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Carman LE, Samulevich ML, Aneskievich BJ. Repressive Control of Keratinocyte Cytoplasmic Inflammatory Signaling. Int J Mol Sci 2023; 24:11943. [PMID: 37569318 PMCID: PMC10419196 DOI: 10.3390/ijms241511943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023] Open
Abstract
The overactivity of keratinocyte cytoplasmic signaling contributes to several cutaneous inflammatory and immune pathologies. An important emerging complement to proteins responsible for this overactivity is signal repression brought about by several proteins and protein complexes with the native role of limiting inflammation. The signaling repression by these proteins distinguishes them from transmembrane receptors, kinases, and inflammasomes, which drive inflammation. For these proteins, defects or deficiencies, whether naturally arising or in experimentally engineered skin inflammation models, have clearly linked them to maintaining keratinocytes in a non-activated state or returning cells to a post-inflamed state after a signaling event. Thus, together, these proteins help to resolve acute inflammatory responses or limit the development of chronic cutaneous inflammatory disease. We present here an integrated set of demonstrated or potentially inflammation-repressive proteins or protein complexes (linear ubiquitin chain assembly complex [LUBAC], cylindromatosis lysine 63 deubiquitinase [CYLD], tumor necrosis factor alpha-induced protein 3-interacting protein 1 [TNIP1], A20, and OTULIN) for a comprehensive view of cytoplasmic signaling highlighting protein players repressing inflammation as the needed counterpoints to signal activators and amplifiers. Ebb and flow of players on both sides of this inflammation equation would be of physiological advantage to allow acute response to damage or pathogens and yet guard against chronic inflammatory disease. Further investigation of the players responsible for repressing cytoplasmic signaling would be foundational to developing new chemical-entity pharmacologics to stabilize or enhance their function when clinical intervention is needed to restore balance.
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Affiliation(s)
- Liam E. Carman
- Graduate Program in Pharmacology & Toxicology, University of Connecticut, Storrs, CT 06269-3092, USA; (L.E.C.); (M.L.S.)
| | - Michael L. Samulevich
- Graduate Program in Pharmacology & Toxicology, University of Connecticut, Storrs, CT 06269-3092, USA; (L.E.C.); (M.L.S.)
| | - Brian J. Aneskievich
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269-3092, USA
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2
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Gregor JB, Xu D, French ME. Assembly and disassembly of branched ubiquitin chains. Front Mol Biosci 2023; 10:1197272. [PMID: 37325469 PMCID: PMC10267395 DOI: 10.3389/fmolb.2023.1197272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023] Open
Abstract
Protein ubiquitylation is an essential post-translational modification that regulates nearly all aspects of eukaryotic cell biology. A diverse collection of ubiquitylation signals, including an extensive repertoire of polymeric ubiquitin chains, leads to a range of different functional outcomes for the target protein. Recent studies have shown that ubiquitin chains can be branched and that branched chains have a direct impact on the stability or the activity of the target proteins they are attached to. In this mini review, we discuss the mechanisms that control the assembly and disassembly of branched chains by the enzymes of the ubiquitylation and deubiquitylation machinery. Existing knowledge regarding the activities of chain branching ubiquitin ligases and the deubiquitylases responsible for cleaving branched chains is summarized. We also highlight new findings concerning the formation of branched chains in response to small molecules that induce the degradation of otherwise stable proteins and examine the selective debranching of heterotypic chains by the proteasome-bound deubiquitylase UCH37.
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Affiliation(s)
- Justin B. Gregor
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Dantong Xu
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Michael E. French
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
- Department of Chemistry and Biochemistry, University of Tampa, Tampa, FL, United States
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3
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Assembly and function of branched ubiquitin chains. Trends Biochem Sci 2022; 47:759-771. [DOI: 10.1016/j.tibs.2022.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/23/2022] [Accepted: 04/05/2022] [Indexed: 12/11/2022]
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4
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New classes of E3 ligases illuminated by chemical probes. Curr Opin Struct Biol 2022; 73:102341. [DOI: 10.1016/j.sbi.2022.102341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 11/23/2022]
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5
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Funyu T, Kanemaru Y, Onoda H, Arita K. Preparation of the ubiquitination-triggered active form of SETDB1 in E. coli for biochemical and structural analyses. J Biochem 2021; 170:655-662. [PMID: 34324684 DOI: 10.1093/jb/mvab087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/23/2021] [Indexed: 11/13/2022] Open
Abstract
Trimethylation of histone H3 at K9 by the lysine methyltransferase, SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) plays a pivotal role in silencing tissue-specific genes and retrotransposable elements. In mammalian cells, SETDB1 undergoes monoubiquitination in the insertion region of the SET domain in an E3 ubiquitin ligase-independent manner. This ubiquitination has been shown to enhance the histone H3-K9 methyltransferase activity of SETDB1; however, the molecular mechanism underlying SETDB1 activation by ubiquitination is unknown. In this study, we developed an E. coli ubiquitination plasmid for the preparation of ubiquitinated SETDB1. Western blotting and mutational analyses showed that coexpression of the SET domain of SETDB1 with the proteins encoded by the ubiquitination plasmid led to site-specific monoubiquitination of the SET domain at K867. An in vitro histone H3 methylation assay demonstrated that the ubiquitinated SET domain of SETDB1 acquired enzymatic activity. Taken together, these findings demonstrate successful preparation of the active form of SETDB1 with the E. coli ubiquitination system, which will aid biochemical and structural studies of ubiquitinated SETDB1.
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Affiliation(s)
- Tomoko Funyu
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yuka Kanemaru
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroki Onoda
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kyohei Arita
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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6
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Pluska L, Jarosch E, Zauber H, Kniss A, Waltho A, Bagola K, von Delbrück M, Löhr F, Schulman BA, Selbach M, Dötsch V, Sommer T. The UBA domain of conjugating enzyme Ubc1/Ube2K facilitates assembly of K48/K63-branched ubiquitin chains. EMBO J 2021; 40:e106094. [PMID: 33576509 PMCID: PMC7957398 DOI: 10.15252/embj.2020106094] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/22/2020] [Accepted: 01/05/2021] [Indexed: 12/23/2022] Open
Abstract
The assembly of a specific polymeric ubiquitin chain on a target protein is a key event in the regulation of numerous cellular processes. Yet, the mechanisms that govern the selective synthesis of particular polyubiquitin signals remain enigmatic. The homologous ubiquitin-conjugating (E2) enzymes Ubc1 (budding yeast) and Ube2K (mammals) exclusively generate polyubiquitin linked through lysine 48 (K48). Uniquely among E2 enzymes, Ubc1 and Ube2K harbor a ubiquitin-binding UBA domain with unknown function. We found that this UBA domain preferentially interacts with ubiquitin chains linked through lysine 63 (K63). Based on structural modeling, in vitro ubiquitination experiments, and NMR studies, we propose that the UBA domain aligns Ubc1 with K63-linked polyubiquitin and facilitates the selective assembly of K48/K63-branched ubiquitin conjugates. Genetic and proteomics experiments link the activity of the UBA domain, and hence the formation of this unusual ubiquitin chain topology, to the maintenance of cellular proteostasis.
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Affiliation(s)
- Lukas Pluska
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Ernst Jarosch
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Henrik Zauber
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Andreas Kniss
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic ResonanceGoethe UniversityFrankfurt am MainGermany
| | - Anita Waltho
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Katrin Bagola
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | | | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic ResonanceGoethe UniversityFrankfurt am MainGermany
| | - Brenda A Schulman
- Department of Molecular Machines and SignalingMax Planck Institute of BiochemistryMartinsriedGermany
| | - Matthias Selbach
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
- Charité – Universitätsmedizin BerlinBerlinGermany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic ResonanceGoethe UniversityFrankfurt am MainGermany
| | - Thomas Sommer
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
- Institute for BiologyHumboldt‐Universität zu BerlinBerlinGermany
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7
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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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8
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Kaiho-Soma A, Akizuki Y, Igarashi K, Endo A, Shoda T, Kawase Y, Demizu Y, Naito M, Saeki Y, Tanaka K, Ohtake F. TRIP12 promotes small-molecule-induced degradation through K29/K48-branched ubiquitin chains. Mol Cell 2021; 81:1411-1424.e7. [PMID: 33567268 DOI: 10.1016/j.molcel.2021.01.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/13/2020] [Accepted: 01/20/2021] [Indexed: 12/19/2022]
Abstract
Targeted protein degradation is an emerging therapeutic paradigm. Small-molecule degraders such as proteolysis-targeting chimeras (PROTACs) induce the degradation of neo-substrates by hijacking E3 ubiquitin ligases. Although ubiquitylation of endogenous substrates has been extensively studied, the mechanism underlying forced degradation of neo-substrates is less well understood. We found that the ubiquitin ligase TRIP12 promotes PROTAC-induced and CRL2VHL-mediated degradation of BRD4 but is dispensable for the degradation of the endogenous CRL2VHL substrate HIF-1α. TRIP12 associates with BRD4 via CRL2VHL and specifically assembles K29-linked ubiquitin chains, facilitating the formation of K29/K48-branched ubiquitin chains and accelerating the assembly of K48 linkage by CRL2VHL. Consequently, TRIP12 promotes the PROTAC-induced apoptotic response. TRIP12 also supports the efficiency of other degraders that target CRABP2 or TRIM24 or recruit CRBN. These observations define TRIP12 and K29/K48-branched ubiquitin chains as accelerators of PROTAC-directed targeted protein degradation, revealing a cooperative mechanism of branched ubiquitin chain assembly unique to the degradation of neo-substrates.
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Affiliation(s)
- Ai Kaiho-Soma
- Institute for Advanced Life Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Yoshino Akizuki
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Katsuhide Igarashi
- Institute for Advanced Life Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan; School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Akinori Endo
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Takuji Shoda
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa 210-9501, Japan
| | - Yasuko Kawase
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa 210-9501, Japan
| | - Mikihiko Naito
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa 210-9501, Japan; Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa 210-9501, Japan
| | - Yasushi Saeki
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Keiji Tanaka
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Fumiaki Ohtake
- Institute for Advanced Life Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan; School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan; Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
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9
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Ali MS, Panuzzo C, Calabrese C, Maglione A, Piazza R, Cilloni D, Saglio G, Pergolizzi B, Bracco E. The Giant HECT E3 Ubiquitin Ligase HERC1 Is Aberrantly Expressed in Myeloid Related Disorders and It Is a Novel BCR-ABL1 Binding Partner. Cancers (Basel) 2021; 13:cancers13020341. [PMID: 33477751 PMCID: PMC7832311 DOI: 10.3390/cancers13020341] [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: 12/31/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The pathological role/s of the HERC family members has recently been initiated to be explored in few solid tumors and the assessment of their transcript amount reveals that they might act as effective prognostic factors. However, evidence concerning the non-solid tumors, and especially myeloid related neoplasms, is currently lacking. In the present article for the first time we provide original data for a clear and well-defined association between the gene expression level of a giant HERC E3 ubiquitin ligase family member, HERC1, and some myeloid related disorders, namely Acute Myeloid Leukemia, Myeloproliferative neoplasms and Chronic Myeloid Leukemia. Furthermore, our findings unveil that the HERC1 protein physically interacts, likely forming a very large supramolecular complex, and it is a putative BCR-ABL1 tyrosine kinase substrate. We hope that this work will contribute to the advance of our understanding of the roles played by the giant HERCs in myeloid related neoplasms. Abstract HERC E3 subfamily members are parts of the E3 ubiquitin ligases and key players for a wide range of cellular functions. Though the involvement of the Ubiquitin Proteasome System in blood disorders has been broadly studied, so far the role of large HERCs in this context remains unexplored. In the present study we examined the expression of the large HECT E3 Ubiquitin Ligase, HERC1, in blood disorders. Our findings revealed that HERC1 gene expression was severely downregulated both in acute and in chronic myelogenous leukemia at diagnosis, while it is restored after complete remission achievement. Instead, in Philadelphia the negative myeloproliferative neoplasm HERC1 level was peculiarly controlled, being very low in Primary Myelofibrosis and significantly upregulated in those Essential Thrombocytemia specimens harboring the mutation in the calreticulin gene. Remarkably, in CML cells HERC1 mRNA level was associated with the BCR-ABL1 kinase activity and the HERC1 protein physically interacted with BCR-ABL1. Furthermore, we found that HERC1 was directly tyrosine phosphorylated by the ABL kinase. Overall and for the first time, we provide original evidence on the potential tumor-suppressing or -promoting properties, depending on the context, of HERC1 in myeloid related blood disorders.
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Affiliation(s)
- Muhammad Shahzad Ali
- Department of Clinical and Biological Science, Medical School, University of Torino, 10043 Orbassano, Italy; (M.S.A.); (C.P.); (C.C.); (A.M.); (D.C.); (G.S.)
| | - Cristina Panuzzo
- Department of Clinical and Biological Science, Medical School, University of Torino, 10043 Orbassano, Italy; (M.S.A.); (C.P.); (C.C.); (A.M.); (D.C.); (G.S.)
| | - Chiara Calabrese
- Department of Clinical and Biological Science, Medical School, University of Torino, 10043 Orbassano, Italy; (M.S.A.); (C.P.); (C.C.); (A.M.); (D.C.); (G.S.)
| | - Alessandro Maglione
- Department of Clinical and Biological Science, Medical School, University of Torino, 10043 Orbassano, Italy; (M.S.A.); (C.P.); (C.C.); (A.M.); (D.C.); (G.S.)
| | - Rocco Piazza
- Department of Health Sciences, University of Milano-Bicocca, 20900 Monza, Italy;
| | - Daniela Cilloni
- Department of Clinical and Biological Science, Medical School, University of Torino, 10043 Orbassano, Italy; (M.S.A.); (C.P.); (C.C.); (A.M.); (D.C.); (G.S.)
| | - Giuseppe Saglio
- Department of Clinical and Biological Science, Medical School, University of Torino, 10043 Orbassano, Italy; (M.S.A.); (C.P.); (C.C.); (A.M.); (D.C.); (G.S.)
| | - Barbara Pergolizzi
- Department of Clinical and Biological Science, Medical School, University of Torino, 10043 Orbassano, Italy; (M.S.A.); (C.P.); (C.C.); (A.M.); (D.C.); (G.S.)
- Correspondence: (B.P.); (E.B.)
| | - Enrico Bracco
- Department of Oncology, Medical School, University of Torino, 10043 Orbassano, Italy
- Correspondence: (B.P.); (E.B.)
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Sardana R, Emr SD. Membrane Protein Quality Control Mechanisms in the Endo-Lysosome System. Trends Cell Biol 2021; 31:269-283. [PMID: 33414051 DOI: 10.1016/j.tcb.2020.11.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 01/12/2023]
Abstract
Protein quality control (PQC) machineries play a critical role in selective identification and removal of mistargeted, misfolded, and aberrant proteins. This task is extremely complicated due to the enormous diversity of the proteome. It also requires nuanced and careful differentiation between 'normal' and 'folding intermediates' from 'abnormal' and 'misfolded' protein states. Multiple genetic and proteomic approaches have started to delineate the molecular underpinnings of how these machineries recognize their target and how their activity is regulated. In this review, we summarize our understanding of the various E3 ubiquitin ligases and associated machinery that mediate PQC in the endo-lysosome system in yeast and humans, how they are regulated, and mechanisms of target selection, with the intent of guiding future research in this area.
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Affiliation(s)
- Richa Sardana
- Weill Institute of Cell and Molecular Biology, Cornell University, Ithaca, NY, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Scott D Emr
- Weill Institute of Cell and Molecular Biology, Cornell University, Ithaca, NY, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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RNF11 at the Crossroads of Protein Ubiquitination. Biomolecules 2020; 10:biom10111538. [PMID: 33187263 PMCID: PMC7697665 DOI: 10.3390/biom10111538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/18/2022] Open
Abstract
RNF11 (Ring Finger Protein 11) is a 154 amino-acid long protein that contains a RING-H2 domain, whose sequence has remained substantially unchanged throughout vertebrate evolution. RNF11 has drawn attention as a modulator of protein degradation by HECT E3 ligases. Indeed, the large number of substrates that are regulated by HECT ligases, such as ITCH, SMURF1/2, WWP1/2, and NEDD4, and their role in turning off the signaling by ubiquitin-mediated degradation, candidates RNF11 as the master regulator of a plethora of signaling pathways. Starting from the analysis of the primary sequence motifs and from the list of RNF11 protein partners, we summarize the evidence implicating RNF11 as an important player in modulating ubiquitin-regulated processes that are involved in transforming growth factor beta (TGF-β), nuclear factor-κB (NF-κB), and Epidermal Growth Factor (EGF) signaling pathways. This connection appears to be particularly significant, since RNF11 is overexpressed in several tumors, even though its role as tumor growth inhibitor or promoter is still controversial. The review highlights the different facets and peculiarities of this unconventional small RING-E3 ligase and its implication in tumorigenesis, invasion, neuroinflammation, and cancer metastasis.
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12
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Gutiérrez-Flores J, Hernández-Lemus E, Cortés-Guzmán F, Ramos E. Do weak interactions affect the biological behavior of DNA? A DFT study of CpG island-like chains. J Mol Model 2020; 26:266. [PMID: 32918237 DOI: 10.1007/s00894-020-04501-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/03/2020] [Indexed: 01/06/2023]
Abstract
The origin, stability, and contribution to the formation of noncovalent interactions, such as hydrogen bonds and π - π stacking, have been already widely discussed. However, there are few discussions about the relevance of these weak interactions in DNA performance. In this work, we seek to shed light on the effect of hydrogen bonds and π - π stacking interactions on the biological behavior of DNA through the description of these intermolecular forces in CpG island-like (GC-rich) chains. Furthermore, we made some comparisons with TATA box-like (TA-rich) chains in order to describe hydrogen bond and π - π stacking interactions as a function of the DNA sequence. For hydrogen bonds, we found that there is not a significant effect related to the number of base pairs. Whereas for π - π stacking interactions, the energy tended to decrease as the number of base pairs increased. We observed anticooperative effects for both hydrogen bonds and π - π stacking interactions. These results are in contrast with those of TATA box-like chains since cooperative and additive effects were found for both hydrogen bonds and π - π stacking, respectively. Based on the chemical hardness and density of states, we can conclude that proteins may interact easier with GC-rich chains. We conclude that regardless of the chain length, a protein could interact more easily with these genomics regions because the π - π stacking energies did not increase as a function of the number of base pairs, making, for the first time, a first approximation of the influence of noncovalent interaction on DNA behavior. We did all this work by means of DFT framework included in the DMol3 code (M06-L/DNP). Graphical Abstract Cartoon representation of how nocovalent interactions affect the interaction of DNA with a protein, i.e., how hydrogen bond and π - π stacking interactions influence the biological behavior of DNA.
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Affiliation(s)
- Jorge Gutiérrez-Flores
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, CDMX, México
| | | | - Fernando Cortés-Guzmán
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, CDMX, México
| | - Estrella Ramos
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, CDMX, México.
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Nagi K, Kaur S, Bai Y, Shenoy SK. In-frame fusion of SUMO1 enhances βarrestin2's association with activated GPCRs as well as with nuclear pore complexes. Cell Signal 2020; 75:109759. [PMID: 32860951 DOI: 10.1016/j.cellsig.2020.109759] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/17/2020] [Accepted: 08/22/2020] [Indexed: 01/11/2023]
Abstract
Small ubiquitin like modifier (SUMO) conjugation or SUMOylation of βarrestin2 promotes its association with the clathrin adaptor protein AP2 and facilitates rapid β2 adrenergic receptor (β2AR) internalization. However, disruption of the consensus SUMOylation site in βarrestin2, did not prevent βarrestin2's association with activated β2ARs, dopamine D2 receptors (D2Rs), angiotensin type 1a receptors (AT1aRs) and V2 vasopressin receptors (V2Rs). To address the role of SUMOylation in the trafficking of βarrestin and GPCR complexes, we generated and characterized a yellow fluorescent protein (YFP) tagged βarrestin2-SUMO1 chimeric protein, which is resistant to de-SUMOylation. In HEK-293 cells, YFP-SUMO1 predominantly localized in the nucleus, whereas YFP-βarrestin2 is cytoplasmic. YFP-βarrestin2-SUMO1 in addition to being cytoplasmic, is localized at the nuclear membrane. Nonetheless, βarrestin2-SUMO1 associated robustly with agonist-activated β2ARs as evaluated by co-immunoprecipitation, confocal microscopy and bioluminescence resonance energy transfer (BRET). βarrestin2-SUMO1 associated strongly with the D2R, which forms transient complexes with βarrestin2. But, βarrestin2-SUMO1 and βarrestin2 showed equivalent binding with the V2R, which forms stable complexes with βarrestin2. βarrestin2 expression level directly correlated with the steady state levels of the unmodified form of RanGAP1, which upon SUMOylation associates with nuclear membrane. On the other hand, βarrestin2-SUMO1 not only localized at the nuclear membrane, but also formed a macromolecular complex with RanGAP1. Taken together, our data suggest that SUMOylation of βarrestin2 promotes its protein interactions at both cell and nuclear membranes. Furthermore, βarrestin2-SUMO1 presents as a useful tool to characterize βarrestin2 recruitment to GPCRs, which form transient and unstable complex with βarrestin2.
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Affiliation(s)
- Karim Nagi
- Department of Medicine, Division of Cardiology, Duke University Medical Center, Durham, NC 27710, USA; College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Suneet Kaur
- Department of Medicine, Division of Cardiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Yushi Bai
- Department of Medicine, Division of Cardiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Sudha K Shenoy
- Department of Medicine, Division of Cardiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.
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14
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Ubiquitin in disguise unveils a cryptic binding site in 1.2-MDa anaphase-promoting complex/cyclosome. Proc Natl Acad Sci U S A 2019; 116:17142-17144. [PMID: 31371495 DOI: 10.1073/pnas.1911388116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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15
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Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site. Proc Natl Acad Sci U S A 2019; 116:17280-17289. [PMID: 31350353 DOI: 10.1073/pnas.1902889116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ubiquitin (Ub)-mediated proteolysis is a fundamental mechanism used by eukaryotic cells to maintain homeostasis and protein quality, and to control timing in biological processes. Two essential aspects of Ub regulation are conjugation through E1-E2-E3 enzymatic cascades and recognition by Ub-binding domains. An emerging theme in the Ub field is that these 2 properties are often amalgamated in conjugation enzymes. In addition to covalent thioester linkage to Ub's C terminus for Ub transfer reactions, conjugation enzymes often bind noncovalently and weakly to Ub at "exosites." However, identification of such sites is typically empirical and particularly challenging in large molecular machines. Here, studying the 1.2-MDa E3 ligase anaphase-promoting complex/cyclosome (APC/C), which controls cell division and many aspects of neurobiology, we discover a method for identifying unexpected Ub-binding sites. Using a panel of Ub variants (UbVs), we identify a protein-based inhibitor that blocks Ub ligation to APC/C substrates in vitro and ex vivo. Biochemistry, NMR, and cryo-electron microscopy (cryo-EM) structurally define the UbV interaction, explain its inhibitory activity through binding the surface on the APC2 subunit that recruits the E2 enzyme UBE2C, and ultimately reveal that this APC2 surface is also a Ub-binding exosite with preference for K48-linked chains. The results provide a tool for probing APC/C activity, have implications for the coordination of K48-linked Ub chain binding by APC/C with the multistep process of substrate polyubiquitylation, and demonstrate the power of UbV technology for identifying cryptic Ub-binding sites within large multiprotein complexes.
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16
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Deol KK, Lorenz S, Strieter ER. Enzymatic Logic of Ubiquitin Chain Assembly. Front Physiol 2019; 10:835. [PMID: 31333493 PMCID: PMC6624479 DOI: 10.3389/fphys.2019.00835] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022] Open
Abstract
Protein ubiquitination impacts virtually every biochemical pathway in eukaryotic cells. The fate of a ubiquitinated protein is largely dictated by the type of ubiquitin modification with which it is decorated, including a large variety of polymeric chains. As a result, there have been intense efforts over the last two decades to dissect the molecular details underlying the synthesis of ubiquitin chains by ubiquitin-conjugating (E2) enzymes and ubiquitin ligases (E3s). In this review, we highlight these advances. We discuss the evidence in support of the alternative models of transferring one ubiquitin at a time to a growing substrate-linked chain (sequential addition model) versus transferring a pre-assembled ubiquitin chain (en bloc model) to a substrate. Against this backdrop, we outline emerging principles of chain assembly: multisite interactions, distinct mechanisms of chain initiation and elongation, optimal positioning of ubiquitin molecules that are ultimately conjugated to each other, and substrate-assisted catalysis. Understanding the enzymatic logic of ubiquitin chain assembly has important biomedical implications, as the misregulation of many E2s and E3s and associated perturbations in ubiquitin chain formation contribute to human disease. The resurgent interest in bifunctional small molecules targeting pathogenic proteins to specific E3s for polyubiquitination and subsequent degradation provides an additional incentive to define the mechanisms responsible for efficient and specific chain synthesis and harness them for therapeutic benefit.
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Affiliation(s)
- Kirandeep K Deol
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States
| | - Sonja Lorenz
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States.,Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, United States
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17
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Bellia F, Lanza V, García-Viñuales S, Ahmed IMM, Pietropaolo A, Iacobucci C, Malgieri G, D'Abrosca G, Fattorusso R, Nicoletti VG, Sbardella D, Tundo GR, Coletta M, Pirone L, Pedone E, Calcagno D, Grasso G, Milardi D. Ubiquitin binds the amyloid β peptide and interferes with its clearance pathways. Chem Sci 2019; 10:2732-2742. [PMID: 30996991 PMCID: PMC6419943 DOI: 10.1039/c8sc03394c] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/09/2019] [Indexed: 12/22/2022] Open
Abstract
Several lines of evidence point to a compromised proteostasis associated with a reduction of the Ubiquitin Proteasome System (UPS) activity in patients affected by Alzheimer's Disease (AD) and suggest that the amyloid β peptide (Aβ) is an important player in the game. Inspired also by many reports, underlining the presence of ubiquitin (Ub) in the amyloid plaques of AD brains, here we set out to test whether Ub may bind the Aβ peptide and have any effect on its clearance pathways. By using an integrated array of MALDI-TOF/UPLC-HRMS, fluorescence, NMR, SPR, Microscale Thermophoresis (MST) and molecular dynamics studies, we consistently demonstrated that Aβ40 binds Ub with a 1 : 1 stoichiometry and K d in the high micromolar range. In particular, we show that the N-terminal domain of the Aβ peptide (through residues D1, E3 and R5) interacts with the C-terminal tail of Ub (involving residues K63 and E64), inducing the central region of Aβ (14HQKLVFFAEDVGSNK28) to adopt a mixed α-helix/β-turn structure. ELISA assays, carried out in neuroblastoma cell lysates, suggest that Aβ competitively binds Ub also in the presence of the entire pool of cytosolic Ub binding proteins. Ub-bound Aβ has a lower tendency to aggregate into amyloid-like fibrils and is more slowly degraded by the Insulin Degrading Enzyme (IDE). Finally, we observe that the water soluble fragment Aβ1-16 significantly inhibits Ub chain growth reactions. These results evidence how the non-covalent interaction between Aβ peptides and Ub may have relevant effects on the regulation of the upstream events of the UPS and pave the way to future in vivo studies addressing the role played by Aβ peptide in the malfunction of proteome maintenance occurring in AD.
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Affiliation(s)
- F Bellia
- Consiglio Nazionale delle Ricerche , Istituto di Biostrutture e Bioimmagini , Via P. Gaifami 18 , 95126 Catania , Italy .
| | - V Lanza
- Consiglio Nazionale delle Ricerche , Istituto di Biostrutture e Bioimmagini , Via P. Gaifami 18 , 95126 Catania , Italy .
| | - S García-Viñuales
- Consiglio Nazionale delle Ricerche , Istituto di Biostrutture e Bioimmagini , Via P. Gaifami 18 , 95126 Catania , Italy .
| | - I M M Ahmed
- Consiglio Nazionale delle Ricerche , Istituto di Biostrutture e Bioimmagini , Via P. Gaifami 18 , 95126 Catania , Italy .
| | - A Pietropaolo
- Dipartimento di Scienze della Salute , Università degli Studi Magna Graecia di Catanzaro , Viale Europa , 88100 , Catanzaro , Italy
| | - C Iacobucci
- Department of Pharmaceutical Chemistry & Bioanalytics , Institute of Pharmacy , Martin Luther University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - G Malgieri
- Department of Environmental , Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy
| | - G D'Abrosca
- Department of Environmental , Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy
| | - R Fattorusso
- Department of Environmental , Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy
| | - V G Nicoletti
- Dipartimento di Scienze Biomediche e Biotecnologiche (BIOMETEC) , sez. Biochimica medica , Università di Catania , Via Santa Sofia 97 , 95124 Catania , Italy
| | - D Sbardella
- Dipartimento di Scienze Cliniche e Medicina Traslazionale , Università di Roma Tor Vergata , Via Montpellier 1 , 00133 , Roma , Italy
| | - G R Tundo
- Dipartimento di Scienze Cliniche e Medicina Traslazionale , Università di Roma Tor Vergata , Via Montpellier 1 , 00133 , Roma , Italy
| | - M Coletta
- Dipartimento di Scienze Cliniche e Medicina Traslazionale , Università di Roma Tor Vergata , Via Montpellier 1 , 00133 , Roma , Italy
| | - L Pirone
- Consiglio Nazionale delle Ricerche , Istituto di Biostrutture e Bioimmagini , Via Mezzocannone, 16 , Naples I-80134 , Italy
| | - E Pedone
- Consiglio Nazionale delle Ricerche , Istituto di Biostrutture e Bioimmagini , Via Mezzocannone, 16 , Naples I-80134 , Italy
| | - D Calcagno
- Dipartimento di Scienze Chimiche , Università di Catania , V.le Andrea Doria 6 , 95125 Catania , Italy .
| | - G Grasso
- Dipartimento di Scienze Chimiche , Università di Catania , V.le Andrea Doria 6 , 95125 Catania , Italy .
| | - D Milardi
- Consiglio Nazionale delle Ricerche , Istituto di Biostrutture e Bioimmagini , Via P. Gaifami 18 , 95126 Catania , Italy .
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18
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Mattern M, Sutherland J, Kadimisetty K, Barrio R, Rodriguez MS. Using Ubiquitin Binders to Decipher the Ubiquitin Code. Trends Biochem Sci 2019; 44:599-615. [PMID: 30819414 DOI: 10.1016/j.tibs.2019.01.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/13/2022]
Abstract
Post-translational modifications (PTMs) by ubiquitin (Ub) are versatile, highly dynamic, and involved in nearly all aspects of eukaryote biological function. The reversibility and heterogeneity of Ub chains attached to protein substrates have complicated their isolation, quantification, and characterization. Strategies have emerged to isolate endogenous ubiquitylated targets, including technologies based on the use of Ub-binding peptides, such as tandem-repeated Ub-binding entities (TUBEs). TUBEs allow the identification and characterization of Ub chains, and novel substrates for deubiquitylases (DUBs) and Ub ligases (E3s). Here we review their impact on purification, analysis of pan or chain-selective polyubiquitylated proteins and underline the biological relevance of this information. Together with peptide aptamers and other Ub affinity-based approaches, TUBEs will contribute to unraveling the secrets of the Ub code.
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Affiliation(s)
- Michael Mattern
- Progenra Inc., 277 Great Valley Parkway, Malvern 19355, Pennsylvania, USA; These authors contributed equally
| | - James Sutherland
- CIC bioGUNE, Technology Park of Bizkaia, Bldg. 801A, 48160 Derio, Spain; These authors contributed equally
| | - Karteek Kadimisetty
- LifeSensors Inc., 271 Great Valley Parkway, Malvern 19355, Pennsylvania, USA
| | - Rosa Barrio
- CIC bioGUNE, Technology Park of Bizkaia, Bldg. 801A, 48160 Derio, Spain
| | - Manuel S Rodriguez
- ITAV-IPBS-UPS CNRS USR3505, 1 place Pierre Potier, Oncopole entrée B, 31106 Toulouse, France.
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19
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Roles of ubiquitin in autophagy and cell death. Semin Cell Dev Biol 2018; 93:125-135. [PMID: 30195063 PMCID: PMC6854449 DOI: 10.1016/j.semcdb.2018.09.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/28/2018] [Accepted: 09/03/2018] [Indexed: 01/12/2023]
Abstract
The balance between cell survival and cell death is often lost in human pathologies such as inflammation and cancer. Autophagy plays a critical role in cell survival: essential nutrients are generated by autophagy-dependent degradation and recycling of cellular garbage. On the other hand, cell death is induced by different programs, such as apoptosis, pyroptosis, and necroptosis. Emerging evidence is revealing how cell survival and cell death pathways are coordinated to determine cell fate. For instance, posttranslational modification of proteins with ubiquitin regulates many steps of autophagy and cell death pathways. In this review article, we will discuss how the ubiquitin system influences cell death and autophagy.
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20
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Budhidarmo R, Zhu J, Middleton AJ, Day CL. The RING domain of RING Finger 11 (RNF11) protein binds Ubc13 and inhibits formation of polyubiquitin chains. FEBS Lett 2018. [PMID: 29537486 DOI: 10.1002/1873-3468.13029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The Really Interesting New Gene (RING) Finger protein 11 (RNF11) is a subunit of the A20 ubiquitin-editing complex that ensures the transient nature of inflammatory responses. Although the role of RNF11 as a negative regulator of NF-κB signalling is well-documented, the molecular mechanisms that underpin this function are poorly understood. Here, we show that RNF11 binds both Ubc13 and the Ubc13~ubiquitin conjugate tightly and with similar affinity, but has minimal E3 ligase activity. Remarkably, RNF11 appears to bind Ubc13 so tightly that it outcompetes the E1 and an active E3 ligase. As a consequence, RNF11 may regulate the activity of E3s that rely on Ubc13 for ubiquitin chain assembly by limiting the availability of Ubc13 and its conjugate.
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Affiliation(s)
- Rhesa Budhidarmo
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jingyi Zhu
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Adam J Middleton
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Catherine L Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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21
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Abstract
Attachment of ubiquitin to proteins relies on a sophisticated enzyme cascade that is tightly regulated. The machinery of ubiquitylation responds to a range of signals, which remarkably includes ubiquitin itself. Thus, ubiquitin is not only the central player in the ubiquitylation cascade but also a key regulator. The ubiquitin E3 ligases provide specificity to the cascade and often bind the substrate, while the ubiquitin-conjugating enzymes (E2s) have a pivotal role in determining chain linkage and length. Interaction of ubiquitin with the E2 is important for activity, but the weak nature of these contacts has made them hard to identify and study. By reviewing available crystal structures, we identify putative ubiquitin binding sites on E2s, which may enhance E2 processivity and the assembly of chains of a defined linkage. The implications of these new sites are discussed in the context of known E2-ubiquitin interactions.
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22
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Lee BL, Singh A, Mark Glover JN, Hendzel MJ, Spyracopoulos L. Molecular Basis for K63-Linked Ubiquitination Processes in Double-Strand DNA Break Repair: A Focus on Kinetics and Dynamics. J Mol Biol 2017; 429:3409-3429. [PMID: 28587922 DOI: 10.1016/j.jmb.2017.05.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/20/2017] [Accepted: 05/30/2017] [Indexed: 11/18/2022]
Abstract
Cells are exposed to thousands of DNA damage events on a daily basis. This damage must be repaired to preserve genetic information and prevent development of disease. The most deleterious damage is a double-strand break (DSB), which is detected and repaired by mechanisms known as non-homologous end-joining (NHEJ) and homologous recombination (HR), which are components of the DNA damage response system. NHEJ is an error-prone first line of defense, whereas HR invokes error-free repair and is the focus of this review. The functions of the protein components of HR-driven DNA repair are regulated by the coordinated action of post-translational modifications including lysine acetylation, phosphorylation, ubiquitination, and SUMOylation. The latter two mechanisms are fundamental for recognition of DSBs and reorganizing chromatin to facilitate repair. We focus on the structures and molecular mechanisms for the protein components underlying synthesis, recognition, and cleavage of K63-linked ubiquitin chains, which are abundant at damage sites and obligatory for DSB repair. The forward flux of the K63-linked ubiquitination cascade is driven by the combined activity of E1 enzyme, the heterodimeric E2 Mms2-Ubc13, and its cognate E3 ligases RNF8 and RNF168, which is balanced through the binding and cleavage of chains by the deubiquitinase BRCC36, and the proteasome, and through the binding of chains by recognition modules on repair proteins such as RAP80. We highlight a number of aspects regarding our current understanding for the role of kinetics and dynamics in determining the function of the enzymes and chain recognition modules that drive K63 ubiquitination.
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Affiliation(s)
- Brian L Lee
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Anamika Singh
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - J N Mark Glover
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Leo Spyracopoulos
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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23
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Kumar A, Chaugule VK, Condos TEC, Barber KR, Johnson C, Toth R, Sundaramoorthy R, Knebel A, Shaw GS, Walden H. Parkin-phosphoubiquitin complex reveals cryptic ubiquitin-binding site required for RBR ligase activity. Nat Struct Mol Biol 2017; 24:475-483. [PMID: 28414322 PMCID: PMC5420311 DOI: 10.1038/nsmb.3400] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/16/2017] [Indexed: 12/20/2022]
Abstract
RING-between-RING (RBR) E3 ligases are a class of ubiquitin ligases distinct from RING or HECT E3 ligases. An important RBR ligase is Parkin, mutations in which lead to early-onset hereditary Parkinsonism. Parkin and other RBR ligases share a catalytic RBR module but are usually autoinhibited and activated via distinct mechanisms. Recent insights into Parkin regulation predict large, unknown conformational changes during Parkin activation. However, current data on active RBR ligases reflect the absence of regulatory domains. Therefore, it remains unclear how individual RBR ligases are activated, and whether they share a common mechanism. We now report the crystal structure of a human Parkin-phosphoubiquitin complex, which shows that phosphoubiquitin binding induces movement in the 'in-between RING' (IBR) domain to reveal a cryptic ubiquitin-binding site. Mutation of this site negatively affects Parkin's activity. Furthermore, ubiquitin binding promotes cooperation between Parkin molecules, which suggests a role for interdomain association in the RBR ligase mechanism.
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Affiliation(s)
- Atul Kumar
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Viduth K Chaugule
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Tara E C Condos
- Department of Biochemistry, Schulich School of Medicine and
Dentistry, University of Western Ontario, London, ON, Canada
| | - Kathryn R Barber
- Department of Biochemistry, Schulich School of Medicine and
Dentistry, University of Western Ontario, London, ON, Canada
| | - Clare Johnson
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | | | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Gary S Shaw
- Department of Biochemistry, Schulich School of Medicine and
Dentistry, University of Western Ontario, London, ON, Canada
| | - Helen Walden
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
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24
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Filipčík P, Curry JR, Mace PD. When Worlds Collide-Mechanisms at the Interface between Phosphorylation and Ubiquitination. J Mol Biol 2017; 429:1097-1113. [PMID: 28235544 DOI: 10.1016/j.jmb.2017.02.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 02/08/2023]
Abstract
Phosphorylation and ubiquitination are pervasive post-translational modifications that impact all processes inside eukaryotic cells. The role of each modification has been studied for decades, and functional interplay between the two has long been demonstrated and even more widely postulated. However, our understanding of the molecular features that allow phosphorylation to control protein ubiquitination and ubiquitin to control phosphorylation has only recently begun to build. Here, we review examples of regulation between ubiquitination and phosphorylation, aiming to describe mechanisms at the molecular level. In general, these examples illustrate phosphorylation as a versatile switch throughout ubiquitination pathways, and ubiquitination primarily impacting kinase signalling in a more emphatic manner through scaffolding or degradation. Examples of regulation between these two processes are likely to grow even further as advances in molecular biology, proteomics, and computation allow a system-level understanding of signalling. Many new cases could involve similar principles to those described here, but the extensive co-regulation of these two systems leaves no doubt that they still have many surprises in store.
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Affiliation(s)
- Pavel Filipčík
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Jack R Curry
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand.
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