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Hoedt E, Zhang G, Neubert TA. Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) for Quantitative Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:531-539. [PMID: 31347069 DOI: 10.1007/978-3-030-15950-4_31] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful approach for high-throughput quantitative proteomics. SILAC allows highly accurate protein quantitation through metabolic encoding of whole cell proteomes using stable isotope labeled amino acids. Since its introduction in 2002, SILAC has become increasingly popular. In this chapter we review the methodology and application of SILAC, with an emphasis on three research areas: dynamics of posttranslational modifications, protein-protein interactions, and protein turnover.
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Affiliation(s)
- Esthelle Hoedt
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Guoan Zhang
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
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Abreha MH, Dammer EB, Ping L, Zhang T, Duong DM, Gearing M, Lah JJ, Levey AI, Seyfried NT. Quantitative Analysis of the Brain Ubiquitylome in Alzheimer's Disease. Proteomics 2018; 18:e1800108. [PMID: 30230243 PMCID: PMC6283072 DOI: 10.1002/pmic.201800108] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 08/16/2018] [Indexed: 12/15/2022]
Abstract
Several neurodegenerative diseases including Alzheimer's Disease (AD) are characterized by ubiquitin-positive pathological protein aggregates. Here, an immunoaffinity approach is utilized to enrich ubiquitylated isopeptides after trypsin digestion from five AD and five age-matched control postmortem brain tissues. Label-free MS-based proteomic analysis identifies 4291 unique ubiquitylation sites mapping to 1682 unique proteins. Differential enrichment analysis shows that over 800 ubiquitylation sites are significantly altered between AD and control cases. Of these, ≈80% are increased in AD, including seven poly ubiquitin linkages, which is consistent with proteolytic stress and high burden of ubiquitylated pathological aggregates in AD. The microtubule associated protein Tau, the core component of neurofibrillary tangles, has the highest number of increased sites of ubiquitylation per any protein in AD. Tau poly ubiquitylation from AD brain homogenates is confirmed by reciprocal co-immunoprecipitation and by affinity capture using tandem ubiquitin binding entities. Co-modified peptides, with both ubiquitylation and phosphorylation sites, are also enriched in AD. Notably, many of the co-modified peptides mapped to Tau within KXGS motifs in the microtubule binding region suggesting that crosstalk between phosphorylation and ubiquitylation occurs on Tau in AD. Overall, these findings highlight the utility of MS to map ubiquitylated substrates in human brain and provides insight into mechanisms underlying pathological protein posttranslational modification in AD.
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Affiliation(s)
- Measho H. Abreha
- Center for Neurodegenerative Diseases, Emory University
School of Medicine, Atlanta, GA, 30322
| | - Eric B. Dammer
- Department of Biochemistry, Emory University School of
Medicine, Atlanta, GA, 30322
- Center for Neurodegenerative Diseases, Emory University
School of Medicine, Atlanta, GA, 30322
| | - Lingyan Ping
- Department of Biochemistry, Emory University School of
Medicine, Atlanta, GA, 30322
- Center for Neurodegenerative Diseases, Emory University
School of Medicine, Atlanta, GA, 30322
| | - Tian Zhang
- Department of Biochemistry, Emory University School of
Medicine, Atlanta, GA, 30322
- Center for Neurodegenerative Diseases, Emory University
School of Medicine, Atlanta, GA, 30322
| | - Duc M. Duong
- Department of Biochemistry, Emory University School of
Medicine, Atlanta, GA, 30322
- Center for Neurodegenerative Diseases, Emory University
School of Medicine, Atlanta, GA, 30322
| | - Marla Gearing
- Department of Pathology and Laboratory Medicine, Emory
University School of Medicine, Atlanta, GA, 30322
- Center for Neurodegenerative Diseases, Emory University
School of Medicine, Atlanta, GA, 30322
| | - James J. Lah
- Department of Neurology, Emory University School of
Medicine, Atlanta, GA, 30322
- Center for Neurodegenerative Diseases, Emory University
School of Medicine, Atlanta, GA, 30322
| | - Allan I. Levey
- Department of Neurology, Emory University School of
Medicine, Atlanta, GA, 30322
- Center for Neurodegenerative Diseases, Emory University
School of Medicine, Atlanta, GA, 30322
| | - Nicholas T. Seyfried
- Department of Biochemistry, Emory University School of
Medicine, Atlanta, GA, 30322
- Department of Neurology, Emory University School of
Medicine, Atlanta, GA, 30322
- Center for Neurodegenerative Diseases, Emory University
School of Medicine, Atlanta, GA, 30322
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Identification, Quantification, and Site Localization of Protein Posttranslational Modifications via Mass Spectrometry-Based Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:345-382. [PMID: 27975226 DOI: 10.1007/978-3-319-41448-5_17] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Posttranslational modifications (PTMs) are important biochemical processes for regulating various signaling pathways and determining specific cell fate. Mass spectrometry (MS)-based proteomics has been developed extensively in the past decade and is becoming the standard approach for systematic characterization of different PTMs on a global scale. In this chapter, we will explain the biological importance of various PTMs, summarize key innovations in PTMs enrichment strategies, high-performance liquid chromatography (HPLC)-based fractionation approaches, mass spectrometry detection methods, and lastly bioinformatic tools for PTMs related data analysis. With great effort in recent years by the proteomics community, highly efficient enriching methods and comprehensive resources have been developed. This chapter will specifically focus on five major types of PTMs; phosphorylation, glycosylation, ubiquitination/sumosylation, acetylation, and methylation.
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Tong Z, Kim MS, Pandey A, Espenshade PJ. Identification of candidate substrates for the Golgi Tul1 E3 ligase using quantitative diGly proteomics in yeast. Mol Cell Proteomics 2014; 13:2871-82. [PMID: 25078903 DOI: 10.1074/mcp.m114.040774] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Maintenance of protein homeostasis is essential for cellular survival. Central to this regulation are mechanisms of protein quality control in which misfolded proteins are recognized and degraded by the ubiquitin-proteasome system. One well-studied protein quality control pathway requires endoplasmic reticulum (ER)-resident, multi-subunit E3 ubiquitin ligases that function in ER-associated degradation. Using fission yeast, our lab identified the Golgi Dsc E3 ligase as required for proteolytic activation of fungal sterol regulatory element-binding protein transcription factors. The Dsc E3 ligase contains five integral membrane subunits and structurally resembles ER-associated degradation E3 ligases. Saccharomyces cerevisiae codes for homologs of Dsc E3 ligase subunits, including the Dsc1 E3 ligase homolog Tul1 that functions in Golgi protein quality control. Interestingly, S. cerevisiae lacks sterol regulatory element-binding protein homologs, indicating that novel Tul1 E3 ligase substrates exist. Here, we show that the S. cerevisiae Tul1 E3 ligase consists of Tul1, Dsc2, Dsc3, and Ubx3 and define Tul1 complex architecture. Tul1 E3 ligase function required each subunit as judged by vacuolar sorting of the artificial substrate Pep12D. Genetic studies demonstrated that Tul1 E3 ligase was required in cells lacking the multivesicular body pathway and under conditions of ubiquitin depletion. To identify candidate substrates, we performed quantitative diGly proteomics using stable isotope labeling by amino acids in cell culture to survey ubiquitylation in wild-type and tul1Δ cells. We identified 3116 non-redundant ubiquitylation sites, including 10 sites in candidate substrates. Quantitative proteomics found 4.5% of quantified proteins (53/1172) to be differentially expressed in tul1Δ cells. Correcting the diGly dataset for these differences increased the number of Tul1-dependent ubiquitylation sites. Together, our data demonstrate that the Tul1 E3 ligase functions in protein homeostasis under non-stress conditions and support a role in protein quality control. This quantitative diGly proteomics methodology will serve as a robust platform for screening for stress conditions that require Tul1 E3 ligase activity.
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Affiliation(s)
- Zongtian Tong
- From the ‡Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Min-Sik Kim
- §McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Akhilesh Pandey
- §McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; ¶Departments of Biological Chemistry, Oncology and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; ‖Adrienne Helis Malvin Medical Research Foundation, New Orleans, Louisiana 70130; **Diana Helis Henry Medical Research Foundation, New Orleans, Louisiana 70130
| | - Peter J Espenshade
- From the ‡Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
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Abstract
Analysis of proteins and their posttranslational modifications is important for understanding different biological events. For analysis of viral proteomes, an optimal protocol includes production of a highly purified virus that can be investigated with a high-resolving analytical method. In this Methods in Molecular Biology paper we describe a working strategy for how structural proteins in the Adenovirus particle can be studied using liquid chromatography-high-resolving mass spectrometry. This method provides information on the chemical composition of the virus particle. Further, knowledge about amino acids carrying modifications that could be essential for any part of the virus life cycle is collected. We describe in detail alternatives available for preparation of virus for proteome analysis as well as choice of mass spectrometric instrumentation suitable for this kind of analysis.
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Affiliation(s)
- Sara Bergström Lind
- Department of Immunology, Genetics, and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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Hoedt E, Zhang G, Neubert TA. Stable isotope labeling by amino acids in cell culture (SILAC) for quantitative proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:93-106. [PMID: 24952180 DOI: 10.1007/978-3-319-06068-2_5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful approach for high-throughput quantitative proteomics. SILAC allows highly accurate protein quantitation through metabolic encoding of whole cell proteomes using stable isotope labeled amino acids. Since its introduction in 2002, SILAC has become increasingly popular. In this chapter we review the methodology and application of SILAC, with an emphasis on three research areas: dynamics of posttranslational modifications, protein-protein interactions, and protein turnover.
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Affiliation(s)
- Esthelle Hoedt
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 540 First Avenue, New York, NY, 10016, USA
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Kessler BM. Ubiquitin - omics reveals novel networks and associations with human disease. Curr Opin Chem Biol 2013; 17:59-65. [PMID: 23339974 DOI: 10.1016/j.cbpa.2012.12.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 12/18/2012] [Accepted: 12/30/2012] [Indexed: 01/27/2023]
Abstract
Human neurodegenerative and infectious diseases and tumorigenesis are associated with alterations in ubiquitin pathways. Over 10% of the genome encode for genes that either bind or manipulate ubiquitin to affect a large proportion of biological processes. This has been the basis for the development of approaches allowing the enrichment of ubiquitinated proteins for comparisons using proteomics and mass spectrometry. Tools such as tagged tandem ubiquitin binding domains, chemically derivatized ubiquitin or anti-gly-gly-lys antibodies combined with mass spectrometry have contributed to surveys of poly-ubiquitinated proteins, poly-ubiquitin linkage diversity and protein ubiquitination sites and their relation to other posttranslational modifications at a proteome wide level, providing insights in to how dynamic alterations in ubiquitination and deubiquitination steps are associated with normal physiology and pathogenesis.
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Affiliation(s)
- Benedikt M Kessler
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, Roosevelt Drive, University of Oxford, OX3 7BN, UK.
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