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Kaval Oğuz E, Oğuz AR, Özok N, Alkan Z, Ergöz Azizoğlu B, Örgi E, Erdemir AN, Yeşilbaş A. Investigation of the therapeutic effect of melatonin on deltamethrin applied mouse primary hepatocyte culture. Arch Physiol Biochem 2024:1-8. [PMID: 39101831 DOI: 10.1080/13813455.2024.2387696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/31/2024] [Accepted: 07/28/2024] [Indexed: 08/06/2024]
Abstract
OBJECTIVE In recent years, it has been known that the melatonin hormone, secreted from the pineal gland, possesses significant antioxidant activity. This study explores the therapeutic effect of melatonin on the deleterious effects of deltamethrin, a pyrethroid pesticide extensively used worldwide, including in Türkiye, on mouse liver cells. METHODS Hepatocytes from Balb/C mice were isolated using a two-stage perfusion method, resulting in over 85% live hepatocytes. The isolated cells were cultured with different doses of deltamethrin (1 and 10 µM) and melatonin (100 µM) for 24 and 48 hours. At the conclusion of the culture period, hepatocytes were extracted at the 24th and 48th hours, and Malondialdehyde (MDA), Total Antioxidant Capacity (TAC), Total Oxidation Status (TOS), and DNA damages (8-hydroxy-2'-deoxyguanosine (8-OHdG)) were examined. RESULTS While an increase in MDA, TOS, and DNA damage was observed in the deltamethrin-administered groups of hepatocytes, a decrease in TAC level was noted. It was determined that the applied deltamethrin had no effect on cell viability throughout the application period. CONCLUSION Furthermore, it was observed that melatonin, when administered concurrently with deltamethrin, reduced the toxic effect of deltamethrin. This study suggests that melatonin has a protective effect against deltamethrin-induced damage in mouse hepatocyte cells.
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Affiliation(s)
- Elif Kaval Oğuz
- Faculty of Education, Science Education, Van Yüzüncü Yıl University, Van, Türkiye
| | - Ahmet Regaib Oğuz
- Department of Biology, Faculty of Science, Van Yüzüncü Yıl University, Van, Türkiye
| | - Necati Özok
- Department of Biology, Faculty of Science, Van Yüzüncü Yıl University, Van, Türkiye
| | - Zehra Alkan
- Department of Biology, Faculty of Science, Van Yüzüncü Yıl University, Van, Türkiye
| | - Burcu Ergöz Azizoğlu
- Department of Biology, Faculty of Science, Van Yüzüncü Yıl University, Van, Türkiye
| | - Elif Örgi
- Department of Biology, Faculty of Science, Van Yüzüncü Yıl University, Van, Türkiye
| | - Ayşe Nur Erdemir
- Department of Biology, Faculty of Science, Van Yüzüncü Yıl University, Van, Türkiye
| | - Ayşe Yeşilbaş
- Department of Biology, Faculty of Science, Van Yüzüncü Yıl University, Van, Türkiye
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2
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Lim Kam Sian TCC, Sun C, Cain JE, Steele JR, Hanchapola I, Stoychev S, Schittenhelm RB, Faridi P. A Semiautomated Proteomics and Phosphoproteomics Protocol for the Identification of Novel Therapeutic Targets and Predictive Biomarkers in In Vivo Xenograft Models of Pediatric Cancers. Methods Mol Biol 2024; 2806:229-242. [PMID: 38676807 DOI: 10.1007/978-1-0716-3858-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2024]
Abstract
Genomic profiling has identified therapeutic targets for precision treatment of certain cancers, but many patients lack actionable mutations. Additional omics approaches, like proteomics and phosphoproteomics, are essential for comprehensive mapping of cancer-associated molecular phenotypes. In vivo models, such as cell line and patient-derived xenografts (PDX), offer valuable insights into cancer biology and treatment strategies.This chapter presents a semiautomated high-throughput workflow for integrated proteomics and phosphoproteomics analysis on the Kingfish platform coupled with MagReSyn® Zr-IMAC HP. It enhances protein extraction from in vivo xenograft samples and provides better insights into cancers with poor prognosis. The approach successfully identified over 11,000 unique phosphosites and ~6000 proteins in SJSA-1 pediatric osteosarcoma xenografts, demonstrating its efficacy. This workflow is a valuable tool for studying tumor biology and developing precision oncology strategies.
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Affiliation(s)
- Terry C C Lim Kam Sian
- Monash Proteomics and Metabolomics Platform, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Department of Medicine, Sub-Faculty of Clinical and Molecular Medicine, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Christie Sun
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Jason E Cain
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Joel R Steele
- Monash Proteomics and Metabolomics Platform, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Iresha Hanchapola
- Monash Proteomics and Metabolomics Platform, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | | | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Platform, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Pouya Faridi
- Monash Proteomics and Metabolomics Platform, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- Department of Medicine, Sub-Faculty of Clinical and Molecular Medicine, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, Australia.
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia.
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia.
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3
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Claes Z, Bollen M. A split-luciferase lysate-based approach to identify small-molecule modulators of phosphatase subunit interactions. Cell Chem Biol 2023; 30:1666-1679.e6. [PMID: 37625414 DOI: 10.1016/j.chembiol.2023.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/31/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023]
Abstract
An emerging strategy for the therapeutic targeting of protein phosphatases involves the use of compounds that interfere with the binding of regulatory subunits or substrates. However, high-throughput screening strategies for such interfering molecules are scarce. Here, we report on the conversion of the NanoBiT split-luciferase system into a robust assay for the quantification of phosphatase subunit and substrate interactions in cell lysates. The assay is suitable to screen small-molecule libraries for interfering compounds. We designed and validated split-luciferase sensors for a broad range of PP1 and PP2A holoenzymes, including sensors that selectively report on weak interaction sites. To facilitate efficient hit triaging in large-scale screening campaigns, deselection procedures were developed to eliminate assay-interfering molecules with high fidelity. As a proof-of-principle, we successfully applied the split-luciferase screening tool to identify small-molecule disruptors of the interaction between the C-terminus of PP1β and the ankyrin-repeat domain of the myosin-phosphatase targeting subunit MYPT1.
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Affiliation(s)
- Zander Claes
- Laboratory of Biosignaling and Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium
| | - Mathieu Bollen
- Laboratory of Biosignaling and Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium.
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4
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Low TY, Mohtar MA, Lee PY, Omar N, Zhou H, Ye M. WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT. MASS SPECTROMETRY REVIEWS 2021; 40:309-333. [PMID: 32491218 DOI: 10.1002/mas.21636] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Phosphorylation is a form of protein posttranslational modification (PTM) that regulates many biological processes. Whereas phosphoproteomics is a scientific discipline that identifies and quantifies the phosphorylated proteome using mass spectrometry (MS). This task is extremely challenging as ~30% of the human proteome is phosphorylated; and each phosphoprotein may exist as multiple phospho-isoforms that are present in low abundance and stoichiometry. Hence, phosphopeptide enrichment techniques are indispensable to (phospho)proteomics laboratories. These enrichment methods encompass widely-adopted techniques such as (i) affinity-based chromatography; (ii) ion exchange and mixed-mode chromatography (iii) enrichment with phospho-specific antibodies and protein domains, and (iv) functionalized polymers and other less common but emerging technologies such as hydroxyapatite chromatography and precipitation with inorganic ions. Here, we review these techniques, their history, continuous development and evaluation. Besides, we outline associating challenges of phosphoproteomics that are linked to experimental design, sample preparation, and proteolytic digestion. In addition, we also discuss about the future outlooks in phosphoproteomics, focusing on elucidating the noncanonical phosphoproteome and deciphering the "dark phosphoproteome". © 2020 John Wiley & Sons Ltd.
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Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Nursyazwani Omar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Houjiang Zhou
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Centre, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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Humphrey SJ, Karayel O, James DE, Mann M. High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform. Nat Protoc 2019; 13:1897-1916. [PMID: 30190555 DOI: 10.1038/s41596-018-0014-9] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mass spectrometry has transformed the field of cell signaling by enabling global studies of dynamic protein phosphorylation ('phosphoproteomics'). Recent developments are enabling increasingly sophisticated phosphoproteomics studies, but practical challenges remain. The EasyPhos workflow addresses these and is sufficiently streamlined to enable the analysis of hundreds of phosphoproteomes at a depth of >10,000 quantified phosphorylation sites. Here we present a detailed and updated workflow that further ensures high performance in sample-limited conditions while also reducing sample preparation time. By eliminating protein precipitation steps and performing the entire protocol, including digestion, in a single 96-well plate, we now greatly minimize opportunities for sample loss and variability. This results in very high reproducibility and a small sample size requirement (≤200 μg of protein starting material). After cell culture or tissue collection, the protocol takes 1 d, whereas mass spectrometry measurements require ~1 h per sample. Applied to glioblastoma cells acutely treated with epidermal growth factor (EGF), EasyPhos quantified 20,132 distinct phosphopeptides from 200 μg of protein in less than 1 d of measurement time, revealing thousands of EGF-regulated phosphorylation events.
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Affiliation(s)
- Sean J Humphrey
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia. .,The Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.
| | - Ozge Karayel
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David E James
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.,The Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Matthias Mann
- Max Planck Institute of Biochemistry, Martinsried, Germany. .,NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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Goel RK, Meyer M, Paczkowska M, Reimand J, Vizeacoumar F, Vizeacoumar F, Lam TT, Lukong KE. Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates. Proteome Sci 2018; 16:16. [PMID: 30140170 PMCID: PMC6098843 DOI: 10.1186/s12953-018-0143-7] [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: 03/24/2018] [Accepted: 07/19/2018] [Indexed: 01/27/2023] Open
Abstract
Background The non-receptor tyrosine kinase, SRMS (Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites) is a member of the BRK family kinases (BFKs) which represents an evolutionarily conserved relative of the Src family kinases (SFKs). Tyrosine kinases are known to regulate a number of cellular processes and pathways via phosphorylating substrate proteins directly and/or by partaking in signaling cross-talks leading to the indirect modulation of various signaling intermediates. In a previous study, we profiled the tyrosine-phosphoproteome of SRMS and identified multiple candidate substrates of the kinase. The broader cellular signaling intermediates of SRMS are unknown. Methods In order to uncover the broader SRMS-regulated phosphoproteome and identify the SRMS-regulated indirect signaling intermediates, we performed label-free global phosphoproteomics analysis on cells expressing wild-type SRMS. Using computational database searching and bioinformatics analyses we characterized the dataset. Results Our analyses identified 60 hyperphosphorylated (phosphoserine/phosphothreonine) proteins mapped from 140 hyperphosphorylated peptides. Bioinfomatics analyses identified a number of significantly enriched biological and cellular processes among which DNA repair pathways were found to be upregulated while apoptotic pathways were found to be downregulated. Analyses of motifs derived from the upregulated phosphosites identified Casein kinase 2 alpha (CK2α) as one of the major potential kinases contributing to the SRMS-dependent indirect regulation of signaling intermediates. Conclusions Overall, our phosphoproteomics analyses identified serine/threonine phosphorylation dynamics as important secondary events of the SRMS-regulated phosphoproteome with implications in the regulation of cellular and biological processes. Electronic supplementary material The online version of this article (10.1186/s12953-018-0143-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Raghuveera Kumar Goel
- 1Department of Biochemistry, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada
| | - Mona Meyer
- 2Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3 Canada
| | - Marta Paczkowska
- 2Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3 Canada
| | - Jüri Reimand
- 2Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3 Canada.,3Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON M5G 1L7 Canada
| | - Frederick Vizeacoumar
- 4Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Franco Vizeacoumar
- 4Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada.,5Saskatchewan Cancer Agency, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada
| | - TuKiet T Lam
- 6Department of Molecular Biophysics and Biochemistry and MS & Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT USA
| | - Kiven Erique Lukong
- 1Department of Biochemistry, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada
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7
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Wattacheril J, Rose KL, Hill S, Lanciault C, Murray CR, Washington K, Williams B, English W, Spann M, Clements R, Abumrad N, Flynn CR. Non-alcoholic fatty liver disease phosphoproteomics: A functional piece of the precision puzzle. Hepatol Res 2017; 47:1469-1483. [PMID: 28258704 PMCID: PMC5583035 DOI: 10.1111/hepr.12885] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/27/2017] [Accepted: 02/28/2017] [Indexed: 12/24/2022]
Abstract
BACKGROUND Molecular signaling events associated with the necroinflammatory changes in nonalcoholic steatohepatitis (NASH) are not well understood. AIMS To understand the molecular basis of NASH, we evaluated reversible phosphorylation events in hepatic tissue derived from Class III obese subjects by phosphoproteomic means with the aim of highlighting key regulatory pathways that distinguish NASH from non-alcoholic fatty liver disease (also known as simple steatosis; SS). MATERIALS & METHODS Class III obese subjects undergoing bariatric surgery underwent liver biopsy (eight normal patients, eight with simple steatosis, and eight NASH patients). Our strategy was unbiased, comparing global differences in liver protein reversible phosphorylation events across the 24 subjects. RESULTS Of the 3078 phosphorylation sites assigned (2465 phosphoserine, 445 phosphothreonine, 165 phosphotyrosine), 53 were altered by a factor of 2 among cohorts, and of those, 12 were significantly increased or decreased by ANOVA (P < 0.05). DISCUSSION Statistical analyses of canonical signaling pathways identified carbohydrate metabolism and RNA post-transcriptional modification among the most over-represented networks. CONCLUSION Collectively, these results raise the possibility of abnormalities in carbohydrate metabolism as an important trigger for the development of NASH, in parallel with already established abnormalities in lipid metabolism.
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Affiliation(s)
- Julia Wattacheril
- Center for Liver Disease and Transplantation, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, United States of America
| | - Kristie L. Rose
- Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Salisha Hill
- Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Christian Lanciault
- Department of Pathology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Clark R. Murray
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Kay Washington
- Department of Pathology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Brandon Williams
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Wayne English
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Matthew Spann
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Ronald Clements
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Naji Abumrad
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Charles Robb Flynn
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America,Corresponding author: Charles Flynn, PhD, Assistant Professor, Department of Surgery, Vanderbilt University, MRBIV Room 8465A, 2213 Garland Ave, Nashville, TN 37232,
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8
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Rosa-Fernandes L, Rocha VB, Carregari VC, Urbani A, Palmisano G. A Perspective on Extracellular Vesicles Proteomics. Front Chem 2017; 5:102. [PMID: 29209607 PMCID: PMC5702361 DOI: 10.3389/fchem.2017.00102] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/03/2017] [Indexed: 12/15/2022] Open
Abstract
Increasing attention has been given to secreted extracellular vesicles (EVs) in the past decades, especially in the portrayal of their molecular cargo and role as messengers in both homeostasis and pathophysiological conditions. This review presents the state-of-the-art proteomic technologies to identify and quantify EVs proteins along with their PTMs, interacting partners and structural details. The rapid growth of mass spectrometry-based analytical strategies for protein sequencing, PTMs and structural characterization has improved the level of molecular details that can be achieved from limited amount of EVs isolated from different biological sources. Here we will provide a perspective view on the achievements and challenges on EVs proteome characterization using mass spectrometry. A detailed bioinformatics approach will help us to picture the molecular fingerprint of EVs and understand better their pathophysiological function.
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Affiliation(s)
- Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Victória Bombarda Rocha
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Andrea Urbani
- Proteomic and Metabonomic Laboratory, Fondazione Santa Lucia, Rome, Italy.,Institute of Biochemistry and Biochemical Clinic, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Proteomic and Metabonomic Laboratory, Fondazione Santa Lucia, Rome, Italy
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9
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Imperlini E, Gnecchi M, Rognoni P, Sabidò E, Ciuffreda MC, Palladini G, Espadas G, Mancuso FM, Bozzola M, Malpasso G, Valentini V, Palladini G, Orrù S, Ferraro G, Milani P, Perlini S, Salvatore F, Merlini G, Lavatelli F. Proteotoxicity in cardiac amyloidosis: amyloidogenic light chains affect the levels of intracellular proteins in human heart cells. Sci Rep 2017; 7:15661. [PMID: 29142197 PMCID: PMC5688098 DOI: 10.1038/s41598-017-15424-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 10/27/2017] [Indexed: 12/31/2022] Open
Abstract
AL amyloidosis is characterized by widespread deposition of immunoglobulin light chains (LCs) as amyloid fibrils. Cardiac involvement is frequent and leads to life-threatening cardiomyopathy. Besides the tissue alteration caused by fibrils, clinical and experimental evidence indicates that cardiac damage is also caused by proteotoxicity of prefibrillar amyloidogenic species. As in other amyloidoses, the damage mechanisms at cellular level are complex and largely undefined. We have characterized the molecular changes in primary human cardiac fibroblasts (hCFs) exposed in vitro to soluble amyloidogenic cardiotoxic LCs from AL cardiomyopathy patients. To evaluate proteome alterations caused by a representative cardiotropic LC, we combined gel-based with label-free shotgun analysis and performed bioinformatics and data validation studies. To assess the generalizability of our results we explored the effects of multiple LCs on hCF viability and on levels of a subset of cellular proteins. Our results indicate that exposure of hCFs to cardiotropic LCs translates into proteome remodeling, associated with apoptosis activation and oxidative stress. The proteome alterations affect proteins involved in cytoskeletal organization, protein synthesis and quality control, mitochondrial activity and metabolism, signal transduction and molecular trafficking. These results support and expand the concept that soluble amyloidogenic cardiotropic LCs exert toxic effects on cardiac cells.
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Affiliation(s)
- Esther Imperlini
- IRCCS SDN, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Massimiliano Gnecchi
- Coronary Care Unit and Laboratory of Experimental Cardiology for Cell and Molecular Therapy, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Molecular Medicine, Unit of Cardiology, University of Pavia, Pavia, Italy.,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Paola Rognoni
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Eduard Sabidò
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Maria Chiara Ciuffreda
- Coronary Care Unit and Laboratory of Experimental Cardiology for Cell and Molecular Therapy, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giovanni Palladini
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Guadalupe Espadas
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesco Mattia Mancuso
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Margherita Bozzola
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Giuseppe Malpasso
- Coronary Care Unit and Laboratory of Experimental Cardiology for Cell and Molecular Therapy, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Veronica Valentini
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Giuseppina Palladini
- Department of Internal Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Stefania Orrù
- IRCCS SDN, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy.,Department of Movement Sciences, "Parthenope" University, Naples, Italy
| | - Giovanni Ferraro
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Paolo Milani
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Stefano Perlini
- Department of Internal Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate, Naples, Italy. .,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Pavia, Italy.
| | - Giampaolo Merlini
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy.
| | - Francesca Lavatelli
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
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10
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Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtiö J. Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome. Sci Rep 2017; 7:4513. [PMID: 28674419 PMCID: PMC5495806 DOI: 10.1038/s41598-017-04798-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/13/2017] [Indexed: 02/06/2023] Open
Abstract
Protein phosphorylation is involved in the regulation of most eukaryotic cells functions and mass spectrometry-based analysis has made major contributions to our understanding of this regulation. However, low abundance of phosphorylated species presents a major challenge in achieving comprehensive phosphoproteome coverage and robust quantification. In this study, we developed a workflow employing titanium dioxide phospho-enrichment coupled with isobaric labeling by Tandem Mass Tags (TMT) and high-resolution isoelectric focusing (HiRIEF) fractionation to perform in-depth quantitative phosphoproteomics starting with a low sample quantity. To benchmark the workflow, we analyzed HeLa cells upon pervanadate treatment or cell cycle arrest in mitosis. Analyzing 300 µg of peptides per sample, we identified 22,712 phosphorylation sites, of which 19,075 were localized with high confidence and 1,203 are phosphorylated tyrosine residues, representing 6.3% of all detected phospho-sites. HiRIEF fractions with the most acidic isoelectric points are enriched in multiply phosphorylated peptides, which represent 18% of all the phospho-peptides detected in the pH range 2.5–3.7. Cross-referencing with the PhosphoSitePlus database reveals 1,264 phosphorylation sites that have not been previously reported and kinase association analysis suggests that a subset of these may be functional during the mitotic phase.
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Affiliation(s)
- Elena Panizza
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Rui M M Branca
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | | | - Lukas M Orre
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Janne Lehtiö
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
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11
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Grundt K, Thiede B, Østvold AC. Identification of kinases phosphorylating 13 sites in the nuclear, DNA-binding protein NUCKS. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:359-369. [PMID: 28011258 DOI: 10.1016/j.bbapap.2016.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/05/2016] [Accepted: 12/19/2016] [Indexed: 12/27/2022]
Abstract
NUCKS is a vertebrate specific, nuclear and DNA-binding phospho protein. The protein is highly expressed in rapidly dividing cells, and is overexpressed in a number of cancer tissues. The phosphorylation of NUCKS is cell cycle and DNA-damage regulated, but little is known about the responsible kinases. By utilizing in vitro and in vivo phosphorylation assays using isolated NUCKS as well as synthetic NUCKS-derived peptides in combination with mass spectrometry, phosphopeptide mapping, phosphphoamino acid analyses, phosphospecific antibodies and the use of specific kinase inhibitors, we found that NUCKS is phosphorylated on 11 sites by CK2. At least 7 of the CK2 sites are phosphorylated in vivo. We also found that NUCKS is phosphorylated on two sites by ATM kinase and DNA-PK in vitro, and is phosphorylated in vivo by ATM kinase in γ-irradiated cells. All together, we identified three kinases phosphorylating 13 out of 39 in vivo phosphorylated sites in mammalian NUCKS. The identification of CK2 and PIKK kinases as kinases phosphorylating NUCKS in vivo provide further evidence for the involvement of NUCKS in cell cycle control and DNA repair.
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Affiliation(s)
- Kirsten Grundt
- University of Oslo, Institute of Basic Medical Sciences, Department of Biochemistry, P.O. Box 1112, Blindern N-0317, Oslo, Norway
| | - Bernd Thiede
- University of Oslo, Department of Biosciences, P.O. Box 1066, Blindern N-0316, Oslo, Norway
| | - Anne Carine Østvold
- University of Oslo, Institute of Basic Medical Sciences, Department of Biochemistry, P.O. Box 1112, Blindern N-0317, Oslo, Norway.
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12
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Hatano A, Matsumoto M, Nakayama KI. Phosphoproteomics analyses show subnetwork systems in T-cell receptor signaling. Genes Cells 2016; 21:1095-1112. [DOI: 10.1111/gtc.12406] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/02/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Atsushi Hatano
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation; Kyushu University; 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation; Kyushu University; 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Keiichi I. Nakayama
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation; Kyushu University; 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
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13
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Soares NC, Blackburn JM. Mass Spectrometry Targeted Assays as a Tool to Improve Our Understanding of Post-translational Modifications in Pathogenic Bacteria. Front Microbiol 2016; 7:1216. [PMID: 27540373 PMCID: PMC4972818 DOI: 10.3389/fmicb.2016.01216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/21/2016] [Indexed: 01/03/2023] Open
Affiliation(s)
- Nelson C. Soares
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape TownCape Town, South Africa
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14
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Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins. Proc Natl Acad Sci U S A 2016; 113:E3461-7. [PMID: 27247408 DOI: 10.1073/pnas.1603799113] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Absolute values of protein expression levels in cells are crucial information for understanding cellular biological systems. Precise quantification of proteins can be achieved by liquid chromatography (LC)-mass spectrometry (MS) analysis of enzymatic digests of proteins in the presence of isotope-labeled internal standards. Thus, development of a simple and easy way for the preparation of internal standards is advantageous for the analyses of multiple target proteins, which will allow systems-level studies. Here we describe a method, termed MS-based Quantification By isotope-labeled Cell-free products (MS-QBiC), which provides the simple and high-throughput preparation of internal standards by using a reconstituted cell-free protein synthesis system, and thereby facilitates both multiplexed and sensitive quantification of absolute amounts of target proteins. This method was applied to a systems-level dynamic analysis of mammalian circadian clock proteins, which consist of transcription factors and protein kinases that govern central and peripheral circadian clocks in mammals. Sixteen proteins from 20 selected circadian clock proteins were successfully quantified from mouse liver over a 24-h time series, and 14 proteins had circadian variations. Quantified values were applied to detect internal body time using a previously developed molecular timetable method. The analyses showed that single time-point data from wild-type mice can predict the endogenous state of the circadian clock, whereas data from clock mutant mice are not applicable because of the disappearance of circadian variation.
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15
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Frades I, Andreasson E. Phytophthora infestans specific phosphorylation patterns and new putative control targets. Fungal Biol 2016; 120:631-644. [PMID: 27020162 DOI: 10.1016/j.funbio.2016.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/16/2015] [Accepted: 01/06/2016] [Indexed: 11/15/2022]
Abstract
In this study we applied biomathematical searches of gene regulatory mechanisms to learn more about oomycete biology and to identify new putative targets for pesticides or biological control against Phytophthora infestans. First, oomycete phylum-specific phosphorylation motifs were found by discriminative n-gram analysis. We found 11.600 P. infestans specific n-grams, mapping 642 phosphoproteins. The most abundant group among these related to phosphatidylinositol metabolism. Due to the large number of possible targets found and our hypothesis that multi-level control is a sign of usefulness as targets for intervention, we identified overlapping targets with a second screen. This was performed to identify proteins dually regulated by small RNA and phosphorylation. We found 164 proteins to be regulated by both sRNA and phosphorylation and the dominating functions where phosphatidylinositol signalling/metabolism, endocytosis, and autophagy. Furthermore we performed a similar regulatory study and discriminative n-gram analysis of proteins with no clear orthologs in other species and proteins that are known to be unique to P. infestans such as the RxLR effectors, Crinkler (CRN) proteins and elicitins. We identified CRN proteins with specific phospho-motifs present in all life stages. PITG_12626, PITG_14042 and PITG_23175 are CRN proteins that have species-specific phosphorylation motifs and are subject to dual regulation.
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Affiliation(s)
- Itziar Frades
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden.
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden
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16
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Kwon OK, Kim SJ, Lee YM, Lee YH, Bae YS, Kim JY, Peng X, Cheng Z, Zhao Y, Lee S. Global analysis of phosphoproteome dynamics in embryonic development of zebrafish (Danio rerio). Proteomics 2015; 16:136-49. [DOI: 10.1002/pmic.201500017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 09/04/2015] [Accepted: 10/01/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Oh Kwang Kwon
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
| | - Sun Ju Kim
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
| | - You-Mie Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
| | - Young-Hoon Lee
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program); Kyungpook National University; Daegu Korea
| | - Young-Seuk Bae
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program); Kyungpook National University; Daegu Korea
| | - Jin Young Kim
- Mass Spectrometry Research Center; Korea Basic Science Institute; Ochang Chungbuk Republic of Korea
| | - Xiaojun Peng
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd; Hangzhou P. R. China
| | - Zhongyi Cheng
- Advanced Institute of Translational Medicine; Tongji University; Shanghai P. R. China
| | - Yingming Zhao
- Ben May Department for Cancer Research; University of Chicago; Chicago IL USA
| | - Sangkyu Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
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17
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Kwon OK, Sim J, Kim SJ, Sung E, Kim JY, Jeong TC, Lee S. Comprehensive Analysis of in Vivo Phosphoproteome of Mouse Liver Microsomes. J Proteome Res 2015; 14:5215-24. [PMID: 26487105 DOI: 10.1021/acs.jproteome.5b00812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Protein phosphorylation at serine, threonine, and tyrosine residues are some of the most widespread reversible post-translational modifications. Microsomes are vesicle-like bodies, not ordinarily present within living cells, which form from pieces of the endoplasmic reticulum (ER), plasma membrane, mitochondria, or Golgi apparatus of broken eukaryotic cells. Here we investigated the total phosphoproteome of mouse liver microsomes (MLMs) using TiO2 enrichment of phosphopeptides coupled to on-line 2D-LC-MS/MS. In total, 699 phosphorylation sites in 527 proteins were identified in MLMs. When compared with the current phosphoSitePlus database, 155 novel phosphoproteins were identified in MLM. The distributions of phosphosites were 89.4, 8.0, and 2.6% for phosphoserine, phosphotheronine, and phosphotyrosine, respectively. By Motif-X analysis, eight Ser motifs and one Thr motif were found, and five acidic, two basophilic-, and two proline-directed motifs were assigned. The potential functions of phosphoproteins in MLM were assigned by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. In GO annotation, phosphorylated microsomal proteins were involved in mRNA processing, mRNA metabolic processes, and RNA splicing. In the KEGG pathway analysis, phosphorylated microsomal proteins were highly enriched in ribosome protein processing in ER and ribosomes and in RNA transport. Furthermore, we determined that 52 and 23 phosphoproteins were potential substrates of cAMP-dependent protein kinase A and casein kinase II, respectively, many of which are 40S/60S ribosomal proteins. Overall, our results provide an overview of features of protein phosphorylation in MLMs that should be a valuable resource for the future understanding of protein synthesis or translation involving phosphorylation.
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Affiliation(s)
- Oh Kwang Kwon
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University , Daegu 41566, Republic of Korea
| | - JuHee Sim
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University , Daegu 41566, Republic of Korea
| | - Sun Ju Kim
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University , Daegu 41566, Republic of Korea
| | - Eunji Sung
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University , Daegu 41566, Republic of Korea
| | - Jin Young Kim
- Mass Spectrometry Research Center, Korea Basic Science Institute , Ochang, Chungbuk 28115, Republic of Korea
| | - Tae Cheon Jeong
- College of Pharmacy, Yeungnam University , Gyeongsan 38541, Republic of Korea
| | - Sangkyu Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University , Daegu 41566, Republic of Korea
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18
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Noberini R, Uggetti A, Pruneri G, Minucci S, Bonaldi T. Pathology Tissue-quantitative Mass Spectrometry Analysis to Profile Histone Post-translational Modification Patterns in Patient Samples. Mol Cell Proteomics 2015; 15:866-77. [PMID: 26463340 PMCID: PMC4813706 DOI: 10.1074/mcp.m115.054510] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Indexed: 12/18/2022] Open
Abstract
Histone post-translational modifications (hPTMs) generate a complex combinatorial code that has been implicated with various pathologies, including cancer. Dissecting such a code in physiological and diseased states may be exploited for epigenetic biomarker discovery, but hPTM analysis in clinical samples has been hindered by technical limitations. Here, we developed a method (PAThology tissue analysis of Histones by Mass Spectrometry - PAT-H-MS) that allows to perform a comprehensive, unbiased and quantitative MS-analysis of hPTM patterns on formalin-fixed paraffin-embedded (FFPE) samples. In pairwise comparisons, histone extracted from formalin-fixed paraffin-embedded tissues showed patterns similar to fresh frozen samples for 24 differentially modified peptides from histone H3. In addition, when coupled with a histone-focused version of the super-SILAC approach, this method allows the accurate quantification of modification changes among breast cancer patient samples. As an initial application of the PAThology tissue analysis of Histones by Mass Spectrometry method, we analyzed breast cancer samples, revealing significant changes in histone H3 methylation patterns among Luminal A-like and Triple Negative disease subtypes. These results pave the way for retrospective epigenetic studies that combine the power of MS-based hPTM analysis with the extensive clinical information associated with formalin-fixed paraffin-embedded archives.
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Affiliation(s)
- Roberta Noberini
- From the ‡Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy
| | - Andrea Uggetti
- §Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Via Ripamonti 435, 20141 Milano
| | - Giancarlo Pruneri
- §Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Via Ripamonti 435, 20141 Milano; ¶School of Medicine, University of Milan, 20122 Milan, Italy
| | - Saverio Minucci
- ‖Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; **Drug Development Program, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; ‡‡Department of Bioscience, University of Milan, 20133 Milan, Italy
| | - Tiziana Bonaldi
- ‖Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy;
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19
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Study of the activated macrophage transcriptome. Exp Mol Pathol 2015; 99:575-80. [PMID: 26439118 DOI: 10.1016/j.yexmp.2015.09.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 09/30/2015] [Indexed: 11/22/2022]
Abstract
Transcriptome analysis is a powerful modern tool to study possible alterations of gene expression associated with human diseases. It turns out to be especially promising for evaluation of gene expression changes in immunopathology, as immune cells have flexible gene expression patterns that can be switched in response to infection, inflammatory stimuli and exposure to various cytokines. In particular, macrophage polarization towards pro-inflammatory (M1) and anti-inflammatory (M2) phenotypes can be successfully studied using the modern transcriptome analysis approaches. The two mostly used techniques for transcriptome analysis are microarray and next generation sequencing. In this review we will provide an overview of known gene expression changes associated with immunopathology and discuss the advantage and limitations of different methods of transcriptome analysis.
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20
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Frades I, Resjö S, Andreasson E. Comparison of phosphorylation patterns across eukaryotes by discriminative N-gram analysis. BMC Bioinformatics 2015. [PMID: 26224486 PMCID: PMC4520095 DOI: 10.1186/s12859-015-0657-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background How protein phosphorylation relates to kingdom/phylum divergence is largely unknown and the amino acid residues surrounding the phosphorylation site have profound importance on protein kinase–substrate interactions. Standard motif analysis is not adequate for large scale comparative analysis because each phophopeptide is assigned to a unique motif and perform poorly with the unbalanced nature of the input datasets. Results First the discriminative n-grams of five species from five different kingdom/phyla were identified. A signature with 5540 discriminative n-grams that could be found in other species from the same kingdoms/phyla was created. Using a test data set, the ability of the signature to classify species in their corresponding kingdom/phylum was confirmed using classification methods. Lastly, ortholog proteins among proteins with n-grams were identified in order to determine to what degree was the identity of the detected n-grams a property of phosphosites rather than a consequence of species-specific or kingdom/phylum-specific protein inventory. The motifs were grouped in clusters of equal physico-chemical nature and their distribution was similar between species in the same kingdom/phylum while clear differences were found among species of different kingdom/phylum. For example, the animal-specific top discriminative n-grams contained many basic amino acids and the plant-specific motifs were mainly acidic. Secondary structure prediction methods show that the discriminative n-grams in the majority of the cases lack from a regular secondary structure as on average they had 88 % of random coil compared to 66 % found in the phosphoproteins they were derived from. Conclusions The discriminative n-grams were able to classify organisms in their corresponding kingdom/phylum, they show different patterns among species of different kingdom/phylum and these regions can contribute to evolutionary divergence as they are in disordered regions that can evolve rapidly. The differences found possibly reflect group-specific differences in the kinomes of the different groups of species. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0657-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Itziar Frades
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden.
| | - Svante Resjö
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden.
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden.
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21
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Zappacosta F, Scott GF, Huddleston MJ, Annan RS. An Optimized Platform for Hydrophilic Interaction Chromatography–Immobilized Metal Affinity Chromatography Enables Deep Coverage of the Rat Liver Phosphoproteome. J Proteome Res 2015; 14:997-1009. [DOI: 10.1021/pr501025e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Francesca Zappacosta
- Proteomics
and Biological
Mass Spectrometry Laboratory, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Gilbert F. Scott
- Proteomics
and Biological
Mass Spectrometry Laboratory, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Michael J. Huddleston
- Proteomics
and Biological
Mass Spectrometry Laboratory, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Roland S. Annan
- Proteomics
and Biological
Mass Spectrometry Laboratory, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
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22
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Abstract
The family of transmembrane receptor kinase is the largest protein kinase family in Arabidopsis. However many of these kinases have yet uncharacterized functions and little is known about direct substrates of these kinases. Here, we present a large-scale phosphoproteomics method involving label-free quantitation-based comparative phosphopeptide profiling of knockout mutants in receptor-like kinases. This approach, among other physiological and cell biological experiments, is one step in understanding the functional roles of plant kinases in the context of their signaling networks.
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Affiliation(s)
- Xu Na Wu
- Department of Plant Systems Biology, Universität Hohenheim, Fruwirthstraße 12, Stuttgart, 70593, Germany
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23
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St-Germain JR, Taylor P, Zhang W, Li Z, Ketela T, Moffat J, Neel BG, Trudel S, Moran MF. Differential regulation of FGFR3 by PTPN1 and PTPN2. Proteomics 2014; 15:419-33. [PMID: 25311528 DOI: 10.1002/pmic.201400259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 09/04/2014] [Accepted: 10/08/2014] [Indexed: 11/06/2022]
Abstract
Aberrant expression and activation of FGFR3 is associated with disease states including bone dysplasia and malignancies of bladder, cervix, and bone marrow. MS analysis of protein-phosphotyrosine in multiple myeloma cells revealed a prevalent phosphorylated motif, D/EYYR/K, derived from the kinase domain activation loops of tyrosine kinases including FGFR3 corresponding to a recognition sequence of protein-tyrosine phosphatase PTPN1. Knockdown of PTPN1 or the related enzyme PTPN2 by RNAi resulted in ligand-independent activation of FGFR3. Modulation of FGFR3 activation loop phosphorylation by both PTPN1 and PTPN2 was a function of receptor trafficking and phosphotyrosine phosphatase (PTP) compartmentalization. The FGFR3 activation loop motif DYYKK(650) is altered to DYYKE(650) in the oncogenic variant FGFR3(K650E) , and consequently it is constitutively fully activated and unaffected by activation loop phosphorylation. FGFR3(K650E) was nevertheless remarkably sensitive to negative regulation by PTPN1 and PTPN2. This suggests that in addition to modulating FGFR3 phosphorylation, PTPN1 and PTPN2 constrain the kinase domain by fostering an inactive-state. Loss of this constraint in response to ligand or impaired PTPN1/N2 may initiate FGFR3 activation. These results suggest a model wherein PTP expression levels may define conditions that select for ectopic FGFR3 expression and activation during tumorigenesis.
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Affiliation(s)
- Jonathan R St-Germain
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Canada
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24
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A novel toxicogenomics-based approach to categorize (non-)genotoxic carcinogens. Arch Toxicol 2014; 89:2413-27. [DOI: 10.1007/s00204-014-1368-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/04/2014] [Indexed: 10/24/2022]
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25
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Wu X, Sklodowski K, Encke B, Schulze WX. A kinase-phosphatase signaling module with BSK8 and BSL2 involved in regulation of sucrose-phosphate synthase. J Proteome Res 2014; 13:3397-409. [PMID: 24924143 DOI: 10.1021/pr5003164] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
External supply of sucrose to carbon-starved Arabidopsis seedlings induced changes in phosphorylation of Brassinosteroid Signaling Kinase 8 (BSK8) at two different sites. Serine S(20) lies within a phosphorylation hotspot at the N-terminal region of the protein, while S(213) is located within the kinase domain of BSK8. Upon sucrose supply phosphorylation of BSK8(S20) and BSK8(S213) showed opposite behavior with increasing phosphorylation of S(213) and decreased phosphorylation of S(20) at 5 min after sucrose supply. Here we aim to systematically analyze the effects of BSK8 mutations on downstream cellular regulatory events and characterize molecular functions of BSK8 and its phosphorylation. Comparative phosphoproteomic profiling of a bsk8 knockout mutant and wild type revealed potential targets in sucrose metabolism. Activity of sucrose-phosphate synthase (SPS) was decreased by phosphorylation at S(152), and SPS phosphorylation inversely correlated with sucrose-induced BSK8 activity. Furthermore, BSK8 was found to interact with BSL2, a Kelch-type phosphatase. On the basis of a combination of kinase activity measurements, SPS activity assays, and phosphorylation site mutations in BSK8 at S(20) and S(213), we conclude that regulation of SPS by BSK8 occurs through activation of a phosphatase that in turn may dephosphorylate SPS and thus activates the enzyme.
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Affiliation(s)
- XuNa Wu
- Max Planck Institute for Molecular Plant Physiology , Am Mühlenberg 1, 14476 Golm, Germany
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26
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Sjoelund V, Smelkinson M, Nita-Lazar A. Phosphoproteome profiling of the macrophage response to different toll-like receptor ligands identifies differences in global phosphorylation dynamics. J Proteome Res 2014; 13:5185-97. [PMID: 24941444 PMCID: PMC4227906 DOI: 10.1021/pr5002466] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Toll-like
receptors (TLRs) are among the first sensors that detect
infection and drive immune response. Macrophages encountering a pathogen
are usually stimulated not by one TLR, but by a combination of TLRs
engaged by distinct microbe ligands. To understand the integrated
signaling under complex conditions, we investigated the differences
in the phosphoprotein signaling cascades triggered by TLR2, TLR4,
and TLR7 ligands using a single responding cell population. We performed
a global, quantitative, early poststimulation kinetic analysis of
the mouse macrophage phosphoproteome using stable isotope labeling
with amino acids coupled to phosphopeptide enrichment and high-resolution
mass spectrometry. For each TLR ligand, we found marked elevation
of phosphorylation of cytoskeleton components, GTPases of the Rho
family, and phospholipase C signaling pathway proteins. Phosphorylation
of proteins involved in phagocytosis was only seen in response to
TLR2 and TLR4 but not to TLR7 activation. Changes in the phosphorylation
of proteins involved in endocytosis were delayed in response to TLR2
as compared to TLR4 ligands. These findings reveal that the phosphoproteomic
response to stimulation of distinct TLRs varies both in the major
modification targets and the phosphorylation dynamics. These results
advance the understanding of how macrophages sense and respond to
a diverse set of TLR stimuli.
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Affiliation(s)
- Virginie Sjoelund
- Laboratory of Systems Biology, and §Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
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27
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Deroyer C, Rénert AF, Merville MP, Fillet M. New role for EMD (emerin), a key inner nuclear membrane protein, as an enhancer of autophagosome formation in the C16-ceramide autophagy pathway. Autophagy 2014; 10:1229-40. [PMID: 24819607 DOI: 10.4161/auto.28777] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
To date, precise roles of EMD (emerin) remain poorly described. In this paper, we investigated the role of EMD in the C16-ceramide autophagy pathway. Ceramides are bioactive signaling molecules acting notably in the regulation of cell growth, differentiation, or cell death. However, the mechanisms by which they mediate these pathways are not fully understood. We found that C16-ceramide induces EMD phosphorylation on its LEM domain through PRKACA. Upon ceramide treatment, phosphorylated EMD binds MAP1LC3B leading to an increase of autophagosome formation. These data suggest a new role of EMD as an enhancer of autophagosome formation in the C16-ceramide autophagy pathway in colon cancer cells.
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Affiliation(s)
- Céline Deroyer
- GIGA-R Proteomic Unit; University of Liège; Liège, Belgium
| | | | - Marie-Paule Merville
- Department of Clinical Chemistry; Centre Hospitalier Universitaire de Liège; Liège, Belgium
| | - Marianne Fillet
- GIGA-R Proteomic Unit; University of Liège; Liège, Belgium; Department of Analytical Pharmaceutical Chemistry; Department of Pharmacy; Centre Interfacultaire de Recherche du Médicament; University of Liège; Liège, Belgium
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Kwon OK, Sim J, Yun KN, Kim JY, Lee S. Global Phosphoproteomic Analysis of Daphnia pulex Reveals Evolutionary Conservation of Ser/Thr/Tyr Phosphorylation. J Proteome Res 2014; 13:1327-35. [DOI: 10.1021/pr400911x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Oh Kwang Kwon
- College
of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - JuHee Sim
- College
of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Ki Na Yun
- Mass
Spectrometry Research Center, Korea Basic Science Institute, Ochang, Chungbuk 363-883, Republic of Korea
| | - Jin Young Kim
- Mass
Spectrometry Research Center, Korea Basic Science Institute, Ochang, Chungbuk 363-883, Republic of Korea
| | - Sangkyu Lee
- College
of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 702-701, Republic of Korea
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29
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30
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Wiese H, Kuhlmann K, Wiese S, Stoepel NS, Pawlas M, Meyer HE, Stephan C, Eisenacher M, Drepper F, Warscheid B. Comparison of alternative MS/MS and bioinformatics approaches for confident phosphorylation site localization. J Proteome Res 2014; 13:1128-37. [PMID: 24364495 DOI: 10.1021/pr400402s] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Over the past years, phosphoproteomics has advanced to a prime tool in signaling research. Since then, an enormous amount of information about in vivo protein phosphorylation events has been collected providing a treasure trove for gaining a better understanding of the molecular processes involved in cell signaling. Yet, we still face the problem of how to achieve correct modification site localization. Here we use alternative fragmentation and different bioinformatics approaches for the identification and confident localization of phosphorylation sites. Phosphopeptide-enriched fractions were analyzed by multistage activation, collision-induced dissociation and electron transfer dissociation (ETD), yielding complementary phosphopeptide identifications. We further found that MASCOT, OMSSA and Andromeda each identified a distinct set of phosphopeptides allowing the number of site assignments to be increased. The postsearch engine SLoMo provided confident phosphorylation site localization, whereas different versions of PTM-Score integrated in MaxQuant differed in performance. Based on high-resolution ETD and higher collisional dissociation (HCD) data sets from a large synthetic peptide and phosphopeptide reference library reported by Marx et al. [Nat. Biotechnol. 2013, 31 (6), 557-564], we show that an Andromeda/PTM-Score probability of 1 is required to provide an false localization rate (FLR) of 1% for HCD data, while 0.55 is sufficient for high-resolution ETD spectra. Additional analyses of HCD data demonstrated that for phosphotyrosine peptides and phosphopeptides containing two potential phosphorylation sites, PTM-Score probability cutoff values of <1 can be applied to ensure an FLR of 1%. Proper adjustment of localization probability cutoffs allowed us to significantly increase the number of confident sites with an FLR of <1%.Our findings underscore the need for the systematic assessment of FLRs for different score values to report confident modification site localization.
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Affiliation(s)
- Heike Wiese
- Faculty of Biology, Functional Proteomics, University of Freiburg , 79104 Freiburg, Germany
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31
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Tian M, Chen X, Xiong Q, Xiong J, Xiao C, Ge F, Yang F, Miao W. Phosphoproteomic analysis of protein phosphorylation networks in Tetrahymena thermophila, a model single-celled organism. Mol Cell Proteomics 2013; 13:503-19. [PMID: 24200585 DOI: 10.1074/mcp.m112.026575] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Tetrahymena thermophila is a widely used unicellular eukaryotic model organism in biological research and contains more than 1000 protein kinases and phosphatases with specificity for Ser/Thr/Tyr residues. However, only a few dozen phosphorylation sites in T. thermophila are known, presenting a major obstacle to further understanding of the regulatory roles of reversible phosphorylation in this organism. In this study, we used high-accuracy mass-spectrometry-based proteomics to conduct global and site-specific phosphoproteome profiling of T. thermophila. In total, 1384 phosphopeptides and 2238 phosphorylation sites from 1008 T. thermophila proteins were identified through the combined use of peptide prefractionation, TiO2 enrichment, and two-dimensional LC-MS/MS analysis. The identified phosphoproteins are implicated in the regulation of various biological processes such as transport, gene expression, and mRNA metabolic process. Moreover, integrated analysis of the T. thermophila phosphoproteome and gene network revealed the potential biological functions of many previously unannotated proteins and predicted some putative kinase-substrate pairs. Our data provide the first global survey of phosphorylation in T. thermophila using a phosphoproteomic approach and suggest a wide-ranging regulatory scope of this modification. The provided dataset is a valuable resource for the future understanding of signaling pathways in this important model organism.
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Affiliation(s)
- Miao Tian
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
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32
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Hao P, Ren Y, Tam JP, Sze SK. Correction of Errors in Tandem Mass Spectrum Extraction Enhances Phosphopeptide Identification. J Proteome Res 2013; 12:5548-57. [DOI: 10.1021/pr4004486] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Piliang Hao
- School of Biological Sciences and ‡Singapore Centre
on Environmental Life Sciences
Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Yan Ren
- School of Biological Sciences and ‡Singapore Centre
on Environmental Life Sciences
Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - James P. Tam
- School of Biological Sciences and ‡Singapore Centre
on Environmental Life Sciences
Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Siu Kwan Sze
- School of Biological Sciences and ‡Singapore Centre
on Environmental Life Sciences
Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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33
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Wu XN, Sanchez Rodriguez C, Pertl-Obermeyer H, Obermeyer G, Schulze WX. Sucrose-induced receptor kinase SIRK1 regulates a plasma membrane aquaporin in Arabidopsis. Mol Cell Proteomics 2013; 12:2856-73. [PMID: 23820729 PMCID: PMC3790296 DOI: 10.1074/mcp.m113.029579] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 06/30/2013] [Indexed: 11/06/2022] Open
Abstract
The transmembrane receptor kinase family is the largest protein kinase family in Arabidopsis, and it contains the highest fraction of proteins with yet uncharacterized functions. Here, we present functions of SIRK1, a receptor kinase that was previously identified with rapid transient phosphorylation after sucrose resupply to sucrose-starved seedlings. SIRK1 was found to be an active kinase with increasing activity in the presence of an external sucrose supply. In sirk1 T-DNA insertional mutants, the sucrose-induced phosphorylation patterns of several membrane proteins were strongly reduced; in particular, pore-gating phosphorylation sites in aquaporins were affected. SIRK1-GFP fusions were found to directly interact with aquaporins in affinity pull-down experiments on microsomal membrane vesicles. Furthermore, protoplast swelling assays of sirk1 mutants and SIRK1-GFP expressing lines confirmed a direct functional interaction of receptor kinase SIRK1 and aquaporins as substrates for phosphorylation. A lack of SIRK1 expression resulted in the failure of mutant protoplasts to control water channel activity upon changes in external sucrose concentrations. We propose that SIRK1 is involved in the regulation of sucrose-specific osmotic responses through direct interaction with and activation of an aquaporin via phosphorylation and that the duration of this response is controlled by phosphorylation-dependent receptor internalization.
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Affiliation(s)
- Xu Na Wu
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm, Germany
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34
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Pozo-Guisado E, Martin-Romero FJ. The regulation of STIM1 by phosphorylation. Commun Integr Biol 2013; 6:e26283. [PMID: 24505502 PMCID: PMC3914909 DOI: 10.4161/cib.26283] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 08/27/2013] [Indexed: 12/31/2022] Open
Abstract
Calcium ion (Ca(2+)) concentration plays a key role in cell signaling in eukaryotic cells. At the cellular level, Ca(2+) directly participates in such diverse cellular events as adhesion and migration, differentiation, contraction, secretion, synaptic transmission, fertilization, and cell death. As a consequence of these diverse actions, the cytosolic concentration of free Ca(2+) is tightly regulated by the coordinated activity of Ca(2+) channels, Ca(2+) pumps, and Ca(2+)-binding proteins. Although many of these regulators have been studied in depth, other proteins have been described recently, and naturally far less is known about their contribution to cell physiology. Within this last group of proteins, STIM1 has emerged as a major contributor to Ca(2+) signaling by means of its activity as Ca(2+) channel regulator. STIM1 is a protein resident mainly, but not exclusively, in the endoplasmic reticulum (ER), and activates a set of plasma membrane Ca(2+) channels termed store-operated calcium channels (SOCs) when the concentration of free Ca(2+) within the ER drops transiently as a result of Ca(2+) release from this compartment. Knowledge regarding the molecular architecture of STIM1 has grown considerably during the last years, and several structural domains within STIM1 have been reported to be required for the specific molecular interactions with other important players in Ca(2+) signaling, such as Ca(2+) channels and microtubules. Within the modulators of STIM1, phosphorylation has been shown to both activate and inactivate STIM1-dependent Ca(2+) entry depending on the cell type, cell cycle phase, and the specific residue that becomes modified. Here we shall review current knowledge regarding the modulation of STIM1 by phosphorylation.
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Affiliation(s)
- Eulalia Pozo-Guisado
- Department of Biochemistry and Molecular Biology; School of Life Sciences; University of Extremadura; Badajoz, Spain
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35
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Popovic M, Zlatev V, Hodnik V, Anderluh G, Felli IC, Pongor S, Pintar A. Flexibility of the PDZ-binding motif in the micelle-bound form of Jagged-1 cytoplasmic tail. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1818:1706-16. [PMID: 22465068 DOI: 10.1016/j.bbamem.2012.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 01/07/2023]
Abstract
Human Jagged-1, one of the ligands of Notch receptors, is a transmembrane protein composed of a large extracellular region and a 125-residue cytoplasmic tail which bears a C-terminal PDZ recognition motif. To investigate the interaction between Jagged-1 cytoplasmic tail and the inner leaflet of the plasma membrane we determined, by solution NMR, the secondary structure and dynamics of the recombinant protein corresponding to the intracellular region of Jagged-1, J1_tmic, bound to negatively charged lysophospholipid micelles. NMR showed that the PDZ binding motif is preceded by four alpha-helical segments and that, despite the extensive interaction between J1_tmic and the micelle, the PDZ binding motif remains highly flexible. Binding of J1_tmic to negatively charged, but not to zwitterionic vesicles, was confirmed by surface plasmon resonance. To study the PDZ binding region in more detail, we prepared a peptide corresponding to the last 24 residues of Jagged-1, J1C24, and different phosphorylated variants of it. J1C24 displays a marked helical propensity and undergoes a coil-helix transition in the presence of negatively charged, but not zwitterionic, lysophospholipid micelles. Phosphorylation at different positions drastically decreases the helical propensity of the peptides and abolishes the coil-helix transition triggered by lysophospholipid micelles. We propose that phosphorylation of residues upstream of the PDZ binding motif may shift the equilibrium from an ordered, membrane-bound, interfacial form of Jagged-1 C-terminal region to a more disordered form with an increased accessibility of the PDZ recognition motif, thus playing an indirect role in the interaction between Jagged-1 and the PDZ-containing target protein.
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Affiliation(s)
- Matija Popovic
- International Centre for Genetic Engineering and Biotechnology, AREA Science Park Padriciano 99, 1-34149 Trieste, Italy
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36
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Jünger MA, Aebersold R. Mass spectrometry-driven phosphoproteomics: patterning the systems biology mosaic. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2013; 3:83-112. [PMID: 24902836 DOI: 10.1002/wdev.121] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein phosphorylation is the best-studied posttranslational modification and plays a role in virtually every biological process. Phosphoproteomics is the analysis of protein phosphorylation on a proteome-wide scale, and mainly uses the same instrumentation and analogous strategies as conventional mass spectrometry (MS)-based proteomics. Measurements can be performed either in a discovery-type, also known as shotgun mode, or in a targeted manner which monitors a set of a priori known phosphopeptides, such as members of a signal transduction pathway, across biological samples. Here, we delineate the different experimental levels at which measures can be taken to optimize the scope, reliability, and information content of phosphoproteomic analyses. Various chromatographic and chemical protocols exist to physically enrich phosphopeptides from proteolytic digests of biological samples. Subsequent mass spectrometric analysis revolves around peptide ion fragmentation to generate sequence information and identify the backbone sequence of phosphopeptides as well as the phosphate group attachment site(s), and different modes of fragmentation like collision-induced dissociation (CID), electron transfer dissociation (ETD), and higher energy collisional dissociation (HCD) have been established for phosphopeptide analysis. Computational tools are important for the identification and quantification of phosphopeptides and mapping of phosphorylation sites, the deposition of large-scale phosphoproteome datasets in public databases, and the extraction of biologically meaningful information by data mining, integration with other data types, and descriptive or predictive modeling. Finally, we discuss how orthogonal experimental approaches can be employed to validate newly identified phosphorylation sites on a biochemical, mechanistic, and physiological level.
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Affiliation(s)
- Martin A Jünger
- Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
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37
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Gauss GH, Kleven MD, Sendamarai AK, Fleming MD, Lawrence CM. The crystal structure of six-transmembrane epithelial antigen of the prostate 4 (Steap4), a ferri/cuprireductase, suggests a novel interdomain flavin-binding site. J Biol Chem 2013; 288:20668-82. [PMID: 23733181 DOI: 10.1074/jbc.m113.479154] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Steap4 is a cell surface metalloreductase linked to obesity-associated insulin resistance. Initial characterization of its cell surface metalloreductase activity has been reported, but thorough biochemical characterization of this activity is lacking. Here, we report detailed kinetic analysis of the Steap4 cell surface metalloreductase activities. Steap4 shows physiologically relevant Km values for both Fe(3+) and Cu(2+) and retains activity at acidic pH, suggesting it may also function within intracellular organelles to reduce these metals. Flavin-dependent NADPH oxidase activity that was much greater than the equivalent Steap3 construct was observed for the isolated N-terminal oxidoreductase domain. The crystal structure of the Steap4 oxidoreductase domain was determined, providing a structural explanation for these differing activities. Structure-function work also suggested Steap4 utilizes an interdomain flavin-binding site to shuttle electrons between the oxidoreductase and transmembrane domains, and it showed that the disordered N-terminal residues do not contribute to enzymatic activity.
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Affiliation(s)
- George H Gauss
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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38
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Phosphoproteome dynamics reveal novel ERK1/2 MAP kinase substrates with broad spectrum of functions. Mol Syst Biol 2013; 9:669. [PMID: 23712012 PMCID: PMC4188273 DOI: 10.1038/msb.2013.25] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 04/18/2013] [Indexed: 01/23/2023] Open
Abstract
The ERK1/2 MAP kinase pathway is an evolutionarily conserved signaling module that controls many fundamental physiological processes. Deregulated activity of ERK1/2 MAP kinases is associated with developmental syndromes and several human diseases. Despite the importance of this pathway, a comprehensive picture of the natural substrate repertoire and biochemical mechanisms regulated by ERK1/2 is still lacking. In this study, we used large-scale quantitative phosphoproteomics and bioinformatics analyses to identify novel candidate ERK1/2 substrates based on their phosphorylation signature and kinetic profiles in epithelial cells. We identified a total of 7936 phosphorylation sites within 1861 proteins, of which 155 classify as candidate ERK1/2 substrates, including 128 new targets. Candidate ERK1/2 substrates are involved in diverse cellular processes including transcriptional regulation, chromatin remodeling, RNA splicing, cytoskeleton dynamics, cellular junctions and cell signaling. Detailed characterization of one newly identified substrate, the transcriptional regulator JunB, revealed that ERK1/2 phosphorylate JunB on a serine adjacent to the DNA-binding domain, resulting in increased DNA-binding affinity and transcriptional activity. Our study expands the spectrum of cellular functions controlled by ERK1/2 kinases.
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39
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Soares NC, Spät P, Krug K, Macek B. Global dynamics of the Escherichia coli proteome and phosphoproteome during growth in minimal medium. J Proteome Res 2013; 12:2611-21. [PMID: 23590516 DOI: 10.1021/pr3011843] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent phosphoproteomics studies have generated relatively large data sets of bacterial proteins phosphorylated on serine, threonine, and tyrosine, implicating this type of phosphorylation in the regulation of vital processes of a bacterial cell; however, most phosphoproteomics studies in bacteria were so far qualitative. Here we applied stable isotope labeling by amino acids in cell culture (SILAC) to perform a quantitative analysis of proteome and phosphoproteome dynamics of Escherichia coli during five distinct phases of growth in the minimal medium. Combining two triple-SILAC experiments, we detected a total of 2118 proteins and quantified relative dynamics of 1984 proteins in all measured phases of growth, including 570 proteins associated with cell wall and membrane. In the phosphoproteomic experiment, we detected 150 Ser/Thr/Tyr phosphorylation events, of which 108 were localized to a specific amino acid residue and 76 were quantified in all phases of growth. Clustering analysis of SILAC ratios revealed distinct sets of coregulated proteins for each analyzed phase of growth and overrepresentation of membrane proteins in transition between exponential and stationary phases. The proteomics data indicated that proteins related to stress response typically associated with the stationary phase, including RpoS-dependent proteins, had increasing levels already during earlier phases of growth. Application of SILAC enabled us to measure median occupancies of phosphorylation sites, which were generally low (<12%). Interestingly, the phosphoproteome analysis showed a global increase of protein phosphorylation levels in the late stationary phase, pointing to a likely role of this modification in later phases of growth.
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40
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Gnad F, Young A, Zhou W, Lyle K, Ong CC, Stokes MP, Silva JC, Belvin M, Friedman LS, Koeppen H, Minden A, Hoeflich KP. Systems-wide analysis of K-Ras, Cdc42, and PAK4 signaling by quantitative phosphoproteomics. Mol Cell Proteomics 2013; 12:2070-80. [PMID: 23608596 DOI: 10.1074/mcp.m112.027052] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Although K-Ras, Cdc42, and PAK4 signaling are commonly deregulated in cancer, only a few studies have sought to comprehensively examine the spectrum of phosphorylation-mediated signaling downstream of each of these key signaling nodes. In this study, we completed a label-free quantitative analysis of oncogenic K-Ras, activated Cdc42, and PAK4-mediated phosphorylation signaling, and report relative quantitation of 2152 phosphorylated peptides on 1062 proteins. We define the overlap in phosphopeptides regulated by K-Ras, Cdc42, and PAK4, and find that perturbation of these signaling components affects phosphoproteins associated with microtubule depolymerization, cytoskeletal organization, and the cell cycle. These findings provide a resource for future studies to characterize novel targets of oncogenic K-Ras signaling and validate biomarkers of PAK4 inhibition.
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Affiliation(s)
- Florian Gnad
- Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, California 94080, USA.
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41
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Phang HQ, Hoon JL, Lai SK, Zeng Y, Chiam KH, Li HY, Koh CG. POPX2 phosphatase regulates the KIF3 kinesin motor complex. J Cell Sci 2013; 127:727-39. [DOI: 10.1242/jcs.126482] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The kinesin motors are important in the regulation of cellular functions such as protein trafficking, spindle organization and centrosome separation. In this study, we have identified POPX2, a serine-threonine phosphatase, as an interacting partner of the KAP3 subunit of the kinesin-2 motor. The kinesin-2 motor is a heterotrimeric complex composed of KIF3A, KIF3B motor subunits and KAP3, the non-motor subunit, which binds the cargo. Here we report that the phosphatase POPX2 is a negative regulator of the trafficking of N-cadherin and other cargoes; consequently, it markedly influences cell-cell adhesion. POPX2 affects trafficking by determining the phosphorylation status of KIF3A at serine-690. This is consistent with the observation that KIF3A-S690A mutant is defective in cargo trafficking. Our studies also implicate CaMKII as the kinase that phosphorylates KIF3A at serine-690. These results strongly suggest POPX2 and CaMKII as the phosphatase-kinase pair that regulates kinesin-mediated transport and cell-cell adhesion.
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42
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Kim YM, Kim DH. dRAGging amino acid-mTORC1 signaling by SH3BP4. Mol Cells 2013; 35:1-6. [PMID: 23274731 PMCID: PMC3887856 DOI: 10.1007/s10059-013-2249-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 12/04/2012] [Accepted: 12/04/2012] [Indexed: 10/27/2022] Open
Abstract
Mammalian target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth and autophagy. Its activity is regulated by the availability of amino acids and growth factors. The activation of mTORC1 by growth factors, such as insulin and insulin-like growth factor-1 (IGF-1), is mediated by tuberous sclerosis complex (TSC) 1 and 2 and Rheb GTPase. Relative to the growth factor-regulated mTORC1 pathway, the evolutionarily ancient amino acid-mTORC1 pathway remains not yet clearly defined. The amino acid-mTORC1 pathway is mediated by Rag GTPase heterodimers. Several binding proteins of Rag GTPases were discovered in recent studies. Here, we discuss the functions and mechanisms of the newly-identified binders of Rag GTPases. In particular, this review focuses on SH3 binding protein 4 (SH3BP4), the protein recently identifed as a negative regulator of Rag GTPases.
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Affiliation(s)
- Young-Mi Kim
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455,
USA
| | - Do-Hyung Kim
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455,
USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455,
USA
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43
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Hahn B, D'Alessandro LA, Depner S, Waldow K, Boehm ME, Bachmann J, Schilling M, Klingmüller U, Lehmann WD. Cellular ERK phospho-form profiles with conserved preference for a switch-like pattern. J Proteome Res 2012; 12:637-46. [PMID: 23210697 DOI: 10.1021/pr3007232] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ERK is a member of the MAPK pathway with essential functions in cell proliferation, differentiation, and survival. Complete ERK activation by the kinase MEK requires dual phosphorylation at T and Y within the activation motif TEY. We show that exposure of primary mouse hepatocytes to hepatocyte growth factor (HGF) results in phosphorylation at the activation motif, but not of other residues nearby. To determine the relative abundances of unphosphorylated ERK and the three ERK phospho-forms pT, pY, and pTpY, we employed an extended one-source peptide/phosphopeptide standard method in combination with nanoUPLC-MS. This method enabled us to determine the abundances of phospho-forms with a relative variability of ≤5% (SD). We observed a switch-like preference of ERK phospho-form abundances toward the active, doubly phosphorylated and the inactive, unphosphorylated form. Interestingly, ERK phospho-form profiles were similar upon growth factor and cytokine stimulation. A screening of several murine and human cell systems revealed that the balance between TY- and pTpY-ERK is conserved while the abundances of pT- and pY-ERK are more variable within cell types. We show that the phospho-form profiles do not change by blocking MEK activity suggesting that cellular phosphatases determine the ERK phospho-form distribution. This study provides novel quantitative insights into multisite phosphorylation.
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Affiliation(s)
- Bettina Hahn
- Molecular Structure Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
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44
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Li QR, Ning ZB, Yang XL, Wu JR, Zeng R. Complementary workflow for global phosphoproteome analysis. Electrophoresis 2012; 33:3291-8. [DOI: 10.1002/elps.201200124] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 07/26/2012] [Accepted: 09/05/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Qing-Run Li
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai; China
| | - Zhi-Bin Ning
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai; China
| | - Xing-Lin Yang
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai; China
| | - Jia-Rui Wu
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai; China
| | - Rong Zeng
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai; China
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45
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Pham K, Langlais P, Zhang X, Chao A, Zingsheim M, Yi Z. Insulin-stimulated phosphorylation of protein phosphatase 1 regulatory subunit 12B revealed by HPLC-ESI-MS/MS. Proteome Sci 2012; 10:52. [PMID: 22937917 PMCID: PMC3546068 DOI: 10.1186/1477-5956-10-52] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 07/31/2012] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED BACKGROUND Protein phosphatase 1 (PP1) is one of the major phosphatases responsible for protein dephosphorylation in eukaryotes. Protein phosphatase 1 regulatory subunit 12B (PPP1R12B), one of the regulatory subunits of PP1, can bind to PP1cδ, one of the catalytic subunits of PP1, and modulate the specificity and activity of PP1cδ against its substrates. Phosphorylation of PPP1R12B on threonine 646 by Rho kinase inhibits the activity of the PP1c-PPP1R12B complex. However, it is not currently known whether PPP1R12B phosphorylation at threonine 646 and other sites is regulated by insulin. We set out to identify phosphorylation sites in PPP1R12B and to quantify the effect of insulin on PPP1R12B phosphorylation by using high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry. RESULTS 14 PPP1R12B phosphorylation sites were identified, 7 of which were previously unreported. Potential kinases were predicted for these sites. Furthermore, relative quantification of PPP1R12B phosphorylation sites for basal and insulin-treated samples was obtained by using peak area-based label-free mass spectrometry of fragment ions. The results indicate that insulin stimulates the phosphorylation of PPP1R12B significantly at serine 29 (3.02 ± 0.94 fold), serine 504 (11.67 ± 3.33 fold), and serine 645/threonine 646 (2.34 ± 0.58 fold). CONCLUSION PPP1R12B was identified as a phosphatase subunit that undergoes insulin-stimulated phosphorylation, suggesting that PPP1R12B might play a role in insulin signaling. This study also identified novel targets for future investigation of the regulation of PPP1R12B not only in insulin signaling in cell models, animal models, and in humans, but also in other signaling pathways.
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Affiliation(s)
- Kimberly Pham
- Center for Metabolic and Vascular Biology, Arizona State University, Tempe, AZ, USA
| | - Paul Langlais
- Center for Metabolic and Vascular Biology, Arizona State University, Tempe, AZ, USA
| | - Xiangmin Zhang
- Center for Metabolic and Vascular Biology, Arizona State University, Tempe, AZ, USA.,Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy/Health Sciences, Wayne State University, 259 Mack Ave., Detroit, MI, USA
| | - Alex Chao
- Center for Metabolic and Vascular Biology, Arizona State University, Tempe, AZ, USA
| | - Morgan Zingsheim
- Center for Metabolic and Vascular Biology, Arizona State University, Tempe, AZ, USA
| | - Zhengping Yi
- Center for Metabolic and Vascular Biology, Arizona State University, Tempe, AZ, USA.,Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy/Health Sciences, Wayne State University, 259 Mack Ave., Detroit, MI, USA
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Mack HID, Zheng B, Asara JM, Thomas SM. AMPK-dependent phosphorylation of ULK1 regulates ATG9 localization. Autophagy 2012; 8:1197-214. [PMID: 22932492 DOI: 10.4161/auto.20586] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Autophagy is activated in response to a variety of cellular stresses including metabolic stress. While elegant genetic studies in yeast have identified the core autophagy machinery, the signaling pathways that regulate this process are less understood. AMPK is an energy sensing kinase and several studies have suggested that AMPK is required for autophagy. The biochemical connections between AMPK and autophagy, however, have not been elucidated. In this report, we identify a biochemical connection between a critical regulator of autophagy, ULK1, and the energy sensing kinase, AMPK. ULK1 forms a complex with AMPK, and AMPK activation results in ULK1 phosphorylation. Moreover, we demonstrate that the immediate effect of AMPK-dependent phosphorylation of ULK1 results in enhanced binding of the adaptor protein YWHAZ/14-3-3ζ; and this binding alters ULK1 phosphorylation in vitro. Finally, we provide evidence that both AMPK and ULK1 regulate localization of a critical component of the phagophore, ATG9, and that some of the AMPK phosphorylation sites on ULK1 are important for regulating ATG9 localization. Taken together these data identify an ULK1-AMPK signaling cassette involved in regulation of the autophagy machinery.
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Affiliation(s)
- Hildegard I D Mack
- Cancer Biology Program, Division of Hematology/Oncology, Department of Medicine Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
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Cirulli C, Coccetti P, Alberghina L, Tripodi F. A surface-activated chemical ionization approach allows quantitative phosphorylation analysis of the cyclin-dependent kinase inhibitor Sic1 phosphorylated on Ser201. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:1527-1532. [PMID: 22638969 DOI: 10.1002/rcm.6251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RATIONALE Quantitative phosphoproteomics represents a front line for functional proteomics and hence for systems biology. Here we present a new application of the surface-activated chemical ionization (SACI) technology for quantitative phosphoproteomics analysis. The main advantages of SACI-MS technology are high sensitivity, quantitative accuracy and matrix effect reduction, which allow quantitative estimations. METHODS A SACI-MS approach was used to investigate the quantitative in vivo phosphorylation of the cyclin-dependent kinase inhibitor Sic1, a low-abundance protein of Saccharomyces cerevisiae, which is phosphorylated on Ser201 by casein kinase 2 (CK2) and compared its phosphorylation status in cells growing in two different carbon sources (glucose or ethanol). RESULTS Our relative quantification indicated that the Sic1-Ser201 phosphorylation level is about 2-fold higher in ethanol- than in glucose-growing cells, proportional to the Sic1 protein level. This finding is coherent with results of western blot analysis using anti-phospho-Ser201-specific antibody, validating the results obtained with this new SACI approach. CONCLUSIONS The findings presented in this paper indicate that the innovative LC/SACI-MS method, coupled with immunoprecipitation, is a powerful device to obtain quantitative information on the phosphorylation state of low abundance proteins.
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Affiliation(s)
- Claudia Cirulli
- Università degli Studi di Milano-Bicocca, Dipartimento di Biotecnologie e Bioscienze, Piazza della Scienza 2, 20126 Milano, Italy.
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SH3BP4 is a negative regulator of amino acid-Rag GTPase-mTORC1 signaling. Mol Cell 2012; 46:833-46. [PMID: 22575674 DOI: 10.1016/j.molcel.2012.04.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 03/12/2012] [Accepted: 04/05/2012] [Indexed: 11/21/2022]
Abstract
Amino acids stimulate cell growth and suppress autophagy through activation of mTORC1. The activation of mTORC1 by amino acids is mediated by Rag guanosine triphosphatase (GTPase) heterodimers on the lysosome. The molecular mechanism by which amino acids regulate the Rag GTPase heterodimers remains to be elucidated. Here, we identify SH3 domain-binding protein 4 (SH3BP4) as a binding protein and a negative regulator of Rag GTPase complex. SH3BP4 binds to the inactive Rag GTPase complex through its Src homology 3 (SH3) domain under conditions of amino acid starvation and inhibits the formation of active Rag GTPase complex. As a consequence, the binding abrogates the interaction of mTORC1 with Rag GTPase complex and the recruitment of mTORC1 to the lysosome, thus inhibiting amino acid-induced mTORC1 activation and cell growth and promoting autophagy. These results demonstrate that SH3BP4 is a negative regulator of the Rag GTPase complex and amino acid-dependent mTORC1 signaling.
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Nacerddine K, Beaudry JB, Ginjala V, Westerman B, Mattiroli F, Song JY, van der Poel H, Ponz OB, Pritchard C, Cornelissen-Steijger P, Zevenhoven J, Tanger E, Sixma TK, Ganesan S, van Lohuizen M. Akt-mediated phosphorylation of Bmi1 modulates its oncogenic potential, E3 ligase activity, and DNA damage repair activity in mouse prostate cancer. J Clin Invest 2012; 122:1920-32. [PMID: 22505453 DOI: 10.1172/jci57477] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 02/29/2012] [Indexed: 11/17/2022] Open
Abstract
Prostate cancer (PCa) is a major lethal malignancy in men, but the molecular events and their interplay underlying prostate carcinogenesis remain poorly understood. Epigenetic events and the upregulation of polycomb group silencing proteins including Bmi1 have been described to occur during PCa progression. Here, we found that conditional overexpression of Bmi1 in mice induced prostatic intraepithelial neoplasia, and elicited invasive adenocarcinoma when combined with PTEN haploinsufficiency. In addition, Bmi1 and the PI3K/Akt pathway were coactivated in a substantial fraction of human high-grade tumors. We found that Akt mediated Bmi1 phosphorylation, enhancing its oncogenic potential in an Ink4a/Arf-independent manner. This process also modulated the DNA damage response and affected genomic stability. Together, our findings demonstrate the etiological role of Bmi1 in PCa, unravel an oncogenic collaboration between Bmi1 and the PI3K/Akt pathway, and provide mechanistic insights into the modulation of Bmi1 function by phosphorylation during prostate carcinogenesis.
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Affiliation(s)
- Karim Nacerddine
- Division of Molecular Genetics and Center for Biomedical Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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Yan GR, Yin XF, Xiao CL, Tan ZL, Xu SH, He QY. Identification of novel signaling components in genistein-regulated signaling pathways by quantitative phosphoproteomics. J Proteomics 2011; 75:695-707. [DOI: 10.1016/j.jprot.2011.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 09/09/2011] [Accepted: 09/09/2011] [Indexed: 12/27/2022]
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