation pathways function at the INM. Protein degradation machineries in the ER/NE target a wide variety of substrates in multiple cellular compartments, including the cytoplasm, nucleoplasm, ER lumen, ER membrane, and the NE. Here, we review the protein degradation machineries of the ER and NE and the underlying mechanisms dictating recognition and processing of substrates by these machineries.
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Affiliation(s)
- Adrian B Mehrtash
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, 06520, CT, USA.
| | - Mark Hochstrasser
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA; Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, 06520, CT, USA.
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159
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Emerging Roles of Ubiquitin-like Proteins in Pre-mRNA Splicing. Trends Biochem Sci 2018; 43:896-907. [PMID: 30269981 DOI: 10.1016/j.tibs.2018.09.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/31/2018] [Accepted: 09/06/2018] [Indexed: 12/12/2022]
Abstract
Ubiquitin-like proteins (UBLs) belong to the protein family whose members share a globular beta-grasp fold structure. The archetypal member, ubiquitin, is known for its function in proteasome-mediated protein degradation. UBLs have been shown to play several crucial roles besides protein turnover, including DNA damage response, cell cycle control, cellular signaling, protein trafficking, and innate immunity activation. In the past few years, accumulating evidence illustrates that four UBLs, namely, ubiquitin, SUMO, Hub1, and Sde2, are involved in eukaryotic pre-mRNA splicing. They modify the spliceosomes and promote splicing by adding new surfaces for intermolecular interactions, thereby refining the outcome of gene expression. In this review article, we highlight recent discoveries with an emphasis on the emerging roles of UBLs in splicing regulation.
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160
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Stewart L, D M Edgar J, Blakely G, Patrick S. Antigenic mimicry of ubiquitin by the gut bacterium Bacteroides fragilis: a potential link with autoimmune disease. Clin Exp Immunol 2018; 194:153-165. [PMID: 30076785 PMCID: PMC6194340 DOI: 10.1111/cei.13195] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/18/2018] [Accepted: 07/28/2018] [Indexed: 01/09/2023] Open
Abstract
Ubiquitin is highly conserved across eukaryotes and is essential for normal eukaryotic cell function. The bacterium Bacteroides fragilis is a member of the normal human gut microbiota, and the only bacterium known to encode a homologue of eukaryotic ubiquitin. The B. fragilis gene sequence indicates a past horizontal gene transfer event from a eukaryotic source. It encodes a protein (BfUbb) with 63% identity to human ubiquitin which is exported from the bacterial cell. The aim of this study was (i) to determine if there was antigenic cross‐reactivity between B. fragilis ubiquitin and human ubiquitin and (ii) to determine if humans produced antibodies to BfUbb. Molecular model comparisons of BfUbb and human ubiquitin predicted a high level (99·8% confidence) of structural similarity. Linear epitope mapping identified epitopes in BfUbb and human ubiquitin that cross‐react. BfUbb also has epitope(s) that do not cross‐react with human ubiquitin. The reaction of human serum (n = 474) to BfUbb and human ubiquitin from the following four groups of subjects was compared by enzyme‐linked immunosorbent assay (ELISA): (1) newly autoantibody‐positive patients, (2) allergen‐specific immunoglobulin (Ig)E‐negative patients, (3) ulcerative colitis patients and (4) healthy volunteers. We show that the immune system of some individuals has been exposed to BfUbb which has resulted in the generation of IgG antibodies. Serum from patients referred for first‐time testing to an immunology laboratory for autoimmune disease are more likely to have a high level of antibodies to BfUbb than healthy volunteers. Molecular mimicry of human ubiquitin by BfUbb could be a trigger for autoimmune disease.
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Affiliation(s)
- L Stewart
- School School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - J D M Edgar
- Regional Immunology Laboratory, Belfast Health and Social Care Trust, Belfast, UK.,The Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - G Blakely
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - S Patrick
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,The Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
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161
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Expression profiling of ubiquitin-related genes in LKB1 mutant lung adenocarcinoma. Sci Rep 2018; 8:13221. [PMID: 30185829 PMCID: PMC6125361 DOI: 10.1038/s41598-018-31592-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 08/20/2018] [Indexed: 12/12/2022] Open
Abstract
Liver kinase B1 (LKB1) is a tumor suppressor, and there is a very high proportion of LKB1 mutation in lung adenocarcinoma. The function of LKB1 is closely related to that of ubiquitin related genes. Our objective is to analyze the changes in ubiquitin-related genes in LKB1 mutant lung adenocarcinoma. We searched The Cancer Genome Atlas (TCGA) and obtained gene expression profiles from 230 lung adenocarcinoma patients, which were then analyzed using R software. Kaplan–Meier curves and Cox proportional hazards regression were applied to estimate survival. Real-time reverse transcription PCR was used to verify gene expression. Gene function was explored by gene set enrichment analysis. There were significantly expressed differences in the ubiquitin-related gene SH3RF1 between the LKB1 mutant and wild-type lung adenocarcinoma patients (p = 9.78013E-05). Patients with LKB1 mutation and high expression of SH3RF1 had a better prognosis than the low expression group (HR 0.356, 95% CI 0.136–0.929, p = 0.035). SH3RF1 can influence cell cycle, apoptosis, DNA replication and the p53 signaling pathway. SH3RF1 might have great clinical value act as a diagnostic biomarker and indicator to evaluate the prognosis of LKB1 mutant lung adenocarcinoma patients. This gene also can become a new treatment target for LKB1 mutant lung adenocarcinoma patients.
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162
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Garrido E, Srivastava AK, Sadanandom A. Exploiting protein modification systems to boost crop productivity: SUMO proteases in focus. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4625-4632. [PMID: 29897480 PMCID: PMC6117578 DOI: 10.1093/jxb/ery222] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In recent years, post-translational modification (PTM) of proteins has emerged as a key process that integrates plant growth and response to a changing environment. During the processes of domestication and breeding, plants were selected for various yield and adaptational characteristics. The post-translational modifier small ubiquitin-like modifier (SUMO) protein is known to have a role in the regulation of a number of these characteristics. Using bioinformatics, we mined the genomes of cereal and Brassica crops and their non-crop relatives Arabidopsis thaliana and Brachypodium distachyon for ubiquitin-like protease (ULP) SUMO protease sequences. We discovered that the SUMO system in cereal crops is disproportionately elaborate in comparison with that in B. distachyon. We use these data to propose deSUMOylation as a mechanism for specificity in the SUMO system.
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Affiliation(s)
- Emma Garrido
- Department of Biosciences, Durham University, Stockton Road, Durham, UK
| | | | - Ari Sadanandom
- Department of Biosciences, Durham University, Stockton Road, Durham, UK
- Correspondence:
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163
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Ubiquitin-Mimicking Peptides Transfer Differentiates by E1 and E2 Enzymes. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6062520. [PMID: 30246024 PMCID: PMC6136576 DOI: 10.1155/2018/6062520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/18/2018] [Accepted: 08/01/2018] [Indexed: 12/15/2022]
Abstract
Ubiquitin and ubiquitin like proteins (UBLs) play key roles in eukaryotes. These proteins are attached to their target proteins through an E1-E2-E3 cascade and modify the functions of these proteins. Since the discovery of ubiquitin, several UBLs have been identified, including Nedd8, SUMO, ISG15, and Atg8. Ubiquitin and UBLs share a similar three-dimensional structure: β-grasp fold and an X-X-[R/A/E/K]-X-X-[G/X]-G motif at the C-terminus. We have previously reported that ubiquitin, Nedd8, and SUMO mimicking peptides which all contain the conserved motif X-X-[R/A/E/K]-X-X-[G/X]-G still retained their reactivity toward their corresponding E1, E2, and E3 enzymes. In our current study, we investigated whether such C-terminal peptides could still be transferred onto related pathway enzymes to probe the function of these enzymes when they are fused with a protein. By bioinformatic search of protein databases, we selected eight proteins carrying the X-X-[R/A/E/K]-X-X-[G/X]-G motif at the C-terminus of the β-grasp fold. We synthesized the C-terminal sequences of these candidates as short peptides and found that three of them showed significant reactivity with the ubiquitin E1 enzyme Ube1. We next fused the three reactive short peptides to three different protein frames, including their respective native protein frames, a ubiquitin frame and a peptidyl carrier protein (PCP) frame, and measured the reactivities of these peptide-fused proteins with Ube1. Peptide-fused proteins on ubiquitin and PCP frames showed obvious reactivity with Ube1. However, when we measured E2 UbcH7 transfer, we found that the PCP-peptide fusions lost their reactivity with UbcH7. Taken together, these results suggested that the recognition of E2 enzymes with peptide-fused proteins depended not only on the C-terminal sequences of the ubiquitin-mimicking peptides, but also on the overall structures of the protein frames.
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164
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Feng T, Deng L, Lu X, Pan W, Wu Q, Dai J. Ubiquitin-conjugating enzyme UBE2J1 negatively modulates interferon pathway and promotes RNA virus infection. Virol J 2018; 15:132. [PMID: 30157886 PMCID: PMC6114777 DOI: 10.1186/s12985-018-1040-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/10/2018] [Indexed: 12/11/2022] Open
Abstract
Background Viral infection activates innate immune pathways and interferons (IFNs) play a pivotal role in the outcome of a viral infection. Ubiquitin modifications of host and viral proteins significantly influence the progress of virus infection. Ubiquitin-conjugating enzyme E2s (UBE2) have the capacity to determine ubiquitin chain topology and emerge as key mediators of chain assembly. Methods In this study, we screened the functions of 34 E2 genes using an RNAi library during Dengue virus (DENV) infection. RNAi and gene overexpression approaches were used to study the gene function in viral infection and interferon signaling. Results We found that silencing UBE2J1 significantly impaired DENV infection, while overexpression of UBE2J1 enhanced DENV infection. Further studies suggested that type I IFN expression was significantly increased in UBE2J1 silenced cells and decreased in UBE2J1 overexpressed cells. Reporter assay suggested that overexpression of UBE2J1 dramatically suppressed RIG-I directed IFNβ promoter activation. Finally, we have confirmed that UBE2J1 can facilitate the ubiquitination and degradation of transcription factor IFN regulatory factor 3 (IRF3). Conclusion These results suggest that UBE2 family member UBE2J1 can negatively regulate type I IFN expression, thereby promote RNA virus infection. Electronic supplementary material The online version of this article (10.1186/s12985-018-1040-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tingting Feng
- Institute of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, 199 Ren-ai Road, Suzhou, 215123, People's Republic of China
| | - Lei Deng
- Institute of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, 199 Ren-ai Road, Suzhou, 215123, People's Republic of China
| | - Xiaochuan Lu
- Institute of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, 199 Ren-ai Road, Suzhou, 215123, People's Republic of China
| | - Wen Pan
- Institute of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, 199 Ren-ai Road, Suzhou, 215123, People's Republic of China
| | - Qihan Wu
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai Institute of Planned Parenthood Research, Shanghai, 200032, People's Republic of China.
| | - Jianfeng Dai
- Institute of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, 199 Ren-ai Road, Suzhou, 215123, People's Republic of China. .,Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai Institute of Planned Parenthood Research, Shanghai, 200032, People's Republic of China.
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165
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Fuchs ACD, Maldoner L, Wojtynek M, Hartmann MD, Martin J. Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system. Nat Commun 2018; 9:2696. [PMID: 30002364 PMCID: PMC6043591 DOI: 10.1038/s41467-018-05198-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/22/2018] [Indexed: 12/05/2022] Open
Abstract
While protein ubiquitination was long believed to be a truly eukaryotic feature, recently sequenced genomes revealed complete ubiquitin (Ub) modification operons in archaea. Here, we present the structural and mechanistic characterization of an archaeal Rpn11 deubiquitinase from Caldiarchaeum subterraneum, CsRpn11, and its role in the processing of CsUb precursor and ubiquitinated proteins. CsRpn11 activity is affected by the catalytic metal ion type, small molecule inhibitors, sequence characteristics at the cleavage site, and the folding state of CsUb-conjugated proteins. Comparison of CsRpn11 and CsRpn11-CsUb crystal structures reveals a crucial conformational switch in the CsRpn11 Ins-1 site, which positions CsUb for catalysis. The presence of this transition in a primordial soluble Rpn11 thus predates the evolution of eukaryotic Rpn11 immobilized in the proteasomal lid. Complementing phylogenetic studies, which designate CsRpn11 and CsUb as close homologs of the respective eukaryotic proteins, our results provide experimental support for an archaeal origin of protein ubiquitination.
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Affiliation(s)
- Adrian C D Fuchs
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Lorena Maldoner
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Matthias Wojtynek
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Jörg Martin
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
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166
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Hua Z, Doroodian P, Vu W. Contrasting duplication patterns reflect functional diversities of ubiquitin and ubiquitin-like protein modifiers in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:296-311. [PMID: 29738099 DOI: 10.1111/tpj.13951] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 03/29/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
Ubiquitin (Ub) and Ub-like proteins, collectively forming the ubiquiton family, regulate nearly all aspects of cellular processes via post-translational modifications. Studies devoted to specific members suggested a large expansion of this family in plants; however, a lack of systematic analysis hinders the comparison of individual members at both evolutionary history and functional divergence levels, which may provide new insight into biological functions. In this work, we first retrieved a total of 5856 members of 17 known ubiquiton subfamilies in 50 plant genomes by searching both prior annotations and missing loci in each genome. We then applied this list to analyze the duplication history of major ubiquiton subfamilies in plants. We show that autophagy-related protein 8 (ATG8), membrane-anchored Ub-fold (MUB), small Ub-like modifier (SUMO) and Ub loci encode 88% of the plant ubiquiton family. Although whole genome duplications (WGDs) significantly expanded the family, we discovered contrasting duplication patterns both in species and in subfamilies. Within the family, the ATG8 and MUB members were primarily duplicated through WGDs, whereas a significant number of Ub and SUMO loci were generated through retroposition and tandem duplications, respectively. Although Ub coding regions are highly conserved in plants, promoter activity analysis demonstrated lineage-specific expression patterns of polyUb genes in Oryza sativa (rice) and Arabidopsis, confirming their retroposition origin. Based on the theory of dosage balance constraints, our study suggests that ubiquiton members duplicated through WGDs play crucial roles in plants, and that the regulatory pathways involving ATG8 and MUB are more conserved than those controlled by Ub and SUMO.
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Affiliation(s)
- Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH, 45701, USA
| | - Paymon Doroodian
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
| | - William Vu
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
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167
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Qu Q, Pan M, Gao S, Zheng Q, Yu Y, Su J, Li X, Hu H. A Highly Efficient Synthesis of Polyubiquitin Chains. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018; 5:1800234. [PMID: 30027052 PMCID: PMC6051384 DOI: 10.1002/advs.201800234] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 04/17/2018] [Indexed: 06/08/2023]
Abstract
A robust, microwave-assisted, highly efficient, solid-phase peptide synthesis method for preparing isopeptide-linked 62-mer and 76-mer isoubiquitins and polyubiquitin is developed. The strategy avoids the use of costly resins and pseudoprolines, and the isopeptide-linked building blocks can be assembled with high initial purity within 1 day. All seven diubiquitins are successfully synthesized on a multi-milligram scale; a four-segment, three-ligation method is used to obtain a K33-/K11-linked mixed triubiquitin in excellent yield. Circular dichroism and crystallographic analyses are used to verify the structures of the well-folded, synthetic polyubiquitin chains. The facile synthetic strategy is expected to be generally applicable for the rapid synthesis of isopeptide-linked isoUbs and to pave the way for the study of longer polyubiquitin chains.
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Affiliation(s)
- Qian Qu
- School of PharmacySecond Military Medical University325 Guohe RoadShanghai200433China
- Tsinghua‐Peking Center for Life SciencesTsinghua UniversityBeijing100084China
| | - Man Pan
- Tsinghua‐Peking Center for Life SciencesTsinghua UniversityBeijing100084China
| | - Shuai Gao
- Tsinghua‐Peking Center for Life SciencesTsinghua UniversityBeijing100084China
| | - Qing‐Yun Zheng
- Tsinghua‐Peking Center for Life SciencesTsinghua UniversityBeijing100084China
| | - Yuan‐Yuan Yu
- Tsinghua‐Peking Center for Life SciencesTsinghua UniversityBeijing100084China
| | - Jia‐Can Su
- Changhai HospitalSecond Military Medical University168 Changhai RoadShanghai200433China
| | - Xiang Li
- School of PharmacySecond Military Medical University325 Guohe RoadShanghai200433China
| | - Hong‐Gang Hu
- School of PharmacySecond Military Medical University325 Guohe RoadShanghai200433China
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168
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Regulation of Aspergillus nidulans CreA-Mediated Catabolite Repression by the F-Box Proteins Fbx23 and Fbx47. mBio 2018; 9:mBio.00840-18. [PMID: 29921666 PMCID: PMC6016232 DOI: 10.1128/mbio.00840-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The attachment of one or more ubiquitin molecules by SCF (Skp-Cullin-F-box) complexes to protein substrates targets them for subsequent degradation by the 26S proteasome, allowing the control of numerous cellular processes. Glucose-mediated signaling and subsequent carbon catabolite repression (CCR) are processes relying on the functional regulation of target proteins, ultimately controlling the utilization of this carbon source. In the filamentous fungus Aspergillus nidulans, CCR is mediated by the transcription factor CreA, which modulates the expression of genes encoding biotechnologically relevant enzymes. Although CreA-mediated repression of target genes has been extensively studied, less is known about the regulatory pathways governing CCR and this work aimed at further unravelling these events. The Fbx23 F-box protein was identified as being involved in CCR and the Δfbx23 mutant presented impaired xylanase production under repressing (glucose) and derepressing (xylan) conditions. Mass spectrometry showed that Fbx23 is part of an SCF ubiquitin ligase complex that is bridged via the GskA protein kinase to the CreA-SsnF-RcoA repressor complex, resulting in the degradation of the latter under derepressing conditions. Upon the addition of glucose, CreA dissociates from the ubiquitin ligase complex and is transported into the nucleus. Furthermore, casein kinase is important for CreA function during glucose signaling, although the exact role of phosphorylation in CCR remains to be determined. In summary, this study unraveled novel mechanistic details underlying CreA-mediated CCR and provided a solid basis for studying additional factors involved in carbon source utilization which could prove useful for biotechnological applications.IMPORTANCE The production of biofuels from plant biomass has gained interest in recent years as an environmentally friendly alternative to production from petroleum-based energy sources. Filamentous fungi, which naturally thrive on decaying plant matter, are of particular interest for this process due to their ability to secrete enzymes required for the deconstruction of lignocellulosic material. A major drawback in fungal hydrolytic enzyme production is the repression of the corresponding genes in the presence of glucose, a process known as carbon catabolite repression (CCR). This report provides previously unknown mechanistic insights into CCR through elucidating part of the protein-protein interaction regulatory system that governs the CreA transcriptional regulator in the reference organism Aspergillus nidulans in the presence of glucose and the biotechnologically relevant plant polysaccharide xylan.
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169
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Pozzi B, Mammi P, Bragado L, Giono LE, Srebrow A. When SUMO met splicing. RNA Biol 2018; 15:689-695. [PMID: 29741121 PMCID: PMC6152442 DOI: 10.1080/15476286.2018.1457936] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/22/2018] [Accepted: 03/20/2018] [Indexed: 12/12/2022] Open
Abstract
Spliceosomal proteins have been revealed as SUMO conjugation targets. Moreover, we have reported that many of these are in a SUMO-conjugated form when bound to a pre-mRNA substrate during a splicing reaction. We demonstrated that SUMOylation of Prp3 (PRPF3), a component of the U4/U6 di-snRNP, is required for U4/U6•U5 tri-snRNP formation and/or recruitment to active spliceosomes. Expanding upon our previous results, we have shown that the splicing factor SRSF1 stimulates SUMO conjugation to several spliceosomal proteins. Given the relevance of the splicing process, as well as the complex and dynamic nature of its governing machinery, the spliceosome, the molecular mechanisms that modulate its function represent an attractive topic of research. We posit that SUMO conjugation could represent a way of modulating spliceosome assembly and thus, splicing efficiency. How cycles of SUMOylation/de-SUMOylation of spliceosomal proteins become integrated throughout the highly choreographed spliceosomal cycle awaits further investigation.
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Affiliation(s)
- Berta Pozzi
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE, UBA- CONICET); Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Pablo Mammi
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE, UBA- CONICET); Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Laureano Bragado
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE, UBA- CONICET); Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Luciana E. Giono
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE, UBA- CONICET); Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Anabella Srebrow
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE, UBA- CONICET); Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
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170
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Yalla K, Elliott C, Day JP, Findlay J, Barratt S, Hughes ZA, Wilson L, Whiteley E, Popiolek M, Li Y, Dunlop J, Killick R, Adams DR, Brandon NJ, Houslay MD, Hao B, Baillie GS. FBXW7 regulates DISC1 stability via the ubiquitin-proteosome system. Mol Psychiatry 2018; 23:1278-1286. [PMID: 28727686 PMCID: PMC5984089 DOI: 10.1038/mp.2017.138] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 01/27/2023]
Abstract
Disrupted in schizophrenia 1 (DISC1) is a multi-functional scaffolding protein that has been associated with neuropsychiatric disease. The role of DISC1 is to assemble protein complexes that promote neural development and signaling, hence tight control of the concentration of cellular DISC1 in neurons is vital to brain function. Using structural and biochemical techniques, we show for we believe the first time that not only is DISC1 turnover elicited by the ubiquitin proteasome system (UPS) but that it is orchestrated by the F-Box protein, FBXW7. We present the structure of FBXW7 bound to the DISC1 phosphodegron motif and exploit this information to prove that disruption of the FBXW7-DISC1 complex results in a stabilization of DISC1. This action can counteract DISC1 deficiencies observed in neural progenitor cells derived from induced pluripotent stem cells from schizophrenia patients with a DISC1 frameshift mutation. Thus manipulation of DISC1 levels via the UPS may provide a novel method to explore DISC1 function.
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Affiliation(s)
- K Yalla
- College of Veterinary Medical and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - C Elliott
- College of Veterinary Medical and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
- Institute of Psychiatry, Psychology and Neuroscience, King’s College, London, UK
| | - J P Day
- College of Veterinary Medical and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - J Findlay
- College of Veterinary Medical and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - S Barratt
- College of Veterinary Medical and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Z A Hughes
- Neuroscience Research Unit, Pfizer Inc, Cambridge, MA, USA
| | - L Wilson
- Neuroscience Research Unit, Pfizer Inc, Cambridge, MA, USA
| | - E Whiteley
- College of Veterinary Medical and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - M Popiolek
- Neuroscience Research Unit, Pfizer Inc, Cambridge, MA, USA
| | - Y Li
- Department of Molecular Biology and Biophysics, University of Connecticut Health Centre, Farmington, CT, USA
| | - J Dunlop
- AstraZeneca, Neuroscience, Innovative Medicines & Early Development, Waltham, MA, USA
| | - R Killick
- Institute of Psychiatry, Psychology and Neuroscience, King’s College, London, UK
| | - D R Adams
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, UK
| | - N J Brandon
- AstraZeneca, Neuroscience, Innovative Medicines & Early Development, Waltham, MA, USA
| | - M D Houslay
- Institute of Pharmaceutical Science, King’s College, London, UK
| | - B Hao
- Department of Molecular Biology and Biophysics, University of Connecticut Health Centre, Farmington, CT, USA
| | - G S Baillie
- College of Veterinary Medical and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
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171
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Fang S, Qiu J, Wu Z, Bai T, Guo W. Down-regulation of UBC9 increases the sensitivity of hepatocellular carcinoma to doxorubicin. Oncotarget 2018; 8:49783-49795. [PMID: 28572537 PMCID: PMC5564807 DOI: 10.18632/oncotarget.17939] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/05/2017] [Indexed: 12/21/2022] Open
Abstract
UBC9 is an E2-conjugating enzyme that is required for SUMOylation and has been implicated in regulating several critical cellular pathways. UBC9 is overexpressed in certain tumors, such as lung adenocarcinoma, ovarian carcinoma and melanoma, which implies that it has special clinical significance. However, the role of UBC9 in Hepatocellular carcinoma (HCC) drug responsiveness is not clear. In this study, we investigated the clinicopathological significance of UBC9 in HCC and investigated the mechanism of UBC9-mediated chemosensitivity to doxorubicin (DOX) in hepatocellular carcinoma cells. We found that relative to adjacent normal tissues, UBC9 was markedly overexpressed in HCC, which closely correlated with tumor size, tumor microsatellite formation, and tumor encapsulation. Our results also showed that down-regulation of UBC9 by shRNA reduced the expression of Bcl-2 and Bcl-xl and increased the expression of cleaved-Caspase3, which is a proapoptotic protein. These changes were associated with reduced apoptosis in response to DOX. Furthermore, we observed a mechanism involving modulation of the P38 and ERK1/2 signaling pathways. Together, our results indicate that down-regulation of UBC9 sensitizes cells to anticancer drugs, is possibly associated with the regulation of ERK1/2 and P38 activation and interacts with the intrinsic apoptosis pathway. Thus, knockdown of UBC9 may have a tumor suppressor effect and UBC9 could be a potential target for the treatment of HCC cancer.
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Affiliation(s)
- Sufen Fang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Junyao Qiu
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Zheng Wu
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Tao Bai
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Wuhua Guo
- Department of Interventional Radiology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
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172
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Neddylation mediates ventricular chamber maturation through repression of Hippo signaling. Proc Natl Acad Sci U S A 2018; 115:E4101-E4110. [PMID: 29632206 DOI: 10.1073/pnas.1719309115] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
During development, ventricular chamber maturation is a crucial step in the formation of a functionally competent postnatal heart. Defects in this process can lead to left ventricular noncompaction cardiomyopathy and heart failure. However, molecular mechanisms underlying ventricular chamber development remain incompletely understood. Neddylation is a posttranslational modification that attaches ubiquitin-like protein NEDD8 to protein targets via NEDD8-specific E1-E2-E3 enzymes. Here, we report that neddylation is temporally regulated in the heart and plays a key role in cardiac development. Cardiomyocyte-specific knockout of NAE1, a subunit of the E1 neddylation activating enzyme, significantly decreased neddylated proteins in the heart. Mice lacking NAE1 developed myocardial hypoplasia, ventricular noncompaction, and heart failure at late gestation, which led to perinatal lethality. NAE1 deletion resulted in dysregulation of cell cycle-regulatory genes and blockade of cardiomyocyte proliferation in vivo and in vitro, which was accompanied by the accumulation of the Hippo kinases Mst1 and LATS1/2 and the inactivation of the YAP pathway. Furthermore, reactivation of YAP signaling in NAE1-inactivated cardiomyocytes restored cell proliferation, and YAP-deficient hearts displayed a noncompaction phenotype, supporting an important role of Hippo-YAP signaling in NAE1-depleted hearts. Mechanistically, we found that neddylation regulates Mst1 and LATS2 degradation and that Cullin 7, a NEDD8 substrate, acts as the ubiquitin ligase of Mst1 to enable YAP signaling and cardiomyocyte proliferation. Together, these findings demonstrate a role for neddylation in heart development and, more specifically, in the maturation of ventricular chambers and also identify the NEDD8 substrate Cullin 7 as a regulator of Hippo-YAP signaling.
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173
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Roy S, Jagus R, Morse D. Translation and Translational Control in Dinoflagellates. Microorganisms 2018; 6:microorganisms6020030. [PMID: 29642465 PMCID: PMC6027434 DOI: 10.3390/microorganisms6020030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 12/24/2022] Open
Abstract
Dinoflagellates are unicellular protists that feature a multitude of unusual nuclear features, including large genomes, packaging of DNA without histones, and multiple gene copies organized as tandem gene arrays. Furthermore, all dinoflagellate mRNAs experience trans-splicing with a common 22-nucleotide splice leader (SL) sequence. These features challenge some of the concepts and assumptions about the regulation of gene expression derived from work on model eukaryotes such as yeasts and mammals. Translational control in the dinoflagellates, based on extensive study of circadian bioluminescence and by more recent microarray and transcriptome analyses, is now understood to be a crucial element in regulating gene expression. A picture of the translation machinery of dinoflagellates is emerging from the recent availability of transcriptomes of multiple dinoflagellate species and the first complete genome sequences. The components comprising the translational control toolkit of dinoflagellates are beginning to take shape and are outlined here.
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Affiliation(s)
- Sougata Roy
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke East, Montréal, QC H1X 2B2, Canada.
| | - Rosemary Jagus
- Institute of Marine & Environmental Technology, University of Maryland Center for Environmental Science701 E. Pratt St., Baltimore, MD 21202, USA.
| | - David Morse
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke East, Montréal, QC H1X 2B2, Canada.
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174
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Carrier M, Lutzing R, Gaouar S, Rochette-Egly C. TRIM24 mediates the interaction of the retinoic acid receptor alpha with the proteasome. FEBS Lett 2018; 592:1426-1433. [PMID: 29543331 DOI: 10.1002/1873-3468.13033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/16/2018] [Accepted: 02/16/2018] [Indexed: 12/17/2022]
Abstract
The nuclear retinoic acid (RA) receptors (RARα, β and γ) are ligand-dependent regulators of transcription. Upon activation by RA, they are recruited at the promoters of target genes together with several coregulators. Then, they are degraded by the ubiquitin proteasome system. Here, we report that the degradation of the RARα subtype involves ubiquitination and the tripartite motif protein TRIM24, which was originally identified as a ligand-dependent corepressor of RARα. We show that in response to RA, TRIM24 serves as an adapter linking RARα to the proteasome for its degradation. In addition, TRIM24 and the proteasome are recruited with RARα to the promoters of target genes and thus are inherently linked to RARα transcriptional activity.
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Affiliation(s)
- Marilyn Carrier
- Department of Functional Genomics and Cancer, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM, U964, CNRS, UMR7104, Université de Strasbourg, Illkirch Cedex, France
| | - Regis Lutzing
- Department of Functional Genomics and Cancer, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM, U964, CNRS, UMR7104, Université de Strasbourg, Illkirch Cedex, France
| | - Samia Gaouar
- Department of Functional Genomics and Cancer, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM, U964, CNRS, UMR7104, Université de Strasbourg, Illkirch Cedex, France
| | - Cécile Rochette-Egly
- Department of Functional Genomics and Cancer, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM, U964, CNRS, UMR7104, Université de Strasbourg, Illkirch Cedex, France
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175
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Haahr P, Borgermann N, Guo X, Typas D, Achuthankutty D, Hoffmann S, Shearer R, Sixma TK, Mailand N. ZUFSP Deubiquitylates K63-Linked Polyubiquitin Chains to Promote Genome Stability. Mol Cell 2018; 70:165-174.e6. [PMID: 29576528 DOI: 10.1016/j.molcel.2018.02.024] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/17/2018] [Accepted: 02/15/2018] [Indexed: 12/12/2022]
Abstract
Deubiquitylating enzymes (DUBs) enhance the dynamics of the versatile ubiquitin (Ub) code by reversing and regulating cellular ubiquitylation processes at multiple levels. Here we discovered that the uncharacterized human protein ZUFSP (zinc finger with UFM1-specific peptidase domain protein/C6orf113/ZUP1), which has been annotated as a potentially inactive UFM1 protease, and its fission yeast homolog Mug105 define a previously unrecognized class of evolutionarily conserved cysteine protease DUBs. Human ZUFSP selectively interacts with and cleaves long K63-linked poly-Ub chains by means of tandem Ub-binding domains, whereas it displays poor activity toward mono- or di-Ub substrates. In cells, ZUFSP is recruited to and regulates K63-Ub conjugates at genotoxic stress sites, promoting chromosome stability upon replication stress in a manner dependent on its catalytic activity. Our findings establish ZUFSP as a new type of linkage-selective cysteine peptidase DUB with a role in genome maintenance pathways.
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Affiliation(s)
- Peter Haahr
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Nikoline Borgermann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Xiaohu Guo
- Division of Biochemistry, Cancer Genomics Center, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Dimitris Typas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Divya Achuthankutty
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Center for Chromosome Stability, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Saskia Hoffmann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Robert Shearer
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Titia K Sixma
- Division of Biochemistry, Cancer Genomics Center, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Niels Mailand
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Center for Chromosome Stability, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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176
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ISG15 promotes esophageal squamous cell carcinoma tumorigenesis via c-MET/Fyn/β-catenin signaling pathway. Exp Cell Res 2018; 367:47-55. [PMID: 29555370 DOI: 10.1016/j.yexcr.2018.03.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 12/30/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most malignant tumors in China with a poor prognosis. Most ESCC patients were diagnosed at advanced stages, losing the opportunity for surgical excision. Hence, it remains a pressing work to identify biomarkers for early detection, prognosis prediction and targeting therapies in ESCC. Interferon-stimulated gene 15 (ISG15) encodes a 15-kDa protein, and is involved in the post-translational modification (PTMs) of multiple proteins. However, the molecular functions of ISG15 in ESCC remain unclear. In this work, we found that ISG15 was aberrantly expressed in ESCC tissues and cell lines. Enhanced protein level of ISG15 promoted cellular malignant phenotypes including proliferation, migration, invasion and tumor formation in vivo. Consistently, reduction of ISG15 attenuated the cellular malignant phenotype in ESCC cell lines. Furthermore, gene-expression profiles suggested that the differentially expressed ISG15 affected the expression of a panel of genes enriched in the cell adherens junction, such as c-MET. Notably, as a secreted protein, the concentration of ISG15 was elevated in ESCC plasma than healthy individuals, acting as a potential diagnostic marker. Taken together, our results suggested a tumor promotion role of ISG15 in ESCC via c-MET/Fyn/β-catenin pathway.
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177
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Sun S, Liu S, Zhang Z, Zeng W, Sun C, Tao T, Lin X, Feng XH. Phosphatase UBLCP1 controls proteasome assembly. Open Biol 2018; 7:rsob.170042. [PMID: 28539385 PMCID: PMC5451543 DOI: 10.1098/rsob.170042] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/20/2017] [Indexed: 12/26/2022] Open
Abstract
Ubiquitin-like domain-containing C-terminal domain phosphatase 1 (UBLCP1), an FCP/SCP phosphatase family member, was identified as the first proteasome phosphatase. UBLCP1 binds to proteasome subunit Rpn1 and dephosphorylates the proteasome in vitro. However, it is still unclear which proteasome subunit(s) are the bona fide substrate(s) of UBLCP1 and the precise mechanism for proteasome regulation remains elusive. Here, we show that UBLCP1 selectively binds to the 19S regulatory particle (RP) through its interaction with Rpn1, but not the 20S core particle (CP) or the 26S proteasome holoenzyme. In the RP, UBLCP1 dephosphorylates the subunit Rpt1, impairs its ATPase activity, and consequently disrupts the 26S proteasome assembly, yet it has no effects on the RP assembly from precursor complexes. The Rpn1-binding and phosphatase activities of UBLCP1 are essential for its function on Rpt1 dephosphorylation and proteasome activity both in vivo and in vitro. Our study establishes the essential role of the UBLCP1/Rpn1/Rpt1 complex in regulating proteasome assembly.
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Affiliation(s)
- Shuangwu Sun
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Sisi Liu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Zhengmao Zhang
- Michael E. DeBakey, Department of Surgery, Houston, TX, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Wang Zeng
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Chuang Sun
- Michael E. DeBakey, Department of Surgery, Houston, TX, USA
| | - Tao Tao
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Xia Lin
- Michael E. DeBakey, Department of Surgery, Houston, TX, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Xin-Hua Feng
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China .,Michael E. DeBakey, Department of Surgery, Houston, TX, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
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178
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Trans-Binding Mechanism of Ubiquitin-like Protein Activation Revealed by a UBA5-UFM1 Complex. Cell Rep 2018; 16:3113-3120. [PMID: 27653677 DOI: 10.1016/j.celrep.2016.08.067] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 07/07/2016] [Accepted: 08/19/2016] [Indexed: 01/14/2023] Open
Abstract
Modification of proteins by ubiquitin or ubiquitin-like proteins (UBLs) is a critical cellular process implicated in a variety of cellular states and outcomes. A prerequisite for target protein modification by a UBL is the activation of the latter by activating enzymes (E1s). Here, we present the crystal structure of the non-canonical homodimeric E1, UBA5, in complex with its cognate UBL, UFM1, and supporting biochemical experiments. We find that UBA5 binds to UFM1 via a trans-binding mechanism in which UFM1 interacts with distinct sites in both subunits of the UBA5 dimer. This binding mechanism requires a region C-terminal to the adenylation domain that brings UFM1 to the active site of the adjacent UBA5 subunit. We also find that transfer of UFM1 from UBA5 to the E2, UFC1, occurs via a trans mechanism, thereby requiring a homodimer of UBA5. These findings explicitly elucidate the role of UBA5 dimerization in UFM1 activation.
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179
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Epigenetic regulation in B-cell maturation and its dysregulation in autoimmunity. Cell Mol Immunol 2018; 15:676-684. [PMID: 29375128 PMCID: PMC6123482 DOI: 10.1038/cmi.2017.133] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 12/11/2022] Open
Abstract
B cells have a critical role in the initiation and acceleration of autoimmune diseases, especially those mediated by autoantibodies. In the peripheral lymphoid system, mature B cells are activated by self or/and foreign antigens and signals from helper T cells for differentiating into either memory B cells or antibody-producing plasma cells. Accumulating evidence has shown that epigenetic regulations modulate somatic hypermutation and class switch DNA recombination during B-cell activation and differentiation. Any abnormalities in these complex regulatory processes may contribute to aberrant antibody production, resulting in autoimmune pathogenesis such as systemic lupus erythematosus. Newly generated knowledge from advanced modern technologies such as next-generation sequencing, single-cell sequencing and DNA methylation sequencing has enabled us to better understand B-cell biology and its role in autoimmune development. Thus this review aims to summarize current research progress in epigenetic modifications contributing to B-cell activation and differentiation, especially under autoimmune conditions such as lupus, rheumatoid arthritis and type 1 diabetes.
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180
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Gopinath P, Ohayon S, Nawatha M, Brik A. Chemical and semisynthetic approaches to study and target deubiquitinases. Chem Soc Rev 2018; 45:4171-98. [PMID: 27049734 DOI: 10.1039/c6cs00083e] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ubiquitination is a key posttranslational modification, which affects numerous biological processes and is reversed by a class of enzymes known as deubiquitinases (DUBs). This family of enzymes cleaves mono-ubiquitin or poly-ubiquitin chains from a target protein through different mechanisms and mode of interactions with their substrates. Studying the role of DUBs in health and diseases has been a major goal for many laboratories both in academia and in industry. However, the field has been challenged by the difficulties in obtaining native substrates and novel reagents using traditional enzymatic and molecular biology approaches. Recent advancements in the synthesis and semisynthesis of proteins made it possible to prepare several unique ubiquitin conjugates to study various aspects of DUBs such as their specificities and structures. Moreover, these approaches enable the preparation of novel activity based probes and assays to monitor DUB activities in vitro and in cellular contexts. Efforts made to bring new chemical entities for the selective inhibition of DUBs based on these tools are also highlighted with selected examples.
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Affiliation(s)
- Pushparathinam Gopinath
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Shimrit Ohayon
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Mickal Nawatha
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
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181
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Guo Y, Song Y, Guo Z, Hu M, Liu B, Duan H, Wang L, Yuan T, Wang D. Function of RAD6B and RNF8 in spermatogenesis. Cell Cycle 2018; 17:162-173. [PMID: 28825854 DOI: 10.1080/15384101.2017.1361066] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Histone ubiquitination regulates sperm formation and is important for nucleosome removal during spermatogenesis. RNF8 is an E3 ubiquitin ligase, and RAD6B is an E2 ubiquitin-conjugating enzyme. Both proteins participate in DNA damage repair processes via histone ubiquitination. Loss of RNF8 or RAD6B can lead to sterility in male mice. However, the specific mechanisms regulating these ubiquitin-mediated processes are unclear. In this study, we found that RNF8 knockout mice were either subfertile or sterile based on the numbers of offspring they produced. We explored the mechanism by which RAD6B and RNF8 knockouts cause infertility in male mice and compared the effects of their loss on spermatogenesis. Our results demonstrate that RAD6B can polyubiquitinate histones H2 A and H2B. In addition, RNF8 was shown to monoubiquitinate histones H2 A and H2B. Furthermore, we observed that absence of histone ubiquitination was not the only reason for infertility. Senescence played a role in intensifying male sterility by affecting the number of germ cells during spermatogenesis. In summary, both histone ubiquitination and senescence play important roles in spermatogenesis.
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Affiliation(s)
- Yingli Guo
- a Department of Anatomy and Histology , Lanzhou University , School of Basic Medical Sciences , Lanzhou , China
| | - Yanfeng Song
- a Department of Anatomy and Histology , Lanzhou University , School of Basic Medical Sciences , Lanzhou , China
| | - Zhao Guo
- a Department of Anatomy and Histology , Lanzhou University , School of Basic Medical Sciences , Lanzhou , China
| | - Mengjin Hu
- a Department of Anatomy and Histology , Lanzhou University , School of Basic Medical Sciences , Lanzhou , China
| | - Bing Liu
- a Department of Anatomy and Histology , Lanzhou University , School of Basic Medical Sciences , Lanzhou , China
| | - Hongyu Duan
- a Department of Anatomy and Histology , Lanzhou University , School of Basic Medical Sciences , Lanzhou , China
| | - Le Wang
- a Department of Anatomy and Histology , Lanzhou University , School of Basic Medical Sciences , Lanzhou , China
| | - Tianxia Yuan
- a Department of Anatomy and Histology , Lanzhou University , School of Basic Medical Sciences , Lanzhou , China
| | - Degui Wang
- a Department of Anatomy and Histology , Lanzhou University , School of Basic Medical Sciences , Lanzhou , China
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182
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Fu H, Xu J, Chen J, Li G, Zhao X, Chen P. Microarray analysis reveals Tmub1 as a cell cycle-associated protein in rat hepatocytes. Mol Med Rep 2018; 17:4337-4344. [PMID: 29344642 PMCID: PMC5802207 DOI: 10.3892/mmr.2018.8451] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 01/11/2018] [Indexed: 12/18/2022] Open
Abstract
Transmembrane and ubiquitin-like domain containing protein 1 (Tmub1), formerly known as hepatocyte odd protein shuttling (HOPS) has been recognized as a ubiquitously expressed shuttling protein that moves between the nucleus and cytoplasm in hepatocytes. Tmub1 is involved in liver regeneration and functions as a bridging protein in tumor cell proliferation. To investigate the transcriptional profile and potential biological processes affected by Tmub1 expression in normal rat hepatocytes, microarray and bioinformatics experiments were used to identify 127 mRNAs differentially expressed between Tmub1-overexpression, Tmub1-knockdown and normal BRL-3A cells (fold-change ≥2.5). The expression levels of 17 key node genes associated with the cell cycle were confirmed by reverse transcription-quantitative polymerase chain reaction analysis. Flow cytometry, 5-Ethynyl-20-deoxyuridine, Cell Counting Kit-8 and western blotting experiments revealed the effects on the cell cycle and the inhibition of proliferation in BRL-3A cells overexpressing Tmub1. Further co-immunoprecipitation assays demonstrated that Tmub1 interacts with cyclin A2 during the cell cycle and that the overexpression of Tmub1 may postpone cyclin A2 and cyclin B1 degradation in the M phase. The results of the present study indicated that Tmub1 functions as a cell proliferation inhibitor and cell cycle-associated protein.
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Affiliation(s)
- Hangwei Fu
- Department of Hepatobiliary Surgery, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
| | - Jianhua Xu
- Department of Hepatobiliary Surgery, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
| | - Jian Chen
- Department of Hepatobiliary Surgery, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
| | - Guangyao Li
- Department of Hepatobiliary Surgery, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
| | - Xiaobiao Zhao
- Department of Hepatobiliary Surgery, 187 Military Hospital, Haikou, Hainan 571159, P.R. China
| | - Ping Chen
- Department of Hepatobiliary Surgery, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
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183
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Sumoylation of histone deacetylase 1 regulates MyoD signaling during myogenesis. Exp Mol Med 2018; 50:e427. [PMID: 29328071 PMCID: PMC5799798 DOI: 10.1038/emm.2017.236] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 02/07/2023] Open
Abstract
Sumoylation, the conjugation of a small ubiquitin-like modifier (SUMO) protein to a target, has diverse cellular effects. However, the functional roles of the SUMO modification during myogenesis have not been fully elucidated. Here, we report that basal sumoylation of histone deacetylase 1 (HDAC1) enhances the deacetylation of MyoD in undifferentiated myoblasts, whereas further sumoylation of HDAC1 contributes to switching its binding partners from MyoD to Rb to induce myocyte differentiation. Differentiation in C2C12 skeletal myoblasts induced new immunoblot bands above HDAC1 that were gradually enhanced during differentiation. Using SUMO inhibitors and sumoylation assays, we showed that the upper band was caused by sumoylation of HDAC1 during differentiation. Basal deacetylase activity was not altered in the SUMO modification-resistant mutant HDAC1 K444/476R (HDAC1 2R). Either differentiation or transfection of SUMO1 increased HDAC1 activity that was attenuated in HDAC1 2R. Furthermore, HDAC1 2R failed to deacetylate MyoD. Binding of HDAC1 to MyoD was attenuated by K444/476R. Binding of HDAC1 to MyoD was gradually reduced after 2 days of differentiation. Transfection of SUMO1 induced dissociation of HDAC1 from MyoD but potentiated its binding to Rb. SUMO1 transfection further attenuated HDAC1-induced inhibition of muscle creatine kinase luciferase activity that was reversed in HDAC1 2R. HDAC1 2R failed to inhibit myogenesis and muscle gene expression. In conclusion, HDAC1 sumoylation plays a dual role in MyoD signaling: enhancement of HDAC1 deacetylation of MyoD in the basally sumoylated state of undifferentiated myoblasts and dissociation of HDAC1 from MyoD during myogenesis.
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184
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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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185
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Moreno-Gonzalo O, Fernandez-Delgado I, Sanchez-Madrid F. Post-translational add-ons mark the path in exosomal protein sorting. Cell Mol Life Sci 2018; 75:1-19. [PMID: 29080091 PMCID: PMC11105655 DOI: 10.1007/s00018-017-2690-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/11/2017] [Accepted: 10/23/2017] [Indexed: 02/07/2023]
Abstract
Extracellular vesicles (EVs) are released by cells to the extracellular environment to mediate inter-cellular communication. Proteins, lipids, nucleic acids and metabolites shuttled in these vesicles modulate specific functions in recipient cells. The enrichment of selected sets of proteins in EVs compared with global cellular levels suggests the existence of specific sorting mechanisms to specify EV loading. Diverse post-translational modifications (PTMs) of proteins participate in the loading of specific elements into EVs. In this review, we offer a perspective on PTMs found in EVs and discuss the specific role of some PTMs, specifically Ubiquitin and Ubiquitin-like modifiers, in exosomal sorting of protein components. The understanding of these mechanisms will provide new strategies for biomedical applications. Examples include the presence of defined PTM marks on EVs as novel biomarkers for the diagnosis and prognosis of certain diseases, or the specific import of immunogenic components into EVs for vaccine generation.
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Affiliation(s)
- Olga Moreno-Gonzalo
- Vascular Pathophysiology Research Area, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Servicio de Inmunología, Instituto Investigación Sanitaria Princesa, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Irene Fernandez-Delgado
- Vascular Pathophysiology Research Area, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Servicio de Inmunología, Instituto Investigación Sanitaria Princesa, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Francisco Sanchez-Madrid
- Vascular Pathophysiology Research Area, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain.
- Servicio de Inmunología, Instituto Investigación Sanitaria Princesa, Universidad Autónoma de Madrid (UAM), Madrid, Spain.
- CIBERCV, Madrid, Spain.
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186
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Streich FC, Lima CD. Strategies to Trap Enzyme-Substrate Complexes that Mimic Michaelis Intermediates During E3-Mediated Ubiquitin-Like Protein Ligation. Methods Mol Biol 2018; 1844:169-196. [PMID: 30242710 DOI: 10.1007/978-1-4939-8706-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Most cellular functions rely on pathways that catalyze posttranslational modification of cellular proteins by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins. Like other posttranslational modifications that require distinct writers, readers, and erasers during signaling, Ub/Ubl pathways employ distinct enzymes that catalyze Ub/Ubl attachment, Ub/Ubl recognition, and Ub/Ubl removal. Ubl protein conjugation typically relies on parallel but distinct enzymatic cascades catalyzed by an E1-activating enzyme, an E2 carrier protein, and an E3 ubiquitin-like protein ligase. One major class of E3, with ca. 600 members, harbors RING or the RING-like SP-RING or Ubox domains. These RING/RING-like domains bind and activate the E2-Ubl thioester by stabilizing a conformation that is optimal for nucleophilic attack by the side chain residue (typically lysine) on the substrate. These RING/RING-like domains typically function together with other domains or protein complexes that often serve to recruit particular substrates. How these RING/RING-like E3 domains function to activate the E2-Ubl thioester while engaged with substrate remains poorly understood. We describe a strategy to generate and purify a unique E2Ubc9-UblSUMO thioester mimetic that can be cross-linked to the SubstratePCNA at Lys164, a conjugation site that is only observed in the presence of E3Siz1. We describe two techniques to cross-link the E2Ubc9-UblSUMO thioester mimetic active site to the site of modification on PCNA and the subsequent purification of these complexes. Finally, we describe the reconstitution and purification of the E2Ubc9-UblSUMO-PCNA complex with the E3Siz1 and purification that enabled its crystallization and structure determination. We think this technique can be extended to other E2-Ubl-substrate/E3 complexes to better probe the function and specificity of RING-based E3 Ubl ligases.
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Affiliation(s)
- Frederick C Streich
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, USA.
- Howard Hughes Medical Institute, 1275 York Ave, New York, NY, USA.
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187
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BAH1 an E3 Ligase from Arabidopsis thaliana Stabilizes Heat Shock Factor σ 32 of Escherichia coli by Interacting with DnaK/DnaJ Chaperone Team. Curr Microbiol 2017; 75:450-455. [PMID: 29260303 DOI: 10.1007/s00284-017-1401-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/15/2017] [Indexed: 10/18/2022]
Abstract
In Escherichia coli, the DnaK/DnaJ chaperone can control the stability and activity of σ32, which is the key factor in heat shock response. Heterologous expression of eukaryotic molecular chaperones protects E. coli from heat stress. Here, we show that BAH1, an E3 ligase from plant that has a similar zinc finger domain to DnaJ, can perform block the effect of DnaK on σ32 in Escherichia coli. By constructing a chimeric DnaJ protein, with the J-domain of DnaJ fused to BAH1, we found BAH1 could partially compensate for the DnaJ' zinc finger domain in vivo, and that it was dependent on the zinc finger domain of BAH1. Furthermore, BAH1 could interact with both σ32 and DnaK to increase the level of HSPs, such as GroEL, DnaK, and σ32. These results suggested that the zinc finger domain was conserved during evolution.
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188
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Naik MT, Kang M, Ho CC, Liao PH, Hsieh YL, Naik NM, Wang SH, Chang I, Shih HM, Huang TH. Molecular mechanism of K65 acetylation-induced attenuation of Ubc9 and the NDSM interaction. Sci Rep 2017; 7:17391. [PMID: 29234076 PMCID: PMC5727262 DOI: 10.1038/s41598-017-17465-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/27/2017] [Indexed: 11/09/2022] Open
Abstract
The negatively charged amino acid-dependent sumoylation motif (NDSM) carries an additional stretch of acidic residues downstream of the consensus Ψ-K-x-E/D sumoylation motif. We have previously shown that acetylation of the SUMO E2 conjugase enzyme, Ubc9, at K65 downregulates its binding to the NDSM and renders a selective decrease in sumoylation of substrates with the NDSM motif. Here, we provide detailed structural, thermodynamic, and kinetics results of the interactions between Ubc9 and its K65 acetylated variant (Ac-Ubc9K65) with three NDSMs derived from Elk1, CBP, and Calpain2 to rationalize the mechanism beneath this reduced binding. Our nuclear magnetic resonance (NMR) data rule out a direct interaction between the NDSM and the K65 residue of Ubc9. Similarly, we found that NDSM binding was entropy-driven and unlikely to be affected by the negative charge by K65 acetylation. Moreover our NMR, mutagenesis and molecular dynamics simulation studies defined the sequence of the NDSM as Ψ-K-x-E/D-x1-x2-(x3/E/D)-(x4/E/D)-xn and determined that K74 and K76 were critical Ubc9 residues interacting with the negatively charged residues of the NDSM.
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Affiliation(s)
- Mandar T Naik
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.,Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, 02903, USA
| | - Mooseok Kang
- Department of Physics, Pusan National University, Busan, 46241, Korea
| | - Chun-Chen Ho
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Pei-Hsin Liao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yung-Lin Hsieh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Nandita M Naik
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Szu-Huan Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Iksoo Chang
- Center for Proteome Biophysics, Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988, Korea.
| | - Hsiu-Ming Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, 35053, Taiwan.
| | - Tai-Huang Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.
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189
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Zhang SY, Cao N, Chen MK, Zhang LD, Bai YQ, Ding SZ, Yang YX. FAT 10 protein as a potential serological marker in the diagnosis of hepatocellullar carcinoma. Clin Res Hepatol Gastroenterol 2017; 41:711-714. [PMID: 28754570 DOI: 10.1016/j.clinre.2017.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/19/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Si-Yu Zhang
- Department of Gastroenterology and Hepatology, People's Hospital of Zhengzhou University, No. 7 Wei Wu Road, 450003 Zhengzhou, Henan, P.R. China; Department of Gastroenterology and Hepatology, Zhengzhou Second Hospital, Zhengzhou, Henan, P.R. China
| | - Na Cao
- Henan Police College, Zhengzhou, Henan, China
| | - Min-Kai Chen
- Department of Gastroenterology and Hepatology, People's Hospital of Zhengzhou University, No. 7 Wei Wu Road, 450003 Zhengzhou, Henan, P.R. China
| | - Li-Da Zhang
- Department of Gastroenterology and Hepatology, People's Hospital of Zhengzhou University, No. 7 Wei Wu Road, 450003 Zhengzhou, Henan, P.R. China
| | - Yang-Qiu Bai
- Department of Gastroenterology and Hepatology, People's Hospital of Zhengzhou University, No. 7 Wei Wu Road, 450003 Zhengzhou, Henan, P.R. China
| | - Song-Ze Ding
- Department of Gastroenterology and Hepatology, People's Hospital of Zhengzhou University, No. 7 Wei Wu Road, 450003 Zhengzhou, Henan, P.R. China
| | - Yu-Xiu Yang
- Department of Gastroenterology and Hepatology, People's Hospital of Zhengzhou University, No. 7 Wei Wu Road, 450003 Zhengzhou, Henan, P.R. China.
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190
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Zaky W, Manton C, Miller CP, Khatua S, Gopalakrishnan V, Chandra J. The ubiquitin-proteasome pathway in adult and pediatric brain tumors: biological insights and therapeutic opportunities. Cancer Metastasis Rev 2017; 36:617-633. [PMID: 29071526 DOI: 10.1007/s10555-017-9700-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nearly 20 years ago, the concept of targeting the proteasome for cancer therapy began gaining momentum. This concept was driven by increased understanding of the biology/structure and function of the 26S proteasome, insight into the role of the proteasome in transformed cells, and the synthesis of pharmacological inhibitors with clinically favorable features. Subsequent in vitro, in vivo, and clinical testing culminated in the FDA approval of three proteasome inhibitors-bortezomib, carfilzomib, and ixazomib -for specific hematological malignancies. However, despite in vitro and in vivo studies pointing towards efficacy in solid tumors, clinical responses broadly have been evasive. For brain tumors, a malignancy in dire need of new approaches both in adult and pediatric patients, this has also been the case. Elucidation of proteasome-dependent processes in specific types of brain tumors, the evolution of newer proteasome targeting strategies, and the use of proteasome inhibitors in combination strategies will clarify how these agents can be leveraged more effectively to treat central nervous system malignancies. Since brain tumors represent a heterogeneous subset of solid tumors, and in particular, pediatric brain tumors possess distinct biology from adult brain tumors, tailoring of proteasome inhibitor-based strategies to specific subtypes of these tumors will be critical for advancing care for affected patients, and will be discussed in this review.
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Affiliation(s)
- Wafik Zaky
- Children's Cancer Hospital, Division of Pediatrics, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Christa Manton
- Children's Cancer Hospital, Division of Pediatrics, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Claudia P Miller
- Children's Cancer Hospital, Division of Pediatrics, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Soumen Khatua
- Children's Cancer Hospital, Division of Pediatrics, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Vidya Gopalakrishnan
- Children's Cancer Hospital, Division of Pediatrics, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Joya Chandra
- Children's Cancer Hospital, Division of Pediatrics, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.
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191
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Abstract
Ubiquitination is a widespread post-translational modification that controls multiple steps in autophagy, a major lysosome-mediated intracellular degradation pathway. A variety of ubiquitin chains are attached as selective labels on protein aggregates and dysfunctional organelles, thus promoting their autophagy-dependent degradation. Moreover, ubiquitin modification of autophagy regulatory components is essential to positively or negatively regulate autophagy flux in both non-selective and selective pathways. We review the current findings that elucidate the components, timing, and kinetics of the multivalent role of ubiquitin signals in control of amplitude and selectivity of autophagy pathways as well as their impact on the development of human diseases.
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Affiliation(s)
- Paolo Grumati
- From the Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60590 Frankfurt am Main and
| | - Ivan Dikic
- From the Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60590 Frankfurt am Main and .,the Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt-Riedberg Campus, 60438 Frankfurt am Main, Germany
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192
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van der Heden van Noort GJ, Kooij R, Elliott PR, Komander D, Ovaa H. Synthesis of Poly-Ubiquitin Chains Using a Bifunctional Ubiquitin Monomer. Org Lett 2017; 19:6490-6493. [PMID: 29172548 PMCID: PMC5735377 DOI: 10.1021/acs.orglett.7b03085] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
An optimized large scale and highly
reproducible route to orthogonally
protected γ-thiolysine is reported. Its utility in the synthesis
of bifunctional ubiquitin monomers is demonstrated. These ubiquitin
synthons are employed in polymerization reactions giving access to
synthetic poly-ubiquitin chains of defined linkage.
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Affiliation(s)
| | - Raymond Kooij
- Department of Chemical Immunology, Leiden University Medical Centre , 2333 ZC Leiden, The Netherlands
| | - Paul R Elliott
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Huib Ovaa
- Department of Chemical Immunology, Leiden University Medical Centre , 2333 ZC Leiden, The Netherlands
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193
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Schick M, Habringer S, Nilsson JA, Keller U. Pathogenesis and therapeutic targeting of aberrant MYC expression in haematological cancers. Br J Haematol 2017; 179:724-738. [DOI: 10.1111/bjh.14917] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Markus Schick
- Internal Medicine III; School of Medicine; Technische Universität München; Munich Germany
| | - Stefan Habringer
- Internal Medicine III; School of Medicine; Technische Universität München; Munich Germany
| | - Jonas A. Nilsson
- Department of Surgery; Sahlgrenska Cancer Center; Gothenburg University; Gothenburg Sweden
| | - Ulrich Keller
- Internal Medicine III; School of Medicine; Technische Universität München; Munich Germany
- German Cancer Consortium (DKTK); German Cancer Research Center (DKFZ); Heidelberg Germany
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194
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Bailey-Elkin BA, Knaap RCM, Kikkert M, Mark BL. Structure and Function of Viral Deubiquitinating Enzymes. J Mol Biol 2017; 429:3441-3470. [PMID: 28625850 PMCID: PMC7094624 DOI: 10.1016/j.jmb.2017.06.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 01/12/2023]
Abstract
Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including innate and adaptive immune responses. Ubiquitin-mediated control over these processes can be reversed by cellular deubiquitinating enzymes (DUBs), which remove ubiquitin from cellular targets and depolymerize polyubiquitin chains. The importance of protein ubiquitination to host immunity has been underscored by the discovery of viruses that encode proteases with deubiquitinating activity, many of which have been demonstrated to actively corrupt cellular ubiquitin-dependent processes to suppress innate antiviral responses and promote viral replication. DUBs have now been identified in diverse viral lineages, and their characterization is providing valuable insights into virus biology and the role of the ubiquitin system in host antiviral mechanisms. Here, we provide an overview of the structural biology of these fascinating viral enzymes and their role innate immune evasion and viral replication.
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Affiliation(s)
- Ben A Bailey-Elkin
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - Robert C M Knaap
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada.
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195
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Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein. Antiviral Res 2017; 149:58-74. [PMID: 29128390 PMCID: PMC7113668 DOI: 10.1016/j.antiviral.2017.11.001] [Citation(s) in RCA: 423] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/29/2017] [Accepted: 11/02/2017] [Indexed: 12/11/2022]
Abstract
The multi-domain non-structural protein 3 (Nsp3) is the largest protein encoded by the coronavirus (CoV) genome, with an average molecular mass of about 200 kD. Nsp3 is an essential component of the replication/transcription complex. It comprises various domains, the organization of which differs between CoV genera, due to duplication or absence of some domains. However, eight domains of Nsp3 exist in all known CoVs: the ubiquitin-like domain 1 (Ubl1), the Glu-rich acidic domain (also called “hypervariable region”), a macrodomain (also named “X domain”), the ubiquitin-like domain 2 (Ubl2), the papain-like protease 2 (PL2pro), the Nsp3 ectodomain (3Ecto, also called “zinc-finger domain”), as well as the domains Y1 and CoV-Y of unknown functions. In addition, the two transmembrane regions, TM1 and TM2, exist in all CoVs. The three-dimensional structures of domains in the N-terminal two thirds of Nsp3 have been investigated by X-ray crystallography and/or nuclear magnetic resonance (NMR) spectroscopy since the outbreaks of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) in 2003 as well as Middle-East Respiratory Syndrome coronavirus (MERS-CoV) in 2012. In this review, the structures and functions of these domains of Nsp3 are discussed in depth. Nonstructural protein 3 (∼200 kD) is a multifunctional protein comprising up to 16 different domains and regions. Nsp3 binds to viral RNA, nucleocapsid protein, as well as other viral proteins, and participates in polyprotein processing. The papain-like protease of Nsp3 is an established target for new antivirals. Through its de-ADP-ribosylating, de-ubiquitinating, and de-ISGylating activities, Nsp3 counteracts host innate immunity. Structural data are available for the N-terminal two thirds of Nsp3, but domains in the remainder are poorly characterized.
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196
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Zhao X, Lutz J, Höllmüller E, Scheffner M, Marx A, Stengel F. Identification of Proteins Interacting with Ubiquitin Chains. Angew Chem Int Ed Engl 2017; 56:15764-15768. [DOI: 10.1002/anie.201705898] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 09/01/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Xiaohui Zhao
- Departments of Chemistry and Biology; Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Joachim Lutz
- Departments of Chemistry and Biology; Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Eva Höllmüller
- Departments of Chemistry and Biology; Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Martin Scheffner
- Departments of Chemistry and Biology; Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Andreas Marx
- Departments of Chemistry and Biology; Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Florian Stengel
- Departments of Chemistry and Biology; Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
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197
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Zhao X, Lutz J, Höllmüller E, Scheffner M, Marx A, Stengel F. Identifizierung von Interaktoren von Ubiquitinketten. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705898] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiaohui Zhao
- Fachbereich Chemie und Biologie; Konstanz Research School Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Joachim Lutz
- Fachbereich Chemie und Biologie; Konstanz Research School Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Eva Höllmüller
- Fachbereich Chemie und Biologie; Konstanz Research School Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Martin Scheffner
- Fachbereich Chemie und Biologie; Konstanz Research School Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Andreas Marx
- Fachbereich Chemie und Biologie; Konstanz Research School Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Florian Stengel
- Fachbereich Chemie und Biologie; Konstanz Research School Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
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198
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Herhaus L, Dikic I. Regulation of Salmonella-host cell interactions via the ubiquitin system. Int J Med Microbiol 2017; 308:176-184. [PMID: 29126744 DOI: 10.1016/j.ijmm.2017.11.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/01/2017] [Accepted: 11/05/2017] [Indexed: 01/29/2023] Open
Abstract
Salmonella infections cause acute intestinal inflammatory responses through the action of bacterial effector proteins secreted into the host cytosol. These proteins promote Salmonella survival, amongst others, by deregulating the host innate immune system and interfering with host cell ubiquitylation signaling. This review describes the recent findings of dynamic changes of the host ubiquitinome during pathogen infection, how bacterial effector proteins modulate the host ubiquitin system and how the host innate immune system counteracts Salmonella invasion by using these pathogens as signaling platforms to initiate immune responses.
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Affiliation(s)
- Lina Herhaus
- Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, 60590 Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, 60438 Frankfurt am Main, Germany.
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199
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Méndez-Hernández LE, Robledo-Rivera AY, Macías-Silva M, Calera MR, Sánchez-Olea R. Gpn3 is polyubiquitinated on lysine 216 and degraded by the proteasome in the cell nucleus in a Gpn1-inhibitable manner. FEBS Lett 2017; 591:3757-3770. [DOI: 10.1002/1873-3468.12883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Marina Macías-Silva
- Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México
| | - Mónica R. Calera
- Instituto de Física; Universidad Autónoma de San Luis Potosí; México
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200
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Efficient protein production by yeast requires global tuning of metabolism. Nat Commun 2017; 8:1131. [PMID: 29070809 PMCID: PMC5656615 DOI: 10.1038/s41467-017-00999-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 08/09/2017] [Indexed: 01/20/2023] Open
Abstract
The biotech industry relies on cell factories for production of pharmaceutical proteins, of which several are among the top-selling medicines. There is, therefore, considerable interest in improving the efficiency of protein production by cell factories. Protein secretion involves numerous intracellular processes with many underlying mechanisms still remaining unclear. Here, we use RNA-seq to study the genome-wide transcriptional response to protein secretion in mutant yeast strains. We find that many cellular processes have to be attuned to support efficient protein secretion. In particular, altered energy metabolism resulting in reduced respiration and increased fermentation, as well as balancing of amino-acid biosynthesis and reduced thiamine biosynthesis seem to be particularly important. We confirm our findings by inverse engineering and physiological characterization and show that by tuning metabolism cells are able to efficiently secrete recombinant proteins. Our findings provide increased understanding of which cellular regulations and pathways are associated with efficient protein secretion. The contribution of metabolic pathways to protein secretion is largely unknown. Here, the authors find conserved metabolic patterns in yeast by examining genome-wide transcriptional responses in high protein secretion mutants and reveal critical factors that can be tuned for efficient protein secretion.
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