1
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Purser N, Tripathi-Giesgen I, Li J, Scott DC, Horn-Ghetko D, Baek K, Schulman BA, Alpi AF, Kleiger G. Catalysis of non-canonical protein ubiquitylation by the ARIH1 ubiquitin ligase. Biochem J 2023; 480:1817-1831. [PMID: 37870100 PMCID: PMC10657180 DOI: 10.1042/bcj20230373] [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: 08/31/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 10/24/2023]
Abstract
Protein ubiquitylation typically involves isopeptide bond formation between the C-terminus of ubiquitin to the side-chain amino group on Lys residues. However, several ubiquitin ligases (E3s) have recently been identified that ubiquitylate proteins on non-Lys residues. For instance, HOIL-1 belongs to the RING-in-between RING (RBR) class of E3s and has an established role in Ser ubiquitylation. Given the homology between HOIL-1 and ARIH1, an RBR E3 that functions with the large superfamily of cullin-RING E3 ligases (CRLs), a biochemical investigation was undertaken, showing ARIH1 catalyzes Ser ubiquitylation to CRL-bound substrates. However, the efficiency of ubiquitylation was exquisitely dependent on the location and chemical environment of the Ser residue within the primary structure of the substrate. Comprehensive mutagenesis of the ARIH1 Rcat domain identified residues whose mutation severely impacted both oxyester and isopeptide bond formation at the preferred site for Ser ubiquitylation while only modestly affecting Lys ubiquitylation at the physiological site. The results reveal dual isopeptide and oxyester protein ubiquitylation activities of ARIH1 and set the stage for physiological investigations into this function of emerging importance.
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Affiliation(s)
- Nicholas Purser
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, U.S.A
| | - Ishita Tripathi-Giesgen
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, U.S.A
| | - Daniel C. Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, U.S.A
| | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A. Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, U.S.A
| | - Arno F. Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, U.S.A
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2
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Ma W, Liu H, Li X. Chemical Synthesis of Peptides and Proteins Bearing Base-Labile Post-Translational Modifications: Evolution of the Methods in Four Decades. Chembiochem 2023; 24:e202300348. [PMID: 37380612 DOI: 10.1002/cbic.202300348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023]
Abstract
The S-palmitoylation on Cys residue and O-acetylation on Ser/Thr residues are two types of base-labile post-translational modifications (PTMs) in cells. The lability of these PTMs to bases and nucleophiles makes the peptides/proteins bearing S-palmitoyl or O-acetyl groups challenging synthetic targets, which cannot be prepared via the standard Fmoc-SPPS and native chemical ligation. In this review, we summarized the efforts towards their preparation in the past 40 years, with the focus on the evolution of synthetic methods.
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Affiliation(s)
- Wenjie Ma
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Han Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
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3
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Lin Z, Li S, Xiao H, Xu Z, Li C, Zeng J, Wang S, Liu Z, Huang H. The degradation of TGR5 mediated by Smurf1 contributes to diabetic nephropathy. Cell Rep 2023; 42:112851. [PMID: 37481723 DOI: 10.1016/j.celrep.2023.112851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/07/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023] Open
Abstract
The multiple roles of TGR5 in the regulation of glucose metabolism, inflammation, and oxidative stress have drawn attention as therapeutic candidates for diabetes-related kidney disease. However, diabetes induces downregulation of renal TGR5 protein expression, and the regulatory mechanisms have not been clarified. Here, we identify that Smurf1, an E3 ubiquitin ligase, is a critical interactor of TGR5 and mediates the ubiquitination and proteasomal degradation of TGR5 under high glucose stimulation in glomerular mesangial cells. Genetic deficiency of Smurf1 restores TGR5 protein expression and attenuates renal injuries in diabetic mice. Mechanistically, Smurf1 interacts with the TGR5 ICL2 region by its HECT domain and induces K11/K48-linked polyubiquitination of TGR5 at K306 residue. Moreover, restoration of TGR5 protects db/db mice from diabetic nephropathy. These observations elucidate the critical role of Smurf1 in regulating TGR5 stability, suggesting that pharmacological targeting of the interaction between Smurf1 and TGR5 could serve as a promising therapeutic strategy against diabetic nephropathy.
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Affiliation(s)
- Zeyuan Lin
- Laboratory of Pharmacology & Toxicology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Shanshan Li
- Laboratory of Pharmacology & Toxicology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Haiming Xiao
- Laboratory of Pharmacology & Toxicology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhanchi Xu
- Laboratory of Pharmacology & Toxicology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Chuting Li
- Laboratory of Pharmacology & Toxicology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jingran Zeng
- Laboratory of Pharmacology & Toxicology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Shaogui Wang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Zhongqiu Liu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Heqing Huang
- Laboratory of Pharmacology & Toxicology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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4
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Abstract
The traditional textbook describes ubiquitylation as the conjugation of ubiquitin to a target by forming a covalent bond connecting ubiquitin's carboxy-terminal glycine residue with an acceptor amino acid like lysine or amino-terminal methionine in the substrate protein. While this adequately depicts a significant fraction of cellular ubiquitylation processes, a growing number of ubiquitin modifications do not follow this rule. Recent data demonstrate that ubiquitin can also be efficiently attached to other amino acids, such as cysteine, serine, and threonine, via ester bonding. Initially observed for a virus-encoded ubiquitin ligase, which targets a cysteine residue in a host protein to initiate its degradation, ester-linked ubiquitylation is now shown to also drive regular cellular processes. These ubiquitylation events expand the complexity and diversity of ubiquitin signaling and broaden the capability of cellular messages in the so-called ubiquitin code. Still, questions on the prevalence, relevance, and involvement in physiological and cellular functions await clearing. In this review, we aim to summarize our knowledge on ester-linked ubiquitylation and introduce experimental strategies to circumvent technical issues that complicate analysis of this uncommon posttranslational modification.
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Affiliation(s)
- Alba Ferri-Blazquez
- Max-Delbrück-Center for Molecular Medicine in the Helmholz Association, Berlin Buch, Germany.
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Ernst Jarosch
- Max-Delbrück-Center for Molecular Medicine in the Helmholz Association, Berlin Buch, Germany
| | - Thomas Sommer
- Max-Delbrück-Center for Molecular Medicine in the Helmholz Association, Berlin Buch, Germany
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
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5
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Kelsall IR. Non-lysine ubiquitylation: Doing things differently. Front Mol Biosci 2022; 9:1008175. [PMID: 36200073 PMCID: PMC9527308 DOI: 10.3389/fmolb.2022.1008175] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/01/2022] [Indexed: 11/23/2022] Open
Abstract
The post-translational modification of proteins with ubiquitin plays a central role in nearly all aspects of eukaryotic biology. Historically, studies have focused on the conjugation of ubiquitin to lysine residues in substrates, but it is now clear that ubiquitylation can also occur on cysteine, serine, and threonine residues, as well as on the N-terminal amino group of proteins. Paradigm-shifting reports of non-proteinaceous substrates have further extended the reach of ubiquitylation beyond the proteome to include intracellular lipids and sugars. Additionally, results from bacteria have revealed novel ways to ubiquitylate (and deubiquitylate) substrates without the need for any of the enzymatic components of the canonical ubiquitylation cascade. Focusing mainly upon recent findings, this review aims to outline the current understanding of non-lysine ubiquitylation and speculate upon the molecular mechanisms and physiological importance of this non-canonical modification.
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6
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Harnessing the ubiquitin code to respond to environmental cues. Essays Biochem 2022; 66:111-121. [PMID: 35880291 PMCID: PMC9400065 DOI: 10.1042/ebc20210094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/13/2022] [Accepted: 06/27/2022] [Indexed: 12/15/2022]
Abstract
Ubiquitination is an essential post-translational signal that allows cells to adapt and respond to environmental stimuli. Substrate modifications range from a single ubiquitin molecule to complex polyubiquitin chains, where diverse chain topologies constitute a code that is utilized to modify the functions of proteins in numerous cellular signalling pathways. Diverse ubiquitin chain topologies are generated by linking the C-terminus of ubiquitin to one of seven lysine residues or the N-terminal methionine 1 residue of the preceding ubiquitin. Cooperative action between a large array of E2 conjugating and E3 ligase enzymes supports the formation of not only homotypic ubiquitin chains but also heterotypic mixed or branched chains. This complex array of chain topologies is recognized by proteins containing linkage-specific ubiquitin-binding domains and regulates numerous cellular pathways. Although many functions of the ubiquitin code in plants remain unknown, recent work suggests that specific chain topologies are associated with particular molecular processes. Deciphering the ubiquitin code and how plants utilize it to cope with the changing environment is essential to understand the regulatory mechanisms that underpin myriad stress responses and establishment of environmental tolerance.
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7
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Ma Q, Lei H, Cao Y. Intramolecular covalent bonds in Gram-positive bacterial surface proteins. Chembiochem 2022; 23:e202200316. [PMID: 35801833 DOI: 10.1002/cbic.202200316] [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: 06/03/2022] [Revised: 07/07/2022] [Indexed: 11/09/2022]
Abstract
Gram-positive bacteria experience considerable mechanical perturbation when adhering to host surfaces during colonization and infection. They have evolved various adhesion proteins that are mechanically robust to ensure strong surface adhesion. Recently, it was discovered that these adhesion proteins contain rare, extra intramolecular covalent bonds that stabilize protein structures and participate in surface bonding. These intramolecular covalent bonds include isopeptides, thioesters, and ester bonds, which often form spontaneously without the need for additional enzymes. With the development of single-molecule force spectroscopy techniques, the detailed mechanical roles of these intramolecular covalent bonds have been revealed. In this review, we summarize the recent advances in this area of research, focusing on the link between the mechanical stability and function of these covalent bonds in Gram-positive bacterial surface proteins. We also highlight the potential impact of these discoveries on the development of novel antibiotics and chemical biology tools.
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Affiliation(s)
- Quan Ma
- Nanjing University, Department of Physics, CHINA
| | - Hai Lei
- Nanjing University, Department of Physics, CHINA
| | - Yi Cao
- Nanjing University, Department of Physics, 22 Hankou Road, 210093, Nanjing, CHINA
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8
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LUBAC: a new player in polyglucosan body disease. Biochem Soc Trans 2021; 49:2443-2454. [PMID: 34709403 PMCID: PMC8589444 DOI: 10.1042/bst20210838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 12/13/2022]
Abstract
Altered protein ubiquitination is associated with the pathobiology of numerous diseases; however, its involvement in glycogen metabolism and associated polyglucosan body (PB) disease has not been investigated in depth. In PB disease, excessively long and less branched glycogen chains (polyglucosan bodies, PBs) are formed, which precipitate in different tissues causing myopathy, cardiomyopathy and/or neurodegeneration. Linear ubiquitin chain assembly complex (LUBAC) is a multi-protein complex composed of two E3 ubiquitin ligases HOIL-1L and HOIP and an adaptor protein SHARPIN. Together they are responsible for M1-linked ubiquitination of substrates primarily related to immune signaling and cell death pathways. Consequently, severe immunodeficiency is a hallmark of many LUBAC deficient patients. Remarkably, all HOIL-1L deficient patients exhibit accumulation of PBs in different organs especially skeletal and cardiac muscle resulting in myopathy and cardiomyopathy with heart failure. This emphasizes LUBAC's important role in glycogen metabolism. To date, neither a glycogen metabolism-related LUBAC substrate nor the molecular mechanism are known. Hence, current reviews on LUBAC's involvement in glycogen metabolism are lacking. Here, we aim to fill this gap by describing LUBAC's involvement in PB disease. We present a comprehensive review of LUBAC structure, its role in M1-linked and other types of atypical ubiquitination, PB pathology in human patients and findings in new mouse models to study the disease. We conclude the review with recent drug developments and near-future gene-based therapeutic approaches to treat LUBAC related PB disease.
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9
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Zhao H, Song Y, Li J, Zhang Y, Huang H, Li Q, Zhang Y, Xue Y. Primary restriction of S-RNase cytotoxicity by a stepwise ubiquitination and degradation pathway in Petunia hybrida. THE NEW PHYTOLOGIST 2021; 231:1249-1264. [PMID: 33932295 PMCID: PMC8361771 DOI: 10.1111/nph.17438] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/20/2021] [Indexed: 05/15/2023]
Abstract
In self-incompatible Petunia species, the pistil S-RNase acts as cytotoxin to inhibit self-pollination but is polyubiquitinated by the pollen-specific nonself S-locus F-box (SLF) proteins and subsequently degraded by the ubiquitin-proteasome system (UPS), allowing cross-pollination. However, it remains unclear how S-RNase is restricted by the UPS. Using biochemical analyses, we first show that Petunia hybrida S3 -RNase is largely ubiquitinated by K48-linked polyubiquitin chains at three regions, R I, R II and R III. R I is ubiquitinated in unpollinated, self-pollinated and cross-pollinated pistils, indicating its occurrence before PhS3 -RNase uptake into pollen tubes, whereas R II and R III are exclusively ubiquitinated in cross-pollinated pistils. Transgenic analyses showed that removal of R II ubiquitination resulted in significantly reduced seed sets from cross-pollination and that of R I and R III to a lesser extent, indicating their increased cytotoxicity. Consistent with this, the mutated R II of PhS3 -RNase resulted in a marked reduction of its degradation, whereas that of R I and R III resulted in less reduction. Taken together, we demonstrate that PhS3 -RNase R II functions as a major ubiquitination region for its destruction and R I and R III as minor ones, revealing that its cytotoxicity is primarily restricted by a stepwise UPS mechanism for cross-pollination in P. hybrida.
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Affiliation(s)
- Hong Zhao
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yanzhai Song
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Junhui Li
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yue Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Huaqiu Huang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Qun Li
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
| | - Yu’e Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
| | - Yongbiao Xue
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
- Beijing Institute of GenomicsChinese Academy of Sciences and National Centre for BioinformationBeijing100101China
- Jiangsu Co‐Innovation Centre for Modern Production Technology of Grain CropsYangzhou UniversityYangzhou225009China
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10
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D'Amico F, Mukhopadhyay R, Ovaa H, Mulder MPC. Targeting TRIM Proteins: A Quest towards Drugging an Emerging Protein Class. Chembiochem 2021; 22:2011-2031. [PMID: 33482040 PMCID: PMC8251876 DOI: 10.1002/cbic.202000787] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/22/2021] [Indexed: 02/06/2023]
Abstract
The ubiquitylation machinery regulates several fundamental biological processes from protein homeostasis to a wide variety of cellular signaling pathways. As a consequence, its dysregulation is linked to diseases including cancer, neurodegeneration, and autoimmunity. With this review, we aim to highlight the therapeutic potential of targeting E3 ligases, with a special focus on an emerging class of RING ligases, named tri-partite motif (TRIM) proteins, whose role as targets for drug development is currently gaining pharmaceutical attention. TRIM proteins exert their catalytic activity as scaffolds involved in many protein-protein interactions, whose multidomains and adapter-like nature make their druggability very challenging. Herein, we give an overview of the current understanding of this class of single polypeptide RING E3 ligases and discuss potential targeting options.
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Affiliation(s)
- Francesca D'Amico
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
| | - Rishov Mukhopadhyay
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
| | - Monique P. C. Mulder
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
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11
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Chain reactions: molecular mechanisms of RBR ubiquitin ligases. Biochem Soc Trans 2021; 48:1737-1750. [PMID: 32677670 PMCID: PMC7458406 DOI: 10.1042/bst20200237] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Ubiquitination is a fundamental post-translational modification that regulates almost all aspects of cellular signalling and is ultimately catalysed by the action of E3 ubiquitin ligases. The RING-between-RING (RBR) family of E3 ligases encompasses 14 distinct human enzymes that are defined by a unique domain organisation and catalytic mechanism. Detailed characterisation of several RBR ligase family members in the last decade has revealed common structural and mechanistic features. At the same time these studies have highlighted critical differences with respect to autoinhibition, activation and catalysis. Importantly, the majority of RBR E3 ligases remain poorly studied, and thus the extent of diversity within the family remains unknown. In this mini-review we outline the current understanding of the RBR E3 mechanism, structure and regulation with a particular focus on recent findings and developments that will shape the field in coming years.
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12
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Kang JA, Jeon YJ. How Is the Fidelity of Proteins Ensured in Terms of Both Quality and Quantity at the Endoplasmic Reticulum? Mechanistic Insights into E3 Ubiquitin Ligases. Int J Mol Sci 2021; 22:ijms22042078. [PMID: 33669844 PMCID: PMC7923238 DOI: 10.3390/ijms22042078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
The endoplasmic reticulum (ER) is an interconnected organelle that plays fundamental roles in the biosynthesis, folding, stabilization, maturation, and trafficking of secretory and transmembrane proteins. It is the largest organelle and critically modulates nearly all aspects of life. Therefore, in the endoplasmic reticulum, an enormous investment of resources, including chaperones and protein folding facilitators, is dedicated to adequate protein maturation and delivery to final destinations. Unfortunately, the folding and assembly of proteins can be quite error-prone, which leads to the generation of misfolded proteins. Notably, protein homeostasis, referred to as proteostasis, is constantly exposed to danger by flows of misfolded proteins and subsequent protein aggregates. To maintain proteostasis, the ER triages and eliminates terminally misfolded proteins by delivering substrates to the ubiquitin–proteasome system (UPS) or to the lysosome, which is termed ER-associated degradation (ERAD) or ER-phagy, respectively. ERAD not only eliminates misfolded or unassembled proteins via protein quality control but also fine-tunes correctly folded proteins via protein quantity control. Intriguingly, the diversity and distinctive nature of E3 ubiquitin ligases determine efficiency, complexity, and specificity of ubiquitination during ERAD. ER-phagy utilizes the core autophagy machinery and eliminates ERAD-resistant misfolded proteins. Here, we conceptually outline not only ubiquitination machinery but also catalytic mechanisms of E3 ubiquitin ligases. Further, we discuss the mechanistic insights into E3 ubiquitin ligases involved in the two guardian pathways in the ER, ERAD and ER-phagy. Finally, we provide the molecular mechanisms by which ERAD and ER-phagy conduct not only protein quality control but also protein quantity control to ensure proteostasis and subsequent organismal homeostasis.
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Affiliation(s)
- Ji An Kang
- Department of Biochemistry, College of Medicine, Chungnam National University, Daejeon 35015, Korea;
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Young Joo Jeon
- Department of Biochemistry, College of Medicine, Chungnam National University, Daejeon 35015, Korea;
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
- Correspondence:
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13
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He D, Damaris RN, Li M, Khan I, Yang P. Advances on Plant Ubiquitylome-From Mechanism to Application. Int J Mol Sci 2020; 21:E7909. [PMID: 33114409 PMCID: PMC7663383 DOI: 10.3390/ijms21217909] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/13/2020] [Accepted: 10/17/2020] [Indexed: 12/11/2022] Open
Abstract
Post-translational modifications (PTMs) of proteins enable modulation of their structure, function, localization and turnover. To date, over 660 PTMs have been reported, among which, reversible PTMs are regarded as the key players in cellular signaling. Signaling mediated by PTMs is faster than re-initiation of gene expression, which may result in a faster response that is particularly crucial for plants due to their sessile nature. Ubiquitylation has been widely reported to be involved in many aspects of plant growth and development and it is largely determined by its target protein. It is therefore of high interest to explore new ubiquitylated proteins/sites to obtain new insights into its mechanism and functions. In the last decades, extensive protein profiling of ubiquitylation has been achieved in different plants due to the advancement in ubiquitylated proteins (or peptides) affinity and mass spectrometry techniques. This obtained information on a large number of ubiquitylated proteins/sites helps crack the mechanism of ubiquitylation in plants. In this review, we have summarized the latest advances in protein ubiquitylation to gain comprehensive and updated knowledge in this field. Besides, the current and future challenges and barriers are also reviewed and discussed.
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Affiliation(s)
- Dongli He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (D.H.); (R.N.D.); (M.L.)
| | - Rebecca Njeri Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (D.H.); (R.N.D.); (M.L.)
| | - Ming Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (D.H.); (R.N.D.); (M.L.)
| | - Imran Khan
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19014, USA;
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (D.H.); (R.N.D.); (M.L.)
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14
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Proteomic approaches for the profiling of ubiquitylation events and their applications in drug discovery. J Proteomics 2020; 231:103996. [PMID: 33017648 DOI: 10.1016/j.jprot.2020.103996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/27/2020] [Accepted: 09/27/2020] [Indexed: 01/23/2023]
Abstract
Protein ubiquitylation regulates almost all aspects of the biological processes including gene expression, DNA repair, cell proliferation and apoptosis in eukaryotic cells. Dysregulation of protein ubiquitylation caused by abnormal expression of enzymes in the ubiquitin system results in the onset of many diseases including cancer, neurodegenerative diseases, and metabolic syndromes. Therefore, targeting the ubiquitin system becomes a promising research area in drug discovery. Identification of protein ubiquitylation sites is critical for revealing the key ubiquitylation events associated with diseases and specific signaling pathways and for elucidating the biological functions of the specific ubiquitylation events. Many approaches that enrich for the ubiquitylated proteins and ubiquitylated peptides at the protein and peptide levels have been developed to facilitate their identification by MS. In this paper, we will review the proteomic approaches available for the identification of ubiquitylation events at the proteome scale and discuss their advantages and limitations. We will also brief the application of the profiling of ubiquitylation events in drug target discovery and in target validation for proteolysis-targeting chimera (PROTAC). Possible future research directions in this field will also be discussed. SIGNIFICANCE: Ubiquitylation plays critical roles in regulating many biological processes in eukaryotic cells. Identification of ubiquitylation sites can provide the essential information for the functional study of the specific modified substrates. Since ubiquitylated proteins have much lower abundance than non-ubiquitylated proteins, enrichment of ubiquitylated proteins or peptides is critical for their identification by MS. This review focuses on different enrichment approaches that facilitate their isolation and identification by MS and discusses the advantages and drawbacks of these approaches. The application of the profiling of ubiquitylation events in drug target discovery and future research directions will be beneficial to the research community.
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15
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Chen Y, Jin J. The application of ubiquitin ligases in the PROTAC drug design. Acta Biochim Biophys Sin (Shanghai) 2020; 52:776-790. [PMID: 32506133 DOI: 10.1093/abbs/gmaa053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/13/2022] Open
Abstract
Protein ubiquitylation plays important roles in many biological activities. Protein ubiquitylation is a unique process that is mainly controlled by ubiquitin ligases. The ubiquitin-proteasome system (UPS) is the main process to degrade short-lived and unwanted proteins in eukaryotes. Many components in the UPS are attractive drug targets. Recent studies indicated that ubiquitin ligases can be employed as tools in proteolysis-targeting chimeras (PROTACs) for drug discovery. In this review article, we will discuss the recent progress of the application of ubiquitin ligases in the PROTAC drug design. We will also discuss advantages and existing problems of PROTACs. Moreover, we will propose a few principles for selecting ubiquitin ligases in PROTAC applications.
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Affiliation(s)
- Yilin Chen
- Life Science Institute, Zhejiang University, Hangzhou 310058, China
| | - Jianping Jin
- Life Science Institute, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
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16
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Deng L, Meng T, Chen L, Wei W, Wang P. The role of ubiquitination in tumorigenesis and targeted drug discovery. Signal Transduct Target Ther 2020; 5:11. [PMID: 32296023 PMCID: PMC7048745 DOI: 10.1038/s41392-020-0107-0] [Citation(s) in RCA: 341] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 02/08/2023] Open
Abstract
Ubiquitination, an important type of protein posttranslational modification (PTM), plays a crucial role in controlling substrate degradation and subsequently mediates the "quantity" and "quality" of various proteins, serving to ensure cell homeostasis and guarantee life activities. The regulation of ubiquitination is multifaceted and works not only at the transcriptional and posttranslational levels (phosphorylation, acetylation, methylation, etc.) but also at the protein level (activators or repressors). When regulatory mechanisms are aberrant, the altered biological processes may subsequently induce serious human diseases, especially various types of cancer. In tumorigenesis, the altered biological processes involve tumor metabolism, the immunological tumor microenvironment (TME), cancer stem cell (CSC) stemness and so on. With regard to tumor metabolism, the ubiquitination of some key proteins such as RagA, mTOR, PTEN, AKT, c-Myc and P53 significantly regulates the activity of the mTORC1, AMPK and PTEN-AKT signaling pathways. In addition, ubiquitination in the TLR, RLR and STING-dependent signaling pathways also modulates the TME. Moreover, the ubiquitination of core stem cell regulator triplets (Nanog, Oct4 and Sox2) and members of the Wnt and Hippo-YAP signaling pathways participates in the maintenance of CSC stemness. Based on the altered components, including the proteasome, E3 ligases, E1, E2 and deubiquitinases (DUBs), many molecular targeted drugs have been developed to combat cancer. Among them, small molecule inhibitors targeting the proteasome, such as bortezomib, carfilzomib, oprozomib and ixazomib, have achieved tangible success. In addition, MLN7243 and MLN4924 (targeting the E1 enzyme), Leucettamol A and CC0651 (targeting the E2 enzyme), nutlin and MI-219 (targeting the E3 enzyme), and compounds G5 and F6 (targeting DUB activity) have also shown potential in preclinical cancer treatment. In this review, we summarize the latest progress in understanding the substrates for ubiquitination and their special functions in tumor metabolism regulation, TME modulation and CSC stemness maintenance. Moreover, potential therapeutic targets for cancer are reviewed, as are the therapeutic effects of targeted drugs.
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Affiliation(s)
- Lu Deng
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, China.
| | - Tong Meng
- Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, 389 Xincun Road, Shanghai, China
| | - Lei Chen
- Division of Laboratory Safety and Services, Northwest A&F University, Yangling Shaanxi, 712100, China
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Ping Wang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, Tongji University, Shanghai, 200092, China.
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17
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Garcia-Barcena C, Osinalde N, Ramirez J, Mayor U. How to Inactivate Human Ubiquitin E3 Ligases by Mutation. Front Cell Dev Biol 2020; 8:39. [PMID: 32117970 PMCID: PMC7010608 DOI: 10.3389/fcell.2020.00039] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/16/2020] [Indexed: 12/24/2022] Open
Abstract
E3 ubiquitin ligases are the ultimate enzymes involved in the transfer of ubiquitin to substrate proteins, a process that determines the fate of the modified protein. Numerous diseases are caused by defects in the ubiquitin-proteasome machinery, including when the activity of a given E3 ligase is hampered. Thus, inactivation of E3 ligases and the resulting effects at molecular or cellular level have been the focus of many studies during the last few years. For this purpose, site-specific mutation of key residues involved in either protein interaction, substrate recognition or ubiquitin transfer have been reported to successfully inactivate E3 ligases. Nevertheless, it is not always trivial to predict which mutation(s) will block the catalytic activity of a ligase. Here we review over 250 site-specific inactivating mutations that have been carried out in 120 human E3 ubiquitin ligases. We foresee that the information gathered here will be helpful for the design of future experimental strategies.
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Affiliation(s)
- Cristina Garcia-Barcena
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Nerea Osinalde
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain.,Ikerbasque - Basque Foundation for Science, Bilbao, Spain
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18
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McClellan AJ, Laugesen SH, Ellgaard L. Cellular functions and molecular mechanisms of non-lysine ubiquitination. Open Biol 2019; 9:190147. [PMID: 31530095 PMCID: PMC6769291 DOI: 10.1098/rsob.190147] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Protein ubiquitination is of great cellular importance through its central role in processes such as degradation, DNA repair, endocytosis and inflammation. Canonical ubiquitination takes place on lysine residues, but in the past 15 years non-lysine ubiquitination on serine, threonine and cysteine has been firmly established. With the emerging importance of non-lysine ubiquitination, it is crucial to identify the responsible molecular machinery and understand the mechanistic basis for non-lysine ubiquitination. Here, we first provide an overview of the literature that has documented non-lysine ubiquitination. Informed by these examples, we then discuss the molecular mechanisms and cellular implications of non-lysine ubiquitination, and conclude by outlining open questions and future perspectives in the field.
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Affiliation(s)
- Amie J McClellan
- Division of Science and Mathematics, Bennington College, 1 College Drive, Bennington, VT 05201, USA
| | - Sophie Heiden Laugesen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Lars Ellgaard
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen N, Denmark
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19
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Abstract
Posttranslational protein modification by ubiquitin (Ub) regulates aspects of biology, including protein turnover and the cell cycle. Proteins and enzymes that promote Ub conjugation are therapeutic targets because they are sometimes dysregulated in cancer, neurodegenerative diseases, and other disorders. Ub conjugation is initiated by a Ub-activating enzyme that adopts different conformations to catalyze Ub activation, Ub-activating enzyme thioester bond formation, and thioester bond transfer to Ub-conjugating enzymes. Here, we illuminate 2 uncharacterized states for Ub-activating enzyme, one bound to pyrophosphate prior to thioester bond formation and one captured during thioester bond formation. These structures reveal key differences and similarities among activating enzymes for Ub and SUMO with respect to conformational changes that accompany thioester formation. The ubiquitin (Ub) and Ub-like (Ubl) protein-conjugation cascade is initiated by E1 enzymes that catalyze Ub/Ubl activation through C-terminal adenylation, thioester bond formation with an E1 catalytic cysteine, and thioester bond transfer to Ub/Ubl E2 conjugating enzymes. Each of these reactions is accompanied by conformational changes of the E1 domain that contains the catalytic cysteine (Cys domain). Open conformations of the Cys domain are associated with adenylation and thioester transfer to E2s, while a closed conformation is associated with pyrophosphate release and thioester bond formation. Several structures are available for Ub E1s, but none has been reported in the open state before pyrophosphate release or in the closed state. Here, we describe the structures of Schizosaccharomyces pombe Ub E1 in these two states, captured using semisynthetic Ub probes. In the first, with a Ub-adenylate mimetic (Ub-AMSN) bound, the E1 is in an open conformation before release of pyrophosphate. In the second, with a Ub-vinylsulfonamide (Ub-AVSN) bound covalently to the catalytic cysteine, the E1 is in a closed conformation required for thioester bond formation. These structures provide further insight into Ub E1 adenylation and thioester bond formation. Conformational changes that accompany Cys-domain rotation are conserved for SUMO and Ub E1s, but changes in Ub E1 involve additional surfaces as mutational and biochemical analysis of residues within these surfaces alter Ub E1 activities.
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20
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The E3 ligase HOIL-1 catalyses ester bond formation between ubiquitin and components of the Myddosome in mammalian cells. Proc Natl Acad Sci U S A 2019; 116:13293-13298. [PMID: 31209050 PMCID: PMC6613137 DOI: 10.1073/pnas.1905873116] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The linear ubiquitin assembly complex (LUBAC) comprises 3 components: HOIP, HOIL-1, and Sharpin, of which HOIP and HOIL-1 are both members of the RBR subfamily of E3 ubiquitin ligases. HOIP catalyses the formation of Met1-linked ubiquitin oligomers (also called linear ubiquitin), but the function of the E3 ligase activity of HOIL-1 is unknown. Here, we report that HOIL-1 is an atypical E3 ligase that forms oxyester bonds between the C terminus of ubiquitin and serine and threonine residues in its substrates. Exploiting the sensitivity of HOIL-1-generated oxyester bonds to cleavage by hydroxylamine, and macrophages from knock-in mice expressing the E3 ligase-inactive HOIL-1[C458S] mutant, we identify IRAK1, IRAK2, and MyD88 as physiological substrates of the HOIL-1 E3 ligase during Toll-like receptor signaling. HOIL-1 is a monoubiquitylating E3 ubiquitin ligase that initiates the de novo synthesis of polyubiquitin chains that are attached to these proteins in macrophages. HOIL-1 also catalyses its own monoubiquitylation in cells and most probably the monoubiquitylation of Sharpin, in which ubiquitin is also attached by an oxyester bond. Our study establishes that oxyester-linked ubiquitylation is used as an intracellular signaling mechanism.
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21
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El Magraoui F, Brinkmeier R, Mastalski T, Hupperich A, Strehl C, Schwerter D, Girzalsky W, Meyer HE, Warscheid B, Erdmann R, Platta HW. The deubiquitination of the PTS1-import receptor Pex5p is required for peroxisomal matrix protein import. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:199-213. [PMID: 30408545 DOI: 10.1016/j.bbamcr.2018.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/13/2018] [Accepted: 11/02/2018] [Indexed: 12/28/2022]
Abstract
Peroxisomal biogenesis depends on the correct import of matrix proteins into the lumen of the organelle. Most peroxisomal matrix proteins harbor the peroxisomal targeting-type 1 (PTS1), which is recognized by the soluble PTS1-receptor Pex5p in the cytosol. Pex5p ferries the PTS1-proteins to the peroxisomal membrane and releases them into the lumen. Finally, the PTS1-receptor is monoubiquitinated on the conserved cysteine 6 in Saccharomyces cerevisiae. The monoubiquitinated Pex5p is recognized by the peroxisomal export machinery and is retrotranslocated into the cytosol for further rounds of protein import. However, the functional relevance of deubiquitination has not yet been addressed. In this study, we have analyzed a Pex5p-truncation lacking Cys6 [(Δ6)Pex5p], a construct with a ubiquitin-moiety genetically fused to the truncation [Ub-(Δ6)Pex5p], as well as a construct with a reduced susceptibility to deubiquitination [Ub(G75/76A)-(Δ6)Pex5p]. While the (Δ6)Pex5p-truncation is not functional, the Ub-(Δ6)Pex5p chimeric protein can facilitate matrix protein import. In contrast, the Ub(G75/76A)-(Δ6)Pex5p chimera exhibits a complete PTS1-import defect. The data show for the first time that not only ubiquitination but also deubiquitination rates are tightly regulated and that efficient deubiquitination of Pex5p is essential for peroxisomal biogenesis.
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Affiliation(s)
- Fouzi El Magraoui
- Biomedizinische Forschung, Leibniz-Insitute for Analytische Wissenschaften - ISAS e.V. - (ISAS e.V.), 44139 Dortmund, Germany; Systembiochemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Rebecca Brinkmeier
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Thomas Mastalski
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Alexander Hupperich
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Christofer Strehl
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | | | | | - Helmut E Meyer
- Biomedizinische Forschung, Leibniz-Insitute for Analytische Wissenschaften - ISAS e.V. - (ISAS e.V.), 44139 Dortmund, Germany
| | - Bettina Warscheid
- Functional Proteomics, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Ralf Erdmann
- Systembiochemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44801 Bochum, Germany.
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22
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Deubiquitinating Enzymes Related to Autophagy: New Therapeutic Opportunities? Cells 2018; 7:cells7080112. [PMID: 30126257 PMCID: PMC6116007 DOI: 10.3390/cells7080112] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/13/2018] [Accepted: 08/17/2018] [Indexed: 12/21/2022] Open
Abstract
Autophagy is an evolutionary conserved catabolic process that allows for the degradation of intracellular components by lysosomes. This process can be triggered by nutrient deprivation, microbial infections or other challenges to promote cell survival under these stressed conditions. However, basal levels of autophagy are also crucial for the maintenance of proper cellular homeostasis by ensuring the selective removal of protein aggregates and dysfunctional organelles. A tight regulation of this process is essential for cellular survival and organismal health. Indeed, deregulation of autophagy is associated with a broad range of pathologies such as neuronal degeneration, inflammatory diseases, and cancer progression. Ubiquitination and deubiquitination of autophagy substrates, as well as components of the autophagic machinery, are critical regulatory mechanisms of autophagy. Here, we review the main evidence implicating deubiquitinating enzymes (DUBs) in the regulation of autophagy. We also discuss how they may constitute new therapeutic opportunities in the treatment of pathologies such as cancers, neurodegenerative diseases or infections.
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23
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Xu CC, Zhang D, Hann DR, Xie ZP, Staehelin C. Biochemical properties and in planta effects of NopM, a rhizobial E3 ubiquitin ligase. J Biol Chem 2018; 293:15304-15315. [PMID: 30120198 DOI: 10.1074/jbc.ra118.004444] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/25/2018] [Indexed: 01/18/2023] Open
Abstract
Nodulation outer protein M (NopM) is an IpaH family type three (T3) effector secreted by the nitrogen-fixing nodule bacterium Sinorhizobium sp. strain NGR234. Previous work indicated that NopM is an E3 ubiquitin ligase required for an optimal symbiosis between NGR234 and the host legume Lablab purpureus Here, we continued to analyze the function of NopM. Recombinant NopM was biochemically characterized using an in vitro ubiquitination system with Arabidopsis thaliana proteins. In this assay, NopM forms unanchored polyubiquitin chains and possesses auto-ubiquitination activity. In a NopM variant lacking any lysine residues, auto-ubiquitination was not completely abolished, indicating noncanonical auto-ubiquitination of the protein. In addition, we could show intermolecular ubiquitin transfer from NopM to C338A (enzymatically inactive NopM form) in vitro Bimolecular fluorescence complementation analysis provided clues about NopM-NopM interactions at plasma membranes in planta NopM, but not C338A, expressed in tobacco cells induced cell death, suggesting that E3 ubiquitin ligase activity of NopM induced effector-triggered immunity responses. Likewise, expression of NopM in Lotus japonicus caused reduced nodule formation, whereas expression of C338A showed no obvious effects on symbiosis. Further experiments indicated that serine residue 26 of NopM is phosphorylated in planta and that NopM can be phosphorylated in vitro by salicylic acid-induced protein kinase (NtSIPK), a mitogen-activated protein kinase (MAPK) of tobacco. Hence, NopM is a phosphorylated T3 effector that can interact with itself, with ubiquitin, and with MAPKs.
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Affiliation(s)
- Chang-Chao Xu
- From the State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China
| | - Di Zhang
- From the State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China
| | - Dagmar R Hann
- the Institute of Genetics, Ludwig-Maximilians-Universität München, D-82152 Martinsried, Germany, and
| | - Zhi-Ping Xie
- From the State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China, .,the Shenzhen Research and Development Center of State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Baoan, Shenzhen 518057, China
| | - Christian Staehelin
- From the State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China, .,the Shenzhen Research and Development Center of State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Baoan, Shenzhen 518057, China
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24
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Abstract
Ubiquitylation is an essential posttranslational modification that controls cell division, differentiation, and survival in all eukaryotes. By combining multiple E3 ligases (writers), ubiquitin-binding effectors (readers), and de-ubiquitylases (erasers) with functionally distinct ubiquitylation tags, the ubiquitin system constitutes a powerful signaling network that is employed in similar ways from yeast to humans. Here, we discuss conserved principles of ubiquitin-dependent signaling that illustrate how this posttranslational modification shapes intracellular signaling networks to establish robust development and homeostasis throughout the eukaryotic kingdom.
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Affiliation(s)
- Eugene Oh
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA; .,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - David Akopian
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Michael Rape
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA; .,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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25
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Pao KC, Wood NT, Knebel A, Rafie K, Stanley M, Mabbitt PD, Sundaramoorthy R, Hofmann K, van Aalten DMF, Virdee S. Activity-based E3 ligase profiling uncovers an E3 ligase with esterification activity. Nature 2018; 556:381-385. [PMID: 29643511 DOI: 10.1038/s41586-018-0026-1] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 03/07/2018] [Indexed: 12/21/2022]
Abstract
Ubiquitination is initiated by transfer of ubiquitin (Ub) from a ubiquitin-activating enzyme (E1) to a ubiquitin-conjugating enzyme (E2), producing a covalently linked intermediate (E2-Ub) 1 . Ubiquitin ligases (E3s) of the 'really interesting new gene' (RING) class recruit E2-Ub via their RING domain and then mediate direct transfer of ubiquitin to substrates 2 . By contrast, 'homologous to E6-AP carboxy terminus' (HECT) E3 ligases undergo a catalytic cysteine-dependent transthiolation reaction with E2-Ub, forming a covalent E3-Ub intermediate3,4. Additionally, RING-between-RING (RBR) E3 ligases have a canonical RING domain that is linked to an ancillary domain. This ancillary domain contains a catalytic cysteine that enables a hybrid RING-HECT mechanism 5 . Ubiquitination is typically considered a post-translational modification of lysine residues, as there are no known human E3 ligases with non-lysine activity. Here we perform activity-based protein profiling of HECT or RBR-like E3 ligases and identify the neuron-associated E3 ligase MYCBP2 (also known as PHR1) as the apparent single member of a class of RING-linked E3 ligase with esterification activity and intrinsic selectivity for threonine over serine. MYCBP2 contains two essential catalytic cysteine residues that relay ubiquitin to its substrate via thioester intermediates. Crystallographic characterization of this class of E3 ligase, which we designate RING-Cys-relay (RCR), provides insights into its mechanism and threonine selectivity. These findings implicate non-lysine ubiquitination in cellular regulation of higher eukaryotes and suggest that E3 enzymes have an unappreciated mechanistic diversity.
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Affiliation(s)
- Kuan-Chuan Pao
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Nicola T Wood
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Karim Rafie
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Mathew Stanley
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Peter D Mabbitt
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | | | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Daan M F van Aalten
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
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26
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Sun H, Meledin R, Mali SM, Brik A. Total chemical synthesis of ester-linked ubiquitinated proteins unravels their behavior with deubiquitinases. Chem Sci 2018; 9:1661-1665. [PMID: 29675213 PMCID: PMC5887810 DOI: 10.1039/c7sc04518b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/19/2017] [Indexed: 12/27/2022] Open
Abstract
The novel synthetic strategy for preparation of ester linked ubiquitinated proteins was developed. We found that the ester linkage could be cleaved by deubiquitinases with different efficiency relative to the isopeptide-linked substrate.
Ester-linked ubiquitinated proteins have been reported by several groups to be involved in ubiquitin signalling. However, due to the lack of the suitable tools to homogeneously produce such conjugates, their exact physiological roles and biochemical behavior remain enigmatic. Here, we report for the first time on the development of a novel synthetic strategy based on total chemical synthesis of proteins to construct ubiquitinated proteins, where ubiquitin is linked to the substrate via an ester bond. In this study, we prepared ester- and isopeptide-linked ubiquitinated α-globin and examined their relative behaviors with various deubiquitinases. We found that deubiquitinases are able to cleave the ester linkage with different efficiency relative to the isopeptide-linked substrate. These results may indicate that ester-linked ubiquitinated proteins are natural substrates for deubiquitinases.
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Affiliation(s)
- Hao Sun
- Schulich Faculty of Chemistry , Technion Israel Institute of Technology , Haifa , 3200008 , Israel .
| | - Roman Meledin
- Schulich Faculty of Chemistry , Technion Israel Institute of Technology , Haifa , 3200008 , Israel .
| | - Sachitanand M Mali
- Schulich Faculty of Chemistry , Technion Israel Institute of Technology , Haifa , 3200008 , Israel .
| | - Ashraf Brik
- Schulich Faculty of Chemistry , Technion Israel Institute of Technology , Haifa , 3200008 , Israel .
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27
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Kwon YT, Ciechanover A. The Ubiquitin Code in the Ubiquitin-Proteasome System and Autophagy. Trends Biochem Sci 2017; 42:873-886. [DOI: 10.1016/j.tibs.2017.09.002] [Citation(s) in RCA: 374] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/05/2017] [Accepted: 09/07/2017] [Indexed: 12/14/2022]
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28
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Schwerter DP, Grimm I, Platta HW, Erdmann R. ATP-driven processes of peroxisomal matrix protein import. Biol Chem 2017; 398:607-624. [PMID: 27977397 DOI: 10.1515/hsz-2016-0293] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/11/2016] [Indexed: 12/13/2022]
Abstract
In peroxisomal matrix protein import two processes directly depend on the binding and hydrolysis of ATP, both taking place at the late steps of the peroxisomal import cycle. First, ATP hydrolysis is required to initiate a ubiquitin-transfer cascade to modify the import (co-)receptors. These receptors display a dual localization in the cytosol and at the peroxisomal membrane, whereas only the membrane bound fraction receives the ubiquitin modification. The second ATP-dependent process of the import cycle is carried out by the two AAA+-proteins Pex1p and Pex6p. These ATPases form a heterohexameric complex, which is recruited to the peroxisomal import machinery by the membrane anchor protein Pex15p. The Pex1p/Pex6p complex recognizes the ubiquitinated import receptors, pulls them out of the membrane and releases them into the cytosol. There the deubiquitinated receptors are provided for further rounds of import. ATP binding and hydrolysis are required for Pex1p/Pex6p complex formation and receptor export. In this review, we summarize the current knowledge on the peroxisomal import cascade. In particular, we will focus on the ATP-dependent processes, which are so far best understood in the model organism Saccharomyces cerevisiae.
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Affiliation(s)
- Daniel P Schwerter
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum
| | - Immanuel Grimm
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum
| | - Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Medizinische Fakultät der Ruhr-Universität Bochum, D-44780 Bochum
| | - Ralf Erdmann
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum
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29
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The DUB blade goes snicker-snack: Novel ubiquitin cleavage by a Legionella effector protein. Cell Res 2017; 27:845-846. [PMID: 28574056 DOI: 10.1038/cr.2017.80] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Recently, a Legionella pneumophila effector protein was shown to have an unprecedented ATP-independent ubiquitin ligase activity that couples phosphoribosylated ubiquitin (PR-Ub) to serine residues of host proteins. A new study published in Cell Research by Qiu et al. reveals that another Legionella effector protein, SidJ, catalyzes deubiquitination of PR-Ub by cleavage of the substrate-linked phosphodiester bond.
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Bhogaraju S, Kalayil S, Liu Y, Bonn F, Colby T, Matic I, Dikic I. Phosphoribosylation of Ubiquitin Promotes Serine Ubiquitination and Impairs Conventional Ubiquitination. Cell 2017; 167:1636-1649.e13. [PMID: 27912065 DOI: 10.1016/j.cell.2016.11.019] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 10/28/2016] [Accepted: 11/10/2016] [Indexed: 01/13/2023]
Abstract
Conventional ubiquitination involves the ATP-dependent formation of amide bonds between the ubiquitin C terminus and primary amines in substrate proteins. Recently, SdeA, an effector protein of pathogenic Legionella pneumophila, was shown to mediate NAD-dependent and ATP-independent ubiquitin transfer to host proteins. Here, we identify a phosphodiesterase domain in SdeA that efficiently catalyzes phosphoribosylation of ubiquitin on a specific arginine via an ADP-ribose-ubiquitin intermediate. SdeA also catalyzes a chemically and structurally distinct type of substrate ubiquitination by conjugating phosphoribosylated ubiquitin to serine residues of protein substrates via a phosphodiester bond. Furthermore, phosphoribosylation of ubiquitin prevents activation of E1 and E2 enzymes of the conventional ubiquitination cascade, thereby impairing numerous cellular processes including mitophagy, TNF signaling, and proteasomal degradation. We propose that phosphoribosylation of ubiquitin potently modulates ubiquitin functions in mammalian cells.
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Affiliation(s)
- Sagar Bhogaraju
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Sissy Kalayil
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Yaobin Liu
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Florian Bonn
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Thomas Colby
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Ivan Matic
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; Department of Immunology and Medical Genetics, University of Split, School of Medicine, Soltanska 2, 21000 Split, Croatia.
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31
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Regulation of G Protein-Coupled Receptors by Ubiquitination. Int J Mol Sci 2017; 18:ijms18050923. [PMID: 28448471 PMCID: PMC5454836 DOI: 10.3390/ijms18050923] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/20/2017] [Accepted: 04/23/2017] [Indexed: 02/07/2023] Open
Abstract
G protein-coupled receptors (GPCRs) comprise the largest family of membrane receptors that control many cellular processes and consequently often serve as drug targets. These receptors undergo a strict regulation by mechanisms such as internalization and desensitization, which are strongly influenced by posttranslational modifications. Ubiquitination is a posttranslational modification with a broad range of functions that is currently gaining increased appreciation as a regulator of GPCR activity. The role of ubiquitination in directing GPCRs for lysosomal degradation has already been well-established. Furthermore, this modification can also play a role in targeting membrane and endoplasmic reticulum-associated receptors to the proteasome. Most recently, ubiquitination was also shown to be involved in GPCR signaling. In this review, we present current knowledge on the molecular basis of GPCR regulation by ubiquitination, and highlight the importance of E3 ubiquitin ligases, deubiquitinating enzymes and β-arrestins. Finally, we discuss classical and newly-discovered functions of ubiquitination in controlling GPCR activity.
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Nordgren M, Francisco T, Lismont C, Hennebel L, Brees C, Wang B, Van Veldhoven PP, Azevedo JE, Fransen M. Export-deficient monoubiquitinated PEX5 triggers peroxisome removal in SV40 large T antigen-transformed mouse embryonic fibroblasts. Autophagy 2016; 11:1326-40. [PMID: 26086376 DOI: 10.1080/15548627.2015.1061846] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Peroxisomes are ubiquitous cell organelles essential for human health. To maintain a healthy cellular environment, dysfunctional and superfluous peroxisomes need to be selectively removed. Although emerging evidence suggests that peroxisomes are mainly degraded by pexophagy, little is known about the triggers and molecular mechanisms underlying this process in mammalian cells. In this study, we show that PEX5 proteins fused to a bulky C-terminal tag trigger peroxisome degradation in SV40 large T antigen-transformed mouse embryonic fibroblasts. In addition, we provide evidence that this process is autophagy-dependent and requires monoubiquitination of the N-terminal cysteine residue that marks PEX5 for recycling. As our findings also demonstrate that the addition of a bulky tag to the C terminus of PEX5 does not interfere with PEX5 monoubiquitination but strongly inhibits its export from the peroxisomal membrane, we hypothesize that such a tag mimics a cargo protein that cannot be released from PEX5, thus keeping monoubiquitinated PEX5 at the membrane for a sufficiently long time to be recognized by the autophagic machinery. This in turn suggests that monoubiquitination of the N-terminal cysteine of peroxisome-associated PEX5 not only functions to recycle the peroxin back to the cytosol, but also serves as a quality control mechanism to eliminate peroxisomes with a defective protein import machinery.
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Affiliation(s)
- Marcus Nordgren
- a Laboratory of Lipid Biochemistry and Protein Interactions; Department of Cellular and Molecular Medicine; University of Leuven - KU Leuven ; Leuven , Belgium
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33
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Boomsma W, Nielsen SV, Lindorff-Larsen K, Hartmann-Petersen R, Ellgaard L. Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases. PeerJ 2016; 4:e1725. [PMID: 26966660 PMCID: PMC4782732 DOI: 10.7717/peerj.1725] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/02/2016] [Indexed: 12/28/2022] Open
Abstract
The ubiquitin-proteasome system targets misfolded proteins for degradation. Since the accumulation of such proteins is potentially harmful for the cell, their prompt removal is important. E3 ubiquitin-protein ligases mediate substrate ubiquitination by bringing together the substrate with an E2 ubiquitin-conjugating enzyme, which transfers ubiquitin to the substrate. For misfolded proteins, substrate recognition is generally delegated to molecular chaperones that subsequently interact with specific E3 ligases. An important exception is San1, a yeast E3 ligase. San1 harbors extensive regions of intrinsic disorder, which provide both conformational flexibility and sites for direct recognition of misfolded targets of vastly different conformations. So far, no mammalian ortholog of San1 is known, nor is it clear whether other E3 ligases utilize disordered regions for substrate recognition. Here, we conduct a bioinformatics analysis to examine >600 human and S. cerevisiae E3 ligases to identify enzymes that are similar to San1 in terms of function and/or mechanism of substrate recognition. An initial sequence-based database search was found to detect candidates primarily based on the homology of their ordered regions, and did not capture the unique disorder patterns that encode the functional mechanism of San1. However, by searching specifically for key features of the San1 sequence, such as long regions of intrinsic disorder embedded with short stretches predicted to be suitable for substrate interaction, we identified several E3 ligases with these characteristics. Our initial analysis revealed that another remarkable trait of San1 is shared with several candidate E3 ligases: long stretches of complete lysine suppression, which in San1 limits auto-ubiquitination. We encode these characteristic features into a San1 similarity-score, and present a set of proteins that are plausible candidates as San1 counterparts in humans. In conclusion, our work indicates that San1 is not a unique case, and that several other yeast and human E3 ligases have sequence properties that may allow them to recognize substrates by a similar mechanism as San1.
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Affiliation(s)
- Wouter Boomsma
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , Copenhagen , Denmark
| | - Sofie V Nielsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , Copenhagen , Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , Copenhagen , Denmark
| | - Rasmus Hartmann-Petersen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , Copenhagen , Denmark
| | - Lars Ellgaard
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , Copenhagen , Denmark
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Ramirez J, Min M, Barrio R, Lindon C, Mayor U. Isolation of Ubiquitinated Proteins to High Purity from In Vivo Samples. Methods Mol Biol 2016; 1449:193-202. [PMID: 27613036 DOI: 10.1007/978-1-4939-3756-1_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Ubiquitination pathways are widely used within eukaryotic cells. The complexity of ubiquitin signaling gives rise to a number of problems in the study of specific pathways. One problem is that not all processes regulated by ubiquitin are shared among the different cells of an organism (e.g., neurotransmitter release is only carried out in neuronal cells). Moreover, these processes are often highly temporally dynamic. It is essential therefore to use the right system for each biological question, so that we can characterize pathways specifically in the tissue or cells of interest. However, low stoichiometry, and the unstable nature of many ubiquitin conjugates, presents a technical barrier to studying this modification in vivo. Here, we describe two approaches to isolate ubiquitinated proteins to high purity. The first one favors isolation of the whole mixture of ubiquitinated material from a given tissue or cell type, generating a survey of the ubiquitome landscape for a specific condition. The second one favors the isolation of just one specific protein, in order to facilitate the characterization of its ubiquitinated fraction. In both cases, highly stringent denaturing buffers are used to minimize the presence of contaminating material in the sample.
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Affiliation(s)
- Juanma Ramirez
- Biokimika eta Biologia Molekularra Saila, Zientzia eta Teknologia Fakultatea, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
| | - Mingwei Min
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Catherine Lindon
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
| | - Ugo Mayor
- Biokimika eta Biologia Molekularra Saila, Zientzia eta Teknologia Fakultatea, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain.
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35
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KLHL12 Promotes Non-Lysine Ubiquitination of the Dopamine Receptors D4.2 and D4.4, but Not of the ADHD-Associated D4.7 Variant. PLoS One 2015; 10:e0145654. [PMID: 26717573 PMCID: PMC4738440 DOI: 10.1371/journal.pone.0145654] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/07/2015] [Indexed: 01/11/2023] Open
Abstract
DOPAMINE D4 RECEPTOR POLYMORPHISM The dopamine D4 receptor has an important polymorphism in its third intracellular loop that is intensively studied and has been associated with several abnormal conditions, among others, attention deficit hyperactivity disorder. KLHL12 PROMOTES UBIQUITINATION OF THE DOPAMINE D4 RECEPTOR ON NON-LYSINE RESIDUES In previous studies we have shown that KLHL12, a BTB-Kelch protein, specifically interacts with the polymorphic repeats of the dopamine D4 receptor and enhances its ubiquitination, which, however, has no influence on receptor degradation. In this study we provide evidence that KLHL12 promotes ubiquitination of the dopamine D4 receptor on non-lysine residues. By using lysine-deficient receptor mutants and chemical approaches we concluded that ubiquitination on cysteine, serine and/or threonine is possible. DIFFERENTIAL UBIQUITINATION OF THE DOPAMINE D4 RECEPTOR POLYMORPHIC VARIANTS Additionally, we show that the dopamine D4.7 receptor variant, which is associated with a predisposition to develop attention deficient hyperactivity disorder, is differentially ubiquitinated compared to the other common receptor variants D4.2 and D4.4. Together, our study suggests that GPCR ubiquitination is a complex and variable process.
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36
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Beaudette P, Popp O, Dittmar G. Proteomic techniques to probe the ubiquitin landscape. Proteomics 2015; 16:273-87. [PMID: 26460060 DOI: 10.1002/pmic.201500290] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/03/2015] [Accepted: 10/06/2015] [Indexed: 01/06/2023]
Abstract
Protein ubiquitination is a powerful modulator of cellular functions. Classically linked to the degradation of proteins, it also plays a role in intracellular localization, DNA damage response, vesicle fusion events, and the immune and transcriptional responses. Ubiquitin is versatile and can code for several distinct signals, either by adding a single ubiquitin or forming a chain of ubiquitins on the target protein. The enzymatic cascade associated with the cellular process determines the nature of the modification. Numerous efforts have been made for the identification of ubiquitin acceptor sites in the target proteins using genetic, biochemical or MS-based proteomic methods, such as affinity-based enrichment of ubiquitinated proteins, and antibody-based enrichment of modified peptides. Modern instrumentation enables quantitative MS strategies to identify and characterize hundreds of ubiquitin substrates in a single analysis making it the dominant method for ubiquitin site detection. Characterization of the interubiquitin connectivity in ubiquitin polymers has also moved into focus, with the field of targeted proteomics techniques proving invaluable for identifying and quantifying linkage types found in such polyubiquitin chains. This review seeks to provide an overview of the many MS-based proteomics techniques available for exploring this dynamic field.
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Affiliation(s)
- Patrick Beaudette
- Department of Mass Spectrometry, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Oliver Popp
- Department of Mass Spectrometry, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Gunnar Dittmar
- Department of Mass Spectrometry, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
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37
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Platta HW, Brinkmeier R, Reidick C, Galiani S, Clausen MP, Eggeling C. Regulation of peroxisomal matrix protein import by ubiquitination. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:838-49. [PMID: 26367801 DOI: 10.1016/j.bbamcr.2015.09.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/09/2015] [Accepted: 09/10/2015] [Indexed: 02/02/2023]
Abstract
Peroxisomes are organelles that play an important role in many cellular tasks. The functionality of peroxisomes depends on the proper import of their matrix proteins. Peroxisomal matrix proteins are imported posttranslationally in a folded, sometimes even oligomeric state. They harbor a peroxisomal targeting sequence (PTS), which is recognized by dynamic PTS-receptors in the cytosol. The PTS-receptors ferry the cargo to the peroxisomal membrane, where they become part of a transient import pore and then release the cargo into the peroxisomal lumen. Subsequentially, the PTS-receptors are ubiquitinated in order to mark them for the export-machinery, which releases them back to the cytosol. Upon deubiquitination, the PTS-receptors can facilitate further rounds of cargo import. Because the ubiquitination of the receptors is an essential step in the import cycle, it also represents a central regulatory element that governs peroxisomal dynamics. In this review we want to give an introduction to the functional role played by ubiquitination during peroxisomal protein import and highlight the mechanistic concepts that have emerged based on data derived from different species since the discovery of the first ubiquitinated peroxin 15years ago. Moreover, we discuss future tasks and the potential of using advanced technologies for investigating further details of peroxisomal protein transport.
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Affiliation(s)
- Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Rebecca Brinkmeier
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Christina Reidick
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Silvia Galiani
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Mathias P Clausen
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom.
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Gilkerson J, Kelley DR, Tam R, Estelle M, Callis J. Lysine Residues Are Not Required for Proteasome-Mediated Proteolysis of the Auxin/Indole Acidic Acid Protein IAA1. PLANT PHYSIOLOGY 2015; 168:708-20. [PMID: 25888615 PMCID: PMC4453792 DOI: 10.1104/pp.15.00402] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 04/16/2015] [Indexed: 05/21/2023]
Abstract
Although many ubiquitin-proteasome substrates have been characterized in plants, very little is known about the corresponding ubiquitin attachment(s) underlying regulated proteolysis. Current dogma asserts that ubiquitin is typically covalently attached to a substrate through an isopeptide bond between the ubiquitin carboxy terminus and a substrate lysyl amino group. However, nonlysine (non-Lys) ubiquitin attachment has been observed in other eukaryotes, including the N terminus, cysteine, and serine/threonine modification. Here, we investigate site(s) of ubiquitin attachment on indole-3-acetic acid1 (IAA1), a short-lived Arabidopsis (Arabidopsis thaliana) Auxin/indole-3-acetic acid (Aux/IAA) family member. Most Aux/IAA proteins function as negative regulators of auxin responses and are targeted for degradation after ubiquitination by the ubiquitin ligase SCF(TIR1/AFB) (for S-Phase Kinase-Associated Protein1, Cullin, F-box [SCF] with Transport Inhibitor Response1 [TIR1]/Auxin Signaling F-box [AFB]) by an interaction directly facilitated by auxin. Surprisingly, using a Histidine-Hemaglutinin (HIS(6x)-HA(3x)) epitope-tagged version expressed in vivo, Lys-less IAA1 was ubiquitinated and rapidly degraded in vivo. Lys-substituted versions of IAA1 localized to the nucleus as Yellow Fluorescent Protein fusions and interacted with both TIR1 and IAA7 in yeast (Saccharomyces cerevisiae) two-hybrid experiments, indicating that these proteins were functional. Ubiquitination on both HIS(6x)-HA(3x)-IAA1 and Lys-less HIS(6x)-HA(3x)-IAA1 proteins was sensitive to sodium hydroxide treatment, indicative of ubiquitin oxyester formation on serine or threonine residues. Additionally, base-resistant forms of ubiquitinated IAA1 were observed for HIS(6x)-HA(3x)-IAA1, suggesting additional lysyl-linked ubiquitin on this protein. Characterization of other Aux/IAA proteins showed that they have diverse degradation rates, adding additional complexity to auxin signaling. Altogether, these data indicate that Aux/IAA family members have protein-specific degradation rates and that ubiquitination of Aux/IAAs can occur on multiple types of amino residues to promote rapid auxin-mediated degradation.
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Affiliation(s)
- Jonathan Gilkerson
- Department of Molecular and Cellular Biology and Plant Biology Graduate Group, University of California, Davis, California 95616 (J.G., R.T., J.C.); andDivision of Biological Sciences and Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0116 (D.R.K., M.E.)
| | - Dior R Kelley
- Department of Molecular and Cellular Biology and Plant Biology Graduate Group, University of California, Davis, California 95616 (J.G., R.T., J.C.); andDivision of Biological Sciences and Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0116 (D.R.K., M.E.)
| | - Raymond Tam
- Department of Molecular and Cellular Biology and Plant Biology Graduate Group, University of California, Davis, California 95616 (J.G., R.T., J.C.); andDivision of Biological Sciences and Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0116 (D.R.K., M.E.)
| | - Mark Estelle
- Department of Molecular and Cellular Biology and Plant Biology Graduate Group, University of California, Davis, California 95616 (J.G., R.T., J.C.); andDivision of Biological Sciences and Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0116 (D.R.K., M.E.)
| | - Judy Callis
- Department of Molecular and Cellular Biology and Plant Biology Graduate Group, University of California, Davis, California 95616 (J.G., R.T., J.C.); andDivision of Biological Sciences and Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0116 (D.R.K., M.E.)
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39
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Cysteine-specific ubiquitination protects the peroxisomal import receptor Pex5p against proteasomal degradation. Biosci Rep 2015; 35:BSR20150103. [PMID: 26182377 PMCID: PMC4613714 DOI: 10.1042/bsr20150103] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 05/01/2015] [Indexed: 11/22/2022] Open
Abstract
Peroxisomal import receptors cycle between the peroxisomal membrane and the cytosol. A monoubiquitinated cysteine is required for efficient recycling of the peroxisomal import receptor Pex5p and prevents the protein from polyubiquitination, which leads to a rapid degradation of the protein. Peroxisomal matrix protein import is mediated by dynamic import receptors, which cycle between the peroxisomal membrane and the cytosol. Proteins with a type 1 peroxisomal targeting signal (PTS1) are bound by the import receptor Pex5p in the cytosol and guided to the peroxisomal membrane. After cargo translocation into the peroxisomal matrix, the receptor is released from the membrane back to the cytosol in an ATP-dependent manner by the AAA-type ATPases Pex1p and Pex6p. These mechanoenzymes recognize ubiquitinated Pex5p-species as substrates for membrane extraction. The PTS1-receptor is either polyubiquitinated via peptide bonds at two certain lysines and results in proteasomal degradation or monoubiquitinated via a thioester-bond at a conserved cysteine, which enables the recycling of Pex5p and further rounds of matrix protein import. To investigate the physiological relevance of the conserved N-terminal cysteine of Pex5p, the known target amino acids for ubiquitination were substituted by site-directed mutagenesis. In contrast with Pex5pC6A, Pex5pC6K turned out to be functional in PTS1 import and utilization of oleic acid, independent of the lysines at position 18 and 24. In contrast with wild-type Pex5p, Pex5pC6K displays an ubiquitination pattern, similar to the polyubiquitination pattern of Pex4p or Pex22p mutant strains. Moreover, Pex5pC6K displays a significantly reduced steady-state level when the deubiquitinating enzyme Ubp15p is missing. Thus, our results indicate that not the cysteine residue but the position of ubiquitination is important for Pex5p function. The presence of the cysteine prevents polyubiquitination and rapid degradation of Pex5p.
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40
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Kennedy JE, Marchese A. Regulation of GPCR Trafficking by Ubiquitin. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 132:15-38. [PMID: 26055053 DOI: 10.1016/bs.pmbts.2015.02.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
G protein-coupled receptor (GPCR)-promoted signaling mediates cellular responses to a variety of stimuli involved in diverse physiological processes. In addition, GPCRs are also the largest class of target for many drugs used to treat a variety of diseases. Despite the role of GPCR signaling in health and disease, the molecular mechanisms governing GPCR signaling remain poorly understanding. Classically, GPCR signaling is tightly regulated by GPCR kinases and β-arrestins, which act in a concerted fashion to govern GPCR desensitization and also GPCR trafficking. Ubiquitination has now emerged as an important posttranslational modification that has multiple roles, either directly or indirectly, in governing GPCR trafficking. Recent studies have revealed a mechanistic link between GPCR phosphorylation, β-arrestins, and ubiquitination. Here, we review recent developments in our understanding of how ubiquitin regulates GPCR trafficking within the endocytic pathway.
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Affiliation(s)
- Justine E Kennedy
- Department of Molecular Pharmacology and Therapeutics, Loyola University Chicago, Health Sciences Division, Maywood, Illinois, USA
| | - Adriano Marchese
- Department of Molecular Pharmacology and Therapeutics, Loyola University Chicago, Health Sciences Division, Maywood, Illinois, USA.
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41
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Abstract
Ubiquitin is a small 8.5 kDa protein that is conjugated to a target protein in a concerted three step enzymatic process. Ubiquitin addition can drastically affect function or target the modified protein for degradation. Ubiquitin modifications have important regulatory roles in disease progression, such as in cancer and neurodegenerative diseases to name a few. As a consequence, it is imperative to identify important ubiquitin targets to elucidate the role of the modification. Proteomic studies have sought to understand this role by identifying proteome-wide ubiquitylated proteins. Two central ideas have developed to characterize the ubiquitylome: affinity purification of ubiquitylated proteins and optimization of GG-peptide enrichment. In this review, we will discuss recent advances in both approaches and discuss how these studies are essential to pharmacoproteomics.
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Affiliation(s)
- Tanya R Porras-Yakushi
- California Institute of Technology, Beckman Institute, 1200 E. California Blvd, Pasadena, CA 91125, USA
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42
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Abstract
Protein ubiquitination is an important post-translational modification that regulates almost every aspect of cellular function and many cell signaling pathways in eukaryotes. Alterations of protein ubiquitination have been linked to many diseases, such as cancer, neurodegenerative diseases, cardiovascular diseases, immunological disorders and inflammatory diseases. To understand the roles of protein ubiquitination in these diseases and in cell signaling pathways, it is necessary to identify ubiquitinated proteins and their modification sites. However, owing to the nature of protein ubiquitination, it is challenging to identify the exact modification sites under physiological conditions. Recently, ubiquitin-remnant profiling, an immunoprecipitation approach, which uses monoclonal antibodies specifically to enrich for peptides derived from the ubiquitinated portion of proteins and mass spectrometry for their identification, was developed to determine ubiquitination events from cell lysates. This approach has now been widely applied to profile protein ubiquitination in several cellular contexts. In this review, we discuss mass-spectrometry-based methods for the identification of protein ubiquitination sites, analyze their advantages and disadvantages, and discuss their application for proteomic analysis of ubiquitination.
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Affiliation(s)
- Guoqiang Xu
- a Laboratory of Chemical Biology, Department of Pharmacology , College of Pharmaceutical Sciences, Soochow University , Suzhou , China
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43
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Ashida H, Kim M, Sasakawa C. Exploitation of the host ubiquitin system by human bacterial pathogens. Nat Rev Microbiol 2014; 12:399-413. [DOI: 10.1038/nrmicro3259] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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44
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Lectez B, Migotti R, Lee SY, Ramirez J, Beraza N, Mansfield B, Sutherland JD, Martinez-Chantar ML, Dittmar G, Mayor U. Ubiquitin profiling in liver using a transgenic mouse with biotinylated ubiquitin. J Proteome Res 2014; 13:3016-26. [PMID: 24730562 DOI: 10.1021/pr5001913] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ubiquitination is behind most cellular processes, with ubiquitin substrates being regulated variously according to the number of covalently conjugated ubiquitin molecules and type of chain formed. Here we report the first mammalian system for ubiquitin proteomics allowing direct validation of the MS-identified proteins. We created a transgenic mouse expressing biotinylated ubiquitin and demonstrate its use for the isolation of ubiquitinated proteins from liver and other tissues. The specificity and strength of the biotin-avidin interaction allow very stringent washes, so only proteins conjugated to ubiquitin are isolated. In contrast with recently available antibody-based approaches, our strategy allows direct validation by immunoblotting, therefore revealing the type of ubiquitin chains (mono or poly) formed in vivo. We also identify the conjugating E2 enzymes that are ubiquitin-loaded in the mouse tissue. Furthermore, our strategy allows the identification of candidate cysteine-ubiquitinated proteins, providing a strategy to identify those on a proteomic scale. The novel in vivo system described here allows broad access to tissue-specific ubiquitomes and can be combined with established mouse disease models to investigate ubiquitin-dependent therapeutical approaches.
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Affiliation(s)
- Benoît Lectez
- CIC bioGUNE, Bizkaia Teknologia Parkea , Building 801-A, 48160 Derio, Basque Country, Spain
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45
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Platta HW, Hagen S, Reidick C, Erdmann R. The peroxisomal receptor dislocation pathway: to the exportomer and beyond. Biochimie 2013; 98:16-28. [PMID: 24345375 DOI: 10.1016/j.biochi.2013.12.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 12/05/2013] [Indexed: 12/29/2022]
Abstract
The biogenesis of peroxisomes is an ubiquitin-dependent process. In particular, the import of matrix proteins into the peroxisomal lumen requires the modification of import receptors with ubiquitin. The matrix proteins are synthesized on free polyribosomes in the cytosol and are recognized by import receptors via a peroxisomal targeting sequence (PTS). Subsequent to the transport of the receptor/cargo-complex to the peroxisomal membrane and the release of the cargo into the peroxisomal lumen, the PTS-receptors are exported back to the cytosol for further rounds of matrix protein import. The exportomer represents the molecular machinery required for the retrotranslocation of the PTS-receptors. It comprises enzymes for the ubiquitination as well as for the ATP-dependent extraction of the PTS-receptors from the peroxisomal membrane. Furthermore, recent evidence indicates a mechanistic interconnection of the ATP-dependent removal of the PTS-receptors with the translocation of the matrix protein into the organellar lumen. Interestingly, the components of the peroxisomal exportomer seem also to be involved in cellular tasks that are distinct from the ubiquitination and dislocation of the peroxisomal PTS-receptors. This includes work that indicates a central function of this machinery in the export of peroxisomal matrix proteins in plants, while a subset of exportomer components is involved in the meiocyte formation in some fungi, the peroxisome-chloroplast contact during photorespiration in plants and possibly even the selective degradation of peroxisomes via pexophagy. In this review, we want to discuss the central role of the exportomer during matrix protein import, but also highlight distinct roles of exportomer constituents in additional cellular processes. This article is part of a Special Issue entitled: Peroxisomes: biogenesis, functions and diseases.
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Affiliation(s)
- Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
| | - Stefanie Hagen
- Systembiochemie, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Christina Reidick
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Ralf Erdmann
- Systembiochemie, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
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46
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Apanasets O, Grou CP, Van Veldhoven PP, Brees C, Wang B, Nordgren M, Dodt G, Azevedo JE, Fransen M. PEX5, the shuttling import receptor for peroxisomal matrix proteins, is a redox-sensitive protein. Traffic 2013; 15:94-103. [PMID: 24118911 DOI: 10.1111/tra.12129] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/03/2013] [Accepted: 10/07/2013] [Indexed: 01/11/2023]
Abstract
Peroxisome maintenance depends on the import of nuclear-encoded proteins from the cytosol. The vast majority of these proteins is destined for the peroxisomal lumen and contains a C-terminal peroxisomal targeting signal, called PTS1. This targeting signal is recognized in the cytosol by the receptor PEX5. After docking at the peroxisomal membrane and release of the cargo into the organelle matrix, PEX5 is recycled to the cytosol through a process requiring monoubiquitination of an N-terminal, cytosolically exposed cysteine residue (Cys11 in the human protein). At present, the reason why a cysteine, and not a lysine residue, is the target of ubiquitination remains unclear. Here, we provide evidence that PTS1 protein import into human fibroblasts is a redox-sensitive process. We also demonstrate that Cys11 in human PEX5 functions as a redox switch that regulates PEX5 activity in response to intracellular oxidative stress. Finally, we show that exposure of human PEX5 to oxidized glutathione results in a ubiquitination-deficient PEX5 molecule, and that substitution of Cys11 by a lysine can counteract this effect. In summary, these findings reveal that the activity of PEX5, and hence PTS1 import, is controlled by the redox state of the cytosol. The potential physiological implications of these findings are discussed.
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Affiliation(s)
- Oksana Apanasets
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU, Leuven, Belgium
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47
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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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48
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Platta HW, Hagen S, Erdmann R. The exportomer: the peroxisomal receptor export machinery. Cell Mol Life Sci 2013; 70:1393-411. [PMID: 22983384 PMCID: PMC11113987 DOI: 10.1007/s00018-012-1136-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 07/30/2012] [Accepted: 08/13/2012] [Indexed: 12/21/2022]
Abstract
Peroxisomes constitute a dynamic compartment of almost all eukaryotic cells. Depending on environmental changes and cellular demands peroxisomes can acquire diverse metabolic roles. The compartmentalization of peroxisomal matrix enzymes is a prerequisite to carry out their physiologic function. The matrix proteins are synthesized on free ribosomes in the cytosol and are ferried to the peroxisomal membrane by specific soluble receptors. Subsequent to cargo release into the peroxisomal matrix, the receptors are exported back to the cytosol to facilitate further rounds of matrix protein import. This dislocation step is accomplished by a remarkable machinery, which comprises enzymes required for the ubiquitination as well as the ATP-dependent extraction of the receptor from the membrane. Interestingly, receptor ubiquitination and dislocation are the only known energy-dependent steps in the peroxisomal matrix protein import process. The current view is that the export machinery of the receptors might function as molecular motor not only in the dislocation of the receptors but also in the import step of peroxisomal matrix protein by coupling ATP-dependent removal of the peroxisomal import receptor with cargo translocation into the organelle. In this review we will focus on the architecture and function of the peroxisomal receptor export machinery, the peroxisomal exportomer.
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Affiliation(s)
- Harald W. Platta
- Abteilung für Systembiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Ruhr-Universität Bochum, Universitätsstr. 150, 44780 Bochum, Germany
| | - Stefanie Hagen
- Abteilung für Systembiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Ruhr-Universität Bochum, Universitätsstr. 150, 44780 Bochum, Germany
| | - Ralf Erdmann
- Abteilung für Systembiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Ruhr-Universität Bochum, Universitätsstr. 150, 44780 Bochum, Germany
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49
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Liu X, Subramani S. Unique requirements for mono- and polyubiquitination of the peroxisomal targeting signal co-receptor, Pex20. J Biol Chem 2013; 288:7230-40. [PMID: 23344950 DOI: 10.1074/jbc.m112.424911] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Pichia pastoris, the peroxisomal targeting signal 2 (PTS2)-dependent peroxisomal matrix protein import pathway requires the receptor, Pex7, and its co-receptor Pex20. A conserved lysine (Lys(19)) near the N terminus of Pex20 is required for its polyubiquitination and proteasomal degradation, whereas a conserved cysteine (Cys(8)) is essential for its recycling. In this study, we found that Cys(8) is required for the DTT-sensitive mono- and diubiquitination of Pex20. We also show that the PTS2 cargo receptor, Pex7, is required for Pex20 polyubiquitination. Pex4, the E2 ubiquitin-conjugation enzyme, is required for monoubiquitination of Pex20. However, it is also necessary for polyubiquitination of Pex20, making its behavior distinct from the ubiquitination described for other PTS receptors. Unlike the roles of specific RING peroxins in Pex5 ubiquitination, we found that all the RING peroxins (Pex2, Pex10, and Pex12) are required as E3 ubiquitin ligases for Pex20 mono- and polyubiquitination. A model for Pex20 ubiquitination is proposed based on these observations. This is the first description of the complete ubiquitination pathway of Pex20, which provides a better understanding of the recycling and degradation of this PTS2 cargo co-receptor.
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Affiliation(s)
- Xueqian Liu
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093-0322, USA
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50
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Abstract
Archaea contain, both a functional proteasome and an ubiquitin-like protein conjugation system (termed sampylation) that is related to the ubiquitin proteasome system (UPS) of eukaryotes. Archaeal proteasomes have served as excellent models for understanding how proteins are degraded by the central energy-dependent proteolytic machine of eukaryotes, the 26S proteasome. While sampylation has only recently been discovered, it is thought to be linked to proteasome-mediated degradation in archaea. Unlike eukaryotes, sampylation only requires an E1 enzyme homolog of the E1-E2-E3 ubiquitylation cascade to mediate protein conjugation. Furthermore, recent evidence suggests that archaeal and eurkaryotic E1 enzyme homologs can serve dual roles in mediating protein conjugation and activating sulfur for incorporation into biomolecules. The focus of this book chapter is the energy-dependent proteasome and sampylation systems of Archaea.
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Affiliation(s)
- Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611-0700, USA,
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