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Koszela J, Pham NT, Shave S, St-Cyr D, Ceccarelli DF, Orlicky S, Marinier A, Sicheri F, Tyers M, Auer M. A Novel Confocal Scanning Protein-Protein Interaction Assay (PPI-CONA) Reveals Exceptional Selectivity and Specificity of CC0651, a Small Molecule Binding Enhancer of the Weak Interaction between the E2 Ubiquitin-Conjugating Enzyme CDC34A and Ubiquitin. Bioconjug Chem 2024; 35:1441-1449. [PMID: 39167708 PMCID: PMC11417995 DOI: 10.1021/acs.bioconjchem.4c00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024]
Abstract
Protein-protein interactions (PPIs) are some of the most challenging target classes in drug discovery. Highly sensitive detection techniques are required for the identification of chemical modulators of PPIs. Here, we introduce PPI confocal nanoscanning (PPI-CONA), a miniaturized, microbead based high-resolution fluorescence imaging assay. We demonstrate the capabilities of PPI-CONA by detecting low affinity ternary complex formation between the human CDC34A ubiquitin-conjugating (E2) enzyme, ubiquitin, and CC0651, a small molecule enhancer of the CDC34A-ubiquitin interaction. We further exemplify PPI-CONA with an E2 enzyme binding study on CC0651 and a CDC34A binding specificity study of a series of CC0651 analogues. Our results indicate that CC0651 is highly selective toward CDC34A. We further demonstrate how PPI-CONA can be applied to screening very low affinity interactions. PPI-CONA holds potential for high-throughput screening for modulators of PPI targets and characterization of their affinity, specificity, and selectivity.
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Affiliation(s)
- Joanna Koszela
- School
of Molecular Biosciences, University of
Glasgow, Glasgow G12 8QQ, U.K.
| | - Nhan T. Pham
- School
of Biological Sciences, University of Edinburgh, Edinburgh, Scotland EH9 3BF, U.K.
- College
of Medicine and Veterinary Medicine, Institute for Regeneration and
Repair, University of Edinburgh, 4-5 Little France Drive, Edinburgh EH16 4UU, U.K.
| | - Steven Shave
- School
of Biological Sciences, University of Edinburgh, Edinburgh, Scotland EH9 3BF, U.K.
- Edinburgh
Cancer Research, Cancer Research UK Scotland Centre, Institute of
Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, U.K.
| | - Daniel St-Cyr
- X-Chem
Inc., Montréal, Québec H4S 1Z9, Canada
- Institute
for Research in Immunology and Cancer, University
of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Derek F. Ceccarelli
- Centre
for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Steven Orlicky
- Centre
for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Anne Marinier
- Institute
for Research in Immunology and Cancer, University
of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Frank Sicheri
- Centre
for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Mike Tyers
- Institute
for Research in Immunology and Cancer, University
of Montreal, Montreal, Québec H3T 1J4, Canada
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Manfred Auer
- School
of Biological Sciences, University of Edinburgh, Edinburgh, Scotland EH9 3BF, U.K.
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2
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Hou Z, Sun A, Li Y, Song X, Liu S, Hu X, Luan Y, Guan H, He C, Sun Y, Chen J. What Are the Reliable Plasma Biomarkers for Mild Cognitive Impairment? A Clinical 4D Proteomics Study and Validation. Mediators Inflamm 2024; 2024:7709277. [PMID: 38883967 PMCID: PMC11178428 DOI: 10.1155/2024/7709277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/20/2024] [Accepted: 04/30/2024] [Indexed: 06/18/2024] Open
Abstract
Objective At present, Alzheimer's disease (AD) lacks effective treatment means, and early diagnosis and intervention are the keys to treatment. Therefore, for mild cognitive impairment (MCI) and AD patients, blood sample analysis using the 4D nonstandard (label-free) proteomic in-depth quantitative analysis, looking for specific protein marker expression differences, is important. These marker levels change as AD progresses, and the analysis of these biomarkers changes with this method, which has the potential to show the degree of disease progression and can be used for the diagnosis and preventive treatment of MCI and AD. Materials and Methods Patients were recruited according to the inclusion and exclusion criteria and divided into three groups according to scale scores. Elderly patients diagnosed with AD were selected as the AD group (n = 9). Patients diagnosed with MCI were classified into the MCI group (n = 10). Cognitively healthy elderly patients were included in the normal cognition control group (n = 10). Patients' blood samples were used for 4D label-free proteomic in-depth quantitative analysis to identify potential blood biomarkers. The sample size of each group was expanded (n = 30), and the selected biomarkers were verified by enzyme-linked immunosorbent assay (ELISA) to verify the accuracy of the proteomic prediction. Results Six specific blood markers, namely, APOE, MMP9, UBR5, PLA2G7, STAT5B, and S100A8, were detected by 4D label-free proteomic quantitative analysis. These markers showed a statistically significant upregulation trend in the MCI and AD groups compared with the normal cognition control group (P < 0.05). ELISA results showed that the levels of these six proteins in the MCI group were significantly higher than those in the normal cognition control group, and the levels of these six proteins in the AD group were significantly higher than those in the MCI group (P < 0.05). Conclusion The plasma levels of APOE, MMP9, UBR5, PLA2G7, STAT5B, and S100A8 in cognitively healthy elderly patients and patients with MCI and AD were significantly different and, more importantly, showed a trend of increasing expression. These results indicate that these six human plasma markers have important diagnostic and therapeutic potential in the identification of cognitive impairment and have value for in-depth research and clinical application.
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Affiliation(s)
- Zhitao Hou
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania, Philadelphia 19104, PA, USA
- Key Laboratory of Chinese Internal Medicine of the Ministry of Education Dongzhimen Hospital Affiliated with Beijing University of Chinese Medicine, Beijing 100700, China
- The First Hospital Affiliated with Heilongjiang University of Chinese Medicine, Harbin 150010, Heilongjiang, China
| | - Ailin Sun
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
- Pudong Hospital Affiliated with Fudan University, Shanghai 200120, China
| | - Yan Li
- The First Hospital Affiliated with Heilongjiang University of Chinese Medicine, Harbin 150010, Heilongjiang, China
| | - Xiaochen Song
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
| | - Shu Liu
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
| | - Xinying Hu
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
| | - Yihan Luan
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
| | - Huibo Guan
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
| | - Changyuan He
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
| | - Yuefeng Sun
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
| | - Jing Chen
- College of Basic Medical and Sciences Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang, China
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3
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Mikhailovskii O, Izmailov SA, Xue Y, Case DA, Skrynnikov NR. X-ray Crystallography Module in MD Simulation Program Amber 2023. Refining the Models of Protein Crystals. J Chem Inf Model 2024; 64:18-25. [PMID: 38147516 DOI: 10.1021/acs.jcim.3c01531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
The MD simulation package Amber offers an attractive platform to refine crystallographic structures of proteins: (i) state-of-the-art force fields help to regularize protein coordinates and reconstruct the poorly diffracting elements of the structure, such as flexible loops; (ii) MD simulations restrained by the experimental diffraction data provide an effective strategy to optimize structural models of protein crystals, including explicitly modeled interstitial solvent as well as crystal contacts. Here, we present the new crystallography module xray, released as a part of the Amber 2023 package. This module contains functions to calculate and scale structure factors (including the contributions from bulk solvent), evaluate the maximum-likelihood-type crystallographic potential, and compute its derivative forces. The X-ray functionality of Amber no longer relies on external dependencies so that the full advantage of GPU acceleration can be taken. This makes it possible to refine in a short time hundreds of crystal models, including supercell models comprised of multiple unit cells. The new automated Amber-based refinement procedure leads to an appreciable improvement in Rfree (in some cases, by as much as 0.067) as well as MolProbity scores.
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Affiliation(s)
- Oleg Mikhailovskii
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Sergei A Izmailov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Yi Xue
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - David A Case
- Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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Nawarathnage S, Tseng YJ, Soleimani S, Smith T, Pedroza Romo MJ, Abiodun WO, Egbert CM, Madhusanka D, Bunn D, Woods B, Tsubaki E, Stewart C, Brown S, Doukov T, Andersen JL, Moody JD. Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain. Structure 2023; 31:1589-1603.e6. [PMID: 37776857 PMCID: PMC10843481 DOI: 10.1016/j.str.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/11/2023] [Accepted: 09/04/2023] [Indexed: 10/02/2023]
Abstract
Human thirty-eight-negative kinase-1 (TNK1) is implicated in cancer progression. The TNK1 ubiquitin-associated (UBA) domain binds polyubiquitin and plays a regulatory role in TNK1 activity and stability. No experimentally determined molecular structure of this unusual UBA domain is available. We fused the UBA domain to the 1TEL variant of the translocation ETS leukemia protein sterile alpha motif (TELSAM) crystallization chaperone and obtained crystals diffracting as far as 1.53 Å. GG and GSGG linkers allowed the UBA to reproducibly find a productive binding mode against its host 1TEL polymer and crystallize at protein concentrations as low as 0.2 mg/mL. Our studies support a mechanism of 1TEL fusion crystallization and show that 1TEL fusion crystals require fewer crystal contacts than traditional protein crystals. Modeling and experimental validation suggest the UBA domain may be selective for both the length and linkages of polyubiquitin chains.
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Affiliation(s)
| | - Yi Jie Tseng
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Sara Soleimani
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Tobin Smith
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Maria J Pedroza Romo
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Wisdom O Abiodun
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Christina M Egbert
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA; Fritz B. Burns Cancer Research Laboratory, Brigham Young University, Provo, UT, USA
| | - Deshan Madhusanka
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA; Fritz B. Burns Cancer Research Laboratory, Brigham Young University, Provo, UT, USA
| | - Derick Bunn
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Bridger Woods
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Evan Tsubaki
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Cameron Stewart
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Seth Brown
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Tzanko Doukov
- Macromolecular Crystallography Group, Structural Molecular Biology Resource, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA
| | - Joshua L Andersen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA; Fritz B. Burns Cancer Research Laboratory, Brigham Young University, Provo, UT, USA.
| | - James D Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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5
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Nawarathnage S, Tseng YJ, Soleimani S, Smith T, Romo MJP, Abiodun WO, Egbert CM, Madhusanka D, Bunn D, Woods B, Tsubaki E, Stewart C, Brown S, Doukov T, Andersen JL, Moody JD. Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544429. [PMID: 37398013 PMCID: PMC10312729 DOI: 10.1101/2023.06.14.544429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Human thirty-eight-negative kinase-1 (TNK1) is implicated in cancer progression. The TNK1-UBA domain binds polyubiquitin and plays a regulatory role in TNK1 activity and stability. Sequence analysis suggests an unusual architecture for the TNK1 UBA domain, but an experimentally-validated molecular structure is undetermined. To gain insight into TNK1 regulation, we fused the UBA domain to the 1TEL crystallization chaperone and obtained crystals diffracting as far as 1.53 Å. A 1TEL search model enabled solution of the X-ray phases. GG and GSGG linkers allowed the UBA to reproducibly find a productive binding mode against its host 1TEL polymer and to crystallize at protein concentrations as low as 0.1 mg/mL. Our studies support a mechanism of TELSAM fusion crystallization and show that TELSAM fusion crystals require fewer crystal contacts than traditional protein crystals. Modeling and experimental validation suggest the UBA domain may be selective for both the length and linkages of polyubiquitin chains.
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Affiliation(s)
- Supeshala Nawarathnage
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
- These authors contributed equally to this work
| | - Yi Jie Tseng
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
- These authors contributed equally to this work
| | - Sara Soleimani
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
- These authors contributed equally to this work
| | - Tobin Smith
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Maria J Pedroza Romo
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Wisdom Oshireku Abiodun
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Christina M. Egbert
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Deshan Madhusanka
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Derick Bunn
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Bridger Woods
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Evan Tsubaki
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Cameron Stewart
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Seth Brown
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Tzanko Doukov
- Macromolecular Crystallography Group, Structural Molecular Biology Resource, Stanford Synchrotron Radiation Lightsource, Menlo Park, California, United States of America
| | - Joshua L. Andersen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - James D. Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
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6
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Wagh AR, Sulakshane P, Glickman MH. Alzheimer's disease-associated mutant ubiquitin (UBB +1) is secreted through an autophagosome-like vesicle-mediated unconventional pathway. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194936. [PMID: 37075976 DOI: 10.1016/j.bbagrm.2023.194936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/28/2023] [Accepted: 04/13/2023] [Indexed: 04/21/2023]
Abstract
Misfolded protein aggregation at both intracellular and extracellular milieus is thought to be the major etiology of Alzheimer's disease (AD). UBB+1, a frameshift variant of the ubiquitin B gene (UBB) results in a folded ubiquitin domain fused to a flexible unstructured extension. Accumulation of UBB+1 in extracellular plaques in the brains of AD patients undoubtedly suggests a role of the ubiquitin-proteasome system in AD. However, the exact mechanism of extracellular secretion of UBB+1 remains unknown. In an attempt to understand the molecular mechanism of UBB+1 secretion, we performed a survey of secretory pathways and identified the involvement of unconventional autophagosome-mediated UBB+1 secretion. Expression of UBB+1 was sufficient to stimulate LC3B/Atg8 conversion from LC3B-I to LC3B-II, which indicates initiation of the autophagy pathway. Furthermore, deficiency of ATG5 - a key player in autophagosome formation - inhibited UBB+1 secretion. Based on immunofluorescence 3D structured illumination (SIM) microscopy and co-immunoprecipitation, we provide evidence that UBB+1 is associated with the secretory autophagosome marker, SEC22B, while HSP90 possibly acts as a carrier. Using LC-MS/MS and mutagenesis we found that in cells, UBB+1 is ubiquitinated on lysine 11, 29, and 48, however, this ubiquitination does not contribute to its secretion. By contrast, proteasome or lysosome inhibition slightly enhanced secretion. Taken together, this study suggests that by ridding cells of UBB+1, secretory autophagosomes may alleviate the cellular stress associated with UBB+1, yet simultaneously mediate the spreading of a mutant specie with disordered characteristics to the extracellular milieu.
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Affiliation(s)
- Ajay R Wagh
- The Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Prasad Sulakshane
- The Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Michael H Glickman
- The Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel.
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7
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Middleton AJ, Day CL. From seeds to trees: how E2 enzymes grow ubiquitin chains. Biochem Soc Trans 2023; 51:353-362. [PMID: 36645006 PMCID: PMC9987950 DOI: 10.1042/bst20220880] [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: 11/24/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/17/2023]
Abstract
Modification of proteins by ubiquitin is a highly regulated process that plays a critical role in eukaryotes, from the construction of signalling platforms to the control of cell division. Aberrations in ubiquitin transfer are associated with many diseases, including cancer and neurodegenerative disorders. The ubiquitin machinery generates a rich code on substrate proteins, spanning from single ubiquitin modifications to polyubiquitin chains with diverse linkage types. Central to this process are the E2 enzymes, which often determine the exact nature of the ubiquitin code. The focus of this mini-review is on the molecular details of how E2 enzymes can initiate and grow ubiquitin chains. In particular, recent developments and biochemical breakthroughs that help explain how the degradative E2 enzymes, Ube2s, Ube2k, and Ube2r, generate complex ubiquitin chains with exquisite specificity will be discussed.
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Affiliation(s)
- Adam J. Middleton
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Catherine L. Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
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8
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Characterization of the chimeric protein cUBC1 engineered by substituting the linker of E2-25K into UBC1 enzyme of Saccharomyces cerevisiae. Int J Biol Macromol 2022; 209:991-1000. [PMID: 35429515 DOI: 10.1016/j.ijbiomac.2022.04.057] [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: 12/03/2021] [Revised: 03/27/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022]
Abstract
Ubiquitination is an important posttranslational modification of proteins in eukaryotic cells, wherein ubiquitin molecules are conjugated to target proteins. Ubiquitination is catalyzed by the cascade of ubiquitin activating enzyme (E1), ubiquitin conjugating enzyme (E2), and ubiquitin ligase (E3). The number of E2s encoded in eukaryotes partly explains their contribution to the inherent specificity of the ubiquitin system. The ubiquitin conjugating enzyme UBC1 of Saccharomyces cerevisiae participates the degradation of short-lived and abnormal proteins. UBC1 consists of two well-defined domains separated by a long flexible linker. E2-25K, the human homolog of UBC1 is crucial to neurons and its failure leads to neurodegenerative disorders. The linker of UBC1 is of 22 amino acids, while that of E2-25K has 6 amino acids. To understand the importance of the linker, the chimeric protein, cUBC1 was constructed by substituting the linker of E2-25K in UBC1. cUBC1 shows minor changes in its secondary structure. cUBC1 expression in ubc1 deletion mutants showed no effect over growth, thermotolerance and resistance to antibiotic stress. However, survival under heat stress was enhanced with cUBC1. Western blot analysis of the enzymatic activity showed cUBC1 performed equally well as UBC1. Hence, cUBC1 demonstrates that the shorter linker increased the stability of UBC1.
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9
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Nakasone MA, Majorek KA, Gabrielsen M, Sibbet GJ, Smith BO, Huang DT. Structure of UBE2K-Ub/E3/polyUb reveals mechanisms of K48-linked Ub chain extension. Nat Chem Biol 2022; 18:422-431. [PMID: 35027744 PMCID: PMC8964413 DOI: 10.1038/s41589-021-00952-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/30/2021] [Indexed: 01/03/2023]
Abstract
Ubiquitin (Ub) chain types govern distinct biological processes. K48-linked polyUb chains target substrates for proteasomal degradation, but the mechanism of Ub chain synthesis remains elusive due to the transient nature of Ub handover. Here, we present the structure of a chemically trapped complex of the E2 UBE2K covalently linked to donor Ub and acceptor K48-linked di-Ub, primed for K48-linked Ub chain synthesis by a RING E3. The structure reveals the basis for acceptor Ub recognition by UBE2K active site residues and the C-terminal Ub-associated (UBA) domain, to impart K48-linked Ub specificity and catalysis. Furthermore, the structure unveils multiple Ub-binding surfaces on the UBA domain that allow distinct binding modes for K48- and K63-linked Ub chains. This multivalent Ub-binding feature serves to recruit UBE2K to ubiquitinated substrates to overcome weak acceptor Ub affinity and thereby promote chain elongation. These findings elucidate the mechanism of processive K48-linked polyUb chain formation by UBE2K.
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Affiliation(s)
| | | | - Mads Gabrielsen
- Cancer Research UK Beatson Institute, Glasgow, UK
- MVLS Structural Biology and Biophysical Characterisation Facility, University of Glasgow, Glasgow, UK
| | | | - Brian O Smith
- Institute of Molecular Cell and System Biology, University of Glasgow, Glasgow, UK
| | - Danny T Huang
- Cancer Research UK Beatson Institute, Glasgow, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
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10
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Mikhailovskii O, Xue Y, Skrynnikov NR. Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber. IUCRJ 2022; 9:114-133. [PMID: 35059216 PMCID: PMC8733891 DOI: 10.1107/s2052252521011891] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
A procedure has been developed for the refinement of crystallographic protein structures based on the biomolecular simulation program Amber. The procedure constructs a model representing a crystal unit cell, which generally contains multiple protein molecules and is fully hydrated with TIP3P water. Periodic boundary conditions are applied to the cell in order to emulate the crystal lattice. The refinement is conducted in the form of a specially designed short molecular-dynamics run controlled by the Amber ff14SB force field and the maximum-likelihood potential that encodes the structure-factor-based restraints. The new Amber-based refinement procedure has been tested on a set of 84 protein structures. In most cases, the new procedure led to appreciably lower R free values compared with those reported in the original PDB depositions or obtained by means of the industry-standard phenix.refine program. In particular, the new method has the edge in refining low-accuracy scrambled models. It has also been successful in refining a number of molecular-replacement models, including one with an r.m.s.d. of 2.15 Å. In addition, Amber-refined structures consistently show superior MolProbity scores. The new approach offers a highly realistic representation of protein-protein interactions in the crystal, as well as of protein-water interactions. It also offers a realistic representation of protein crystal dynamics (akin to ensemble-refinement schemes). Importantly, the method fully utilizes the information from the available diffraction data, while relying on state-of-the-art molecular-dynamics modeling to assist with those elements of the structure that do not diffract well (for example mobile loops or side chains). Finally, it should be noted that the protocol employs no tunable parameters, and the calculations can be conducted in a matter of several hours on desktop computers equipped with graphical processing units or using a designated web service.
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Affiliation(s)
- Oleg Mikhailovskii
- Laboratory of Biomolecular NMR, St Petersburg State University, St Petersburg 199034, Russian Federation
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Yi Xue
- School of Life Sciences, Tsinghua University, Beijing 100084, People’s Republic of China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, People’s Republic of China
- Tsinghua University–Peking University Joint Center for Life Sciences, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Nikolai R. Skrynnikov
- Laboratory of Biomolecular NMR, St Petersburg State University, St Petersburg 199034, Russian Federation
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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11
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Banasiak K, Szulc NA, Pokrzywa W. The Dose-Dependent Pleiotropic Effects of the UBB +1 Ubiquitin Mutant. Front Mol Biosci 2021; 8:650730. [PMID: 33842548 PMCID: PMC8032880 DOI: 10.3389/fmolb.2021.650730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/02/2021] [Indexed: 11/23/2022] Open
Abstract
The proteolytic machinery activity diminishes with age, leading to abnormal accumulation of aberrant proteins; furthermore, a decline in protein degradation capacity is associated with multiple age-related proteinopathies. Cellular proteostasis can be maintained via the removal of ubiquitin (Ub)-tagged damaged and redundant proteins by the ubiquitin-proteasome system (UPS). However, during aging, central nervous system (CNS) cells begin to express a frameshift-mutated Ub, UBB+1. Its accumulation is a neuropathological hallmark of tauopathy, including Alzheimer’s disease and polyglutamine diseases. Mechanistically, in cell-free and cell-based systems, an increase in the UBB+1 concentration disrupts proteasome processivity, leading to increased aggregation of toxic proteins. On the other hand, a low level of UBB+1 improves stress resistance and extends lifespan. Here we summarize recent findings regarding the impact of UBB+1 on Ub signaling and neurodegeneration. We also review the molecular basis of how UBB+1 affects UPS components as well as its dose-dependent switch between cytoprotective and cytotoxic roles.
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Affiliation(s)
- Katarzyna Banasiak
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Natalia A Szulc
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
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12
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Pluska L, Jarosch E, Zauber H, Kniss A, Waltho A, Bagola K, von Delbrück M, Löhr F, Schulman BA, Selbach M, Dötsch V, Sommer T. The UBA domain of conjugating enzyme Ubc1/Ube2K facilitates assembly of K48/K63-branched ubiquitin chains. EMBO J 2021; 40:e106094. [PMID: 33576509 PMCID: PMC7957398 DOI: 10.15252/embj.2020106094] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/22/2020] [Accepted: 01/05/2021] [Indexed: 12/23/2022] Open
Abstract
The assembly of a specific polymeric ubiquitin chain on a target protein is a key event in the regulation of numerous cellular processes. Yet, the mechanisms that govern the selective synthesis of particular polyubiquitin signals remain enigmatic. The homologous ubiquitin-conjugating (E2) enzymes Ubc1 (budding yeast) and Ube2K (mammals) exclusively generate polyubiquitin linked through lysine 48 (K48). Uniquely among E2 enzymes, Ubc1 and Ube2K harbor a ubiquitin-binding UBA domain with unknown function. We found that this UBA domain preferentially interacts with ubiquitin chains linked through lysine 63 (K63). Based on structural modeling, in vitro ubiquitination experiments, and NMR studies, we propose that the UBA domain aligns Ubc1 with K63-linked polyubiquitin and facilitates the selective assembly of K48/K63-branched ubiquitin conjugates. Genetic and proteomics experiments link the activity of the UBA domain, and hence the formation of this unusual ubiquitin chain topology, to the maintenance of cellular proteostasis.
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Affiliation(s)
- Lukas Pluska
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Ernst Jarosch
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Henrik Zauber
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Andreas Kniss
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic ResonanceGoethe UniversityFrankfurt am MainGermany
| | - Anita Waltho
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Katrin Bagola
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | | | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic ResonanceGoethe UniversityFrankfurt am MainGermany
| | - Brenda A Schulman
- Department of Molecular Machines and SignalingMax Planck Institute of BiochemistryMartinsriedGermany
| | - Matthias Selbach
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
- Charité – Universitätsmedizin BerlinBerlinGermany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic ResonanceGoethe UniversityFrankfurt am MainGermany
| | - Thomas Sommer
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
- Institute for BiologyHumboldt‐Universität zu BerlinBerlinGermany
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13
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Wang Q, Dong Z, Su J, Huang J, Xiao P, Tian L, Chen Y, Ma L, Chen X. Ixazomib inhibits myeloma cell proliferation by targeting UBE2K. Biochem Biophys Res Commun 2021; 549:1-7. [PMID: 33647537 DOI: 10.1016/j.bbrc.2021.02.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/11/2021] [Indexed: 11/26/2022]
Abstract
PURPOSE Ixazomib is a selective, effective, and reversible inhibitor of 20S proteasome and is approved for the treatment of multiple myeloma. Ubiquitin-conjugating enzyme E2 (UBE2K) is involved in the synthesis of K48-linked ubiquitin chains and is the target of certain drugs used for the treatment of tumors. The purpose of this study was to investigate the relationship between ixazomib and UBE2K in myeloma cells. METHODS We used CCK-8 and Annexin V-FITC/propidium iodide kit to detect the effects of ixazomib on survival and apoptosis of RPMI-8226 and U-266 myeloma cell lines. Quantitative polymerase chain reaction and western blot were used to detect the change in gene and protein expression levels of myeloma cells treated with ixazomib. Furthermore, the regulatory effects of ixazomib on UBE2K and its downstream targets were investigated following the overexpression of UBE2K. RESULTS In myeloma cells, ixazomib decreased cell survival and increased apoptosis in a dose-dependent manner. Ixazomib significantly increased the expression of HIST1H2BD, MNAT1, NEK3, and TARS2, while decreasing the expression of HSPA1B and UBE2K. In addition, ixazomib inhibited the proliferation of myeloma cells, blocked cell cycle, induced cell apoptosis, and increased the production of reactive oxygen species by inhibiting UBE2K expression. Lastly, ixazomib regulates mitosis- and apoptosis-related genes by lowering UBE2K expression. CONCLUSION In summary, ixazomib leads to impaired proliferation of myeloma cells by targeting UBE2K.
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Affiliation(s)
- Qingqing Wang
- Blood Rheumatism Immunology Department, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, Fujian, China.
| | - Zhigao Dong
- Blood Rheumatism Immunology Department, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, Fujian, China.
| | - Junnan Su
- Blood Rheumatism Immunology Department, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, Fujian, China.
| | - Jinmei Huang
- Blood Rheumatism Immunology Department, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, Fujian, China.
| | - Pingping Xiao
- Blood Rheumatism Immunology Department, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, Fujian, China.
| | - Lihong Tian
- Blood Rheumatism Immunology Department, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, Fujian, China.
| | - Yongquan Chen
- Blood Rheumatism Immunology Department, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, Fujian, China.
| | - Lili Ma
- Blood Rheumatism Immunology Department, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, Fujian, China.
| | - Xuyan Chen
- Blood Rheumatism Immunology Department, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, Fujian, China.
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14
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Watson ME, Scott D, Jamieson C, Layfield R, Mason AM. Design, synthesis and evaluation of E2‐25K derived stapled peptides. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Morag E. Watson
- Department of Pure and Applied Chemistry University of Strathclyde Glasgow UK
| | - Daniel Scott
- School of Life Sciences, University of Nottingham Medical School Nottingham UK
| | - Craig Jamieson
- Department of Pure and Applied Chemistry University of Strathclyde Glasgow UK
| | - Robert Layfield
- School of Life Sciences, University of Nottingham Medical School Nottingham UK
| | - Andrew M. Mason
- Medicinal Sciences and Technology, GlaxoSmithKline Research and Development, Medicines Research Centre Stevenage Herts UK
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15
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Cook BW, Lacoursiere RE, Shaw GS. Recruitment of Ubiquitin within an E2 Chain Elongation Complex. Biophys J 2020; 118:1679-1689. [PMID: 32101714 DOI: 10.1016/j.bpj.2020.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/26/2022] Open
Abstract
The ubiquitin (Ub) proteolysis pathway uses an E1, E2, and E3 enzyme cascade to label substrate proteins with ubiquitin and target them for degradation. The mechanisms of ubiquitin chain formation remain unclear and include a sequential addition model, in which polyubiquitin chains are built unit by unit on the substrate, or a preassembly model, in which polyubiquitin chains are preformed on the E2 or E3 enzyme and then transferred in one step to the substrate. The E2 conjugating enzyme UBE2K has a 150-residue catalytic core domain and a C-terminal ubiquitin-associated (UBA) domain. Polyubiquitin chains anchored to the catalytic cysteine and free in solution are formed by UBE2K supporting a preassembly model. To study how UBE2K might assemble polyubiquitin chains, we synthesized UBE2K-Ub and UBE2K-Ub2 covalent complexes and analyzed E2 interactions with the covalently attached Ub and Ub2 moieties using NMR spectroscopy. The UBE2K-Ub complex exists in multiple conformations, including the catalytically competent closed state independent of the UBA domain. In contrast, the UBE2K-Ub2 complex takes on a more extended conformation directed by interactions between the classic I44 hydrophobic face of the distal Ub and the conserved MGF hydrophobic patch of the UBA domain. Our results indicate there are distinct differences between the UBE2K-Ub and UBE2K-Ub2 complexes and show how the UBA domain can alter the position of a polyubiquitin chain attached to the UBE2K active site. These observations provide structural insights into the unique Ub chain-building capacity for UBE2K.
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Affiliation(s)
- Benjamin W Cook
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Rachel E Lacoursiere
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Gary S Shaw
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada.
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16
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Lee JG, Youn HS, Kang JY, Park SY, Kidera A, Yoo YJ, Eom SH. Crystal structure of the Ube2K/E2-25K and K48-linked di-ubiquitin complex provides structural insight into the mechanism of K48-specific ubiquitin chain synthesis. Biochem Biophys Res Commun 2018; 506:102-107. [DOI: 10.1016/j.bbrc.2018.10.067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 10/10/2018] [Indexed: 02/08/2023]
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17
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Synthesis and purification of linkage-specific polyubiquitin chains of distinct length for structural studies. Anal Biochem 2018; 559:1-4. [PMID: 30107157 DOI: 10.1016/j.ab.2018.08.007] [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: 01/22/2018] [Accepted: 08/08/2018] [Indexed: 11/22/2022]
Abstract
Polyubiquitylation is one of the most versatile post-translational modifications involved in the regulation of numerous intracellular signaling processes. An assembly procedure that is simple, robust, and efficient to synthesize and purify linkage-specific polyubiquitin chains of defined length at a preparative scale is required in biophysical and structural studies. Here, we have optimized known enzymatic procedures in the form of a protocol to obtain multi-milligrams of Lys48-and Lys63-linked polyubiquitin chain types with more than 99% purity. Mass spectrometry (ESI/MS) analysis of K48- and K63-linked diubiquitin confirmed that the enzymes used in the preparation generated homogeneous linkages with no promiscuity.
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18
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Hip2 ubiquitin-conjugating enzyme has a role in UV-induced G1/S arrest and re-entry. Genes Genomics 2018; 41:159-166. [PMID: 30264212 DOI: 10.1007/s13258-018-0747-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/19/2018] [Indexed: 12/13/2022]
Abstract
Regulation of cell cycle arrest and re-entry triggered by DNA damage is vital for cell division and growth and is also involved in cell survival. UV radiation can generate lesions in the DNA, which results in cell cycle arrest and the induction of the DNA repair process. However, the mechanism of promoting cell cycle progression following DNA repair is elusive. The primary aim of this study is to investigate whether Hip2 ubiquitin-conjugating enzyme has a role in UV-induced G1/S arrest and re-entry. The phase of HEK293 cells was synchronized at the G1/S border using thymidine. The synchronously proliferating cells were exposed to UV radiation to cause DNA damage. We investigated the expression of p53, Hip2, p21, cyclin D and E proteins that are involved in the cell cycle progression. Finally, we examined changes in the phosphorylation of Hip2 after UV radiation treatment using the pIMAGO™ assay. When cells were exposed to UV radiation, expression of p53 was elevated, and the cell cycle was arrested at the G1/S boundary. In response to the increased p53 level, Hip2 became phosphorylated and activated through the inhibition of its degradation. The phosphorylated Hip2 inhibited p53, thereby suppressing the expression of p21, a downstream signal, and sequentially stimulating cyclin D and cyclin E to induce re-entry to the cell cycle. Our studies demonstrate that Hip2 works as a regulator in UV-induced cell cycle arrest and re-entry.
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19
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Muñoz-Arellano AJ, Chen X, Molt A, Meza E, Petranovic D. Different Expression Levels of Human Mutant Ubiquitin B +1 (UBB +1) Can Modify Chronological Lifespan or Stress Resistance of Saccharomyces cerevisiae. Front Mol Neurosci 2018; 11:200. [PMID: 29950972 PMCID: PMC6008557 DOI: 10.3389/fnmol.2018.00200] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 05/18/2018] [Indexed: 11/13/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is the main pathway responsible for the degradation of misfolded proteins, and its dysregulation has been implicated in several neurodegenerative diseases, including Alzheimer's disease (AD). UBB+1, a mutant variant of ubiquitin B, was found to accumulate in neurons of AD patients and it has been linked to UPS dysfunction and neuronal death. Using the yeast Saccharomyces cerevisiae as a model system, we constitutively expressed UBB+1 to evaluate its effects on proteasome function and cell death, particularly under conditions of chronological aging. We showed that the expression of UBB+1 caused inhibition of the three proteasomal proteolytic activities (caspase-like (β1), trypsin-like (β2) and chymotrypsin-like (β5) activities) in yeast. Interestingly, this inhibition did not alter cell viability of growing cells. Moreover, we showed that cells expressing UBB+1 at lower level displayed an increased capacity to degrade induced misfolded proteins. When we evaluated cells during chronological aging, UBB+1 expression at lower level, prevented cells to accumulate reactive oxygen species (ROS) and avert apoptosis, dramatically increasing yeast life span. Since proteasome inhibition by UBB+1 has previously been shown to induce chaperone expression and thus protect against stress, we evaluated our UBB+1 model under heat shock and oxidative stress. Higher expression of UBB+1 caused thermotolerance in yeast due to induction of chaperones, which occurred to a lesser extent at lower expression level of UBB+1 (where we observed the phenotype of extended life span). Altering UPS capacity by differential expression of UBB+1 protects cells against several stresses during chronological aging. This system can be valuable to study the effects of UBB+1 on misfolded proteins involved in neurodegeneration and aging.
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Affiliation(s)
- Ana Joyce Muñoz-Arellano
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Xin Chen
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Andrea Molt
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Eugenio Meza
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Dina Petranovic
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
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20
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Active Site Gate Dynamics Modulate the Catalytic Activity of the Ubiquitination Enzyme E2-25K. Sci Rep 2018; 8:7002. [PMID: 29725124 PMCID: PMC5934386 DOI: 10.1038/s41598-018-25476-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/23/2018] [Indexed: 12/13/2022] Open
Abstract
The ubiquitin proteasome system (UPS) signals for degradation of proteins through attachment of K48-linked polyubiquitin chains, or alterations in protein-protein recognition through attachment of K63-linked chains. Target proteins are ubiquitinated in three sequential chemical steps by a three-component enzyme system. Ubiquitination, or E2 enzymes, catalyze the central step by facilitating reaction of a target protein lysine with the C-terminus of Ub that is attached to the active site cysteine of the E2 through a thioester bond. E2 reactivity is modulated by dynamics of an active site gate, whose central residue packs against the active site cysteine in a closed conformation. Interestingly, for the E2 Ubc13, which specifically catalyzes K63-linked ubiquitination, the central gate residue adopts an open conformation. We set out to determine if active site gate dynamics play a role in catalysis for E2-25K, which adopts the canonical, closed gate conformation, and which selectively synthesizes K48-linked ubiquitin chains. Gate dynamics were characterized using mutagenesis of key residues, combined with enzyme kinetics measurements, and main chain NMR relaxation. The experimental data were interpreted with all atom MD simulations. The data indicate that active site gate opening and closing rates for E2-25K are precisely balanced.
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21
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Munari F, Bortot A, Assfalg M, D'Onofrio M. Alzheimer's disease-associated ubiquitin mutant Ubb +1: Properties of the carboxy-terminal domain and its influence on biomolecular interactions. Int J Biol Macromol 2017; 108:24-31. [PMID: 29175520 DOI: 10.1016/j.ijbiomac.2017.11.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/17/2017] [Accepted: 11/19/2017] [Indexed: 12/19/2022]
Abstract
Ubb+1, a ubiquitin (Ub) mutant protein originating from misreading of the Ub B gene, is found accumulated in brain tissues of Alzheimer's disease patients. The mutant attracts strong interest due to its possible participation in the molecular events leading to neurodegeneration. Ubb+1 is composed of the globular domain of Ub, linked to a 19-residue C-terminal peptide. Based on NMR relaxation and solvent accessibility measurements we obtained new insight into the molecular properties of Ubb+1. We further determined the thermal stability of Ubb+1 in the monomeric form, and in Lys48- and Lys63-linked dimers. Finally, we explored the influence of the C-terminal fragment on the interactions of Ubb+1 with an isolated UBA2 domain and with membrane mimics. Our data indicate that the C-terminal fragment of Ubb+1 is overall highly flexible, except for a short stretch which appears less solvent-exposed. While influencing the hydrodynamic properties of the globular domain, the fragment does not establish long-lived interactions with the globular domain. It results that the structure and stability of Ub are minimally perturbed by the peptide extension. However, binding to UBA2 and to membrane mimics are both affected, exemplifying possible changes in biomolecular recognition experienced by the disease-associated Ubb+1 compared to the wild-type protein.
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Affiliation(s)
- Francesca Munari
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Andrea Bortot
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
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22
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Searching for Correlations Between the Development of Neurodegenerative Hallmarks: Targeting Huntingtin as a Contributing Factor. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [PMID: 28971465 DOI: 10.1007/978-3-319-57379-3_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
This paper aims to study four general hallmarks of neurodegeneration and the correlations between them, with emphasis on the huntingtin (htt) interactions contributing to their prevention or promotion in its wild-type and mutated forms. Most of the neurodegenerative diseases share same or similar cell dysfunctions and huntingtin seems to associate in an polyglutamine-length dependent manner with components of the mechanisms that can go impaired. Therefore, the protein is proposed as contributing factor to the development of selective neurodegeneration.
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23
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Singh RK, Kazansky Y, Wathieu D, Fushman D. Hydrophobic Patch of Ubiquitin is Important for its Optimal Activation by Ubiquitin Activating Enzyme E1. Anal Chem 2017; 89:7852-7860. [PMID: 28686836 PMCID: PMC5573600 DOI: 10.1021/acs.analchem.6b04194] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein ubiquitination plays a role in essentially every process in eukaryotic cells. The attachment of ubiquitin (Ub) or Ub-like (UBL) proteins to target proteins is achieved by parallel but distinct cascades of enzymatic reactions involving three enzymes: E1, E2, and E3. The E1 enzyme functions at the apex of this pathway and plays a critical role in activating the C-terminus of ubiquitin or UBL, which is an essential step that triggers subsequent downstream transfer to their cognate E2s resulting in the fidelity of the Ub/UBL conjugation machinery. Despite the central role of the E1 enzyme in protein modification, a quantitative method to measure Ub/UBL activation by E1 is lacking. Here, we present a mass spectrometry-based assay to accurately measure the activation of Ub/UBL by E1 independent of the E2/E3 enzymes. Our method does not require radiolabeling of any components and therefore can be used in any biochemical laboratory having access to a mass spectrometer. This method allowed us to dissect the concerted process of E1-E2-catalyzed Ub conjugation in order to separately characterize the process of Ub activation and how it is affected by select mutations and other factors. We found that the hydrophobic patch of Ub is important for the optimal activation of Ub by E1. We further show that the blockers of the Ub-proteasome system such as ubistatin and fullerenol inhibit Ub activation by E1. Interestingly, our data indicate that the phosphorylation of Ub at the S65 position augments its activation by the E1 enzyme.
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Affiliation(s)
- Rajesh K Singh
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland , College Park, Maryland 20742, United States
| | - Yaniv Kazansky
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland , College Park, Maryland 20742, United States
| | - Donald Wathieu
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland , College Park, Maryland 20742, United States
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland , College Park, Maryland 20742, United States
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24
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E2-25K SUMOylation inhibits proteasome for cell death during cerebral ischemia/reperfusion. Cell Death Dis 2016; 7:e2573. [PMID: 28032866 PMCID: PMC5261013 DOI: 10.1038/cddis.2016.428] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 01/12/2023]
Abstract
Cerebral ischemia/reperfusion (I/R) causes brain damage accompanied by ubiquitin accumulation and impairment of proteasome activity. In this study, we report that E2-25K, an E2-conjugating enzyme, is SUMOylated during oxidative stress and regulates cerebral I/R-induced damage. Knockdown of E2-25K expression protects against oxygen/glucose deprivation and reoxygenation (OGD/R)-induced neuronal cell death, whereas ectopic expression of E2-25K stimulates it. Compared with the control mice, cerebral infarction lesions and behavioral/neurological disorders are ameliorated in E2-25K knockout mice during middle cerebral artery occlusion and reperfusion. In particular, E2-25K is SUMOylated at Lys14 under oxidative stress, OGD/R and I/R to prompt cell death. Further, E2-25K downregulates the proteasome subunit S5a to impair proteasome complex and thus restrain proteasome activity under oxidative stress. This proteasome inhibitory activity of E2-25K is dependent on its SUMOylation. These results suggest that E2-25K has a crucial role in oxidative stress and cerebral I/R-induced damage through inhibiting proteasome via its SUMOylation.
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25
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Chojnacki M, Zhang D, Talarowska M, Gałecki P, Szemraj J, Fushman D, Nakasone MA. Characterizing polyubiquitinated forms of the neurodegenerative ubiquitin mutant UBB +1. FEBS Lett 2016; 590:4573-4585. [PMID: 27861798 DOI: 10.1002/1873-3468.12484] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/23/2016] [Accepted: 10/31/2016] [Indexed: 01/18/2023]
Abstract
The ubiquitin mutant UBB+1 has been identified as a hallmark of neurodegenerative diseases. In this study, we characterize polyubiquitinated forms of UBB+1 in vitro and from patient samples. The ability of UBB+1 to be readily ubiquitinated by several E2 enzymes provided a mechanism for the controlled synthesis and purification of defined conjugates. This allowed us to utilize polyUb-UBB+1 conjugates for biochemical assays, as well as solution NMR. Coupled with our immunoassay for detection of ubiquitinated forms of UBB+1 in patient blood samples, we gain a clearer picture of the molecular mechanisms underlying neurodegenerative diseases.
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Affiliation(s)
- Michal Chojnacki
- Department of Medical Biochemistry, Medical University of Łódź, Poland
| | - Daoning Zhang
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, USA
| | | | - Piotr Gałecki
- Department of Adult Psychiatry, Medical University of Łódź, Poland
| | - Janusz Szemraj
- Department of Medical Biochemistry, Medical University of Łódź, Poland
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, USA
| | - Mark A Nakasone
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, USA
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26
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Morimoto D, Shirakawa M. The evolving world of ubiquitin: transformed polyubiquitin chains. Biomol Concepts 2016; 7:157-67. [PMID: 27226101 DOI: 10.1515/bmc-2016-0009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/15/2016] [Indexed: 12/22/2022] Open
Abstract
The regulation of diverse cellular events by proteins that have undergone post-translational modification with ubiquitin is well documented. Ubiquitin can be polymerized and eight types of polyubiquitin chain contribute to the complexity and specificity of the ubiquitin signal. Unexpectedly, recent studies have shown that ubiquitin itself undergoes post-translational modification by acetylation and phosphorylation; moreover, amyloid-like fibrils comprised of polyubiquitin chains have been discovered. Thus, ubiquitin is not only conjugated to substrate proteins, but also modified and transformed itself. Here, we review these novel forms of ubiquitin signal, with a focus on fibril formation of polyubiquitin chains and its underlying biological relevance.
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Chen X, Petranovic D. Role of frameshift ubiquitin B protein in Alzheimer's disease. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2016; 8:300-13. [DOI: 10.1002/wsbm.1340] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/10/2016] [Accepted: 03/19/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Xin Chen
- Systems and Synthetic Biology, Department of Biology and Biological Engineering; Chalmers University of Technology; Göteborg Sweden
| | - Dina Petranovic
- Systems and Synthetic Biology, Department of Biology and Biological Engineering; Chalmers University of Technology; Göteborg Sweden
- Novo Nordisk Foundation Center for Biosustainability; Chalmers University of Technology; Göteborg Sweden
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28
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Middleton AJ, Day CL. The molecular basis of lysine 48 ubiquitin chain synthesis by Ube2K. Sci Rep 2015; 5:16793. [PMID: 26592444 PMCID: PMC4655369 DOI: 10.1038/srep16793] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/20/2015] [Indexed: 12/14/2022] Open
Abstract
The post-translational modification of proteins by ubiquitin is central to the regulation of eukaryotic cells. Substrate-bound ubiquitin chains linked by lysine 11 and 48 target proteins to the proteasome for degradation and determine protein abundance in cells, while other ubiquitin chain linkages regulate protein interactions. The specificity of chain-linkage type is usually determined by ubiquitin-conjugating enzymes (E2s). The degradative E2, Ube2K, preferentially catalyses formation of Lys48-linked chains, but like most E2s, the molecular basis for chain formation is not well understood. Here we report the crystal structure of a Ube2K~ubiquitin conjugate and demonstrate that even though it is monomeric, Ube2K can synthesize Lys48-linked ubiquitin chains. Using site-directed mutagenesis and modelling, our studies reveal a molecular understanding of the catalytic complex and identify key features required for synthesis of degradative Lys48-linked chains. The position of the acceptor ubiquitin described here is likely conserved in other E2s that catalyse Lys48-linked ubiquitin chain synthesis.
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Affiliation(s)
- Adam J Middleton
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Catherine L Day
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
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29
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Gentier RJ, van Leeuwen FW. Misframed ubiquitin and impaired protein quality control: an early event in Alzheimer's disease. Front Mol Neurosci 2015; 8:47. [PMID: 26388726 PMCID: PMC4557111 DOI: 10.3389/fnmol.2015.00047] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/18/2015] [Indexed: 12/21/2022] Open
Abstract
Amyloid β (Aβ) plaque formation is a prominent cellular hallmark of Alzheimer's disease (AD). To date, immunization trials in AD patients have not been effective in terms of curing or ameliorating dementia. In addition, γ-secretase inhibitor strategies await clinical improvements in AD. These approaches were based upon the idea that autosomal dominant mutations in amyloid precursor protein (APP) and Presenilin 1 (PS1) genes are predictive for treatment of all AD patients. However most AD patients are of the sporadic form which partly explains the failures to treat this multifactorial disease. The major risk factor for developing sporadic AD (SAD) is aging whereas the Apolipoprotein E polymorphism (ε4 variant) is the most prominent genetic risk factor. Other medium-risk factors such as triggering receptor expressed on myeloid cells 2 (TREM2) and nine low risk factors from Genome Wide Association Studies (GWAS) were associated with AD. Recently, pooled GWAS studies identified protein ubiquitination as one of the key modulators of AD. In addition, a brain site specific strategy was used to compare the proteomes of AD patients by an Ingenuity Pathway Analysis. This strategy revealed numerous proteins that strongly interact with ubiquitin (UBB) signaling, and pointing to a dysfunctional ubiquitin proteasome system (UPS) as a causal factor in AD. We reported that DNA-RNA sequence differences in several genes including ubiquitin do occur in AD, the resulting misframed protein of which accumulates in the neurofibrillary tangles (NFTs). This suggests again a functional link between neurodegeneration of the AD type and loss of protein quality control by the UPS. Progress in this field is discussed and modulating the activity of the UPS opens an attractive avenue of research towards slowing down the development of AD and ameliorating its effects by discovering prime targets for AD therapeutics.
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Affiliation(s)
- Romina J. Gentier
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht UniversityMaastricht, Netherlands
| | - Fred W. van Leeuwen
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht UniversityMaastricht, Netherlands
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The HIP2~ubiquitin conjugate forms a non-compact monomeric thioester during di-ubiquitin synthesis. PLoS One 2015; 10:e0120318. [PMID: 25799589 PMCID: PMC4370575 DOI: 10.1371/journal.pone.0120318] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/05/2015] [Indexed: 11/30/2022] Open
Abstract
Polyubiquitination is a post-translational event used to control the degradation of damaged or unwanted proteins by modifying the target protein with a chain of ubiquitin molecules. One potential mechanism for the assembly of polyubiquitin chains involves the dimerization of an E2 conjugating enzyme allowing conjugated ubiquitin molecules to be put into close proximity to assist reactivity. HIP2 (UBE2K) and Ubc1 (yeast homolog of UBE2K) are unique E2 conjugating enzymes that each contain a C-terminal UBA domain attached to their catalytic domains, and they have basal E3-independent polyubiquitination activity. Although the isolated enzymes are monomeric, polyubiquitin formation activity assays show that both can act as ubiquitin donors or ubiquitin acceptors when in the activated thioester conjugate suggesting dimerization of the E2-ubiquitin conjugates. Stable disulfide complexes, analytical ultracentrifugation and small angle x-ray scattering were used to show that the HIP2-Ub and Ubc1-Ub thioester complexes remain predominantly monomeric in solution. Models of the HIP2-Ub complex derived from SAXS data show the complex is not compact but instead forms an open or backbent conformation similar to UbcH5b~Ub or Ubc13~Ub where the UBA domain and covalently attached ubiquitin reside on opposite ends of the catalytic domain. Activity assays showed that full length HIP2 exhibited a five-fold increase in the formation rate of di-ubiquitin compared to a HIP2 lacking the UBA domain. This difference was not observed for Ubc1 and may be attributed to the closer proximity of the UBA domain in HIP2 to the catalytic core than for Ubc1.
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31
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Ohtake F, Saeki Y, Sakamoto K, Ohtake K, Nishikawa H, Tsuchiya H, Ohta T, Tanaka K, Kanno J. Ubiquitin acetylation inhibits polyubiquitin chain elongation. EMBO Rep 2014; 16:192-201. [PMID: 25527407 DOI: 10.15252/embr.201439152] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Ubiquitylation is a versatile post-translational modification (PTM). The diversity of ubiquitylation topologies, which encompasses different chain lengths and linkages, underlies its widespread cellular roles. Here, we show that endogenous ubiquitin is acetylated at lysine (K)-6 (AcK6) or K48. Acetylated ubiquitin does not affect substrate monoubiquitylation, but inhibits K11-, K48-, and K63-linked polyubiquitin chain elongation by several E2 enzymes in vitro. In cells, AcK6-mimetic ubiquitin stabilizes the monoubiquitylation of histone H2B-which we identify as an endogenous substrate of acetylated ubiquitin-and of artificial ubiquitin fusion degradation substrates. These results characterize a mechanism whereby ubiquitin, itself a PTM, is subject to another PTM to modulate mono- and polyubiquitylation, thus adding a new regulatory layer to ubiquitin biology.
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Affiliation(s)
- Fumiaki Ohtake
- Division of Cellular and Molecular Toxicology, Biological Safety Research Center, National Institute of Health Sciences, Setagaya-ku Tokyo, Japan
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Sciences, Setagaya-ku Tokyo, Japan
| | - Kensaku Sakamoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi Yokohama, Japan
| | - Kazumasa Ohtake
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi Yokohama, Japan
| | - Hiroyuki Nishikawa
- Institute of Advanced Medical Science, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Hikaru Tsuchiya
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Sciences, Setagaya-ku Tokyo, Japan
| | - Tomohiko Ohta
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Sciences, Setagaya-ku Tokyo, Japan
| | - Jun Kanno
- Division of Cellular and Molecular Toxicology, Biological Safety Research Center, National Institute of Health Sciences, Setagaya-ku Tokyo, Japan
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Krutauz D, Reis N, Nakasone MA, Siman P, Zhang D, Kirkpatrick DS, Gygi SP, Brik A, Fushman D, Glickman MH. Extended ubiquitin species are protein-based DUB inhibitors. Nat Chem Biol 2014; 10:664-70. [PMID: 24997605 PMCID: PMC4466224 DOI: 10.1038/nchembio.1574] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 05/27/2014] [Indexed: 01/16/2023]
Abstract
A frameshift mutation in the transcript of the ubiquitin-B gene leads to a C-terminally extended ubiquitin (Ub), UBB(+1). UBB(+1) has been considered to inhibit proteasomes and as such to be the underlying cause for toxic protein buildup correlated with certain neuropathological conditions. We demonstrate that expression of extended Ub variants leads to accumulation of heterogeneously linked polyubiquitin conjugates, indicating a pervasive effect on Ub-dependent turnover. 20S proteasomes selectively proteolyzed Ub extensions, yet no evidence for inhibition of 26S holoenzymes was found. However, among susceptible targets for inhibition was Ubp6, the primary enzyme responsible for disassembly of Lys48 linkages at 26S proteasomes. Processing of Lys48 and Lys63 linkages by other deubiquitinating enzymes (DUBs) was also inhibited. Disruption of Ub-dependent degradation by extended Ub variants may therefore be attributed to their inhibitory effect on select DUBs, thus shifting research efforts related to protein accumulation in neurodegenerative processes from proteasomes to DUBs.
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Affiliation(s)
- Daria Krutauz
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Noa Reis
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Mark A Nakasone
- 1] Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel. [2] Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, USA
| | - Peter Siman
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Daoning Zhang
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, USA
| | | | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ashraf Brik
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, USA
| | - Michael H Glickman
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
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33
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Yim N, Ryu SW, Han EC, Yoon J, Choi K, Choi C. Mutant ubiquitin UBB+1 induces mitochondrial fusion by destabilizing mitochondrial fission-specific proteins and confers resistance to oxidative stress-induced cell death in astrocytic cells. PLoS One 2014; 9:e99937. [PMID: 24941066 PMCID: PMC4062464 DOI: 10.1371/journal.pone.0099937] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 05/20/2014] [Indexed: 11/28/2022] Open
Abstract
Mutant ubiquitin UBB+1 is observed in a variety of aging-related neurodegenerative diseases and acts as a potent inhibitor of the ubiquitin proteasome system (UPS). In the present study, we investigated the relationship between impaired UPS (using ectopic expression of UBB+1) and mitochondrial dynamics in astrocytes, which are the most abundant glial cells in the central nervous system. Immunocytochemistry and fluorescence recovery after photobleaching revealed that ectopic expression of UBB+1 induced mitochondrial elongation. We further demonstrated that overexpression of UBB+1 destabilized mitochondrial fission-specific proteins including Drp1, Fis1, and OPA3, but not the mitochondrial fusion-specific proteins Mfn1, Mfn2, and OPA1. The reduction in mitochondrial fission-specific proteins by UBB+1 was prevented by inhibiting the 26 S proteasome using chemical inhibitors, including MG132, lactacystin and epoxomicin. We then assessed the involvement of proteases that target mitochondrial proteins by using various protease inhibitors. Finally, we confirmed that either overexpression of UBB+1 or inhibiting the proteasome can protect astrocytic cells from H2O2-induced cell death compared with control cells. Our results suggest that UBB+1 destabilizes mitochondrial fission-specific proteins, leading to mitochondrial fusion and the subsequent resistance to oxidative stress. We therefore propose a protective role of UBB+1 overexpression or the proteasome inhibition in astrocytes in degenerative brains.
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Affiliation(s)
- Nambin Yim
- Cell Signaling and BioImaging Laboratory, Department of Bio and Brain Engineering, KAIST, Daejeon, Korea
| | - Seung-Wook Ryu
- Cell Signaling and BioImaging Laboratory, Department of Bio and Brain Engineering, KAIST, Daejeon, Korea
- KI for the BioCentury, KAIST, Daejeon, Korea
| | - Eun Chun Han
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea
| | - Jonghee Yoon
- Cell Signaling and BioImaging Laboratory, Department of Bio and Brain Engineering, KAIST, Daejeon, Korea
| | - Kyungsun Choi
- Cell Signaling and BioImaging Laboratory, Department of Bio and Brain Engineering, KAIST, Daejeon, Korea
- * E-mail: (KC); (CC)
| | - Chulhee Choi
- Cell Signaling and BioImaging Laboratory, Department of Bio and Brain Engineering, KAIST, Daejeon, Korea
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea
- KI for the BioCentury, KAIST, Daejeon, Korea
- * E-mail: (KC); (CC)
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Sokratous K, Hadjisavvas A, Diamandis EP, Kyriacou K. The role of ubiquitin-binding domains in human pathophysiology. Crit Rev Clin Lab Sci 2014; 51:280-90. [PMID: 24901807 DOI: 10.3109/10408363.2014.915287] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ubiquitination, a fundamental post-translational modification (PTM) resulting in the covalent attachment of ubiquitin (Ub) to a target protein, is currently implicated in several key cellular processes. Although ubiquitination was initially associated with protein degradation, it is becoming increasingly evident that proteins labeled with polyUb chains of specific topology and length are activated in an ever-expanding repertoire of specific cellular processes. In addition to their involvement in the classical protein degradation pathways they are involved in DNA repair, kinase regulation and nuclear factor-κB (NF-κB) signaling. The sorting and processing of distinct Ub signals is mediated by small protein motifs, known as Ub-binding domains (UBDs), which are found in proteins that execute disparate biological functions. The involvement of UBDs in several biological pathways has been revealed by several studies which have highlighted the vital role of UBDs in cellular homeostasis. Importantly, functional impairment of UBDs in key regulatory pathways has been related to the development of pathophysiological conditions, including immune disorders and cancer. In this review, we present an up-to-date account of the crucial role of UBDs and their functions, with a special emphasis on their functional impairment in key biological pathways and the pathogenesis of several human diseases. The still under-investigated topic of Ub-UBD interactions as a target for developing novel therapeutic strategies against many diseases is also discussed.
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35
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Fecto F, Esengul YT, Siddique T. Protein recycling pathways in neurodegenerative diseases. ALZHEIMERS RESEARCH & THERAPY 2014; 6:13. [PMID: 25031631 PMCID: PMC4055009 DOI: 10.1186/alzrt243] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many progressive neurodegenerative diseases, including Alzheimer disease, Parkinson disease, Huntington disease, amyotrophic lateral sclerosis, and frontotemporal lobe dementia, are associated with the formation of insoluble intracellular proteinaceous inclusions. It is therefore imperative to understand the factors that regulate normal, as well as abnormal, protein recycling in neurons. Dysfunction of the ubiquitin-proteasome or autophagy pathways might contribute to the pathology of various neurodegenerative diseases. Induction of these pathways may offer a rational therapeutic strategy for a number of these diseases.
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Affiliation(s)
- Faisal Fecto
- Division of Neuromuscular Medicine, Davee Department of Neurology and Clinical Neurosciences, Northwestern University Feinberg School of Medicine, Tarry Building, Room 13-715, 303 East Chicago Avenue, Chicago, IL 60611, USA
| | - Y Taylan Esengul
- Division of Neuromuscular Medicine, Davee Department of Neurology and Clinical Neurosciences, Northwestern University Feinberg School of Medicine, Tarry Building, Room 13-715, 303 East Chicago Avenue, Chicago, IL 60611, USA
| | - Teepu Siddique
- Division of Neuromuscular Medicine, Davee Department of Neurology and Clinical Neurosciences, Northwestern University Feinberg School of Medicine, Tarry Building, Room 13-715, 303 East Chicago Avenue, Chicago, IL 60611, USA ; Interdepartmental Neuroscience Program, Northwestern University, Chicago, IL 60611, USA ; Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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36
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Hong L, Huang HC, Jiang ZF. Relationship between amyloid-beta and the ubiquitin–proteasome system in Alzheimer’s disease. Neurol Res 2014; 36:276-82. [DOI: 10.1179/1743132813y.0000000288] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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37
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Anuppalle M, Maddirevula S, Huh TL, Rhee M. Ubiquitin proteasome system networks in the neurological disorders. Anim Cells Syst (Seoul) 2013. [DOI: 10.1080/19768354.2013.855256] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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38
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Moon S, Shin J, Lee D, Seong RH, Lee W. 1H, 15N, and 13C resonance assignments and secondary structure of the SWIRM domain of human BAF155, a chromatin remodeling complex component. Mol Cells 2013; 36:333-9. [PMID: 23996527 PMCID: PMC3887986 DOI: 10.1007/s10059-013-0119-5] [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: 04/16/2013] [Revised: 07/05/2013] [Accepted: 07/08/2013] [Indexed: 10/26/2022] Open
Abstract
Mammalian SWI/SNF complexes are evolutionary conserved, ATP-dependent chromatin remodeling units. BAF155 in the SWI/SNF complex contains several highly conserved domains, including SANT, SWIRM, and leucine zipper domains. The biological roles of the SWIRM domain remain unclear; however, both structural and biochemical analyses of this domain have suggested that it could mediate protein-protein or protein-DNA interactions during the chromatin remodeling process. The human BAF155 SWIRM domain was cloned into the Escherichia coli expression vector pMAL-c2X and purified using affinity chromatography for structural analysis. We report the backbone (1)H, (15)N, and (13)C resonance assignments and secondary structure of this domain using nuclear magnetic resonance (NMR) spectroscopy and the TALOS+ program. The secondary structure consists of five α-helices that form a typical histone fold for DNA interactions. Our data suggest that the BAF155 SWIRM domain interacts with nucleosome DNA (Kd = 0.47 μM).
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Affiliation(s)
- Sunjin Moon
- Structural Biochemistry and Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-740, Korea
| | - Joon Shin
- Structural Biochemistry and Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-740, Korea
| | - Dongju Lee
- Structural Biochemistry and Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-740, Korea
| | | | - Weontae Lee
- Structural Biochemistry and Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-740, Korea
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39
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Dasuri K, Zhang L, Keller JN. Oxidative stress, neurodegeneration, and the balance of protein degradation and protein synthesis. Free Radic Biol Med 2013; 62:170-185. [PMID: 23000246 DOI: 10.1016/j.freeradbiomed.2012.09.016] [Citation(s) in RCA: 260] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/05/2012] [Accepted: 09/11/2012] [Indexed: 12/12/2022]
Abstract
Oxidative stress occurs in a variety of disease settings and is strongly linked to the development of neuron death and neuronal dysfunction. Cells are equipped with numerous pathways to prevent the genesis, as well as the consequences, of oxidative stress in the brain. In this review we discuss the various forms and sources of oxidative stress in the brain and briefly discuss some of the complexities in detecting the presence of oxidative stress. We then focus the review on the interplay between the diverse cellular proteolytic pathways and their roles in regulating oxidative stress in the brain. Additionally, we discuss the involvement of protein synthesis in regulating the downstream effects of oxidative stress. Together, these components of the review demonstrate that the removal of damaged proteins by effective proteolysis and the synthesis of new and protective proteins are vital in the preservation of brain homeostasis during periods of increased levels of reactive oxygen species. Last, studies from our laboratory and others have demonstrated that protein synthesis is intricately linked to the rates of protein degradation, with impairment of protein degradation sufficient to decrease the rates of protein synthesis, which has important implications for successfully responding to periods of oxidative stress. Specific neurodegenerative diseases, including Alzheimer disease, Parkinson disease, amyotrophic lateral sclerosis, and stroke, are discussed in this context. Taken together, these findings add to our understanding of how oxidative stress is effectively managed in the healthy brain and help elucidate how impairments in proteolysis and/or protein synthesis contribute to the development of neurodegeneration and neuronal dysfunction in a variety of clinical settings.
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Affiliation(s)
- Kalavathi Dasuri
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Le Zhang
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Jeffrey N Keller
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA.
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40
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Hong SB, Kim BW, Kim JH, Song HK. Structure of the autophagic E2 enzyme Atg10. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1409-17. [PMID: 22993095 DOI: 10.1107/s0907444912034166] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 07/31/2012] [Indexed: 12/19/2022]
Abstract
Autophagy is a regulated degradation pathway that plays a critical role in all eukaryotic life cycles. One interesting feature of the core autophagic process, autophagosome formation, is similar to ubiquitination. One of two autophagic E2 enzymes, Atg10, interacts with Atg7 to receive Atg12, a ubiquitin-like molecule, and is also involved in the Atg12-Atg5 conjugation reaction. To date, no information on the interaction between Atg10 and Atg7 has been reported, although structural information is available pertaining to the individual components. Here, the crystal structure of Atg10 from Saccharomyces cerevisiae is described at 2.7 Å resolution. A significant improvement of the diffraction limit by heavy-atom derivatization was essential for structure determination. The core fold of yeast Atg10 is well conserved compared with those of Atg3 and other E2 enzymes. In contrast to other E2 enzymes, however, the autophagic E2 enzymes Atg3 and Atg10 possess insertion regions in the middle of the core fold and may be involved in protein function. The missing segment, which was termed the `FR-region', in Atg10 may be important for interaction with the E1 enzyme Atg7. This study provides a framework for understanding the E2 conjugation reaction in autophagy.
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Affiliation(s)
- Seung Beom Hong
- School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Republic of Korea
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41
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van Tijn P, Dennissen FJA, Gentier RJG, Hobo B, Hermes D, Steinbusch HWM, Van Leeuwen FW, Fischer DF. Mutant ubiquitin decreases amyloid β plaque formation in a transgenic mouse model of Alzheimer's disease. Neurochem Int 2012; 61:739-48. [PMID: 22797007 DOI: 10.1016/j.neuint.2012.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 07/02/2012] [Accepted: 07/04/2012] [Indexed: 12/12/2022]
Abstract
The mutant ubiquitin UBB(+1) is a substrate as well as an inhibitor of the ubiquitin-proteasome system (UPS) and accumulates in the neuropathological hallmarks of Alzheimer's disease (AD). A role for the UPS has been suggested in the generation of amyloid β (Aβ) plaques in AD. To investigate the effect of UBB(+1) expression on amyloid pathology in vivo, we crossed UBB(+1) transgenic mice with a transgenic line expressing AD-associated mutant amyloid precursor protein (APPSwe) and mutant presenilin 1 (PS1dE9), resulting in APPPS1/UBB(+1) triple transgenic mice. In these mice, we determined the Aβ levels at 3, 6, 9 and 11 months of age. Surprisingly, we found a significant decrease in Aβ deposition in amyloid plaques and levels of soluble Aβ(42) in APPPS1/UBB(+1) transgenic mice compared to APPPS1 mice at 6 months of age, without alterations in UBB(+1) protein levels or proteasomal chymotrypsin activity. These lowering effects of UBB(+1) on Aβ deposition were transient, as this relative decrease in plaque load was not significant in APPPS1/UBB(+1) mice at 9 and 11 months of age. We also show that APPPS1/UBB(+1) mice exhibit astrogliosis, indicating that they may not be improved functionally compared to APPPS1 mice despite the Aβ reduction. The molecular mechanism underlying this decrease in Aβ deposition in APPPS1/UBB(+1) mice is more complex than previously assumed because UBB(+1) is also ubiquitinated at K63 opening the possibility of additional effects of UBB(+1) (e.g. kinase activation).
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Affiliation(s)
- Paula van Tijn
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA Amsterdam, The Netherlands
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42
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Chadwick L, Gentle L, Strachan J, Layfield R. Review: unchained maladie - a reassessment of the role of Ubb(+1) -capped polyubiquitin chains in Alzheimer's disease. Neuropathol Appl Neurobiol 2012; 38:118-31. [PMID: 22082077 DOI: 10.1111/j.1365-2990.2011.01236.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular misreading allows the formation of mutant proteins in the absence of gene mutations. A mechanism has been proposed by which a frameshift mutant of the ubiquitin protein, Ubb(+1) , which accumulates in an age-dependent manner as a result of molecular misreading, contributes to neuropathology in Alzheimer's disease (Lam et al. 2000). Specifically, in the Ubb(+1) -mediated proteasome inhibition hypothesis Ubb(+1) 'caps' unanchored (that is, nonsubstrate linked) polyubiquitin chains, which then act as dominant inhibitors of the 26S proteasome. A review of subsequent literature indicates that this original hypothesis is broadly supported, and offers new insights into the mechanisms accounting for the age-dependent accumulation of Ubb(+1) , and how Ubb(+1) -mediated proteasome inhibition may contribute to Alzheimer's disease. Further, recent studies have highlighted a physiological role for free endogenous unanchored polyubiquitin chains in the direct activation of certain protein kinases. This raises the possibility that Ubb(+1) -capped unanchored polyubiquitin chains could also exert harmful effects through the aberrant activation of tau or other ubiquitin-dependent kinases, neuronal NF-κB activity or NF-κB-mediated neuroinflammatory processes.
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Affiliation(s)
- L Chadwick
- School of Biomedical Sciences, University of Nottingham, UK
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Arrigoni A, Grillo B, Vitriolo A, De Gioia L, Papaleo E. C-terminal acidic domain of ubiquitin-conjugating enzymes: A multi-functional conserved intrinsically disordered domain in family 3 of E2 enzymes. J Struct Biol 2012; 178:245-59. [DOI: 10.1016/j.jsb.2012.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Revised: 04/01/2012] [Accepted: 04/03/2012] [Indexed: 11/30/2022]
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Dennissen FJA, Kholod N, van Leeuwen FW. The ubiquitin proteasome system in neurodegenerative diseases: culprit, accomplice or victim? Prog Neurobiol 2012; 96:190-207. [PMID: 22270043 DOI: 10.1016/j.pneurobio.2012.01.003] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 12/18/2011] [Accepted: 01/05/2012] [Indexed: 12/14/2022]
Abstract
A shared hallmark for many neurodegenerative disorders is the accumulation of toxic protein species which is assumed to be the cause for these diseases. Since the ubiquitin proteasome system (UPS) is the most important pathway for selective protein degradation it is likely that it is involved in the aetiology neurodegenerative disorders. Indeed, impairment of the UPS has been reported to occur during neurodegeneration. Although accumulation of toxic protein species (amyloid β) are in turn known to impair the UPS the relationship is not necessarily causal. We provide an overview of the most recent insights in the roles the UPS plays in protein degradation and other processes. Additionally, we discuss the role of the UPS in clearance of the toxic proteins known to accumulate in the hallmarks of neurodegenerative diseases. The present paper will focus on critically reviewing the involvement of the UPS in specific neurodegenerative diseases and will discuss if UPS impairment is a cause, a consequence or both of the disease.
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Affiliation(s)
- F J A Dennissen
- Department of Neuroscience, Faculty of Health Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
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Helms KM, Wilson RC, Ogungbe IV, Setzer WN, Twigg PD. Vitexin Inhibits Polyubiquitin Synthesis by the Ubiquitin-conjugating Enzyme E2-25K. Nat Prod Commun 2011. [DOI: 10.1177/1934578x1100601001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
An extract of bark from the tropical rainforest plant Byrsonima crassifolia was screened for inhibition of diubiquitin formation by the human ubiquitin-conjugating enzyme E2-25K. Activity assays with both the full-length enzyme and a truncated, active catalytic UBC domain revealed that the extract contained inhibitory properties. Separation of the extract into individual components and additional screens identified vitexin as the active inhibitor. An IC50 for vitexin was calculated to be approximately 0.5 mM. Molecular modeling simulations were used to predict the mode of inhibition and NMR spectra were used to confirm the binding site of vitexin to E2-25K.
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Affiliation(s)
- Kimberli M. Helms
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
- Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Randall C. Wilson
- Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Ifedayo V. Ogungbe
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - William N. Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Pamela D. Twigg
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
- Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, AL 35899, USA
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Wilson RC, Edmondson SP, Flatt JW, Helms K, Twigg PD. The E2-25K ubiquitin-associated (UBA) domain aids in polyubiquitin chain synthesis and linkage specificity. Biochem Biophys Res Commun 2011; 405:662-6. [PMID: 21281599 DOI: 10.1016/j.bbrc.2011.01.089] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 01/25/2011] [Indexed: 11/18/2022]
Abstract
E2-25K is an ubiquitin-conjugating enzyme with the ability to synthesize Lys48-linked polyubiquitin chains. E2-25K and its homologs represent the only known E2 enzymes which contain a C-terminal ubiquitin-associated (UBA) domain as well as the conserved catalytic ubiquitin-conjugating (UBC) domain. As an additional non-covalent binding surface for ubiquitin, the UBA domain must provide some functional specialization. We mapped the protein-protein interface involved in the E2-25K UBA/ubiquitin complex by solution nuclear magnetic resonance (NMR) spectroscopy and subsequently modeled the structure of the complex. Domain-domain interactions between the E2-25K catalytic UBC domain and the UBA domain do not induce significant structural changes in the UBA domain or alter the affinity of the UBA domain for ubiquitin. We determined that one of the roles of the C-terminal UBA domain, in the context of E2-25K, is to increase processivity in Lys48-linked polyubiquitin chain synthesis, possibly through increased binding to the ubiquitinated substrate. Additionally, we see evidence that the UBA domain directs specificity in polyubiquitin chain linkage.
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Affiliation(s)
- Randall C Wilson
- Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, AL 35899, USA
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