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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.
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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
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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).
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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
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3
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Pinheiro T, Lip KYF, García-Ríos E, Querol A, Teixeira J, van Gulik W, Guillamón JM, Domingues L. Differential proteomic analysis by SWATH-MS unravels the most dominant mechanisms underlying yeast adaptation to non-optimal temperatures under anaerobic conditions. Sci Rep 2020; 10:22329. [PMID: 33339840 PMCID: PMC7749138 DOI: 10.1038/s41598-020-77846-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 10/20/2020] [Indexed: 12/28/2022] Open
Abstract
Elucidation of temperature tolerance mechanisms in yeast is essential for enhancing cellular robustness of strains, providing more economically and sustainable processes. We investigated the differential responses of three distinct Saccharomyces cerevisiae strains, an industrial wine strain, ADY5, a laboratory strain, CEN.PK113-7D and an industrial bioethanol strain, Ethanol Red, grown at sub- and supra-optimal temperatures under chemostat conditions. We employed anaerobic conditions, mimicking the industrial processes. The proteomic profile of these strains in all conditions was performed by sequential window acquisition of all theoretical spectra-mass spectrometry (SWATH-MS), allowing the quantification of 997 proteins, data available via ProteomeXchange (PXD016567). Our analysis demonstrated that temperature responses differ between the strains; however, we also found some common responsive proteins, revealing that the response to temperature involves general stress and specific mechanisms. Overall, sub-optimal temperature conditions involved a higher remodeling of the proteome. The proteomic data evidenced that the cold response involves strong repression of translation-related proteins as well as induction of amino acid metabolism, together with components related to protein folding and degradation while, the high temperature response mainly recruits amino acid metabolism. Our study provides a global and thorough insight into how growth temperature affects the yeast proteome, which can be a step forward in the comprehension and improvement of yeast thermotolerance.
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Affiliation(s)
- Tânia Pinheiro
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Ka Ying Florence Lip
- Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Estéfani García-Ríos
- Food Biotechnology Department, Instituto de Agroquímica Y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Amparo Querol
- Food Biotechnology Department, Instituto de Agroquímica Y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - José Teixeira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Walter van Gulik
- Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - José Manuel Guillamón
- Food Biotechnology Department, Instituto de Agroquímica Y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.
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4
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Huseinovic A, van Dijk M, Vermeulen NPE, van Leeuwen F, Kooter JM, Vos JC. Drug toxicity profiling of a Saccharomyces cerevisiae deubiquitinase deletion panel shows that acetaminophen mimics tyrosine. Toxicol In Vitro 2017; 47:259-268. [PMID: 29258884 DOI: 10.1016/j.tiv.2017.12.007] [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: 08/14/2017] [Revised: 12/05/2017] [Accepted: 12/13/2017] [Indexed: 10/18/2022]
Abstract
Post-translational protein modification by addition or removal of the small polypeptide ubiquitin is involved in a range of critical cellular processes, like proteasomal protein degradation, DNA repair, gene expression, internalization of membrane proteins, and drug sensitivity. We recently identified genes important for acetaminophen (APAP) toxicity in a comprehensive screen and our findings suggested that a small set of yeast strains carrying deletions of ubiquitin-related genes can be informative for drug toxicity profiling. In yeast, approximately 20 different deubiquitinating enzymes (DUBs) have been identified, of which only one is essential for viability. We investigated whether the toxicity profile of DUB deletion yeast strains would be informative about the toxicological mode of action of APAP. A set of DUB deletion strains was tested for sensitivity and resistance to a diverse series of compounds, including APAP, quinine, ibuprofen, rapamycin, cycloheximide, cadmium, peroxide and amino acids and a cluster analysis was performed. Most DUB deletion strains showed an altered growth pattern when exposed to these compounds by being either more sensitive or more resistant than WT. Toxicity profiling of the DUB strains revealed a remarkable overlap between the amino acid tyrosine and acetaminophen (APAP), but not its stereoisomer AMAP. Furthermore, co-exposure of cells to both APAP and tyrosine showed an enhancement of the cellular growth inhibition, suggesting that APAP and tyrosine have a similar mode of action.
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Affiliation(s)
- Angelina Huseinovic
- AIMMS, Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Marc van Dijk
- AIMMS, Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Nico P E Vermeulen
- AIMMS, Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
| | - Jan M Kooter
- AIMMS, Department of Molecular Cell Biology, Section Genetics, VU University Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - J Chris Vos
- AIMMS, Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HZ Amsterdam, The Netherlands.
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5
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Huseinovic A, van Leeuwen JS, van Welsem T, Stulemeijer I, van Leeuwen F, Vermeulen NPE, Kooter JM, Vos JC. The effect of acetaminophen on ubiquitin homeostasis in Saccharomyces cerevisiae. PLoS One 2017; 12:e0173573. [PMID: 28291796 PMCID: PMC5349473 DOI: 10.1371/journal.pone.0173573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/23/2017] [Indexed: 02/05/2023] Open
Abstract
Acetaminophen (APAP), although considered a safe drug, is one of the major causes of acute liver failure by overdose, and therapeutic chronic use can cause serious health problems. Although the reactive APAP metabolite N-acetyl-p-benzoquinoneimine (NAPQI) is clearly linked to liver toxicity, toxicity of APAP is also found without drug metabolism of APAP to NAPQI. To get more insight into mechanisms of APAP toxicity, a genome-wide screen in Saccharomyces cerevisiae for APAP-resistant deletion strains was performed. In this screen we identified genes related to the DNA damage response. Next, we investigated the link between genotype and APAP-induced toxicity or resistance by performing a more detailed screen with a library containing mutants of 1522 genes related to nuclear processes, like DNA repair and chromatin remodelling. We identified 233 strains that had an altered growth rate relative to wild type, of which 107 showed increased resistance to APAP and 126 showed increased sensitivity. Gene Ontology analysis identified ubiquitin homeostasis, regulation of transcription of RNA polymerase II genes, and the mitochondria-to-nucleus signalling pathway to be associated with APAP resistance, while histone exchange and modification, and vesicular transport were connected to APAP sensitivity. Indeed, we observed a link between ubiquitin levels and APAP resistance, whereby ubiquitin deficiency conferred resistance to APAP toxicity while ubiquitin overexpression resulted in sensitivity. The toxicity profile of various chemicals, APAP, and its positional isomer AMAP on a series of deletion strains with ubiquitin deficiency showed a unique resistance pattern for APAP. Furthermore, exposure to APAP increased the level of free ubiquitin and influenced the ubiquitination of proteins. Together, these results uncover a role for ubiquitin homeostasis in APAP-induced toxicity.
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Affiliation(s)
- Angelina Huseinovic
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Jolanda S. van Leeuwen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Iris Stulemeijer
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nico P. E. Vermeulen
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Jan M. Kooter
- AIMMS-Department of Molecular Cell Biology, Section Genetics, VU University Amsterdam, Amsterdam, The Netherlands
| | - J. Chris Vos
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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6
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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.
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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,
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7
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Reed BJ, Locke MN, Gardner RG. A Conserved Deubiquitinating Enzyme Uses Intrinsically Disordered Regions to Scaffold Multiple Protein Interaction Sites. J Biol Chem 2015; 290:20601-12. [PMID: 26149687 DOI: 10.1074/jbc.m115.650952] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Indexed: 12/24/2022] Open
Abstract
In the canonical view of protein function, it is generally accepted that the three-dimensional structure of a protein determines its function. However, the past decade has seen a dramatic growth in the identification of proteins with extensive intrinsically disordered regions (IDRs), which are conformationally plastic and do not appear to adopt single three-dimensional structures. One current paradigm for IDR function is that disorder enables IDRs to adopt multiple conformations, expanding the ability of a protein to interact with a wide variety of disparate proteins. The capacity for many interactions is an important feature of proteins that occupy the hubs of protein networks, in particular protein-modifying enzymes that usually have a broad spectrum of substrates. One such protein modification is ubiquitination, where ubiquitin is attached to proteins through ubiquitin ligases (E3s) and removed through deubiquitinating enzymes. Numerous proteomic studies have found that thousands of proteins are dynamically regulated by cycles of ubiquitination and deubiquitination. Thus, how these enzymes target their wide array of substrates is of considerable importance for understanding the function of the cell's diverse ubiquitination networks. Here, we characterize a yeast deubiquitinating enzyme, Ubp10, that possesses IDRs flanking its catalytic protease domain. We show that Ubp10 possesses multiple, distinct binding modules within its IDRs that are necessary and sufficient for directing protein interactions important for Ubp10's known roles in gene silencing and ribosome biogenesis. The human homolog of Ubp10, USP36, also has IDRs flanking its catalytic domain, and these IDRs similarly contain binding modules important for protein interactions. This work highlights the significant protein interaction scaffolding abilities of IDRs in the regulation of dynamic protein ubiquitination.
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Affiliation(s)
- Benjamin J Reed
- From the Department of Pharmacology, University of Washington, Seattle, Washington 98195
| | - Melissa N Locke
- From the Department of Pharmacology, University of Washington, Seattle, Washington 98195
| | - Richard G Gardner
- From the Department of Pharmacology, University of Washington, Seattle, Washington 98195
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8
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Han S, Shin D, Choi H, Lee S. Molecular determinants of the interaction between Doa1 and Hse1 involved in endosomal sorting. Biochem Biophys Res Commun 2014; 446:352-7. [PMID: 24607902 DOI: 10.1016/j.bbrc.2014.02.118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 02/25/2014] [Indexed: 12/31/2022]
Abstract
Yeast Doa1/Ufd3 is an adaptor protein for Cdc48 (p97 in mammal), an AAA type ATPase associated with endoplasmic reticulum-associated protein degradation pathway and endosomal sorting into multivesicular bodies. Doa1 functions in the endosomal sorting by its association with Hse1, a component of endosomal sorting complex required for transport (ESCRT) system. The association of Doa1 with Hse1 was previously reported to be mediated between PFU domain of Doa1 and SH3 of Hse1. However, it remains unclear which residues are specifically involved in the interaction. Here we report that Doa1/PFU interacts with Hse1/SH3 with a moderate affinity of 5 μM. Asn-438 of Doa1/PFU and Trp-254 of Hse1/SH3 are found to be critical in the interaction while Phe-434, implicated in ubiquitin binding via a hydrophobic interaction, is not. Small-angle X-ray scattering measurements combined with molecular docking and biochemical analysis yield the solution structure of the Doa1/PFU:Hse1/SH3 complex. Taken together, our results suggest that hydrogen bonding is a major determinant in the interaction of Doa1/PFU with Hse1/SH3.
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Affiliation(s)
- Seungsu Han
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Donghyuk Shin
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Hoon Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, South Korea.
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9
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A novel role of the N terminus of budding yeast histone H3 variant Cse4 in ubiquitin-mediated proteolysis. Genetics 2013; 194:513-8. [PMID: 23525333 DOI: 10.1534/genetics.113.149898] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Regulating levels of centromeric histone H3 (CenH3) variant is crucial for genome stability. Interaction of Psh1, an E3 ligase, with the C terminus of Cse4 has been shown to contribute to its proteolysis. Here, we demonstrate a role for ubiquitination of the N terminus of Cse4 in regulating Cse4 proteolysis for faithful chromosome segregation and a role for Doa1 in ubiquitination of Cse4.
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10
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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.
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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
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11
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Enserink JM, Kolodner RD. What makes the engine hum: Rad6, a cell cycle supercharger. Cell Cycle 2012; 11:249-52. [PMID: 22214660 DOI: 10.4161/cc.11.2.19023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Deregulated CDK activity drives cell proliferation of the majority of human tumors, making CDKs highly relevant research subjects. Cdc28 controls cell cycle progression in the budding yeast Saccharomyces cerevisiae, but the identity of many genes that function in conjunction with CDC28 to regulate the cell cycle and cell viability remains obscure. In a recent study, we used a chemical-genetic screen to identify the genetic network of CDC28. Through this analysis, we discovered that the Rad6-Bre1 pathway functions in this network and links ubiquitin levels to cell cycle progression by increasing transcription of cyclin genes. Thus, Rad6 boosts the activity of the cell cycle machinery.
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Affiliation(s)
- Jorrit M Enserink
- Department of Molecular Biology, Institute of Medical Microbiology and Centre of Molecular Biology and Neuroscience, Oslo University Hospital, Oslo, Norway.
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12
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A chemical-genetic screen to unravel the genetic network of CDC28/CDK1 links ubiquitin and Rad6-Bre1 to cell cycle progression. Proc Natl Acad Sci U S A 2011; 108:18748-53. [PMID: 22042866 DOI: 10.1073/pnas.1115885108] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) control the eukaryotic cell cycle, and a single CDK, Cdc28 (also known as Cdk1), is necessary and sufficient for cell cycle regulation in the budding yeast Saccharomyces cerevisiae. Cdc28 regulates cell cycle-dependent processes such as transcription, DNA replication and repair, and chromosome segregation. To gain further insight into the functions of Cdc28, we performed a high-throughput chemical-genetic array (CGA) screen aimed at unraveling the genetic network of CDC28. We identified 107 genes that strongly genetically interact with CDC28. Although these genes serve multiple cellular functions, genes involved in cell cycle regulation, transcription, and chromosome metabolism were overrepresented. DOA1, which is involved in maintaining free ubiquitin levels, as well as the RAD6-BRE1 pathway, which is involved in transcription, displayed particularly strong genetic interactions with CDC28. We discovered that DOA1 is important for cell cycle entry by supplying ubiquitin. Furthermore, we found that the RAD6-BRE1 pathway functions downstream of DOA1/ubiquitin but upstream of CDC28, by promoting transcription of cyclins. These results link cellular ubiquitin levels and the Rad6-Bre1 pathway to cell cycle progression.
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13
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McDonagh B, Requejo R, Fuentes-Almagro C, Ogueta S, Bárcena J, Padilla C. Thiol redox proteomics identifies differential targets of cytosolic and mitochondrial glutaredoxin-2 isoforms in Saccharomyces cerevisiae. Reversible S-glutathionylation of DHBP synthase (RIB3). J Proteomics 2011; 74:2487-97. [DOI: 10.1016/j.jprot.2011.04.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 03/08/2011] [Accepted: 04/18/2011] [Indexed: 12/24/2022]
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14
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Liu XH, Zhuang FL, Lu JP, Lin FC. Identification and molecular cloning Moplaa gene, a homologue of Homo sapiens PLAA, in Magnaporthe oryzae. Microbiol Res 2011; 167:8-13. [PMID: 21482087 DOI: 10.1016/j.micres.2011.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Revised: 02/20/2011] [Accepted: 02/21/2011] [Indexed: 11/25/2022]
Abstract
Magnaporthe oryzae has been used as a model fungal pathogen to study the molecular basis of plant-fungus interactions due to its economic and genetic importance. In this study, we identified a novel gene, Moplaa, which is the homologue of Homo sapiens PLAA encoding a phospholipase A(2)-activating protein. Moplaa is conserved in some eukaryotic organisms by multiple alignment analysis. The function of the Moplaa gene was studied using the gene target replacement method. The Moplaa deletion mutant exhibited retarded growth and conidial germination, reduced conidiation, appressorial turgor pressure and pathogenicity to rice CO-39. Reintroduction of the gene restored defects of the Moplaa deletion mutant.
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Affiliation(s)
- Xiao-Hong Liu
- State Key Laboratory for Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou, China
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15
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Genetic analysis implicates the Set3/Hos2 histone deacetylase in the deposition and remodeling of nucleosomes containing H2A.Z. Genetics 2011; 187:1053-66. [PMID: 21288874 DOI: 10.1534/genetics.110.125419] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Histone variants and histone modification complexes act to regulate the functions of chromatin. In Saccharomyces cerevisiae the histone variant H2A.Z is encoded by HTZ1. Htz1 is dispensable for viability in budding yeast, but htz1Δ is synthetic sick or lethal with the null alleles of about 200 nonessential genes. One of the strongest of these interactions is with the deletion of SET3, which encodes a subunit of the Set3/Hos2 histone deacetylase complex. Little is known about the functions of Set3, and interpreting these genetic interactions remains a highly challenging task. Here we report the results of a forward genetic screen to identify bypass suppressors of the synthetic slow-growth phenotype of htz1Δ set3Δ. Among the identified loss-of-function suppressors are genes encoding subunits of the HDA1 deacetylase complex, the SWR1 complex, the H2B deubiquitination module of SAGA, the proteasome, Set1, and Sir3. This constellation of suppressor genes is uncommon among the global set of htz1Δ synthetic interactions. BDF1, AHC1, RMR1, and CYC8 were identified as high-copy suppressors. We also identified interactions with SLX5 and SLX8, encoding the sumoylation-targeted ubiquitin ligase complex. In the context of htz1Δ set3Δ, suppressors in the SWR1 and the H2B deubiquitination complexes show strong functional similarity, as do suppressors in the silencing genes and the proteasome. Surprisingly, while both htz1Δ set3Δ and swr1Δ set3Δ have severe slow-growth phenotypes, the htz1Δ swr1Δ set3Δ triple mutant grows relatively well. We propose that Set3 has previously unrecognized functions in the dynamic deposition and remodeling of nucleosomes containing H2A.Z.
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16
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Cellular functions of Ufd2 and Ufd3 in proteasomal protein degradation depend on Cdc48 binding. Mol Cell Biol 2011; 31:1528-39. [PMID: 21282470 DOI: 10.1128/mcb.00962-10] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The chaperone-related AAA ATPase Cdc48 (p97/VCP in higher eukaryotes) segregates ubiquitylated proteins for subsequent degradation by the 26S proteasome or for nonproteolytic fates. The specific outcome of Cdc48 activity is controlled by the evolutionary conserved cofactors Ufd2 and Ufd3, which antagonistically regulate the substrates' ubiquitylation states. In contrast to the interaction of Ufd3 and Cdc48, the interaction between the ubiquitin chain elongating enzyme Ufd2 and Cdc48 has not been precisely mapped. Consequently, it is still unknown whether physiological functions of Ufd2 in fact require Cdc48 binding. Here, we show that Ufd2 binds to the C-terminal tail of Cdc48, unlike the human Ufd2 homologue E4B, which interacts with the N domain of p97. The binding sites for Ufd2 and Ufd3 on Cdc48 overlap and depend critically on the conserved residue Y834 but are not identical. Saccharomyces cerevisiae cdc48 mutants altered in residue Y834 or lacking the C-terminal tail are viable and exhibit normal growth. Importantly, however, loss of Ufd2 and Ufd3 binding in these mutants phenocopies defects of Δufd2 and Δufd3 mutants in the ubiquitin fusion degradation (UFD) and Ole1 fatty acid desaturase activation (OLE) pathways. These results indicate that key cellular functions of Ufd2 and Ufd3 in proteasomal protein degradation require their interaction with Cdc48.
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17
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Gatti L, Hoe KL, Hayles J, Righetti SC, Carenini N, Bo LD, Kim DU, Park HO, Perego P. Ubiquitin-proteasome genes as targets for modulation of cisplatin sensitivity in fission yeast. BMC Genomics 2011; 12:44. [PMID: 21247416 PMCID: PMC3032702 DOI: 10.1186/1471-2164-12-44] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 01/19/2011] [Indexed: 12/28/2022] Open
Abstract
Background The ubiquitin(Ub)-proteasome pathway is implicated in the regulation of a variety of cellular functions and plays a major role in stress response in eukaryotic cells, by targeting misfolded and damaged proteins for degradation. In addition, in the presence of DNA damage, the Ub-proteasome system regulates proteins involved in sensing, repairing, and/or tolerating the damage. Antitumor agents such as cisplatin can activate the pathway, but the role of specific pathway components in cell sensitivity/response to the drug is not known. Since platinum compounds represent clinically relevant antitumor agents and a major limitation to their use is the development of drug resistance, there is an urgent need for identifying targets for improving their efficacy. Results In the present study, we performed a genome-wide screening for sensitivity to cisplatin using non-essential haploid deletion mutants of the fission yeast Schizosaccharomyces pombe, belonging to a collection of haploid strains constructed through homologous recombination. Using this approach, we identified three Ub-proteasome mutants exhibiting hypersensitivity to cisplatin (ubp16, ubc13 and pmt3) and ten mutants (including ufd2, beta7 20S, rpt6/let1) resistant to the drug. In addition, the importance of lub1 gene emerged from the comparison between the present screening and gene expression profile data previously obtained in fission yeast. Conclusions The factors identified in the present study allowed us to highlight most finely the close relationship between the Ub-proteasome system and DNA damage response mechanisms, thus establishing a comprehensive framework of regulators likely relevant also in higher eukaryotes. Our results provide the proof of principle of the involvement of specific genes modulated by cisplatin treatment in cell response to the drug, suggesting their potential role as targets for modulating cisplatin sensitivity. In this regard, the prospective identification of novel targets for modulation of cisplatin sensitivity in an eukaryotic model organism appears particularly intriguing towards the discovery of strategies to overcome cisplatin resistance in human tumors.
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Affiliation(s)
- Laura Gatti
- Fondazione IRCCS, Istituto Nazionale per Studio e Cura dei Tumori, 20133 Milan, Italy
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18
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Pashkova N, Gakhar L, Winistorfer SC, Yu L, Ramaswamy S, Piper RC. WD40 repeat propellers define a ubiquitin-binding domain that regulates turnover of F box proteins. Mol Cell 2010; 40:433-43. [PMID: 21070969 DOI: 10.1016/j.molcel.2010.10.018] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 06/01/2010] [Accepted: 08/18/2010] [Indexed: 11/24/2022]
Abstract
WD40-repeat β-propellers are found in a wide range of proteins involved in distinct biological activities. We define a large subset of WD40 β-propellers as a class of ubiquitin-binding domains. Using the β-propeller from Doa1/Ufd3 as a paradigm, we find the conserved top surface of the Doa1 β-propeller binds the hydrophobic patch of ubiquitin centered on residues I44, L8, and V70. Mutations that disrupt ubiquitin binding abrogate Doa1 function, demonstrating the importance of this interaction. We further demonstrate that WD40 β-propellers from a functionally diverse set of proteins bind ubiquitin in a similar fashion. This set includes members of the F box family of SCF ubiquitin E3 ligase adaptors. Using mutants defective in binding, we find that ubiquitin interaction by the F box protein Cdc4 promotes its autoubiquitination and turnover. Collectively, our results reveal a molecular mechanism that may account for how ubiquitin controls a broad spectrum of cellular activities.
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Affiliation(s)
- Natasha Pashkova
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA
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19
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Mirzaei H, Rogers RS, Grimes B, Eng J, Aderem A, Aebersold R. Characterizing the connectivity of poly-ubiquitin chains by selected reaction monitoring mass spectrometry. MOLECULAR BIOSYSTEMS 2010; 6:2004-14. [PMID: 20694217 DOI: 10.1039/c005242f] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Protein ubiquitination is an essential post-translational modification (PTM) involved in the regulation of a variety of cellular functions, including transcription and protein degradation. Proteins can be both mono- or poly-ubiquitinated. Poly-ubiquitin chains vary in the manner by which the ubiquitin proteins are linked and their total length. Different poly-ubiquitin structures are thought to specify different fates for the target protein but the correlation between poly-ubiquitin structures and their specific cellular function(s) is not well understood. We have developed a set of specific and quantitative targeted mass spectrometry assays to determine the frequency of different types of inter-ubiquitin linkages in poly-ubiquitin chains relative to the total ubiquitin concentration. We chemically synthesized heavy isotope labeled reference peptides that represent the products generated by tryptic digestion of the known forms of inter-ubiquitin links for the yeast Saccharomyces cerevisiae and human, in addition to all peptides from tryptic digestion of a single ubiquitin molecule for these two species. We used these peptides to develop optimized Selected Reaction Monitoring (SRM) assays for their unambiguous detection in biological samples. We used these assays to profile the frequency of the different types of inter-ubiquitin linkages in a mixture of in vitro assembled human poly-ubiquitin chains and 15 isolated poly-ubiquitinated proteins from S. cerevisiae. We then applied the method to detect toxin induced changes in the poly-ubiquitination profile in complex and enriched protein samples.
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Affiliation(s)
- Hamid Mirzaei
- Institute for Systems Biology, Seattle, WA 98103, USA
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20
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O'Quin JB, Bourassa L, Zhang D, Shockey JM, Gidda SK, Fosnot S, Chapman KD, Mullen RT, Dyer JM. Temperature-sensitive post-translational regulation of plant omega-3 fatty-acid desaturases is mediated by the endoplasmic reticulum-associated degradation pathway. J Biol Chem 2010; 285:21781-96. [PMID: 20452984 PMCID: PMC2898375 DOI: 10.1074/jbc.m110.135236] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Indexed: 11/06/2022] Open
Abstract
Changes in ambient temperature represent a major physiological challenge to membranes of poikilothermic organisms. In plants, the endoplasmic reticulum (ER)-localized omega-3 fatty-acid desaturases (Fad3) increase the production of polyunsaturated fatty acids at cooler temperatures, but the FAD3 genes themselves are typically not up-regulated during this adaptive response. Here, we expressed two closely related plant FAD3 genes in yeast cells and found that their enzymes produced significantly different amounts of omega-3 fatty acids and that these differences correlated to differences in rates of protein turnover. Domain-swapping and mutagenesis experiments revealed that each protein contained a degradation signal in its N terminus and that the charge density of a PEST-like sequence within this region was largely responsible for the differences in rates of protein turnover. The half-life of each Fad3 protein was increased at cooler temperatures, and protein degradation required specific components of the ER-associated degradation pathway including the Cdc48 adaptor proteins Doa1, Shp1, and Ufd2. Expression of the Fad3 proteins in tobacco cells incubated with the proteasomal inhibitor MG132 further confirmed that they were degraded via the proteasomal pathway in plants. Collectively, these findings indicate that Fad3 protein abundance is regulated by a combination of cis-acting degradation signals and the ubiquitin-proteasome pathway and that modulation of Fad3 protein amounts in response to temperature may represent one mechanism of homeoviscous adaptation in plants.
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Affiliation(s)
- Jami B. O'Quin
- From the Department of Biological Sciences, University of New Orleans, New Orleans, Louisiana 70124
| | - Linda Bourassa
- From the Department of Biological Sciences, University of New Orleans, New Orleans, Louisiana 70124
| | - Daiyuan Zhang
- the Department of Biological Sciences, University of North Texas, Denton, Texas 76203
- the United States Arid-Land Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service, Maricopa, Arizona 85138
| | - Jay M. Shockey
- the Southern Regional Research Center, United States Department of Agriculture-Agricultural Research Service, New Orleans, Louisiana 70124, and
| | - Satinder K. Gidda
- the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario NWG 2W1, Canada
| | - Spencer Fosnot
- the United States Arid-Land Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service, Maricopa, Arizona 85138
| | - Kent D. Chapman
- the Department of Biological Sciences, University of North Texas, Denton, Texas 76203
| | - Robert T. Mullen
- the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario NWG 2W1, Canada
| | - John M. Dyer
- the United States Arid-Land Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service, Maricopa, Arizona 85138
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21
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Kimura Y, Tanaka K. Regulatory mechanisms involved in the control of ubiquitin homeostasis. J Biochem 2010; 147:793-8. [PMID: 20418328 DOI: 10.1093/jb/mvq044] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Ubiquitin (Ub) modification plays an essential role in the regulation of various cellular processes. Ub performs a remarkable array of cellular tasks through the production of a large number of ubiquitinated proteins; such tasks require many Ubs. Ubs are expressed abundantly from several Ub encoding genes, though not in excess. Rather, Ub expression is tightly regulated through various control mechanisms. Recent studies have shown that the cellular Ub level is regulated by balanced activities of deubiquitinating enzymes and their regulators. Here, we review the current understandings of the regulatory mechanisms that control Ub expression and its metabolism and maintain Ub homeostasis.
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Affiliation(s)
- Yoko Kimura
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
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22
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Qiu L, Pashkova N, Walker JR, Winistorfer S, Allali-Hassani A, Akutsu M, Piper R, Dhe-Paganon S. Structure and function of the PLAA/Ufd3-p97/Cdc48 complex. J Biol Chem 2009; 285:365-72. [PMID: 19887378 PMCID: PMC2804184 DOI: 10.1074/jbc.m109.044685] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
PLAA (ortholog of yeast Doa1/Ufd3, also know as human PLAP or phospholipase A2-activating protein) has been implicated in a variety of disparate biological processes that involve the ubiquitin system. It is linked to the maintenance of ubiquitin levels, but the mechanism by which it accomplishes this is unclear. The C-terminal PUL (PLAP, Ufd3p, and Lub1p) domain of PLAA binds p97, an AAA ATPase, which among other functions helps transfer ubiquitinated proteins to the proteasome for degradation. In yeast, loss of Doa1 is suppressed by altering p97/Cdc48 function indicating that physical interaction between PLAA and p97 is functionally important. Although the overall regions of interaction between these proteins are known, the structural basis has been unavailable. We solved the high resolution crystal structure of the p97-PLAA complex showing that the PUL domain forms a 6-mer Armadillo-containing domain. Its N-terminal extension folds back onto the inner curvature forming a deep ridge that is positively charged with residues that are phylogenetically conserved. The C terminus of p97 binds in this ridge, where the side chain of p97-Tyr805, implicated in phosphorylation-dependent regulation, is buried. Expressed in doa1Δ null cells, point mutants of the yeast ortholog Doa1 that disrupt this interaction display slightly reduced ubiquitin levels, but unlike doa1Δ null cells, showed only some of the growth phenotypes. These data suggest that the p97-PLAA interaction is important for a subset of PLAA-dependent biological processes and provides a framework to better understand the role of these complex molecules in the ubiquitin system.
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Affiliation(s)
- Liyan Qiu
- Structural Genomics Consortium, Department of Physiology, University of Toronto, Toronto, Ontario M5G 1L7,Canada
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23
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An Armadillo motif in Ufd3 interacts with Cdc48 and is involved in ubiquitin homeostasis and protein degradation. Proc Natl Acad Sci U S A 2009; 106:16197-202. [PMID: 19805280 DOI: 10.1073/pnas.0908321106] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The yeast AAA-ATPase Cdc48 and the ubiquitin fusion degradation (UFD) proteins play important, evolutionarily conserved roles in ubiquitin dependent protein degradation. The N-terminal domain of Cdc48 interacts with substrate-recruiting cofactors, whereas the C terminus of Cdc48 binds to proteins such as Ufd3 that process substrates. Ufd3 is essential for efficient protein degradation and for maintaining cellular ubiquitin levels. This protein contains an N-terminal WD40 domain, a central ubiquitin-binding domain, and a C-terminal Cdc48-binding PUL domain. The crystal structure of the PUL domain reveals an Armadillo repeat with high structural similarity to importin-alpha, and the Cdc48-binding site could be mapped to the concave surface of the PUL domain by biochemical studies. Alterations of the Cdc48 binding site of Ufd3 by site-directed mutagenesis resulted in a depletion of cellular ubiquitin pools and reduced activity of the ubiquitin fusion degradation pathway. Therefore, our data provide direct evidence that the functions of Ufd3 in ubiquitin homeostasis and protein degradation depend on its interaction with the C terminus of Cdc48.
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24
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McDonagh B, Ogueta S, Lasarte G, Padilla CA, Bárcena JA. Shotgun redox proteomics identifies specifically modified cysteines in key metabolic enzymes under oxidative stress in Saccharomyces cerevisiae. J Proteomics 2009; 72:677-89. [PMID: 19367685 DOI: 10.1016/j.jprot.2009.01.023] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Post-translational redox modification of thiol groups can form the molecular basis of antioxidative protection and redox control. We have implemented a shotgun redox proteomic technique to identify the precise cysteines reversibly oxidised in key proteins. The method was applied to Saccharomyces cerevisiae subjected to peroxide treatment. Enrichment by covalent redox affinity chromatography allowed the isolation of a "redox subpeptidome" that was analysed by LC-MS/MS. Unique peptides containing specific reversibly oxidised cysteines were used to identify over 70 proteins in control and treated samples of which 27 were consistently present in all replicates. In most cases, the redox modification negatively affects their function and slows down their metabolic pathways. Integration of the data provides a snapshot consistent with a metabolic defensive strategy, regulating key enzymes by redox modification, redirecting energy toward ribulose-5-phosphate recycling for NADPH production and antioxidative defence.This generally applicable method has allowed us to discover new redox regulated proteins (DAHP and carbamoylphosphate synthases, Doa1p) and to precisely identify target cysteines in a number of known ones.
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Affiliation(s)
- Brian McDonagh
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Universidad de Córdoba, Cordoba, Spain
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25
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Fu QS, Zhou CJ, Gao HC, Jiang YJ, Zhou ZR, Hong J, Yao WM, Song AX, Lin DH, Hu HY. Structural basis for ubiquitin recognition by a novel domain from human phospholipase A2-activating protein. J Biol Chem 2009; 284:19043-52. [PMID: 19423704 DOI: 10.1074/jbc.m109.009126] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ubiquitin (Ub) is an essential modifier conserved in all eukaryotes from yeast to human. Phospholipase A(2)-activating protein (PLAA), a mammalian homolog of yeast DOA1/UFD3, has been proposed to be able to bind with Ub, which plays important roles in endoplasmic reticulum-associated degradation, vesicle formation, and DNA damage response. We have identified a core domain from the PLAA family ubiquitin-binding region of human PLAA (residues 386-465, namely PFUC) that can bind Ub and elucidated its solution structure and Ub-binding mode by NMR approaches. The PFUC domain possesses equal population of two conformers in solution by cis/trans-isomerization, whereas the two isomers exhibit almost equivalent Ub binding abilities. This domain structure takes a novel fold consisting of four beta-strands and two alpha-helices, and the Ub-binding site on PFUC locates in the surface of alpha2-helix, which is to some extent analogous to those of UBA, CUE, and UIM domains. This study provides structural basis and biochemical information for Ub recognition of the novel PFU domain from a PLAA family protein that may connect ubiquitination and degradation in endoplasmic reticulum-associated degradation.
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Affiliation(s)
- Qing-Shan Fu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Ren J, Pashkova N, Winistorfer S, Piper RC. DOA1/UFD3 plays a role in sorting ubiquitinated membrane proteins into multivesicular bodies. J Biol Chem 2008; 283:21599-611. [PMID: 18508771 PMCID: PMC2490793 DOI: 10.1074/jbc.m802982200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 05/19/2008] [Indexed: 12/23/2022] Open
Abstract
Ubiquitin (Ub) is a sorting signal that targets integral membrane proteins to the interior of the vacuole/lysosome by directing them into lumenal vesicles of multivesicular bodies (MVBs). The Vps27-Hse1 complex, which is homologous to the Hrs-STAM complex in mammalian cells, serves as a Ub-sorting receptor at the surface of early endosomes. We have found that Hse1 interacts with Doa1/Ufd3. Doa1 is known to interact with Cdc48/p97 and Ub and is required for maintaining Ub levels. We find that the Hse1 Src homology 3 domain binds directly to the central PFU domain of Doa1. Mutations in Doa1 that block Hse1 binding but not Ub binding do not alter Ub levels but do result in the missorting of the MVB cargo GFP-Cps1. Loss of Doa1 also causes a synthetic growth defect when combined with loss of Vps27. Unlike the loss of Doa1 alone, the doa1Delta vps27Delta double mutant phenotype is not suppressed by Ub overexpression, demonstrating that the effect is not due to indirect consequence of lowered Ub levels. Loss of Doa1 results in a defect in the accumulation of GFP-Ub within yeast vacuoles, implying that there is a reduction in the flux of ubiquitinated membrane proteins through the MVB pathway. This defect was also reflected by an inability to properly sort Vph1-GFP-Ub, a modified subunit of the multiprotein vacuolar ATPase complex, which carries an in-frame fusion of Ub as an MVB sorting signal. These results reveal novel roles for Doa1 in helping to process ubiquitinated membrane proteins for sorting into MVBs.
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Affiliation(s)
- Jihui Ren
- Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA
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Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells. Nat Cell Biol 2008; 10:483-8. [DOI: 10.1038/ncb1712] [Citation(s) in RCA: 287] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 01/08/2008] [Indexed: 01/22/2023]
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Pabla R, Rozario D, Siede W. Regulation of Saccharomyces cerevisiae DNA polymerase eta transcript and protein. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2008; 47:157-68. [PMID: 17874115 DOI: 10.1007/s00411-007-0132-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Accepted: 09/03/2007] [Indexed: 05/17/2023]
Abstract
RAD30-encoded DNA polymerase eta functions as a translesion polymerase that can bypass the most frequent types of UV-induced pyrimidine photoproducts in an error-free manner. Although its transcript is UV-inducible in Saccharomyces cerevisiae, Rad30 (studied as a Rad30-Myc fusion) is a stable protein whose levels do not fluctuate following UV treatment or during cell cycle progression. Rad30 protein is subject to monoubiquitination whose level is upregulated in G1 and downregulated during S-phase reentry. This downregulation is accelerated in UV-treated cells. A missense mutation (L577Q) of the ubiquitin binding domain (UBZ) confers a reduced degree of ubiquitination outside of G1 and a complete failure to stably interact with ubiquitinated substrates. This mutation confers a phenotype resembling a complete RAD30 deletion, thus attesting to the significance of the UBZ motif for polymerase eta function in vivo.
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Affiliation(s)
- Ritu Pabla
- Department of Cell Biology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
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Kunze D, MacCallum D, Odds FC, Hube B. Multiple functions of DOA1 in Candida albicans. MICROBIOLOGY-SGM 2007; 153:1026-1041. [PMID: 17379712 DOI: 10.1099/mic.0.2006/002741-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
While searching for regulators of virulence attributes of the human-pathogenic fungus Candida albicans, a gene was identified similar to the genes encoding the mammalian phospholipase A2-activating protein (PLAP) and the Saccharomyces cerevisiae protein Doa1, which is known to play a key role during ubiquitin (Ub)-dependent protein degradation. All three proteins contain WD-repeats. Both PLAP and CaDoa1 contain a mellitin-like sequence with a central 'KVL'. This mellitin-like sequence was shown to be necessary for full function of CaDoa1. CaDOA1 was expressed under all conditions investigated. Gene disruption of CaDOA1 caused phenotypes including modified colony morphologies, temperature sensitivity, reduced secretion of hydrolytic enzymes and hypersensitivity to various compounds such as propranolol, butanol, caffeine, chelators, azoles, nocodazole and cadmium. Strikingly, mutants lacking DOA1 were filamentous and grew as pseudohyphae and true hyphae under conditions that normally support yeast growth. Transcriptional profiling of Deltadoa1 indicated that several genes associated with Ub-mediated proteolysis, including CDC48 and UBI4, are upregulated. These data suggest that DOA1 of C. albicans, like its orthologue in S. cerevisiae, is associated with Ub-mediated proteolysis and has multiple functions. However, some functions of CaDoa1 seem to be unique for C. albicans. These results support the hypothesis that Ub-mediated proteolysis plays an important role in the regulation of morphology in C. albicans.
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Affiliation(s)
- Donika Kunze
- Robert Koch-Institut, Nordufer 20, D-13353, Berlin, Germany
| | - Donna MacCallum
- Aberdeen Fungal Group, School of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Frank C Odds
- Aberdeen Fungal Group, School of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Lelbniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute Jena (HKI), Beutenbergstraße 11a, D-07745 Jena, Germany
- Friedrich-Schiller-University, Jena, Germany
- Robert Koch-Institut, Nordufer 20, D-13353, Berlin, Germany
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30
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Groothuis TAM, Dantuma NP, Neefjes J, Salomons FA. Ubiquitin crosstalk connecting cellular processes. Cell Div 2006; 1:21. [PMID: 17007633 PMCID: PMC1613237 DOI: 10.1186/1747-1028-1-21] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Accepted: 09/28/2006] [Indexed: 11/10/2022] Open
Abstract
The polypeptide ubiquitin is used in many processes as different as endocytosis, multivesicular body formation, and regulation of gene transcription. Conjugation of a single ubiquitin moiety is typically used in these processes. A polymer of ubiquitin moieties is required for tagging proteins for proteasomal degradation. Besides its role in protein degradation, ubiquitin is also engaged as mono- or polymer in intracellular signalling and DNA repair. Since free ubiquitin is present in limiting amounts in cells, changes in the demands for ubiquitin in any of these processes is likely to indirectly affect other ubiquitin modifications. For example, proteotoxic stress strongly increases poly-ubiquitylated proteins at the cost of mono-ubiquitylated histones resulting in chromatin remodelling and altered transcription. Here we discuss the interconnection between ubiquitin-dependent processes and speculate on the functional significance of the ubiquitin equilibrium as a signalling route translating cellular stress into molecular responses.
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Affiliation(s)
- Tom AM Groothuis
- Division of Tumor Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Nico P Dantuma
- Department of Cell and Molecular Biology, The Medical Nobel Institute, Karolinska Institutet, Von Eulers väg 3, S-17177, Stockholm, Sweden
| | - Jacques Neefjes
- Division of Tumor Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Florian A Salomons
- Department of Cell and Molecular Biology, The Medical Nobel Institute, Karolinska Institutet, Von Eulers väg 3, S-17177, Stockholm, Sweden
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