1
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Min Y, Yu H, Li Q. Transcriptional and post-translational regulation of MITF mediated by bHLH domain during the melanogenesis and melanocyte proliferation in Crassostrea gigas. Int J Biol Macromol 2024; 266:131138. [PMID: 38547943 DOI: 10.1016/j.ijbiomac.2024.131138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/07/2024] [Accepted: 03/23/2024] [Indexed: 04/06/2024]
Abstract
Melanocyte differentiation is orchestrated by the master regulator transcription factor MITF. However, its ability to discern distinct binding sites linked to effective gene regulation remains poorly understood. This study aims to assess how co-activator acetyltransferase interacts with MITF to modulate their related lysine action, thereby mediating downstream gene regulation, including DNA affinity, stability, transcriptional activity, particularly in the process of shell pigmentation. Here, we have demonstrated that the CgMITF protein can be acetylated, further enabling selective amplification of the melanocyte maturation program. Collaboration with transcriptional co-regulator p300 advances MITF dynamically interplay with downstream targeted gene promoters. We have established that MITF activation was partially dependent on the bHLH domain, which was well conserved across species. The bHLH domain contained conserved lysine residues, including K6 and K43, which interacted with the E-box motif of downstream targeted-genes. Mutations at K6 and K43 lead to a decrease in the binding affinity of the E-box motif. CgMITF protein bound to the E-box motif within the promoter regions of the tyrosinase-related genes, contributing to melanogenesis, and also interacted with the E-box motif within the TBX2 promoter regions, associated with melanocyte proliferation. We elucidated how the bHLH domain links the transcriptional regulation and acetylation modifications in the melanocyte development in C. gigas.
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Affiliation(s)
- Yue Min
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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2
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Arnesen T, Kjosås I, McTiernan N. Protein N-terminal acetylation is entering the degradation end game. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00723-1. [PMID: 38519774 DOI: 10.1038/s41580-024-00723-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Affiliation(s)
- Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, Bergen, Norway.
| | - Ine Kjosås
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Nina McTiernan
- Department of Biomedicine, University of Bergen, Bergen, Norway.
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3
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van de Kooij B, de Vries E, Rooswinkel RW, Janssen GMC, Kok FK, van Veelen PA, Borst J. N-terminal acetylation can stabilize proteins independent of their ubiquitination. Sci Rep 2023; 13:5333. [PMID: 37005459 PMCID: PMC10067848 DOI: 10.1038/s41598-023-32380-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/27/2023] [Indexed: 04/04/2023] Open
Abstract
The majority of proteins in mammalian cells are modified by covalent attachment of an acetyl-group to the N-terminus (Nt-acetylation). Paradoxically, Nt-acetylation has been suggested to inhibit as well as to promote substrate degradation. Contrasting these findings, proteome-wide stability measurements failed to detect any correlation between Nt-acetylation status and protein stability. Accordingly, by analysis of protein stability datasets, we found that predicted Nt-acetylation positively correlates with protein stability in case of GFP, but this correlation does not hold for the entire proteome. To further resolve this conundrum, we systematically changed the Nt-acetylation and ubiquitination status of model substrates and assessed their stability. For wild-type Bcl-B, which is heavily modified by proteasome-targeting lysine ubiquitination, Nt-acetylation did not correlate with protein stability. For a lysine-less Bcl-B mutant, however, Nt-acetylation correlated with increased protein stability, likely due to prohibition of ubiquitin conjugation to the acetylated N-terminus. In case of GFP, Nt-acetylation correlated with increased protein stability, as predicted, but our data suggest that Nt-acetylation does not affect GFP ubiquitination. Similarly, in case of the naturally lysine-less protein p16, Nt-acetylation correlated with protein stability, regardless of ubiquitination on its N-terminus or on an introduced lysine residue. A direct effect of Nt-acetylation on p16 stability was supported by studies in NatB-deficient cells. Together, our studies argue that Nt-acetylation can stabilize proteins in human cells in a substrate-specific manner, by competition with N-terminal ubiquitination, but also by other mechanisms that are independent of protein ubiquitination status.
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Affiliation(s)
- Bert van de Kooij
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Department of Medical Oncology, University Medical Center Groningen, Groningen, the Netherlands.
| | - Evert de Vries
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Immunology and Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Rogier W Rooswinkel
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Frédérique K Kok
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Leiden Academic Centre for Drug Research, Leiden, the Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jannie Borst
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Department of Immunology and Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands.
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4
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Narooka AR, Apte A, Yadav P, Murillo JR, Goto-Silva L, Junqueira M, Datta S. EhRho6 mediated actin degradation in Entamoeba histolytica is associated with compromised pathogenicity. Mol Microbiol 2022; 117:1121-1137. [PMID: 35324049 DOI: 10.1111/mmi.14896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/14/2022] [Accepted: 03/16/2022] [Indexed: 11/27/2022]
Abstract
Entamoeba histolytica causes amoebiasis which is a major health concern in developing countries. E. histolytica pathogenicity has been implicated to a large repertoire of small GTPases which switch between the inactive GDP bound state and the active GTP bound state with the help of guanine nucleotide exchange factors (GEFs) and GTPase activating protein (GAPs). Rho family of small GTPases are well known to modulate the actin cytoskeletal dynamics which plays a major role in E. histolytica pathogenicity. Here we report an atypical amoebic RhoGEF, and its preferred substrate EhRho6, which, upon overexpression abrogated the pathogenic behavior of the amoeba such as adhesion to host cell, monolayer destruction, erythrophagocytosis, and formation of actin dots. A causative immunoblot analysis revealed actin degradation in the EhRho6 overexpressing trophozoites that could be inhibited by blocking the amoebic proteasomal pathway. A careful analysis of the results from a previously published transcriptomics study, in conjunction with our observations, led to the identification of a clade of Rho GTPases in this pathogenic amoeba which we hypothesize to have implications during the amoebic encystation.
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Affiliation(s)
- Anil Raj Narooka
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Achala Apte
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Pooja Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Jimmy Rodriguez Murillo
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Livia Goto-Silva
- D'Or Institute for Research and Education (IDOR), Rua Diniz Cordeiro, 30 - Botafogo, Rio de Janeiro, RJ, Brazil
| | - Magno Junqueira
- Laboratório de Espectrometria de Massa Biológica - LEMB, do Departamento de Bioquímica do Instituto de Química UFRJ, Rio de Janeiro, RJ, Brasil
| | - Sunando Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
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5
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Boontem P, Yamashima T. Hydroxynonenal causes Langerhans cell degeneration in the pancreas of Japanese macaque monkeys. PLoS One 2021; 16:e0245702. [PMID: 34748564 PMCID: PMC8575276 DOI: 10.1371/journal.pone.0245702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 09/18/2021] [Indexed: 11/21/2022] Open
Abstract
Background For their functions of insulin biosynthesis and glucose- and fatty acid- mediated insulin secretion, Langerhans β-cells require an intracellular milieu rich in oxygen. This requirement makes β-cells, with their constitutively low antioxidative defense, susceptible to the oxidative stress. Although much progress has been made in identifying its molecular basis in experimental systems, whether the oxidative stress due to excessive fatty acids plays a crucial role in the Langerhans cell degeneration in primates is still debated. Methods Focusing on Hsp70.1, which has dual functions as molecular chaperone and lysosomal stabilizer, the mechanism of lipotoxicity to Langerhans cells was studied using macaque monkeys after the consecutive injections of the lipid peroxidation product ‘hydroxynonenal’. Based on the ‘calpain-cathepsin hypothesis’ formulated in 1998, calpain activation, Hsp70.1 cleavage, and lysosomal integrity were studied by immunofluorescence histochemistry, electron microscopy, and Western blotting. Results Light microscopy showed more abundant vacuole formation in the hydroxynonenal-treated islet cells than the control cells. Electron microscopy showed that vacuolar changes, which were identified as enlarged rough ER, occurred mainly in β-cells followed by δ-cells. Intriguingly, both cell types showed a marked decrease in insulin and somatostatin granules. Furthermore, they exhibited marked increases in peroxisomes, autophagosomes/autolysosomes, lysosomal and peroxisomal membrane rupture/permeabilization, and mitochondrial degeneration. Disrupted peroxisomes were often localized in the close vicinity of degenerating mitochondria or autolysosomes. Immunofluorescence histochemical analysis showed an increased co-localization of activated μ-calpain and Hsp70.1 with the extralysosomal release of cathepsin B. Western blotting showed increases in μ-calpain activation, Hsp70.1 cleavage, and expression of the hydroxynonenal receptor GPR109A. Conclusions Taken together, these data implicate hydroxynonenal in both oxidation of Hsp70.1 and activation of μ-calpain. The calpain-mediated cleavage of the carbonylated Hsp70.1, may cause lysosomal membrane rupture/permeabilization. The low defense of primate Langerhans cells against hydroxynonenal and peroxisomally-generated hydrogen peroxide, was presumably overwhelmed to facilitate cell degeneration.
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Affiliation(s)
| | - Tetsumori Yamashima
- Departments of Cell Metabolism and Nutrition, Kanazawa, Japan
- Psychiatry and Behavioral Science, Kanazawa, Japan
- * E-mail:
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6
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Kashina AS. Regulation of actin isoforms in cellular and developmental processes. Semin Cell Dev Biol 2020; 102:113-121. [PMID: 32001148 DOI: 10.1016/j.semcdb.2019.12.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022]
Abstract
Actin is one of the most abundant and essential intracellular proteins that mediates nearly every form of cellular movement and underlies such key processes as embryogenesis, tissue integrity, cell division and contractility of all types of muscle and non-muscle cells. In mammals, actin is represented by six isoforms, which are encoded by different genes but produce proteins that are 95-99 % identical to each other. The six actin genes have vastly different functions in vivo, and the small amino acid differences between the proteins they encode are rigorously maintained through evolution, but the underlying differences behind this distinction, as well as the importance of specific amino acid sequences for each actin isoform, are not well understood. This review summarizes different levels of actin isoform-specific regulation in cellular and developmental processes, starting with the nuclear actin's role in transcription, and covering the gene-level, mRNA-level, and protein-level regulation, with a special focus on mammalian actins in non-muscle cells.
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Affiliation(s)
- Anna S Kashina
- University of Pennsylvania, Philadelphia, PA, 19104, United States.
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7
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Fernández-Nogales M, Lucas JJ. Altered Levels and Isoforms of Tau and Nuclear Membrane Invaginations in Huntington's Disease. Front Cell Neurosci 2020; 13:574. [PMID: 32009905 PMCID: PMC6978886 DOI: 10.3389/fncel.2019.00574] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/12/2019] [Indexed: 12/13/2022] Open
Abstract
Since the early reports of neurofibrillary Tau pathology in brains of some Huntington’s disease (HD) patients, mounting evidence of multiple alterations of Tau in HD brain tissue has emerged in recent years. Such Tau alterations range from increased total levels, imbalance of isoforms generated by alternative splicing (increased 4R-/3R-Tau ratio) or by post-translational modifications such as hyperphosphorylation or truncation. Besides, the detection in HD brains of a new Tau histopathological hallmark known as Tau nuclear rods (TNRs) or Tau-positive nuclear indentations (TNIs) led to propose HD as a secondary Tauopathy. After their discovery in HD brains, TNIs have also been reported in hippocampal neurons of early Braak stage AD cases and in frontal and temporal cortical neurons of FTD-MAPT cases due to the intronic IVS10+16 mutation in the Tau gene (MAPT) which results in an increased 4R-/3R-Tau ratio similar to that observed in HD. TNIs are likely pathogenic for contributing to the disturbed nucleocytoplasmic transport observed in HD. A key question is whether correction of any of the mentioned Tau alterations might have positive therapeutic implications for HD. The beneficial effect of decreasing Tau expression in HD mouse models clearly implicates Tau in HD pathogenesis. Such beneficial effect might be exerted by diminishing the excess total levels of Tau or specifically by diminishing the excess 4R-Tau, as well as any of their downstream effects. In any case, since gene silencing drugs are under development to attenuate both Huntingtin (HTT) expression for HD and MAPT expression for FTD-MAPT, it is conceivable that the combined therapy in HD patients might be more effective than HTT silencing alone.
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Affiliation(s)
| | - José J Lucas
- Centro de Biología Molecular Severo Ochoa (CBMSO)(CSIC-UAM), Madrid, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
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8
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Hong H, Cai Y, Zhang S, Ding H, Wang H, Han A. Molecular Basis of Substrate Specific Acetylation by N-Terminal Acetyltransferase NatB. Structure 2017; 25:641-649.e3. [PMID: 28380339 DOI: 10.1016/j.str.2017.03.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/24/2017] [Accepted: 03/09/2017] [Indexed: 11/29/2022]
Abstract
The NatB N-terminal acetyltransferase specifically acetylates the N-terminal group of substrate protein peptides starting with Met-Asp/Glu/Asn/Gln. How NatB recognizes and acetylates these substrates remains unknown. Here, we report crystal structures of a NatB holoenzyme from Candida albicans in the presence of its co-factor CoA and substrate peptides. The auxiliary subunit Naa25 of NatB forms a horseshoe-like deck to hold specifically its catalytic subunit Naa20. The first two amino acids Met and Asp of a substrate peptide mediate the major interactions with the active site in the Naa20 subunit. The hydrogen bonds between the substrate Asp and pocket residues of Naa20 are essential to determine the NatB substrate specificity. Moreover, a hydrogen bond between the amino group of the substrate Met and a carbonyl group in the Naa20 active site directly anchors the substrate toward acetyl-CoA. Together, these structures define a unique molecular mechanism of specific N-terminal acetylation acted by NatB.
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Affiliation(s)
- Haiyan Hong
- State Key Laboratory for Cellular Stress Biology, Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Yongfei Cai
- State Key Laboratory for Cellular Stress Biology, Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Shijun Zhang
- State Key Laboratory for Cellular Stress Biology, Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Hongyan Ding
- State Key Laboratory for Cellular Stress Biology, Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Haitao Wang
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Aidong Han
- State Key Laboratory for Cellular Stress Biology, Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China.
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9
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Cohen-Kaplan V, Livneh I, Avni N, Fabre B, Ziv T, Kwon YT, Ciechanover A. p62- and ubiquitin-dependent stress-induced autophagy of the mammalian 26S proteasome. Proc Natl Acad Sci U S A 2016; 113:E7490-E7499. [PMID: 27791183 PMCID: PMC5127335 DOI: 10.1073/pnas.1615455113] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ubiquitin-proteasome system and autophagy are the two main proteolytic systems involved in, among other functions, the maintenance of cell integrity by eliminating misfolded and damaged proteins and organelles. Both systems remove their targets after their conjugation with ubiquitin. An interesting, yet incompletely understood problem relates to the fate of the components of the two systems. Here we provide evidence that amino acid starvation enhances polyubiquitination on specific sites of the proteasome, a modification essential for its targeting to the autophagic machinery. The uptake of the ubiquitinated proteasome is mediated by its interaction with the ubiquitin-associated domain of p62/SQSTM1, a process that also requires interaction with LC3. Importantly, deletion of the PB1 domain of p62, which is important for the targeting of ubiquitinated substrates to the proteasome, has no effect on stress-induced autophagy of this proteolytic machinery, suggesting that the domain of p62 that binds to the proteasome determines the function of p62 in either targeting substrates to the proteasome or targeting the proteasome to autophagy.
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Affiliation(s)
- Victoria Cohen-Kaplan
- Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109602, Israel
| | - Ido Livneh
- Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109602, Israel
| | - Noa Avni
- Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109602, Israel
| | - Bertrand Fabre
- Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109602, Israel
| | - Tamar Ziv
- Smoler Proteomic Center and Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yong Tae Kwon
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea
| | - Aaron Ciechanover
- Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109602, Israel;
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea
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10
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Tooley JG, Schaner Tooley CE. New roles for old modifications: emerging roles of N-terminal post-translational modifications in development and disease. Protein Sci 2014; 23:1641-9. [PMID: 25209108 DOI: 10.1002/pro.2547] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 09/08/2014] [Indexed: 01/07/2023]
Abstract
The importance of internal post-translational modification (PTM) in protein signaling and function has long been known and appreciated. However, the significance of the same PTMs on the alpha amino group of N-terminal amino acids has been comparatively understudied. Historically considered static regulators of protein stability, additional functional roles for N-terminal PTMs are now beginning to be elucidated. New findings show that N-terminal methylation, along with N-terminal acetylation, is an important regulatory modification with significant roles in development and disease progression. There are also emerging studies on the enzymology and functional roles of N-terminal ubiquitylation and N-terminal propionylation. Here, will discuss the recent advances in the functional studies of N-terminal PTMs, recount the new N-terminal PTMs being identified, and briefly examine the possibility of dynamic N-terminal PTM exchange.
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Affiliation(s)
- John G Tooley
- Department of Biochemistry and Molecular Biology, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, Kentucky
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11
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Jiang Y, Pore SK, Lee JH, Sriram S, Mai BK, Han DH, Agarwalla P, Zakrzewska A, Kim Y, Banerjee R, Lee SH, Lee MJ. Characterization of mammalian N-degrons and development of heterovalent inhibitors of the N-end rule pathway. Chem Sci 2013. [DOI: 10.1039/c3sc51059j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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12
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Sriram SM, Kim BY, Kwon YT. The N-end rule pathway: emerging functions and molecular principles of substrate recognition. Nat Rev Mol Cell Biol 2011; 12:735-47. [PMID: 22016057 DOI: 10.1038/nrm3217] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The N-end rule defines the protein-destabilizing activity of a given amino-terminal residue and its post-translational modification. Since its discovery 25 years ago, the pathway involved in the N-end rule has been thought to target only a limited set of specific substrates of the ubiquitin-proteasome system. Recent studies have provided insights into the components, substrates, functions and structural basis of substrate recognition. The N-end rule pathway is now emerging as a major cellular proteolytic system, in which the majority of proteins are born with or acquire specific N-terminal degradation determinants through protein-specific or global post-translational modifications.
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Affiliation(s)
- Shashikanth M Sriram
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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13
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Dougan DA, Micevski D, Truscott KN. The N-end rule pathway: from recognition by N-recognins, to destruction by AAA+proteases. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:83-91. [PMID: 21781991 DOI: 10.1016/j.bbamcr.2011.07.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 07/03/2011] [Accepted: 07/06/2011] [Indexed: 11/26/2022]
Abstract
Intracellular proteolysis is a tightly regulated process responsible for the targeted removal of unwanted or damaged proteins. The non-lysosomal removal of these proteins is performed by processive enzymes, which belong to the AAA+superfamily, such as the 26S proteasome and Clp proteases. One important protein degradation pathway, that is common to both prokaryotes and eukaryotes, is the N-end rule. In this pathway, proteins bearing a destabilizing amino acid residue at their N-terminus are degraded either by the ClpAP protease in bacteria, such as Escherichia coli or by the ubiquitin proteasome system in the eukaryotic cytoplasm. A suite of enzymes and other molecular components are also required for the successful generation, recognition and delivery of N-end rule substrates to their cognate proteases. In this review we examine the similarities and differences in the N-end rule pathway of bacterial and eukaryotic systems, focusing on the molecular determinants of this pathway.
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Affiliation(s)
- D A Dougan
- Department of Biochemistry, L Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Australia.
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14
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Camargo H, Nusspaumer G, Abia D, Briceño V, Remacha M, Ballesta JPG. The amino terminal end determines the stability and assembling capacity of eukaryotic ribosomal stalk proteins P1 and P2. Nucleic Acids Res 2011; 39:3735-43. [PMID: 21247875 PMCID: PMC3089481 DOI: 10.1093/nar/gkq1356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The eukaryotic ribosomal proteins P1 and P2 bind to protein P0 through their N-terminal domain to form the essential ribosomal stalk. A mutational analysis points to amino acids at positions 2 and 3 as determinants for the drastic difference of Saccharomyces cerevisiae P1 and P2 half-life, and suggest different degradation mechanisms for each protein type. Moreover, the capacity to form P1/P2 heterodimers is drastically affected by mutations in the P2β four initial amino acids, while these mutations have no effect on P1β. Binding of P2β and, to a lesser extent, P1β to the ribosome is also seriously affected showing the high relevance of the amino acids in the first turn of the NTD α-helix 1 for the stalk assembly. The negative effect of some mutations on ribosome binding can be reversed by the presence of the second P1/P2 couple in the ribosome, indicating a stabilizing structural influence between the two heterodimers. Unexpectedly, some mutations totally abolish heterodimer formation but allow significant ribosome binding and, therefore, a previous P1 and P2 association seems not to be an absolute requirement for stalk assembly. Homology modeling of the protein complexes suggests that the mutated residues can affect the overall protein conformation.
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Affiliation(s)
- Hendricka Camargo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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15
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Dougan DA, Truscott KN, Zeth K. The bacterial N-end rule pathway: expect the unexpected. Mol Microbiol 2010; 76:545-58. [DOI: 10.1111/j.1365-2958.2010.07120.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Hwang CS, Shemorry A, Varshavsky A. N-terminal acetylation of cellular proteins creates specific degradation signals. Science 2010; 327:973-7. [PMID: 20110468 DOI: 10.1126/science.1183147] [Citation(s) in RCA: 490] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The retained N-terminal methionine (Met) residue of a nascent protein is often N-terminally acetylated (Nt-acetylated). Removal of N-terminal Met by Met-aminopeptidases frequently leads to Nt-acetylation of the resulting N-terminal alanine (Ala), valine (Val), serine (Ser), threonine (Thr), and cysteine (Cys) residues. Although a majority of eukaryotic proteins (for example, more than 80% of human proteins) are cotranslationally Nt-acetylated, the function of this extensively studied modification is largely unknown. Using the yeast Saccharomyces cerevisiae, we found that the Nt-acetylated Met residue could act as a degradation signal (degron), targeted by the Doa10 ubiquitin ligase. Moreover, Doa10 also recognized the Nt-acetylated Ala, Val, Ser, Thr, and Cys residues. Several examined proteins of diverse functions contained these N-terminal degrons, termed AcN-degrons, which are a prevalent class of degradation signals in cellular proteins.
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Affiliation(s)
- Cheol-Sang Hwang
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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17
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Peña MMO, Melo SP, Xing YY, White K, Barbour KW, Berger FG. The intrinsically disordered N-terminal domain of thymidylate synthase targets the enzyme to the ubiquitin-independent proteasomal degradation pathway. J Biol Chem 2009; 284:31597-607. [PMID: 19797058 DOI: 10.1074/jbc.m109.038455] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ubiquitin-independent proteasomal degradation pathway is increasingly being recognized as important in regulation of protein turnover in eukaryotic cells. One substrate of this pathway is the pyrimidine biosynthetic enzyme thymidylate synthase (TS; EC 2.1.1.45), which catalyzes the reductive methylation of dUMP to form dTMP and is essential for DNA replication during cell growth and proliferation. Previous work from our laboratory showed that degradation of TS is ubiquitin-independent and mediated by an intrinsically disordered 27-residue region at the N-terminal end of the molecule. In the current study we show that this region, in cooperation with an alpha-helix formed by the next 15 residues, functions as a degron, i.e. it is capable of destabilizing a heterologous protein to which it is fused. Comparative analysis of the primary sequence of TS from a number of mammalian species revealed that the N-terminal domain is hypervariable among species yet is conserved with regard to its disordered nature, its high Pro content, and the occurrence of Pro at the penultimate site. Characterization of mutant proteins showed that Pro-2 protects the N terminus against N(alpha)-acetylation, a post-translational process that inhibits TS degradation. However, although a free amino group at the N terminus is necessary, it is not sufficient for degradation of the polypeptide. The implications of these findings to the proteasome-targeting function of the N-terminal domain, particularly with regard to its intrinsic flexibility, are discussed.
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Affiliation(s)
- Maria Marjorette O Peña
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
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18
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Sakurai N, Moriya K, Suzuki T, Sofuku K, Mochiki H, Nishimura O, Utsumi T. Detection of co- and posttranslational protein N-myristoylation by metabolic labeling in an insect cell-free protein synthesis system. Anal Biochem 2007; 362:236-44. [PMID: 17266917 DOI: 10.1016/j.ab.2006.12.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Revised: 12/11/2006] [Accepted: 12/14/2006] [Indexed: 10/23/2022]
Abstract
To establish a simple and sensitive method to detect protein N-myristoylation, the usefulness of a newly developed cell-free protein synthesis system derived from insect cells for detecting protein N-myristoylation by in vitro metabolic labeling was examined. The results showed that in vitro translation of cDNA coding for N-myristoylated protein in the presence of [(3)H]myristic acid followed by SDS-PAGE and fluorography is a useful method for rapid detection of protein N-myristoylation. Differential labeling of N-myristoylated model proteins with [(3)H]leucine, [(3)H]myristic acid, and [(35)S]methionine revealed that the removal of the initiating Met during the N-myristoylation reaction could be detected using this system. Analysis of the N-myristoylation of a series of model proteins with mutated N-myristoylation motifs revealed that the amino acid sequence requirements for the N-myristoylation reaction in this system are quite similar to those observed in the rabbit reticulocyte lysate system. N-myristoylation of tBid (a posttranslationally N-myristoylated cytotoxic protein that could not be expressed in transfected cells) was successfully detected in this assay system. Thus, metabolic labeling in an insect cell-free protein synthesis system is an effective strategy to detect co- and posttranslational protein N-myristoylation irrespective of the cytotoxicity of the protein.
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Affiliation(s)
- Nagisa Sakurai
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan
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19
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Suzuki T, Ito M, Ezure T, Shikata M, Ando E, Utsumi T, Tsunasawa S, Nishimura O. N-Terminal protein modifications in an insect cell-free protein synthesis system and their identification by mass spectrometry. Proteomics 2006; 6:4486-95. [PMID: 16835852 DOI: 10.1002/pmic.200600126] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
To evaluate the ability of an insect cell-free protein synthesis system to generate proper N-terminal cotranslational protein modifications such as removal of the initiating Met, N-acetylation, and N-myristoylation, several mutants were constructed using truncated human gelsolin (tGelsolin) as a model protein. Tryptic digests of these mutants were analyzed by MALDI-TOF MS and MALDI-quadrupole-IT-TOF MS. The wild-type tGelsolin, which is an N-myristoylated protein, was found to be N-myristoylated when myristoyl-CoA was added to the in vitro translation reaction mixture. N-myristoylation did not occur on the Gly-2 to Ala mutant, in which the N-myristoylation motif was disrupted, whereas this mutant was found to be N-acetylated after removal of the initiating Met. Analyses of Gly-2 to His and Leu-3 to Asp mutants revealed that the amino acids at positions 2 and 3 strongly affect the susceptibility of the nascent peptide chain to removal of the initiating Met and to N-acetylation, respectively. These results suggest that N-terminal modifications occurring in the insect cell-free protein synthesis system are quite similar to those observed in the mammalian protein synthesis system. Thus, a combination of the cell-free protein synthesis system with MS is an effective strategy to analyze protein modifications.
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Affiliation(s)
- Takashi Suzuki
- Life Science Laboratory, Analytical and Measuring Instruments Division, Shimadzu Corporation, Kyoto, Japan.
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20
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Erbse A, Schmidt R, Bornemann T, Schneider-Mergener J, Mogk A, Zahn R, Dougan DA, Bukau B. ClpS is an essential component of the N-end rule pathway in Escherichia coli. Nature 2006; 439:753-6. [PMID: 16467841 DOI: 10.1038/nature04412] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2005] [Accepted: 11/07/2005] [Indexed: 11/09/2022]
Abstract
The N-end rule states that the half-life of a protein is determined by the nature of its amino-terminal residue. Eukaryotes and prokaryotes use N-terminal destabilizing residues as a signal to target proteins for degradation by the N-end rule pathway. In eukaryotes an E3 ligase, N-recognin, recognizes N-end rule substrates and mediates their ubiquitination and degradation by the proteasome. In Escherichia coli, N-end rule substrates are degraded by the AAA + chaperone ClpA in complex with the ClpP peptidase (ClpAP). Little is known of the molecular mechanism by which N-end rule substrates are initially selected for proteolysis. Here we report that the ClpAP-specific adaptor, ClpS, is essential for degradation of N-end rule substrates by ClpAP in bacteria. ClpS binds directly to N-terminal destabilizing residues through its substrate-binding site distal to the ClpS-ClpA interface, and targets these substrates to ClpAP for degradation. Degradation by the N-end rule pathway is more complex than anticipated and several other features are involved, including a net positive charge near the N terminus and an unstructured region between the N-terminal signal and the folded protein substrate. Through interaction with this signal, ClpS converts the ClpAP machine into a protease with exquisitely defined specificity, ideally suited to regulatory proteolysis.
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Affiliation(s)
- A Erbse
- Zentrum für Molekulare Biologie Heidelberg, Universität Heidelberg, INF 282, Heidelberg D-69120, Germany
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21
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Hegde AN. Ubiquitin-proteasome-mediated local protein degradation and synaptic plasticity. Prog Neurobiol 2004; 73:311-57. [PMID: 15312912 DOI: 10.1016/j.pneurobio.2004.05.005] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2003] [Accepted: 05/28/2004] [Indexed: 02/07/2023]
Abstract
A proteolytic pathway in which attachment of a small protein, ubiquitin, marks the substrates for degradation by a multi-subunit complex called the proteasome has been shown to function in synaptic plasticity and in several other physiological processes of the nervous system. Attachment of ubiquitin to protein substrates occurs through a series of highly specific and regulated steps. Degradation by the proteasome is subject to multiple levels of regulation as well. How does the ubiquitin-proteasome pathway contribute to synaptic plasticity? Long-lasting, protein synthesis-dependent, changes in the synaptic strength occur through activation of molecular cascades in the nucleus in coordination with signaling events in specific synapses. Available evidence indicates that ubiquitin-proteasome-mediated degradation has a role in the molecular mechanisms underlying synaptic plasticity that operate in the nucleus as well as at the synapse. Since the ubiquitin-proteasome pathway has been shown to be versatile in having roles in addition to proteolysis in several other cellular processes relevant to synaptic plasticity, such as endocytosis and transcription, this pathway is highly suited for a localized role in the neuron. Because of its numerous roles, malfunctioning of this pathway leads to several diseases and disorders of the nervous system. In this review, I examine the ubiquitin-proteasome pathway in detail and describe the role of regulated proteolysis in long-term synaptic plasticity. Also, using synaptic tagging theory of synapse-specific plasticity, I provide a model on the possible roles and regulation of local protein degradation by the ubiquitin-proteasome pathway.
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Affiliation(s)
- Ashok N Hegde
- Department of Neurobiology and Anatomy, Medical Center Boulevard, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA.
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22
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Avila J, Lucas JJ, Perez M, Hernandez F. Role of tau protein in both physiological and pathological conditions. Physiol Rev 2004; 84:361-84. [PMID: 15044677 DOI: 10.1152/physrev.00024.2003] [Citation(s) in RCA: 641] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The morphology of a neuron is determined by its cytoskeletal scaffolding. Thus proteins that associate with the principal cytoskeletal components such as the microtubules have a strong influence on both the morphology and physiology of neurons. Tau is a microtubule-associated protein that stabilizes neuronal microtubules under normal physiological conditions. However, in certain pathological situations, tau protein may undergo modifications, mainly through phosphorylation, that can result in the generation of aberrant aggregates that are toxic to neurons. This process occurs in a number of neurological disorders collectively known as tauopathies, the most commonly recognized of which is Alzheimer's disease. The purpose of this review is to define the role of tau protein under normal physiological conditions and to highlight the role of the protein in different tauopathies.
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Affiliation(s)
- Jesus Avila
- Centro de Biología Molecular "Severo Ochoa", Facultad de Ciencias, Campus de Cantoblanco, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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23
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Utsumi T, Nakano K, Funakoshi T, Kayano Y, Nakao S, Sakurai N, Iwata H, Ishisaka R. Vertical-scanning mutagenesis of amino acids in a model N-myristoylation motif reveals the major amino-terminal sequence requirements for protein N-myristoylation. ACTA ACUST UNITED AC 2004; 271:863-74. [PMID: 14764103 DOI: 10.1111/j.1432-1033.2004.03991.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In order to determine the amino-terminal sequence requirements for protein N-myristoylation, site-directed mutagenesis of the N-terminal region was performed using tumor necrosis factor (TNF) mutants as model substrate proteins. Subsequently, the susceptibility of these mutants to protein N-myristoylation was evaluated by metabolic labeling in an in vitro translation system using rabbit reticulocyte lysate. A TNF mutant having the sequence MGAAAAAAAA at its N-terminus was used as the starting sequence to identify elements critical for protein N-myristoylation. Sequential vertical-scanning mutagenesis of amino acids at a distinct position in this model N-terminal sequence revealed the major sequence requirements for protein N-myristoylation: the combination of amino acids at position 3 and 6 constitutes a major determinant for the susceptibility to protein N-myristoylation. When Ser was located at position 6, 11 amino acids (Gly, Ala, Ser, Cys, Thr, Val, Asn, Leu, Ile, Gln, His) were permitted at position 3 to direct efficient protein N-myristoylation. In this case, the presence of Lys at position 7 was found to affect the amino acid requirement at position 3 and Lys became permitted at this position. When Ser was not located at position 6, only 3 amino acids (Ala, Asn, Gln) were permitted at position 3 to direct efficient protein N-myristoylation. The amino acid requirements found in this study were fully consistent with the N-terminal sequence of 78 N-myristoylated proteins in which N-myristoylation was experimentally verified. These observations strongly indicate that the combination of amino acids at position 3, 6 and 7 is a major determinant for protein N-myristoylation.
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Affiliation(s)
- Toshihiko Utsumi
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan.
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24
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Thomae BA, Rifki OF, Theobald MA, Eckloff BW, Wieben ED, Weinshilboum RM. Human catecholamine sulfotransferase (SULT1A3) pharmacogenetics: functional genetic polymorphism. J Neurochem 2004; 87:809-19. [PMID: 14622112 DOI: 10.1046/j.1471-4159.2003.02027.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sulfotransferase (SULT) 1A3 catalyzes the sulfate conjugation of catecholamines and structurally related drugs. As a step toward studies of the possible contribution of inherited variation in SULT1A3 to the pathophysiology of human disease and/or variation in response to drugs related to catecholamines, we have resequenced all seven coding exons, three upstream non-coding exons, exon-intron splice junctions and the 5'-flanking region of SULT1A3 using DNA samples from 60 African-American (AA) and 60 Caucasian-American (CA) subjects. Eight single nucleotide polymorphisms (SNPs) were observed in AA and five in CA subjects, including one non-synonymous cSNP (Lys234Asn) that was observed only in AA subjects with an allele frequency of 4.2%. This change in amino acid sequence resulted in only 28 +/- 4.5% (mean +/- SEM) of the enzyme activity of the wild-type (WT) sequence after transient expression in COS-1 cells, with a parallel decrease (54 +/- 2.2% of WT) in level of SULT1A3 immunoreactive protein. Substrate kinetic studies failed to show significant differences in apparent Km values of the two allozymes for either dopamine (10.5 versus 10.2 micro m for WT and variant, respectively) or the cosubstrate 3'-phosphoadenosine 5'-phosphosulfate (0.114 versus 0.122 micro m, respectively). The decrease in level of immunoreactive protein in response to this single change in amino acid sequence was due, at least in part, to accelerated SULT1A3 degradation through a proteasome-mediated process. These observations raise the possibility of ethnic-specific inherited alterations in catecholamine sulfation in humans.
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Affiliation(s)
- Bianca A Thomae
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Medical School-Mayo Clinic, Rochester, Minnesota 55905, USA
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25
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Gautschi M, Just S, Mun A, Ross S, Rücknagel P, Dubaquié Y, Ehrenhofer-Murray A, Rospert S. The yeast N(alpha)-acetyltransferase NatA is quantitatively anchored to the ribosome and interacts with nascent polypeptides. Mol Cell Biol 2003; 23:7403-14. [PMID: 14517307 PMCID: PMC230319 DOI: 10.1128/mcb.23.20.7403-7414.2003] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The majority of cytosolic proteins in eukaryotes contain a covalently linked acetyl moiety at their very N terminus. The mechanism by which the acetyl moiety is efficiently transferred to a large variety of nascent polypeptides is currently only poorly understood. Yeast N(alpha)-acetyltransferase NatA, consisting of the known subunits Nat1p and the catalytically active Ard1p, recognizes a wide range of sequences and is thought to act cotranslationally. We found that NatA was quantitatively bound to ribosomes via Nat1p and contained a previously unrecognized third subunit, the N(alpha)-acetyltransferase homologue Nat5p. Nat1p not only anchored Ard1p and Nat5p to the ribosome but also was in close proximity to nascent polypeptides, independent of whether they were substrates for N(alpha)-acetylation or not. Besides Nat1p, NAC (nascent polypeptide-associated complex) and the Hsp70 homologue Ssb1/2p interact with a variety of nascent polypeptides on the yeast ribosome. A direct comparison revealed that Nat1p required longer nascent polypeptides for interaction than NAC and Ssb1/2p. Delta nat1 or Delta ard1 deletion strains were temperature sensitive and showed derepression of silent mating type loci while Delta nat5 did not display any obvious phenotype. Temperature sensitivity and derepression of silent mating type loci caused by Delta nat1 or Delta ard1 were partially suppressed by overexpression of SSB1. The combination of data suggests that Nat1p presents the N termini of nascent polypeptides for acetylation and might serve additional roles during protein synthesis.
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Affiliation(s)
- Matthias Gautschi
- Max Planck Research Unit Enzymology of Protein Folding, D-06120 Halle, Germany
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26
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Jason LJM, Moore SC, Lewis JD, Lindsey G, Ausió J. Histone ubiquitination: a tagging tail unfolds? Bioessays 2002; 24:166-74. [PMID: 11835281 DOI: 10.1002/bies.10038] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Despite the fact that histone H2A ubiquitination affects about 10-15% of this histone in most eukaryotic cells, histone ubiquitination is among one of the less-well-characterized post-translational histone modifications. Nevertheless, some important observations have been made in recent years. Whilst several enzymes had been known to ubiquitinate histones in vitro, recent studies in yeast have led to the unequivocal identification of the enzyme responsible for this post-translational modification in this organism. A strong functional co-relation to meiosis and spermiogenesis has also now been well documented, although its participation in other functional aspects of chromatin metabolism, such as transcription or DNA repair, still remains rather speculative and controversial. Because of its nature, histone ubiquitination represents the most bulky structural change to histones and as such it would be expected to exert an important effect on chromatin structure. Past and recent structural studies, however, indicate a surprising lack of effect of (H2A/H2B) ubiquitination on nucleosome architecture and of uH2A on chromatin folding. These results suggest that this modification may serve as a signal for recognition by functionally relevant trans-acting factors and/or operate synergistically in conjunction with other post-translational modifications such as for instance acetylation.
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Affiliation(s)
- Laure J M Jason
- Department of Biochemistry, University of Cape Town, South Africa
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27
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Utsumi T, Sato M, Nakano K, Takemura D, Iwata H, Ishisaka R. Amino acid residue penultimate to the amino-terminal gly residue strongly affects two cotranslational protein modifications, N-myristoylation and N-acetylation. J Biol Chem 2001; 276:10505-13. [PMID: 11124252 DOI: 10.1074/jbc.m006134200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To examine the amino-terminal sequence requirements for cotranslational protein N-myristoylation, a series of site-directed mutagenesis of N-terminal region were performed using tumor necrosis factor as a nonmyristoylated model protein. Subsequently, the susceptibility of these mutants to protein N-myristoylation was evaluated by metabolic labeling in an in vitro translation system or in transfected cells. It was found that the amino acid residue at position 3 in an N-myristoylation consensus motif, Met-Gly-X-X-X-Ser-X-X-X, strongly affected the susceptibility of the protein to two different cotranslational protein modifications, N-myristoylation and N-acetylation; 10 amino acids (Ala, Ser, Cys, Thr, Val, Asn, Leu, Ile, Gln, and His) with a radius of gyration smaller than 1.80 A directed N-myristoylation, two negatively charged residues (Asp and Glu) directed N-acetylation, and two amino acids (Gly and Met) directed heterogeneous modification with both N-myristoylation and N-acetylation. The amino acid requirements at this position for the two modifications were dramatically changed when Ser at position 6 in the consensus motif was replaced with Ala. Thus, the amino acid residue penultimate to the N-terminal Gly residue strongly affected two cotranslational protein modifications, N-myristoylation and N-acetylation, and the amino acid requirements at this position for these two modifications were significantly affected by downstream residues.
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Affiliation(s)
- T Utsumi
- Department of Biological Chemistry and Department of Veterinary Medicine, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan.
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28
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Affiliation(s)
- B Polevoda
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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29
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Nusspaumer G, Remacha M, Ballesta JP. Phosphorylation and N-terminal region of yeast ribosomal protein P1 mediate its degradation, which is prevented by protein P2. EMBO J 2000; 19:6075-84. [PMID: 11080154 PMCID: PMC305824 DOI: 10.1093/emboj/19.22.6075] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2000] [Revised: 09/06/2000] [Accepted: 09/22/2000] [Indexed: 11/14/2022] Open
Abstract
The stalk proteins P1 and P2, which are fundamental for ribosome activity, are the only ribosomal components for which there is a cytoplasmic pool. Accumulation of these two proteins is differentially regulated in Saccharomyces cerevisiae by degradation. In the absence of P2, the amount of P1 is drastically reduced; in contrast, P2 proteins are not affected by a deficiency in P1. However, association with P2 protects P1 proteins. The half-life of P1 is a few minutes, while that of P2 is several hours. The proteasome is not involved in the degradation of P1 proteins. The different sensitivity to degradation of these two proteins is associated with two structural features: phosphorylation and N-terminus structure. A phosphorylation site at the C-terminus is required for P1 proteolysis. P2 proteins, despite being phosphorylated, are protected by their N-terminal peptide. An exchange of the first five amino acids between the two types of protein makes P1 resistant and P2 sensitive to degradation.
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Affiliation(s)
- G Nusspaumer
- Centro de Biología Molecular, CSIC and UAM, Canto Blanco, 28049 Madrid, Spain
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30
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Hershko A, Ciechanover A, Varshavsky A. Basic Medical Research Award. The ubiquitin system. Nat Med 2000; 6:1073-81. [PMID: 11017125 DOI: 10.1038/80384] [Citation(s) in RCA: 517] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- A Hershko
- Unit of Biochemistry, Technion-Israel Institute of Technology, Faculty of Medicine, P.O. Box 9649, Haifa, 31096, Israel
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31
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Yagüe J, Alvarez I, Rognan D, Ramos M, Vázquez J, de Castro JAL. An N-acetylated natural ligand of human histocompatibility leukocyte antigen (HLA)-B39. Classical major histocompatibility complex class I proteins bind peptides with a blocked NH(2) terminus in vivo. J Exp Med 2000; 191:2083-92. [PMID: 10859333 PMCID: PMC2193201 DOI: 10.1084/jem.191.12.2083] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Sequence-independent interactions involving the free peptidic NH(2) terminus are thought to be an essential feature of peptide binding to classical major histocompatibility complex (MHC) class I proteins. Challenging this paradigm, a natural Nalpha-acetylated ligand of human histocompatibility leukocyte antigen (HLA)-B39 was identified in this study. It matched the NH(2)-terminal sequence of two human helicases, was resistant to aminopeptidase M, and was produced with high yield from a synthetic 30 mer with the sequence of the putative parental protein by the 20S proteasome. This is the first reported natural ligand of classical MHC class I antigens that has a blocked NH(2) terminus.
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Affiliation(s)
- Jesús Yagüe
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Facultad de Ciencias, 28049 Madrid, Spain
| | - Iñaki Alvarez
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Facultad de Ciencias, 28049 Madrid, Spain
| | - Didier Rognan
- Department of Applied Biosciences, Eidgenössiche Technische Hochschule, CH-8057 Zürich, Switzerland
| | - Manuel Ramos
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Facultad de Ciencias, 28049 Madrid, Spain
| | - Jesús Vázquez
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Facultad de Ciencias, 28049 Madrid, Spain
| | - José A. López de Castro
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Facultad de Ciencias, 28049 Madrid, Spain
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32
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Teckman JH, Gilmore R, Perlmutter DH. Role of ubiquitin in proteasomal degradation of mutant alpha(1)-antitrypsin Z in the endoplasmic reticulum. Am J Physiol Gastrointest Liver Physiol 2000; 278:G39-48. [PMID: 10644560 DOI: 10.1152/ajpgi.2000.278.1.g39] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A delay in intracellular degradation of the mutant alpha(1)-antitrypsin (alpha(1)AT)Z molecule is associated with greater retention within the endoplasmic reticulum (ER) and susceptibility to liver disease in a subgroup of patients with alpha(1)AT deficiency. Recent studies have shown that alpha(1)ATZ is ordinarily degraded in the ER by a mechanism that involves the proteasome, as demonstrated in intact cells using human fibroblast cell lines engineered for expression of alpha(1)ATZ and in a cell-free microsomal translocation assay system programmed with purified alpha(1)ATZ mRNA. To determine whether the ubiquitin system is required for proteasomal degradation of alpha(1)ATZ and whether specific components of the ubiquitin system can be implicated, we have now used two approaches. First, we overexpressed a dominant-negative ubiquitin mutant (UbK48R-G76A) by transient transfection in the human fibroblast cell lines expressing alpha(1)ATZ. The results showed that there was marked, specific, and selective inhibition of alpha(1)ATZ degradation mediated by UbK48R-G76A, indicating that the ubiquitin system is at least in part involved in ER degradation of alpha(1)ATZ. Second, we subjected reticulocyte lysate to DE52 chromatography and tested the resulting well-characterized fractions in the cell-free system. The results showed that there were both ubiquitin-dependent and -independent proteasomal mechanisms for degradation of alpha(1)ATZ and that the ubiquitin-conjugating enzyme E2-F1 may play a role in the ubiquitin-dependent proteasomal mechanism.
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Affiliation(s)
- J H Teckman
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
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33
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Thual C, Komar AA, Bousset L, Fernandez-Bellot E, Cullin C, Melki R. Structural characterization of Saccharomyces cerevisiae prion-like protein Ure2. J Biol Chem 1999; 274:13666-74. [PMID: 10224139 DOI: 10.1074/jbc.274.19.13666] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sacchromyces cerevisiae prion-like protein Ure2 was expressed in Escherichia coli and was purified to homogeneity. We show here that Ure2p is a soluble protein that can assemble into fibers that are similar to the fibers observed in the case of PrP in its scrapie prion filaments form or that form on Sup35 self-assembly. Ure2p self-assembly is a cooperative process where one can distinguish a lag phase followed by an elongation phase preceding a plateau. A combination of size exclusion chromatography, sedimentation velocity, and electron microscopy demonstrates that the soluble form of Ure2p consists at least of three forms of the protein as follows: a monomeric, dimeric, and tetrameric form whose abundance is concentration-dependent. By the use of limited proteolysis, intrinsic fluorescence, and circular dichroism measurements, we bring strong evidence for the existence of at least two structural domains in Ure2p molecules. Indeed, Ure2p NH2-terminal region is found poorly structured, whereas its COOH-terminal domain appears to be compactly folded. Finally, we show that only slight conformational changes accompany Ure2p assembly into insoluble high molecular weight oligomers. These changes essentially affect the COOH-terminal part of the molecule. The properties of Ure2p are compared in the discussion to that of other prion-like proteins such as Sup35 and mammalian prion protein PrP.
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Affiliation(s)
- C Thual
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette Cedex, France
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van Leyen K, Duvoisin RM, Engelhardt H, Wiedmann M. A function for lipoxygenase in programmed organelle degradation. Nature 1998; 395:392-5. [PMID: 9759730 DOI: 10.1038/26500] [Citation(s) in RCA: 216] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Membrane-enclosed organelles, a defining characteristic of eukaryotic cells, are lost during differentiation of specific cell types such as reticulocytes (an intermediate in differentiation of erythrocytes), central fibre cells of the eye lens, and keratinocytes. The degradation of these organelles must be tightly regulated with respect to both the time of activation and the specificity of membrane degradation. The expression of 15-lipoxygenase (15-LOX) peaks in reticulocytes immediately before organelle degradation. Here we show that 15-LOX integrates into the membranes of various organelles, allowing release of proteins from the organelle lumen and access of proteases to both lumenal and integral membrane proteins. In addition, by sparing the plasma membrane, 15-LOX shows the required specificity for organellar membranes. Thus, the action of 15-LOX provides a mechanism by which the natural degradation process can be explained. This conclusion is supported by our finding that lipoxygenase expression in the eye lens is restricted to the region at which organelle degradation occurs.
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Affiliation(s)
- K van Leyen
- Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
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35
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Mitton KP, Tumminia SJ, Arora J, Zelenka P, Epstein DL, Russell P. Transient loss of alphaB-crystallin: an early cellular response to mechanical stretch. Biochem Biophys Res Commun 1997; 235:69-73. [PMID: 9196037 DOI: 10.1006/bbrc.1997.6737] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Human trabecular meshwork (HTM) is distended and stretched with increases in intraocular pressure. During this stretching, there is a rearrangement of actin filaments. The HTM cells express alpha B-crystallin, a small heat shock protein that may have a role in the stabilization and regulation of the cytoskeleton in mammalian cells. The levels of alpha B-crystallin were examined in trabecular meshwork cells after mechanical stretch. Human TM primary cell cultures, plated onto silicone sheets, were subjected to a single 10% linear stretch and samples were prepared at various times after stretch for immunoblotting or Northern blotting. Immunoblots of total protein extracts with antibody specific for alpha B-crystallin detected a 26% decrease of cellular alpha B-crystallin levels within 2 minutes. After 1 hour alpha B-crystallin levels had decreased 90% compared to control cells. The levels of alpha B-crystallin began to recover in cells stretched for 2 hours and returned to initial levels by 24 hours. Northern blots probed with alpha B-crystallin exon III cDNA detected a transcript of 0.65 kb in human TM cells and the levels of the alpha B mRNA remained constant during alpha B-crystallin protein decrease. Later, levels of the 0.65 kb transcript of alpha B-crystallin increased during the cellular recovery. These results suggest that decreased levels of alpha B-crystallin after mechanical stretch were probably not due to transcriptional changes but rather to increased degradation of alpha B-crystallin protein. An increase in mRNA levels may play a role in the recovery of alpha B-crystallin during reorganization of the cytoskeleton and attachment to the substratum. These data raise the possibility of a specific proteolysis of alpha B-crystallin protein in cells after a physiological challenge.
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Affiliation(s)
- K P Mitton
- Laboratory for Mechanisms of Ocular Diseases, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Bercovich B, Stancovski I, Mayer A, Blumenfeld N, Laszlo A, Schwartz AL, Ciechanover A. Ubiquitin-dependent degradation of certain protein substrates in vitro requires the molecular chaperone Hsc70. J Biol Chem 1997; 272:9002-10. [PMID: 9083024 DOI: 10.1074/jbc.272.14.9002] [Citation(s) in RCA: 215] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Degradation of a protein via the ubiquitin system involves two discrete steps, signaling by covalent conjugation of multiple moieties of ubiquitin and degradation of the tagged substrate. Conjugation is catalyzed via a three-step mechanism that involves three distinct enzymes that act successively: E1, E2, and E3. The first two enzymes catalyze activation of ubiquitin and transfer of the activated moiety to E3, respectively. E3, to which the substrate is specifically bound, catalyzes formation of a polyubiquitin chain that is anchored to the targeted protein. The polyubiquitin-tagged protein is degraded by the 26 S proteasome, and free and reutilizable ubiquitin is released. In addition to the three conjugating enzymes, targeting of certain proteins requires association with ancillary proteins and/or post-translational modification(s). Using a specific antibody to deplete cell extract from the molecular chaperone Hsc70, we demonstrate that this protein is required for the degradation of actin, alpha-crystallin, glyceraldehyde-3-phosphate dehydrogenase, alpha-lactalbumin, and histone H2A. In contrast, the degradation of bovine serum albumin, lysozyme, and oxidized RNase A is Hsc70-independent. Mechanistic analysis revealed that the chaperone is required for the conjugation reaction; however, it does not substitute for E3. Involvement of the chaperone in the proteolytic process requires complex formation with the substrate. Formation of this complex appears to be essential in the proteolytic process. In addition, the proper function of the chaperone in the proteolytic process requires the presence of K+, which allows rapid cycles of dissociation and association of the complex. The chaperone may act by binding to the substrate and unfolding it to expose a ubiquitin ligase-binding site. In addition, it can also act directly on the ubiquitination machinery.
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Affiliation(s)
- B Bercovich
- Department of Biochemistry and the Rappaport Institute for Research in the Medical Sciences, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
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37
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Iwaya K, Nishibori H, Osada T, Matsuno Y, Tsuda H, Sato S, Kono H, Fukutomi T, Suzuki M, Torikata C, Iwamatsu A, Hirohashi S. Immunoreaction at 43 kDa with anti-ubiquitin antibody in breast neoplasms. Jpn J Cancer Res 1997; 88:273-80. [PMID: 9140112 PMCID: PMC5921380 DOI: 10.1111/j.1349-7006.1997.tb00378.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Protein ubiquitination has been implicated in ATP-dependent protein turnover and normal cell proliferation. To investigate whether the ubiquitin-mediated system is functionally involved in the cancerous state, we examined changes in protein ubiquitination in 52 surgically resected primary breast tumors. Immunohistochemically, ubiquitin (Ub) was identified in the cytoplasm of cancer cells, which were stained more strongly than adjacent normal ductal epithelium. Corresponding immunoblot analysis of normal and neoplastic regions of human breast showed that the immunoreaction for Ub at about 43 kDa was increased in all of the tumors (100%), regardless of the clinical stage or histologic grade. This protein, which gave a single spot on two-dimensional gel electrophoresis, had partial amino acid sequences which were identical to those of actin family members. Our results suggest that ubiquitination of this 43-kDa protein may be involved in the carcinogenesis or biological characteristics of human breast neoplasms.
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Affiliation(s)
- K Iwaya
- Pathology Division, National Cancer Center Research Institute, Tokyo
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38
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Solomon V, Goldberg AL. Importance of the ATP-ubiquitin-proteasome pathway in the degradation of soluble and myofibrillar proteins in rabbit muscle extracts. J Biol Chem 1996; 271:26690-7. [PMID: 8900146 DOI: 10.1074/jbc.271.43.26690] [Citation(s) in RCA: 304] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Recent studies have suggested that activation of the ubiquitin-proteasome pathway is primarily responsible for the rapid loss of muscle proteins in various types of atrophy. The present studies were undertaken to test if different classes of muscle proteins are degraded by this pathway. In extracts of rabbit psoas muscle, the complete degradation of soluble proteins to amino acids was stimulated up to 6-fold by ATP. Peptide aldehyde inhibitors of the proteasome or the removal of proteasomes markedly inhibited only the ATP-dependent process. Addition of purified myosin, actin, troponin, or tropomyosin to these extracts showed that these proteins served as substrates for the ubiquitin-proteasome pathway. By contrast, degradation of myoglobin did not require ATP, proteasomes, or any known proteases in muscles. When myosin, actin, and troponin were added as actomyosin complexes or as intact myofibrils to these extracts, they were not hydrolyzed at a significant rate, probably because in these multicomponent complexes, these proteins are protected from degradation. Accordingly, actin (but not albumin or troponin) inhibited the degradation of 125I-myosin, and actin was found to selectively inhibit ubiquitin conjugation to 125I-myosin. Also, the presence of tropomyosin inhibited the degradation of 125I-troponin. However, neither actin nor tropomyosin inhibited the degradation of 125I-lysozyme or soluble muscle proteins. Thus, specific interactions between the myofibrillar proteins appear to protect them from ubiquitin-dependent degradation, and the rate-limiting step in their degradation is probably their dissociation from the myofibril.
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Affiliation(s)
- V Solomon
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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39
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Gonen H, Stancovski I, Shkedy D, Hadari T, Bercovich B, Bengal E, Mesilati S, Abu-Hatoum O, Schwartz AL, Ciechanover A. Isolation, characterization, and partial purification of a novel ubiquitin-protein ligase, E3. Targeting of protein substrates via multiple and distinct recognition signals and conjugating enzymes. J Biol Chem 1996; 271:302-10. [PMID: 8550577 DOI: 10.1074/jbc.271.1.302] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Degradation of a protein via the ubiquitin system involves two discrete steps, conjugation of ubiquitin to the substrate and degradation of the adduct. Conjugation follows a three-step mechanism. First, ubiquitin is activated by the ubiquitin-activating enzyme, E1. Following activation, one of several E2 enzymes (ubiquitin-carrier proteins or ubiquitin-conjugating enzymes, UBCs) transfers ubiquitin from E1 to the protein substrate that is bound to one of several ubiquitin-protein ligases, E3s. These enzymes catalyze the last step in the process, covalent attachment of ubiquitin to the protein substrate. The binding of the substrate to E3 is specific and implies that E3s play a major role in recognition and selection of proteins for conjugation and subsequent degradation. So far, only a few ligases have been identified, and it is clear that many more have not been discovered yet. Here, we describe a novel ligase that is involved in the conjugation and degradation of non "N-end rule" protein substrates such as actin, troponin T, and MyoD. This substrate specificity suggests that the enzyme may be involved in degradation of muscle proteins. The ligase acts in concert with E2-F1, a previously described non N-end rule UBC. Interestingly, it is also involved in targeting lysozyme, a bona fide N-end substrate that is recognized by E3 alpha and E2-14 kDa. The novel ligase recognizes lysozyme via a signal(s) that is distinct from the N-terminal residue of the protein. Thus, it appears that certain proteins can be targeted via multiple recognition motifs and distinct pairs of conjugating enzymes. We have purified the ligase approximately 200-fold and demonstrated that it is different from other known E3s, including E3 alpha/UBR1, E3 beta, and E6-AP. The native enzyme has an apparent molecular mass of approximately 550 kDa and appears to be a homodimer. Because of its unusual size, we designated this novel ligase E3L (large). E3L contains an -SH group that is essential for its activity. Like several recently described E3 enzymes, including E6-AP and the ligase involved in the processing of p105, the NF-kappa B precursor, the novel ligase is found in mammalian tissues but not in wheat germ.
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Affiliation(s)
- H Gonen
- Department of Biochemistry, Carmel Medical Center, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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Abstract
Contrary to widespread belief, the regulation and mechanism of degradation for the mass of intracellular proteins (i.e. differential, selective protein turnover) in vertebrate tissues is still a major biological enigma. There is no evidence for the conclusion that ubiquitin plays any role in these processes. The primary function of the ubiquitin-dependent protein degradation pathway appears to lie in the removal of abnormal, misfolded, denatured or foreign proteins in some eukaryotic cells. ATP/ubiquitin-dependent proteolysis probably also plays a role in the degradation of some so-called 'short-lived' proteins. Evidence obtained from the covalent modification of such natural substrates as calmodulin, histones (H2A, H2B) and some cell membrane receptors with ubiquitin indicates that the reversible interconversion of proteins with ubiquitin followed by concomitant functional changes may be of prime importance.
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Affiliation(s)
- H P Jennissen
- Institut für Physiologische Chemie, Universität-GHS-Essen, Germany
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41
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Obin M, Nowell T, Taylor A. A comparison of ubiquitin-dependent proteolysis of rod outer segment proteins in reticulocyte lysate and a retinal pigment epithelial cell line. Curr Eye Res 1995; 14:751-60. [PMID: 8529413 DOI: 10.3109/02713689508995796] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We compared ATP- and ubiquitin-dependent proteolysis in supernatants of rabbit reticulocyte lysate and a human retinal pigment epithelial (RPE) cell line. At pH 7.8, both preparations catalyzed the conjugation of [125I]ubiquitin to endogenous proteins, generating an equivalent amount of high mass (> 150 kDa) [125I]ubiquitin-protein adducts. Both preparations degraded exogenous histone 2A, oxRNase and beta-lactoglobulin in an ATP-dependent manner. Addition of ubiquitin (12 or 120 microM) to reticulocyte lysate stimulated (1.4-fold) ATP-dependent degradation only of histone 2A. Addition of 12 microM ubiquitin to RPE supernatant resulted in > or = 3-fold enhancement in degradation of all three substrates. Next, we compared the ability of the two proteolysis systems to degrade bovine rod outer segment (ROS) nonintegral membrane proteins. [125I]ROS protein degradation by reticulocyte lysate was almost exclusively ATP-dependent and was completely inhibited by hemin and vanadate, inhibitors of ATP- and ubiquitin-dependent proteolysis. RPE supernatant also degraded ROS proteins by an ATP-dependent mechanism, and, unlike results obtained in reticulocyte assays, this degradation increased (2-fold) upon ubiquitin supplementation. Both proteolysis systems degraded ROS proteins of molecular mass approximately 10, 30, 37, 40 and 60 kDa, with coincident formation of high mass species. Reticulocyte lysate also degraded 100 and 150 kDa ROS proteins, whereas RPE supernatant did not. The 10, 37 and 40 kDa species were identified by western blot as the gamma-, beta- and alpha- subunits of rod transducin (Gt), respectively. RPE supernatant generated (some) ROS proteolysis products that remained acid-precipitable. As compared with patterns of proteolysis in reticulocytes, RPE supernatant (1) degraded 100% more Gt beta gamma, (2) generated > 10-fold the amount of high mass (putative ubiquitin-ROS protein) conjugates and (3) preferentially degraded Gt beta gamma relative to G t alpha. The ubiquitin-dependent enhancement of ATP-dependent degradation of all proteins tested in RPE supernatant makes the RPE system a valuable experimental tool for the explicit demonstration of ubiquitin-dependent proteolysis.
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Affiliation(s)
- M Obin
- USDA-JMHNRCA, Tufts University, Boston, MA 02111, USA
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42
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Tamaoka A, Mizusawa H, Mori H, Shoji S. Ubiquitinated alpha B-crystallin in glial cytoplasmic inclusions from the brain of a patient with multiple system atrophy. J Neurol Sci 1995; 129:192-8. [PMID: 7608736 DOI: 10.1016/0022-510x(94)00275-s] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Glial cytoplasmic inclusions (GCIs) have been observed in oligodendroglia-like cells, specifically in the brains of patients with multiple system atrophy (striatonigral degeneration, olivopontocerebellar atrophy and Shy-Drager syndrome). We have investigated GCIs from brains of patients with multiple system atrophy biochemically and immunochemically. While most GCIs have been reported positive for both ubiquitin and alpha B-crystallin in immunocytochemical studies, the components of GCIs have not been identified biochemically. GCI-bearing cells were partially purified from the OPCA brain by sieving with nylon meshes and discontinuous sucrose density gradient centrifugation. The fraction containing GCI-bearing cells was also found to contain a 32 kDa and a 40 kDa protein, both of which were specifically recognized by anti-ubiquitin and anti-alpha B-crystallin antibodies, neither of which was found in the same fraction derived from control brain. These immunochemical results suggest that ubiquitinated alpha B-crystallin is present in GCIs from the brains of patients with multiple system atrophy.
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Affiliation(s)
- A Tamaoka
- Department of Neurology, University of Tsukuba, Ibaraki-ken, Japan
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43
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Shang F, Taylor A. Oxidative stress and recovery from oxidative stress are associated with altered ubiquitin conjugating and proteolytic activities in bovine lens epithelial cells. Biochem J 1995; 307 ( Pt 1):297-303. [PMID: 7717989 PMCID: PMC1136776 DOI: 10.1042/bj3070297] [Citation(s) in RCA: 125] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Roles for ubiquitin (an 8.5 kDa polypeptide) involve its conjugation to proteins as a signal to initiate degradation and as a stress protein. We investigated ubiquitin conjugation and ubiquitin-dependent proteolytic activities in cultured bovine lens epithelial cells (BLECs) upon oxidative challenge. A 44% decrease in intracellular glutathione confirmed oxidative stress upon incubation with 1 mM H2O2. After 30 min incubation, endogenous high-molecular-mass ubiquitin conjugates decreased 73%, and intracellular proteolysis decreased about 50%. In the supernatants of the oxidatively treated BLECs, the ability to form high-molecular-mass ubiquitin conjugates with exogenous 125I-labelled ubiquitin decreased 28%, and ATP-dependent degradation of oxidized alpha-crystallin decreased 36%. When the H2O2-treated BLECs were allowed to recover for 60 min, intracellular proteolysis returned to the level of control cells. There was also a subsequent transient enhancement of intracellular proteolysis and a simultaneous recovery of endogenous high-molecular-mass ubiquitin conjugates. In parallel cell-free experiments, conjugating activity with exogenous 125I-labelled ubiquitin and ATP-dependent degradation of oxidized alpha-crystallin increased 35% and 72% respectively compared with non-oxidatively treated BLECs. ATP-independent proteolysis showed little response to exposure or removal of H2O2. These results indicate that (1) the rate of intracellular proteolysis in BLECs is associated with the level of endogenous high-molecular-mass ubiquitin conjugates and (2) oxidative stress may inactivate the ubiquitin conjugation activity with coordinate depression of proteolytic capability. Enhancement in ubiquitin conjugation and proteolytic activities during recovery from oxidative stress may be important in removal of damaged proteins and restoration of normal function of BLECs. The inactivation of ubiquitin-dependent proteolysis by oxidation may be involved in the accumulation of altered proteins and other adverse sequelae in the oxidatively challenged aging lens.
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Affiliation(s)
- F Shang
- Laboratory for Nutrition and Vision Research, USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA
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44
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Wing SS, Jain P. Molecular cloning, expression and characterization of a ubiquitin conjugation enzyme (E2(17)kB) highly expressed in rat testis. Biochem J 1995; 305 ( Pt 1):125-32. [PMID: 7826319 PMCID: PMC1136439 DOI: 10.1042/bj3050125] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Ubiquitin-conjugating enzymes (E2s) play a key role in ubiquitin-mediated proteolysis by catalysing the conjugation of ubiquitin to protein substrates. We have previously reported the cDNA cloning of a 14 kDa conjugating enzyme [E2(14)k; Wing, Dumas and Banville (1992) J. Biol. Chem. 267, 6495-6501] that efficiently supported ubiquitination and protein degradation in reticulocyte extracts. Surprisingly, the structure of this E2 was markedly more similar to the Saccharomyces cerevisiae DNA repair gene RAD6, than to the S. cerevisiae UBC4/UBC5 genes which are required for the degradation of short-lived proteins and support much of the ubiquitination of yeast proteins. This suggested that mammalian homologues of UBC4/UBC5 remained to be identified. Using oligonucleotides derived from the S. cerevisiae UBC4 sequence as primers in a PCR reaction with rat muscle cDNA as a template, a 390 bp DNA fragment was amplified which predicted an amino acid sequence that was 83% identical to yeast UBC4. Screening a rat testes cDNA library identified a family of cDNAs which predicted two very similar proteins with basic pIs and molecular masses of approx. 16,700 Da. Isoform 2E was expressed in Escherichia coli and purified to homogeneity. It supported ubiquitination to reticulocyte and testis proteins more rapidly in vitro and produced larger conjugates than E2(14)k. Examination of RNA from different tissues indicated that this type of E2 was expressed in a broad spectrum of tissues but at particularly high levels in the testis. Fractionation of a testis extract by anion-exchange chromatography identified several putative ubiquitin protein ligase activities with which this E2 could interact in promoting conjugation of ubiquitin to proteins. One of these activities supported conjugation of ubiquitin to histone H2A, a substrate degraded in the ubiquitin system by a non-N-end rule mechanism. This paper reports the first cloning of a apparent mammalian homologue of S. cerevisiae UBC4/UBC5. Its high expression in testis and ability to efficiently support conjugation to testis proteins suggest that this family of E2s may play a role in the proteolysis that occurs during spermatogenesis.
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Affiliation(s)
- S S Wing
- Department of Medicine, McGill University, Montreal, Quebec, Canada
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45
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Shaeffer J. Monoubiquitinated alpha globin is an intermediate in the ATP-dependent proteolysis of alpha globin. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)31777-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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46
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Gonen H, Smith CE, Siegel NR, Kahana C, Merrick WC, Chakraburtty K, Schwartz AL, Ciechanover A. Protein synthesis elongation factor EF-1 alpha is essential for ubiquitin-dependent degradation of certain N alpha-acetylated proteins and may be substituted for by the bacterial elongation factor EF-Tu. Proc Natl Acad Sci U S A 1994; 91:7648-52. [PMID: 8052636 PMCID: PMC44459 DOI: 10.1073/pnas.91.16.7648] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Targeting of different cellular proteins for conjugation and subsequent degradation via the ubiquitin pathway involves diverse recognition signals and distinct enzymatic factors. A few proteins are recognized via their N-terminal amino acid residue and conjugated by a ubiquitin-protein ligase that recognizes this residue. Most substrates, including the N alpha-acetylated proteins that constitute the vast majority of cellular proteins, are targeted by different signals and are recognized by yet unknown ligases. We have previously shown that degradation of N-terminally blocked proteins requires a specific factor, designated FH, and that the factor acts along with the 26S protease complex to degrade ubiquitin-conjugated proteins. Here, we demonstrate that FH is the protein synthesis elongation factor EF-1 alpha. (a) Partial sequence analysis reveals 100% identity to EF-1 alpha. (b) Like EF-1 alpha, FH binds to immobilized GTP (or GDP) and can be purified in one step using the corresponding nucleotide for elution. (c) Guanine nucleotides that bind to EF-1 alpha protect the ubiquitin system-related activity of FH from heat inactivation, and nucleotides that do not bind do not exert this effect. (d) EF-Tu, the homologous bacterial elongation factor, can substitute for FH/EF-1 alpha in the proteolytic system. This last finding is of particular interest since the ubiquitin system has not been identified in prokaryotes. The activities of both EF-1 alpha and EF-Tu are strongly and specifically inhibited by ubiquitin-aldehyde, a specific inhibitor of ubiquitin isopeptidases. It appears, therefore, that EF-1 alpha may be involved in releasing ubiquitin from multiubiquitin chains, thus rendering the conjugates susceptible to the action of the 26S protease complex.
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Affiliation(s)
- H Gonen
- Department of Biochemistry, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa
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47
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Mifflin L, Cohen R. Characterization of denatured protein inducers of the heat shock (stress) response in Xenopus laevis oocytes. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)40739-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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48
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Shang F, Huang L, Taylor A. Degradation of native and oxidized beta- and gamma-crystallin using bovine lens epithelial cell and rabbit reticulocyte extracts. Curr Eye Res 1994; 13:423-31. [PMID: 7924406 DOI: 10.3109/02713689408999870] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In many types of cells, modified proteins are selectively and rapidly removed by various proteolytic systems. In eye lens, as in most cells, there appears to be a multiplicity of proteolytic pathways, including ubiquitin-dependent, ATP-dependent and ATP-independent pathways. Each of these appears to be involved in the degradation of alpha-crystallins. The objective of this study was to determine if oxidized beta- and gamma-crystallins would be selectively degraded and which proteolytic systems might be involved. beta- and gamma-crystallins were oxidized by exposure to 137Cs radiation under N2O. This system generates *OH primarily. Oxidation of beta- and gamma-crystallins was indicated by decreased protein sulfhydryl content and tryptophan fluorescence, as well as by increased levels of carbonyl and high molecular weight aggregates with increasing radiation dose. gamma-crystallin was more susceptible than beta-crystallin to oxidation based on loss of native crystallin, increase in aggregates and fragmentation products, and loss of tryptophan. Low molecular mass polymers (dimers) appear to be the precursors of high mass aggregates induced upon oxidation. At a specific level of oxidative insult interchain covalent bonds in addition to disulfides were more extensive in the polymers of gamma-crystallin as compared to beta-crystallin. Except for beta-crystallin irradiated with 1 krad, the degradation rate of crystallins using both reticulocyte and bovine lens epithelial cells (BLEC) proteolytic systems increased in proportion to the extent of oxidation. Proteolysis of oxidized gamma-crystallins increased 1775% and 900%, respectively, using reticulocytes and BLEC supernatants as the source of proteases.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- F Shang
- Laboratory for Nutrition and Vision Research, USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111
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49
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Purification and characterization of a novel species of ubiquitin-carrier protein, E2, that is involved in degradation of non-“N-end rule” protein substrates. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)36920-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Wang MB, Boulter D, Gatehouse JA. Characterization and sequencing of cDNA clone encoding the phloem protein PP2 of Cucurbita pepo. PLANT MOLECULAR BIOLOGY 1994; 24:159-170. [PMID: 8111014 DOI: 10.1007/bf00040582] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Direct N-terminal amino acid sequencing of the phloem protein 2 (PP2) from 3-month old Cucurbita pepo L. (pumpkin), purified by SDS-PAGE and blotted onto PVDF membrane, showed that the protein had a blocked N-terminus. However, after in situ cleavage of the polypeptide in a gel slice by cyanogen bromide, 75 residues of sequences on two cyanogen bromide fragments were determined. An oligonucleotide probe based on this amino acid sequence was used to screen a cDNA library, constructed from mRNA of 3-5-day old seedling hypocotyls, in lambda ZAP II. A cDNA clone (p11A) predicted an amino acid sequence of 218 residues, in full agreement with the sequences determined for two CNBr fragments of PP2, and suggests that the N-terminus of the protein is a blocked methionine residue which is cleaved off by CNBr. Two additional cDNA clones were sequenced but no heterogeneity in the PP2 sequence was found. The deduced amino acid sequence of C. pepo differs in nine residues from the recently published sequence of Cucurbita maxima (Bostwick et al., Plant Cell 4 (1992) 1539-1548). Southern blot showed that PP2 is encoded by a gene family with a relatively large number of members (estimated as 7-15 per haploid genome).
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Affiliation(s)
- M B Wang
- Department of Biological Sciences, University of Durham, UK
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