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Shehzada S, Noto T, Saksouk J, Mochizuki K. A SUMO E3 ligase promotes long non-coding RNA transcription to regulate small RNA-directed DNA elimination. eLife 2024; 13:e95337. [PMID: 38197489 PMCID: PMC10830130 DOI: 10.7554/elife.95337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024] Open
Abstract
Small RNAs target their complementary chromatin regions for gene silencing through nascent long non-coding RNAs (lncRNAs). In the ciliated protozoan Tetrahymena, the interaction between Piwi-associated small RNAs (scnRNAs) and the nascent lncRNA transcripts from the somatic genome has been proposed to induce target-directed small RNA degradation (TDSD), and scnRNAs not targeted for TDSD later target the germline-limited sequences for programmed DNA elimination. In this study, we show that the SUMO E3 ligase Ema2 is required for the accumulation of lncRNAs from the somatic genome and thus for TDSD and completing DNA elimination to make viable sexual progeny. Ema2 interacts with the SUMO E2 conjugating enzyme Ubc9 and enhances SUMOylation of the transcription regulator Spt6. We further show that Ema2 promotes the association of Spt6 and RNA polymerase II with chromatin. These results suggest that Ema2-directed SUMOylation actively promotes lncRNA transcription, which is a prerequisite for communication between the genome and small RNAs.
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Affiliation(s)
- Salman Shehzada
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
| | - Tomoko Noto
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
| | - Julie Saksouk
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
| | - Kazufumi Mochizuki
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
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2
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Michaelides IN, Collie GW. E3 Ligases Meet Their Match: Fragment-Based Approaches to Discover New E3 Ligands and to Unravel E3 Biology. J Med Chem 2023; 66:3173-3194. [PMID: 36821822 PMCID: PMC10009759 DOI: 10.1021/acs.jmedchem.2c01882] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Indexed: 02/25/2023]
Abstract
Ubiquitination is a key post-translational modification of proteins, affecting the regulation of multiple cellular processes. Cells are equipped with over 600 ubiquitin orchestrators, called E3 ubiquitin ligases, responsible for directing the covalent attachment of ubiquitin to substrate proteins. Due to their regulatory role in cells, significant efforts have been made to discover ligands for E3 ligases. The recent emergence of the proteolysis targeting chimera (PROTAC) and molecular glue degrader (MGD) modalities has further increased interest in E3 ligases as drug targets. This perspective focuses on how fragment based lead discovery (FBLD) methods have been used to discover new ligands for this important target class. In some cases these efforts have led to clinical candidates; in others, they have provided tools for deepening our understanding of E3 ligase biology. Recently, FBLD-derived ligands have inspired the design of PROTACs that are able to artificially modulate protein levels in cells.
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Affiliation(s)
- Iacovos N. Michaelides
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
| | - Gavin W. Collie
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
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3
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Ginkgolic acid improves bleomycin-induced pulmonary fibrosis by inhibiting SMAD4 SUMOylation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8002566. [PMID: 35707278 PMCID: PMC9192210 DOI: 10.1155/2022/8002566] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 04/24/2022] [Accepted: 05/20/2022] [Indexed: 11/18/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a refractory chronic respiratory disease with progressively exacerbating symptoms and a high mortality rate. There are currently only two effective drugs for IPF; thus, there is an urgent need to develop new therapeutics. Previous experiments have shown that ginkgolic acid (GA), as a SUMO-1 inhibitor, exerted an inhibitory effect on cardiac fibrosis induced by myocardial infarction. Regarding the pathogenesis of PF, previous studies have concluded that small ubiquitin-like modifier (SUMO) polypeptides bind multiple target proteins and participate in fibrosis of multiple organs, including PF. In this study, we found altered expression of SUMO family members in lung tissues from IPF patients. GA mediated the reduced expression of SUMO1/2/3 and the overexpression of SENP1 in a PF mouse model, which improved PF phenotypes. At the same time, the protective effect of GA on PF was also confirmed in the SENP1-KO transgenic mice model. Subsequent experiments showed that SUMOylation of SMAD4 was involved in PF. It was inhibited by TGF-β1, but GA could reverse the effects of TGF-β1. SENP1 also inhibited the SUMOylation of SMAD4 and then participated in epithelial-mesenchymal transition (EMT) downstream of TGF-β1. We also found that SENP1 regulation of SMAD4 SUMOylation affected reactive oxygen species (ROS) production during TGF-β1-induced EMT and that GA prevented this oxidative stress through SENP1. Therefore, GA may inhibit the SUMOylation of SMAD4 through SENP1 and participate in TGF-β1-mediated pulmonary EMT, all of which reduce the degree of PF. This study provided potential novel targets and a new alternative for the future clinical testing in PF.
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4
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Li X, Zhou S, Liu Z, Lu L, Dang H, Li H, Chu B, Chen P, Ma Z, Zhao S, Li Z, van Nocker S, Ma F, Guan Q. Fine-tuning of SUMOylation modulates drought tolerance of apple. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:903-919. [PMID: 34978131 PMCID: PMC9055824 DOI: 10.1111/pbi.13772] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
SUMOylation is involved in various aspects of plant biology, including drought stress. However, the relationship between SUMOylation and drought stress tolerance is complex; whether SUMOylation has a crosstalk with ubiquitination in response to drought stress remains largely unclear. In this study, we found that both increased and decreased SUMOylation led to increased survival of apple (Malus × domestica) under drought stress: both transgenic MdSUMO2A overexpressing (OE) plants and MdSUMO2 RNAi plants exhibited enhanced drought tolerance. We further confirmed that MdDREB2A is one of the MdSUMO2 targets. Both transgenic MdDREB2A OE and MdDREB2AK192R OE plants (which lacked the key site of SUMOylation by MdSUMO2A) were more drought tolerant than wild-type plants. However, MdDREB2AK192R OE plants had a much higher survival rate than MdDREB2A OE plants. We further showed SUMOylated MdDREB2A was conjugated with ubiquitin by MdRNF4 under drought stress, thereby triggering its protein degradation. In addition, MdRNF4 RNAi plants were more tolerant to drought stress. These results revealed the molecular mechanisms that underlie the relationship of SUMOylation with drought tolerance and provided evidence for the tight control of MdDREB2A accumulation under drought stress mediated by SUMOylation and ubiquitination.
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Affiliation(s)
- Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Shuangxi Zhou
- Department of Biological SciencesMacquarie UniversityNorth RydeNSWAustralia
| | - Zeyuan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Liyuan Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Huan Dang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Huimin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Baohua Chu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Ziqing Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Shuang Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Steve van Nocker
- Department of HorticultureMichigan State UniversityEast LansingMIUSA
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
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5
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Hu Z, Crews CM. Recent Developments in PROTAC-Mediated Protein Degradation: From Bench to Clinic. Chembiochem 2022; 23:e202100270. [PMID: 34494353 PMCID: PMC9395155 DOI: 10.1002/cbic.202100270] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/02/2021] [Indexed: 01/21/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs), an emerging paradigm-shifting technology, hijacks the ubiquitin-proteasome system for targeted protein degradation. PROTACs induce ternary complexes between an E3 ligase and POI, and this induced proximity leads to polyUb chain formation on substrates and eventual proteasomal-mediated POI degradation. PROTACs have shown great therapeutic potential by degrading many disease-causing proteins, such as the androgen receptor and BRD4. The PROTAC technology has advanced significantly in the last two decades, with the repertoire of PROTAC targets increased tremendously. Herein, we describe recent developments of PROTAC technology, focusing on mechanistic and kinetic studies, pharmacokinetic study, spatiotemporal control of PROTACs, covalent PROTACs, resistance to PROTACs, and new E3 ligands.
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Affiliation(s)
- Zhenyi Hu
- Department of Molecular, Cellular and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven CT 06511 (USA)
| | - Craig M. Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven CT 06511 (USA),Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06511(USA),Department of Pharmacology, Yale University, 333 Cedar Street New Haven, CT 06511 (USA)
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6
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Zhang Y, Zeng L. Crosstalk between Ubiquitination and Other Post-translational Protein Modifications in Plant Immunity. PLANT COMMUNICATIONS 2020; 1:100041. [PMID: 33367245 PMCID: PMC7748009 DOI: 10.1016/j.xplc.2020.100041] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/07/2020] [Accepted: 03/19/2020] [Indexed: 05/05/2023]
Abstract
Post-translational modifications (PTMs) are central to the modulation of protein activity, stability, subcellular localization, and interaction with partners. They greatly expand the diversity and functionality of the proteome and have taken the center stage as key players in regulating numerous cellular and physiological processes. Increasing evidence indicates that in addition to a single regulatory PTM, many proteins are modified by multiple different types of PTMs in an orchestrated manner to collectively modulate the biological outcome. Such PTM crosstalk creates a combinatorial explosion in the number of proteoforms in a cell and greatly improves the ability of plants to rapidly mount and fine-tune responses to different external and internal cues. While PTM crosstalk has been investigated in depth in humans, animals, and yeast, the study of interplay between different PTMs in plants is still at its infant stage. In the past decade, investigations showed that PTMs are widely involved and play critical roles in the regulation of interactions between plants and pathogens. In particular, ubiquitination has emerged as a key regulator of plant immunity. This review discusses recent studies of the crosstalk between ubiquitination and six other PTMs, i.e., phosphorylation, SUMOylation, poly(ADP-ribosyl)ation, acetylation, redox modification, and glycosylation, in the regulation of plant immunity. The two basic ways by which PTMs communicate as well as the underlying mechanisms and diverse outcomes of the PTM crosstalk in plant immunity are highlighted.
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7
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Fu H, Zhang Y, Chen J, Zhou B, Chen G, Chen P. Tmub1 Suppresses Hepatocellular Carcinoma by Promoting the Ubiquitination of ΔNp63 Isoforms. MOLECULAR THERAPY-ONCOLYTICS 2020; 18:126-136. [PMID: 32671188 PMCID: PMC7338996 DOI: 10.1016/j.omto.2020.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/01/2020] [Indexed: 12/29/2022]
Abstract
Transmembrane and ubiquitin-like domain-containing 1 (Tmub1) inhibits hepatocyte proliferation during liver regeneration, but its role in hepatocellular carcinoma (HCC) has yet to be revealed. In this study, we show that the levels of Tmub1 were significantly lower in HCC tissues and cells than they were in adjacent tissues and normal hepatic cells, and the low levels of Tmub1 indicated a poor prognosis in HCC patients. Xenograft growth assay revealed that Tmub1 represses HCC growth in vivo. In addition, Tmub1 formed a protein complex with apoptosis-associated protein tumor protein 63 (p63), especially with the ΔN isoforms (ΔNp63α, β, and γ). Further loss- and gain-of-function analyses indicated that Tmub1 promotes apoptosis of Hep3B and MHCC-LM3 cells. Tmub1 decreased the protein expression of ΔNp63, and the pro-apoptotic effect of Tmub1 can be reversed by ΔNp63 isoforms (α, β, and γ). Additionally, we report that Tmub1 promotes the ubiquitination and degradation of ΔNp63 proteins. Finally, we confirmed in HCC tissues that Tmub1 is negatively correlated with ΔNp63 and positively correlated with the level of apoptosis. Taken together, Tmub1 suppresses HCC by enhancing the ubiquitination and degradation of ΔNp63 isoforms to induce HCC cell apoptosis. These findings provide a potential strategy for the management of HCC.
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Affiliation(s)
- Hangwei Fu
- Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Yida Zhang
- Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Junying Chen
- Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Bo Zhou
- Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Geng Chen
- Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, Chongqing 400042, China
- Corresponding author: Geng Chen, Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, #10 Changjiangzhilu Daping, Yuzhong District, Chongqing 400042, China.
| | - Ping Chen
- Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, Chongqing 400042, China
- Corresponding author: Ping Chen, Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, #10 Changjiangzhilu Daping, Yuzhong District, Chongqing 400042, China.
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8
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Wu HQ, Baker D, Ovaa H. Small molecules that target the ubiquitin system. Biochem Soc Trans 2020; 48:479-497. [PMID: 32196552 PMCID: PMC7200645 DOI: 10.1042/bst20190535] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 02/07/2023]
Abstract
Eukaryotic life depends upon the interplay between vast networks of signaling pathways composed of upwards of 109-1010 proteins per cell. The integrity and normal operation of the cell requires that these proteins act in a precise spatial and temporal manner. The ubiquitin system is absolutely central to this process and perturbation of its function contributes directly to the onset and progression of a wide variety of diseases, including cancer, metabolic syndromes, neurodegenerative diseases, autoimmunity, inflammatory disorders, infectious diseases, and muscle dystrophies. Whilst the individual components and the overall architecture of the ubiquitin system have been delineated in some detail, how ubiquitination might be successfully targeted, or harnessed, to develop novel therapeutic approaches to the treatment of disease, currently remains relatively poorly understood. In this review, we will provide an overview of the current status of selected small molecule ubiquitin system inhibitors. We will further discuss the unique challenges of targeting this ubiquitous and highly complex machinery, and explore and highlight potential ways in which these challenges might be met.
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Affiliation(s)
- Hai Qiu Wu
- Oncode Institute, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - David Baker
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Huib Ovaa
- Oncode Institute, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
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9
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Wang L, Qi H, Tang Y, Shen HM. Post-translational Modifications of Key Machinery in the Control of Mitophagy. Trends Biochem Sci 2020; 45:58-75. [DOI: 10.1016/j.tibs.2019.08.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/05/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022]
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10
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Ward CC, Kleinman JI, Brittain SM, Lee PS, Chung CYS, Kim K, Petri Y, Thomas JR, Tallarico JA, McKenna JM, Schirle M, Nomura DK. Covalent Ligand Screening Uncovers a RNF4 E3 Ligase Recruiter for Targeted Protein Degradation Applications. ACS Chem Biol 2019; 14:2430-2440. [PMID: 31059647 DOI: 10.1021/acschembio.8b01083] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Targeted protein degradation has arisen as a powerful strategy for drug discovery allowing the targeting of undruggable proteins for proteasomal degradation. This approach most often employs heterobifunctional degraders consisting of a protein-targeting ligand linked to an E3 ligase recruiter to ubiquitinate and mark proteins of interest for proteasomal degradation. One challenge with this approach, however, is that only a few E3 ligase recruiters currently exist for targeted protein degradation applications, despite the hundreds of known E3 ligases in the human genome. Here, we utilized activity-based protein profiling (ABPP)-based covalent ligand screening approaches to identify cysteine-reactive small-molecules that react with the E3 ubiquitin ligase RNF4 and provide chemical starting points for the design of RNF4-based degraders. The hit covalent ligand from this screen reacted with either of two zinc-coordinating cysteines in the RING domain, C132 and C135, with no effect on RNF4 activity. We further optimized the potency of this hit and incorporated this potential RNF4 recruiter into a bifunctional degrader linked to JQ1, an inhibitor of the BET family of bromodomain proteins. We demonstrate that the resulting compound CCW 28-3 is capable of degrading BRD4 in a proteasome- and RNF4-dependent manner. In this study, we have shown the feasibility of using chemoproteomics-enabled covalent ligand screening platforms to expand the scope of E3 ligase recruiters that can be exploited for targeted protein degradation applications.
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Affiliation(s)
- Carl C. Ward
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jordan I. Kleinman
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Scott M. Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Lee
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Clive Yik Sham Chung
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Kenneth Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
| | - Yana Petri
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jason R. Thomas
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - John A. Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Jeffrey M. McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Daniel K. Nomura
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
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11
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Shi P, Su Y, Li R, Zhang L, Chen C, Zhang L, Faaberg K, Huang J. Dual Regulation of Host TRAIP Post-translation and Nuclear/Plasma Distribution by Porcine Reproductive and Respiratory Syndrome Virus Non-structural Protein 1α Promotes Viral Proliferation. Front Immunol 2018; 9:3023. [PMID: 30619364 PMCID: PMC6305329 DOI: 10.3389/fimmu.2018.03023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/06/2018] [Indexed: 12/11/2022] Open
Abstract
In this study, we show that porcine reproductive and respiratory syndrome virus (PRRSV) non-structural protein 1α (nsp1α) facilitates PRRSV escape from innate immune by modulating nuclear to cytoplasmic translocation and distribution ratio of TRAIP to promote virus proliferation. Mechanistically, TRAIP interacts with PRRSV nsp1α via its K205 site, while NSP1α decreases the SUMOylation and K48 ubiquitination independent of the TRAIP interaction K205 site. Modulation of the dual modification of TRAIP by PRRSV nsp1α results in over-enrichment of TRAIP in the cytoplasm. Enrichment of nsp1α-induced cytoplasmic TRAIP in turn leads to excessive K48 ubiquitination and degradation of serine/threonine-protein kinase (TBK1), thereby antagonizing TBK1-IRF3-IFN signaling. This study proposes a novel mechanism by which PRRSV utilizes host proteins to regulate innate immunity. Findings from this study provides novel perspective to advance our understanding in the pathogenesis of PRRSV.
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Affiliation(s)
- Peidian Shi
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Yanxin Su
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Ruiqiao Li
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Lei Zhang
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Chen Chen
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Lilin Zhang
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Kay Faaberg
- Agricultural Research Service, USDA, National Animal Disease Center, Ames, IA, United States
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, Tianjin, China
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12
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La Barbera G, Capriotti AL, Michelini E, Piovesana S, Calabretta MM, Zenezini Chiozzi R, Roda A, Laganà A. Proteomic analysis and bioluminescent reporter gene assays to investigate effects of simulated microgravity on Caco-2 cells. Proteomics 2018; 17. [PMID: 28727291 DOI: 10.1002/pmic.201700081] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/04/2017] [Accepted: 07/07/2017] [Indexed: 02/03/2023]
Abstract
Microgravity is one of the most important features in spaceflight. Previous evidence from in-vitro studies has shown that significant changes occur under simulated microgravity. For this reason, human colon adenocarcinoma Caco-2 cells were selected as cell model of intestinal epithelial barrier and their response to altered gravity conditions was investigated, especially on the protein level. In this study, we combined label-free shotgun proteomics and bioluminescent reporter gene assays to identify key proteins and pathways involved in the response of Caco-2 cells under reference and microgravity conditions. A two-dimensional clinostat was modified with 3D-printed adaptors to hold conventional T25 culture flasks. The comparative proteome analysis led to identify 38 and 26 proteins differently regulated by simulated microgravity after 48 and 72 h, respectively. Substantial fractions of these proteins are involved in regulation, cellular and metabolic processes and localization. Bioluminescent reporter gene assays were carried out to investigate microgavity-induced alterations on the transcriptional regulation of key targets, such as NF-kB pathway and CYP27A1. While no significant difference was found in the basal transcription, a lower NF-kB basal activation in simulated microgravity conditions was reported, corroborating the hypothesis of reduced immunity in microgravity conditions.
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Affiliation(s)
| | | | - Elisa Michelini
- Dipartimento di Chimica "G.Ciamician", Università di Bologna - Alma Mater Studiorum, Bologna, Italy.,INBB, Istituto Nazionale di Biostrutture e Biosistemi, Rome, Italy
| | - Susy Piovesana
- Dipartimento di Chimica, Sapienza Università di Roma, Rome, Italy
| | | | | | - Aldo Roda
- Dipartimento di Chimica "G.Ciamician", Università di Bologna - Alma Mater Studiorum, Bologna, Italy.,INBB, Istituto Nazionale di Biostrutture e Biosistemi, Rome, Italy
| | - Aldo Laganà
- Dipartimento di Chimica, Sapienza Università di Roma, Rome, Italy
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