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Hu B, Arpag S, Zuchner S, Li J. A novel missense mutation of CMT2P alters transcription machinery. Ann Neurol 2016; 80:834-845. [PMID: 27615052 DOI: 10.1002/ana.24776] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/29/2016] [Accepted: 09/01/2016] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Charcot-Marie-Tooth type 2P (CMT2P) has been associated with frameshift mutations in the RING domain of LRSAM1 (an E3 ligase). This study describes families with a novel missense mutation of LRSAM1 gene and explores pathogenic mechanisms of CMT2P. METHODS Patients with CMT2P were characterized clinically, electrophysiologically, and genetically. A neuronal model with the LRSAM1 mutation was created using CRISPR/Cas9 technology. The neuronal cell line along with fibroblasts isolated from the patients was used to study RNA-binding proteins. RESULTS This American family with dominantly inherited axonal polyneuropathy reveals a phenotype similar to those in previously reported non-US families. The affected members in our family cosegregated with a novel missense mutation Cys694Arg that alters a highly conserved cysteine in the RING domain. This mutation leads to axonal degeneration in the in vitro neuronal cell line. Moreover, using protein mass spectrometry, we identified a group of RNA-binding proteins (including FUS, a protein critically involved in motor neuron degeneration) that interacted with LRSAM1. The interactions were disrupted by the Cys694Arg mutation, which resulted in reduction of intranuclear RNA-binding proteins. INTERPRETATION Our findings suggest that the mutant LRSAM1 may aberrantly affect the formation of transcription machinery. Given that a similar mechanism has been reported in motor neuron degeneration of amyotrophic lateral sclerosis, abnormalities of RNA/RNA-binding protein complex may play a role in the neuronal degeneration of CMT2P. Ann Neurol 2016;80:834-845.
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Affiliation(s)
- Bo Hu
- Department of Neurology, Center for Human Genetic Research, and Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN
| | - Sezgi Arpag
- Department of Neurology, Center for Human Genetic Research, and Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN
| | - Stephan Zuchner
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL
| | - Jun Li
- Department of Neurology, Center for Human Genetic Research, and Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN
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352
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Wright JD, Mace PD, Day CL. Noncovalent Ubiquitin Interactions Regulate the Catalytic Activity of Ubiquitin Writers. Trends Biochem Sci 2016; 41:924-937. [PMID: 27614784 DOI: 10.1016/j.tibs.2016.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/26/2016] [Accepted: 08/01/2016] [Indexed: 11/27/2022]
Abstract
Covalent modification of substrate proteins with ubiquitin is the end result of an intricate network of protein-protein interactions. The inherent ability of the E1, E2, and E3 proteins of the ubiquitylation cascade (the ubiquitin writers) to interact with ubiquitin facilitates this process. Importantly, contact between ubiquitin and the E2/E3 writers is required for catalysis and the assembly of chains of a given linkage. However, ubiquitin is also an activator of ubiquitin-writing enzymes, with many recent studies highlighting the ability of ubiquitin to regulate activity and substrate modification. Here, we review the interactions between ubiquitin-writing enzymes and regulatory ubiquitin molecules that promote activity, and highlight the potential of these interactions to promote processive ubiquitin transfer.
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Affiliation(s)
- Joshua D Wright
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand; The Francis Crick Institute, London NW1 1AT, UK
| | - Peter D Mace
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Catherine L Day
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand.
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353
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Weber A, Cohen I, Popp O, Dittmar G, Reiss Y, Sommer T, Ravid T, Jarosch E. Sequential Poly-ubiquitylation by Specialized Conjugating Enzymes Expands the Versatility of a Quality Control Ubiquitin Ligase. Mol Cell 2016; 63:827-39. [PMID: 27570077 DOI: 10.1016/j.molcel.2016.07.020] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 06/07/2016] [Accepted: 07/20/2016] [Indexed: 12/13/2022]
Abstract
The Doa10 quality control ubiquitin (Ub) ligase labels proteins with uniform lysine 48-linked poly-Ub (K48-pUB) chains for proteasomal degradation. Processing of Doa10 substrates requires the activity of two Ub conjugating enzymes. Here we show that the non-canonical conjugating enzyme Ubc6 attaches single Ub molecules not only to lysines but also to hydroxylated amino acids. These Ub moieties serve as primers for subsequent poly-ubiquitylation by Ubc7. We propose that the evolutionary conserved propensity of Ubc6 to mount Ub on diverse amino acids augments the number of ubiquitylation sites within a substrate and thereby increases the target range of Doa10. Our work provides new insights on how the consecutive activity of two specialized conjugating enzymes facilitates the attachment of poly-Ub to very heterogeneous client molecules. Such stepwise ubiquitylation reactions most likely represent a more general cellular phenomenon that extends the versatility yet sustains the specificity of the Ub conjugation system.
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Affiliation(s)
- Annika Weber
- Intracellular Proteolysis, Max-Delbrueck-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Itamar Cohen
- Department of Biological Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Oliver Popp
- Mass Spectrometric Core Facility, Max-Delbrueck-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Gunnar Dittmar
- Mass Spectrometric Core Facility, Max-Delbrueck-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Yuval Reiss
- Department of Biological Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Thomas Sommer
- Intracellular Proteolysis, Max-Delbrueck-Center for Molecular Medicine, 13125 Berlin, Germany; Institute of Biology, Humboldt University Berlin, 10099 Berlin, Germany.
| | - Tommer Ravid
- Department of Biological Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel.
| | - Ernst Jarosch
- Intracellular Proteolysis, Max-Delbrueck-Center for Molecular Medicine, 13125 Berlin, Germany.
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354
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Kaneko M, Iwase I, Yamasaki Y, Takai T, Wu Y, Kanemoto S, Matsuhisa K, Asada R, Okuma Y, Watanabe T, Imaizumi K, Nomura Y. Genome-wide identification and gene expression profiling of ubiquitin ligases for endoplasmic reticulum protein degradation. Sci Rep 2016; 6:30955. [PMID: 27485036 PMCID: PMC4971459 DOI: 10.1038/srep30955] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 07/08/2016] [Indexed: 11/30/2022] Open
Abstract
Endoplasmic reticulum (ER)-associated degradation (ERAD) is a mechanism by which unfolded proteins that accumulate in the ER are transported to the cytosol for ubiquitin–proteasome-mediated degradation. Ubiquitin ligases (E3s) are a group of enzymes responsible for substrate selectivity and ubiquitin chain formation. The purpose of this study was to identify novel E3s involved in ERAD. Thirty-seven candidate genes were selected by searches for proteins with RING-finger motifs and transmembrane regions, which are the major features of ERAD E3s. We performed gene expression profiling for the identified E3s in human and mouse tissues. Several genes were specifically or selectively expressed in both tissues; the expression of four genes (RNFT1, RNF185, CGRRF1 and RNF19B) was significantly upregulated by ER stress. To determine the involvement of the ER stress-responsive genes in ERAD, we investigated their ER localisation, in vitro autoubiquitination activity and ER stress resistance. All were partially localised to the ER, whereas CGRRF1 did not possess E3 activity. RNFT1 and RNF185, but not CGRRF1 and RNF19B, exhibited significant resistance to ER stressor in an E3 activity-dependent manner. Thus, these genes are possible candidates for ERAD E3s.
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Affiliation(s)
- Masayuki Kaneko
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Ikuko Iwase
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Yuki Yamasaki
- Otsuka GEN Research Institute, Otsuka Pharmaceutical Co., Ltd., Tokushima 771-0192, Japan
| | - Tomoko Takai
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Yan Wu
- Department of Biochemistry, Graduate school of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Soshi Kanemoto
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Koji Matsuhisa
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Rie Asada
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Yasunobu Okuma
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science, Choshi, Chiba 288-0025, Japan
| | - Takeshi Watanabe
- Otsuka GEN Research Institute, Otsuka Pharmaceutical Co., Ltd., Tokushima 771-0192, Japan
| | - Kazunori Imaizumi
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Yausyuki Nomura
- Department of Pharmacology, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
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355
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Lazzari E, Meroni G. TRIM32 ubiquitin E3 ligase, one enzyme for several pathologies: From muscular dystrophy to tumours. Int J Biochem Cell Biol 2016; 79:469-477. [PMID: 27458054 DOI: 10.1016/j.biocel.2016.07.023] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 01/01/2023]
Abstract
TRIM32 is a member of the TRIpartite Motif family characterised by the presence of an N-terminal three-domain-module that includes a RING domain, which confers E3 ubiquitin ligase activity, one or two B-box domains and a Coiled-Coil region that mediates oligomerisation. Several TRIM32 substrates were identified including muscular proteins and proteins involved in cell cycle regulation and cell motility. As ubiquitination is a versatile post-translational modification that can affect target turnover, sub-cellular localisation or activity, it is likely that diverse substrates may be differentially affected by TRIM32-mediated ubiquitination, reflecting its multi-faceted roles in muscle physiology, cancer and immunity. With particular relevance for muscle physiology, mutations in TRIM32 are associated with autosomal recessive Limb-Girdle Muscular Dystrophy 2H, a muscle-wasting disease with variable clinical spectrum ranging from almost asymptomatic to wheelchair-bound patients. In this review, we will focus on the ability of TRIM32 to mark specific substrates for proteasomal degradation discussing how the TRIM32-proteasome axis may (i) be important for muscle homeostasis and for the pathogenesis of muscular dystrophy; and (ii) define either an oncogenic or tumour suppressive role for TRIM32 in the context of different types of cancer.
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Affiliation(s)
- Elisa Lazzari
- Department of Life Sciences, University of Trieste and Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Germana Meroni
- Department of Life Sciences, University of Trieste and Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy.
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356
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A C2HC zinc finger is essential for the RING-E2 interaction of the ubiquitin ligase RNF125. Sci Rep 2016; 6:29232. [PMID: 27411375 PMCID: PMC4944129 DOI: 10.1038/srep29232] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 06/14/2016] [Indexed: 12/02/2022] Open
Abstract
The activity of RING ubiquitin ligases (E3s) depends on an interaction between the RING domain and ubiquitin conjugating enzymes (E2), but posttranslational events or additional structural elements, yet largely undefined, are frequently required to enhance or regulate activity. Here, we show for the ubiquitin ligase RNF125 that, in addition to the RING domain, a C2HC Zn finger (ZnF) is crucial for activity, and a short linker sequence (Li2120-128) enhances activity. The contribution of these regions was first shown with truncated proteins, and the essential role of the ZnF was confirmed with mutations at the Zn chelating Cys residues. Using NMR, we established that the C2HC ZnF/Li2120-128 region is crucial for binding of the RING domain to the E2 UbcH5a. The partial X-ray structure of RNF125 revealed the presence of extensive intramolecular interactions between the RING and C2HC ZnF. A mutation at one of the contact residues in the C2HC ZnF, a highly conserved M112, resulted in the loss of ubiquitin ligase activity. Thus, we identified the structural basis for an essential role of the C2HC ZnF and conclude that this domain stabilizes the RING domain, and is therefore required for binding of RNF125 to an E2.
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357
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Densham RM, Garvin AJ, Stone HR, Strachan J, Baldock RA, Daza-Martin M, Fletcher A, Blair-Reid S, Beesley J, Johal B, Pearl LH, Neely R, Keep NH, Watts FZ, Morris JR. Human BRCA1-BARD1 ubiquitin ligase activity counteracts chromatin barriers to DNA resection. Nat Struct Mol Biol 2016; 23:647-55. [PMID: 27239795 PMCID: PMC6522385 DOI: 10.1038/nsmb.3236] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/02/2016] [Indexed: 01/03/2023]
Abstract
The opposing activities of 53BP1 and BRCA1 influence pathway choice in DNA double-strand-break repair. How BRCA1 counteracts the inhibitory effect of 53BP1 on DNA resection and homologous recombination is unknown. Here we identify the site of BRCA1-BARD1 required for priming ubiquitin transfer from E2∼ubiquitin and demonstrate that BRCA1-BARD1's ubiquitin ligase activity is required for repositioning 53BP1 on damaged chromatin. We confirm H2A ubiquitination by BRCA1-BARD1 and show that an H2A-ubiquitin fusion protein promotes DNA resection and repair in BARD1-deficient cells. BRCA1-BARD1's function in homologous recombination requires the chromatin remodeler SMARCAD1. SMARCAD1 binding to H2A-ubiquitin and optimal localization to sites of damage and activity in DNA repair requires its ubiquitin-binding CUE domains. SMARCAD1 is required for 53BP1 repositioning, and the need for SMARCAD1 in olaparib or camptothecin resistance is alleviated by 53BP1 loss. Thus, BRCA1-BARD1 ligase activity and subsequent SMARCAD1-dependent chromatin remodeling are critical regulators of DNA repair.
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Affiliation(s)
- Ruth M Densham
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Alexander J Garvin
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Helen R Stone
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Joanna Strachan
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Robert A Baldock
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Manuel Daza-Martin
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Alice Fletcher
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sarah Blair-Reid
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - James Beesley
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Balraj Johal
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Laurence H Pearl
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Robert Neely
- School of Chemistry, University of Birmingham, Birmingham, UK
| | - Nicholas H Keep
- Department of Biological Sciences, Institute for Structural and Molecular Biology, Birkbeck, University of London, London, UK
| | - Felicity Z Watts
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Joanna R Morris
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
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358
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Li T, Giagtzoglou N, Eberl DF, Jaiswal SN, Cai T, Godt D, Groves AK, Bellen HJ. The E3 ligase Ubr3 regulates Usher syndrome and MYH9 disorder proteins in the auditory organs of Drosophila and mammals. eLife 2016; 5. [PMID: 27331610 PMCID: PMC4978524 DOI: 10.7554/elife.15258] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/21/2016] [Indexed: 01/08/2023] Open
Abstract
Myosins play essential roles in the development and function of auditory organs and multiple myosin genes are associated with hereditary forms of deafness. Using a forward genetic screen in Drosophila, we identified an E3 ligase, Ubr3, as an essential gene for auditory organ development. Ubr3 negatively regulates the mono-ubiquitination of non-muscle Myosin II, a protein associated with hearing loss in humans. The mono-ubiquitination of Myosin II promotes its physical interaction with Myosin VIIa, a protein responsible for Usher syndrome type IB. We show that ubr3 mutants phenocopy pathogenic variants of Myosin II and that Ubr3 interacts genetically and physically with three Usher syndrome proteins. The interactions between Myosin VIIa and Myosin IIa are conserved in the mammalian cochlea and in human retinal pigment epithelium cells. Our work reveals a novel mechanism that regulates protein complexes affected in two forms of syndromic deafness and suggests a molecular function for Myosin IIa in auditory organs.
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Affiliation(s)
- Tongchao Li
- Program in Developmental Biology, Baylor College of Medicine, Houston, United States
| | - Nikolaos Giagtzoglou
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Department of Neurology, Baylor College of Medicine, Houston, United States
| | - Daniel F Eberl
- Department of Biology, University of Iowa, Iowa City, United States
| | - Sonal Nagarkar Jaiswal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, United States
| | - Tiantian Cai
- Department of Neuroscience, Baylor College of Medicine, Houston, United States
| | - Dorothea Godt
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Andrew K Groves
- Program in Developmental Biology, Baylor College of Medicine, Houston, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Department of Neuroscience, Baylor College of Medicine, Houston, United States
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine, Houston, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, United States.,Department of Neuroscience, Baylor College of Medicine, Houston, United States
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359
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Rotavirus NSP1 Associates with Components of the Cullin RING Ligase Family of E3 Ubiquitin Ligases. J Virol 2016; 90:6036-48. [PMID: 27099313 DOI: 10.1128/jvi.00704-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 12/17/2022] Open
Abstract
UNLABELLED The rotavirus nonstructural protein NSP1 acts as an antagonist of the host antiviral response by inducing degradation of key proteins required to activate interferon (IFN) production. Protein degradation induced by NSP1 is dependent on the proteasome, and the presence of a RING domain near the N terminus has led to the hypothesis that NSP1 is an E3 ubiquitin ligase. To examine this hypothesis, pulldown assays were performed, followed by mass spectrometry to identify components of the host ubiquitination machinery that associate with NSP1. Multiple components of cullin RING ligases (CRLs), which are essential multisubunit ubiquitination complexes, were identified in association with NSP1. The mass spectrometry was validated in both transfected and infected cells to show that the NSP1 proteins from different strains of rotavirus associated with key components of CRL complexes, most notably the cullin scaffolding proteins Cul3 and Cul1. In vitro binding assays using purified proteins confirmed that NSP1 specifically interacted with Cul3 and that the N-terminal region of Cul3 was responsible for binding to NSP1. To test if NSP1 used CRL3 to induce degradation of the target protein IRF3 or β-TrCP, Cul3 levels were knocked down using a small interfering RNA (siRNA) approach. Unexpectedly, loss of Cul3 did not rescue IRF3 or β-TrCP from degradation in infected cells. The results indicate that, rather than actively using CRL complexes to induce degradation of target proteins required for IFN production, NSP1 may use cullin-containing complexes to prevent another cellular activity. IMPORTANCE The ubiquitin-proteasome pathway plays an important regulatory role in numerous cellular functions, and many viruses have evolved mechanisms to exploit or manipulate this pathway to enhance replication and spread. Rotavirus, a major cause of severe gastroenteritis in young children that causes approximately 420,000 deaths worldwide each year, utilizes the ubiquitin-proteasome system to subvert the host innate immune response by inducing the degradation of key components required for the production of interferon (IFN). Here, we show that NSP1 proteins from different rotavirus strains associate with the scaffolding proteins Cul1 and Cul3 of CRL ubiquitin ligase complexes. Nonetheless, knockdown of Cul1 and Cul3 suggests that NSP1 induces the degradation of some target proteins independently of its association with CRL complexes, stressing a need to further investigate the mechanistic details of how NSP1 subverts the host IFN response.
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360
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Zattas D, Berk JM, Kreft SG, Hochstrasser M. A Conserved C-terminal Element in the Yeast Doa10 and Human MARCH6 Ubiquitin Ligases Required for Selective Substrate Degradation. J Biol Chem 2016; 291:12105-18. [PMID: 27068744 PMCID: PMC4933261 DOI: 10.1074/jbc.m116.726877] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/08/2016] [Indexed: 11/06/2022] Open
Abstract
Specific proteins are modified by ubiquitin at the endoplasmic reticulum (ER) and are degraded by the proteasome, a process referred to as ER-associated protein degradation. In Saccharomyces cerevisiae, two principal ER-associated protein degradation ubiquitin ligases (E3s) reside in the ER membrane, Doa10 and Hrd1. The membrane-embedded Doa10 functions in the degradation of substrates in the ER membrane, nuclear envelope, cytoplasm, and nucleoplasm. How most E3 ligases, including Doa10, recognize their protein substrates remains poorly understood. Here we describe a previously unappreciated but highly conserved C-terminal element (CTE) in Doa10; this cytosolically disposed 16-residue motif follows the final transmembrane helix. A conserved CTE asparagine residue is required for ubiquitylation and degradation of a subset of Doa10 substrates. Such selectivity suggests that the Doa10 CTE is involved in substrate discrimination and not general ligase function. Functional conservation of the CTE was investigated in the human ortholog of Doa10, MARCH6 (TEB4), by analyzing MARCH6 autoregulation of its own degradation. Mutation of the conserved Asn residue (N890A) in the MARCH6 CTE stabilized the normally short lived enzyme to the same degree as a catalytically inactivating mutation (C9A). We also report the localization of endogenous MARCH6 to the ER using epitope tagging of the genomic MARCH6 locus by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated genome editing. These localization and CTE analyses support the inference that MARCH6 and Doa10 are functionally similar. Moreover, our results with the yeast enzyme suggest that the CTE is involved in the recognition and/or ubiquitylation of specific protein substrates.
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Affiliation(s)
- Dimitrios Zattas
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and
| | - Jason M Berk
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and
| | - Stefan G Kreft
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and the Department of Biology, University of Konstanz, Universitaetsstrasse 10, 78457 Konstanz, Germany
| | - Mark Hochstrasser
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and
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361
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Koliopoulos MG, Esposito D, Christodoulou E, Taylor IA, Rittinger K. Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity. EMBO J 2016; 35:1204-18. [PMID: 27154206 PMCID: PMC4864278 DOI: 10.15252/embj.201593741] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/06/2016] [Indexed: 12/30/2022] Open
Abstract
TRIM E3 ubiquitin ligases regulate a wide variety of cellular processes and are particularly important during innate immune signalling events. They are characterized by a conserved tripartite motif in their N-terminal portion which comprises a canonical RING domain, one or two B-box domains and a coiled-coil region that mediates ligase dimerization. Self-association via the coiled-coil has been suggested to be crucial for catalytic activity of TRIMs; however, the precise molecular mechanism underlying this observation remains elusive. Here, we provide a detailed characterization of the TRIM ligases TRIM25 and TRIM32 and show how their oligomeric state is linked to catalytic activity. The crystal structure of a complex between the TRIM25 RING domain and an ubiquitin-loaded E2 identifies the structural and mechanistic features that promote a closed E2~Ub conformation to activate the thioester for ubiquitin transfer allowing us to propose a model for the regulation of activity in the full-length protein. Our data reveal an unexpected diversity in the self-association mechanism of TRIMs that might be crucial for their biological function.
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Affiliation(s)
- Marios G Koliopoulos
- Mill Hill LaboratoryMolecular Structure of Cell Signalling LaboratoryThe Francis Crick InstituteLondonUK
| | - Diego Esposito
- Mill Hill LaboratoryMolecular Structure of Cell Signalling LaboratoryThe Francis Crick InstituteLondonUK
| | | | - Ian A Taylor
- Mill Hill LaboratoryMacromolecular Structure LaboratoryThe Francis Crick InstituteLondonUK
| | - Katrin Rittinger
- Mill Hill LaboratoryMolecular Structure of Cell Signalling LaboratoryThe Francis Crick InstituteLondonUK
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362
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Characterisation of assembly and ubiquitylation by the RBCC motif of Trim5α. Sci Rep 2016; 6:26837. [PMID: 27230667 PMCID: PMC4882581 DOI: 10.1038/srep26837] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/09/2016] [Indexed: 12/17/2022] Open
Abstract
The post-entry restriction factor Trim5α blocks infection of retroviral pathogens shortly after the virus gains entry to the cell, preventing reverse transcription and integration into the host genome. Central to the mechanism of restriction is recognition of the lattice of capsid protein that forms the inner-shell of the retrovirus. To recognise this lattice, Trim5α has been shown to assemble into a large hexagonal array, complementary to the capsid lattice. Structures of the Trim5α coiled-coil region reveal an elongated anti-parallel dimer consistent with the edges of this array placing the Bbox domain at each end of the coiled-coil to facilitate assembly. To investigate the nature of this assembly we have designed and characterised a monomeric version of the TRIM RBCC motif with a truncated coiled-coil. Biophysical characterisation by SEC-MALLS, AUC, and SAXS demonstrate that this construct forms compact folded domain that assembles into a trimer that would support the formation of a hexagonal lattice. Furthermore, the RING domain and elements of the coiled-coil region are shown to contribute to assembly. Ubiquitylation assays demonstrate that this assembly increases ubiquitylation activity providing a link from recognition of the capsid lattice and assembly to the activation of innate immune signalling and restriction.
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363
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The Ubiquitination of NF-κB Subunits in the Control of Transcription. Cells 2016; 5:cells5020023. [PMID: 27187478 PMCID: PMC4931672 DOI: 10.3390/cells5020023] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/03/2016] [Accepted: 05/06/2016] [Indexed: 02/06/2023] Open
Abstract
Nuclear factor (NF)-κB has evolved as a latent, inducible family of transcription factors fundamental in the control of the inflammatory response. The transcription of hundreds of genes involved in inflammation and immune homeostasis require NF-κB, necessitating the need for its strict control. The inducible ubiquitination and proteasomal degradation of the cytoplasmic inhibitor of κB (IκB) proteins promotes the nuclear translocation and transcriptional activity of NF-κB. More recently, an additional role for ubiquitination in the regulation of NF-κB activity has been identified. In this case, the ubiquitination and degradation of the NF-κB subunits themselves plays a critical role in the termination of NF-κB activity and the associated transcriptional response. While there is still much to discover, a number of NF-κB ubiquitin ligases and deubiquitinases have now been identified which coordinate to regulate the NF-κB transcriptional response. This review will focus the regulation of NF-κB subunits by ubiquitination, the key regulatory components and their impact on NF-κB directed transcription.
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364
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Wright FA, Wojcikiewicz RJH. Chapter 4 - Inositol 1,4,5-Trisphosphate Receptor Ubiquitination. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 141:141-59. [PMID: 27378757 DOI: 10.1016/bs.pmbts.2016.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Inositol 1,4,5-trisphosphate receptors (IP3Rs) are large (∼300kDa) proteins that associate into tetrameric ion channels in the endoplasmic reticulum (ER) membrane. Activation and opening of the channel upon binding of IP3 and Ca(2+) allows the flow of Ca(2+) ions from stores within the ER lumen to the cytosol, thereby promoting a number of Ca(2+)-dependent cellular events, such as secretion, neurotransmitter release, and cell division. Intriguingly, it appears that the same conformational change that IP3Rs undergo during activation makes them a target for degradation by the ubiquitin-proteasome pathway and that this mode of processing allows the cell to tune its internal Ca(2+) response to extracellular signals. Here, we review recent studies showing that activated IP3Rs interact with an array of proteins that mediate their degradation, that IP3Rs are modified by a complex array of ubiquitin conjugates, that this ubiquitination and degradation functions to regulate IP3-mediated Ca(2+) responses in the cell, and that mutations to different proteins involved in IP3R degradation result in a set of similar diseases.
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Affiliation(s)
- F A Wright
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - R J H Wojcikiewicz
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY, United States.
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365
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Abstract
Ubiquitin-conjugating enzymes (E2s) are the central players in the trio of enzymes responsible for the attachment of ubiquitin (Ub) to cellular proteins. Humans have ∼40 E2s that are involved in the transfer of Ub or Ub-like (Ubl) proteins (e.g., SUMO and NEDD8). Although the majority of E2s are only twice the size of Ub, this remarkable family of enzymes performs a variety of functional roles. In this review, we summarize common functional and structural features that define unifying themes among E2s and highlight emerging concepts in the mechanism and regulation of E2s.
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366
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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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367
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Hodge CD, Ismail IH, Edwards RA, Hura GL, Xiao AT, Tainer JA, Hendzel MJ, Glover JNM. RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment. J Biol Chem 2016; 291:9396-410. [PMID: 26903517 DOI: 10.1074/jbc.m116.715698] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Indexed: 01/31/2023] Open
Abstract
DNA double strand break (DSB) responses depend on the sequential actions of the E3 ubiquitin ligases RNF8 and RNF168 plus E2 ubiquitin-conjugating enzyme Ubc13 to specifically generate histone Lys-63-linked ubiquitin chains in DSB signaling. Here, we defined the activated RNF8-Ubc13∼ubiquitin complex by x-ray crystallography and its functional solution conformations by x-ray scattering, as tested by separation-of-function mutations imaged in cells by immunofluorescence. The collective results show that the RING E3 RNF8 targets E2 Ubc13 to DSB sites and plays a critical role in damage signaling by stimulating polyubiquitination through modulating conformations of ubiquitin covalently linked to the Ubc13 active site. Structure-guided separation-of-function mutations show that the RNF8 E2 stimulating activity is essential for DSB signaling in mammalian cells and is necessary for downstream recruitment of 53BP1 and BRCA1. Chromatin-targeted RNF168 rescues 53BP1 recruitment involved in non-homologous end joining but not BRCA1 recruitment for homologous recombination. These findings suggest an allosteric approach to targeting the ubiquitin-docking cleft at the E2-E3 interface for possible interventions in cancer and chronic inflammation, and moreover, they establish an independent RNF8 role in BRCA1 recruitment.
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Affiliation(s)
- Curtis D Hodge
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Ismail H Ismail
- the Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada, the Biophysics Department, Faculty of Science, Cairo University, 12613 Giza, Egypt
| | - Ross A Edwards
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Greg L Hura
- the Lawrence Berkeley National Laboratory, Berkeley, California 94704
| | - Andrew T Xiao
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - John A Tainer
- the Lawrence Berkeley National Laboratory, Berkeley, California 94704, the Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, and
| | - Michael J Hendzel
- the Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada
| | - J N Mark Glover
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada,
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368
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Gu H. Infected cell protein 0 functional domains and their coordination in herpes simplex virus replication. World J Virol 2016; 5:1-13. [PMID: 26870669 PMCID: PMC4735549 DOI: 10.5501/wjv.v5.i1.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 10/28/2015] [Accepted: 12/08/2015] [Indexed: 02/05/2023] Open
Abstract
Herpes simplex virus 1 (HSV-1) is a ubiquitous human pathogen that establishes latent infection in ganglia neurons. Its unique life cycle requires a balanced “conquer and compromise” strategy to deal with the host anti-viral defenses. One of HSV-1 α (immediate early) gene products, infected cell protein 0 (ICP0), is a multifunctional protein that interacts with and modulates a wide range of cellular defensive pathways. These pathways may locate in different cell compartments, which then migrate or exchange factors upon stimulation, for the purpose of a concerted and effective defense. ICP0 is able to simultaneously attack multiple host pathways by either degrading key restrictive factors or modifying repressive complexes. This is a viral protein that contains an E3 ubiquitin ligase, translocates among different cell compartments and interacts with major defensive complexes. The multiple functional domains of ICP0 can work independently and at the same time coordinate with each other. Dissecting the functional domains of ICP0 and delineating the coordination of these domains will help us understand HSV-1 pathogenicity as well as host defense mechanisms. This article focuses on describing individual ICP0 domains, their biochemical properties and their implication in HSV-1 infection. By putting individual domain functions back into the picture of host anti-viral defense network, this review seeks to elaborate the complex interactions between HSV-1 and its host.
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369
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Uddin S, Bhat AA, Krishnankutty R, Mir F, Kulinski M, Mohammad RM. Involvement of F-BOX proteins in progression and development of human malignancies. Semin Cancer Biol 2016; 36:18-32. [PMID: 26410033 DOI: 10.1016/j.semcancer.2015.09.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 12/13/2022]
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370
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Nowotny M, Gaur V. Structure and mechanism of nucleases regulated by SLX4. Curr Opin Struct Biol 2016; 36:97-105. [PMID: 26827285 DOI: 10.1016/j.sbi.2016.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 01/08/2023]
Abstract
SLX4 is a multidomain platform that regulates various proteins that are involved in genome maintenance and stability. Among these proteins are three structure-selective nucleases (SSEs). XPF-ERCC1 and MUS81-EME1 are structurally similar and function as heterodimers of highly similar subunits, in which only one is active. Two independent modules are formed from subunits of the heterodimers - a dimer of nuclease and nuclease-like domains and a dimer of tandem helix-hairpin-helix HhH2 domains. Both modules are responsible for substrate recognition. The third SSE, SLX1, contains GIY-YIG and RING domains and is a promiscuous nuclease. Structural data imply that SLX1 exists in free form as an autoinhibited homodimer. Association with SLX4 platform disrupts the homodimer and activates SLX1. This review discusses the available structural and mechanistic information on SLX4-regulated SSEs.
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Affiliation(s)
- Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland.
| | - Vineet Gaur
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland.
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371
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Lechtenberg BC, Rajput A, Sanishvili R, Dobaczewska MK, Ware CF, Mace PD, Riedl SJ. Structure of a HOIP/E2~ubiquitin complex reveals RBR E3 ligase mechanism and regulation. Nature 2016; 529:546-50. [PMID: 26789245 PMCID: PMC4856479 DOI: 10.1038/nature16511] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/03/2015] [Indexed: 02/07/2023]
Abstract
Ubiquitination is a central process affecting all facets of cellular signaling and function1. A critical step in ubiquitination is the transfer of ubiquitin from an E2 ubiquitin-conjugating enzyme to a substrate or a growing ubiquitin chain, which is mediated by E3 ubiquitin ligases. RING-type E3 ligases typically facilitate the transfer of ubiquitin from the E2 directly to the substrate2,3. The RBR family of RING-type E3 ligases, however, breaks this paradigm by forming a covalent intermediate with ubiquitin similarly to HECT-type E3 ligases4–6. The RBR family includes Parkin4 and HOIP, the central catalytic factor of the linear ubiquitin chain assembly complex (LUBAC)7. While structural insights into the RBR E3 ligases Parkin and HHARI in their overall autoinhibited forms are available8–13, no structures exist of intact fully active RBR E3 ligases or any of their complexes. Thus, the RBR mechanism of action has remained largely enigmatic. Here we present the first structure of the fully active HOIP-RBR in its transfer complex with an E2~ubiquitin conjugate, which elucidates the intricate nature of RBR E3 ligases. The active HOIP-RBR adopts a conformation markedly different from that of autoinhibited RBRs. HOIP-RBR binds the E2~ubiquitin conjugate in an elongated fashion, with the E2 and E3 catalytic centers ideally aligned for ubiquitin transfer, which structurally both requires and enables a HECT-like mechanism. In addition, surprisingly, three distinct helix–IBR-fold motifs inherent to RBRs form ubiquitin-binding regions that engage the activated ubiquitin of the E2~Ub conjugate as well as an additional regulatory ubiquitin molecule. The features uncovered reveal critical states of the HOIP-RBR E3 ligase cycle, and comparison with Parkin and HHARI suggests a general mechanism for RBR E3 ligases.
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Affiliation(s)
- Bernhard C Lechtenberg
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Akhil Rajput
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Ruslan Sanishvili
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Małgorzata K Dobaczewska
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Carl F Ware
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Peter D Mace
- Biochemistry Department, University of Otago, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Stefan J Riedl
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
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372
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Speranzini V, Pilotto S, Sixma TK, Mattevi A. Touch, act and go: landing and operating on nucleosomes. EMBO J 2016; 35:376-88. [PMID: 26787641 DOI: 10.15252/embj.201593377] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/10/2015] [Indexed: 12/16/2022] Open
Abstract
Chromatin-associated enzymes are responsible for the installation, removal and reading of precise post-translation modifications on DNA and histone proteins. They are specifically recruited to the target gene by associated factors, and as a result of their activity, they contribute in modulating cell identity and differentiation. Structural and biophysical approaches are broadening our knowledge on these processes, demonstrating that DNA, histone tails and histone surfaces can each function as distinct yet functionally interconnected anchoring points promoting nucleosome binding and modification. The mechanisms underlying nucleosome recognition have been described for many histone modifiers and related readers. Here, we review the recent literature on the structural organization of these nucleosome-associated proteins, the binding properties that drive nucleosome modification and the methodological advances in their analysis. The overarching conclusion is that besides acting on the same substrate (the nucleosome), each system functions through characteristic modes of action, which bring about specific biological functions in gene expression regulation.
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Affiliation(s)
| | - Simona Pilotto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
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373
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Wang D, Tan J, Xu Y, Han M, Tu Y, Zhu Z, Dou C, Xin J, Tan X, Zeng JP, Zhao G, Liu Z. The ubiquitin ligase RNF43 downregulation increases membrane expression of frizzled receptor in pancreatic ductal adenocarcinoma. Tumour Biol 2016; 37:627-31. [PMID: 26240024 DOI: 10.1007/s13277-015-3499-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 04/23/2015] [Indexed: 01/04/2023] Open
Abstract
RNF43 is a novel tumor suppressor protein and known to be expressed in a multitude of tissue and dysregulated in cancers of these organs including ovarian and colorectal tissues. RNF43 expression has been shown to be expressed in mutated forms in several pancreatic cell lines. RNF43, by virtue of being an ubiquitin ligase, has the potential to ubiquitinylate membrane receptors like frizzled that subserves sensing Wnt soluble signals at the cell membrane. Thus, normally, RNF43 downregulates Wnt signaling by removing frizzled receptor from the membrane. In the present study, the expression of the tumor suppressor RNF43 was examined in human patient samples of pancreatic ductal adenocarcinoma (PDAC). Reduced levels of expression of RNF43 in PDAC were demonstrated by Western blotting. We incorporated membrane biotinylation assay to examine the expression of frizzled6 receptor in the membrane and demonstrated that it is significantly increased in PDAC tissues. This may be responsible for enhanced Wnt/beta-catenin signaling and provides the first level of evidence of a possible role of this well-known pathway in pancreatic exocrine carcinogenesis. We have utilized appropriate controls to ensure the true positivity of the findings of the present study. The contribution of Wnt/beta-catenin/RNF43 pathway in pancreatic carcinogenesis may provide for utilization of pharmacologic resources for precision-based approaches to treat pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Dadong Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hostpial of Chinese PLA General Hospital, Beijing, 100048, China
| | - Jingwang Tan
- Department of Hepatobiliary Surgery, The First Affiliated Hostpial of Chinese PLA General Hospital, Beijing, 100048, China
| | - Yong Xu
- Department of Hepatobiliary Surgery, The First Affiliated Hostpial of Chinese PLA General Hospital, Beijing, 100048, China
| | - Mingming Han
- Department of Hepatobiliary Surgery, The First Affiliated Hostpial of Chinese PLA General Hospital, Beijing, 100048, China
| | - Yuliang Tu
- Department of Hepatobiliary Surgery, The First Affiliated Hostpial of Chinese PLA General Hospital, Beijing, 100048, China
| | - Ziman Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hostpial of Chinese PLA General Hospital, Beijing, 100048, China
| | - Chunqing Dou
- Department of Hepatobiliary Surgery, The First Affiliated Hostpial of Chinese PLA General Hospital, Beijing, 100048, China
| | - Jin Xin
- Department of Hepatobiliary Surgery, The First Affiliated Hostpial of Chinese PLA General Hospital, Beijing, 100048, China
| | - Xianglong Tan
- Department of Hepatobiliary Surgery, The First Affiliated Hostpial of Chinese PLA General Hospital, Beijing, 100048, China
| | - Jian-Ping Zeng
- Department of Hepatobiliary Surgery, The First Affiliated Hostpial of Chinese PLA General Hospital, Beijing, 100048, China
| | - Gang Zhao
- Department of Emergency Surgery, Qianfoshang Hospital Affiliated to Shandong University, No 16766, Jingshi Road, Lixia Distict, Jinan, 250014, China.
| | - Zhiwei Liu
- Department of Hepatobiliary Surgery, Chinese PLA General Hospital, No.28, Fuxing Road, Haidian District, Beijing, 100853, China.
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374
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Chapter Six - The Ubiquitin Network in the Control of EGFR Endocytosis and Signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 141:225-76. [DOI: 10.1016/bs.pmbts.2016.03.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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375
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Isolation, expression analysis and characterization of NEFA-interacting nuclear protein 30 and RING finger and SPRY domain containing 1 in skeletal muscle. Gene 2016; 576:319-32. [DOI: 10.1016/j.gene.2015.10.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 10/07/2015] [Accepted: 10/16/2015] [Indexed: 11/18/2022]
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376
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McDowell G, Philpott A. New Insights Into the Role of Ubiquitylation of Proteins. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 325:35-88. [DOI: 10.1016/bs.ircmb.2016.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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377
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Schaefer JS, Klein JR. Roquin--a multifunctional regulator of immune homeostasis. Genes Immun 2015; 17:79-84. [PMID: 26673963 PMCID: PMC4777649 DOI: 10.1038/gene.2015.58] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 11/06/2015] [Indexed: 12/20/2022]
Abstract
Roquin-1 (Rc3h1) is an E3 ubiquitin ligase originally discovered in a mutational screen for genetic factors contributory to systemic lupus erythematosus-like symptoms in mice. A single base-pair mutation in the Rc3h1 gene resulted in the manifestation of autoantibody production and sustained immunological inflammation characterized by excessive T follicular helper cell activation and formation of germinal centers. Subsequent studies have uncovered a multifactorial process by which Roquin-1 contributes to the maintenance of immune homeostasis. Through its interactions with partner proteins, Roquin-1 targets mRNAs for decay with inducible costimulator being a primary target. In this review, we discuss newly discovered functions of Roquin-1 in the immune system and inflammation, and in disease manifestation, and discuss avenues of further research. A model is presented for the role of Roquin in health and disease.
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Affiliation(s)
- J S Schaefer
- Department of Diagnostic and Biomedical Sciences, The University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX, USA
| | - J R Klein
- Department of Diagnostic and Biomedical Sciences, The University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX, USA
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378
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Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity. Nat Struct Mol Biol 2015; 23:45-52. [PMID: 26656854 DOI: 10.1038/nsmb.3142] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/13/2015] [Indexed: 11/09/2022]
Abstract
RING-domain E3 ligases enhance transfer of ubiquitin to substrate proteins by stabilizing the RING-bound thioester-linked E2∼ubiquitin conjugate in a defined conformation that primes the active site for nucleophilic attack. Here we report that the monomeric RING domains from the human E3 ligases Arkadia and Ark2C bind directly to free ubiquitin with an affinity comparable to that of other dedicated ubiquitin-binding domains. Further work showed that the Ark-like RING domain and the noncovalently bound ubiquitin molecule coordinately stabilize the E2-conjugated ubiquitin (donor ubiquitin) in the 'closed' conformation. Our studies identify the RING domain of Arkadia as a ubiquitin-binding domain and provide insight into a new ubiquitin-dependent mechanism used by monomeric RING domains to activate ubiquitin transfer. This study also suggests how substrates that have been monoubiquitinated could be favored for further ubiquitination.
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379
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Wertz IE, Newton K, Seshasayee D, Kusam S, Lam C, Zhang J, Popovych N, Helgason E, Schoeffler A, Jeet S, Ramamoorthi N, Kategaya L, Newman RJ, Horikawa K, Dugger D, Sandoval W, Mukund S, Zindal A, Martin F, Quan C, Tom J, Fairbrother WJ, Townsend M, Warming S, DeVoss J, Liu J, Dueber E, Caplazi P, Lee WP, Goodnow CC, Balazs M, Yu K, Kolumam G, Dixit VM. Phosphorylation and linear ubiquitin direct A20 inhibition of inflammation. Nature 2015; 528:370-5. [PMID: 26649818 DOI: 10.1038/nature16165] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 10/11/2015] [Indexed: 12/26/2022]
Abstract
Inactivation of the TNFAIP3 gene, encoding the A20 protein, is associated with critical inflammatory diseases including multiple sclerosis, rheumatoid arthritis and Crohn's disease. However, the role of A20 in attenuating inflammatory signalling is unclear owing to paradoxical in vitro and in vivo findings. Here we utilize genetically engineered mice bearing mutations in the A20 ovarian tumour (OTU)-type deubiquitinase domain or in the zinc finger-4 (ZnF4) ubiquitin-binding motif to investigate these discrepancies. We find that phosphorylation of A20 promotes cleavage of Lys63-linked polyubiquitin chains by the OTU domain and enhances ZnF4-mediated substrate ubiquitination. Additionally, levels of linear ubiquitination dictate whether A20-deficient cells die in response to tumour necrosis factor. Mechanistically, linear ubiquitin chains preserve the architecture of the TNFR1 signalling complex by blocking A20-mediated disassembly of Lys63-linked polyubiquitin scaffolds. Collectively, our studies reveal molecular mechanisms whereby A20 deubiquitinase activity and ubiquitin binding, linear ubiquitination, and cellular kinases cooperate to regulate inflammation and cell death.
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Affiliation(s)
- Ingrid E Wertz
- Discovery Oncology, Genentech, South San Francisco, California 94080, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Kim Newton
- Physiological Chemistry, Genentech, South San Francisco, California 94080, USA
| | - Dhaya Seshasayee
- Immunology, Genentech, South San Francisco, California 94080, USA
| | - Saritha Kusam
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Cynthia Lam
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Juan Zhang
- Immunology, Genentech, South San Francisco, California 94080, USA
| | - Nataliya Popovych
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Elizabeth Helgason
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Allyn Schoeffler
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Surinder Jeet
- Immunology, Genentech, South San Francisco, California 94080, USA
| | | | - Lorna Kategaya
- Discovery Oncology, Genentech, South San Francisco, California 94080, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Robert J Newman
- Molecular Biology, Genentech, South San Francisco, California 94080, USA
| | - Keisuke Horikawa
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Debra Dugger
- Physiological Chemistry, Genentech, South San Francisco, California 94080, USA
| | - Wendy Sandoval
- Protein Chemistry, Genentech, South San Francisco, California 94080, USA
| | - Susmith Mukund
- Structural Biology, Genentech, South San Francisco, California 94080, USA
| | - Anuradha Zindal
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Flavius Martin
- Immunology, Genentech, South San Francisco, California 94080, USA
| | - Clifford Quan
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Jeffrey Tom
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Wayne J Fairbrother
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Michael Townsend
- Immunology, Genentech, South San Francisco, California 94080, USA
| | - Søren Warming
- Molecular Biology, Genentech, South San Francisco, California 94080, USA
| | - Jason DeVoss
- Immunology, Genentech, South San Francisco, California 94080, USA
| | - Jinfeng Liu
- Bioinformatics, Genentech, South San Francisco, California 94080, USA
| | - Erin Dueber
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Patrick Caplazi
- Pathology, Genentech, South San Francisco, California 94080, USA
| | - Wyne P Lee
- Immunology, Genentech, South San Francisco, California 94080, USA
| | - Christopher C Goodnow
- Immunogenomics Laboratory, Immunology Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Sydney, Australia
| | - Mercedesz Balazs
- Immunology, Genentech, South San Francisco, California 94080, USA
| | - Kebing Yu
- Protein Chemistry, Genentech, South San Francisco, California 94080, USA
| | - Ganesh Kolumam
- Molecular Biology, Genentech, South San Francisco, California 94080, USA
| | - Vishva M Dixit
- Physiological Chemistry, Genentech, South San Francisco, California 94080, USA
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380
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Tournillon AS, López I, Malbert-Colas L, Naski N, Olivares-Illana V, Fåhraeus R. The alternative translated MDMX(p60) isoform regulates MDM2 activity. Cell Cycle 2015; 14:449-58. [PMID: 25659040 PMCID: PMC4615104 DOI: 10.4161/15384101.2014.977081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Isoforms derived from alternative splicing, mRNA translation initiation or promoter usage extend the functional repertoire of the p53, p63 and p73 genes family and of their regulators MDM2 and MDMX. Here we show cap-independent translation of an N-terminal truncated isoform of hMDMX, hMDMXp60, which is initiated at the 7th AUG codon downstream of the initiation site for full length hMDMXFL at position +384. hMDMXp60 lacks the p53 binding motif but retains the RING domain and interacts with hMDM2 and hMDMXFL. hMDMXp60 shows higher affinity for hMDM2, as compared to hMDMXFL. In vitro data reveal a positive cooperative interaction between hMDMXp60 and hMDM2 and in cellulo data show that low levels of hMDMXp60 promote degradation of hMDM2 whereas higher levels stabilize hMDM2 and prevent hMDM2-mediated degradation of hMDMXFL. These results describe a novel alternatively translated hMDMX isoform that exhibits unique regulatory activity toward hMDM2 autoubiquitination. The data illustrate how the N-terminus of hMDMX regulates its C-terminal RING domain and the hMDM2 activity.
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Affiliation(s)
- Anne-Sophie Tournillon
- a Cibles Thérapeutiques, Equipe Labellisée la Ligue Contre le Cancer, Institut National de la Santé et de la Recherche Médicale UMR1162; Institut de Génétique Moléculaire , Université Paris 7 ; Hôpital St. Louis; Paris , France
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381
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Sánchez-Martín P, Romá-Mateo C, Viana R, Sanz P. Ubiquitin conjugating enzyme E2-N and sequestosome-1 (p62) are components of the ubiquitination process mediated by the malin–laforin E3-ubiquitin ligase complex. Int J Biochem Cell Biol 2015; 69:204-14. [DOI: 10.1016/j.biocel.2015.10.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/28/2015] [Accepted: 10/30/2015] [Indexed: 11/26/2022]
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382
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Mikami S, Nakaura M, Kawahara A, Mizoguchi T, Itoh M. Mindbomb 2 is dispensable for embryonic development and Notch signalling in zebrafish. Biol Open 2015; 4:1576-82. [PMID: 26519518 PMCID: PMC4728363 DOI: 10.1242/bio.014225] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Mindbomb E3 ubiquitin protein ligase (Mib) family of proteins, Mib1 and Mib2, are RING finger ubiquitin ligases that share specific substrates. Mib1 is known to play essential roles in Notch signalling by ubiquitinating Notch ligands in vivo. Conversely, the functions of Mib2 in vivo are not fully understood, although Mib2 ubiquitinates multiple substrates, including Notch ligands, in vitro. To determine the Notch-dependent and Notch-independent functions of Mib2 in vivo, we generated mutant alleles of zebrafish mib2 using transcription activator-like effector nucleases (TALENs). We found that mib2 homozygous mutants were viable and fertile. Notch-mediated functions, such as early neurogenesis, somitogenesis, and pigment cell development, were not affected in mib2 mutant embryos. The lack of Notch-deficient phenotypes in mib2 mutants was not due to compensation by a mib2 maternal gene product because mib2 maternal-zygotic mutants also did not exhibit a distinct phenotype. We also showed that Mib2 does not redundantly act with Mib1 because the genetic ablation of mib2 neither enhanced mibtfi91-null phenotypes nor did it alleviate antimorphic mibta52b phenotypes. Furthermore, the postulated Notch-independent roles of Mib2 in maintaining muscular integrity and N-methyl-D-aspartate receptor (NMDAR) activity were not evident: mib2 mutants did not show phenotypes different from that of the control embryos. These observations suggest that Mib2 is dispensable for embryonic development and does not have redundant functions with Mib1 in Notch signalling at least during early development stages in zebrafish. Summary: Mib2 is dispensable for embryonic development and does not have redundant functions with Mib1 in Notch signalling, at least during early development stages in zebrafish.
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Affiliation(s)
- Shohei Mikami
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
| | - Mizuki Nakaura
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
| | - Atsuo Kawahara
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Takamasa Mizoguchi
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
| | - Motoyuki Itoh
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
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383
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Li S, Liang YH, Mariano J, Metzger MB, Stringer DK, Hristova VA, Li J, Randazzo PA, Tsai YC, Ji X, Weissman AM. Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B. J Biol Chem 2015; 290:30225-39. [PMID: 26475854 DOI: 10.1074/jbc.m115.685867] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Indexed: 11/06/2022] Open
Abstract
RING proteins constitute the largest class of E3 ubiquitin ligases. Unlike most RINGs, AO7 (RNF25) binds the E2 ubiquitin-conjugating enzyme, UbcH5B (UBE2D2), with strikingly high affinity. We have defined, by co-crystallization, the distinctive means by which AO7 binds UbcH5B. AO7 contains a structurally unique UbcH5B binding region (U5BR) that is connected by an 11-amino acid linker to its RING domain, forming a clamp surrounding the E2. The U5BR interacts extensively with a region of UbcH5B that is distinct from both the active site and the RING-interacting region, referred to as the backside of the E2. An apparent paradox is that the high-affinity binding of the AO7 clamp to UbcH5B, which is dependent on the U5BR, decreases the rate of ubiquitination. We establish that this is a consequence of blocking the stimulatory, non-covalent, binding of ubiquitin to the backside of UbcH5B. Interestingly, when non-covalent backside ubiquitin binding cannot occur, the AO7 clamp now enhances the rate of ubiquitination. The high-affinity binding of the AO7 clamp to UbcH5B has also allowed for the co-crystallization of previously described and functionally important RING mutants at the RING-E2 interface. We show that mutations having marked effects on function only minimally affect the intermolecular interactions between the AO7 RING and UbcH5B, establishing a high degree of complexity in activation through the RING-E2 interface.
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Affiliation(s)
- Shengjian Li
- From the Laboratory of Protein Dynamics and Signaling
| | - Yu-He Liang
- Macromolecular Crystallography Laboratory, and
| | | | | | | | | | - Jess Li
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702 and
| | - Paul A Randazzo
- the Laboratory of Cell and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yien Che Tsai
- From the Laboratory of Protein Dynamics and Signaling
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, and
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384
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Lake CM, Nielsen RJ, Guo F, Unruh JR, Slaughter BD, Hawley RS. Vilya, a component of the recombination nodule, is required for meiotic double-strand break formation in Drosophila. eLife 2015; 4:e08287. [PMID: 26452093 PMCID: PMC4703084 DOI: 10.7554/elife.08287] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 10/08/2015] [Indexed: 01/25/2023] Open
Abstract
Meiotic recombination begins with the induction of programmed double-strand breaks (DSBs). In most organisms only a fraction of DSBs become crossovers. Here we report a novel meiotic gene, vilya, which encodes a protein with homology to Zip3-like proteins shown to determine DSB fate in other organisms. Vilya is required for meiotic DSB formation, perhaps as a consequence of its interaction with the DSB accessory protein Mei-P22, and localizes to those DSB sites that will mature into crossovers. In early pachytene Vilya localizes along the central region of the synaptonemal complex and to discrete foci. The accumulation of Vilya at foci is dependent on DSB formation. Immuno-electron microscopy demonstrates that Vilya is a component of recombination nodules, which mark the sites of crossover formation. Thus Vilya links the mechanism of DSB formation to either the selection of those DSBs that will become crossovers or to the actual process of crossing over.
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Affiliation(s)
- Cathleen M Lake
- Stowers Institute for Medical Research, Kansas City, United States
| | - Rachel J Nielsen
- Stowers Institute for Medical Research, Kansas City, United States
| | - Fengli Guo
- Stowers Institute for Medical Research, Kansas City, United States
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, United States
| | | | - R Scott Hawley
- Stowers Institute for Medical Research, Kansas City, United States.,Department of Molecular and Integrative Physiology, Kansas University Medical Center, Kansas City, United States
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385
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Phillips AH, Corn JE. Using protein motion to read, write, and erase ubiquitin signals. J Biol Chem 2015; 290:26437-44. [PMID: 26354440 DOI: 10.1074/jbc.r115.653675] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eukaryotes use a tiny protein called ubiquitin to send a variety of signals, most often by post-translationally attaching ubiquitins to substrate proteins and to each other, thereby forming polyubiquitin chains. A combination of biophysical, biochemical, and biological studies has shown that complex macromolecular dynamics are central to many aspects of ubiquitin signaling. This review focuses on how equilibrium fluctuations and coordinated motions of ubiquitin itself, the ubiquitin conjugation machinery, and deubiquitinating enzymes enable activity and regulation on many levels, with implications for how such a tiny protein can send so many signals.
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Affiliation(s)
- Aaron H Phillips
- From the Innovative Genomics Initiative, University of California, Berkeley, California 94702
| | - Jacob E Corn
- From the Innovative Genomics Initiative, University of California, Berkeley, California 94702
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386
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Grou CP, Pinto MP, Mendes AV, Domingues P, Azevedo JE. The de novo synthesis of ubiquitin: identification of deubiquitinases acting on ubiquitin precursors. Sci Rep 2015; 5:12836. [PMID: 26235645 PMCID: PMC4522658 DOI: 10.1038/srep12836] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 07/09/2015] [Indexed: 12/24/2022] Open
Abstract
Protein ubiquitination, a major post-translational modification in eukaryotes, requires an adequate pool of free ubiquitin. Cells maintain this pool by two pathways, both involving deubiquitinases (DUBs): recycling of ubiquitin from ubiquitin conjugates and processing of ubiquitin precursors synthesized de novo. Although many advances have been made in recent years regarding ubiquitin recycling, our knowledge on ubiquitin precursor processing is still limited, and questions such as when are these precursors processed and which DUBs are involved remain largely unanswered. Here we provide data suggesting that two of the four mammalian ubiquitin precursors, UBA52 and UBA80, are processed mostly post-translationally whereas the other two, UBB and UBC, probably undergo a combination of co- and post-translational processing. Using an unbiased biochemical approach we found that UCHL3, USP9X, USP7, USP5 and Otulin/Gumby/FAM105b are by far the most active DUBs acting on these precursors. The identification of these DUBs together with their properties suggests that each ubiquitin precursor can be processed in at least two different manners, explaining the robustness of the ubiquitin de novo synthesis pathway.
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Affiliation(s)
- Cláudia P Grou
- 1] Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal [2] Organelle Biogenesis and Function Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Manuel P Pinto
- 1] Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal [2] Organelle Biogenesis and Function Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Andreia V Mendes
- 1] Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal [2] Organelle Biogenesis and Function Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Pedro Domingues
- Mass Spectrometry Centre, UI-QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Jorge E Azevedo
- 1] Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal [2] Organelle Biogenesis and Function Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal [3] Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
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387
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Xie L, Lang-Mladek C, Richter J, Nigam N, Hauser MT. UV-B induction of the E3 ligase ARIADNE12 depends on CONSTITUTIVELY PHOTOMORPHOGENIC 1. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 93:18-28. [PMID: 25817546 PMCID: PMC4503874 DOI: 10.1016/j.plaphy.2015.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 03/20/2015] [Indexed: 05/05/2023]
Abstract
The UV-B inducible ARIADNE12 (ARI12) gene of Arabidopsis thaliana is a member of the RING-between-RING (RBR) family of E3 ubiquitin ligases for which a novel ubiquitination mechanism was identified in mammalian homologs. This RING-HECT hybrid mechanism needs a conserved cysteine which is replaced by serine in ARI12 and might affect the E3 ubiquitin ligase activity. We have shown that under photomorphogenic UV-B, ARI12 is a downstream target of the classical ultraviolet B (UV-B) UV Resistance Locus 8 (UVR8) pathway. However, under high fluence rate of UV-B ARI12 was induced independently of UVR8 and the UV-A/blue light and red/far-red photoreceptors. A key component of several light signaling pathways is Constitutively Photomorphogenic 1 (COP1). Upon UV-B COP1 is trapped in the nucleus through interaction with UVR8 permitting the activation of genes that regulate the biosynthesis of UV-B protective metabolites and growth adaptations. To clarify the role of COP1 in the regulation of ARI12 mRNA expression and ARI12 protein stability, localization and interaction with COP1 was assessed with and without UV-B. We found that COP1 controls ARI12 in white light, low and high fluence rate of UV-B. Furthermore we show that ARI12 is indeed an E3 ubiquitin ligase which is mono-ubiquitinated, a prerequisite for the RING-HECT hybrid mechanism. Finally, genetic analyses with transgenes expressing a genomic pmARI12:ARI12-GFP construct confirm the epistatic interaction between COP1 and ARI12 in growth responses to high fluence rate UV-B.
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Affiliation(s)
- Lisi Xie
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Christina Lang-Mladek
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Julia Richter
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Neha Nigam
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Marie-Theres Hauser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
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388
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Branigan E, Plechanovová A, Jaffray EG, Naismith JH, Hay RT. Structural basis for the RING-catalyzed synthesis of K63-linked ubiquitin chains. Nat Struct Mol Biol 2015; 22:597-602. [PMID: 26148049 PMCID: PMC4529489 DOI: 10.1038/nsmb.3052] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 06/02/2015] [Indexed: 11/17/2022]
Abstract
RING E3 ligase-catalyzed formation of K63-linked ubiquitin chains by the Ube2V2-Ubc13 E2 complex is required in many important biological processes. Here we report the structure of the RING-domain dimer of rat RNF4 in complex with a human Ubc13∼Ub conjugate and Ube2V2. The structure has captured Ube2V2 bound to the acceptor (priming) ubiquitin with K63 in a position favorable for attack on the linkage between Ubc13 and the donor (second) ubiquitin held in the active 'folded back' conformation by the RING domain of RNF4. We verified the interfaces identified in the structure by in vitro ubiquitination assays of site-directed mutants. To our knowledge, this represents the first view of synthesis of K63-linked ubiquitin chains in which both substrate ubiquitin and ubiquitin-loaded E2 are juxtaposed to allow E3 ligase-mediated catalysis.
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Affiliation(s)
- Emma Branigan
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Anna Plechanovová
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Ellis G Jaffray
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - James H Naismith
- 1] Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, UK. [2] State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
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389
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Yudina Z, Roa A, Johnson R, Biris N, de Souza Aranha Vieira DA, Tsiperson V, Reszka N, Taylor AB, Hart PJ, Demeler B, Diaz-Griffero F, Ivanov DN. RING Dimerization Links Higher-Order Assembly of TRIM5α to Synthesis of K63-Linked Polyubiquitin. Cell Rep 2015. [PMID: 26212332 DOI: 10.1016/j.celrep.2015.06.072] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Members of the tripartite motif (TRIM) protein family of RING E3 ubiquitin (Ub) ligases promote innate immune responses by catalyzing synthesis of polyubiquitin chains linked through lysine 63 (K63). Here, we investigate the mechanism by which the TRIM5α retroviral restriction factor activates Ubc13, the K63-linkage-specific E2. Structural, biochemical, and functional characterization of the TRIM5α:Ubc13-Ub interactions reveals that activation of the Ubc13-Ub conjugate requires dimerization of the TRIM5α RING domain. Our data explain how higher-order oligomerization of TRIM5α, which is promoted by the interaction with the retroviral capsid, enhances the E3 Ub ligase activity of TRIM5α and contributes to its antiretroviral function. This E3 mechanism, in which RING dimerization is transient and depends on the interaction of the TRIM protein with the ligand, is likely to be conserved in many members of the TRIM family and may have evolved to facilitate recognition of repetitive epitope patterns associated with infection.
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Affiliation(s)
- Zinaida Yudina
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Amanda Roa
- Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Rory Johnson
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Nikolaos Biris
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | | | - Vladislav Tsiperson
- Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Natalia Reszka
- Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Alexander B Taylor
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA; X-ray Crystallography Core Laboratory, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - P John Hart
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA; X-ray Crystallography Core Laboratory, University of Texas Health Science Center, San Antonio, TX 78229, USA; Geriatric Research, Education, and Clinical Center, Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX 78229, USA
| | - Borries Demeler
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Felipe Diaz-Griffero
- Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Dmitri N Ivanov
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA.
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390
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Vittal V, Stewart MD, Brzovic PS, Klevit RE. Regulating the Regulators: Recent Revelations in the Control of E3 Ubiquitin Ligases. J Biol Chem 2015; 290:21244-51. [PMID: 26187467 DOI: 10.1074/jbc.r115.675165] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Since its discovery as a post-translational signal for protein degradation, our understanding of ubiquitin (Ub) has vastly evolved. Today, we recognize that the role of Ub signaling is expansive and encompasses diverse processes including cell division, the DNA damage response, cellular immune signaling, and even organismal development. With such a wide range of functions comes a wide range of regulatory mechanisms that control the activity of the ubiquitylation machinery. Ub attachment to substrates occurs through the sequential action of three classes of enzymes, E1s, E2s, and E3s. In humans, there are 2 E1s, ∼ 35 E2s, and hundreds of E3s that work to attach Ub to thousands of cellular substrates. Regulation of ubiquitylation can occur at each stage of the stepwise Ub transfer process, and substrates can also impact their own modification. Recent studies have revealed elegant mechanisms that have evolved to control the activity of the enzymes involved. In this minireview, we highlight recent discoveries that define some of the various mechanisms by which the activities of E3-Ub ligases are regulated.
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Affiliation(s)
- Vinayak Vittal
- From the Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742
| | - Mikaela D Stewart
- From the Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742
| | - Peter S Brzovic
- From the Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742
| | - Rachel E Klevit
- From the Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742
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391
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Kato A, Komatsu K. RNF20-SNF2H Pathway of Chromatin Relaxation in DNA Double-Strand Break Repair. Genes (Basel) 2015; 6:592-606. [PMID: 26184323 PMCID: PMC4584319 DOI: 10.3390/genes6030592] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/25/2023] Open
Abstract
Rapid progress in the study on the association of histone modifications with chromatin remodeling factors has broadened our understanding of chromatin dynamics in DNA transactions. In DNA double-strand break (DSB) repair, the well-known mark of histones is the phosphorylation of the H2A variant, H2AX, which has been used as a surrogate marker of DSBs. The ubiquitylation of histone H2B by RNF20 E3 ligase was recently found to be a DNA damage-induced histone modification. This modification is required for DSB repair and regulated by a distinctive pathway from that of histone H2AX phosphorylation. Moreover, the connection between H2B ubiquitylation and the chromatin remodeling activity of SNF2H has been elucidated. In this review, we summarize the current knowledge of RNF20-mediated processes and the molecular link to H2AX-mediated processes during DSB repair.
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Affiliation(s)
- Akihiro Kato
- Division of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Yoshida-konoecho, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Kenshi Komatsu
- Division of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Yoshida-konoecho, Sakyo-ku, Kyoto 606-8501, Japan.
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392
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Taherbhoy AM, Huang OW, Cochran AG. BMI1–RING1B is an autoinhibited RING E3 ubiquitin ligase. Nat Commun 2015; 6:7621. [DOI: 10.1038/ncomms8621] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 05/26/2015] [Indexed: 01/21/2023] Open
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393
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Jiang S, Park DW, Gao Y, Ravi S, Darley-Usmar V, Abraham E, Zmijewski JW. Participation of proteasome-ubiquitin protein degradation in autophagy and the activation of AMP-activated protein kinase. Cell Signal 2015; 27:1186-97. [PMID: 25728513 PMCID: PMC4380640 DOI: 10.1016/j.cellsig.2015.02.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/04/2015] [Accepted: 02/23/2015] [Indexed: 01/05/2023]
Abstract
Although activation of the AMP-activated protein kinase (AMPK) as well as of ubiquitin/proteasome degradative pathways play an essential role in the preservation of metabolic homeostasis, little is known concerning interactions between protein turnover and AMPK activity. In the present studies, we found that inhibition of the 26S proteasome resulted in rapid activation of AMPK in macrophages, epithelial and endothelial cells. This was associated with increased levels of non-degraded Ub-protein conjugates, in both cytosolic and mitochondrial fractions. Selective inhibitors of ubiquitination or siRNA-dependent knockdown of Ub-ligase E1 diminished AMPK activation in cells treated with MG132, a 26S proteasome inhibitor. In addition to inhibition of AMPK activation by Ub-ligase E1 inhibitors, deficiency in Park2 mitochondria-associated Ub-ligase E3 also reduced AMPK activation upon dissipation of mitochondrial membrane potential (Δψm). Accumulation of Ub-proteins was correlated with decreases in cellular bioenergetics, including mitochondria oxidative phosphorylation, and an increase in ROS formation. Antioxidants, such as N-acetyl-L-cysteine or mitochondria-targeted MitoTEMPO, effectively diminished MG132-induced AMPK activation. Glucose-dependent regulation of AMPK or AMPK-mediated autophagy was modulated by alterations in intracellular levels of Ub-protein conjugates. Our results indicate that accumulation of ubiquitinated proteins alter cellular bioenergetics and redox status, leading to AMPK activation.
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Affiliation(s)
- Shaoning Jiang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA
| | - Dae Won Park
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA; Division of Infectious Diseases, Korea University Ansan Hospital, Ansan 425-707, Republic of Korea
| | - Yong Gao
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA
| | - Saranya Ravi
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA; Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA
| | - Victor Darley-Usmar
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA; Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA
| | - Edward Abraham
- Office of the Dean, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jaroslaw W Zmijewski
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA; Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA.
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394
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Wright FA, Lu JP, Sliter DA, Dupré N, Rouleau GA, Wojcikiewicz RJH. A Point Mutation in the Ubiquitin Ligase RNF170 That Causes Autosomal Dominant Sensory Ataxia Destabilizes the Protein and Impairs Inositol 1,4,5-Trisphosphate Receptor-mediated Ca2+ Signaling. J Biol Chem 2015; 290:13948-57. [PMID: 25882839 DOI: 10.1074/jbc.m115.655043] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Indexed: 12/11/2022] Open
Abstract
RNF170 is an endoplasmic reticulum membrane ubiquitin ligase that contributes to the ubiquitination of activated inositol 1,4,5-trisphosphate (IP3) receptors, and also, when point mutated (arginine to cysteine at position 199), causes autosomal dominant sensory ataxia (ADSA), a disease characterized by neurodegeneration in the posterior columns of the spinal cord. Here we demonstrate that this point mutation inhibits RNF170 expression and signaling via IP3 receptors. Inhibited expression of mutant RNF170 was seen in cells expressing exogenous RNF170 constructs and in ADSA lymphoblasts, and appears to result from enhanced RNF170 autoubiquitination and proteasomal degradation. The basis for these effects was probed via additional point mutations, revealing that ionic interactions between charged residues in the transmembrane domains of RNF170 are required for protein stability. In ADSA lymphoblasts, platelet-activating factor-induced Ca(2+) mobilization was significantly impaired, whereas neither Ca(2+) store content, IP3 receptor levels, nor IP3 production were altered, indicative of a functional defect at the IP3 receptor locus, which may be the cause of neurodegeneration. CRISPR/Cas9-mediated genetic deletion of RNF170 showed that RNF170 mediates the addition of all of the ubiquitin conjugates known to become attached to activated IP3 receptors (monoubiquitin and Lys(48)- and Lys(63)-linked ubiquitin chains), and that wild-type and mutant RNF170 have apparently identical ubiquitin ligase activities toward IP3 receptors. Thus, the Ca(2+) mobilization defect seen in ADSA lymphoblasts is apparently not due to aberrant IP3 receptor ubiquitination. Rather, the defect likely reflects abnormal ubiquitination of other substrates, or adaptation to the chronic reduction in RNF170 levels.
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Affiliation(s)
- Forrest A Wright
- From the Department of Pharmacology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Justine P Lu
- From the Department of Pharmacology, SUNY Upstate Medical University, Syracuse, New York 13210
| | | | - Nicolas Dupré
- the Neuromuscular and Neurogenetic Disease Clinic, CHU de Québec, Laval University, Quebec City, Quebec G1J 1Z4, Canada, and
| | - Guy A Rouleau
- the Montreal Neurological Institute and Hospital and Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 2B4, Canada
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395
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Lutz-Nicoladoni C, Wolf D, Sopper S. Modulation of Immune Cell Functions by the E3 Ligase Cbl-b. Front Oncol 2015; 5:58. [PMID: 25815272 PMCID: PMC4356231 DOI: 10.3389/fonc.2015.00058] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/24/2015] [Indexed: 01/10/2023] Open
Abstract
Maintenance of immunological tolerance is a critical hallmark of the immune system. Several signaling checkpoints necessary to balance activating and inhibitory input to immune cells have been described so far, among which the E3 ligase Cbl-b appears to be a central player. Cbl-b is expressed in all leukocyte subsets and regulates several signaling pathways in T cells, NK cells, B cells, and different types of myeloid cells. In most cases, Cbl-b negatively regulates activation signals through antigen or pattern recognition receptors and co-stimulatory molecules. In line with this function, cblb-deficient immune cells display lower activation thresholds and cblb knockout mice spontaneously develop autoimmunity and are highly susceptible to experimental autoimmunity. Interestingly, genetic association studies link CBLB-polymorphisms with autoimmunity also in humans. Vice versa, the increased activation potential of cblb-deficient cells renders them more potent to fight against malignancies or infections. Accordingly, several reports have shown that cblb knockout mice reject tumors, which mainly depends on cytotoxic T and NK cells. Thus, targeting Cbl-b may be an interesting strategy to enhance anti-cancer immunity. In this review, we summarize the findings on the molecular function of Cbl-b in different cell types and illustrate the potential of Cbl-b as target for immunomodulatory therapies.
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Affiliation(s)
- Christina Lutz-Nicoladoni
- Department of Hematology and Oncology, Medical University Innsbruck , Innsbruck , Austria ; Tumor Immunology Laboratory, Tyrolean Cancer Research Institute , Innsbruck , Austria
| | - Dominik Wolf
- Medical Clinic III for Oncology, Haematology and Rheumatology, University Clinic Bonn (UKB) , Bonn , Germany
| | - Sieghart Sopper
- Department of Hematology and Oncology, Medical University Innsbruck , Innsbruck , Austria ; Tumor Immunology Laboratory, Tyrolean Cancer Research Institute , Innsbruck , Austria
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396
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Mitsiades CS. Therapeutic landscape of carfilzomib and other modulators of the ubiquitin-proteasome pathway. J Clin Oncol 2015; 33:782-5. [PMID: 25605842 PMCID: PMC4517049 DOI: 10.1200/jco.2014.55.5748] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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397
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Distinct activation of an E2 ubiquitin-conjugating enzyme by its cognate E3 ligases. Proc Natl Acad Sci U S A 2015; 112:E625-32. [PMID: 25646477 DOI: 10.1073/pnas.1415621112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A significant portion of ubiquitin (Ub)-dependent cellular protein quality control takes place at the endoplasmic reticulum (ER) in a process termed "ER-associated degradation" (ERAD). Yeast ERAD employs two integral ER membrane E3 Ub ligases: Hrd1 (also termed "Der3") and Doa10, which recognize a distinct set of substrates. However, both E3s bind to and activate a common E2-conjugating enzyme, Ubc7. Here we describe a novel feature of the ERAD system that entails differential activation of Ubc7 by its cognate E3s. We found that residues within helix α2 of Ubc7 that interact with donor Ub were essential for polyUb conjugation. Mutagenesis of these residues inhibited the in vitro activity of Ubc7 by preventing the conjugation of donor Ub to the acceptor. Unexpectedly, Ub chain formation by mutant Ubc7 was restored selectively by the Hrd1 RING domain but not by the Doa10 RING domain. In agreement with the in vitro data, Ubc7 α2 helix mutations selectively impaired the in vivo degradation of Doa10 substrates but had no apparent effect on the degradation of Hrd1 substrates. To our knowledge, this is the first example of distinct activation requirements of a single E2 by two E3s. We propose a model in which the RING domain activates Ub transfer by stabilizing a transition state determined by noncovalent interactions between the α2 helix of Ubc7 and Ub and that this transition state may be stabilized further by some E3 ligases, such as Hrd1, through additional interactions outside the RING domain.
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398
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Huang SY, Chang CF, Fang PJ, Naik MT, Güntert P, Shih HM, Huang TH. The RING domain of human promyelocytic leukemia protein (PML). JOURNAL OF BIOMOLECULAR NMR 2015; 61:173-180. [PMID: 25627356 DOI: 10.1007/s10858-015-9901-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 01/19/2015] [Indexed: 06/04/2023]
Affiliation(s)
- Shu-Yu Huang
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, 11529, Taiwan, ROC
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399
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Figueiredo-Pereira ME, Rockwell P, Schmidt-Glenewinkel T, Serrano P. Neuroinflammation and J2 prostaglandins: linking impairment of the ubiquitin-proteasome pathway and mitochondria to neurodegeneration. Front Mol Neurosci 2015; 7:104. [PMID: 25628533 PMCID: PMC4292445 DOI: 10.3389/fnmol.2014.00104] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 12/17/2014] [Indexed: 12/13/2022] Open
Abstract
The immune response of the CNS is a defense mechanism activated upon injury to initiate repair mechanisms while chronic over-activation of the CNS immune system (termed neuroinflammation) may exacerbate injury. The latter is implicated in a variety of neurological and neurodegenerative disorders such as Alzheimer and Parkinson diseases, amyotrophic lateral sclerosis, multiple sclerosis, traumatic brain injury, HIV dementia, and prion diseases. Cyclooxygenases (COX-1 and COX-2), which are key enzymes in the conversion of arachidonic acid into bioactive prostanoids, play a central role in the inflammatory cascade. J2 prostaglandins are endogenous toxic products of cyclooxygenases, and because their levels are significantly increased upon brain injury, they are actively involved in neuronal dysfunction induced by pro-inflammatory stimuli. In this review, we highlight the mechanisms by which J2 prostaglandins (1) exert their actions, (2) potentially contribute to the transition from acute to chronic inflammation and to the spreading of neuropathology, (3) disturb the ubiquitin-proteasome pathway and mitochondrial function, and (4) contribute to neurodegenerative disorders such as Alzheimer and Parkinson diseases, and amyotrophic lateral sclerosis, as well as stroke, traumatic brain injury (TBI), and demyelination in Krabbe disease. We conclude by discussing the therapeutic potential of targeting the J2 prostaglandin pathway to prevent/delay neurodegeneration associated with neuroinflammation. In this context, we suggest a shift from the traditional view that cyclooxygenases are the most appropriate targets to treat neuroinflammation, to the notion that J2 prostaglandin pathways and other neurotoxic prostaglandins downstream from cyclooxygenases, would offer significant benefits as more effective therapeutic targets to treat chronic neurodegenerative diseases, while minimizing adverse side effects.
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Affiliation(s)
- Maria E Figueiredo-Pereira
- Department of Biological Sciences, Hunter College, The Graduate School and University Center, City University of New York New York, NY, USA
| | - Patricia Rockwell
- Department of Biological Sciences, Hunter College, The Graduate School and University Center, City University of New York New York, NY, USA
| | - Thomas Schmidt-Glenewinkel
- Department of Biological Sciences, Hunter College, The Graduate School and University Center, City University of New York New York, NY, USA
| | - Peter Serrano
- Department of Psychology, Hunter College, The Graduate School and University Center, City University of New York New York, NY, USA
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400
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Niewerth D, Jansen G, Assaraf YG, Zweegman S, Kaspers GJ, Cloos J. Molecular basis of resistance to proteasome inhibitors in hematological malignancies. Drug Resist Updat 2015; 18:18-35. [DOI: 10.1016/j.drup.2014.12.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 11/28/2014] [Accepted: 12/03/2014] [Indexed: 12/25/2022]
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