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Cheng S, Fahmi NA, Park M, Sun J, Thao K, Yeh HS, Zhang W, Yong J. mTOR Contributes to the Proteome Diversity through Transcriptome-Wide Alternative Splicing. Int J Mol Sci 2022; 23:ijms232012416. [PMID: 36293270 PMCID: PMC9604279 DOI: 10.3390/ijms232012416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
The mammalian target of rapamycin (mTOR) pathway is crucial in energy metabolism and cell proliferation. Previously, we reported transcriptome-wide 3′-untranslated region (UTR) shortening by alternative polyadenylation upon mTOR activation and its impact on the proteome. Here, we further interrogated the mTOR-activated transcriptome and found that hyperactivation of mTOR promotes transcriptome-wide exon skipping/exclusion, producing short isoform transcripts from genes. This widespread exon skipping confers multifarious regulations in the mTOR-controlled functional proteomics: AS in coding regions widely affects the protein length and functional domains. They also alter the half-life of proteins and affect the regulatory post-translational modifications. Among the RNA processing factors differentially regulated by mTOR signaling, we found that SRSF3 mechanistically facilitates exon skipping in the mTOR-activated transcriptome. This study reveals a role of mTOR in AS regulation and demonstrates that widespread AS is a multifaceted modulator of the mTOR-regulated functional proteome.
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Affiliation(s)
- Sze Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Naima Ahmed Fahmi
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Meeyeon Park
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Jiao Sun
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Kaitlyn Thao
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Hsin-Sung Yeh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Wei Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
- Correspondence: (W.Z.); (J.Y.); Tel.: +1-407-823-2763 (W.Z.); +1-612-626-2420 (J.Y.)
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
- Correspondence: (W.Z.); (J.Y.); Tel.: +1-407-823-2763 (W.Z.); +1-612-626-2420 (J.Y.)
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2
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Electrostatic and steric effects underlie acetylation-induced changes in ubiquitin structure and function. Nat Commun 2022; 13:5435. [PMID: 36114200 PMCID: PMC9481602 DOI: 10.1038/s41467-022-33087-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 08/26/2022] [Indexed: 12/29/2022] Open
Abstract
Covalent attachment of ubiquitin (Ub) to proteins is a highly versatile posttranslational modification. Moreover, Ub is not only a modifier but itself is modified by phosphorylation and lysine acetylation. However, the functional consequences of Ub acetylation are poorly understood. By generation and comprehensive characterization of all seven possible mono-acetylated Ub variants, we show that each acetylation site has a particular impact on Ub structure. This is reflected in selective usage of the acetylated variants by different E3 ligases and overlapping but distinct interactomes, linking different acetylated variants to different cellular pathways. Notably, not only electrostatic but also steric effects contribute to acetylation-induced changes in Ub structure and, thus, function. Finally, we provide evidence that p300 acts as a position-specific Ub acetyltransferase and HDAC6 as a general Ub deacetylase. Our findings provide intimate insights into the structural and functional consequences of Ub acetylation and highlight the general importance of Ub acetylation. Ubiquitin is not only a posttranslational modifier but itself is subject to modifications, such as acetylation. Characterization of distinct acetylated ubiquitin variants reveals that each acetylation site has a particular impact on ubiquitin structure and its protein-protein interaction properties.
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Lacoursiere RE, Hadi D, Shaw GS. Acetylation, Phosphorylation, Ubiquitination (Oh My!): Following Post-Translational Modifications on the Ubiquitin Road. Biomolecules 2022; 12:biom12030467. [PMID: 35327659 PMCID: PMC8946176 DOI: 10.3390/biom12030467] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 02/06/2023] Open
Abstract
Ubiquitination is controlled by a series of E1, E2, and E3 enzymes that can ligate ubiquitin to cellular proteins and dictate the turnover of a substrate and the outcome of signalling events such as DNA damage repair and cell cycle. This process is complex due to the combinatorial power of ~35 E2 and ~1000 E3 enzymes involved and the multiple lysine residues on ubiquitin that can be used to assemble polyubiquitin chains. Recently, mass spectrometric methods have identified that most enzymes in the ubiquitination cascade can be further modified through acetylation or phosphorylation under particular cellular conditions and altered modifications have been noted in different cancers and neurodegenerative diseases. This review provides a cohesive summary of ubiquitination, acetylation, and phosphorylation sites in ubiquitin, the human E1 enzyme UBA1, all E2 enzymes, and some representative E3 enzymes. The potential impacts these post-translational modifications might have on each protein function are highlighted, as well as the observations from human disease.
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Tsang O, Wong JWH. Proteogenomic interrogation of cancer cell lines: an overview of the field. Expert Rev Proteomics 2021; 18:221-232. [PMID: 33877947 DOI: 10.1080/14789450.2021.1914594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Introduction: Cancer cell lines (CCLs) have been a major resource for cancer research. Over the past couple of decades, they have been instrumental in omic profiling method development and as model systems to generate new knowledge in cell and cancer biology. More recently, with the increasing amount of genomic, transcriptomic and proteomic data being generated in hundreds of CCLs, there is growing potential for integrative proteogenomic data analyses to be performed.Areas covered: In this review, we first describe the most commonly used proteome profiling methods in CCLs. We then discuss how these proteomics data can be integrated with genomics data for proteogenomics analyses. Finally, we highlight some of the recent biological discoveries that have arisen from proteogenomics analyses of CCLs.Expert opinion: Protegeonomics analyses of CCLs have so far enabled the discovery of novel proteins and proteoforms. It has also improved our understanding of biological processes including post-transcriptional regulation of protein abundance and the presentation of antigens by major histocompatibility complex alleles. With proteomics data to be generated in hundreds to thousands of CCLs in coming years, there will be further potential for large-scale proteogenomics analyses and data integration with the phenotypically well-characterized CCLs.
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Affiliation(s)
- Olson Tsang
- Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Jason W H Wong
- Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR.,School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
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Jin L, Chen Y, Yan C, Guo X, Jiang T, Guli A, Song X, Wan Q, Shu Q, Ding S. Phosphoproteome Profiling Revealed the Importance of mTOR Inhibition on CDK1 Activation to Further Regulate Cell Cycle Progression. J Proteome Res 2021; 20:2329-2339. [PMID: 33797919 DOI: 10.1021/acs.jproteome.0c00848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mammalian target of rapamycin (mTOR) functions as a critical regulator of cell cycle progression. However, the underlying mechanism by which mTOR regulates cell cycle progression remains elusive. In this study, we used stable isotope labeling of amino acids in cell culture with a two-step strategy for phosphopeptide enrichment and high-throughput quantitative mass spectrometry to perform a global phosphoproteome analysis of mTOR inhibition by rapamycin. By monitoring the phosphoproteome alterations upon rapamycin treatment, downregulation of mTOR signaling pathway was detected and enriched. Further functional analysis of phosphoproteome revealed the involvement of cell cycle events. Specifically, the elevated profile of cell cycle-related substrates was observed, and the activation of CDK1, MAPK1, and MAPK3 kinases was determined. Second, pathway interrogation using kinase inhibitor treatment confirmed that CDK1 activation operated downstream from mTOR inhibition to further regulate cell cycle progression. Third, we found that the activation of CDK1 following 4-12 h of mTOR inhibition was accompanied by the activation of the Greatwall-endosulfine complex. In conclusion, we presented a high-confidence phosphoproteome map inside the cells upon mTOR inhibition by rapamycin. Our data implied that mTOR inhibition could contribute to CDK1 activation for further regulating cell cycle progression, which was mediated by the Greatwall-endosulfine complex.
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Affiliation(s)
- Luqi Jin
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China
| | - Yu Chen
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China
| | - Chunlan Yan
- Department of Biophysics, Key Laboratory of Medical Neurobiology, Ministry of Health of China, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China
| | - Xiaoyuan Guo
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China
| | - Tingting Jiang
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China
| | - Ayiding Guli
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China
| | - Xinghui Song
- The Core Facilities, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China
| | - Qun Wan
- Department of Urinary Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China
| | - Qiang Shu
- Department of Cell Biology and Department of Cardiovascular Surgery, National Clinical Research Center For Child Health, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China
| | - Shiping Ding
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China.,Department of Cell Biology and Department of Cardiovascular Surgery, National Clinical Research Center For Child Health, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China
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Yang L, Fu Q, Miao L, Ding Q, Li X, Wang J, Jiang G, Wang Y. Quantitative acetylome and phosphorylome analysis reveals Girdin affects pancreatic cancer progression through regulating Cortactin. Aging (Albany NY) 2020; 12:7679-7693. [PMID: 32369440 PMCID: PMC7244020 DOI: 10.18632/aging.103032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 02/25/2020] [Indexed: 02/07/2023]
Abstract
The actin-binding protein Girdin is involved in a variety of cellular processes, including pancreatic cancer. The objective of this study is to explore the role and the mechanism of Girdin in pancreatic cancer by quantitative acetylome and phosphorylome analysis. We firstly found that Girdin was overexpressed in pancreatic cancer tissue and increased expression of Girdin was associated with tumor size and stage of patients with pancreatic cancer. We established the shRNA knockdown of Girdin in PANC-1 and Aspc-1 cells, and we found that shGirdin inhibited proliferation, migration and invasion, and promoted apoptosis. Subsequently, we identified and quantified 5,338 phosphorylated sites in 2,263 proteins that changed in response to Girdin knockdown, and identified a similar set of Girdin-responsive acetylome data as well. Additional data revealed that down-regulation of Girdin affected Cortactin phosphorylation and acetylation, suggesting Cortactin as an important regulatory target of Girdin. Moreover, we found that overexpression of Cortactin could rescue the effect of shGirdin on proliferation, apoptosism, migration and invasion of pancreatic cancer cells. In general, our results provided new insights into the mechanisms of Girdin function including cell proliferation, migration and invasion, and offer biomarker candidates for clinical evaluation of Girdin.
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Affiliation(s)
- Lihua Yang
- Medical Center for Digestive Disease, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Qiang Fu
- Medical Center for Digestive Disease, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Lin Miao
- Medical Center for Digestive Disease, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Quchen Ding
- Medical Center for Digestive Disease, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Xiangyu Li
- Medical Center for Digestive Disease, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Juan Wang
- Medical Center for Digestive Disease, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Guobin Jiang
- Medical Center for Digestive Disease, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Yun Wang
- Medical Center for Digestive Disease, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
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Lacoursiere RE, O’Donoghue P, Shaw GS. Programmed ubiquitin acetylation using genetic code expansion reveals altered ubiquitination patterns. FEBS Lett 2020; 594:1226-1234. [DOI: 10.1002/1873-3468.13702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 01/01/2023]
Affiliation(s)
| | - Patrick O’Donoghue
- Department of Biochemistry The University of Western Ontario London Canada
- Department of Chemistry The University of Western Ontario London Canada
| | - Gary S. Shaw
- Department of Biochemistry The University of Western Ontario London Canada
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Pieroni L, Iavarone F, Olianas A, Greco V, Desiderio C, Martelli C, Manconi B, Sanna MT, Messana I, Castagnola M, Cabras T. Enrichments of post-translational modifications in proteomic studies. J Sep Sci 2019; 43:313-336. [PMID: 31631532 DOI: 10.1002/jssc.201900804] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/23/2019] [Accepted: 10/17/2019] [Indexed: 12/14/2022]
Abstract
More than 300 different protein post-translational modifications are currently known, but only a few have been extensively investigated because modified proteoforms are commonly present in sub-stoichiometry amount. For this reason, improvement of specific enrichment techniques is particularly useful for the proteomic characterization of post-translationally modified proteins. Enrichment proteomic strategies could help the researcher in the challenging issue to decipher the complex molecular cross-talk existing between the different factors influencing the cellular pathways. In this review the state of art of the platforms applied for the enrichment of specific and most common post-translational modifications, such as glycosylation and glycation, phosphorylation, sulfation, redox modifications (i.e. sulfydration and nitrosylation), methylation, acetylation, and ubiquitinylation, are described. Enrichments strategies applied to characterize less studied post-translational modifications are also briefly discussed.
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Affiliation(s)
- Luisa Pieroni
- Laboratorio di Proteomica e Metabolomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Federica Iavarone
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica del Sacro Cuore, Rome, Italy.,IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Alessandra Olianas
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Viviana Greco
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica del Sacro Cuore, Rome, Italy.,IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Claudia Desiderio
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Claudia Martelli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Barbara Manconi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Maria Teresa Sanna
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Irene Messana
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Massimo Castagnola
- Laboratorio di Proteomica e Metabolomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Tiziana Cabras
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
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Xu D, Wang X. Lysine Acetylation is an Important Post-Translational Modification that Modulates Heat Shock Response in the Sea Cucumber Apostichopus japonicus. Int J Mol Sci 2019; 20:ijms20184423. [PMID: 31505730 PMCID: PMC6770049 DOI: 10.3390/ijms20184423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/30/2019] [Accepted: 09/04/2019] [Indexed: 12/19/2022] Open
Abstract
Heat stress (HS) is an important factor for the survival of the marine organism Apostichopus japonicus. Lysine acetylation is a pivotal post-translational modification that modulates diverse physiological processes including heat shock response (HSR). In this study, 4028 lysine acetylation sites in 1439 proteins were identified in A. japonicus by acetylproteome sequencing. A total of 13 motifs were characterized around the acetylated lysine sites. Gene Ontology analysis showed that major acetylated protein groups were involved in “oxidation–reduction process”, “ribosome”, and “protein binding” terms. Compared to the control group, the acetylation quantitation of 25 and 41 lysine sites changed after 6 and 48 h HS. Notably, lysine acetyltransferase CREB-binding protein (CBP) was identified to have differential acetylation quantitation at multiple lysine sites under HS. Various chaperones, such as caseinolytic peptidase B protein homolog (CLBP), T-complex protein 1 (TCP1), and cyclophilin A (CYP1), showed differential acetylation quantitation after 48 h HS. Additionally, many translation-associated proteins, such as ribosomal proteins, translation initiation factor (IF), and elongation factors (EFs), had differential acetylation quantitation under HS. These proteins represented specific interaction networks. Collectively, our results offer novel insight into the complex HSR in A. japonicus and provide a resource for further mechanistic studies examining the regulation of protein function by lysine acetylation.
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Affiliation(s)
- Dongxue Xu
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China.
| | - Xuan Wang
- Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China.
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