1
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Guo L, Zhang B, Zhang W, Xie Y, Chen X, Sun X, Watt DS, Liu C, Spielmann HP, Liu X. Inhibition of Carbohydrate Metabolism Potentiated by the Therapeutic Effects of Oxidative Phosphorylation Inhibitors in Colon Cancer Cells. Cancers (Basel) 2024; 16:1399. [PMID: 38611076 PMCID: PMC11010912 DOI: 10.3390/cancers16071399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 04/14/2024] Open
Abstract
Cancer cells undergo a significant level of "metabolic reprogramming" or "remodeling" to ensure an adequate supply of ATP and "building blocks" for cell survival and to facilitate accelerated proliferation. Cancer cells preferentially use glycolysis for ATP production (the Warburg effect); however, cancer cells, including colorectal cancer (CRC) cells, also depend on oxidative phosphorylation (OXPHOS) for ATP production, a finding that suggests that both glycolysis and OXPHOS play significant roles in facilitating cancer progression and proliferation. Our prior studies identified a semisynthetic isoflavonoid, DBI-1, that served as an AMPK activator targeting mitochondrial complex I. Furthermore, DBI-1 and a glucose transporter 1 (GLUT1) inhibitor, BAY-876, synergistically inhibited CRC cell growth in vitro and in vivo. We now report a study of the structure-activity relationships (SARs) in the isoflavonoid family in which we identified a new DBI-1 analog, namely, DBI-2, with promising properties. Here, we aimed to explore the antitumor mechanisms of DBIs and to develop new combination strategies by targeting both glycolysis and OXPHOS. We identified DBI-2 as a novel AMPK activator using an AMPK phosphorylation assay as a readout. DBI-2 inhibited mitochondrial complex I in the Seahorse assays. We performed proliferation and Western blotting assays and conducted studies of apoptosis, necrosis, and autophagy to corroborate the synergistic effects of DBI-2 and BAY-876 on CRC cells in vitro. We hypothesized that restricting the carbohydrate uptake with a KD would mimic the effects of GLUT1 inhibitors, and we found that a ketogenic diet significantly enhanced the therapeutic efficacy of DBI-2 in CRC xenograft mouse models, an outcome that suggested a potentially new approach for combination cancer therapy.
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Affiliation(s)
- Lichao Guo
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory and Center for Drug Innovation and Discovery, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Baochen Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory and Center for Drug Innovation and Discovery, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Wen Zhang
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Yanqi Xie
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Xi Chen
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory and Center for Drug Innovation and Discovery, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Xueke Sun
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory and Center for Drug Innovation and Discovery, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - David S. Watt
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Chunming Liu
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - H. Peter Spielmann
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Xifu Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory and Center for Drug Innovation and Discovery, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
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2
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Teo QW, Wong HH, Heunis T, Stancheva V, Hachim A, Lv H, Siu L, Ho J, Lan Y, Mok CKP, Ulferts R, Sanyal S. Usp25-Erlin1/2 activity limits cholesterol flux to restrict virus infection. Dev Cell 2023; 58:2495-2509.e6. [PMID: 37683630 PMCID: PMC10914638 DOI: 10.1016/j.devcel.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 05/20/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023]
Abstract
Reprogramming lipid metabolic pathways is a critical feature of activating immune responses to infection. However, how these reconfigurations occur is poorly understood. Our previous screen to identify cellular deubiquitylases (DUBs) activated during influenza virus infection revealed Usp25 as a prominent hit. Here, we show that Usp25-deleted human lung epithelial A549 cells display a >10-fold increase in pathogenic influenza virus production, which was rescued upon reconstitution with the wild type but not the catalytically deficient (C178S) variant. Proteomic analysis of Usp25 interactors revealed a strong association with Erlin1/2, which we confirmed as its substrate. Newly synthesized Erlin1/2 were degraded in Usp25-/- or Usp25C178S cells, activating Srebp2, with increased cholesterol flux and attenuated TLR3-dependent responses. Our study therefore defines the function of a deubiquitylase that serves to restrict a range of viruses by reprogramming lipid biosynthetic flux to install appropriate inflammatory responses.
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Affiliation(s)
- Qi Wen Teo
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ho Him Wong
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Tiaan Heunis
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK
| | - Viktoriya Stancheva
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK
| | - Asmaa Hachim
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK
| | - Huibin Lv
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lewis Siu
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Julian Ho
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yun Lan
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Chris Ka Pun Mok
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | | | - Sumana Sanyal
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK; HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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3
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Lan Y, van Leur SW, Fernando JA, Wong HH, Kampmann M, Siu L, Zhang J, Li M, Nicholls JM, Sanyal S. Viral subversion of selective autophagy is critical for biogenesis of virus replication organelles. Nat Commun 2023; 14:2698. [PMID: 37164963 PMCID: PMC10171163 DOI: 10.1038/s41467-023-38377-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/25/2023] [Indexed: 05/12/2023] Open
Abstract
Infection by many (+)RNA viruses is accompanied by ER-expansion and membrane remodelling to form viral replication organelles, followed by assembly and secretion of viral progenies. We previously identified that virus-triggered lipophagy was critical for flaviviral assembly, and is driven by the lipid droplet associated protein Ancient ubiquitin protein 1 (Aup1). A ubiquitin conjugating protein Ube2g2 that functions as a co-factor for Aup1 was identified as a host dependency factor in our study. Here we characterized its function: Ube2g2-deficient cells displayed a dramatic reduction in virus production, which could be rescued by reconstituting the wild-type but not the catalytically deficient (C89K) mutant of Ube2g2, suggesting that its enzymatic activity is necessary. Ube2g2 deficiency did not affect entry of virus particles but resulted in a profound loss in formation of replication organelles, and production of infectious progenies. This phenomenon resulted from its dual activity in (i) triggering lipophagy in conjunction with Aup1, and (ii) degradation of ER chaperones such as Herpud1, SEL1L, Hrd1, along with Sec62 to restrict ER-phagy upon Xbp1-IRE1 triggered ER expansion. Our results therefore underscore an exquisite fine-tuning of selective autophagy by flaviviruses that drive host membrane reorganization during infection to enable biogenesis of viral replication organelles.
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Affiliation(s)
- Yun Lan
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | | | - Julia Ayano Fernando
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Ho Him Wong
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Martin Kampmann
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Lewis Siu
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Jingshu Zhang
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Mingyuan Li
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - John M Nicholls
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Sumana Sanyal
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China.
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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4
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Munnur D, Banducci-Karp A, Sanyal S. ISG15 driven cellular responses to virus infection. Biochem Soc Trans 2022; 50:1837-1846. [PMID: 36416643 DOI: 10.1042/bst20220839] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022]
Abstract
One of the hallmarks of antiviral responses to infection is the production of interferons and subsequently of interferon stimulated genes. Interferon stimulated gene 15 (ISG15) is among the earliest and most abundant proteins induced upon interferon signalling, encompassing versatile functions in host immunity. ISG15 is a ubiquitin like modifier that can be conjugated to substrates in a process analogous to ubiquitylation and referred to as ISGylation. The free unconjugated form can either exist intracellularly or be secreted to function as a cytokine. Interestingly, ISG15 has been reported to be both advantageous and detrimental to the development of immunopathology during infection. This review describes recent findings on the role of ISG15 in antiviral responses in human infection models, with a particular emphasis on autophagy, inflammatory responses and cellular metabolism combined with viral strategies of counteracting them. The field of ISGylation has steadily gained momentum; however much of the previous studies of virus infections conducted in mouse models are in sharp contrast with recent findings in human cells, underscoring the need to summarise our current understanding of its potential antiviral function in humans and identify knowledge gaps which need to be addressed in future studies.
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Affiliation(s)
- Deeksha Munnur
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, U.K
| | - Adrianna Banducci-Karp
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, U.K
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, U.K
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5
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Ren H, Mou Y, Lin L, Wang L, Hu H. Efficient antigen cross-presentation through coating conventional aluminum adjuvant particles with PEI. Am J Transl Res 2021; 13:4092-4102. [PMID: 34150001 PMCID: PMC8205809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
Classical aluminum adjuvant is a deficient antigen carrier for cross-presentation and cross-priming of CD8+ cytotoxic T cells. Our previous research has demonstrated that cross-presentation efficiency significantly increased when antigens are conjugated covalently to α-Al2O3 nanoparticles. Here we found that coating conventional aluminum adjuvants with polyethyleneimine (PEI) could enhance antigen cross-presentation of DCs (dendritic cells) in vitro and in vivo. PEIs exerted differential effects on antigen cross-presentation. These findings provided an alternative approach to promote the rapid translation of alumina nanoparticles adjuvants into clinical application.
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Affiliation(s)
- Hongyan Ren
- Department of Pathology and Pathophysiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese MedicineNanjing 210023, P. R. China
- Laboratory of Cancer Immunobiology, Robert W. Franz Cancer Research Center, Earle A. Chiles Research Institute, Providence Cancer CenterPortland, OR, USA
| | - Yongbin Mou
- Laboratory of Cancer Immunobiology, Robert W. Franz Cancer Research Center, Earle A. Chiles Research Institute, Providence Cancer CenterPortland, OR, USA
- Nanjing Stomatological Hospital, Medical School of Nanjing UniversityNanjing, China
| | - Lin Lin
- Laboratory of Cancer Immunobiology, Robert W. Franz Cancer Research Center, Earle A. Chiles Research Institute, Providence Cancer CenterPortland, OR, USA
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese MedicineChina
| | - Lixin Wang
- School of Medicine, Southeast UniversityNanjing, China
| | - Hongming Hu
- Laboratory of Cancer Immunobiology, Robert W. Franz Cancer Research Center, Earle A. Chiles Research Institute, Providence Cancer CenterPortland, OR, USA
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6
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Qu J, Zou T, Lin Z. The Roles of the Ubiquitin-Proteasome System in the Endoplasmic Reticulum Stress Pathway. Int J Mol Sci 2021; 22:1526. [PMID: 33546413 PMCID: PMC7913544 DOI: 10.3390/ijms22041526] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
The endoplasmic reticulum (ER) is a highly dynamic organelle in eukaryotic cells, which is essential for synthesis, processing, sorting of protein and lipid metabolism. However, the cells activate a defense mechanism called endoplasmic reticulum stress (ER stress) response and initiate unfolded protein response (UPR) as the unfolded proteins exceed the folding capacity of the ER due to the environmental influences or increased protein synthesis. ER stress can mediate many cellular processes, including autophagy, apoptosis and senescence. The ubiquitin-proteasome system (UPS) is involved in the degradation of more than 80% of proteins in the cells. Today, increasing numbers of studies have shown that the two important components of UPS, E3 ubiquitin ligases and deubiquitinases (DUBs), are tightly related to ER stress. In this review, we summarized the regulation of the E3 ubiquitin ligases and DUBs in ER stress.
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Affiliation(s)
| | | | - Zhenghong Lin
- School of Life Sciences, Chongqing University, Chongqing 401331, China; (J.Q.); (T.Z.)
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7
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Lyn kinase regulates egress of flaviviruses in autophagosome-derived organelles. Nat Commun 2020; 11:5189. [PMID: 33060596 PMCID: PMC7564011 DOI: 10.1038/s41467-020-19028-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/25/2020] [Indexed: 02/07/2023] Open
Abstract
Among the various host cellular processes that are hijacked by flaviviruses, few mechanisms have been described with regard to viral egress. Here we investigate how flaviviruses exploit Src family kinases (SFKs) for exit from infected cells. We identify Lyn as a critical component for secretion of Dengue and Zika infectious particles and their corresponding virus like particles (VLPs). Pharmacological inhibition or genetic depletion of the SFKs, Lyn in particular, block virus secretion. Lyn−/− cells are impaired in virus release and are rescued when reconstituted with wild-type Lyn, but not a kinase- or palmitoylation-deficient Lyn mutant. We establish that virus particles are secreted in two distinct populations – one as free virions and the other enclosed within membranes. Lyn is critical for the latter, which consists of proteolytically processed, infectious virus progenies within autophagosome-derived vesicles. This process depends on Ulk1, Rab GTPases and SNARE complexes implicated in secretory but not degradative autophagy and occur with significantly faster kinetics than the conventional secretory pathway. Our study reveals a previously undiscovered Lyn-dependent exit route of flaviviruses in LC3+ secretory organelles that enables them to evade circulating antibodies and might affect tissue tropism. Egress of flaviviruses and involved host pathways are not well understood. Here, the authors show that Lyn is a critical host kinase for Dengue and Zika virus egress resulting in infectious virus progenies within autophagosome-derived vesicles, which might help the virus to evade antibody responses.
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8
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Cho J, Park J, Kim EE, Song EJ. Assay Systems for Profiling Deubiquitinating Activity. Int J Mol Sci 2020; 21:E5638. [PMID: 32781716 PMCID: PMC7460613 DOI: 10.3390/ijms21165638] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 01/22/2023] Open
Abstract
Deubiquitinating enzymes regulate various cellular processes, particularly protein degradation, localization, and protein-protein interactions. The dysregulation of deubiquitinating enzyme (DUB) activity has been linked to several diseases; however, the function of many DUBs has not been identified. Therefore, the development of methods to assess DUB activity is important to identify novel DUBs, characterize DUB selectivity, and profile dynamic DUB substrates. Here, we review various methods of evaluating DUB activity using cell lysates or purified DUBs, as well as the types of probes used in these methods. In addition, we introduce some techniques that can deliver DUB probes into the cells and cell-permeable activity-based probes to directly visualize and quantify DUB activity in live cells. This review could contribute to the development of DUB inhibitors by providing important information on the characteristics and applications of various probes used to evaluate and detect DUB activity in vitro and in vivo.
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Affiliation(s)
- Jinhong Cho
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.C.); (E.E.K.)
| | - Jinyoung Park
- Molecular Recognition Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea;
| | - Eunice EunKyeong Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.C.); (E.E.K.)
| | - Eun Joo Song
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul 03760, Korea
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9
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Jahan AS, Biquand E, Muñoz-Moreno R, Le Quang A, Mok CKP, Wong HH, Teo QW, Valkenburg SA, Chin AWH, Man Poon LL, Te Velthuis A, García-Sastre A, Demeret C, Sanyal S. OTUB1 Is a Key Regulator of RIG-I-Dependent Immune Signaling and Is Targeted for Proteasomal Degradation by Influenza A NS1. Cell Rep 2020; 30:1570-1584.e6. [PMID: 32023470 DOI: 10.1016/j.celrep.2020.01.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/21/2019] [Accepted: 01/02/2020] [Indexed: 12/16/2022] Open
Abstract
Deubiquitylases (DUBs) regulate critical signaling pathways at the intersection of host immunity and viral pathogenesis. Although RIG-I activation is heavily dependent on ubiquitylation, systematic analyses of DUBs that regulate this pathway have not been performed. Using a ubiquitin C-terminal electrophile, we profile DUBs that function during influenza A virus (IAV) infection and isolate OTUB1 as a key regulator of RIG-I-dependent antiviral responses. Upon infection, OTUB1 relocalizes from the nucleus to mitochondrial membranes together with RIG-I, viral PB2, and NS1. Its expression depends on competing effects of interferon stimulation and IAV-triggered degradation. OTUB1 activates RIG-I via a dual mechanism of K48 polyubiquitin hydrolysis and formation of an E2-repressive complex with UBCH5c. We reconstitute this mechanism in a cell-free system comprising [35S]IRF3, purified RIG-I, mitochondrial membranes, and cytosol expressing OTUB1 variants. A range of IAV NS1 proteins trigger proteasomal degradation of OTUB1, antagonizing the RIG-I signaling cascade and antiviral responses.
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Affiliation(s)
- Akhee Sabiha Jahan
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Elise Biquand
- Molecular Genetics of RNA Viruses, CNRS UMR 3569, Université de Paris, Institut Pasteur, Paris, France
| | - Raquel Muñoz-Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Agathe Le Quang
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Chris Ka-Pun Mok
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Ho Him Wong
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Qi Wen Teo
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Alex W H Chin
- School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Leo Lit Man Poon
- School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Artejan Te Velthuis
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Caroline Demeret
- Molecular Genetics of RNA Viruses, CNRS UMR 3569, Université de Paris, Institut Pasteur, Paris, France
| | - Sumana Sanyal
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong; School of Biomedical Sciences, LKS Faculty of Medicine, University of Hong Kong, Hong Kong.
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10
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Ubiquitinated Proteins Isolated From Tumor Cells Are Efficient Substrates for Antigen Cross-Presentation. J Immunother 2018; 40:155-163. [PMID: 28368960 DOI: 10.1097/cji.0000000000000165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have previously shown that inhibition of the proteasome causes defective ribosomal products to be shunted into autophagosomes and subsequently released from tumor cells as defective ribosomal products in Blebs (DRibbles). These DRibbles serve as an excellent source of antigens for cross-priming of tumor-specific T cells. Here, we examine the role of ubiquitinated proteins (Ub-proteins) in this pathway. Using purified Ub-proteins from tumor cells that express endogenous tumor-associated antigen or exogenous viral antigen, we tested the ability of these proteins to stimulate antigen-specific T-cell responses, by activation of monocyte-derived dendritic cells generated from human peripheral blood mononuclear cells. Compared with total cell lysates, we found that purified Ub-proteins from both a gp100-specific melanoma cell line and from a lung cancer cell line expressing cytomegalovirus pp65 antigen produced a significantly higher level of IFN-γ in gp100- or pp65-specific T cells, respectively. In addition, Ub-proteins from an allogeneic tumor cell line could be used to stimulate tumor-infiltrating lymphocytes isolated and expanded from non-small cell lung cancer patients. These results establish that Ub-proteins provide a relevant source of antigens for cross-priming of antitumor immune responses in a variety of settings, including endogenous melanoma and exogenous viral antigen presentation, as well as antigen-specific tumor-infiltrating lymphocytes. Thus, ubiquitin can be used as an affinity tag to enrich for unknown tumor-specific antigens from tumor cell lysates to stimulate tumor-specific T cells ex vivo or to be used as vaccines to target short-lived proteins.
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11
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Yoon JG, Hwang HJ, Cho JA. Application of the biotin-labeled toxin mutant for affinity isolation of associated proteins in the mammalian cells. J Biosci Bioeng 2018; 125:497-504. [PMID: 29291913 DOI: 10.1016/j.jbiosc.2017.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/01/2017] [Accepted: 12/04/2017] [Indexed: 10/18/2022]
Abstract
Cholera toxin (CT), one of the AB5 bacterial toxin families, is produced by Vibrio cholerae, breeches the intestinal epithelial barrier and enters host epithelial cells to cause the massive secretory diarrhea. This study focused on understanding the retro-translocation machinery of the bacterial toxin using biotin-avidin technology to explain toxin trafficking from the endoplasmic reticulum (ER) to the cytosol. Because the association between the A1 chain of CT and other components of the retro-translocation machinery is likely transient or very weak, the successful bioengineering of such a mutant to be trapped as an intermediate in ER is essential for affinity isolation and further analysis. Here, we prepared a mutant toxin that 15 amino acid Biotin Acceptor Peptide (BAP) was fused to the C-terminal of A1 chain of CT. Biotinylation efficiency of the BAP-inserted cholera toxin (BT) was nearly 100%. Moreover, BT was functionally toxic and successfully pulled down by NeutrAvidin in vitro and in vivo. However, NeutrAvidin-bound biotinylated BT was not toxic. These results suggest the possibility of a plug effect of the biotin-NeutrAvidin-BT complex stuck in the ER without retro-translocation to the cytosol. Therefore, this model might identify the interacting proteins with A1 chain of CT in the host cells by holding the moment of retro-translocation of the bacterial toxin. In conclusion, this study established the model using biotin-avidin technology to elucidate the molecular basis for retro-translocation of bacterial toxin from within the lumen of ER to the cytosol.
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Affiliation(s)
- Ju-Gyeong Yoon
- Department of Food and Nutrition, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Dae-Jeon 34134, South Korea
| | - Hye-Jeong Hwang
- Department of Food and Nutrition, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Dae-Jeon 34134, South Korea
| | - Jin Ah Cho
- Department of Food and Nutrition, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Dae-Jeon 34134, South Korea.
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12
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A Plastid Protein That Evolved from Ubiquitin and Is Required for Apicoplast Protein Import in Toxoplasma gondii. mBio 2017; 8:mBio.00950-17. [PMID: 28655825 PMCID: PMC5487736 DOI: 10.1128/mbio.00950-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Apicomplexan parasites cause a variety of important infectious diseases, including malaria, toxoplasma encephalitis, and severe diarrhea due to Cryptosporidium. Most apicomplexans depend on an organelle called the apicoplast which is derived from a red algal endosymbiont. The apicoplast is essential for the parasite as the compartment of fatty acid, heme, and isoprenoid biosynthesis. The majority of the approximate 500 apicoplast proteins are nucleus encoded and have to be imported across the four membranes that surround the apicoplast. Import across the second outermost membrane of the apicoplast, the periplastid membrane, depends on an apicoplast-specific endoplasmic reticulum-associated protein degradation (ERAD) complex and on enzymes of the associated ubiquitination cascade. However, identification of an apicoplast ubiquitin associated with this machinery has long been elusive. Here we identify a plastid ubiquitin-like protein (PUBL), an apicoplast protein that is derived from a ubiquitin ancestor but that has significantly changed in its primary sequence. PUBL is distinct from known ubiquitin-like proteins, and phylogenomic analyses suggest a clade specific to apicomplexans. We demonstrate that PUBL and the AAA ATPase CDC48AP both act to translocate apicoplast proteins across the periplastid membrane during protein import. Conditional null mutants and genetic complementation show that both proteins are critical for this process and for parasite survival. PUBL residues homologous to those that are required for ubiquitin conjugation onto target proteins are essential for this function, while those required for polyubiquitination and preprotein processing are dispensable. Our experiments provide a mechanistic understanding of the molecular machinery that drives protein import across the membranes of the apicoplast. Apicomplexan parasites are responsible for important human diseases. There are no effective vaccines for use in humans, and drug treatment faces multiple challenges, including emerging resistance, lack of efficacy across the lifecycle, and adverse drug effects. The apicoplast is a promising target for novel treatments: this chloroplast-like organelle is derived from an algal symbiont, is absent from the host, and is essential for parasite growth and pathogenesis. We use Toxoplasma gondii as a model to study the apicoplast due to its strong genetic tools and established functional assays. We identify a plastid ubiquitin-like protein (PUBL) which is a novel ubiquitin-like protein and demonstrate its importance and that of the motor protein CDC48AP for apicoplast protein import. These findings broaden our understanding of the evolution and mechanistic workings of a unique parasite organelle and may lead to new opportunities for treatments against important human pathogens.
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13
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A Protocol for Protein Profiling Using Chemoselective Cleavable Linker Probes in Semi-permeabilized Cells. Methods Mol Biol 2016. [PMID: 27778289 DOI: 10.1007/978-1-4939-6439-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Activity-based protein profiling using activity-based probes (ABPs) resulted in the identification of various enzymes that are involved in the onset and progress of diseases. Detection of such proteins, often expressed at low abundance, is greatly enhanced by incorporating chemically cleavable linkers in the ABP of choice. Initial affinity purification, followed by tailored chemical cleavage of the linker, allows for specific release of the captured enzymes and their interaction partners. When the ABPs are delivered directly to semi-permeabilized cells, in contrast to a crude cell lysate, the sensitivity and efficacy of cell impermeable probes can be enhanced even further.
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14
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Jahan AS, Lestra M, Swee LK, Fan Y, Lamers MM, Tafesse FG, Theile CS, Spooner E, Bruzzone R, Ploegh HL, Sanyal S. Usp12 stabilizes the T-cell receptor complex at the cell surface during signaling. Proc Natl Acad Sci U S A 2016; 113:E705-14. [PMID: 26811477 PMCID: PMC4760780 DOI: 10.1073/pnas.1521763113] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Posttranslational modifications are central to the spatial and temporal regulation of protein function. Among others, phosphorylation and ubiquitylation are known to regulate proximal T-cell receptor (TCR) signaling. Here we used a systematic and unbiased approach to uncover deubiquitylating enzymes (DUBs) that participate during TCR signaling in primary mouse T lymphocytes. Using a C-terminally modified vinyl methyl ester variant of ubiquitin (HA-Ub-VME), we captured DUBs that are differentially recruited to the cytosol on TCR activation. We identified ubiquitin-specific peptidase (Usp) 12 and Usp46, which had not been previously described in this pathway. Stimulation with anti-CD3 resulted in phosphorylation and time-dependent translocation of Usp12 from the nucleus to the cytosol. Usp12(-/-) Jurkat cells displayed defective NFκB, NFAT, and MAPK activities owing to attenuated surface expression of TCR, which were rescued on reconstitution of wild type Usp12. Proximity-based labeling with BirA-Usp12 revealed several TCR adaptor proteins acting as interactors in stimulated cells, of which LAT and Trat1 displayed reduced expression in Usp12(-/-) cells. We demonstrate that Usp12 deubiquitylates and prevents lysosomal degradation of LAT and Trat1 to maintain the proximal TCR complex for the duration of signaling. Our approach benefits from the use of activity-based probes in primary cells without any previous genome modification, and underscores the importance of ubiquitin-mediated regulation to refine signaling cascades.
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Affiliation(s)
- Akhee S Jahan
- HKU-Pasteur Research Pole and Center for Influenza Research, School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Maxime Lestra
- HKU-Pasteur Research Pole and Center for Influenza Research, School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Lee Kim Swee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - Ying Fan
- HKU-Pasteur Research Pole and Center for Influenza Research, School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Mart M Lamers
- HKU-Pasteur Research Pole and Center for Influenza Research, School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Fikadu G Tafesse
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | | | - Eric Spooner
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - Roberto Bruzzone
- HKU-Pasteur Research Pole and Center for Influenza Research, School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong; Department of Cell Biology and Infection, Institut Pasteur, 75015 Paris, France
| | - Hidde L Ploegh
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Sumana Sanyal
- HKU-Pasteur Research Pole and Center for Influenza Research, School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong; Department of Cell Biology and Infection, Institut Pasteur, 75015 Paris, France;
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15
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Sasset L, Petris G, Cesaratto F, Burrone OR. The VCP/p97 and YOD1 Proteins Have Different Substrate-dependent Activities in Endoplasmic Reticulum-associated Degradation (ERAD). J Biol Chem 2015; 290:28175-28188. [PMID: 26463207 DOI: 10.1074/jbc.m115.656660] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Indexed: 11/06/2022] Open
Abstract
Endoplasmic reticulum-associated degradation (ERAD) is an essential quality control mechanism of the folding state of proteins in the secretory pathway that targets unfolded/misfolded polypeptides for proteasomal degradation. The cytosolic p97/valosin-containing protein is an essential ATPase for degradation of ERAD substrates. It has been considered necessary during retro-translocation to extract proteins from the endoplasmic reticulum that are otherwise supposed to accumulate in the endoplasmic reticulum lumen. The activity of the p97-associated deubiquitinylase YOD1 is also required for substrate disposal. We used the in vivo biotinylation retro-translocation assay in mammalian cells under conditions of impaired p97 or YOD1 activity to directly discriminate their requirements and diverse functions in ERAD. Using different ERAD substrates, we found that both proteins participate in two distinct retro-translocation steps. For CD4 and MHC-Iα, which are induced to degradation by the HIV-1 protein Vpu and by the CMV immunoevasins US2 and US11, respectively, p97 and YOD1 have a retro-translocation-triggering role. In contrast, for three other spontaneous ERAD model substrates (NS1, NHK-α1AT, and BST-2/Tetherin), p97 and YOD1 are required in the downstream events of substrate deglycosylation and proteasomal degradation.
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Affiliation(s)
- Linda Sasset
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | - Gianluca Petris
- CIBIO, University of Trento, Via delle Regole 101, 38123 Mattarello, Italy.
| | - Francesca Cesaratto
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | - Oscar R Burrone
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
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16
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Type I interferon imposes a TSG101/ISG15 checkpoint at the Golgi for glycoprotein trafficking during influenza virus infection. Cell Host Microbe 2014; 14:510-21. [PMID: 24237697 DOI: 10.1016/j.chom.2013.10.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 08/13/2013] [Accepted: 10/07/2013] [Indexed: 11/20/2022]
Abstract
Several enveloped viruses exploit host pathways, such as the cellular endosomal sorting complex required for transport (ESCRT) machinery, for their assembly and release. The influenza A virus (IAV) matrix protein binds to the ESCRT-I complex, although the involvement of early ESCRT proteins such as Tsg101 in IAV trafficking remain to be established. We find that Tsg101 can facilitate IAV trafficking, but this is effectively restricted by the interferon (IFN)-stimulated protein ISG15. Cytosol from type I IFN-treated cells abolished IAV hemagglutinin (HA) transport to the cell surface in infected semi-intact cells. This inhibition required Tsg101 and could be relieved with deISGylases. Tsg101 is itself ISGylated in IFN-treated cells. Upon infection, intact Tsg101-deficient cells obtained by CRISPR-Cas9 genome editing were defective in the surface display of HA and for infectious virion release. These data support the IFN-induced generation of a Tsg101- and ISG15-dependent checkpoint in the secretory pathway that compromises influenza virus release.
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17
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Divakaruni AS, Rogers GW, Murphy AN. Measuring Mitochondrial Function in Permeabilized Cells Using the Seahorse XF Analyzer or a Clark-Type Oxygen Electrode. ACTA ACUST UNITED AC 2014; 60:25.2.1-16. [PMID: 24865646 DOI: 10.1002/0471140856.tx2502s60] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Measurements of mitochondrial respiration in intact cells can help define metabolism and its dysregulation in fields such as cancer, metabolic disease, immunology, and neurodegeneration. Although cells can be offered various substrates in the assay medium, many cell types can oxidize stored pools of energy substrates. A general bioenergetic profile can therefore be obtained using intact cells, but the inability to control substrate provision to the mitochondria can restrict an in-depth, mechanistic understanding. Mitochondria can be isolated from intact cells, but the yield and quality of the end product is often poor and prone to subselection during isolation. Plasma membrane permeabilization of cells provides a solution to this challenge, allowing experimental control of the medium surrounding the mitochondria. This unit describes techniques to measure respiration in permeabilized adherent cells using a Seahorse XF Analyzer or permeabilized suspended cells in a Hansatech Oxygraph.
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Affiliation(s)
- Ajit S Divakaruni
- Department of Pharmacology, University of California, San Diego, La Jolla, California
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18
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Claessen JHL, Sanyal S, Ploegh HL. The chaperone BAG6 captures dislocated glycoproteins in the cytosol. PLoS One 2014; 9:e90204. [PMID: 24594942 PMCID: PMC3940849 DOI: 10.1371/journal.pone.0090204] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 01/29/2014] [Indexed: 11/29/2022] Open
Abstract
Secretory and membrane (glyco)proteins are subject to quality control in the endoplasmic reticulum (ER) to ensure that only functional proteins reach their destination. Proteins deemed terminally misfolded and hence functionally defective may be dislocated to the cytosol, where the proteasome degrades them. What we know about this process stems mostly from overexpression of tagged misfolded proteins, or from situations where viruses have hijacked the quality control machinery to their advantage. We know of only very few endogenous substrates of ER quality control, most of which are degraded as part of a signaling pathway, such as Insig-1, but such examples do not necessarily represent terminally misfolded proteins. Here we show that endogenous dislocation clients are captured specifically in association with the cytosolic chaperone BAG6, or retrieved en masse via their glycan handle.
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Affiliation(s)
- Jasper H. L. Claessen
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Sumana Sanyal
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Hidde L Ploegh
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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19
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Salabei JK, Gibb AA, Hill BG. Comprehensive measurement of respiratory activity in permeabilized cells using extracellular flux analysis. Nat Protoc 2014; 9:421-38. [PMID: 24457333 DOI: 10.1038/nprot.2014.018] [Citation(s) in RCA: 233] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Extracellular flux (XF) analysis has become a mainstream method for measuring mitochondrial function in cells and tissues. Although this technique is commonly used to measure bioenergetics in intact cells, we outline here a detailed XF protocol for measuring respiration in permeabilized cells. Cells are permeabilized using saponin (SAP), digitonin (DIG) or recombinant perfringolysin O (rPFO) (XF-plasma membrane permeabilizer (PMP) reagent), and they are provided with specific substrates to measure complex I- or complex II-mediated respiratory activity, complex III+IV respiratory activity or complex IV activity. Medium- and long-chain acylcarnitines or glutamine may also be provided for measuring fatty acid (FA) oxidation or glutamine oxidation, respectively. This protocol uses a minimal number of cells compared with other protocols and does not require isolation of mitochondria. The results are highly reproducible, and mitochondria remain well coupled. Collectively, this protocol provides comprehensive and detailed information regarding mitochondrial activity and efficiency, and, after preparative steps, it takes 6-8 h to complete.
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Affiliation(s)
- Joshua K Salabei
- Diabetes and Obesity Center, Institute of Molecular Cardiology, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Andrew A Gibb
- 1] Diabetes and Obesity Center, Institute of Molecular Cardiology, University of Louisville School of Medicine, Louisville, Kentucky, USA. [2] Department of Physiology and Biophysics, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Bradford G Hill
- 1] Diabetes and Obesity Center, Institute of Molecular Cardiology, University of Louisville School of Medicine, Louisville, Kentucky, USA. [2] Department of Physiology and Biophysics, University of Louisville School of Medicine, Louisville, Kentucky, USA. [3] Department of Biochemistry and Molecular Biology, University of Louisville School of Medicine, Louisville, Kentucky, USA
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20
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Establishment of an in vitro transport assay that reveals mechanistic differences in cytosolic events controlling cholera toxin and T-cell receptor α retro-translocation. PLoS One 2013; 8:e75801. [PMID: 24146777 PMCID: PMC3795749 DOI: 10.1371/journal.pone.0075801] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 08/21/2013] [Indexed: 11/19/2022] Open
Abstract
Following retrograde trafficking to the endoplasmic reticulum (ER), cholera toxin A1 (CTA1) subunit hijacks ER-associated degradation (ERAD) machinery and retro-translocates into the cytosol to induce toxicity. We previously established a cell-based in vivo assay to identify ER components that regulate this process. However, elucidating cytosolic events that govern CTA1 retro-translocation using this assay is difficult as manipulating cytosolic factors often perturbs toxin retrograde transport to the ER. To circumvent this problem, we developed an in vitro assay in semi-permeabilized cells that directly monitors CTA1 release from the ER into the cytosol. We demonstrate CTA1 is released into the cytosol as a folded molecule in a p97- and proteasome-independent manner. Release nonetheless involves a GTP-dependent reaction. Upon extending this assay to the canonical ERAD substrate T-cell receptor α (TCRα), we found the receptor is unfolded when released into the cytosol and degraded by membrane-associated proteasome. In this reaction, p97 initially extracts TCRα from the ER membrane, followed by TCRα discharge into the cytosol that requires additional energy-dependent cytosolic activities. Our results reveal mechanistic insights into cytosolic events controlling CTA1 and TCRα retro-translocation, and provide a reliable tool to further probe this process.
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21
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Gastaldello S, Chen X, Callegari S, Masucci MG. Caspase-1 promotes Epstein-Barr virus replication by targeting the large tegument protein deneddylase to the nucleus of productively infected cells. PLoS Pathog 2013; 9:e1003664. [PMID: 24130483 PMCID: PMC3795028 DOI: 10.1371/journal.ppat.1003664] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 08/12/2013] [Indexed: 11/17/2022] Open
Abstract
The large tegument proteins of herpesviruses contain N-terminal cysteine proteases with potent ubiquitin and NEDD8-specific deconjugase activities, but the function of the enzymes during virus replication remains largely unknown. Using as model BPLF1, the homologue encoded by Epstein-Barr virus (EBV), we found that induction of the productive virus cycle does not affect the total level of ubiquitin-conjugation but is accompanied by a BPLF1-dependent decrease of NEDD8-adducts and accumulation of free NEDD8. Expression of BPLF1 promotes cullin degradation and the stabilization of cullin-RING ligases (CRLs) substrates in the nucleus, while cytoplasmic CRLs and their substrates are not affected. The inactivation of nuclear CRLs is reversed by the N-terminus of CAND1, which inhibits the binding of BPLF1 to cullins and prevents efficient viral DNA replication. Targeting of the deneddylase activity to the nucleus is dependent on processing of the catalytic N-terminus by caspase-1. Inhibition of caspase-1 severely impairs viral DNA synthesis and the release of infectious virus, pointing a previously unrecognized role of the cellular response to danger signals triggered by EBV reactivation in promoting virus replication.
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Affiliation(s)
- Stefano Gastaldello
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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22
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Bernardi KM, Williams JM, Inoue T, Schultz A, Tsai B. A deubiquitinase negatively regulates retro-translocation of nonubiquitinated substrates. Mol Biol Cell 2013; 24:3545-56. [PMID: 24068323 PMCID: PMC3826992 DOI: 10.1091/mbc.e13-06-0332] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Although cholera toxin is a nonubiquitinated substrate that undergoes retro-translocation to the cytosol, this study identifies a deubiquitinase that controls toxin retro-translocation. Endoplasmic reticulum (ER) membrane–bound E3 ubiquitin ligases promote ER-associated degradation (ERAD) by ubiquitinating a retro-translocated substrate that reaches the cytosol from the ER, targeting it to the proteasome for destruction. Recent findings implicate ERAD-associated deubiquitinases (DUBs) as positive and negative regulators during ERAD, reflecting the different consequences of deubiquitinating a substrate prior to proteasomal degradation. These observations raise the question of whether a DUB can control the fate of a nonubiquitinated ERAD substrate. In this study, we probed the role of the ERAD-associated DUB, YOD1, during retro-translocation of the nonubiquitinated cholera toxin A1 (CTA1) peptide, a critical intoxication step. Through combining knockdown, overexpression, and binding studies, we demonstrated that YOD1 negatively controls CTA1 retro-translocation, likely by deubiquitinating and inactivating ubiquitinated ERAD components that normally promote toxin retro-translocation. YOD1 also antagonizes the proteasomal degradation of nonglycosylated pro-α factor, a postulated nonubiquitinated yeast ERAD substrate, in mammalian cells. Our findings reveal that a cytosolic DUB exerts a negative function during retro-translocation of nonubiquitinated substrates, potentially by acting on elements of the ERAD machinery.
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Affiliation(s)
- Kaleena M Bernardi
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48103 Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
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23
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Olzmann JA, Kopito RR, Christianson JC. The mammalian endoplasmic reticulum-associated degradation system. Cold Spring Harb Perspect Biol 2013; 5:cshperspect.a013185. [PMID: 23232094 DOI: 10.1101/cshperspect.a013185] [Citation(s) in RCA: 250] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The endoplasmic reticulum (ER) is the site of synthesis for nearly one-third of the eukaryotic proteome and is accordingly endowed with specialized machinery to ensure that proteins deployed to the distal secretory pathway are correctly folded and assembled into native oligomeric complexes. Proteins failing to meet this conformational standard are degraded by ER-associated degradation (ERAD), a complex process through which folding-defective proteins are selected and ultimately degraded by the ubiquitin-proteasome system. ERAD proceeds through four tightly coupled steps involving substrate selection, dislocation across the ER membrane, covalent conjugation with polyubiquitin, and proteasomal degradation. The ERAD machinery shows a modular organization with central ER membrane-embedded ubiquitin ligases linking components responsible for recognition in the ER lumen to the ubiquitin-proteasome system in the cytoplasm. The core ERAD machinery is highly conserved among eukaryotes and much of our basic understanding of ERAD organization has been derived from genetic and biochemical studies of yeast. In this article we discuss how the core ERAD machinery is organized in mammalian cells.
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Affiliation(s)
- James A Olzmann
- Department of Biology, Stanford University, Stanford, California 94305, USA
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24
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Abstract
ER-associated degradation clears the secretory pathway of misfolded proteins and mediates the regulated degradation of some ER resident proteins. Only a minor increase in the interaction between a protein and a ubiquitin ligase is sufficient to signal substrate degradation. Zhang et al. have identified deubiquitination as a signal amplifier.
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Affiliation(s)
- Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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25
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Wang X, Yu YYL, Myers N, Hansen TH. Decoupling the role of ubiquitination for the dislocation versus degradation of major histocompatibility complex (MHC) class I proteins during endoplasmic reticulum-associated degradation (ERAD). J Biol Chem 2013; 288:23295-306. [PMID: 23801327 DOI: 10.1074/jbc.m113.482018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aberrantly or excessively expressed proteins in the endoplasmic reticulum are identified by quality control mechanisms and dislocated to the cytosol for proteasome-mediated, ubiquitin-dependent degradation by a process termed endoplasmic reticulum-associated degradation (ERAD). In addition to its role in degradation, ubiquitination has also been implicated in substrate dislocation, although whether direct ubiquitin conjugation of ERAD substrates is required for dislocation has been difficult to ascertain. An obstacle in probing the mechanism of quality control-induced ERAD is the paucity of ERAD substrates being dislocated and detected at any given time. To obviate this problem, we report here the use of a sensitive biotinylation system to probe the dislocation of major histocompatibility complex I (MHCI) heavy chain substrates in the absence of immune evasion proteins. Using this assay system the dislocation of MHCI heavy chains was found not to require potential ubiquitin conjugation sites in the cytoplasmic tail or Lys residues in the ectodomain. By contrast, dislocation of MHCI heavy chains did require deubiquitinating enzyme activity and rapid proteasome-mediated degradation required Lys residues in MHCI heavy chain ectodomain. These combined findings support the model that the endoplasmic reticulum quality control-induced dislocation of MHCI heavy chains may not require direct ubiquitination/deubiquitination as is required for proteasome-mediated degradation post dislocation.
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Affiliation(s)
- Xiaoli Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
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26
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Thiazolidinediones are acute, specific inhibitors of the mitochondrial pyruvate carrier. Proc Natl Acad Sci U S A 2013; 110:5422-7. [PMID: 23513224 DOI: 10.1073/pnas.1303360110] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Facilitated pyruvate transport across the mitochondrial inner membrane is a critical step in carbohydrate, amino acid, and lipid metabolism. We report that clinically relevant concentrations of thiazolidinediones (TZDs), a widely used class of insulin sensitizers, acutely and specifically inhibit mitochondrial pyruvate carrier (MPC) activity in a variety of cell types. Respiratory inhibition was overcome with methyl pyruvate, localizing the effect to facilitated pyruvate transport, and knockdown of either paralog, MPC1 or MPC2, decreased the EC50 for respiratory inhibition by TZDs. Acute MPC inhibition significantly enhanced glucose uptake in human skeletal muscle myocytes after 2 h. These data (i) report that clinically used TZDs inhibit the MPC, (ii) validate that MPC1 and MPC2 are obligatory components of facilitated pyruvate transport in mammalian cells, (iii) indicate that the acute effect of TZDs may be related to insulin sensitization, and (iv) establish mitochondrial pyruvate uptake as a potential therapeutic target for diseases rooted in metabolic dysfunction.
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27
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Claessen JHL, Witte MD, Yoder NC, Zhu AY, Spooner E, Ploegh HL. Catch-and-release probes applied to semi-intact cells reveal ubiquitin-specific protease expression in Chlamydia trachomatis infection. Chembiochem 2013; 14:343-52. [PMID: 23335262 DOI: 10.1002/cbic.201200701] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Indexed: 12/26/2022]
Abstract
Protein ubiquitylation controls many cellular pathways, and timely removal of ubiquitin by deubiquitylating enzymes (DUBs) is essential to govern these different functions. To map endogenous expression of individual DUBs as well as that of any interacting proteins, we developed a catch-and-release ubiquitin probe. Ubiquitin was equipped with an activity-based warhead and a cleavable linker attached to a biotin affinity-handle through tandem site-specific modification, in which we combined intein chemistry with sortase-mediated ligation. The resulting probe is cell-impermeable and was therefore delivered to the cytosol of perfringolysin O (PFO)-permeabilized cells. This allowed us to retrieve and identify 34 DUBs and their interacting partners. We also noted the expression, in host cells infected with Chlamydia trachomatis, of two additional DUBs. Furthermore, we retrieved and identified chlamydial DUB1 (ChlaDUB1) and DUB2 (ChlaDUB2), demonstrating by experiment that ChlaDUB2, the presence and activity of which had not been detected in infected cells, is in fact expressed during the course of infection.
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Affiliation(s)
- Jasper H L Claessen
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, 02142, Cambridge, MA, USA
| | - Martin D Witte
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, 02142, Cambridge, MA, USA
| | - Nicholas C Yoder
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, 02142, Cambridge, MA, USA
| | - Angela Y Zhu
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, 02142, Cambridge, MA, USA
| | - Eric Spooner
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, 02142, Cambridge, MA, USA
| | - Hidde L Ploegh
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, 02142, Cambridge, MA, USA
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Pick E, Berman TS. Formation of alternative proteasomes: same lady, different cap? FEBS Lett 2013; 587:389-93. [PMID: 23333296 DOI: 10.1016/j.febslet.2013.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/23/2012] [Accepted: 01/07/2013] [Indexed: 11/29/2022]
Abstract
The 26S proteasome is thought to be a homogenous complex, consisting of a 20S proteolytic core and a 19S regulatory particle that is required for its activation. Two groups have recently reported the activation of archeal 20S by a p97-related double-ring AAA+ ATPase complex, in a similar fashion to that reported for 19S. Since p97 is found in eukaryotes, the existence of a parallel setting in higher organisms is intriguing. Herein, we present supporting data and hypothesize that in eukaryotes, p97 and CSN form a promiscuous, hence hard-to-detect, "alternative cap", enabling the prompt and precise elimination of particular substrates.
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Affiliation(s)
- Elah Pick
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 36006, Israel.
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Sortase-mediated modification of αDEC205 affords optimization of antigen presentation and immunization against a set of viral epitopes. Proc Natl Acad Sci U S A 2013; 110:1428-33. [PMID: 23297227 DOI: 10.1073/pnas.1214994110] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A monoclonal antibody against the C-type lectin DEC205 (αDEC205) is an effective vehicle for delivery of antigens to dendritic cells through creation of covalent αDEC205-antigen adducts. These adducts can induce antigen-specific T-cell immune responses or tolerance. We exploit the transpeptidase activity of sortase to install modified peptides and protein-sized antigens onto the heavy chain of αDEC205, including linkers that contain nonnatural amino acids. We demonstrate stoichiometric site-specific labeling on a scale not easily achievable by genetic fusions (49 distinct fusions in this report). We conjugated a biotinylated version of a class I MHC-restricted epitope to unlabeled αDEC205 and monitored epitope generation upon binding of the adduct to dendritic cells. Our results show transfer of αDEC205 heavy chain to the cytoplasm, followed by proteasomal degradation. Introduction of a labile dipeptide linker at the N terminus of a T-cell epitope improves proteasome-dependent class I MHC-restricted peptide cross-presentation when delivered by αDEC205 in vitro and in vivo. We also conjugated αDEC205 with a linker-optimized peptide library of known CD8 T-cell epitopes from the mouse γ-herpes virus 68. Animals immunized with such conjugates displayed a 10-fold reduction in viral load.
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Perfringolysin O as a useful tool to study human sperm physiology. Fertil Steril 2013; 99:99-106.e2. [DOI: 10.1016/j.fertnstert.2012.08.052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/09/2012] [Accepted: 08/22/2012] [Indexed: 11/27/2022]
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