1
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Tessier TM, Chowdhury A, Stekel Z, Fux J, Sartori MA, Teyra J, Jarvik N, Chung J, Kurinov I, Sicheri F, Sidhu SS, Singer AU, Zhang W. Structural and functional validation of a highly specific Smurf2 inhibitor. Protein Sci 2024; 33:e4885. [PMID: 38147466 PMCID: PMC10823456 DOI: 10.1002/pro.4885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/28/2023]
Abstract
Smurf1 and Smurf2 are two closely related member of the HECT (homologous to E6AP carboxy terminus) E3 ubiquitin ligase family and play important roles in the regulation of various cellular processes. Both were initially identified to regulate transforming growth factor-β and bone morphogenetic protein signaling pathways through regulating Smad protein stability and are now implicated in various pathological processes. Generally, E3 ligases, of which over 800 exist in humans, are ideal targets for inhibition as they determine substrate specificity; however, there are few inhibitors with the ability to precisely target a particular E3 ligase of interest. In this work, we explored a panel of ubiquitin variants (UbVs) that were previously identified to bind Smurf1 or Smurf2. In vitro binding and ubiquitination assays identified a highly specific Smurf2 inhibitor, UbV S2.4, which was able to inhibit ligase activity with high potency in the low nanomolar range. Orthologous cellular assays further demonstrated high specificity of UbV S2.4 toward Smurf2 and no cross-reactivity toward Smurf1. Structural analysis of UbV S2.4 in complex with Smurf2 revealed its mechanism of inhibition was through targeting the E2 binding site. In summary, we investigated several protein-based inhibitors of Smurf1 and Smurf2 and identified a highly specific Smurf2 inhibitor that disrupts the E2-E3 protein interaction interface.
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Affiliation(s)
- Tanner M. Tessier
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | - Arvid Chowdhury
- Department of Molecular GeneticsUniversity of TorontoTorontoOntarioCanada
| | - Zane Stekel
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | - Julia Fux
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | | | | | - Nick Jarvik
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Jacky Chung
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Igor Kurinov
- NE‐CAT, Department of Chemistry and Chemical BiologyCornell UniversityArgonneIllinoisUSA
| | - Frank Sicheri
- Lunenfeld‐Tanenbaum Research Institute, Mount Sinai HospitalTorontoOntarioCanada
| | - Sachdev S. Sidhu
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Alex U. Singer
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Wei Zhang
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
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2
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Shestoperova EI, Strieter ER. Uncovering DUB Selectivity through an Ion Mobility-Based Assessment of Ubiquitin Chain Isomers. Anal Chem 2023; 95:17416-17423. [PMID: 37962301 PMCID: PMC11103383 DOI: 10.1021/acs.analchem.3c04622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Ubiquitination is a reversible post-translational modification that maintains cellular homeostasis and regulates protein turnover. Deubiquitinases (DUBs) are a large family of proteases that catalyze the removal of ubiquitin (Ub) along with the dismantling and editing of Ub chains. Assessing the activity and selectivity of DUBs is critical for defining physiological functions. Despite numerous methods for evaluating DUB activity, none are capable of assessing activity and selectivity in the context of multicomponent mixtures of native unlabeled Ub conjugates. Here, we report an ion mobility (IM)-based approach for measuring DUB selectivity in the context of unlabeled mixtures of Ub chains. We show that IM-mass spectrometry (IM-MS) can be used to assess the selectivity of DUBs in a time-dependent manner. Moreover, using the branched Ub chain selective DUB UCH37/UCHL5 along with a mixture of Ub trimers, a strong preference for branched Ub trimers bearing K6 and K48 linkages is revealed. Our results demonstrate that IM-MS is a powerful method for evaluating DUB selectivity under conditions more physiologically relevant than single-component mixtures.
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Affiliation(s)
- Elizaveta I Shestoperova
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Molecular & Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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3
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Shestoperova EI, Strieter ER. Uncovering DUB Selectivity Through Ion-Mobility-Based Assessment of Ubiquitin Chain Isomers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.11.561976. [PMID: 37873305 PMCID: PMC10592704 DOI: 10.1101/2023.10.11.561976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Ubiquitination is a reversible posttranslational modification that maintains cellular homeostasis and regulates protein turnover. Deubiquitinases (DUBs) are a large family of proteases that catalyze the removal of ubiquitin (Ub) along with the dismantling and editing of Ub chains. Assessing the activity and selectivity of DUBs is critical for defining physiological function. Despite numerous methods for evaluating DUB activity, none are capable of assessing activity and selectivity in the context of multicomponent mixtures of native, unlabeled ubiquitin conjugates. Here we report on an ion mobility (IM)-based approach for measuring DUB selectivity in the context of unlabeled mixtures of Ub chains. We show that IM-MS can be used to assess the selectivity of DUBs in a time-dependent manner. Moreover, using the branched Ub chain selective DUB UCH37/UCHL5 along with a mixture of Ub trimers, a strong preference for branched Ub trimers bearing K6 and K48 linkages is revealed. Our results demonstrate that IM coupled with mass spectrometry (IM-MS) is a powerful method for evaluating DUB selectivity under conditions more physiologically relevant than single component mixtures.
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4
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Shestoperova EI, Ivanov DG, Strieter ER. Quantitative Analysis of Diubiquitin Isomers Using Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:931-938. [PMID: 37014729 DOI: 10.1021/jasms.3c00016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The diversity of ubiquitin modifications calls for methods to better characterize ubiquitin chain linkage, length, and morphology. Here, we use multiple linear regression analysis coupled with ion mobility mass spectrometry (IM-MS) to quantify the relative abundance of different ubiquitin dimer isomers. We demonstrate the utility and robustness of this approach by quantifying the relative abundance of different ubiquitin dimers in complex mixtures and comparing the results to the standard, bottom-up ubiquitin AQUA method. Our results provide a foundation for using multiple linear regression analysis and IM-MS to characterize more complex ubiquitin chain architectures.
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Affiliation(s)
- Elizaveta I Shestoperova
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Daniil G Ivanov
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Molecular & Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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5
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Asimaki E, Petriukov K, Renz C, Meister C, Ulrich HD. Fast friends - Ubiquitin-like modifiers as engineered fusion partners. Semin Cell Dev Biol 2022; 132:132-145. [PMID: 34840080 PMCID: PMC9703124 DOI: 10.1016/j.semcdb.2021.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 12/15/2022]
Abstract
Ubiquitin and its relatives are major players in many biological pathways, and a variety of experimental tools based on biological chemistry or protein engineering is available for their manipulation. One popular approach is the use of linear fusions between the modifier and a protein of interest. Such artificial constructs can facilitate the understanding of the role of ubiquitin in biological processes and can be exploited to control protein stability, interactions and degradation. Here we summarize the basic design considerations and discuss the advantages as well as limitations associated with their use. Finally, we will refer to several published case studies highlighting the principles of how they provide insight into pathways ranging from membrane protein trafficking to the control of epigenetic modifications.
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6
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Tao X, Wu X, Zhou P, Yu X, Zhao C, Peng X, Zhang K, Shen L, Peng J, Yang L. UBE2T promotes glioblastoma malignancy through ubiquitination-mediated degradation of RPL6. Cancer Sci 2022; 114:521-532. [PMID: 36156329 PMCID: PMC9899609 DOI: 10.1111/cas.15604] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 01/07/2023] Open
Abstract
Glioblastoma (GBM) is the most frequent and aggressive malignant glioma. Due to patients' poor prognosis, it is of great clinical significance to determine new targets that may improve GBM treatment. In the present study, we showed that ubiquitin (Ub)-conjugating enzyme E2T (UBE2T) was significantly overexpressed in GBM and could promote proliferation, invasion, and inhibit apoptosis of GBM cells. Mechanistically, UBE2T functioned as the Ub enzyme of ribosomal protein L6 (RPL6) and induced the ubiquitination and degradation of RPL6 in an E3 ligase-independent manner through direct modification by K48-linked polyubiquitination, thus contributing to the malignant progression of GBM cells. Furthermore, inhibiting the expression of RPL6 by UBE2T could not only reduce the expression of wild-type p53, but also enhance the gain-of-function of mutant p53. Moreover, knockdown of UBE2T in LN229 cells obviously suppressed tumor growth in LN229 xenograft mouse models. Collectively, our study demonstrated that UBE2T promotes GBM malignancy through ubiquitination-mediated degradation of RPL6 regardless of the p53 mutation status. It will provide new candidates for molecular biomarkers and therapeutic targets for clinical application in GBM.
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Affiliation(s)
- Xuxiu Tao
- Department of OncologyKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaChina,Cancer Research Institute, School of Basic Medicine Science, Central South UniversityChangshaChina
| | - Xia Wu
- Cancer Research Institute, School of Basic Medicine Science, Central South UniversityChangshaChina,Department of PathologyThe Second Xiangya Hospital, Central South UniversityChangshaChina
| | - Peijun Zhou
- Department of OncologyKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaChina,Cancer Research Institute, School of Basic Medicine Science, Central South UniversityChangshaChina
| | - Xuehui Yu
- Department of OncologyKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaChina,Cancer Research Institute, School of Basic Medicine Science, Central South UniversityChangshaChina
| | - Chen Zhao
- Department of OncologyKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaChina,Cancer Research Institute, School of Basic Medicine Science, Central South UniversityChangshaChina
| | - Xingzhi Peng
- Department of OncologyKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaChina,Cancer Research Institute, School of Basic Medicine Science, Central South UniversityChangshaChina
| | - Kun Zhang
- Department of OncologyKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaChina
| | - Liangfang Shen
- Department of OncologyKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaChina
| | - Jinwu Peng
- Department of PathologyXiangya Hospital, Central South UniversityChangshaChina,Department of PathologyXiangya Changde HospitalChangdeChina
| | - Lifang Yang
- Department of OncologyKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaChina,Cancer Research Institute, School of Basic Medicine Science, Central South UniversityChangshaChina
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7
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Zhou L, Ng DSC, Yam JC, Chen LJ, Tham CC, Pang CP, Chu WK. Post-translational modifications on the retinoblastoma protein. J Biomed Sci 2022; 29:33. [PMID: 35650644 PMCID: PMC9161509 DOI: 10.1186/s12929-022-00818-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/26/2022] [Indexed: 11/21/2022] Open
Abstract
The retinoblastoma protein (pRb) functions as a cell cycle regulator controlling G1 to S phase transition and plays critical roles in tumour suppression. It is frequently inactivated in various tumours. The functions of pRb are tightly regulated, where post-translational modifications (PTMs) play crucial roles, including phosphorylation, ubiquitination, SUMOylation, acetylation and methylation. Most PTMs on pRb are reversible and can be detected in non-cancerous cells, playing an important role in cell cycle regulation, cell survival and differentiation. Conversely, altered PTMs on pRb can give rise to anomalies in cell proliferation and tumourigenesis. In this review, we first summarize recent findings pertinent to how individual PTMs impinge on pRb functions. As many of these PTMs on pRb were published as individual articles, we also provide insights on the coordination, either collaborations and/or competitions, of the same or different types of PTMs on pRb. Having a better understanding of how pRb is post-translationally modulated should pave the way for developing novel and specific therapeutic strategies to treat various human diseases.
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Affiliation(s)
- Linbin Zhou
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Danny Siu-Chun Ng
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jason C Yam
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Li Jia Chen
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Clement C Tham
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi Pui Pang
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Kit Chu
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China.
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong Eye Hospital, 147K Argyle Street, Kowloon, Hong Kong, China.
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8
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Zhu Y, Gan Y, Zou R, Sha H, Lu Y, Zhang Y, Feng J. RNF128 suppresses the malignancy of colorectal cancer cells via inhibition of Wnt/β-catenin signaling. Am J Transl Res 2021; 13:13567-13578. [PMID: 35035697 PMCID: PMC8748172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 08/16/2021] [Indexed: 06/14/2023]
Abstract
PURPOSE Colorectal cancer (CRC) is one of the most frequent tumors and causes of mortality worldwide. Ubiquitin ligase was reported to regulate multiple cellular processes, including tumorigenesis. As ubiquitin E3 ligases, RING-finger proteins play a key role in physiological and pathophysiological processes. METHODS We compared the expression levels of RNF128 in CRC tissues by western-blotting and qRT-PCR. Knockdown and overexpression of RNF128 were performed to examine its effect on proliferation and metastasis of CRC cells. Using western blot and co-immunoprecipitation assays, we explored the possible mechanisms underlying the effect of RNF128 in CRC cells. RESULTS We found that the expression level of RNF128 was correlated with the CRC tumorigenicity. Overexpression or knockdown of RNF128 suppressed or elevated CRC cell proliferation, migration and invasion, respectively. We further determined that RNF128 regulated β-catenin ubiquitination and thus inhibited Wnt/β-catenin signaling in CRC cells. CONCLUSION Our research demonstrated that RNF128 inhibited cell proliferation and metastasis of CRC cells via Wnt/β-catenin signaling-mediated deubiquitination.
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Affiliation(s)
- Yue Zhu
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer ResearchNanjing 210009, Jiangsu, China
- Nanjing Jinling HospitalNanjing 210002, Jiangsu, China
| | - Yujie Gan
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer ResearchNanjing 210009, Jiangsu, China
| | - Renrui Zou
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer ResearchNanjing 210009, Jiangsu, China
| | - Huanhuan Sha
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer ResearchNanjing 210009, Jiangsu, China
| | - Ya Lu
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer ResearchNanjing 210009, Jiangsu, China
| | - Yuan Zhang
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer ResearchNanjing 210009, Jiangsu, China
| | - Jifeng Feng
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer ResearchNanjing 210009, Jiangsu, China
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9
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Kunar R, Roy JK. The mRNA decapping protein 2 (DCP2) is a major regulator of developmental events in Drosophila-insights from expression paradigms. Cell Tissue Res 2021; 386:261-280. [PMID: 34536141 DOI: 10.1007/s00441-021-03503-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 07/01/2021] [Indexed: 02/07/2023]
Abstract
The Drosophila genome codes for two decapping proteins, DCP1 and DCP2, out of which DCP2 is the active decapping enzyme. The present endeavour explores the endogenous promoter firing, transcript and protein expression of DCP2 in Drosophila wherein, besides a ubiquitous expression across development, we identify an active expression paradigm during dorsal closure and a plausible moonlighting expression in the Corazonin neurons of the larval brain. We also demonstrate that the ablation of DCP2 leads to embryonic lethality and defects in vital morphogenetic processes whereas a knockdown of DCP2 in the Corazonin neurons reduces the sensitivity to ethanol in adults, thereby ascribing novel regulatory roles to DCP2. Our findings unravel novel putative roles for DCP2 and identify it as a candidate for studies on the regulated interplay of essential molecules during early development in Drosophila, nay the living world.
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Affiliation(s)
- Rohit Kunar
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi, 221005, India
| | - Jagat Kumar Roy
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi, 221005, India.
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10
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Hommen F, Bilican S, Vilchez D. Protein clearance strategies for disease intervention. J Neural Transm (Vienna) 2021; 129:141-172. [PMID: 34689261 PMCID: PMC8541819 DOI: 10.1007/s00702-021-02431-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/10/2021] [Indexed: 02/06/2023]
Abstract
Protein homeostasis, or proteostasis, is essential for cell function and viability. Unwanted, damaged, misfolded and aggregated proteins are degraded by the ubiquitin–proteasome system (UPS) and the autophagy-lysosome pathway. Growing evidence indicates that alterations in these major proteolytic mechanisms lead to a demise in proteostasis, contributing to the onset and development of distinct diseases. Indeed, dysregulation of the UPS or autophagy is linked to several neurodegenerative, infectious and inflammatory disorders as well as cancer. Thus, modulation of protein clearance pathways is a promising approach for therapeutics. In this review, we discuss recent findings and open questions on how targeting proteolytic mechanisms could be applied for disease intervention.
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Affiliation(s)
- Franziska Hommen
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany
| | - Saygın Bilican
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany. .,Faculty of Medicine, University Hospital Cologne, Cologne, Germany.
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11
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The Effect of Neddylation Inhibition on Inflammation-Induced MMP9 Gene Expression in Esophageal Squamous Cell Carcinoma. Int J Mol Sci 2021; 22:ijms22041716. [PMID: 33572115 PMCID: PMC7915196 DOI: 10.3390/ijms22041716] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/27/2022] Open
Abstract
Inhibition of the protein neddylation process by the small-molecule inhibitor MLN4924 has been recently indicated as a promising direction for cancer treatment. However, the knowledge of all biological consequences of MLN4924 for cancer cells is still incomplete. Here, we report that MLN4924 inhibits tumor necrosis factor-alpha (TNF-α)-induced matrix metalloproteinase 9 (MMP9)-driven cell migration. Using real-time polymerase chain reaction (PCR) and gelatin zymography, we found that MLN4924 inhibited expression and activity of MMP9 at the messenger RNA (mRNA) and protein levels in both resting cells and cells stimulated with TNF-α, and this inhibition was closely related to impaired cell migration. We also revealed that MLN4924, similar to TNF-α, induced phosphorylation of inhibitor of nuclear factor kappa B-alpha (IκB-α). However, contrary to TNF-α, MLN4924 did not induce IκB-α degradation in treated cells. In coimmunoprecipitation experiments, nuclear IκB-α which formed complexes with nuclear factor kappa B p65 subunit (NFκB/p65) was found to be highly phosphorylated at Ser32 in the cells treated with MLN4924, but not in the cells treated with TNF-α alone. Moreover, in the presence of MLN4924, nuclear NFκB/p65 complexes were found to be enriched in c-Jun and cyclin dependent kinase inhibitor 1 A (CDKN1A/p21) proteins. In these cells, NFκB/p65 was unable to bind to the MMP9 gene promoter, which was confirmed by the chromatin immunoprecipitation (ChIP) assay. Taken together, our findings identified MLN4924 as a suppressor of TNF-α-induced MMP9-driven cell migration in esophageal squamous cell carcinoma (ESCC), likely acting by affecting the nuclear ubiquitin–proteasome system that governs NFκB/p65 complex formation and its DNA binding activity in regard to the MMP9 promoter, suggesting that inhibition of neddylation might be a new therapeutic strategy to prevent invasion/metastasis in ESCC patients.
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12
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Edler MK, Johnson CT, Ahmed HS, Richardson JR. Age, sex, and regional differences in scavenger receptor CD36 in the mouse brain: Potential relevance to cerebral amyloid angiopathy and Alzheimer's disease. J Comp Neurol 2020; 529:2209-2226. [PMID: 33319367 DOI: 10.1002/cne.25089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/29/2022]
Abstract
Scavenger receptor CD36 contributes significantly to lipid homeostasis, inflammation, and amyloid deposition, while CD36 deficiency is associated with restored cerebrovascular function in an Alzheimer's disease (AD) mouse model. Yet the distribution of CD36 has not been examined in the brain. Here, we characterized CD36 gene and protein expression in the brains of young, middle aged, aged, and elderly male and female C57BL/6J mice. Age-related increases in CD36 mRNA expression were observed in the male hippocampus and female midbrain. Additionally, male mice had greater CD36 mRNA expression than females in the striatum, hippocampus, and midbrain. CD36 protein was primarily expressed intravascularly, and this expression differed by region, age, and sex in the mouse brain. Although male mice brains demonstrated an increase in CD36 protein with age in several cortices, basal ganglia, hippocampus, and midbrain, a decrease with age was observed in female mice in the same regions. These data suggest that distinctive age, region, and sex expression of CD36 in the brain may contribute to Aβ deposition and neuroinflammation in AD.
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Affiliation(s)
- Melissa K Edler
- Department of Anthropology, Kent State University, Kent, Ohio, USA.,School of Biomedical Sciences, Kent State University, Kent, Ohio, USA.,Brain Health Research Institute, Kent State University, Kent, Ohio, USA.,Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Cooper T Johnson
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Hashim S Ahmed
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Jason R Richardson
- Robert Stempel School of Public Health and Social Work, Florida International University, Miami, Florida, USA
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13
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Guha S, Bhaumik SR. Viral regulation of mRNA export with potentials for targeted therapy. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194655. [PMID: 33246183 DOI: 10.1016/j.bbagrm.2020.194655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/15/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
Abstract
Eukaryotic gene expression begins with transcription in the nucleus to synthesize mRNA (messenger RNA), which is subsequently exported to the cytoplasm for translation to protein. Like transcription and translation, mRNA export is an important regulatory step of eukaryotic gene expression. Various factors are involved in regulating mRNA export, and thus gene expression. Intriguingly, some of these factors interact with viral proteins, and such interactions interfere with mRNA export of the host cell, favoring viral RNA export. Hence, viruses hijack host mRNA export machinery for export of their own RNAs from nucleus to cytoplasm for translation to proteins for viral life cycle, suppressing host mRNA export (and thus host gene expression and immune/antiviral response). Therefore, the molecules that can impair the interactions of these mRNA export factors with viral proteins could emerge as antiviral therapeutic agents to suppress viral RNA transport and enhance host mRNA export, thereby promoting host gene expression and immune response. Thus, there has been a number of studies to understand how virus hijacks mRNA export machinery in suppressing host gene expression and promoting its own RNA export to the cytoplasm for translation to proteins required for viral replication/assembly/life cycle towards developing targeted antiviral therapies, as concisely described here.
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Affiliation(s)
- Shalini Guha
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
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14
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Sun T, Liu Z, Yang Q. The role of ubiquitination and deubiquitination in cancer metabolism. Mol Cancer 2020; 19:146. [PMID: 33004065 PMCID: PMC7529510 DOI: 10.1186/s12943-020-01262-x] [Citation(s) in RCA: 208] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023] Open
Abstract
Metabolic reprogramming, including enhanced biosynthesis of macromolecules, altered energy metabolism, and maintenance of redox homeostasis, is considered a hallmark of cancer, sustaining cancer cell growth. Multiple signaling pathways, transcription factors and metabolic enzymes participate in the modulation of cancer metabolism and thus, metabolic reprogramming is a highly complex process. Recent studies have observed that ubiquitination and deubiquitination are involved in the regulation of metabolic reprogramming in cancer cells. As one of the most important type of post-translational modifications, ubiquitination is a multistep enzymatic process, involved in diverse cellular biological activities. Dysregulation of ubiquitination and deubiquitination contributes to various disease, including cancer. Here, we discuss the role of ubiquitination and deubiquitination in the regulation of cancer metabolism, which is aimed at highlighting the importance of this post-translational modification in metabolic reprogramming and supporting the development of new therapeutic approaches for cancer treatment.
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Affiliation(s)
- Tianshui Sun
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang, 110004, China
| | - Zhuonan Liu
- Department of Urology, First Hospital of China Medical University, Shenyang, China
| | - Qing Yang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang, 110004, China.
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15
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Derambure C, Dzangue-Tchoupou G, D’Agostino MA, Lequerré T, Vittecoq O. Gene expression regulated by abatacept associated with methotrexate and correlation with disease activity in rheumatoid arthritis. PLoS One 2020; 15:e0237143. [PMID: 32760165 PMCID: PMC7410313 DOI: 10.1371/journal.pone.0237143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 07/21/2020] [Indexed: 11/18/2022] Open
Abstract
Objectives Abatacept acts as a competitive inhibitor of the CD28/(CD80/86) costimulation signal required for T cell activation. Mechanisms of action of abatacept have not been fully investigated. The objective of this study was to provide detailed insight into the mode of action of Abatacept based on gene expression data. Methods In this ancillary study from the APPRAISE trial, we investigated the global molecular effects of Abatacept in whole blood samples collected prospectively in biologic naive rheumatoid arthritis patients (n = 19) at baseline and 6 months after the initiation of Abatacept therapy concomitant with methotrexate. Whole human genome microarrays (4x44K) were performed on both baseline and 6-month samples from responders and non-responders patients categorized according to EULAR criteria. T-test with Benjamini-Hochberg correction was performed to identify significant gene expression changes. Gene Ontology and Single Experiment Analysis tools allowed us to highlight specific biological mechanisms involved in methotrexate/Abatacept. Results In methotrexate/Abatacept responders, 672 genes were significantly (q<0.05) dysregulated at 6 months compared to baseline. Correlation analysis highlighted 19 genes whose dysregulations were significantly associated with disease activity variation (p<0.05) and whose functions were associated with proliferation, apoptosis of cells and mitochondrial metabolism, suggesting a restoration of oxidative signaling. The other 653 gene expression changes were relative to direct or indirect effects of methotrexate/Abatacept treatment and were significantly (p<0.005) involved in pathways relative to mRNA processing, proteasome, angiogenesis, apoptosis and TCR signaling. This study highlights new mechanisms of action of methotrexate/Abatacept and may provide new therapeutic targets to prevent autoimmunity in rheumatoid arthritis.
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Affiliation(s)
| | | | - Maria Antonietta D’Agostino
- Department of Rheumatology, AP-HP Ambroise Paré Hospital, University of Versailles Saint Quentin en Yvelines, Boulogne-Billancourt, France
| | - Thierry Lequerré
- Normandie Univ, UNIROUEN, Inserm U 1234, Rouen, France
- Department of Rheumatology Inserm CIC/CRB1404, Rouen University Hospital, Rouen Cedex, France
- * E-mail:
| | - Olivier Vittecoq
- Normandie Univ, UNIROUEN, Inserm U 1234, Rouen, France
- Department of Rheumatology Inserm CIC/CRB1404, Rouen University Hospital, Rouen Cedex, France
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16
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Gâtel P, Piechaczyk M, Bossis G. Ubiquitin, SUMO, and Nedd8 as Therapeutic Targets in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:29-54. [PMID: 32274752 DOI: 10.1007/978-3-030-38266-7_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ubiquitin defines a family of approximately 20 peptidic posttranslational modifiers collectively called the Ubiquitin-like (UbLs). They are conjugated to thousands of proteins, modifying their function and fate in many ways. Dysregulation of these modifications has been implicated in a variety of pathologies, in particular cancer. Ubiquitin, SUMO (-1 to -3), and Nedd8 are the best-characterized UbLs. They have been involved in the regulation of the activity and/or the stability of diverse components of various oncogenic or tumor suppressor pathways. Moreover, the dysregulation of enzymes responsible for their conjugation/deconjugation has also been associated with tumorigenesis and cancer resistance to therapies. The UbL system therefore constitutes an attractive target for developing novel anticancer therapeutic strategies. Here, we review the roles and dysregulations of Ubiquitin, SUMO, and Nedd8 pathways in tumorigenesis, as well as recent advances in the identification of small molecules targeting their conjugating machineries for potential application in the fight against cancer.
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Affiliation(s)
- Pierre Gâtel
- Equipe Labellisée Ligue Contre le Cancer, IGMM, Univ Montpellier, CNRS, Montpellier, France
| | - Marc Piechaczyk
- Equipe Labellisée Ligue Contre le Cancer, IGMM, Univ Montpellier, CNRS, Montpellier, France
| | - Guillaume Bossis
- Equipe Labellisée Ligue Contre le Cancer, IGMM, Univ Montpellier, CNRS, Montpellier, France.
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17
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Guil MJ, Schöller MI, Cassinotti LR, Biancardi VC, Pitra S, Bianciotti LG, Stern JE, Vatta MS. Role of endothelin receptor type A on catecholamine regulation in the olfactory bulb of DOCA-salt hypertensive rats: Hemodynamic implications. Biochim Biophys Acta Mol Basis Dis 2019; 1865:165527. [PMID: 31398465 DOI: 10.1016/j.bbadis.2019.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 07/18/2019] [Accepted: 08/05/2019] [Indexed: 01/09/2023]
Abstract
Increasing evidence shows that the olfactory bulb is involved in blood pressure regulation in health and disease. Enhanced noradrenergic transmission in the olfactory bulb was reported in hypertension. Given that endothelins modulate catecholamines and are involved in the pathogenesis of hypertension, in the present study we sought to establish the role of the endothelin receptor type A on tyrosine hydroxylase, the rate limiting enzyme in catecholamine biosynthesis, in the olfactory bulb of DOCA-salt hypertensive rats. Sprague-Dawley male rats, randomly divided into Control and DOCA-Salt hypertensive groups, were used to assess endothelin receptors by Western blot and confocal microscopy, and their co-localization with tyrosine hydroxylase in the olfactory bulb. Blood pressure and heart rate as well as tyrosine hydroxylase expression and activity were assessed following BQ610 (ETA antagonist) applied to the brain. DOCA-Salt hypertensive rats showed enhanced ETA and decreased ETB expression. ETA co-localized with tyrosine hydroxylase positive neurons. Acute ETA blockade reduced blood pressure and heart rate and decreased the expression of total tyrosine hydroxylase and its phosphorylated forms. Furthermore, it also diminished mRNA tyrosine hydroxylase expression and accelerated the enzyme degradation through the proteasome pathway as shown by pretreatment with MG132, (20s proteasome inhibitor) intracerebroventricularly applied. Present findings support that the brain endothelinergic system plays a major role through ETA activation in the increase of catecholaminergic activity in the olfactory bulb of DOCA-Salt hypertensive rats. They provide rationale evidence that this telencephalic structure contributes in a direct or indirect way to the hemodynamic regulation in salt dependent hypertension.
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Affiliation(s)
- María J Guil
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Fisiología, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química y Metabolismo del Fármaco (IQUIMEFA), Buenos Aires, Argentina
| | - Mercedes I Schöller
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Fisiología, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química y Metabolismo del Fármaco (IQUIMEFA), Buenos Aires, Argentina
| | - Luis R Cassinotti
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Fisiología, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química y Metabolismo del Fármaco (IQUIMEFA), Buenos Aires, Argentina
| | | | - Soledad Pitra
- Department of Physiology, Augusta University, Augusta, GA, USA
| | - Liliana G Bianciotti
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Fisiopatología, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Javier E Stern
- Department of Physiology, Augusta University, Augusta, GA, USA
| | - Marcelo S Vatta
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Fisiología, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química y Metabolismo del Fármaco (IQUIMEFA), Buenos Aires, Argentina.
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18
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Pereira Piedade W, Veith S, Famulski JK. Ubiquitin-mediated proteasome degradation regulates optic fissure fusion. Biol Open 2019; 8:bio.044974. [PMID: 31189662 PMCID: PMC6602337 DOI: 10.1242/bio.044974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Optic fissure fusion is a critical event during retinal development. Failure of fusion leads to coloboma, a potentially blinding congenital disorder. Pax2a is an essential regulator of optic fissure fusion and the target of numerous morphogenetic pathways. In our current study, we examined the negative regulator of pax2a expression, Nz2, and the mechanism modulating Nlz2 activity during optic fissure fusion. Upregulation of Nlz2 in zebrafish embryos resulted in downregulation of pax2a expression and fissure fusion failure. Conversely, upregulation of pax2a expression also led to fissure fusion failure suggesting Pax2 levels require modulation to ensure proper fusion. Interestingly, we discovered Nlz2 is a target of the E3 ubiquitin ligase Siah. We show that zebrafish siah1 expression is regulated by Hedgehog signaling and that Siah1 can directly target Nlz2 for proteasomal degradation, in turn regulating the levels of pax2a mRNA. Finally, we show that both activation and inhibition of Siah activity leads to failure of optic fissure fusion dependent on ubiquitin-mediated proteasomal degradation of Nlz2. In conclusion, we outline a novel, proteasome-mediated degradation regulatory pathway involved in optic fissure fusion. Summary: Optic fissure fusion, a key retinal morphogenic event highly sensitive to developmental signaling, is directly regulated by ubiquitin-mediated proteasomal degradation uncovering a novel regulatory pathway potentially correlated to incidence of coloboma.
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Affiliation(s)
| | - Sydney Veith
- University of Kentucky, Department of Biology, 40506, Lexington, KY, USA
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19
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Wiegering A, Rüther U, Gerhardt C. The Role of Primary Cilia in the Crosstalk between the Ubiquitin⁻Proteasome System and Autophagy. Cells 2019; 8:cells8030241. [PMID: 30875746 PMCID: PMC6468794 DOI: 10.3390/cells8030241] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/06/2019] [Accepted: 03/11/2019] [Indexed: 12/22/2022] Open
Abstract
Protein degradation is a pivotal process for eukaryotic development and homeostasis. The majority of proteins are degraded by the ubiquitin⁻proteasome system and by autophagy. Recent studies describe a crosstalk between these two main eukaryotic degradation systems which allows for establishing a kind of safety mechanism. If one of these degradation systems is hampered, the other compensates for this defect. The mechanism behind this crosstalk is poorly understood. Novel studies suggest that primary cilia, little cellular protrusions, are involved in the regulation of the crosstalk between the two degradation systems. In this review article, we summarise the current knowledge about the association between cilia, the ubiquitin⁻proteasome system and autophagy.
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Affiliation(s)
- Antonia Wiegering
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany.
| | - Ulrich Rüther
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany.
| | - Christoph Gerhardt
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany.
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20
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Miikkulainen P, Högel H, Seyednasrollah F, Rantanen K, Elo LL, Jaakkola PM. Hypoxia-inducible factor (HIF)-prolyl hydroxylase 3 (PHD3) maintains high HIF2A mRNA levels in clear cell renal cell carcinoma. J Biol Chem 2019; 294:3760-3771. [PMID: 30617181 DOI: 10.1074/jbc.ra118.004902] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 01/04/2019] [Indexed: 11/06/2022] Open
Abstract
Most clear cell renal cell carcinomas (ccRCCs) have inactivation of the von Hippel-Lindau tumor suppressor protein (pVHL), resulting in the accumulation of hypoxia-inducible factor α-subunits (HIF-α) and their downstream targets. HIF-2α expression is particularly high in ccRCC and is associated with increased ccRCC growth and aggressiveness. In the canonical HIF signaling pathway, HIF-prolyl hydroxylase 3 (PHD3) suppresses HIF-2α protein by post-translational hydroxylation under sufficient oxygen availability. Here, using immunoblotting and immunofluorescence staining, qRT-PCR, and siRNA-mediated gene silencing, we show that unlike in the canonical pathway, PHD3 silencing in ccRCC cells leads to down-regulation of HIF-2α protein and mRNA. Depletion of other PHD family members had no effect on HIF-2α expression, and PHD3 knockdown in non-RCC cells resulted in the expected increase in HIF-2α protein expression. Accordingly, PHD3 knockdown decreased HIF-2α target gene expression in ccRCC cells and expression was restored upon forced HIF-2α expression. The effect of PHD3 depletion was pinpointed to HIF2A mRNA stability. In line with these in vitro results, a strong positive correlation of PHD3 and HIF2A mRNA expression in ccRCC tumors was detected. Our results suggest that in contrast to the known negative regulation of HIF-2α in most cell types, high PHD3 expression in ccRCC cells maintains elevated HIF-2α expression and that of its target genes, which may enhance kidney cancer aggressiveness.
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Affiliation(s)
- Petra Miikkulainen
- From the Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland.,the Department of Medical Biochemistry, Faculty of Medicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Heidi Högel
- From the Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland.,the Department of Medical Biochemistry, Faculty of Medicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Fatemeh Seyednasrollah
- From the Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland.,the Department of Mathematics and Statistics, University of Turku, Vesilinnantie 5, 20520 Turku, Finland, and
| | - Krista Rantanen
- From the Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
| | - Laura L Elo
- From the Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
| | - Panu M Jaakkola
- From the Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland, .,the Department of Medical Biochemistry, Faculty of Medicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland.,Helsinki University Hospital Cancer Center and Department of Oncology, University of Helsinki, Haartmaninkatu 4, 00290 Helsinki, Finland
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21
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Huang X, Wei S, Ni S, Huang Y, Qin Q. Ubiquitin-Proteasome System Is Required for Efficient Replication of Singapore Grouper Iridovirus. Front Microbiol 2018; 9:2798. [PMID: 30534113 PMCID: PMC6275174 DOI: 10.3389/fmicb.2018.02798] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 10/31/2018] [Indexed: 12/20/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) serves as the major intracellular pathway for protein degradation and plays crucial roles in several cellular processes. However, little is known about the potential actions of the UPS during fish virus infection. In this study, we elucidated the possible roles of UPS in the life cycle of Singapore grouper iridovirus (SGIV); a large DNA virus that usually causes serious systemic diseases with high mortality in groupers. Data from transcriptomic analysis of differentially expressed genes illustrated that expression of 65 genes within the UPS pathway, including ubiquitin encoding, ubiquitination, deubiquitination, and proteasome, were up- or down-regulated during SGIV infection. Using different proteasome inhibitors, inhibition of the proteasome decreased SGIV replication in vitro, accompanied by inhibition of virus assembly site formation, and viral gene transcription and protein transportation. Over-expression of ubiquitin partly rescued the inhibitory effect of ubiquitin inhibitor on SGIV replication, suggesting that UPS was required for fish iridovirus infection in vitro. Viral or host proteins regulated by proteasome inhibition during SGIV infection were investigated with two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Sixty-two differentially expressed proteins, including 15 viral and 47 host proteins, were identified after SGIV infection. The host proteins were involved in ubiquitin-mediated protein degradation, metabolism, cytoskeleton, macromolecular biosynthesis, and signal transduction. Among them, 11 proteins were negatively regulated upon MG132 treatment during SGIV infection. This is believed to be the first study to provide evidence that UPS was essential for fish virus infection and replication.
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Affiliation(s)
- Xiaohong Huang
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Shina Wei
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Songwei Ni
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Youhua Huang
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Qiwei Qin
- College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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22
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Wang P, Gong P, Wang W, Li J, Ai Y, Zhang X. An Eimeria acervulina OTU protease exhibits linkage-specific deubiquitinase activity. Parasitol Res 2018; 118:47-55. [PMID: 30415394 DOI: 10.1007/s00436-018-6113-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 10/07/2018] [Indexed: 02/03/2023]
Abstract
Ubiquitination is an important post-translational modification process that regulates many cellular processes. Proteins can be modified at single or multiple lysine residues by a single ubiquitin protein or by ubiquitin oligomers. It is important to note that the type of ubiquitin chains determines the functional outcome of the modification. Ubiquitin or ubiquitin chains can be removed by deubiquitinases (DUBs). In our previous study, the Eimeria tenella ovarian tumour (Et-OTU) DUB was shown to regulate the telomerase activity of E. tenella and affect E. tenella proliferation. The amino acid sequences of Et-OTU (GenBank: XP_013229759.1) and Eimeria acervulina (E. acervulina) ovarian tumour (Ea-OTUD3) DUB (XP_013250378.1) are 74% identical. Although Et-OTU may regulate E. tenella telomerase activity, whether Ea-OTUD3 affects E. acervulina growth and reproduction remains unclear. We show here that Ea-OTUD3 belongs to the OTU domain class of cysteine protease deubiquitinating enzymes. Ea-OTUD3 is highly linkage-specific, cleaving K48 (Lys48)-, K63-, and K6-linked diubiquitin but not K29-, K33-, and K11-linked diubiquitin. The precise linkage preference of Ea-OTUD3 among these three nonlinear diubiquitin chains is K6 > K48 > K63. Recombinant Ea-OTUD3, but not its catalytic-site mutant Ea-OTUD3 (C247A), exhibits activity against diubiquitin. Ea-OTUD3 removes ubiquitin from the K48-, but to a lesser extent from the K63-linked ubiquitinated E. acervulina proteins of the modified target protein, thereby exhibiting the characteristics of deubiquitinase. This study reveals that the Ea-OTUD3 is a novel functional deubiquitinating enzyme. Furthermore, the Ea-OTUD3 protein may regulate the stability of some K48-linked ubiquitinated E. acervulina proteins.
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Affiliation(s)
- Pu Wang
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Pengtao Gong
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Weirong Wang
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Jianhua Li
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yongxing Ai
- College of Animal Science, Jilin University, Changchun, 130062, China.
| | - Xichen Zhang
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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23
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Ji J, Zhou BR, Zhang RH, Li HM, Guo Q, Zhu J, Luo D. MG-132 treatment promotes TRAIL-mediated apoptosis in SEB-1 sebocytes. Life Sci 2018; 210:150-157. [PMID: 30176247 DOI: 10.1016/j.lfs.2018.08.068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/22/2018] [Accepted: 08/30/2018] [Indexed: 11/19/2022]
Abstract
AIMS This study aimed to identify the mechanism of how MG-132 stimulates cell death in SEB-1 sebocytes. MATERIALS AND METHODS TUNEL staining and annexin-FITC/PI flow cytometry were utilized to examine the apoptotic cell number of SEB-1 sebocytes and HaCaT keratinocytes upon MG-132 and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) treatment. MTT assay and CCK-8 assay monitored the proliferative rate and viability of both cell lines with different treatment. Western blotting (WB) and qPCR were performed to detect the expression of TRAIL and members of Bcl-2 family at protein and gene level. Additionally, RNA interfering was used to knockdown the mRNA transcription of TRAIL and BIK gene. KEY FINDINGS MG-132 treatment enhanced cell death in SEB-1 sebocytes but not in HaCaT keratinocytes. Meanwhile, TRAIL concentrations in SEB-1 sebocytes treated with MG-132 were markedly elevated. Furthermore, treatment with TRAIL or the TRAIL receptor-specific monoclonal antibody AY4 at various doses stimulated cell death in SEB-1 sebocytes in a time- and dose-dependent manner. Silencing of TRAIL restored the cell viability of SEB-1 cells to a normal level after MG-132 treatment. Combined treatment of SEB-1 sebocytes with TRAIL and MG-132 synergistically triggered cell death, suppressed cell proliferation and survival, and promoted BIK expression. Furthermore, BCL2 Interacting Killer (BIK) knockdown via RNA interference participated in the recovery of cell survival reduced by treatment with TRAIL and MG-132. SIGNIFICANCE These findings suggest that treatment with the selective proteasome suppressor MG-132 and TRAIL induces cell death in sebocytes through upregulation of BIK, a member of the Bcl-2 family.
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Affiliation(s)
- Jin Ji
- Department of Dermatology, the First Affiliated Hospital of Nanjing Medical University
| | - Bing-Rong Zhou
- Department of Dermatology, the First Affiliated Hospital of Nanjing Medical University
| | - Ruo-Hua Zhang
- Department of Dermatology, The Affiliated Hospital of Nanjing University of Chinese Medicine
| | - Hong-Min Li
- Department of Dermatology, The Affiliated Hospital of Nanjing University of Chinese Medicine
| | - Qin Guo
- Department of Dermatology, The Affiliated Hospital of Nanjing University of Chinese Medicine
| | - Jie Zhu
- Department of Dermatology, The Affiliated Hospital of Nanjing University of Chinese Medicine
| | - Dan Luo
- Department of Dermatology, the First Affiliated Hospital of Nanjing Medical University.
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Geng S, Miyagi A, Umen JG. Evolutionary divergence of the sex-determining gene MID uncoupled from the transition to anisogamy in volvocine algae. Development 2018; 145:dev.162537. [PMID: 29549112 DOI: 10.1242/dev.162537] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/13/2018] [Indexed: 12/28/2022]
Abstract
Volvocine algae constitute a unique comparative model for investigating the evolution of oogamy from isogamous mating types. The sex- or mating type-determining gene MID encodes a conserved RWP-RK transcription factor found in either the MT- or male mating locus of dioecious volvocine species. We previously found that MID from the isogamous species Chlamydomonas reinhardtii (CrMID) could not induce ectopic spermatogenesis when expressed heterologously in Volvox carteri females, suggesting coevolution of Mid function with gamete dimorphism. Here we found that ectopic expression of MID from the anisogamous species Pleodorina starrii (PsMID) could efficiently induce spermatogenesis when expressed in V. carteri females and, unexpectedly, that GpMID from the isogamous species Gonium pectorale was also able to induce V. carteri spermatogenesis. Neither VcMID nor GpMID could complement a C. reinhardtii mid mutant, at least partly owing to instability of heterologous Mid proteins. Our data show that Mid divergence was not a major contributor to the transition between isogamy and anisogamy/oogamy in volvocine algae, and instead implicate changes in cis-regulatory interactions and/or trans-acting factors of the Mid network in the evolution of sexual dimorphism.
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Affiliation(s)
- Sa Geng
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA
| | - Ayano Miyagi
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA
| | - James G Umen
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA
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25
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Wang P, Li J, Gong P, Wang W, Ai Y, Zhang X. An OTU deubiquitinating enzyme in Eimeria tenella interacts with Eimeria tenella virus RDRP. Parasit Vectors 2018; 11:74. [PMID: 29386062 PMCID: PMC5793433 DOI: 10.1186/s13071-018-2626-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 01/08/2018] [Indexed: 01/09/2023] Open
Abstract
Background Chicken coccidiosis, a disease caused by seven species of Eimeria (Apicomplexa: Coccidia), inflicts severe economic losses on the poultry industry. Eimeria tenella is the one of the most virulent species pathogenic to chickens. Many parasitic protozoans are parasitised by double-stranded (ds) RNA viruses, and the influence of protozoan viruses on parasitic protozoans has been extensively reported. E. tenella RNA virus 1 (Etv) was identified in E. tenella, and the complete genome sequence of Etv was analysed. Here, we screened Etv-RNA-dependent RNA polymerase (RDRP)-interacting host protein E. tenella ovarian tumour (OTU) protein-like cysteine protease (Et-OTU) using a yeast two-hybrid system with pGBKT7-RDRP plasmid serving as bait. A previous study demonstrated that Et-OTU could regulate the telomerase activity of E. tenella, indicating that Et-OTU affects E. tenella proliferation. However, whether Etv-RDRP affects the molecular biological characteristics of E. tenella by interacting with OTU remains unclear. Results We obtained seven positive clones from the initial screen, and six of the seven preys were identified as false-positives. Finally, we identified an RDRP-associated protein predicted to be an E. tenella OTU protein. A α-galactosidase assay showed that the bait vector did not activate the GAL4 reporter gene, indicating no autoactivation activity from the RDRP bait fusion. Pull-down and co-immunoprecipitation assays verified the interaction between Et-OTU and Etv-RDRP both intracellularly and extracellularly. Additionally, Et-OTU was able to deconjugate K48- and K6-linked di-ubiquitin (di-Ub) chains in vitro but not K63-, K11-, K29-, or K33-linked di-Ub chains. The C239A and H351A mutations eliminated the deubiquitinase (DUB) activity of Et-OTU, whereas the D236A mutation did not. Additionally, when combined with RDRP, the DUB activity of Et-OTU towards K48- and K6-linked chains was significantly enhanced. Conclusion Etv-RDRP interacts with Et-OTU both intracellularly and extracellularly. Etv-RDRP enhances the hydrolysis of Et-OTU to K6- or K48-linked ubiquitin chains. This study lays the foundation for further research on the relationship between E. tenella and Etv.
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Affiliation(s)
- Pu Wang
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Jianhua Li
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Pengtao Gong
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Weirong Wang
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yongxing Ai
- College of Animal Science, Jilin University, Changchun, 130062, China.
| | - Xichen Zhang
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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26
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Wang F, Wang L, Wu J, Sokirniy I, Nguyen P, Bregnard T, Weinstock J, Mattern M, Bezsonova I, Hancock WW, Kumar S. Active site-targeted covalent irreversible inhibitors of USP7 impair the functions of Foxp3+ T-regulatory cells by promoting ubiquitination of Tip60. PLoS One 2017; 12:e0189744. [PMID: 29236775 PMCID: PMC5728538 DOI: 10.1371/journal.pone.0189744] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/29/2017] [Indexed: 12/22/2022] Open
Abstract
Accumulation of Foxp3+ T-regulatory (Treg) cells in the tumor microenvironment is associated with tumor immune evasion and poor patient outcome in the case of many solid tumors. Current therapeutic strategies for blocking Treg functions are not Treg-specific, and display only modest and transient efficacy. Recent studies revealed that ubiquitin-specific protease 7 (USP7) is essential for Treg functions by stabilizing expression of Tip60 and Foxp3, which together are central to the development and maintenance of the Treg cell lineage. Pharmacological inhibition of USP7 is therefore a promising strategy for suppressing Treg functions and promoting anti-tumor immunity. Previously, we reported the P5091 series of small molecule USP7 inhibitors and demonstrated their direct anti-tumor activity in vivo using xenograft models. However, the precise mechanism of action of these compounds was not well defined. In this study, we report the development and characterization of P217564, a second-generation USP7 inhibitor with improved potency and selectivity. P217564 selectively targets the catalytic cleft of USP7 and modifies its active site cysteine (C223) by forming a covalent adduct. Irreversible inhibition of USP7 results in durable downstream biological responses in cells, including down-regulation of Tip60 and consequent impairment of Treg suppressive function. In addition, we demonstrate that both USP7 and various USP7 substrates are subjected to Lys48-mediated ubiquitin modification, consistent with increased proteasomal degradation of these proteins because of USP7 inhibition.
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Affiliation(s)
- Feng Wang
- Progenra Inc, Malvern, Pennsylvania, United States of America
| | - Liqing Wang
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jian Wu
- Progenra Inc, Malvern, Pennsylvania, United States of America
| | - Ivan Sokirniy
- Progenra Inc, Malvern, Pennsylvania, United States of America
| | - Phuong Nguyen
- Progenra Inc, Malvern, Pennsylvania, United States of America
| | - Thomas Bregnard
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, Connecticut, United States of America
| | | | - Michael Mattern
- Progenra Inc, Malvern, Pennsylvania, United States of America
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, Connecticut, United States of America
| | - Wayne W. Hancock
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Suresh Kumar
- Progenra Inc, Malvern, Pennsylvania, United States of America
- * E-mail:
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27
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The Ubiquitin Ligase (E3) Psh1p Is Required for Proper Segregation of both Centromeric and Two-Micron Plasmids in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2017; 7:3731-3743. [PMID: 28928274 PMCID: PMC5677152 DOI: 10.1534/g3.117.300227] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein degradation by the ubiquitin-proteasome system is essential to many processes. We sought to assess its involvement in the turnover of mitochondrial proteins in Saccharomyces cerevisiae. We find that deletion of a specific ubiquitin ligase (E3), Psh1p, increases the abundance of a temperature-sensitive mitochondrial protein, mia40-4pHA, when it is expressed from a centromeric plasmid. Deletion of Psh1p unexpectedly elevates the levels of other proteins expressed from centromeric plasmids. Loss of Psh1p does not increase the rate of turnover of mia40-4pHA, affect total protein synthesis, or increase the protein levels of chromosomal genes. Instead, psh1Δ appears to increase the incidence of missegregation of centromeric plasmids relative to their normal 1:1 segregation. After generations of growth with selection for the plasmid, ongoing missegregation would lead to elevated plasmid DNA, mRNA, and protein, all of which we observe in psh1Δ cells. The only known substrate of Psh1p is the centromeric histone H3 variant Cse4p, which is targeted for proteasomal degradation after ubiquitination by Psh1p. However, Cse4p overexpression alone does not phenocopy psh1Δ in increasing plasmid DNA and protein levels. Instead, elevation of Cse4p leads to an apparent increase in 1:0 plasmid segregation events. Further, 2 μm high-copy yeast plasmids also missegregate in psh1Δ, but not when Cse4p alone is overexpressed. These findings demonstrate that Psh1p is required for the faithful inheritance of both centromeric and 2 μm plasmids. Moreover, the effects that loss of Psh1p has on plasmid segregation cannot be accounted for by increased levels of Cse4p.
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28
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Kaistha BP, Krattenmacher A, Fredebohm J, Schmidt H, Behrens D, Widder M, Hackert T, Strobel O, Hoheisel JD, Gress TM, Buchholz M. The deubiquitinating enzyme USP5 promotes pancreatic cancer via modulating cell cycle regulators. Oncotarget 2017; 8:66215-66225. [PMID: 29029505 PMCID: PMC5630405 DOI: 10.18632/oncotarget.19882] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/11/2017] [Indexed: 11/25/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal solid tumors. With an overall five-year survival rate remaining below 6%, there is an explicit need to search for new molecular targets for therapeutic interventions. We undertook a barcode labelled short-hairpin (shRNA) library screen in pancreatic cancer cells in order to identify novel genes promoting cancer survival and progression. Among the candidate genes identified in this screen was the deubiquitinase USP5, which subsequent gene expression analyses demonstrated to be significantly upregulated in primary human pancreatic cancer tissues. Using different knockdown approaches, we show that expression of USP5 is essential for the proliferation and survival of pancreatic cancer cells, tested under different 2D and 3D cell culture conditions as well as in in vivo experiments. These growth inhibition effects upon knockdown of USP5 are mediated primarily by the attenuation of G1/S phase transition in the cells, which is accompanied by accumulation of DNA damage, upregulation of p27, and increased apoptosis rates. Since USP5 is overexpressed in cancer tissues, it can thus potentially serve as a new target for therapeutic interventions, especially given the fact that deubiquitinases are currently emerging as new class of attractive drug targets in cancer.
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Affiliation(s)
- Brajesh P Kaistha
- Department of Medicine, Division of Gastroenterology, Endocrinology and Metabolism, Philipps-University Marburg, Marburg, Germany
| | - Anja Krattenmacher
- Department of Medicine, Division of Gastroenterology, Endocrinology and Metabolism, Philipps-University Marburg, Marburg, Germany
| | - Johannes Fredebohm
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Harald Schmidt
- Department of Medicine, Division of Gastroenterology, Endocrinology and Metabolism, Philipps-University Marburg, Marburg, Germany
| | - Diana Behrens
- Experimantal Pharmacology and Oncology (EPO Berlin-Buch), Berlin, Germany
| | - Miriam Widder
- Institute for Bioprocessing and Analytical Measurement Techniques (IBA-Heiligenstadt), Heilbad Heiligenstadt, Germany
| | - Thilo Hackert
- Department of Surgery, University Clinic Heidelberg, Heidelberg, Germany
| | - Oliver Strobel
- Department of Surgery, University Clinic Heidelberg, Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas M Gress
- Department of Medicine, Division of Gastroenterology, Endocrinology and Metabolism, Philipps-University Marburg, Marburg, Germany
| | - Malte Buchholz
- Department of Medicine, Division of Gastroenterology, Endocrinology and Metabolism, Philipps-University Marburg, Marburg, Germany
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29
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Consalvi S, Brancaccio A, Dall'Agnese A, Puri PL, Palacios D. Praja1 E3 ubiquitin ligase promotes skeletal myogenesis through degradation of EZH2 upon p38α activation. Nat Commun 2017; 8:13956. [PMID: 28067271 PMCID: PMC5423270 DOI: 10.1038/ncomms13956] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 11/16/2016] [Indexed: 12/18/2022] Open
Abstract
Polycomb proteins are critical chromatin modifiers that regulate stem cell differentiation via transcriptional repression. In skeletal muscle progenitors Enhancer of zeste homologue 2 (EZH2), the catalytic subunit of Polycomb Repressive Complex 2 (PRC2), contributes to maintain the chromatin of muscle genes in a repressive conformation, whereas its down-regulation allows the progression through the myogenic programme. Here, we show that p38α kinase promotes EZH2 degradation in differentiating muscle cells through phosphorylation of threonine 372. Biochemical and genetic evidence demonstrates that the MYOD-induced E3 ubiquitin ligase Praja1 (PJA1) is involved in regulating EZH2 levels upon p38α activation. EZH2 premature degradation in proliferating myoblasts is prevented by low levels of PJA1, its cytoplasmic localization and the lower activity towards unphosphorylated EZH2. Our results indicate that signal-dependent degradation of EZH2 is a prerequisite for satellite cells differentiation and identify PJA1 as a new player in the epigenetic control of muscle gene expression. In skeletal muscle progenitors, EZH2 maintains myogenic genes in a repressed state, but during differentiation its levels are reduced via unknown mechanisms. Here the authors show that during myogenesis, p38α kinase phosphorylates EZH2 and targets it for degradation by the ubiquitin ligase PRAJA1.
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Affiliation(s)
- Silvia Consalvi
- Laboratory of Epigenetics and Regenerative Pharmacology, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Arianna Brancaccio
- Laboratory of Epigenetics and Signal Transduction, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy.,Department of Anatomy, Histology, Forensic Medicine and Orthopedics, Via Scarpa 14, Sapienza University, 00161 Rome, Italy
| | - Alessandra Dall'Agnese
- Sanford-Burnham-Prebys Medical Discovery Institute, Development Aging and Regeneration Program, La Jolla 92037, California, USA
| | - Pier Lorenzo Puri
- Laboratory of Epigenetics and Regenerative Pharmacology, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy.,Sanford-Burnham-Prebys Medical Discovery Institute, Development Aging and Regeneration Program, La Jolla 92037, California, USA
| | - Daniela Palacios
- Laboratory of Epigenetics and Signal Transduction, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
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30
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Svoboda P, Fulka H, Malik R. Clearance of Parental Products. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 953:489-535. [DOI: 10.1007/978-3-319-46095-6_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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31
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Liu WJ, Ye L, Huang WF, Guo LJ, Xu ZG, Wu HL, Yang C, Liu HF. p62 links the autophagy pathway and the ubiqutin-proteasome system upon ubiquitinated protein degradation. Cell Mol Biol Lett 2016; 21:29. [PMID: 28536631 PMCID: PMC5415757 DOI: 10.1186/s11658-016-0031-z] [Citation(s) in RCA: 593] [Impact Index Per Article: 74.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 12/07/2016] [Indexed: 01/19/2023] Open
Abstract
The ubiquitin–proteasome system (UPS) and autophagy are two distinct and interacting proteolytic systems. They play critical roles in cell survival under normal conditions and during stress. An increasing body of evidence indicates that ubiquitinated cargoes are important markers of degradation. p62, a classical receptor of autophagy, is a multifunctional protein located throughout the cell and involved in many signal transduction pathways, including the Keap1–Nrf2 pathway. It is involved in the proteasomal degradation of ubiquitinated proteins. When the cellular p62 level is manipulated, the quantity and location pattern of ubiquitinated proteins change with a considerable impact on cell survival. Altered p62 levels can even lead to some diseases. The proteotoxic stress imposed by proteasome inhibition can activate autophagy through p62 phosphorylation. A deficiency in autophagy may compromise the ubiquitin–proteasome system, since overabundant p62 delays delivery of the proteasomal substrate to the proteasome despite proteasomal catalytic activity being unchanged. In addition, p62 and the proteasome can modulate the activity of HDAC6 deacetylase, thus influencing the autophagic degradation.
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Affiliation(s)
- Wei Jing Liu
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China.,Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, 100700 China
| | - Lin Ye
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Wei Fang Huang
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Lin Jie Guo
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Zi Gan Xu
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Hong Luan Wu
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Chen Yang
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Hua Feng Liu
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
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32
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Abstract
The post-translational modification of proteins with ubiquitin represents a complex signalling system that co-ordinates essential cellular functions, including proteolysis, DNA repair, receptor signalling and cell communication. DUBs (deubiquitinases), the enzymes that disassemble ubiquitin chains and remove ubiquitin from proteins, are central to this system. Reflecting the complexity and versatility of ubiquitin signalling, DUB activity is controlled in multiple ways. Although several lines of evidence indicate that aberrant DUB function may promote human disease, the underlying molecular mechanisms are often unclear. Notwithstanding, considerable interest in DUBs as potential drug targets has emerged over the past years. The future success of DUB-based therapy development will require connecting the basic science of DUB function and enzymology with drug discovery. In the present review, we discuss new insights into DUB activity regulation and their links to disease, focusing on the role of DUBs as regulators of cell identity and differentiation, and discuss their potential as emerging drug targets.
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33
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Mou C, Zhang Y, Zhang W, Ding Y, Chen L. Lysine residues 639 and 673 of mouse Ncoa3 are ubiquitination sites for the regulation of its stability. Acta Biochim Biophys Sin (Shanghai) 2014; 46:1066-71. [PMID: 25348736 DOI: 10.1093/abbs/gmu096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ncoa3 is a transcriptional coactivator involved in a wide range of biological processes. Regulation of Ncoa3 protein stability is important to control its activity precisely. Here, we found that deleting amino acid residues 614-740 of Ncoa3 enhances the protein expression level. Replacing two lysine residues, K639 and K673, within this region by arginine, increases the stability of the luciferase fusion protein as well as Ncoa3 protein. When these two lysine residues are mutated to arginine, the overall ubiquitination level of Ncoa3 decreases, indicating that lysine 639 and 673 are its ubiquitination sites. Taken together, we identified two ubiquitination sites at lysine 639 and 673 of Ncoa3. Ubiquitination of these two lysine residues leads to proteasomal degradation of Ncoa3.
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Affiliation(s)
- Chunlin Mou
- State key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yanqin Zhang
- State key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Weiyu Zhang
- State key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yu Ding
- State key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lingyi Chen
- State key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics and College of Life Sciences, Nankai University, Tianjin 300071, China
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34
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Functions of the proteasome on chromatin. Biomolecules 2014; 4:1026-44. [PMID: 25422899 PMCID: PMC4279168 DOI: 10.3390/biom4041026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/11/2014] [Accepted: 11/10/2014] [Indexed: 12/11/2022] Open
Abstract
The proteasome is a large self-compartmentalized protease complex that recognizes, unfolds, and destroys ubiquitylated substrates. Proteasome activities are required for a host of cellular functions, and it has become clear in recent years that one set of critical actions of the proteasome occur on chromatin. In this review, we discuss some of the ways in which proteasomes directly regulate the structure and function of chromatin and chromatin regulatory proteins, and how this influences gene transcription. We discuss lingering controversies in the field, the relative importance of proteolytic versus non-proteolytic proteasome activities in this process, and highlight areas that require further investigation. Our intention is to show that proteasomes are involved in major steps controlling the expression of the genetic information, that proteasomes use both proteolytic mechanisms and ATP-dependent protein remodeling to accomplish this task, and that much is yet to be learned about the full spectrum of ways that proteasomes influence the genome.
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35
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The 26S proteasome and initiation of gene transcription. Biomolecules 2014; 4:827-47. [PMID: 25211636 PMCID: PMC4192674 DOI: 10.3390/biom4030827] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 08/20/2014] [Accepted: 09/01/2014] [Indexed: 11/17/2022] Open
Abstract
Transcription activation is the foremost step of gene expression and is modulated by various factors that act in synergy. Misregulation of this process and its associated factors has severe effects and hence requires strong regulatory control. In recent years, growing evidence has highlighted the 26S proteasome as an important contributor to the regulation of transcription initiation. Well known for its role in protein destruction, its contribution to protein synthesis was initially viewed with skepticism. However, studies over the past several years have established the proteasome as an important component of transcription initiation through proteolytic and non-proteolytic activities. In this review, we discuss findings made so far in understanding the connections between transcription initiation and the 26S proteasome complex.
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36
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Lopez-Serra P, Marcilla M, Villanueva A, Ramos-Fernandez A, Palau A, Leal L, Wahi JE, Setien-Baranda F, Szczesna K, Moutinho C, Martinez-Cardus A, Heyn H, Sandoval J, Puertas S, Vidal A, Sanjuan X, Martinez-Balibrea E, Viñals F, Perales JC, Bramsem JB, Ørntoft TF, Andersen CL, Tabernero J, McDermott U, Boxer MB, Heiden MGV, Albar JP, Esteller M. A DERL3-associated defect in the degradation of SLC2A1 mediates the Warburg effect. Nat Commun 2014; 5:3608. [PMID: 24699711 PMCID: PMC3988805 DOI: 10.1038/ncomms4608] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 03/10/2014] [Indexed: 01/03/2023] Open
Abstract
Cancer cells possess aberrant proteomes that can arise by the disruption of genes involved in physiological protein degradation. Here we demonstrate the presence of promoter CpG island hypermethylation-linked inactivation of DERL3 (Derlin-3), a key gene in the endoplasmic reticulum-associated protein degradation pathway, in human tumours. The restoration of in vitro and in vivo DERL3 activity highlights the tumour suppressor features of the gene. Using the stable isotopic labelling of amino acids in cell culture workflow for differential proteome analysis, we identify SLC2A1 (glucose transporter 1, GLUT1) as a downstream target of DERL3. Most importantly, SLC2A1 overexpression mediated by DERL3 epigenetic loss contributes to the Warburg effect in the studied cells and pinpoints a subset of human tumours with greater vulnerability to drugs targeting glycolysis.
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Affiliation(s)
- Paula Lopez-Serra
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Miguel Marcilla
- Proteomics Unit, Spanish National Biotechnology Centre (CNB), CSIC, 28049 Madrid, Spain
| | - Alberto Villanueva
- Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | | | - Anna Palau
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Lucía Leal
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Jessica E. Wahi
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Fernando Setien-Baranda
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Karolina Szczesna
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Catia Moutinho
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Anna Martinez-Cardus
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Holger Heyn
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Juan Sandoval
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Sara Puertas
- Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - August Vidal
- Bellvitge Biomedical Research Institute (IDIBELL), Department of Pathology, Bellvitge University Hospital, L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Xavier Sanjuan
- Bellvitge Biomedical Research Institute (IDIBELL), Department of Pathology, Bellvitge University Hospital, L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Eva Martinez-Balibrea
- Medical Oncology Service, Catalan Institute of Oncology (ICO), l'Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Hospital Germans Trias I Pujol, Badalona, Barcelona, 08916 Catalonia, Spain
| | - Francesc Viñals
- Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Jose C. Perales
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Jesper B. Bramsem
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, Aarhus N, DK-8200 Aarhus, Denmark
| | - Torben F. Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, Aarhus N, DK-8200 Aarhus, Denmark
| | - Claus L. Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, Aarhus N, DK-8200 Aarhus, Denmark
| | - Josep Tabernero
- Medical Oncology Department, Vall d’Hebron University Hospital, Barcelona, 08035 Catalonia, Spain
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Matthew B. Boxer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20891-4874, USA
| | - Matthew G. Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Juan Pablo Albar
- Proteomics Unit, Spanish National Biotechnology Centre (CNB), CSIC, 28049 Madrid, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010 Catalonia, Spain
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37
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Ndoja A, Cohen RE, Yao T. Ubiquitin signals proteolysis-independent stripping of transcription factors. Mol Cell 2014; 53:893-903. [PMID: 24613342 DOI: 10.1016/j.molcel.2014.02.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 10/23/2013] [Accepted: 01/23/2014] [Indexed: 01/10/2023]
Abstract
Ubiquitination of transcription activators has been reported to regulate transcription via both proteolytic and nonproteolytic routes, yet the function of the ubiquitin (Ub) signal in the nonproteolytic process is poorly understood. By use of the heterologous transcription activator LexA-VP16 in Saccharomyces cerevisiae, we show that monoubiquitin fusion of the activator prevents stable interactions between the activator and DNA, leading to transcription inhibition without activator degradation. We identify the AAA(+) ATPase Cdc48 and its cofactors as the Ub receptor responsible for extracting the monoubiquitinated activator from DNA. Our results suggest that deubiquitination of the activator is critical for transcription activation. These findings with LexA-VP16 extend in both yeast and mammalian cells to native transcription activators Met4 and R-Smads, respectively, that are known to be oligo-ubiquitinated. The results illustrate a role for Ub and Cdc48 in transcriptional regulation and gene expression that is independent of proteolysis.
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Affiliation(s)
- Ada Ndoja
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert E Cohen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
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38
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Westerbeck JW, Pasupala N, Guillotte M, Szymanski E, Matson BC, Esteban C, Kerscher O. A SUMO-targeted ubiquitin ligase is involved in the degradation of the nuclear pool of the SUMO E3 ligase Siz1. Mol Biol Cell 2013; 25:1-16. [PMID: 24196836 PMCID: PMC3873881 DOI: 10.1091/mbc.e13-05-0291] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Here we show that the Slx5/Slx8 STUbL complex is involved in the efficient degradation of the nuclear pool of Siz1, a SUMO E3 ligase with many nuclear and cytosolic substrates. This novel finding suggests that STUbLs can regulate cellular SUMO homeostasis by targeting SUMO E3 ligases. The Slx5/Slx8 heterodimer constitutes a SUMO-targeted ubiquitin ligase (STUbL) with an important role in SUMO-targeted degradation and SUMO-dependent signaling. This STUbL relies on SUMO-interacting motifs in Slx5 to aid in substrate targeting and carboxy-terminal RING domains in both Slx5 and Slx8 for substrate ubiquitylation. In budding yeast cells, Slx5 resides in the nucleus, forms distinct foci, and can associate with double-stranded DNA breaks. However, it remains unclear how STUbLs interact with other proteins and their substrates. To examine the targeting and functions of the Slx5/Slx8 STUbL, we constructed and analyzed truncations of the Slx5 protein. Our structure–function analysis reveals a domain of Slx5 involved in nuclear localization and in the interaction with Slx5, SUMO, Slx8, and a novel interactor, the SUMO E3 ligase Siz1. We further analyzed the functional interaction of Slx5 and Siz1 in vitro and in vivo. We found that a recombinant Siz1 fragment is an in vitro ubiquitylation target of the Slx5/Slx8 STUbL. Furthermore, slx5∆ cells accumulate phosphorylated and sumoylated adducts of Siz1 in vivo. Specifically, we show that Siz1 can be ubiquitylated in vivo and is degraded in an Slx5-dependent manner when its nuclear egress is prevented in mitosis. In conclusion, our data provide a first look into the STUbL-mediated regulation of a SUMO E3 ligase.
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Affiliation(s)
- Jason W Westerbeck
- Biology Department, The College of William & Mary, Williamsburg, VA 23187
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39
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Sorek M, Balaban NQ, Loewenstein Y. Stochasticity, bistability and the wisdom of crowds: a model for associative learning in genetic regulatory networks. PLoS Comput Biol 2013; 9:e1003179. [PMID: 23990765 PMCID: PMC3749950 DOI: 10.1371/journal.pcbi.1003179] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 07/01/2013] [Indexed: 11/20/2022] Open
Abstract
It is generally believed that associative memory in the brain depends on multistable synaptic dynamics, which enable the synapses to maintain their value for extended periods of time. However, multistable dynamics are not restricted to synapses. In particular, the dynamics of some genetic regulatory networks are multistable, raising the possibility that even single cells, in the absence of a nervous system, are capable of learning associations. Here we study a standard genetic regulatory network model with bistable elements and stochastic dynamics. We demonstrate that such a genetic regulatory network model is capable of learning multiple, general, overlapping associations. The capacity of the network, defined as the number of associations that can be simultaneously stored and retrieved, is proportional to the square root of the number of bistable elements in the genetic regulatory network. Moreover, we compute the capacity of a clonal population of cells, such as in a colony of bacteria or a tissue, to store associations. We show that even if the cells do not interact, the capacity of the population to store associations substantially exceeds that of a single cell and is proportional to the number of bistable elements. Thus, we show that even single cells are endowed with the computational power to learn associations, a power that is substantially enhanced when these cells form a population.
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Affiliation(s)
- Matan Sorek
- Edmond and Lily Safra Center for Brain Sciences and the Interdisciplinary Center for Neural Computation, The Hebrew University of Jerusalem, Jerusalem, Israel.
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40
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Skalniak L, Koj A, Jura J. Proteasome inhibitor MG-132 induces MCPIP1 expression. FEBS J 2013; 280:2665-74. [PMID: 23551903 PMCID: PMC3806276 DOI: 10.1111/febs.12264] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 03/19/2013] [Accepted: 03/22/2013] [Indexed: 01/14/2023]
Abstract
The proteasome is a protein complex responsible for the degradation of polyubiquitin-tagged proteins. Besides the removal of target proteins, the proteasome also participates in the regulation of gene transcription in both proteolytic and non-proteolytic fashion. In this study the effect of proteasome inhibition on the basal expression of monocyte chemotactic protein-1 induced protein 1 (MCPIP1) was examined. Treatment of HepG2 or HeLa cells with proteasome inhibitor MG-132 resulted in a significant increase of MCPIP1 expression, both at mRNA and protein level. Interestingly, MG-132 did not alter MCPIP1 stability. Instead, the observed protein increase was blocked by actinomycin D, suggesting the involvement of de novo mRNA synthesis in the increase of MCPIP1 protein following MG-132 treatment. Using several inhibitors we determined the participation of extracellular-signal-regulated kinase 1/2 and p38 kinases in MCPIP1 upregulation by MG-132. Our findings show for the first time the impact of proteasome inhibition on MCPIP1 protein expression by modulation of the activity of intracellular signaling pathways. Overexpression of MCPIP1-myc protein decreased the viability of HeLa cells but not HepG2 cells, which correlates with the increased susceptibility of HeLa cells to MG-132 toxicity. Notably, both MG-132 treatment and MCPIP1-myc overexpression led to the activation of apoptosis, as revealed by the induction of caspases 3/7 in both types of cell lines. This suggests the involvement of MCPIP1 upregulation in toxic properties of proteasome inhibition, which is an acknowledged approach to the treatment of several cancer types.
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Affiliation(s)
- Lukasz Skalniak
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
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41
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Chen L, Cheng C, Zhang C, Yao Q, Zhao E. Ubiquitin-conjugating enzyme involved in the immune response caused by pathogens invasion. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/oji.2013.33013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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42
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Ubiquitin-like proteins and their roles in archaea. Trends Microbiol 2012; 21:31-8. [PMID: 23140889 DOI: 10.1016/j.tim.2012.09.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/25/2012] [Accepted: 09/26/2012] [Indexed: 01/01/2023]
Abstract
This review highlights the finding that ubiquitin-like (Ubl) proteins of archaea (termed SAMPs) function not only as sulfur carriers but also as protein modifiers. UbaA (an E1 ubiquitin-activating enzyme homolog of archaea) is required for the SAMPs to be covalently attached to proteins. The SAMPs and UbaA are also needed to form sulfur-containing biomolecules (e.g., thiolated tRNA and molybdenum cofactor). These findings provide a new perspective on how Ubl proteins can serve as both sulfur carriers and protein modifiers in the absence of canonical E2 ubiquitin conjugating or E3 ubiquitin ligase enzyme homologs.
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43
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Janusz G, Kucharzyk KH, Pawlik A, Staszczak M, Paszczynski AJ. Fungal laccase, manganese peroxidase and lignin peroxidase: gene expression and regulation. Enzyme Microb Technol 2012. [PMID: 23199732 DOI: 10.1016/j.enzmictec.2012.10.003] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extensive research efforts have been dedicated to characterizing expression of laccases and peroxidases and their regulation in numerous fungal species. Much attention has been brought to these enzymes broad substrate specificity resulting in oxidation of a variety of organic compounds which brings about possibilities of their utilization in biotechnological and environmental applications. Research attempts have resulted in increased production of both laccases and peroxidases by the aid of heterologous and homologous expression. Through analysis of promoter regions, protein expression patterns and culture conditions manipulations it was possible to compare and identify common pathways of these enzymes' production and secretion. Although laccase and peroxidase proteins have been crystallized and thoroughly analyzed, there are still a lot of questions remaining about their evolutionary origin and the physiological functions. This review describes the present understanding of promoter sequences and correlation between the observed regulatory effects on laccase, manganese peroxidase and lignin peroxidase genes transcript levels and the presence of specific response elements.
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Affiliation(s)
- Grzegorz Janusz
- Department of Biochemistry, Maria Curie-Skłodowska University, Akademicka 19 Street, 20-033 Lublin, Poland.
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