1
|
Zhang H, Chen H, Zhang J, Wang K, Huang B, Wang Z. The role of MrUbp4, a deubiquitinase, in conidial yield, thermotolerance, and virulence in Metarhizium robertsii. J Invertebr Pathol 2024; 204:108111. [PMID: 38631560 DOI: 10.1016/j.jip.2024.108111] [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: 11/04/2023] [Revised: 03/18/2024] [Accepted: 04/14/2024] [Indexed: 04/19/2024]
Abstract
Ubiquitin-specific proteases (UBPs), the largest subfamily of deubiquitinating enzymes, regulate ubiquitin homeostasis and play diverse roles in eukaryotes. Ubp4 is essential for the growth, development, and pathogenicity of various fungal pathogens. However, its functions in the growth, stress responses, and virulence of entomopathogenic fungi remain unclear. In this study, we elucidated the role of the homolog of Ubp4, MrUbp4, in the entomopathogenic fungus Metarhizium robertsii. Deletion of MrUbp4 led to a notable increase in ubiquitination levels, demonstrating the involvement of MrUbp4 in protein deubiquitination. Furthermore, the ΔMrUbp4 mutant displayed a significant reduction in conidial yield, underscoring the pivotal role of MrUbp4 in conidiation. Additionally, the mutant exhibited heightened resistance to conidial heat treatment, emphasizing the role of MrUbp4 in thermotolerance. Notably, insect bioassays unveiled a substantial impairment in the virulence of the ΔMrUbp4 mutant. This was accompanied by a notable decrease in cuticle penetration ability and appressorium formation upon further analysis. In summary, our findings highlight the essential role of MrUbp4 in regulating the conidial yield, thermotolerance, and contributions to the virulence of M. robertsii.
Collapse
Affiliation(s)
- Hongzhi Zhang
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China; Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei 230036, China
| | - Hanyuan Chen
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China; Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei 230036, China
| | - Jianfeng Zhang
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China; Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei 230036, China
| | - Kui Wang
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China; Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei 230036, China
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei 230036, China.
| | - Zhangxun Wang
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China; Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei 230036, China.
| |
Collapse
|
2
|
Noman M, Azizullah, Ahmed T, Gao Y, Wang H, Xiong X, Wang J, Lou J, Li D, Song F. Degradation of α-Subunits, Doa1 and Doa4, are Critical for Growth, Development, Programmed Cell Death Events, Stress Responses, and Pathogenicity in the Watermelon Fusarium Wilt Fungus Fusarium oxysporum f. sp. niveum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37486296 DOI: 10.1021/acs.jafc.3c01785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
The ubiquitin-proteasome system (UPS) regulates protein quality or control and plays essential roles in several biological and biochemical processes in fungi. Here, we present the characterization of two UPS components, FonDoa1 and FonDoa4, in watermelon Fusarium wilt fungus, Fusarium oxysporum f. sp. niveum (Fon), and their biological functions. FonDoa1 localizes in both the nucleus and cytoplasm, while FonDoa4 is predominantly present in the cytoplasm. Both genes show higher expression in germinating macroconidia at 12 h. Deletion of FonDoa1 or FonDoa4 affects vegetative growth, conidiation, conidial germination/morphology, apoptosis, and responses to environmental stressors. FonDoa1, but not FonDoa4, positively regulates autophagy. The targeted disruption mutants exhibit significantly attenuated pathogenicity on watermelon due to defects in the infection process and invasive fungal growth. Further results indicate that the WD40, PFU, and PUL domains are essential for the function of FonDoa1 in Fon pathogenicity and environmental stress responses. These findings demonstrate the previously uncharacterized biological functions of FonDoa1 and FonDoa4 in phytopathogenic fungi, providing potential targets for developing strategies to control watermelon Fusarium wilt.
Collapse
Affiliation(s)
- Muhammad Noman
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Azizullah
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Temoor Ahmed
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Xianghu Laboratory, Hangzhou 311231, China
| | - Yizhou Gao
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Wang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaohui Xiong
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jiajing Wang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jiajun Lou
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dayong Li
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Fengming Song
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| |
Collapse
|
3
|
Wang Y, Lan Q, Cheng X, Gao Y, Chang L, Xu P, Li Y. Quantitative Proteomics-Based Substrate Screening Revealed Cyclophilin Stabilization Regulated by Deubiquitinase Ubp7. J Proteome Res 2023; 22:2281-2292. [PMID: 37341107 DOI: 10.1021/acs.jproteome.2c00853] [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] [Indexed: 06/22/2023]
Abstract
Quantitative proteomics has emerged as a crucial approach to identifying ubiquitinated substrates to investigate the functions of ubiquitination in cells. In this regard, although the substrate screening of certain enzymes in the ubiquitin system has been based on proteome or ubiquitinome level measurements, the direct comparison of these two approaches has not been determined to date. To quantitatively compare the efficiency and effectiveness of substrate screening from the entire proteomics to the ubiquitinomics filter, we used yeast deubiquitinating enzyme, Ubp7, as an example to evaluate it in this study. A total of 112 potential ubiquitinated substrates were identified from the ubiquitinomics level, whereas only 27 regulated substrates were identified from the entire proteomic screening, demonstrating the increased efficiency of ubiquitinomics quantitative analysis. Subsequently, we selected cyclophilin A (Cpr1) protein as an example, which was filtered out at the proteomics level but was a promising candidate according to the ubiquitinomics filter. Additional investigations revealed that Cpr1 possessed a K48-linked ubiquitin chain regulated by Ubp7, which may affect its homeostasis and, consequently, sensitivity to the therapeutic drug cyclosporine (CsA).
Collapse
Affiliation(s)
- Yonghong Wang
- Department of Biomedicine, School of Medicine, Guizhou University, Guiyang 550025, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing 102206, China
| | - Qiuyan Lan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing 102206, China
| | - Xinyu Cheng
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Yuan Gao
- Central Laboratory of College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing 102206, China
| | - Ping Xu
- Department of Biomedicine, School of Medicine, Guizhou University, Guiyang 550025, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing 102206, China
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, School of Life Sciences, Hebei University, Baoding 071002, China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing 102206, China
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, School of Life Sciences, Hebei University, Baoding 071002, China
| |
Collapse
|
4
|
Couvillion M, Harlen KM, Lachance KC, Trotta KL, Smith E, Brion C, Smalec BM, Churchman LS. Transcription elongation is finely tuned by dozens of regulatory factors. eLife 2022; 11:e78944. [PMID: 35575476 PMCID: PMC9154744 DOI: 10.7554/elife.78944] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/15/2022] [Indexed: 11/30/2022] Open
Abstract
Understanding the complex network that regulates transcription elongation requires the quantitative analysis of RNA polymerase II (Pol II) activity in a wide variety of regulatory environments. We performed native elongating transcript sequencing (NET-seq) in 41 strains of Saccharomyces cerevisiae lacking known elongation regulators, including RNA processing factors, transcription elongation factors, chromatin modifiers, and remodelers. We found that the opposing effects of these factors balance transcription elongation and antisense transcription. Different sets of factors tightly regulate Pol II progression across gene bodies so that Pol II density peaks at key points of RNA processing. These regulators control where Pol II pauses with each obscuring large numbers of potential pause sites that are primarily determined by DNA sequence and shape. Antisense transcription varies highly across the regulatory landscapes analyzed, but antisense transcription in itself does not affect sense transcription at the same locus. Our findings collectively show that a diverse array of factors regulate transcription elongation by precisely balancing Pol II activity.
Collapse
Affiliation(s)
- Mary Couvillion
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Kevin M Harlen
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Kate C Lachance
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Kristine L Trotta
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Erin Smith
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Christian Brion
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Brendan M Smalec
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - L Stirling Churchman
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
| |
Collapse
|
5
|
Usp5, Usp34, and Otu1 deubiquitylases mediate DNA repair in Drosophila melanogaster. Sci Rep 2022; 12:5870. [PMID: 35393473 PMCID: PMC8990000 DOI: 10.1038/s41598-022-09703-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/21/2022] [Indexed: 11/29/2022] Open
Abstract
Ubiquitylation is critical for preventing aberrant DNA repair and for efficient maintenance of genome stability. As deubiquitylases (DUBs) counteract ubiquitylation, they must have a great influence on many biological processes, including DNA damage response. To elucidate the role of DUBs in DNA repair in Drosophila melanogaster, systematic siRNA screening was applied to identify DUBs with a reduced survival rate following exposure to ultraviolet and X-ray radiations. As a secondary validation, we applied the direct repeat (DR)-white reporter system with which we induced site-specific DSBs and affirmed the importance of the DUBs Ovarian tumor domain-containing deubiquitinating enzyme 1 (Otu1), Ubiquitin carboxyl-terminal hydrolase 5 (Usp5), and Ubiquitin carboxyl-terminal hydrolase 34 (Usp34) in DSB repair pathways using Drosophila. Our results indicate that the loss of Otu1 and Usp5 induces strong position effect variegation in Drosophila eye following I-SceI-induced DSB deployment. Otu1 and Usp5 are essential in DNA damage-induced cellular response, and both DUBs are required for the fine-tuned regulation of the non-homologous end joining pathway. Furthermore, the Drosophila DR-white assay demonstrated that homologous recombination does not occur in the absence of Usp34, indicating an indispensable role of Usp34 in this process.
Collapse
|
6
|
Rashid S, Correia-Mesquita TO, Godoy P, Omran RP, Whiteway M. SAGA Complex Subunits in Candida albicans Differentially Regulate Filamentation, Invasiveness, and Biofilm Formation. Front Cell Infect Microbiol 2022; 12:764711. [PMID: 35350439 PMCID: PMC8957876 DOI: 10.3389/fcimb.2022.764711] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/11/2022] [Indexed: 11/24/2022] Open
Abstract
SAGA (Spt-Ada-Gcn5-acetyltransferase) is a highly conserved, multiprotein co-activator complex that consists of five distinct modules. It has two enzymatic functions, a histone acetyltransferase (HAT) and a deubiquitinase (DUB) and plays a central role in processes such as transcription initiation, elongation, protein stability, and telomere maintenance. We analyzed conditional and null mutants of the SAGA complex module components in the fungal pathogen Candida albicans; Ngg1, (the HAT module); Ubp8, (the DUB module); Tra1, (the recruitment module), Spt7, (the architecture module) and Spt8, (the TBP interaction unit), and assessed their roles in a variety of cellular processes. We observed that spt7Δ/Δ and spt8Δ/Δ strains have a filamentous phenotype, and both are highly invasive in yeast growing conditions as compared to the wild type, while ngg1Δ/Δ and ubp8Δ/Δ are in yeast-locked state and non-invasive in both YPD media and filamentous induced conditions compared to wild type. RNA-sequencing-based transcriptional profiling of SAGA mutants reveals upregulation of hyphal specific genes in spt7Δ/Δ and spt8Δ/Δ strains and downregulation of ergosterol metabolism pathway. As well, spt7Δ/Δ and spt8Δ/Δ confer susceptibility to antifungal drugs, to acidic and alkaline pH, to high temperature, and to osmotic, oxidative, cell wall, and DNA damage stresses, indicating that these proteins are important for genotoxic and cellular stress responses. Despite having similar morphological phenotypes (constitutively filamentous and invasive) spt7 and spt8 mutants displayed variation in nuclear distribution where spt7Δ/Δ cells were frequently binucleate and spt8Δ/Δ cells were consistently mononucleate. We also observed that spt7Δ/Δ and spt8Δ/Δ mutants were quickly engulfed by macrophages compared to ngg1Δ/Δ and ubp8Δ/Δ strains. All these findings suggest that the SAGA complex modules can have contrasting functions where loss of Spt7 or Spt8 enhances filamentation and invasiveness while loss of Ngg1 or Ubp8 blocks these processes.
Collapse
Affiliation(s)
| | | | | | | | - Malcolm Whiteway
- Department of Biology, Concordia University, Montreal, QC, Canada
| |
Collapse
|
7
|
Eyboulet F, Jeronimo C, Côté J, Robert F. The deubiquitylase Ubp15 couples transcription to mRNA export. eLife 2020; 9:e61264. [PMID: 33226341 PMCID: PMC7682988 DOI: 10.7554/elife.61264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022] Open
Abstract
Nuclear export of messenger RNAs (mRNAs) is intimately coupled to their synthesis. pre-mRNAs assemble into dynamic ribonucleoparticles as they are being transcribed, processed, and exported. The role of ubiquitylation in this process is increasingly recognized but, while a few E3 ligases have been shown to regulate nuclear export, evidence for deubiquitylases is currently lacking. Here we identified deubiquitylase Ubp15 as a regulator of nuclear export in Saccharomyces cerevisiae. Ubp15 interacts with both RNA polymerase II and the nuclear pore complex, and its deletion reverts the nuclear export defect of E3 ligase Rsp5 mutants. The deletion of UBP15 leads to hyper-ubiquitylation of the main nuclear export receptor Mex67 and affects its association with THO, a complex coupling transcription to mRNA processing and involved in the recruitment of mRNA export factors to nascent transcripts. Collectively, our data support a role for Ubp15 in coupling transcription to mRNA export.
Collapse
Affiliation(s)
- Fanny Eyboulet
- Institut de recherches cliniques de MontréalMontréalCanada
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Axe Oncologie du Centre de Recherche du CHU de Québec-Université LavalQuébec CityCanada
| | - Célia Jeronimo
- Institut de recherches cliniques de MontréalMontréalCanada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Axe Oncologie du Centre de Recherche du CHU de Québec-Université LavalQuébec CityCanada
| | - François Robert
- Institut de recherches cliniques de MontréalMontréalCanada
- Département de Médecine, Faculté de Médecine, Université de MontréalMontréalCanada
| |
Collapse
|
8
|
Suresh HG, Pascoe N, Andrews B. The structure and function of deubiquitinases: lessons from budding yeast. Open Biol 2020; 10:200279. [PMID: 33081638 PMCID: PMC7653365 DOI: 10.1098/rsob.200279] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Protein ubiquitination is a key post-translational modification that regulates diverse cellular processes in eukaryotic cells. The specificity of ubiquitin (Ub) signalling for different bioprocesses and pathways is dictated by the large variety of mono-ubiquitination and polyubiquitination events, including many possible chain architectures. Deubiquitinases (DUBs) reverse or edit Ub signals with high sophistication and specificity, forming an integral arm of the Ub signalling machinery, thus impinging on fundamental cellular processes including DNA damage repair, gene expression, protein quality control and organellar integrity. In this review, we discuss the many layers of DUB function and regulation, with a focus on insights gained from budding yeast. Our review provides a framework to understand key aspects of DUB biology.
Collapse
Affiliation(s)
- Harsha Garadi Suresh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Natasha Pascoe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Brenda Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| |
Collapse
|
9
|
The degradation-promoting roles of deubiquitinases Ubp6 and Ubp3 in cytosolic and ER protein quality control. PLoS One 2020; 15:e0232755. [PMID: 32401766 PMCID: PMC7219781 DOI: 10.1371/journal.pone.0232755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/21/2020] [Indexed: 11/19/2022] Open
Abstract
The quality control of intracellular proteins is achieved by degrading misfolded proteins which cannot be refolded by molecular chaperones. In eukaryotes, such degradation is handled primarily by the ubiquitin-proteasome system. However, it remained unclear whether and how protein quality control deploys various deubiquitinases. To address this question, we screened deletions or mutation of the 20 deubiquitinase genes in Saccharomyces cerevisiae and discovered that almost half of the mutations slowed the removal of misfolded proteins whereas none of the remaining mutations accelerated this process significantly. Further characterization revealed that Ubp6 maintains the level of free ubiquitin to promote the elimination of misfolded cytosolic proteins, while Ubp3 supports the degradation of misfolded cytosolic and ER luminal proteins by different mechanisms.
Collapse
|
10
|
Mat Nanyan NSB, Watanabe D, Sugimoto Y, Takagi H. Effect of the deubiquitination enzyme gene UBP6 on the stress-responsive transcription factor Msn2-mediated control of the amino acid permease Gnp1 in yeast. J Biosci Bioeng 2020; 129:423-427. [DOI: 10.1016/j.jbiosc.2019.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/08/2019] [Accepted: 10/01/2019] [Indexed: 11/16/2022]
|
11
|
Dougherty SE, Maduka AO, Inada T, Silva GM. Expanding Role of Ubiquitin in Translational Control. Int J Mol Sci 2020; 21:E1151. [PMID: 32050486 PMCID: PMC7037965 DOI: 10.3390/ijms21031151] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic proteome has to be precisely regulated at multiple levels of gene expression, from transcription, translation, and degradation of RNA and protein to adjust to several cellular conditions. Particularly at the translational level, regulation is controlled by a variety of RNA binding proteins, translation and associated factors, numerous enzymes, and by post-translational modifications (PTM). Ubiquitination, a prominent PTM discovered as the signal for protein degradation, has newly emerged as a modulator of protein synthesis by controlling several processes in translation. Advances in proteomics and cryo-electron microscopy have identified ubiquitin modifications of several ribosomal proteins and provided numerous insights on how this modification affects ribosome structure and function. The variety of pathways and functions of translation controlled by ubiquitin are determined by the various enzymes involved in ubiquitin conjugation and removal, by the ubiquitin chain type used, by the target sites of ubiquitination, and by the physiologic signals triggering its accumulation. Current research is now elucidating multiple ubiquitin-mediated mechanisms of translational control, including ribosome biogenesis, ribosome degradation, ribosome-associated protein quality control (RQC), and redox control of translation by ubiquitin (RTU). This review discusses the central role of ubiquitin in modulating the dynamism of the cellular proteome and explores the molecular aspects responsible for the expanding puzzle of ubiquitin signals and functions in translation.
Collapse
Affiliation(s)
- Shannon E. Dougherty
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| | - Austin O. Maduka
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan;
| | - Gustavo M. Silva
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| |
Collapse
|
12
|
Que Y, Xu Z, Wang C, Lv W, Yue X, Xu L, Tang S, Dai H, Wang Z. The putative deubiquitinating enzyme MoUbp4 is required for infection-related morphogenesis and pathogenicity in the rice blast fungus Magnaporthe oryzae. Curr Genet 2019; 66:561-576. [PMID: 31872271 DOI: 10.1007/s00294-019-01049-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 11/28/2022]
Abstract
Ubiquitination is a key regulatory mechanism that affects numerous important biological processes, including cellular differentiation and pathogenesis in eukaryotic cells. Attachment of proteins to ubiquitin is reversed by specialized proteases, deubiquitinating enzymes (DUBs), which are essential for precursor processing, maintaining ubiquitin homeostasis and promoting protein degradation by recycling ubiquitins. Here, we report the identification of a novel non-pathogenic T-DNA-tagged mutant T612 of Magnaporthe oryzae with a single insertion in the second exon of MoUBP4, which encodes a putative ubiquitin carboxyl-terminal hydrolase. Targeted gene deletion mutants of MoUBP4 are significantly reduced in mycelial growth, conidiation, and increased in tolerance to SDS and CR (Congo red) cell-wall damage. The ΔMoubp4 mutants are blocked in penetration and invasive growth, which results in the loss of pathogenicity. Many conidia produced by the ΔMoubp4 mutants are unable to form appressoria and mobilization and degradation of glycogen and lipid droplets are significantly delayed. Moreover, immunohybridization analysis revealed that total protein ubiquitination levels of the null mutants were significantly increased, indicating that MoUbp4 functions as a deubiquitination enzyme. Taken together, we conclude that MoUbp4 is required for deubiquitination, infection-related morphogenesis and pathogenicity in M. oryzae.
Collapse
Affiliation(s)
- Yawei Que
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zhe Xu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Chunyan Wang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Wuyun Lv
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xiaofeng Yue
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Lin Xu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Shuai Tang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Han Dai
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zhengyi Wang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China.
| |
Collapse
|
13
|
Biot-Pelletier D, Pinel D, Larue K, Martin VJJ. Determinants of selection in yeast evolved by genome shuffling. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:282. [PMID: 30356826 PMCID: PMC6190656 DOI: 10.1186/s13068-018-1283-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/06/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Genome shuffling (GS) is a widely adopted methodology for the evolutionary engineering of desirable traits in industrially relevant microorganisms. We have previously used genome shuffling to generate a strain of Saccharomyces cerevisiae that is tolerant to the growth inhibitors found in a lignocellulosic hydrolysate. In this study, we expand on previous work by performing a population-wide genomic survey of our genome shuffling experiment and dissecting the molecular determinants of the evolved phenotype. RESULTS Whole population whole-genome sequencing was used to survey mutations selected during the experiment and extract allele frequency time series. Using growth curve assays on single point mutants and backcrossed derivatives, we explored the genetic architecture of the selected phenotype and detected examples of epistasis. Our results reveal cohorts of strongly correlated mutations, suggesting prevalent genetic hitchhiking and the presence of pre-existing founder mutations. From the patterns of apparent selection and the results of direct phenotypic assays, our results identify key driver mutations and deleterious hitchhikers. CONCLUSIONS We use these data to propose a model of inhibitor tolerance in our GS mutants. Our results also suggest a role for compensatory evolution and epistasis in our genome shuffling experiment and illustrate the impact of historical contingency on the outcomes of evolutionary engineering.
Collapse
Affiliation(s)
- Damien Biot-Pelletier
- Department of Biology, Centre for Structural and Functional Genomics, Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
- Present Address: Lallemand Inc., Montréal, QC H4P 2R2 Canada
| | - Dominic Pinel
- Department of Biology, Centre for Structural and Functional Genomics, Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
- Present Address: Amyris Inc, Emeryville, CA 94608 USA
| | - Kane Larue
- Department of Biology, Centre for Structural and Functional Genomics, Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
- Present Address: Charles River Laboratories, Senneville, QC H9X 3R3 Canada
| | - Vincent J. J. Martin
- Department of Biology, Centre for Structural and Functional Genomics, Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| |
Collapse
|
14
|
Mapa CE, Arsenault HE, Conti MM, Poti KE, Benanti JA. A balance of deubiquitinating enzymes controls cell cycle entry. Mol Biol Cell 2018; 29:2821-2834. [PMID: 30207830 PMCID: PMC6249862 DOI: 10.1091/mbc.e18-07-0425] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Protein degradation during the cell cycle is controlled by the opposing activities of ubiquitin ligases and deubiquitinating enzymes (DUBs). Although the functions of ubiquitin ligases in the cell cycle have been studied extensively, the roles of DUBs in this process are less well understood. Here, we used an overexpression screen to examine the specificities of each of the 21 DUBs in budding yeast for 37 cell cycle-regulated proteins. We find that DUBs up-regulate specific subsets of proteins, with five DUBs regulating the greatest number of targets. Overexpression of Ubp10 had the largest effect, stabilizing 15 targets and delaying cells in mitosis. Importantly, UBP10 deletion decreased the stability of the cell cycle regulator Dbf4, delayed the G1/S transition, and slowed proliferation. Remarkably, deletion of UBP10 together with deletion of four additional DUBs restored proliferation to near-wild-type levels. Among this group, deletion of the proteasome-associated DUB Ubp6 alone reversed the G1/S delay and restored the stability of Ubp10 targets in ubp10Δ cells. Similarly, deletion of UBP14, another DUB that promotes proteasomal activity, rescued the proliferation defect in ubp10Δ cells. Our results suggest that DUBs function through a complex genetic network in which their activities are coordinated to facilitate accurate cell cycle progression.
Collapse
Affiliation(s)
- Claudine E Mapa
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Heather E Arsenault
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Michelle M Conti
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Kristin E Poti
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Jennifer A Benanti
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| |
Collapse
|
15
|
Schwerter D, Grimm I, Girzalsky W, Erdmann R. Receptor recognition by the peroxisomal AAA complex depends on the presence of the ubiquitin moiety and is mediated by Pex1p. J Biol Chem 2018; 293:15458-15470. [PMID: 30097517 DOI: 10.1074/jbc.ra118.003936] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/23/2018] [Indexed: 01/14/2023] Open
Abstract
The receptor cycle of type I peroxisomal matrix protein import is completed by ubiquitination of the membrane-bound peroxisome biogenesis factor 5 (Pex5p) and its subsequent export back to the cytosol. The receptor export is the only ATP-dependent step of the whole process and is facilitated by two members of the AAA family of proteins (ATPases associated with various cellular activities), namely Pex1p and Pex6p. To gain further insight into substrate recognition by the AAA complex, we generated an N-terminally linked ubiquitin-Pex5p fusion protein. This fusion protein displayed biological activity because it is able to functionally complement a PEX5-deletion in Saccharomyces cerevisiae. In vitro assays revealed its interaction at WT level with the native cargo protein Pcs60p and Pex14p, a constituent of the receptor docking complex. We also demonstrate in vitro deubiquitination by the deubiquitinating enzyme Ubp15p. In vitro pulldown assays and cross-linking studies demonstrate that Pex5p recognition by the AAA complex depends on the presence of the ubiquitin moiety and is mediated by Pex1p.
Collapse
Affiliation(s)
- Daniel Schwerter
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Systems Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Immanuel Grimm
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Systems Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Wolfgang Girzalsky
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Systems Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Ralf Erdmann
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Systems Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| |
Collapse
|
16
|
Albrecht D, Hürlimann HC, Ceschin J, Saint-Marc C, Pinson B, Daignan-Fornier B. Multiple chemo-genetic interactions between a toxic metabolite and the ubiquitin pathway in yeast. Curr Genet 2018; 64:1275-1286. [PMID: 29721631 DOI: 10.1007/s00294-018-0843-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/17/2018] [Accepted: 04/26/2018] [Indexed: 12/21/2022]
Abstract
AICAR is the precursor of ZMP, a metabolite with antiproliferative properties in yeast and human. We aim at understanding how AICAR (and its active form ZMP) affects essential cellular processes. In this work, we found that ZMP accumulation is synthetic lethal with a hypomorphic allele of the ubiquitin-activating enzyme Uba1. A search for gene-dosage suppressors revealed that ubiquitin overexpression was sufficient to restore growth of the uba1 mutant upon AICAR treatment, suggesting that the ubiquitin pool is critical for cells to cope with AICAR. Accordingly, two mutants with constitutive low ubiquitin, ubp6 and doa1, were highly sensitive to AICAR, a phenotype that could be suppressed by ubiquitin overexpression. We established, by genetic means, that these new AICAR-sensitive mutants act in a different pathway from the rad6/bre1 mutants which were previously reported as sensitive to AICAR (Albrecht et al., Genetics 204:1447-1460, 2016). Two ubiquitin-conjugating enzymes (Ubc4 and Cdc34) and a ubiquitin ligase (Cdc4) were found to contribute to the ability of cells to cope with ZMP. This study illustrates the complexity of chemo-genetic interactions and shows how genetic analyses allow deciphering the implicated pathways, the individual gene effects, and their combined phenotypic contribution. Based on additivity and suppression patterns, we conclude that AICAR treatment shows synthetic interactions with distinct branches of the yeast ubiquitin pathway.
Collapse
Affiliation(s)
- Delphine Albrecht
- Université de Bordeaux, IBGC UMR 5095, 1 rue Camille Saint-Saëns, 33077, Bordeaux, France
- Centre National de la Recherche Scientifique, IBGC UMR 5095, 1 rue Camille Saint-Saëns, 33077, Bordeaux, France
| | - Hans C Hürlimann
- Université de Bordeaux, IBGC UMR 5095, 1 rue Camille Saint-Saëns, 33077, Bordeaux, France
- Centre National de la Recherche Scientifique, IBGC UMR 5095, 1 rue Camille Saint-Saëns, 33077, Bordeaux, France
- Institut für Biologie, Martin-Luther Universität, Universität Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Johanna Ceschin
- Université de Bordeaux, IBGC UMR 5095, 1 rue Camille Saint-Saëns, 33077, Bordeaux, France
- Centre National de la Recherche Scientifique, IBGC UMR 5095, 1 rue Camille Saint-Saëns, 33077, Bordeaux, France
| | - Christelle Saint-Marc
- Université de Bordeaux, IBGC UMR 5095, 1 rue Camille Saint-Saëns, 33077, Bordeaux, France
- Centre National de la Recherche Scientifique, IBGC UMR 5095, 1 rue Camille Saint-Saëns, 33077, Bordeaux, France
| | - Benoît Pinson
- Université de Bordeaux, IBGC UMR 5095, 1 rue Camille Saint-Saëns, 33077, Bordeaux, France
- Centre National de la Recherche Scientifique, IBGC UMR 5095, 1 rue Camille Saint-Saëns, 33077, Bordeaux, France
| | - Bertrand Daignan-Fornier
- Université de Bordeaux, IBGC UMR 5095, 1 rue Camille Saint-Saëns, 33077, Bordeaux, France.
- Centre National de la Recherche Scientifique, IBGC UMR 5095, 1 rue Camille Saint-Saëns, 33077, Bordeaux, France.
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 1 rue C. Saint-Saëns CS 61390, 33077, Bordeaux, France.
| |
Collapse
|
17
|
|
18
|
de Poot SAH, Tian G, Finley D. Meddling with Fate: The Proteasomal Deubiquitinating Enzymes. J Mol Biol 2017; 429:3525-3545. [PMID: 28988953 DOI: 10.1016/j.jmb.2017.09.015] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/20/2017] [Accepted: 09/26/2017] [Indexed: 01/06/2023]
Abstract
Three deubiquitinating enzymes-Rpn11, Usp14, and Uch37-are associated with the proteasome regulatory particle. These enzymes allow proteasomes to remove ubiquitin from substrates before they are translocated into the core particle to be degraded. Although the translocation channel is too narrow for folded proteins, the force of translocation unfolds them mechanically. As translocation proceeds, ubiquitin chains bound to substrate are drawn to the channel's entry port, where they can impede further translocation. Rpn11, situated over the port, can remove these chains without compromising degradation because substrates must be irreversibly committed to degradation before Rpn11 acts. This coupling between deubiquitination and substrate degradation is ensured by the Ins-1 loop of Rpn11, which controls ubiquitin access to its catalytic site. In contrast to Rpn11, Usp14 and Uch37 can rescue substrates from degradation by promoting substrate dissociation from the proteasome prior to the commitment step. Uch37 is unique in being a component of both the proteasome and a second multisubunit assembly, the INO80 complex. However, only recruitment into the proteasome activates Uch37. Recruitment to the proteasome likewise activates Usp14. However, the influence of Usp14 on the proteasome depends on the substrate, due to its marked preference for proteins that carry multiple ubiquitin chains. Usp14 exerts complex control over the proteasome, suppressing proteasome activity even when inactive in deubiquitination. A major challenge for the field will be to elucidate the specificities of Rpn11, Usp14, and Uch37 in greater depth, employing not only model in vitro substrates but also their endogenous targets.
Collapse
Affiliation(s)
- Stefanie A H de Poot
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Geng Tian
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| |
Collapse
|
19
|
LaMonte GM, Almaliti J, Bibo-Verdugo B, Keller L, Zou BY, Yang J, Antonova-Koch Y, Orjuela-Sanchez P, Boyle CA, Vigil E, Wang L, Goldgof GM, Gerwick L, O'Donoghue AJ, Winzeler EA, Gerwick WH, Ottilie S. Development of a Potent Inhibitor of the Plasmodium Proteasome with Reduced Mammalian Toxicity. J Med Chem 2017; 60:6721-6732. [PMID: 28696697 PMCID: PMC5554889 DOI: 10.1021/acs.jmedchem.7b00671] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Naturally derived chemical compounds
are the foundation of much
of our pharmacopeia, especially in antiproliferative and anti-infective
drug classes. Here, we report that a naturally derived molecule called
carmaphycin B is a potent inhibitor against both the asexual and sexual
blood stages of malaria infection. Using a combination of in silico
molecular docking and in vitro directed evolution in a well-characterized
drug-sensitive yeast model, we determined that these compounds target
the β5 subunit of the proteasome. These studies were validated
using in vitro inhibition assays with proteasomes isolated from Plasmodium falciparum. As carmaphycin B is toxic to mammalian
cells, we synthesized a series of chemical analogs that reduce host
cell toxicity while maintaining blood-stage and gametocytocidal antimalarial
activity and proteasome inhibition. This study describes a promising
new class of antimalarial compound based on the carmaphycin B scaffold,
as well as several chemical structural features that serve to enhance
antimalarial specificity.
Collapse
Affiliation(s)
- Gregory M LaMonte
- Department of Pediatrics, School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
| | - Jehad Almaliti
- Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States.,Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan , Amman 11942, Jordan
| | - Betsaida Bibo-Verdugo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Faculty of Pharmacy, and School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
| | - Lena Keller
- Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States
| | - Bing Yu Zou
- Department of Pediatrics, School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
| | - Jennifer Yang
- Department of Pediatrics, School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
| | - Yevgeniya Antonova-Koch
- Department of Pediatrics, School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
| | - Pamela Orjuela-Sanchez
- Department of Pediatrics, School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
| | - Colleen A Boyle
- Department of Pediatrics, School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
| | - Edgar Vigil
- Department of Pediatrics, School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
| | - Lawrence Wang
- Department of Pediatrics, School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
| | - Gregory M Goldgof
- Department of Pediatrics, School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
| | - Lena Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Faculty of Pharmacy, and School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Faculty of Pharmacy, and School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Faculty of Pharmacy, and School of Medicine, University of California, San Diego , La Jolla, California 92093, United States.,Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States
| | - Sabine Ottilie
- Department of Pediatrics, School of Medicine, University of California, San Diego , La Jolla, California 92093, United States
| |
Collapse
|
20
|
Hovsepian J, Defenouillère Q, Albanèse V, Váchová L, Garcia C, Palková Z, Léon S. Multilevel regulation of an α-arrestin by glucose depletion controls hexose transporter endocytosis. J Cell Biol 2017; 216:1811-1831. [PMID: 28468835 PMCID: PMC5461024 DOI: 10.1083/jcb.201610094] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/03/2017] [Accepted: 03/28/2017] [Indexed: 01/13/2023] Open
Abstract
Changes in nutrient availability trigger massive rearrangements of the yeast plasma membrane proteome. This work shows that the arrestin-related protein Csr2/Art8 is regulated by glucose signaling at multiple levels, allowing control of hexose transporter ubiquitylation and endocytosis upon glucose depletion. Nutrient availability controls the landscape of nutrient transporters present at the plasma membrane, notably by regulating their ubiquitylation and subsequent endocytosis. In yeast, this involves the Nedd4 ubiquitin ligase Rsp5 and arrestin-related trafficking adaptors (ARTs). ARTs are targeted by signaling pathways and warrant that cargo ubiquitylation and endocytosis appropriately respond to nutritional inputs. Here, we show that glucose deprivation regulates the ART protein Csr2/Art8 at multiple levels to trigger high-affinity glucose transporter endocytosis. Csr2 is transcriptionally induced in these conditions through the AMPK orthologue Snf1 and downstream transcriptional repressors. Upon synthesis, Csr2 becomes activated by ubiquitylation. In contrast, glucose replenishment induces CSR2 transcriptional shutdown and switches Csr2 to an inactive, deubiquitylated form. This glucose-induced deubiquitylation of Csr2 correlates with its phospho-dependent association with 14-3-3 proteins and involves protein kinase A. Thus, two glucose signaling pathways converge onto Csr2 to regulate hexose transporter endocytosis by glucose availability. These data illustrate novel mechanisms by which nutrients modulate ART activity and endocytosis.
Collapse
Affiliation(s)
- Junie Hovsepian
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Quentin Defenouillère
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Véronique Albanèse
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Libuše Váchová
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i. BIOCEV, 252 50 Vestec, Czech Republic.,Faculty of Science, Charles University, BIOCEV, 252 50 Vestec, Czech Republic
| | - Camille Garcia
- Proteomics Facility, Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Zdena Palková
- Faculty of Science, Charles University, BIOCEV, 252 50 Vestec, Czech Republic
| | - Sébastien Léon
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75013 Paris, France
| |
Collapse
|
21
|
Ho HC, MacGurn JA, Emr SD. Deubiquitinating enzymes Ubp2 and Ubp15 regulate endocytosis by limiting ubiquitination and degradation of ARTs. Mol Biol Cell 2017; 28:1271-1283. [PMID: 28298493 PMCID: PMC5415021 DOI: 10.1091/mbc.e17-01-0008] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/27/2017] [Accepted: 02/28/2017] [Indexed: 12/18/2022] Open
Abstract
Endocytic down-regulation of cell-surface proteins is a fundamental cellular process for cell survival and adaptation to environmental stimuli. Ubiquitination of cargo proteins serves as the sorting signal for downstream trafficking and relies on the arrestin-related trafficking adaptor (ART)-Rsp5 ubiquitin ligase adaptor network in yeast. Hence proper regulation of the abundance and activity of these ligase-adaptor complexes is critical for main-tenance of optimal plasma membrane protein composition. Here we report that the stability of ARTs is regulated by the deubiquitinating enzymes (DUBs) Ubp2 and Ubp15. By counteracting the E3 ubiquitin ligase Rsp5, Ubp2 and Ubp15 prevent hyperubiquitination and proteasomal degradation of ARTs. Specifically, we show that loss of both Ubp2 and Ubp15 results in a defect in Hxt6 endocytosis associated with Art4 instability. Our results uncover a novel function for DUBs in the endocytic pathway by which Ubp2 and Ubp15 positively regulate the ART-Rsp5 network.
Collapse
Affiliation(s)
- Hsuan-Chung Ho
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Jason A MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240
| | - Scott D Emr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| |
Collapse
|
22
|
Wolters N, Amerik A. Inactivation of the VID27 gene prevents suppression of the doa4 degradation defect in doa4Δ did3Δ double mutant. Biochem Biophys Res Commun 2016; 482:1341-1345. [PMID: 27939891 DOI: 10.1016/j.bbrc.2016.12.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 12/06/2016] [Indexed: 11/30/2022]
Abstract
Ubiquitination is a key regulatory mechanism that affects numerous cellular processes. This modification is reversible. Deubiquitinating enzymes (DUBs) remove the ubiquitin tag from modified proteins. DUB Doa4 is involved in deubiquitination of conjugates at the late endosome/pre vacuolar compartment. A genetic screen led to isolation of seven extragenic suppressors of the doa4 phenotypic abnormalities. Remarkably, cloned Doa4-independent degradation (DID) genes encode the class E vacuolar protein-sorting factors involved in membrane protein trafficking. Here we provide evidence that inactivation of Vid27 (vacuolar import and degradation) prevents suppression of the doa4 phenotype by did3 mutation. Vid27 is a cytoplasmic protein essential for delivery of fructose-1,6-bisphosphatase into VID vesicles. Thus, our data revealed another connection between Doa4 and vacuolar protein sorting.
Collapse
Affiliation(s)
- Nazia Wolters
- Department of Pharmacology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Alexander Amerik
- Department of Pharmacology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT, 06030, USA; Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow, 119991, Russian Federation.
| |
Collapse
|
23
|
Böhm S, Szakal B, Herken BW, Sullivan MR, Mihalevic MJ, Kabbinavar FF, Branzei D, Clark NL, Bernstein KA. The Budding Yeast Ubiquitin Protease Ubp7 Is a Novel Component Involved in S Phase Progression. J Biol Chem 2016; 291:4442-52. [PMID: 26740628 DOI: 10.1074/jbc.m115.671057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Indexed: 11/06/2022] Open
Abstract
DNA damage must be repaired in an accurate and timely fashion to preserve genome stability. Cellular mechanisms preventing genome instability are crucial to human health because genome instability is considered a hallmark of cancer. Collectively referred to as the DNA damage response, conserved pathways ensure proper DNA damage recognition and repair. The function of numerous DNA damage response components is fine-tuned by posttranslational modifications, including ubiquitination. This not only involves the enzyme cascade responsible for conjugating ubiquitin to substrates but also requires enzymes that mediate directed removal of ubiquitin. Deubiquitinases remove ubiquitin from substrates to prevent degradation or to mediate signaling functions. The Saccharomyces cerevisiae deubiquitinase Ubp7 has been characterized previously as an endocytic factor. However, here we identify Ubp7 as a novel factor affecting S phase progression after hydroxyurea treatment and demonstrate an evolutionary and genetic interaction of Ubp7 with DNA damage repair pathways of homologous recombination and nucleotide excision repair. We find that deletion of UBP7 sensitizes cells to hydroxyurea and cisplatin and demonstrate that factors that stabilize replication forks are critical under these conditions. Furthermore, ubp7Δ cells exhibit an S phase progression defect upon checkpoint activation by hydroxyurea treatment. ubp7Δ mutants are epistatic to factors involved in histone maintenance and modification, and we find that a subset of Ubp7 is chromatin-associated. In summary, our results suggest that Ubp7 contributes to S phase progression by affecting the chromatin state at replication forks, and we propose histone H2B ubiquitination as a potential substrate of Ubp7.
Collapse
Affiliation(s)
- Stefanie Böhm
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania 15213
| | - Barnabas Szakal
- the Department of Molecular Oncology, Fondazione Istituto Fondazione Italiana per la Ricerca sul Cancro di Oncologia Molecolare, Milan 20139, Italy
| | - Benjamin W Herken
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania 15213
| | - Meghan R Sullivan
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania 15213
| | - Michael J Mihalevic
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania 15213
| | - Faiz F Kabbinavar
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania 15213
| | - Dana Branzei
- the Department of Molecular Oncology, Fondazione Istituto Fondazione Italiana per la Ricerca sul Cancro di Oncologia Molecolare, Milan 20139, Italy
| | - Nathan L Clark
- the Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, and
| | - Kara A Bernstein
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania 15213,
| |
Collapse
|
24
|
Isasa M, Rose CM, Elsasser S, Navarrete-Perea J, Paulo JA, Finley DJ, Gygi SP. Multiplexed, Proteome-Wide Protein Expression Profiling: Yeast Deubiquitylating Enzyme Knockout Strains. J Proteome Res 2015; 14:5306-17. [PMID: 26503604 DOI: 10.1021/acs.jproteome.5b00802] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Characterizing a protein's function often requires a description of the cellular state in its absence. Multiplexing in mass spectrometry-based proteomics has now achieved the ability to globally measure protein expression levels in yeast from 10 cell states simultaneously. We applied this approach to quantify expression differences in wild type and nine deubiquitylating enzyme (DUB) knockout strains with the goal of creating "information networks" that might provide deeper, mechanistic insights into a protein's biological role. In total, more than 3700 proteins were quantified with high reproducibility across three biological replicates (30 samples in all). DUB mutants demonstrated different proteomics profiles, consistent with distinct roles for each family member. These included differences in total ubiquitin levels and specific chain linkages. Moreover, specific expression changes suggested novel functions for several DUB family members. For instance, the ubp3Δ mutant showed large expression changes for members of the cytochrome C oxidase complex, consistent with a role for Ubp3 in mitochondrial regulation. Several DUBs also showed broad expression changes for phosphate transporters as well as other components of the inorganic phosphate signaling pathway, suggesting a role for these DUBs in regulating phosphate metabolism. These data highlight the potential of multiplexed proteome-wide analyses for biological investigation and provide a framework for further study of the DUB family. Our methods are readily applicable to the entire collection of yeast deletion mutants and may help facilitate systematic analysis of yeast and other organisms.
Collapse
Affiliation(s)
- Marta Isasa
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Christopher M Rose
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Suzanne Elsasser
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - José Navarrete-Perea
- National Autonomous University of Mexico, Av. Universidad 3000, Mexico City, District Federal 04510, Mexico
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Daniel J Finley
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| |
Collapse
|
25
|
Beckley JR, Chen JS, Yang Y, Peng J, Gould KL. A Degenerate Cohort of Yeast Membrane Trafficking DUBs Mediates Cell Polarity and Survival. Mol Cell Proteomics 2015; 14:3132-41. [PMID: 26412298 DOI: 10.1074/mcp.m115.050039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Indexed: 12/26/2022] Open
Abstract
Deubiquitinating enzymes (DUBs), cysteine or metallo- proteases that cleave ubiquitin chains or protein conjugates, are present in nearly every cellular compartment, with overlapping protein domain structure, localization, and functions. We discovered a cohort of DUBs that are involved in membrane trafficking (ubp4, ubp5, ubp9, ubp15, and sst2) and found that loss of all five of these DUBs but not loss of any combination of four, significantly impacted cell viability in the fission yeast Schizosaccharomyces pombe (1). Here, we delineate the collective and individual functions and activities of these five conserved DUBs using comparative proteomics, biochemistry, and microscopy. We find these five DUBs are degenerate rather than redundant at the levels of cell morphology, substrate selectivity, ubiquitin chain specificity, and cell viability under stress. These studies reveal the complexity of interplay among these enzymes, providing a foundation for understanding DUB biology and providing another example of how cells utilize degeneracy to improve survival.
Collapse
Affiliation(s)
- Janel R Beckley
- From the Cell & Developmental Biology, Vanderbilt University School of Medicine, 1161 21st Avenue South, Nashville, TN 37232
| | - Jun-Song Chen
- From the Cell & Developmental Biology, Vanderbilt University School of Medicine, 1161 21st Avenue South, Nashville, TN 37232
| | - Yanling Yang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Kathleen L Gould
- From the Cell & Developmental Biology, Vanderbilt University School of Medicine, 1161 21st Avenue South, Nashville, TN 37232
| |
Collapse
|
26
|
Grou CP, Pinto MP, Mendes AV, Domingues P, Azevedo JE. The de novo synthesis of ubiquitin: identification of deubiquitinases acting on ubiquitin precursors. Sci Rep 2015; 5:12836. [PMID: 26235645 PMCID: PMC4522658 DOI: 10.1038/srep12836] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 07/09/2015] [Indexed: 12/24/2022] Open
Abstract
Protein ubiquitination, a major post-translational modification in eukaryotes, requires an adequate pool of free ubiquitin. Cells maintain this pool by two pathways, both involving deubiquitinases (DUBs): recycling of ubiquitin from ubiquitin conjugates and processing of ubiquitin precursors synthesized de novo. Although many advances have been made in recent years regarding ubiquitin recycling, our knowledge on ubiquitin precursor processing is still limited, and questions such as when are these precursors processed and which DUBs are involved remain largely unanswered. Here we provide data suggesting that two of the four mammalian ubiquitin precursors, UBA52 and UBA80, are processed mostly post-translationally whereas the other two, UBB and UBC, probably undergo a combination of co- and post-translational processing. Using an unbiased biochemical approach we found that UCHL3, USP9X, USP7, USP5 and Otulin/Gumby/FAM105b are by far the most active DUBs acting on these precursors. The identification of these DUBs together with their properties suggests that each ubiquitin precursor can be processed in at least two different manners, explaining the robustness of the ubiquitin de novo synthesis pathway.
Collapse
Affiliation(s)
- Cláudia P Grou
- 1] Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal [2] Organelle Biogenesis and Function Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Manuel P Pinto
- 1] Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal [2] Organelle Biogenesis and Function Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Andreia V Mendes
- 1] Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal [2] Organelle Biogenesis and Function Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Pedro Domingues
- Mass Spectrometry Centre, UI-QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Jorge E Azevedo
- 1] Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal [2] Organelle Biogenesis and Function Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal [3] Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| |
Collapse
|
27
|
Swaney DL, Rodríguez-Mias RA, Villén J. Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover. EMBO Rep 2015; 16:1131-44. [PMID: 26142280 DOI: 10.15252/embr.201540298] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 06/15/2015] [Indexed: 12/21/2022] Open
Abstract
Ubiquitylation is an essential post-translational modification that regulates numerous cellular processes, most notably protein degradation. Ubiquitin can itself be phosphorylated at nearly every serine, threonine, and tyrosine residue. However, the effect of this modification on ubiquitin function is largely unknown. Here, we characterized the effects of phosphorylation of yeast ubiquitin at serine 65 in vivo and in vitro. We find this post-translational modification to be regulated under oxidative stress, occurring concomitantly with the restructuring of the ubiquitin landscape into a highly polymeric state. Phosphomimetic mutation of S65 recapitulates the oxidative stress phenotype, causing a dramatic accumulation of ubiquitylated proteins and a proteome-wide reduction of protein turnover rates. Importantly, this mutation impacts ubiquitin chain disassembly, chain linkage distribution, ubiquitin interactions, and substrate targeting. These results demonstrate that phosphorylation is an additional mode of ubiquitin regulation with broad implications in cellular physiology.
Collapse
Affiliation(s)
- Danielle L Swaney
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| |
Collapse
|
28
|
Valera MS, de Armas-Rillo L, Barroso-González J, Ziglio S, Batisse J, Dubois N, Marrero-Hernández S, Borel S, García-Expósito L, Biard-Piechaczyk M, Paillart JC, Valenzuela-Fernández A. The HDAC6/APOBEC3G complex regulates HIV-1 infectiveness by inducing Vif autophagic degradation. Retrovirology 2015; 12:53. [PMID: 26105074 PMCID: PMC4479245 DOI: 10.1186/s12977-015-0181-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 06/10/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) has evolved a complex strategy to overcome the immune barriers it encounters throughout an organism thanks to its viral infectivity factor (Vif), a key protein for HIV-1 infectivity and in vivo pathogenesis. Vif interacts with and promotes "apolipoprotein B mRNA-editing enzyme-catalytic, polypeptide-like 3G" (A3G) ubiquitination and subsequent degradation by the proteasome, thus eluding A3G restriction activity against HIV-1. RESULTS We found that cellular histone deacetylase 6 (HDAC6) directly interacts with A3G through its C-terminal BUZ domain (residues 841-1,215) to undergo a cellular co-distribution along microtubules and cytoplasm. The HDAC6/A3G complex occurs in the absence or presence of Vif, competes for Vif-mediated A3G degradation, and accounts for A3G steady-state expression level. In fact, HDAC6 directly interacts with and promotes Vif autophagic clearance, thanks to its C-terminal BUZ domain, a process requiring the deacetylase activity of HDAC6. HDAC6 degrades Vif without affecting the core binding factor β (CBF-β), a Vif-associated partner reported to be key for Vif- mediated A3G degradation. Thus HDAC6 antagonizes the proviral activity of Vif/CBF-β-associated complex by targeting Vif and stabilizing A3G. Finally, in cells producing virions, we observed a clear-cut correlation between the ability of HDAC6 to degrade Vif and to restore A3G expression, suggesting that HDAC6 controls the amount of Vif incorporated into nascent virions and the ability of HIV-1 particles of being infectious. This effect seems independent on the presence of A3G inside virions and on viral tropism. CONCLUSIONS Our study identifies for the first time a new cellular complex, HDAC6/A3G, involved in the autophagic degradation of Vif, and suggests that HDAC6 represents a new antiviral factor capable of controlling HIV-1 infectiveness by counteracting Vif and its functions.
Collapse
Affiliation(s)
- María-Soledad Valera
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, La Laguna, Tenerife, Spain.
| | - Laura de Armas-Rillo
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, La Laguna, Tenerife, Spain.
| | - Jonathan Barroso-González
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, La Laguna, Tenerife, Spain.
| | - Serena Ziglio
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, La Laguna, Tenerife, Spain.
| | - Julien Batisse
- Architecture et Réactivité de l'ARN, CNRS, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg, France.
| | - Noé Dubois
- Architecture et Réactivité de l'ARN, CNRS, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg, France.
| | - Sara Marrero-Hernández
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, La Laguna, Tenerife, Spain.
| | - Sophie Borel
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS) UMR5236 CNRS UMSF, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Laura García-Expósito
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, La Laguna, Tenerife, Spain.
| | - Martine Biard-Piechaczyk
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS) UMR5236 CNRS UMSF, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l'ARN, CNRS, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg, France.
| | - Agustín Valenzuela-Fernández
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, La Laguna, Tenerife, Spain.
| |
Collapse
|
29
|
Ostapenko D, Burton JL, Solomon MJ. The Ubp15 deubiquitinase promotes timely entry into S phase in Saccharomyces cerevisiae. Mol Biol Cell 2015; 26:2205-16. [PMID: 25877870 PMCID: PMC4462939 DOI: 10.1091/mbc.e14-09-1400] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 12/22/2022] Open
Abstract
The anaphase-promoting complex in partnership with its activator, Cdh1, is an E3 ubiquitin ligase responsible for targeting cell cycle proteins during G1 phase. In the budding yeast Saccharomyces cerevisiae, Cdh1 associates with the deubiquitinating enzyme Ubp15, but the significance of this interaction is unclear. To better understand the physiological role(s) of Ubp15, we examined cell cycle phenotypes of cells lacking Ubp15. We found that ubp15∆ cells exhibited delayed progression from G1 into S phase and increased sensitivity to the DNA synthesis inhibitor hydroxyurea. Both phenotypes of ubp15∆ cells were rescued by additional copies of the S-phase cyclin gene CLB5. Clb5 is an unstable protein targeted for proteasome-mediated degradation by several pathways. We found that during G1 phase, the APC(Cdh1)-mediated degradation of Clb5 was accelerated in ubp15∆ cells. Ubp15 interacted with Clb5 independent of Cdh1 and deubiquitinated Clb5 in a reconstituted system. Thus deubiquitination by Ubp15 counteracts APC activity toward cyclin Clb5 to allow Clb5 accumulation and a timely entry into S phase.
Collapse
Affiliation(s)
- Denis Ostapenko
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114
| | - Janet L Burton
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114
| | - Mark J Solomon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114
| |
Collapse
|
30
|
Kelly SP, Bedwell DM. Both the autophagy and proteasomal pathways facilitate the Ubp3p-dependent depletion of a subset of translation and RNA turnover factors during nitrogen starvation in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2015; 21:898-910. [PMID: 25795416 PMCID: PMC4408797 DOI: 10.1261/rna.045211.114] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 01/05/2015] [Indexed: 05/20/2023]
Abstract
Protein turnover is an important regulatory mechanism that facilitates cellular adaptation to changing environmental conditions. Previous studies have shown that ribosome abundance is reduced during nitrogen starvation by a selective autophagy mechanism termed ribophagy, which is dependent upon the deubiquitinase Ubp3p. In this study, we asked whether the abundance of various translation and RNA turnover factors are reduced following the onset of nitrogen starvation in Saccharomyces cerevisiae. We found distinct differences in the abundance of the proteins tested following nitrogen starvation: (1) The level of some did not change; (2) others were reduced with kinetics similar to ribophagy, and (3) a few proteins were rapidly depleted. Furthermore, different pathways differentially degraded the various proteins upon nitrogen starvation. The translation factors eRF3 and eIF4GI, and the decapping enhancer Pat1p, required an intact autophagy pathway for their depletion. In contrast, the deadenylase subunit Pop2p and the decapping enzyme Dcp2p were rapidly depleted by a proteasome-dependent mechanism. The proteasome-dependent depletion of Dcp2p and Pop2p was also induced by rapamycin, suggesting that the TOR1 pathway influences this pathway. Like ribophagy, depletion of eIF4GI, eRF3, Dcp2p, and Pop2p was dependent upon Ubp3p to varying extents. Together, our results suggest that the autophagy and proteasomal pathways degrade distinct translation and RNA turnover factors in a Ubp3p-dependent manner during nitrogen starvation. While ribophagy is thought to mediate the reutilization of scarce resources during nutrient limitation, our results suggest that the selective degradation of specific proteins could also facilitate a broader reprogramming of the post-transcriptional control of gene expression.
Collapse
Affiliation(s)
- Shane P Kelly
- Department of Cell, Developmental and Integrative Biology, Birmingham, Alabama 35294, USA
| | - David M Bedwell
- Department of Cell, Developmental and Integrative Biology, Birmingham, Alabama 35294, USA Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| |
Collapse
|
31
|
Small toxic protein encoded on chromosome VII of Saccharomyces cerevisiae. PLoS One 2015; 10:e0120678. [PMID: 25781884 PMCID: PMC4363601 DOI: 10.1371/journal.pone.0120678] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/25/2015] [Indexed: 11/19/2022] Open
Abstract
In a previous study, we found an unknown element that caused growth inhibition after its copy number increased in the 3' region of DIE2 in Saccharomyces cerevisiae. In this study, we further identified this element and observed that overexpression of a small protein (sORF2) of 57 amino acids encoded in this region caused growth inhibition. The transcriptional response and multicopy suppression of the growth inhibition caused by sORF2 overexpression suggest that sORF2 overexpression inhibits the ergosterol biosynthetic pathway. sORF2 was not required in the normal growth of S. cerevisiae, and not conserved in related yeast species including S. paradoxus. Thus, sORF2 (designated as OTO1) is an orphan ORF that determines the specificity of this species.
Collapse
|
32
|
Kimura Y, Kawawaki J, Kakiyama Y, Shimoda A, Tanaka K. The ESCRT-III adaptor protein Bro1 controls functions of regulator for free ubiquitin chains 1 (Rfu1) in ubiquitin homeostasis. J Biol Chem 2014; 289:21760-9. [PMID: 24962567 DOI: 10.1074/jbc.m114.550871] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Yeast Rfu1 (regulator for free ubiquitin chain 1) localizes to endosomes and plays a role in ubiquitin homeostasis by inhibiting the activity of Doa4. We show that Bro1, a member of the class E vacuolar protein sorting proteins that recruits Doa4 to endosomes and stimulates Doa4 deubiquitinating activity, also recruits Rfu1 to endosomes for involvement in ubiquitin homeostasis. This recruitment was mediated by the direct interaction between a region containing the YPEL motif in Rfu1 and the V domain in Bro1, which could be analogous to the interaction between the mammalian Alix V domain and YPXnL motifs of viral and cellular proteins. Furthermore, overexpression of Bro1, particularly the V domain, prevented Rfu1 degradation in response to heat shock. Thus, Bro1, a Doa4 positive regulator, regulated Rfu1, a negative regulator of Doa4. Rfu1 degradation partly involved the proteasome and a ubiquitin ligase Rsp5, suggesting that Rfu1 stability was regulated by ubiquitin-proteasome pathways.
Collapse
Affiliation(s)
- Yoko Kimura
- From the Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 113-8613 and the Department of Applied Biological Chemistry, Graduate School of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan
| | - Junko Kawawaki
- From the Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 113-8613 and
| | - Yukie Kakiyama
- From the Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 113-8613 and
| | - Ayumi Shimoda
- From the Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 113-8613 and
| | - Keiji Tanaka
- From the Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 113-8613 and
| |
Collapse
|
33
|
Öling D, Eisele F, Kvint K, Nyström T. Opposing roles of Ubp3-dependent deubiquitination regulate replicative life span and heat resistance. EMBO J 2014; 33:747-61. [PMID: 24596250 DOI: 10.1002/embj.201386822] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The interplay between molecular chaperones, ubiquitin/deubiquitinating enzymes, and proteasomes is a critical element in protein homeostasis. Among these factors, the conserved deubiquitinase, Ubp3, has the interesting ability, when overproduced, to suppress the requirement for the major cytosolic Hsp70 chaperones. Here, we show that Ubp3 overproduction counteracts deficiency of Hsp70s by the removal of damaged proteins deposited in inclusion bodies (JUNQ) during both aging and heat stress. Consistent with this, Ubp3 destabilized, deubiquitinated, and diminished the toxicity of the JUNQ-associated misfolded protein Ubc9(ts) in a proteasome-dependent manner. In contrast, another misfolded model protein, ssCPY*, was stabilized by Ubp3-dependent deubiquitination demonstrating a dual role for Ubp3, saving or destroying aberrant protein species depending on the stage at which the damaged protein is committed for destruction. We present genetic evidence for the former of these activities being key to Ubp3-dependent suppression of heat sensitivity in Hsp70-deficient cells, whereas protein destruction suppresses accelerated aging. We discuss the data in view of how heat stress and aging might elicit differential damage and challenges on the protein homeostasis network.
Collapse
Affiliation(s)
- David Öling
- Department of Chemistry and Molecular Biology, Göteborg University, Göteborg, Sweden
| | | | | | | |
Collapse
|
34
|
Schuh AL, Audhya A. The ESCRT machinery: from the plasma membrane to endosomes and back again. Crit Rev Biochem Mol Biol 2014; 49:242-61. [PMID: 24456136 DOI: 10.3109/10409238.2014.881777] [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: 01/13/2023]
Abstract
The manipulation and reorganization of lipid bilayers are required for diverse cellular processes, ranging from organelle biogenesis to cytokinetic abscission, and often involves transient membrane disruption. A set of membrane-associated proteins collectively known as the endosomal sorting complex required for transport (ESCRT) machinery has been implicated in membrane scission steps, which transform a single, continuous bilayer into two distinct bilayers, while simultaneously segregating cargo throughout the process. Components of the ESCRT pathway, which include 5 distinct protein complexes and an array of accessory factors, each serve discrete functions. This review focuses on the molecular mechanisms by which the ESCRT proteins facilitate cargo sequestration and membrane remodeling and highlights their unique roles in cellular homeostasis.
Collapse
Affiliation(s)
- Amber L Schuh
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health , Madison, WI , USA
| | | |
Collapse
|
35
|
Amara F, Colombo R, Cazzaniga P, Pescini D, Csikász-Nagy A, Falconi MM, Besozzi D, Plevani P. In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae. BMC SYSTEMS BIOLOGY 2013; 7:24. [PMID: 23514624 PMCID: PMC3668150 DOI: 10.1186/1752-0509-7-24] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 02/05/2013] [Indexed: 12/23/2022]
Abstract
BACKGROUND The genome of living organisms is constantly exposed to several damaging agents that induce different types of DNA lesions, leading to cellular malfunctioning and onset of many diseases. To maintain genome stability, cells developed various repair and tolerance systems to counteract the effects of DNA damage. Here we focus on Post Replication Repair (PRR), the pathway involved in the bypass of DNA lesions induced by sunlight exposure and UV radiation. PRR acts through two different mechanisms, activated by mono- and poly-ubiquitylation of the DNA sliding clamp, called Proliferating Cell Nuclear Antigen (PCNA). RESULTS We developed a novel protocol to measure the time-course ratios between mono-, di- and tri-ubiquitylated PCNA isoforms on a single western blot, which were used as the wet readout for PRR events in wild type and mutant S. cerevisiae cells exposed to acute UV radiation doses. Stochastic simulations of PCNA ubiquitylation dynamics, performed by exploiting a novel mechanistic model of PRR, well fitted the experimental data at low UV doses, but evidenced divergent behaviors at high UV doses, thus driving the design of further experiments to verify new hypothesis on the functioning of PRR. The model predicted the existence of a UV dose threshold for the proper functioning of the PRR model, and highlighted an overlapping effect of Nucleotide Excision Repair (the pathway effectively responsible to clean the genome from UV lesions) on the dynamics of PCNA ubiquitylation in different phases of the cell cycle. In addition, we showed that ubiquitin concentration can affect the rate of PCNA ubiquitylation in PRR, offering a possible explanation to the DNA damage sensitivity of yeast strains lacking deubiquitylating enzymes. CONCLUSIONS We exploited an in vivo and in silico combinational approach to analyze for the first time in a Systems Biology context the events of PCNA ubiquitylation occurring in PRR in budding yeast cells. Our findings highlighted an intricate functional crosstalk between PRR and other events controlling genome stability, and evidenced that PRR is more complicated and still far less characterized than previously thought.
Collapse
Affiliation(s)
- Flavio Amara
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Riccardo Colombo
- Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Paolo Cazzaniga
- Dipartimento di Scienze Umane e Sociali, Università degli Studi di Bergamo, Bergamo, Italy
| | - Dario Pescini
- Dipartimento di Statistica e Metodi Quantitativi, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Attila Csikász-Nagy
- , The Microsoft Research - Università degli Studi di Trento, Centre for Computational and Systems Biology, Rovereto (Trento), Italy
| | - Marco Muzi Falconi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Daniela Besozzi
- Dipartimento di Informatica, Università degli Studi di Milano, Milano, Italy
| | - Paolo Plevani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| |
Collapse
|
36
|
Li Y, Wang Y. Ras protein/cAMP-dependent protein kinase signaling is negatively regulated by a deubiquitinating enzyme, Ubp3, in yeast. J Biol Chem 2013; 288:11358-65. [PMID: 23476013 DOI: 10.1074/jbc.m112.449751] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ras proteins and cAMP-dependent protein kinase (protein kinase A, PKA) are important components of a nutrient signaling pathway that mediates cellular responses to glucose in yeast. The molecular mechanisms that regulate Ras/PKA-mediated signaling remain to be fully understood. Here, we provide evidence that Ras/PKA signaling is negatively regulated by a deubiquitinating enzyme, Ubp3. Disrupting the activity of Ubp3 leads to hyperactivation of PKA, as evidenced by much enhanced phosphorylation of PKA substrates, decreased accumulation of glycogen, larger cell size, and increased sensitivity to heat shock. Levels of intracellular cAMP and the active forms of Ras proteins are also elevated in the ubp3Δ mutant. Consistent with a possibility that the increased cAMP is responsible for the abnormal signaling behavior of the ubp3Δ mutant, overexpressing PDE2, which encodes a phosphodiesterase that hydrolyzes cAMP, significantly relieves the cell size increase and heat shock sensitivity of the mutant. Further analysis reveals that Ubp3 interacts with a Ras GTPase-accelerating protein, Ira2, and regulates its level of ubiquitination. Together, our data indicate that Ubp3 is a new regulator of the Ras/PKA signaling pathway and suggest that Ubp3 regulates this pathway by controlling the ubiquitination of Ras GTPase-accelerating protein Ira2.
Collapse
Affiliation(s)
- Yang Li
- Department of Biology, Saint Louis University, St. Louis, Missouri 63103, USA
| | | |
Collapse
|
37
|
Hutchins AP, Liu S, Diez D, Miranda-Saavedra D. The repertoires of ubiquitinating and deubiquitinating enzymes in eukaryotic genomes. Mol Biol Evol 2013; 30:1172-87. [PMID: 23393154 PMCID: PMC3670738 DOI: 10.1093/molbev/mst022] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Reversible protein ubiquitination regulates virtually all known cellular activities. Here, we present a quantitatively evaluated and broadly applicable method to predict eukaryotic ubiquitinating enzymes (UBE) and deubiquitinating enzymes (DUB) and its application to 50 distinct genomes belonging to four of the five major phylogenetic supergroups of eukaryotes: unikonts (including metazoans, fungi, choanozoa, and amoebozoa), excavates, chromalveolates, and plants. Our method relies on a collection of profile hidden Markov models, and we demonstrate its superior performance (coverage and classification accuracy >99%) by identifying approximately 25% and approximately 35% additional UBE and DUB genes in yeast and human, which had not been reported before. In yeast, we predict 85 UBE and 24 DUB genes, for 814 UBE and 107 DUB genes in the human genome. Most UBE and DUB families are present in all eukaryotic lineages, with plants and animals harboring massively enlarged repertoires of ubiquitin ligases. Unicellular organisms, on the other hand, typically harbor less than 300 UBEs and less than 40 DUBs per genome. Ninety-one UBE/DUB genes are orthologous across all four eukaryotic supergroups, and these likely represent a primordial core of enzymes of the ubiquitination system probably dating back to the first eukaryotes approximately 2 billion years ago. Our genome-wide predictions are available through the Database of Ubiquitinating and Deubiquitinating Enzymes (www.DUDE-db.org), where users can also perform advanced sequence and phylogenetic analyses and submit their own predictions.
Collapse
Affiliation(s)
- Andrew Paul Hutchins
- Bioinformatics and Genomics Laboratory, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | | | | | | |
Collapse
|
38
|
Finley D, Ulrich HD, Sommer T, Kaiser P. The ubiquitin-proteasome system of Saccharomyces cerevisiae. Genetics 2012; 192:319-60. [PMID: 23028185 PMCID: PMC3454868 DOI: 10.1534/genetics.112.140467] [Citation(s) in RCA: 301] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 07/28/2012] [Indexed: 12/14/2022] Open
Abstract
Protein modifications provide cells with exquisite temporal and spatial control of protein function. Ubiquitin is among the most important modifiers, serving both to target hundreds of proteins for rapid degradation by the proteasome, and as a dynamic signaling agent that regulates the function of covalently bound proteins. The diverse effects of ubiquitylation reflect the assembly of structurally distinct ubiquitin chains on target proteins. The resulting ubiquitin code is interpreted by an extensive family of ubiquitin receptors. Here we review the components of this regulatory network and its effects throughout the cell.
Collapse
Affiliation(s)
- Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Helle D. Ulrich
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, EN6 3LD, United Kingdom
| | - Thomas Sommer
- Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Peter Kaiser
- Department of Biological Chemistry, University of California, Irvine, California 92697
| |
Collapse
|
39
|
Scheuring D, Künzl F, Viotti C, Yan MSW, Jiang L, Schellmann S, Robinson DG, Pimpl P. Ubiquitin initiates sorting of Golgi and plasma membrane proteins into the vacuolar degradation pathway. BMC PLANT BIOLOGY 2012; 12:164. [PMID: 22970698 PMCID: PMC3534617 DOI: 10.1186/1471-2229-12-164] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 07/13/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND In yeast and mammals, many plasma membrane (PM) proteins destined for degradation are tagged with ubiquitin. These ubiquitinated proteins are internalized into clathrin-coated vesicles and are transported to early endosomal compartments. There, ubiquitinated proteins are sorted by the endosomal sorting complex required for transport (ESCRT) machinery into the intraluminal vesicles of multivesicular endosomes. Degradation of these proteins occurs after endosomes fuse with lysosomes/lytic vacuoles to release their content into the lumen. In plants, some PM proteins, which cycle between the PM and endosomal compartments, have been found to be ubiquitinated, but it is unclear whether ubiquitin is sufficient to mediate internalization and thus acts as a primary sorting signal for the endocytic pathway. To test whether plants use ubiquitin as a signal for the degradation of membrane proteins, we have translationally fused ubiquitin to different fluorescent reporters for the plasma membrane and analyzed their transport. RESULTS Ubiquitin-tagged PM reporters localized to endosomes and to the lumen of the lytic vacuole in tobacco mesophyll protoplasts and in tobacco epidermal cells. The internalization of these reporters was significantly reduced if clathrin-mediated endocytosis was inhibited by the coexpression of a mutant of the clathrin heavy chain, the clathrin hub. Surprisingly, a ubiquitin-tagged reporter for the Golgi was also transported into the lumen of the vacuole. Vacuolar delivery of the reporters was abolished upon inhibition of the ESCRT machinery, indicating that the vacuolar delivery of these reporters occurs via the endocytic transport route. CONCLUSIONS Ubiquitin acts as a sorting signal at different compartments in the endomembrane system to target membrane proteins into the vacuolar degradation pathway: If displayed at the PM, ubiquitin triggers internalization of PM reporters into the endocytic transport route, but it also mediates vacuolar delivery if displayed at the Golgi. In both cases, ubiquitin-tagged proteins travel via early endosomes and multivesicular bodies to the lytic vacuole. This suggests that vacuolar degradation of ubiquitinated proteins is not restricted to PM proteins but might also facilitate the turnover of membrane proteins in the early secretory pathway.
Collapse
Affiliation(s)
- David Scheuring
- Department of Plant Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| | - Fabian Künzl
- Department of Developmental Genetics, Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, 72076, Germany
| | - Corrado Viotti
- Department of Plant Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
- Plant Developmental Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| | - Melody San Wan Yan
- School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin NT, Hong Kong, PR China
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin NT, Hong Kong, PR China
| | - Swen Schellmann
- Botanical Institute, Biozentrum Köln, University of Cologne, Cologne, 50674, Germany
| | - David G Robinson
- Department of Plant Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| | - Peter Pimpl
- Department of Developmental Genetics, Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, 72076, Germany
- Department of Plant Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| |
Collapse
|
40
|
D'Arcy P, Linder S. Proteasome deubiquitinases as novel targets for cancer therapy. Int J Biochem Cell Biol 2012; 44:1729-38. [PMID: 22819849 DOI: 10.1016/j.biocel.2012.07.011] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 07/10/2012] [Accepted: 07/11/2012] [Indexed: 12/27/2022]
Abstract
The ubiquitin-proteasome system (UPS) is a conserved pathway regulating numerous biological processes including protein turnover, DNA repair, and intracellular trafficking. Tumor cells are dependent on a functioning UPS, making it an ideal target for the development of novel anti-cancer therapies. The development of bortezomib (Velcade(®)) as a treatment for multiple myeloma and mantle cell lymphoma has verified this and suggests that targeting other components of the UPS may be a viable strategy for the treatment for cancer. We recently described a novel class of proteasome inhibitors that function by an alternative mechanism of action (D'Arcy et al., 2011). The small molecule b-AP15 blocks the deubiquitinase (DUB) activity of the 19S regulatory particle (19S RP) without inhibiting the proteolytic activities of the 20S core particle (20S CP). b-AP15 inhibits two proteasome-associated DUBs, USP14 and UCHL5, resulting in a rapid accumulation of high molecular weight ubiquitin conjugates and a functional proteasome shutdown. Interestingly, b-AP15 displays several differences to bortezomib including insensitivity to over-expression of the anti-apoptotic mediator Bcl-2 and anti-tumor activity in solid tumor models. In this review we will discuss the potential of proteasome deubiquitinase inhibitors as additions to the therapeutic arsenal against cancer.
Collapse
Affiliation(s)
- Pádraig D'Arcy
- Institute for Oncology-Pathology, Cancer Center Karolinska, Karolinska Institute, 17176 Stockholm, Sweden.
| | | |
Collapse
|
41
|
A deubiquitylating complex required for neosynthesis of a yeast mitochondrial ATP synthase subunit. PLoS One 2012; 7:e38071. [PMID: 22723847 PMCID: PMC3378586 DOI: 10.1371/journal.pone.0038071] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 04/29/2012] [Indexed: 02/06/2023] Open
Abstract
The ubiquitin system is known to be involved in maintaining the integrity of mitochondria, but little is known about the role of deubiquitylating (DUB) enzymes in such functions. Budding yeast cells deleted for UBP13 and its close homolog UBP9 displayed a high incidence of petite colonies and slow respiratory growth at 37°C. Both Ubp9 and Ubp13 interacted directly with Duf1 (DUB-associated factor 1), a WD40 motif-containing protein. Duf1 activates the DUB activity of recombinant Ubp9 and Ubp13 in vitro and deletion of DUF1 resulted in the same respiratory phenotype as the deletion of both UBP9 and UBP13. We show that the mitochondrial defects of these mutants resulted from a strong decrease at 37°C in the de novo biosynthesis of Atp9, a membrane-bound component of ATP synthase encoded by mitochondrial DNA. The defect appears at the level of ATP9 mRNA translation, while its maturation remained unchanged in the mutants. This study describes a new role of the ubiquitin system in mitochondrial biogenesis.
Collapse
|
42
|
Fang W, Price MS, Toffaletti DL, Tenor J, Betancourt-Quiroz M, Price JL, Pan WH, Liao WQ, Perfect JR. Pleiotropic effects of deubiquitinating enzyme Ubp5 on growth and pathogenesis of Cryptococcus neoformans. PLoS One 2012; 7:e38326. [PMID: 22719877 PMCID: PMC3375289 DOI: 10.1371/journal.pone.0038326] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 05/03/2012] [Indexed: 12/16/2022] Open
Abstract
Ubiquitination is a reversible protein modification that influences various cellular processes in eukaryotic cells. Deubiquitinating enzymes remove ubiquitin, maintain ubiquitin homeostasis and regulate protein degradation via the ubiquitination pathway. Cryptococcus neoformans is an important basidiomycete pathogen that causes life-threatening meningoencephalitis primarily in the immunocompromised population. In order to understand the possible influence deubiquitinases have on growth and virulence of the model pathogenic yeast Cryptococcus neoformans, we generated deletion mutants of seven putative deubiquitinase genes. Compared to other deubiquitinating enzyme mutants, a ubp5Δ mutant exhibited severely attenuated virulence and many distinct phenotypes, including decreased capsule formation, hypomelanization, defective sporulation, and elevated sensitivity to several external stressors (such as high temperature, oxidative and nitrosative stresses, high salts, and antifungal agents). Ubp5 is likely the major deubiquitinating enzyme for stress responses in C. neoformans, which further delineates the evolutionary divergence of Cryptococcus from the model yeast S. cerevisiae, and provides an important paradigm for understanding the potential role of deubiquitination in virulence by other pathogenic fungi. Other putative deubiquitinase mutants (doa4Δ and ubp13Δ) share some phenotypes with the ubp5Δ mutant, illustrating functional overlap among deubiquitinating enzymes in C. neoformans. Therefore, deubiquitinating enzymes (especially Ubp5) are essential for the virulence composite of C. neoformans and provide an additional yeast survival and propagation advantage in the host.
Collapse
Affiliation(s)
- Wei Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, PLA Key Laboratory of Mycosis, Institute of Dermatology and Mycosis of Changzheng Hospital, Second Military Medical University, Shanghai, China
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael S. Price
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Dena L. Toffaletti
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jennifer Tenor
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Marisol Betancourt-Quiroz
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jennifer L. Price
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Wei-hua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, PLA Key Laboratory of Mycosis, Institute of Dermatology and Mycosis of Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wan-qing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, PLA Key Laboratory of Mycosis, Institute of Dermatology and Mycosis of Changzheng Hospital, Second Military Medical University, Shanghai, China
- * E-mail: (JRP); (W-QL)
| | - John R. Perfect
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail: (JRP); (W-QL)
| |
Collapse
|
43
|
Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes. J Proteomics 2012; 75:3886-97. [PMID: 22634085 DOI: 10.1016/j.jprot.2012.04.055] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 04/15/2012] [Accepted: 04/21/2012] [Indexed: 11/21/2022]
Abstract
Deubiquitylating enzymes (DUBs) are a large group of proteases that regulate ubiquitin-dependent metabolic pathways by cleaving ubiquitin-protein bonds. Here we present a global study aimed at elucidating the effects DUBs have on protein abundance changes in eukaryotic cells. To this end we compare wild-type Saccharomyces cerevisiae to 20 DUB knock-out strains using quantitative proteomics to measure proteome-wide expression of isotope labeled proteins, and analyze the data in the context of known transcription-factor regulatory networks. Overall we find that protein abundances differ widely between individual deletion strains, demonstrating that removing just a single component from the complex ubiquitin system causes major changes in cellular protein expression. The outcome of our analysis confirms many of the known biological roles for characterized DUBs such as Ubp3p and Ubp8p, and we demonstrate that Sec28p is a novel Ubp3p substrate. In addition we find strong associations for several uncharacterized DUBs providing clues for their possible cellular roles. Hierarchical clustering of all deletion strains reveals pronounced similarities between various DUBs, which corroborate current DUB knowledge and uncover novel functional aspects for uncharacterized DUBs. Observations in our analysis support that DUBs induce both direct and indirect effects on protein abundances.
Collapse
|
44
|
Grou CP, Francisco T, Rodrigues TA, Freitas MO, Pinto MP, Carvalho AF, Domingues P, Wood SA, Rodríguez-Borges JE, Sá-Miranda C, Fransen M, Azevedo JE. Identification of ubiquitin-specific protease 9X (USP9X) as a deubiquitinase acting on ubiquitin-peroxin 5 (PEX5) thioester conjugate. J Biol Chem 2012; 287:12815-27. [PMID: 22371489 DOI: 10.1074/jbc.m112.340158] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Peroxin 5 (PEX5), the peroxisomal protein shuttling receptor, binds newly synthesized peroxisomal matrix proteins in the cytosol and promotes their translocation across the organelle membrane. During the translocation step, PEX5 itself becomes inserted into the peroxisomal docking/translocation machinery. PEX5 is then monoubiquitinated at a conserved cysteine residue and extracted back into the cytosol in an ATP-dependent manner. We have previously shown that the ubiquitin-PEX5 thioester conjugate (Ub-PEX5) released into the cytosol can be efficiently disrupted by physiological concentrations of glutathione, raising the possibility that a fraction of Ub-PEX5 is nonenzymatically deubiquitinated in vivo. However, data suggesting that Ub-PEX5 is also a target of a deubiquitinase were also obtained in that work. Here, we used an unbiased biochemical approach to identify this enzyme. Our results suggest that ubiquitin-specific protease 9X (USP9X) is by far the most active deubiquitinase acting on Ub-PEX5, both in female rat liver and HeLa cells. We also show that USP9X is an elongated monomeric protein with the capacity to hydrolyze thioester, isopeptide, and peptide bonds. The strategy described here will be useful in identifying deubiquitinases acting on other ubiquitin conjugates.
Collapse
Affiliation(s)
- Cláudia P Grou
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Schaefer JB, Morgan DO. Protein-linked ubiquitin chain structure restricts activity of deubiquitinating enzymes. J Biol Chem 2011; 286:45186-96. [PMID: 22072716 DOI: 10.1074/jbc.m111.310094] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The attachment of lysine 48 (Lys(48))-linked polyubiquitin chains to proteins is a universal signal for degradation by the proteasome. Here, we report that long Lys(48)-linked chains are resistant to many deubiquitinating enzymes (DUBs). Representative enzymes from this group, Ubp15 from yeast and its human ortholog USP7, rapidly remove mono- and diubiquitin from substrates but are slow to remove longer Lys(48)-linked chains. This resistance is lost if the structure of Lys(48)-linked chains is disrupted by mutation of ubiquitin or if chains are linked through Lys(63). In contrast to Ubp15 and USP7, Ubp12 readily cleaves the ends of long chains, regardless of chain structure. We propose that the resistance to many DUBs of long, substrate-attached Lys(48)-linked chains helps ensure that proteins are maintained free from ubiquitin until a threshold of ubiquitin ligase activity enables degradation.
Collapse
Affiliation(s)
- Jonathan B Schaefer
- Department of Physiology, University of California at San Francisco, San Francisco, California 94158, USA
| | | |
Collapse
|
46
|
Multicopy suppression screening of Saccharomyces cerevisiae Identifies the ubiquitination machinery as a main target for improving growth at low temperatures. Appl Environ Microbiol 2011; 77:7517-25. [PMID: 21908639 DOI: 10.1128/aem.00404-11] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A decrease in ambient temperature alters membrane functionality and impairs the proper interaction between the cell and its external milieu. Understanding how cells adapt membrane properties and modulate the activity of membrane-associated proteins is therefore of major interest from both the basic and the applied points of view. Here, we have isolated multicopy suppressors of the cold sensitivity phenotype of a trp1 strain of Saccharomyces cerevisiae. Three poorly characterized genes, namely, ALY2 encoding the endocytic adaptor, CAJ1 encoding the J protein, and UBP13 encoding the ubiquitin C-terminal hydrolase, were identified as mediating increased growth at 12°C of both Trp⁻ and Trp+ yeast strains. This effect was likely due to the downregulation of cold-instigated degradation of nutrient permeases, since it was missing from cells of the rsp5Δ mutant strain, which contains a point mutation in the gene encoding ubiquitin ligase. Indeed, we found that 12°C treatments reduced the level of several membrane transporters, including Tat1p and Tat2p, two yeast tryptophan transporters, and Gap1, the general amino acid permease. We also found that the lack of Rsp5p increased the steady state level of Tat1p and Tat2p and that ALY2-engineered cells grown at 12°C had higher Tat2p and Gap1p abundance. Nevertheless, the high copy number of ALY2 or UBP13 improved cold growth even in the absence of Tat2p. Consistent with this, ALY2- and UBP13-engineered cells of the industrial QA23 strain grew faster and produced more CO₂ at 12°C than did the parental when maltose was used as the sole carbon source. Hence, the multicopy suppressors isolated in this work appear to contribute to the correct control of the cell surface protein repertoire and their engineering might have potential biotechnological applications.
Collapse
|
47
|
Bozza WP, Zhuang Z. Biochemical characterization of a multidomain deubiquitinating enzyme Ubp15 and the regulatory role of its terminal domains. Biochemistry 2011; 50:6423-32. [PMID: 21710968 DOI: 10.1021/bi200529z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Deubiquitinating enzymes (DUBs) have emerged as essential players in a myriad of cellular processes, yet the regulation of DUB function remains largely unknown. While some DUBs rely on the formation of complex for regulation of enzymatic activity, many DUBs utilize interdomain interactions to regulate catalysis. Here we report the biochemical characterization of a multidomain deubiquitinating enzyme, Ubp15, from Saccharomyces cerevisiae. Steady-state kinetic investigation showed that Ubp15 is a highly active DUB. We identified active-site residues that are required for catalysis. We have also identified key residues on Ubp15 required for ubiquitin binding and catalysis. We further demonstrated that Ubp15's enzymatic activity is regulated by the N- and C-terminal domains that flank the catalytic core domain. Moreover, we demonstrated that Ubp15 physically interacts with a WD40 repeat-containing protein, Cdh1, by copurification experiments. Interestingly, unlike other DUBs that specifically interact with WD40 repeat-containing proteins, Cdh1 does not function in stimulating Ubp15's activity. The possible cellular function of Ubp15 in cell cycle regulation is discussed in view of the specific interaction between Ubp15 and Cdh1, an activator of the anaphase-promoting complex/cyclosome (APC/C).
Collapse
Affiliation(s)
- William P Bozza
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, USA
| | | |
Collapse
|
48
|
Debelyy MO, Platta HW, Saffian D, Hensel A, Thoms S, Meyer HE, Warscheid B, Girzalsky W, Erdmann R. Ubp15p, a ubiquitin hydrolase associated with the peroxisomal export machinery. J Biol Chem 2011; 286:28223-34. [PMID: 21665945 DOI: 10.1074/jbc.m111.238600] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Peroxisomal matrix protein import is facilitated by cycling receptors shuttling between the cytosol and the peroxisomal membrane. One crucial step in this cycle is the ATP-dependent release of the receptors from the peroxisomal membrane. This step is facilitated by the peroxisomal AAA (ATPases associated with various cellular activities) proteins Pex1p and Pex6p with ubiquitination of the receptor being the main signal for its export. Here we report that the AAA complex contains dislocase as well as deubiquitinating activity. Ubp15p, a ubiquitin hydrolase, was identified as a novel constituent of the complex. Ubp15p partially localizes to peroxisomes and is capable of cleaving off ubiquitin moieties from the type I peroxisomal targeting sequence (PTS1) receptor Pex5p. Furthermore, Ubp15p-deficient cells are characterized by a stress-related PTS1 import defect. The results merge into a picture in which removal of ubiquitin from the PTS1 receptor Pex5p is a specific event and might represent a vital step in receptor recycling.
Collapse
Affiliation(s)
- Mykhaylo O Debelyy
- Abteilung für Systembiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Bochum, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Intersection of the multivesicular body pathway and lipid homeostasis in RNA replication by a positive-strand RNA virus. J Virol 2011; 85:5494-503. [PMID: 21430061 DOI: 10.1128/jvi.02031-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Like many positive-strand RNA viruses, brome mosaic virus (BMV) RNA replication occurs in membrane-invaginated vesicular compartments. BMV RNA replication compartments show parallels with membrane-enveloped, budding retrovirus virions, whose release depends on the cellular multivesicular body (MVB) sorting pathway. BMV RNA replication compartments are not released from their parent membranes, but might depend on MVB functions for membrane invagination. Prior results show that BMV RNA replication is severely inhibited by deletion of the crucial MVB gene DOA4 or BRO1. We report here that involvement of DOA4 and BRO1 in BMV RNA replication is not dependent on the MVB pathway's membrane-shaping functions but rather is due to their roles in recycling ubiquitin from MVB cargos. We show that deleting DOA4 or BRO1 inhibits the ubiquitination- and proteasome-dependent activation of homologous transcription factors Mga2p and Spt23p, which regulate many lipid metabolism genes, including the fatty acid desaturase gene OLE1, which is essential for BMV RNA replication. However, Mga2p processing and BMV RNA replication are restored by supplementing free ubiquitin, which is depleted in doa4Δ and bro1Δ cells. The results identify Mga2p and Spt23p processing and lipid regulation as sensitive targets of ubiquitin depletion and correctly predict multiple effects of modulating additional host genes RFU1, UBP6, and UFD3. Our results also show that BMV RNA replication depends on additional Mga2p-regulated genes likely involved in lipid metabolism beyond OLE1. Among other points, these findings show the potential for blocking viral RNA replication by modulating lipid synthesis at multiple levels.
Collapse
|
50
|
Leach MD, Stead DA, Argo E, MacCallum DM, Brown AJP. Molecular and proteomic analyses highlight the importance of ubiquitination for the stress resistance, metabolic adaptation, morphogenetic regulation and virulence of Candida albicans. Mol Microbiol 2011; 79:1574-93. [PMID: 21269335 PMCID: PMC3084552 DOI: 10.1111/j.1365-2958.2011.07542.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Post-translational modifications of proteins play key roles in eukaryotic growth, differentiation and environmental adaptation. In model systems the ubiquitination of specific proteins contributes to the control of cell cycle progression, stress adaptation and metabolic reprogramming. We have combined molecular, cellular and proteomic approaches to examine the roles of ubiquitination in Candida albicans, because little is known about ubiquitination in this major fungal pathogen of humans. Independent null (ubi4/ubi4) and conditional (MET3p-UBI4/ubi4) mutations were constructed at the C. albicans polyubiquitin-encoding locus. These mutants displayed morphological and cell cycle defects, as well as sensitivity to thermal, oxidative and cell wall stresses. Furthermore, ubi4/ubi4 cells rapidly lost viability under starvation conditions. Consistent with these phenotypes, proteins with roles in stress responses (Gnd1, Pst2, Ssb1), metabolism (Acs2, Eno1, Fba1, Gpd2, Pdx3, Pgk1, Tkl1) and ubiquitination (Ubi4, Ubi3, Pre1, Pre3, Rpt5) were among the ubiquitination targets we identified, further indicating that ubiquitination plays key roles in growth, stress responses and metabolic adaptation in C. albicans. Clearly ubiquitination plays key roles in the regulation of fundamental cellular processes that underpin the pathogenicity of this medically important fungus. This was confirmed by the observation that the virulence of C. albicans ubi4/ubi4 cells is significantly attenuated.
Collapse
Affiliation(s)
- Michelle D Leach
- School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | | | | | | | | |
Collapse
|