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Tóth AD, Soltész-Katona E, Kis K, Guti V, Gilzer S, Prokop S, Boros R, Misák Á, Balla A, Várnai P, Turiák L, Ács A, Drahos L, Inoue A, Hunyady L, Turu G. ArreSTick motif controls β-arrestin-binding stability and extends phosphorylation-dependent β-arrestin interactions to non-receptor proteins. Cell Rep 2024; 43:114241. [PMID: 38758647 DOI: 10.1016/j.celrep.2024.114241] [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] [Received: 10/02/2023] [Revised: 03/11/2024] [Accepted: 05/01/2024] [Indexed: 05/19/2024] Open
Abstract
The binding and function of β-arrestins are regulated by specific phosphorylation motifs present in G protein-coupled receptors (GPCRs). However, the exact arrangement of phosphorylated amino acids responsible for establishing a stable interaction remains unclear. We employ a 1D sequence convolution model trained on GPCRs with established β-arrestin-binding properties. With this approach, amino acid motifs characteristic of GPCRs that form stable interactions with β-arrestins can be identified, a pattern that we name "arreSTick." Intriguingly, the arreSTick pattern is also present in numerous non-receptor proteins. Using proximity biotinylation assay and mass spectrometry analysis, we demonstrate that the arreSTick motif controls the interaction between many non-receptor proteins and β-arrestin2. The HIV-1 Tat-specific factor 1 (HTSF1 or HTATSF1), a nuclear transcription factor, contains the arreSTick pattern, and its subcellular localization is influenced by β-arrestin2. Our findings unveil a broader role for β-arrestins in phosphorylation-dependent interactions, extending beyond GPCRs to encompass non-receptor proteins as well.
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Affiliation(s)
- András Dávid Tóth
- Institute of Molecular Life Sciences, Centre of Excellence of the Hungarian Academy of Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok krt. 2., 1117 Budapest, Hungary; Department of Internal Medicine and Haematology, Semmelweis University, Szentkirályi street 46, 1088 Budapest, Hungary
| | - Eszter Soltész-Katona
- Institute of Molecular Life Sciences, Centre of Excellence of the Hungarian Academy of Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok krt. 2., 1117 Budapest, Hungary; Department of Physiology, Semmelweis University, Tűzoltó street 37-47, 1094 Budapest, Hungary
| | - Katalin Kis
- Department of Physiology, Semmelweis University, Tűzoltó street 37-47, 1094 Budapest, Hungary
| | - Viktor Guti
- Department of Physiology, Semmelweis University, Tűzoltó street 37-47, 1094 Budapest, Hungary
| | - Sharon Gilzer
- Department of Physiology, Semmelweis University, Tűzoltó street 37-47, 1094 Budapest, Hungary
| | - Susanne Prokop
- Department of Physiology, Semmelweis University, Tűzoltó street 37-47, 1094 Budapest, Hungary
| | - Roxána Boros
- Department of Physiology, Semmelweis University, Tűzoltó street 37-47, 1094 Budapest, Hungary
| | - Ádám Misák
- Department of Physiology, Semmelweis University, Tűzoltó street 37-47, 1094 Budapest, Hungary
| | - András Balla
- Department of Physiology, Semmelweis University, Tűzoltó street 37-47, 1094 Budapest, Hungary; HUN-REN SE Hungarian Research Network Laboratory of Molecular Physiology, Budapest, Hungary
| | - Péter Várnai
- Department of Physiology, Semmelweis University, Tűzoltó street 37-47, 1094 Budapest, Hungary; HUN-REN SE Hungarian Research Network Laboratory of Molecular Physiology, Budapest, Hungary
| | - Lilla Turiák
- Institute of Organic Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok krt. 2., 1117 Budapest, Hungary
| | - András Ács
- Institute of Organic Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok krt. 2., 1117 Budapest, Hungary
| | - László Drahos
- Institute of Organic Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok krt. 2., 1117 Budapest, Hungary
| | - Asuka Inoue
- Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - László Hunyady
- Institute of Molecular Life Sciences, Centre of Excellence of the Hungarian Academy of Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok krt. 2., 1117 Budapest, Hungary; Department of Physiology, Semmelweis University, Tűzoltó street 37-47, 1094 Budapest, Hungary.
| | - Gábor Turu
- Institute of Molecular Life Sciences, Centre of Excellence of the Hungarian Academy of Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok krt. 2., 1117 Budapest, Hungary; Department of Physiology, Semmelweis University, Tűzoltó street 37-47, 1094 Budapest, Hungary.
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2
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Cyclin-Dependent Kinase-Mediated Phosphorylation of FANCD2 Promotes Mitotic Fidelity. Mol Cell Biol 2021; 41:e0023421. [PMID: 34096775 DOI: 10.1128/mcb.00234-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Fanconi anemia (FA) is a rare genetic disease characterized by increased risk for bone marrow failure and cancer. The FA proteins function together to repair damaged DNA. A central step in the activation of the FA pathway is the monoubiquitination of the FANCD2 and FANCI proteins, which occurs upon exposure to DNA-damaging agents and during the S phase of the cell cycle. The regulatory mechanisms governing S-phase monoubiquitination, in particular, are poorly understood. In this study, we have identified a cyclin-dependent kinase (CDK) regulatory phosphosite (S592) proximal to the site of FANCD2 monoubiquitination. FANCD2 S592 phosphorylation was detected by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and by immunoblotting with an S592 phospho-specific antibody. Mutation of S592 leads to abrogated monoubiquitination of FANCD2 during the S phase. Furthermore, FA-D2 (FANCD2-/-) patient cells expressing S592 mutants display reduced proliferation under conditions of replication stress and increased mitotic aberrations, including micronuclei and multinucleated cells. Our findings describe a novel cell cycle-specific regulatory mechanism for the FANCD2 protein that promotes mitotic fidelity.
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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: 54] [Impact Index Per Article: 18.0] [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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Abstract
Fodrin and its erythroid cell-specific isoform spectrin are actin-associated fibrous proteins that play crucial roles in the maintenance of structural integrity in mammalian cells, which is necessary for proper cell function. Normal cell morphology is altered in diseases such as various cancers and certain neuronal disorders. Fodrin and spectrin are two-chain (αβ) molecules that are encoded by paralogous genes and share many features but also demonstrate certain differences. Fodrin (in humans, typically a heterodimer of the products of the SPTAN1 and SPTBN1 genes) is expressed in nearly all cell types and is especially abundant in neuronal tissues, whereas spectrin (in humans, a heterodimer of the products of the SPTA1 and SPTB1 genes) is expressed almost exclusively in erythrocytes. To fulfill a role in such a variety of different cell types, it was anticipated that fodrin would need to be a more versatile scaffold than spectrin. Indeed, as summarized here, domains unique to fodrin and its regulation by Ca2+, calmodulin, and a variety of posttranslational modifications (PTMs) endow fodrin with additional specific functions. However, how fodrin structural variations and misregulated PTMs may contribute to the etiology of various cancers and neurodegenerative diseases needs to be further investigated.
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Thingholm TE, Rönnstrand L, Rosenberg PA. Why and how to investigate the role of protein phosphorylation in ZIP and ZnT zinc transporter activity and regulation. Cell Mol Life Sci 2020; 77:3085-3102. [PMID: 32076742 PMCID: PMC7391401 DOI: 10.1007/s00018-020-03473-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 01/13/2020] [Accepted: 01/28/2020] [Indexed: 12/20/2022]
Abstract
Zinc is required for the regulation of proliferation, metabolism, and cell signaling. It is an intracellular second messenger, and the cellular level of ionic, mobile zinc is strictly controlled by zinc transporters. In mammals, zinc homeostasis is primarily regulated by ZIP and ZnT zinc transporters. The importance of these transporters is underscored by the list of diseases resulting from changes in transporter expression and activity. However, despite numerous structural studies of the transporters revealing both zinc binding sites and motifs important for transporter function, the exact molecular mechanisms regulating ZIP and ZnT activities are still not clear. For example, protein phosphorylation was found to regulate ZIP7 activity resulting in the release of Zn2+ from intracellular stores leading to phosphorylation of tyrosine kinases and activation of signaling pathways. In addition, sequence analyses predict all 24 human zinc transporters to be phosphorylated suggesting that protein phosphorylation is important for regulation of transporter function. This review describes how zinc transporters are implicated in a number of important human diseases. It summarizes the current knowledge regarding ZIP and ZnT transporter structures and points to how protein phosphorylation seems to be important for the regulation of zinc transporter activity. The review addresses the need to investigate the role of protein phosphorylation in zinc transporter function and regulation, and argues for a pressing need to introduce quantitative phosphoproteomics to specifically target zinc transporters and proteins involved in zinc signaling. Finally, different quantitative phosphoproteomic strategies are suggested.
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Affiliation(s)
- T E Thingholm
- Department of Molecular Medicine, Cancer and Inflammation Research, University of Southern Denmark, J.B. Winsløws Vej 25, 3, 5000, Odense C, Denmark.
| | - L Rönnstrand
- Division of Translational Cancer Research, Lund University, Medicon Village, Building 404, Scheelevägen 2, Lund, Sweden
- Lund Stem Cell Center, Lund University, Medicon Village, Building 404, Scheelevägen 2, Lund, Sweden
- Division of Oncology, Skåne University Hospital, Lund, Sweden
| | - P A Rosenberg
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Neurology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
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6
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Post-Translational Modification and Natural Mutation of TRPC Channels. Cells 2020; 9:cells9010135. [PMID: 31936014 PMCID: PMC7016788 DOI: 10.3390/cells9010135] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/03/2020] [Accepted: 01/03/2020] [Indexed: 02/06/2023] Open
Abstract
Transient Receptor Potential Canonical (TRPC) channels are homologues of Drosophila TRP channel first cloned in mammalian cells. TRPC family consists of seven members which are nonselective cation channels with a high Ca2+ permeability and are activated by a wide spectrum of stimuli. These channels are ubiquitously expressed in different tissues and organs in mammals and exert a variety of physiological functions. Post-translational modifications (PTMs) including phosphorylation, N-glycosylation, disulfide bond formation, ubiquitination, S-nitrosylation, S-glutathionylation, and acetylation play important roles in the modulation of channel gating, subcellular trafficking, protein-protein interaction, recycling, and protein architecture. PTMs also contribute to the polymodal activation of TRPCs and their subtle regulation in diverse physiological contexts and in pathological situations. Owing to their roles in the motor coordination and regulation of kidney podocyte structure, mutations of TRPCs have been implicated in diseases like cerebellar ataxia (moonwalker mice) and focal and segmental glomerulosclerosis (FSGS). The aim of this review is to comprehensively integrate all reported PTMs of TRPCs, to discuss their physiological/pathophysiological roles if available, and to summarize diseases linked to the natural mutations of TRPCs.
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7
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Post-Translational Modifications of the Mini-Chromosome Maintenance Proteins in DNA Replication. Genes (Basel) 2019; 10:genes10050331. [PMID: 31052337 PMCID: PMC6563057 DOI: 10.3390/genes10050331] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/26/2019] [Accepted: 04/26/2019] [Indexed: 12/15/2022] Open
Abstract
The eukaryotic mini-chromosome maintenance (MCM) complex, composed of MCM proteins 2-7, is the core component of the replisome that acts as the DNA replicative helicase to unwind duplex DNA and initiate DNA replication. MCM10 tightly binds the cell division control protein 45 homolog (CDC45)/MCM2-7/ DNA replication complex Go-Ichi-Ni-San (GINS) (CMG) complex that stimulates CMG helicase activity. The MCM8-MCM9 complex may have a non-essential role in activating the pre-replicative complex in the gap 1 (G1) phase by recruiting cell division cycle 6 (CDC6) to the origin recognition complex (ORC). Each MCM subunit has a distinct function achieved by differential post-translational modifications (PTMs) in both DNA replication process and response to replication stress. Such PTMs include phosphorylation, ubiquitination, small ubiquitin-like modifier (SUMO)ylation, O-N-acetyl-D-glucosamine (GlcNAc)ylation, and acetylation. These PTMs have an important role in controlling replication progress and genome stability. Because MCM proteins are associated with various human diseases, they are regarded as potential targets for therapeutic development. In this review, we summarize the different PTMs of the MCM proteins, their involvement in DNA replication and disease development, and the potential therapeutic implications.
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From Synapse to Function: A Perspective on the Role of Neuroproteomics in Elucidating Mechanisms of Drug Addiction. Proteomes 2018; 6:proteomes6040050. [PMID: 30544849 PMCID: PMC6315754 DOI: 10.3390/proteomes6040050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 12/18/2022] Open
Abstract
Drug addiction is a complex disorder driven by dysregulation in molecular signaling across several different brain regions. Limited therapeutic options currently exist for treating drug addiction and related psychiatric disorders in clinical populations, largely due to our incomplete understanding of the molecular pathways that influence addiction pathology. Recent work provides strong evidence that addiction-related behaviors emerge from the convergence of many subtle changes in molecular signaling networks that include neuropeptides (neuropeptidome), protein-protein interactions (interactome) and post-translational modifications such as protein phosphorylation (phosphoproteome). Advancements in mass spectrometry methodology are well positioned to identify these novel molecular underpinnings of addiction and further translate these findings into druggable targets for therapeutic development. In this review, we provide a general perspective of the utility of novel mass spectrometry-based approaches for addressing critical questions in addiction neuroscience, highlighting recent innovative studies that exemplify how functional assessments of the neuroproteome can provide insight into the mechanisms of drug addiction.
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Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.
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Affiliation(s)
- Zoran Minic
- Department of Chemistry and Biomolecular Science, University of Ottawa, John L. Holmes, Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, Room 02, Ottawa, ON K1N 1A2, Canada.
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
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Abe Y, Tada A, Isoyama J, Nagayama S, Yao R, Adachi J, Tomonaga T. Improved phosphoproteomic analysis for phosphosignaling and active-kinome profiling in Matrigel-embedded spheroids and patient-derived organoids. Sci Rep 2018; 8:11401. [PMID: 30061712 PMCID: PMC6065387 DOI: 10.1038/s41598-018-29837-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/04/2018] [Indexed: 11/17/2022] Open
Abstract
Many attempts have been made to reproduce the three-dimensional (3D) cancer behavior. For that purpose, Matrigel, an extracellular matrix from Engelbreth-Holm-Swarm mouse sarcoma cell, is widely used in 3D cancer models such as scaffold-based spheroids and patient-derived organoids. However, severe ion suppression caused by contaminants from Matrigel hampers large-scale phosphoproteomics. In the present study, we successfully performed global phosphoproteomics from Matrigel-embedded spheroids and organoids. Using acetone precipitations of tryptic peptides, we identified more than 20,000 class 1 phosphosites from HCT116 spheroids. Bioinformatic analysis revealed that phosphoproteomic status are significantly affected by the method used for the recovery from the Matrigel, i.e., Dispase or Cell Recovery Solution. Furthermore, we observed the activation of several phosphosignalings only in spheroids and not in adherent cells which are coincident with previous study using 3D culture. Finally, we demonstrated that our protocol enabled us to identify more than 20,000 and nearly 3,000 class 1 phosphosites from 1.4 mg and 150 μg of patient-derived organoid, respectively. Additionally, we were able to quantify phosphosites with high reproducibility (r = 0.93 to 0.95). Our phosphoproteomics protocol is useful for analyzing the phosphosignalings of 3D cancer behavior and would be applied for precision medicine with patient-derived organoids.
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Affiliation(s)
- Yuichi Abe
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan.,Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan
| | - Asa Tada
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan.,Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan
| | - Junko Isoyama
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan.,Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan
| | - Satoshi Nagayama
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 135-8550, Tokyo, Japan
| | - Ryoji Yao
- Division of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 135-8550, Tokyo, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan.,Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan. .,Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan.
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Rhoads SN, Monahan ZT, Yee DS, Shewmaker FP. The Role of Post-Translational Modifications on Prion-Like Aggregation and Liquid-Phase Separation of FUS. Int J Mol Sci 2018; 19:ijms19030886. [PMID: 29547565 PMCID: PMC5877747 DOI: 10.3390/ijms19030886] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 12/13/2022] Open
Abstract
Subcellular mislocalization and aggregation of the human FUS protein occurs in neurons of patients with subtypes of amyotrophic lateral sclerosis and frontotemporal dementia. FUS is one of several RNA-binding proteins that can functionally self-associate into distinct liquid-phase droplet structures. It is postulated that aberrant interactions within the dense phase-separated state can potentiate FUS's transition into solid prion-like aggregates that cause disease. FUS is post-translationally modified at numerous positions, which affect both its localization and aggregation propensity. These modifications may influence FUS-linked pathology and serve as therapeutic targets.
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Affiliation(s)
- Shannon N Rhoads
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
| | - Zachary T Monahan
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
| | - Debra S Yee
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
| | - Frank P Shewmaker
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
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12
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Mcm10: A Dynamic Scaffold at Eukaryotic Replication Forks. Genes (Basel) 2017; 8:genes8020073. [PMID: 28218679 PMCID: PMC5333062 DOI: 10.3390/genes8020073] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/09/2017] [Accepted: 02/09/2017] [Indexed: 12/13/2022] Open
Abstract
To complete the duplication of large genomes efficiently, mechanisms have evolved that coordinate DNA unwinding with DNA synthesis and provide quality control measures prior to cell division. Minichromosome maintenance protein 10 (Mcm10) is a conserved component of the eukaryotic replisome that contributes to this process in multiple ways. Mcm10 promotes the initiation of DNA replication through direct interactions with the cell division cycle 45 (Cdc45)-minichromosome maintenance complex proteins 2-7 (Mcm2-7)-go-ichi-ni-san GINS complex proteins, as well as single- and double-stranded DNA. After origin firing, Mcm10 controls replication fork stability to support elongation, primarily facilitating Okazaki fragment synthesis through recruitment of DNA polymerase-α and proliferating cell nuclear antigen. Based on its multivalent properties, Mcm10 serves as an essential scaffold to promote DNA replication and guard against replication stress. Under pathological conditions, Mcm10 is often dysregulated. Genetic amplification and/or overexpression of MCM10 are common in cancer, and can serve as a strong prognostic marker of poor survival. These findings are compatible with a heightened requirement for Mcm10 in transformed cells to overcome limitations for DNA replication dictated by altered cell cycle control. In this review, we highlight advances in our understanding of when, where and how Mcm10 functions within the replisome to protect against barriers that cause incomplete replication.
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Abstract
Crystal structure determination of an active polycomb repressive complex 2 (PRC2) from a thermophilic fungus, Chaetomium thermophilum, revealed some long-sought structural mechanisms for assembly, catalysis, and regulation of this important enzyme complex, responsible for trimethylation of histone H3K27 (H3K27me3) and silencing of developmentally regulated genes. In light of the crystal structures of the fungal PRC2 captured in the basal and H3K27me3-stimulated states as well as the structural analysis published previously, (1) we examined surface conservation and electrostatic potential distribution to provide additional insights into functional similarity and divergence between the fungal and human PRC2 and for PRC2 binding by nucleic acids. Structure comparison indicated a conformational change of the catalytic SET domain within PRC2 during transition from the inactive to active state. This conserved structural mechanism is also used by another histone methyltransferase family associated with gene activation for enzyme regulation and may underlie the allosteric stimulation of PRC2 as well.
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Affiliation(s)
- Lianying Jiao
- a Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research , Department of Obstetrics and Gynecology , University of Texas Southwestern Medical Center , Dallas , TX , USA.,b Department of Biophysics , University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Xin Liu
- a Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research , Department of Obstetrics and Gynecology , University of Texas Southwestern Medical Center , Dallas , TX , USA.,b Department of Biophysics , University of Texas Southwestern Medical Center , Dallas , TX , USA
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14
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Li XS, Yuan BF, Feng YQ. Recent advances in phosphopeptide enrichment: Strategies and techniques. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Abstract
The comprehensive study of the phosphoproteome is heavily dependent on appropriate enrichment strategies that are most often, but not exclusively, carried out on the peptide level. In this chapter, I give an overview of the most widely used techniques. In addition to dedicated antibodies, phosphopeptides are enriched by their selective interaction with metals in the form of chelated metal ions or metal oxides. The negative charge of the phosphate group is also exploited in a variety of chromatographic fractionation methods that include different types of ion exchange chromatography, hydrophilic interaction chromatography (HILIC), and electrostatic repulsion HILIC (ERLIC) chromatography. Selected examples from the literature will demonstrate how a combination of these techniques with current high-performance mass spectrometry enables the identification of thousands of phosphorylation sites from various sample types.
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Affiliation(s)
- Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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16
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Enrichment of phosphorylated peptides and proteins by selective precipitation methods. Bioanalysis 2015; 7:243-52. [PMID: 25587840 DOI: 10.4155/bio.14.281] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Protein phosphorylation is one of the most prominent post-translational modifications involved in the regulation of cellular processes. Fundamental understanding of biological processes requires appropriate bioanalytical methods for selectively enriching phosphorylated peptides and proteins. Most of the commonly applied enrichment approaches include chromatographic materials including Fe(3+)-immobilized metal-ion affinity chromatography or metal oxides. In the last years, the introduction of several non-chromatographic isolation technologies has increasingly attracted the interest of many scientists. Such approaches are based on the selective precipitation of phosphorylated peptides and proteins by applying various metal cations. The excellent performance of precipitation-based enrichment methods can be explained by the absence of any stationary phase, resin or sorbent, which usually leads to unspecific binding. This review provides an overview of recently published methods for the selective precipitation of phosphorylated peptides and proteins.
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17
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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18
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Torbett BE, Baird A, Eliceiri BP. Understanding the rules of the road: proteomic approaches to interrogate the blood brain barrier. Front Neurosci 2015; 9:70. [PMID: 25788875 PMCID: PMC4349081 DOI: 10.3389/fnins.2015.00070] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/17/2015] [Indexed: 11/13/2022] Open
Abstract
The blood brain barrier (BBB) is often regarded as a passive barrier that protects brain parenchyma from toxic substances, circulating leukocytes, while allowing the passage of selected molecules. Recently, a combination of molecular profiling techniques have characterized the constituents of the BBB based on in vitro models using isolated endothelial cells and ex vivo models analyzing isolated blood vessels. Characterization of gene expression profiles that are specific to the endothelium of brain blood vessels, and the identification of proteins, cells and multi-cellular structure that comprise the BBB have led to a emerging consensus that the BBB is not, in and of itself, a simple barrier of specialized endothelial cells. Instead, regulation of transcytosis, permeability, and drug translocation into the central nervous system is now viewed as a collection of neurovascular units (NVUs) that, together, give the BBB its unique biological properties. We will review recent technology advancing the understanding of the molecular basis of the BBB with a focus on proteomic approaches.
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Affiliation(s)
- Bruce E Torbett
- Molecular and Experimental Medicine, The Scripps Research Institute La Jolla, CA, USA
| | - Andrew Baird
- Department of Surgery, University of California, San Diego San Diego, CA, USA
| | - Brian P Eliceiri
- Department of Surgery, University of California, San Diego San Diego, CA, USA
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19
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Zhang D, Liang Y, Xie Q, Gao G, Wei J, Huang H, Li J, Gao J, Huang C. A novel post-translational modification of nucleolin, SUMOylation at Lys-294, mediates arsenite-induced cell death by regulating gadd45α mRNA stability. J Biol Chem 2015; 290:4784-4800. [PMID: 25561743 PMCID: PMC4335216 DOI: 10.1074/jbc.m114.598219] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 12/30/2014] [Indexed: 11/06/2022] Open
Abstract
Nucleolin is a ubiquitously expressed protein and participates in many important biological processes, such as cell cycle regulation and ribosomal biogenesis. The activity of nucleolin is regulated by intracellular localization and post-translational modifications, including phosphorylation, methylation, and ADP-ribosylation. Small ubiquitin-like modifier (SUMO) is a category of recently verified forms of post-translational modifications and exerts various effects on the target proteins. In the studies reported here, we discovered SUMOylational modification of human nucleolin protein at Lys-294, which facilitated the mRNA binding property of nucleolin by maintaining its nuclear localization. In response to arsenic exposure, nucleolin-SUMO was induced and promoted its binding with gadd45α mRNA, which increased gadd45α mRNA stability and protein expression, subsequently causing GADD45α-mediated cell death. On the other hand, ectopic expression of Mn-SOD attenuated the arsenite-generated superoxide radical level, abrogated nucleolin-SUMO, and in turn inhibited arsenite-induced apoptosis by reducing GADD45α expression. Collectively, our results for the first time demonstrate that nucleolin-SUMO at K294R plays a critical role in its nucleus sequestration and gadd45α mRNA binding activity. This novel biological function of nucleolin is distinct from its conventional role as a proto-oncogene. Therefore, our findings here not only reveal a new modification of nucleolin protein and its novel functional paradigm in mRNA metabolism but also expand our understanding of the dichotomous roles of nucleolin in terms of cancer development, which are dependent on multiple intracellular conditions and consequently the appropriate regulations of its modifications, including SUMOylation.
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Affiliation(s)
- Dongyun Zhang
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, New York 10987 and; Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yuguang Liang
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, New York 10987 and
| | - Qipeng Xie
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Guangxun Gao
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, New York 10987 and
| | - Jinlong Wei
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Haishan Huang
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jingxia Li
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, New York 10987 and
| | - Jimin Gao
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Chuanshu Huang
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, New York 10987 and.
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20
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Zhang H, Amick J, Chakravarti R, Santarriaga S, Schlanger S, McGlone C, Dare M, Nix JC, Scaglione KM, Stuehr DJ, Misra S, Page RC. A bipartite interaction between Hsp70 and CHIP regulates ubiquitination of chaperoned client proteins. Structure 2015; 23:472-482. [PMID: 25684577 DOI: 10.1016/j.str.2015.01.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/24/2014] [Accepted: 01/05/2015] [Indexed: 11/16/2022]
Abstract
The ubiquitin ligase CHIP plays an important role in cytosolic protein quality control by ubiquitinating proteins chaperoned by Hsp70/Hsc70 and Hsp90, thereby targeting such substrate proteins for degradation. We present a 2.91 Å resolution structure of the tetratricopeptide repeat (TPR) domain of CHIP in complex with the α-helical lid subdomain and unstructured tail of Hsc70. Surprisingly, the CHIP-TPR interacts with determinants within both the Hsc70-lid subdomain and the C-terminal PTIEEVD motif of the tail, exhibiting an atypical mode of interaction between chaperones and TPR domains. We demonstrate that the interaction between CHIP and the Hsc70-lid subdomain is required for proper ubiquitination of Hsp70/Hsc70 or Hsp70/Hsc70-bound substrate proteins. Posttranslational modifications of the Hsc70 lid and tail disrupt key contacts with the CHIP-TPR and may regulate CHIP-mediated ubiquitination. Our study shows how CHIP docks onto Hsp70/Hsc70 and defines a bipartite mode of interaction between TPR domains and their binding partners.
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Affiliation(s)
- Huaqun Zhang
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Joseph Amick
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ritu Chakravarti
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Simon Schlanger
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Cameron McGlone
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Michelle Dare
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jay C Nix
- Molecular Biology Consortium, Beamline 4.2.2, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - K Matthew Scaglione
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Dennis J Stuehr
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Saurav Misra
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
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21
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Bekešová S, Komis G, Křenek P, Vyplelová P, Ovečka M, Luptovčiak I, Illés P, Kuchařová A, Šamaj J. Monitoring protein phosphorylation by acrylamide pendant Phos-Tag™ in various plants. FRONTIERS IN PLANT SCIENCE 2015; 6:336. [PMID: 26029234 PMCID: PMC4429547 DOI: 10.3389/fpls.2015.00336] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 04/28/2015] [Indexed: 05/20/2023]
Abstract
The aim of the present study is to rationalize acrylamide pendant Phos-Tag™ in-gel discrimination of phosphorylated and non-phosphorylated plant protein species with standard immunoblot analysis, and optimize sample preparation, efficient electrophoretic separation and transfer. We tested variants of the method including extraction buffers suitable for preservation of phosphorylated protein species in crude extracts from plants and we addressed the importance of the cation (Mn(2+) or Zn(2+)) used in the gel recipe for efficient transfer to PVDF membranes for further immunoblot analysis. We demonstrate the monitoring of Medicago sativa stress-induced mitogen activated protein kinase (SIMK) in stress-treated wild type plants and transgenic SIMKK RNAi line. We further show the hyperosmotically-induced phosphorylation of the previously uncharacterized HvMPK4 of barley. The method is validated using inducible phosphorylation of barley and wheat α-tubulin and of Arabidopsis MPK6. Acrylamide pendant Phos-Tag™offers a flexible tool for studying protein phosphorylation in crops and Arabidopsis circumventing radioactive labeling and the use of phosphorylation specific antibodies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jozef Šamaj
- *Correspondence: Jozef Šamaj, Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Šlechtitelů 27, Olomouc 783 71, Czech Republic
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22
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Yalak G, Vogel V. Ectokinases as novel cancer markers and drug targets in cancer therapy. Cancer Med 2014; 4:404-14. [PMID: 25504773 PMCID: PMC4380966 DOI: 10.1002/cam4.368] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/24/2014] [Accepted: 09/26/2014] [Indexed: 01/13/2023] Open
Abstract
While small-molecule kinase inhibitors became the most prominent anticancer drugs, novel combinatorial strategies need to be developed as the fight against cancer is not yet won. We review emerging literature showing that the release of several ectokinases is significantly upregulated in body fluids from cancer patients and that they leave behind their unique signatures on extracellular matrix (ECM) proteins. Our analysis of proteomic data reveals that fibronectin is heavily phosphorylated in cancer tissues particularly within its growth factor binding sites and on domains that regulate fibrillogenesis. We are thus making the case that cancer is not only a disease of cells but also of the ECM. Targeting extracellular kinases or the extracellular signatures they leave behind might thus create novel opportunities in cancer diagnosis as well as new avenues to interfere with cancer progression and malignancy.
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Affiliation(s)
- Garif Yalak
- Harvard Medical School/Harvard School of Dental Medicine, Department of Developmental Biology, Harvard University, Boston, Massachusetts, 02115; Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, Switzerland
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23
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Marcilla M, Alpízar A, Lombardía M, Ramos-Fernandez A, Ramos M, Albar JP. Increased diversity of the HLA-B40 ligandome by the presentation of peptides phosphorylated at their main anchor residue. Mol Cell Proteomics 2013; 13:462-74. [PMID: 24366607 DOI: 10.1074/mcp.m113.034314] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human leukocyte antigen (HLA) class I molecules bind peptides derived from the intracellular degradation of endogenous proteins and present them to cytotoxic T lymphocytes, allowing the immune system to detect transformed or virally infected cells. It is known that HLA class I-associated peptides may harbor posttranslational modifications. In particular, phosphorylated ligands have raised much interest as potential targets for cancer immunotherapy. By combining affinity purification with high-resolution mass spectrometry, we identified more than 2000 unique ligands bound to HLA-B40. Sequence analysis revealed two major anchor motifs: aspartic or glutamic acid at peptide position 2 (P2) and methionine, phenylalanine, or aliphatic residues at the C terminus. The use of immobilized metal ion and TiO2 affinity chromatography allowed the characterization of 85 phosphorylated ligands. We further confirmed every sequence belonging to this subset by comparing its experimental MS2 spectrum with that obtained upon fragmentation of the corresponding synthetic peptide. Remarkably, three phospholigands lacked a canonical anchor residue at P2, containing phosphoserine instead. Binding assays showed that these peptides bound to HLA-B40 with high affinity. Together, our data demonstrate that the peptidome of a given HLA allotype can be broadened by the presentation of peptides with posttranslational modifications at major anchor positions. We suggest that ligands with phosphorylated residues at P2 might be optimal targets for T-cell-based cancer immunotherapy.
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Affiliation(s)
- Miguel Marcilla
- Proteomics Unit, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain
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24
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Tang S, Bai C, Yang P, Chen X. 14-3-3ε boosts bleomycin-induced DNA damage response by inhibiting the drug-resistant activity of MVP. J Proteome Res 2013; 12:2511-24. [PMID: 23590642 DOI: 10.1021/pr301085c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Major vault protein (MVP) is the predominant constituent of the vault particle, the largest known ribonuclear protein complex. Although emerging evidence have been establishing the links between MVP (vault) and multidrug resistance (MDR), little is known regarding exactly how the MDR activity of MVP is modulated during cellular response to drug-induced DNA damage (DDR). Bleomycin (BLM), an anticancer drug, induces DNA double-stranded breaks (DSBs) and consequently triggers the cellular DDR. Due to its physiological implications in hepatocellular carcinoma (HCC) and cell fate decision, 14-3-3ε was chosen as the pathway-specific bait protein to identify the critical target(s) responsible for HCC MDR. By using an LC-MS/MS-based proteomic approach, MVP was first identified in the BLM-induced 14-3-3ε interactome formed in HCC cells. Biological characterization revealed that MVP possesses specific activity to promote the resistance to the BLM-induced DDR. On the other hand, 14-3-3ε enhances BLM-induced DDR by interacting with MVP. Mechanistic investigation further revealed that 14-3-3ε, in a phosphorylation-dependent manner, binds to the phosphorylated sites at both Thr52 and Ser864 of the monomer of MVP. Consequently, the phosphorylation-dependent binding between 14-3-3ε and MVP inhibits the drug-resistant activity of MVP for an enhanced DDR to BLM treatment. Our findings provide an insight into the mechanism underlying how the BLM-induced interaction between 14-3-3ε and MVP modulates MDR, implicating novel strategy to overcome the chemotherapeutic resistance through interfering specific protein-protein interactions.
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Affiliation(s)
- Siwei Tang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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25
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Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 957] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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26
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Güzel Y, Rainer M, Mirza MR, Messner CB, Bonn GK. Highly selective recovery of phosphopeptides using trypsin-assisted digestion of precipitated lanthanide–phosphoprotein complexes. Analyst 2013; 138:2897-905. [DOI: 10.1039/c3an00066d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Reimand J, Bader GD. Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Mol Syst Biol 2013; 9:637. [PMID: 23340843 PMCID: PMC3564258 DOI: 10.1038/msb.2012.68] [Citation(s) in RCA: 195] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 12/06/2012] [Indexed: 12/20/2022] Open
Abstract
Large-scale cancer genome sequencing has uncovered thousands of gene mutations, but distinguishing tumor driver genes from functionally neutral passenger mutations is a major challenge. We analyzed 800 cancer genomes of eight types to find single-nucleotide variants (SNVs) that precisely target phosphorylation machinery, important in cancer development and drug targeting. Assuming that cancer-related biological systems involve unexpectedly frequent mutations, we used novel algorithms to identify genes with significant phosphorylation-associated SNVs (pSNVs), phospho-mutated pathways, kinase networks, drug targets, and clinically correlated signaling modules. We highlight increased survival of patients with TP53 pSNVs, hierarchically organized cancer kinase modules, a novel pSNV in EGFR, and an immune-related network of pSNVs that correlates with prolonged survival in ovarian cancer. Our findings include multiple actionable cancer gene candidates (FLNB, GRM1, POU2F1), protein complexes (HCF1, ASF1), and kinases (PRKCZ). This study demonstrates new ways of interpreting cancer genomes and presents new leads for cancer research.
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Affiliation(s)
- Jüri Reimand
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Canada
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28
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Yalak G, Vogel V. Extracellular phosphorylation and phosphorylated proteins: not just curiosities but physiologically important. Sci Signal 2012; 5:re7. [PMID: 23250399 DOI: 10.1126/scisignal.2003273] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mining of the literature and high-throughput mass spectrometry data from both healthy and diseased tissues and from body fluids reveals evidence that various extracellular proteins can exist in phosphorylated states. Extracellular kinases and phosphatases (ectokinases and ectophosphatases) are active in extracellular spaces during times of sufficiently high concentrations of adenosine triphosphate. There is evidence for a role of extracellular phosphorylation in various physiological functions, including blood coagulation, immune cell activation, and the formation of neuronal networks. Ectokinase activity is increased in some diseases, including cancer, Alzheimer's disease, and some microbial infections. We summarize the literature supporting the physiological and pathological roles of extracellularly localized protein kinases, protein phosphatases, and phosphorylated proteins and provide an analysis of the available mass spectrometry data to annotate potential extracellular phosphorylated proteins.
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Affiliation(s)
- Garif Yalak
- Department of Health Sciences and Technology, ETH Zurich, Wolfgang Pauli Strasse 10, HCI F443, CH-8093 Zurich, Switzerland
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29
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A novel strategy for phosphopeptide enrichment using lanthanide phosphate co-precipitation. Anal Bioanal Chem 2012; 404:853-62. [DOI: 10.1007/s00216-012-6215-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 06/18/2012] [Accepted: 06/19/2012] [Indexed: 10/28/2022]
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30
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Fonslow BR, Niessen SM, Singh M, Wong CCL, Xu T, Carvalho PC, Choi J, Park SK, Yates JR. Single-step inline hydroxyapatite enrichment facilitates identification and quantitation of phosphopeptides from mass-limited proteomes with MudPIT. J Proteome Res 2012; 11:2697-709. [PMID: 22509746 DOI: 10.1021/pr300200x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein we report the characterization and optimization of single-step inline enrichment of phosphopeptides directly from small amounts of whole cell and tissue lysates (100-500 μg) using a hydroxyapatite (HAP) microcolumn and Multidimensional Protein Identification Technology (MudPIT). In comparison to a triplicate HILIC-IMAC phosphopeptide enrichment study, ∼80% of the phosphopeptides identified using HAP-MudPIT were unique. Similarly, analysis of the consensus phosphorylation motifs between the two enrichment methods illustrates the complementarity of calcium- and iron-based enrichment methods and the higher sensitivity and selectivity of HAP-MudPIT for acidic motifs. We demonstrate how the identification of more multiply phosphorylated peptides from HAP-MudPIT can be used to quantify phosphorylation cooperativity. Through optimization of HAP-MudPIT on a whole cell lysate we routinely achieved identification and quantification of ca. 1000 phosphopeptides from a ∼1 h enrichment and 12 h MudPIT analysis on small quantities of material. Finally, we applied this optimized method to identify phosphorylation sites from a mass-limited mouse brain region, the amygdala (200-500 μg), identifying up to 4000 phosphopeptides per run.
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Affiliation(s)
- Bryan R Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, California 92037, USA
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31
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Güzel Y, Rainer M, Mirza MR, Bonn GK. Highly efficient precipitation of phosphoproteins using trivalent europium, terbium, and erbium ions. Anal Bioanal Chem 2012; 403:1323-31. [DOI: 10.1007/s00216-012-5917-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 02/24/2012] [Accepted: 02/29/2012] [Indexed: 11/29/2022]
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32
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Goel R, Harsha HC, Pandey A, Keshava Prasad TS. Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. MOLECULAR BIOSYSTEMS 2012; 8:453-63. [PMID: 22159132 PMCID: PMC3804167 DOI: 10.1039/c1mb05340j] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human Protein Reference Database (HPRD) is a rich resource of experimentally proven features of human proteins. Protein information in HPRD includes protein-protein interactions, post-translational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization of human proteins. Although, protein-protein interaction data from HPRD has been widely used by the scientific community, its phosphoproteome data has not been exploited to its full potential. HPRD is one of the largest documentations of human phosphoproteins in the public domain. Currently, phosphorylation data in HPRD comprises of 95,016 phosphosites mapped on to 13,041 proteins. Additionally, enzyme-substrate reactions responsible for 5930 phosphorylation events were also documented. Significant improvements in technologies and high-throughput platforms in biomedical investigations led to an exponential increase of biological data and phosphoproteomic data in recent years. Human Proteinpedia, a community annotation portal developed by us, has also contributed to the significant increase in phosphoproteomic data in HPRD. A large number of phosphorylation events have been mapped on to reference sequences available in HPRD and Human Proteinpedia along with associated protein features. This will provide a platform for systems biology approaches to determine the role of protein phosphorylation in protein function, cell signaling, biological processes and their implication in human diseases. This review aims to provide a composite view of phosphoproteomic data pertaining to human proteins in HPRD and Human Proteinpedia.
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Affiliation(s)
- Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India
- Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, 577 451, India
| | - H. C. Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205, Maryland
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, 21205, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, 21205, Maryland
| | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India
- Centre of Excellence in Bioinformatics, Bioinformatics Centre, School of Life Sciences, Pondicherry University, Pondicherry, 605 014, India
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33
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Verma N, Bäuerlein C, Pink M, Rettenmeier AW, Schmitz-Spanke S. Proteome and phosphoproteome of primary cultured pig urothelial cells. Electrophoresis 2011; 32:3600-11. [DOI: 10.1002/elps.201100220] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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34
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Pink M, Verma N, Polato F, Bonn GK, Baba HA, Rettenmeier AW, Schmitz-Spanke S. Precipitation by lanthanum ions: A straightforward approach to isolating phosphoproteins. J Proteomics 2011; 75:375-83. [DOI: 10.1016/j.jprot.2011.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 07/19/2011] [Accepted: 08/03/2011] [Indexed: 12/01/2022]
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35
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Leitner A, Sturm M, Lindner W. Tools for analyzing the phosphoproteome and other phosphorylated biomolecules: a review. Anal Chim Acta 2011; 703:19-30. [PMID: 21843671 DOI: 10.1016/j.aca.2011.07.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 07/07/2011] [Accepted: 07/10/2011] [Indexed: 11/28/2022]
Abstract
Enrichment, separation and mass spectrometric analysis of biomolecules carrying a phosphate group plays an important role in current analytical chemistry. Application areas range from the preparative enrichment of phospholipids for biotechnological purposes and the separation and purification of plasmid DNA or mRNA to the specific preconcentration of phosphoproteins and -peptides to facilitate their later identification and characterization by mass spectrometry. Most of the recent improvements in this field were triggered by the need for phosphopeptide enrichment technology for the analysis of cellular protein phosphorylation events with the help of liquid chromatography-mass spectrometry. The high sensitivity of mass spectrometry and the possibility to combine this technique with different separation modes in liquid chromatography have made it the method of choice for proteome analysis. However, in the case of phosphoprotein analysis, the low abundance of the resulting phosphopeptides and their low quality fragment spectra interfere with the identification of phosphorylation events. Recent developments in phosphopeptide enrichment and fragmentation technologies successfully helped to overcome these limitations. In this review, we will focus on sample preparation techniques in the field of phosphoproteomics, but also highlight recent advancements for the analysis of other phosphorylated biomolecules.
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Pflieger D, Gonnet F, de la Fuente van Bentem S, Hirt H, de la Fuente A. Linking the proteins--elucidation of proteome-scale networks using mass spectrometry. MASS SPECTROMETRY REVIEWS 2011; 30:268-297. [PMID: 21337599 DOI: 10.1002/mas.20278] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 10/05/2009] [Accepted: 10/05/2009] [Indexed: 05/30/2023]
Abstract
Proteomes are intricate. Typically, thousands of proteins interact through physical association and post-translational modifications (PTMs) to give rise to the emergent functions of cells. Understanding these functions requires one to study proteomes as "systems" rather than collections of individual protein molecules. The abstraction of the interacting proteome to "protein networks" has recently gained much attention, as networks are effective representations, that lose specific molecular details, but provide the ability to see the proteome as a whole. Mostly two aspects of the proteome have been represented by network models: proteome-wide physical protein-protein-binding interactions organized into Protein Interaction Networks (PINs), and proteome-wide PTM relations organized into Protein Signaling Networks (PSNs). Mass spectrometry (MS) techniques have been shown to be essential to reveal both of these aspects on a proteome-wide scale. Techniques such as affinity purification followed by MS have been used to elucidate protein-protein interactions, and MS-based quantitative phosphoproteomics is critical to understand the structure and dynamics of signaling through the proteome. We here review the current state-of-the-art MS-based analytical pipelines for the purpose to characterize proteome-scale networks.
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Affiliation(s)
- Delphine Pflieger
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, CNRS UMR 8587, Evry, France
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Rosenqvist H, Ye J, Jensen ON. Analytical strategies in mass spectrometry-based phosphoproteomics. Methods Mol Biol 2011; 753:183-213. [PMID: 21604124 DOI: 10.1007/978-1-61779-148-2_13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Phosphoproteomics, the systematic study of protein phosphorylation events and cell signaling networks in cells and tissues, is a rapidly evolving branch of functional proteomics. Current phosphoproteomics research provides a large toolbox of strategies and protocols that may assist researchers to reveal key regulatory events and phosphorylation-mediated processes in the cell and in whole organisms. We present an overview of sensitive and robust analytical methods for phosphopeptide analysis, including calcium phosphate precipitation and affinity enrichment methods such as IMAC and TiO(2). We then discuss various tandem mass spectrometry approaches for phosphopeptide sequencing and quantification, and we consider aspects of phosphoproteome data analysis and interpretation. Efficient integration of these stages of phosphoproteome analysis is highly important to ensure a successful outcome of large-scale experiments for studies of phosphorylation-mediated protein regulation.
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Affiliation(s)
- Heidi Rosenqvist
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, Scotland, UK
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Harsha HC, Pandey A. Phosphoproteomics in cancer. Mol Oncol 2010; 4:482-95. [PMID: 20937571 DOI: 10.1016/j.molonc.2010.09.004] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 09/20/2010] [Accepted: 09/20/2010] [Indexed: 12/19/2022] Open
Abstract
Reversible protein phosphorylation serves as a basis for regulating a number of cellular processes. Aberrant activation of kinase signaling pathways is commonly associated with several cancers. Recent developments in phosphoprotein/phosphopeptide enrichment strategies and quantitative mass spectrometry have resulted in robust pipelines for high-throughput characterization of phosphorylation in a global fashion. Today, it is possible to profile site-specific phosphorylation events on thousands of proteins in a single experiment. The potential of this approach is already being realized to characterize signaling pathways that govern oncogenesis. In addition, chemical proteomic strategies have been used to unravel targets of kinase inhibitors, which are otherwise difficult to characterize. This review summarizes various approaches used for analysis of the phosphoproteome in general, and protein kinases in particular, highlighting key cancer phosphoproteomic studies.
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Affiliation(s)
- H C Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore, India.
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Rogers LD, Fang Y, Foster LJ. An integrated global strategy for cell lysis, fractionation, enrichment and mass spectrometric analysis of phosphorylated peptides. MOLECULAR BIOSYSTEMS 2010; 6:822-9. [DOI: 10.1039/b915986j] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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40
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The phosphoproteomics data explosion. Curr Opin Chem Biol 2009; 13:414-20. [DOI: 10.1016/j.cbpa.2009.06.022] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 06/24/2009] [Accepted: 06/25/2009] [Indexed: 01/03/2023]
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Lazar IM. Recent advances in capillary and microfluidic platforms with MS detection for the analysis of phosphoproteins. Electrophoresis 2009; 30:262-75. [PMID: 19156662 DOI: 10.1002/elps.200800427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Reversible protein phosphorylation represents a key regulatory mechanism that triggers essential cellular signaling events. The large-scale characterization of protein phosphorylation in a cell represents, therefore, the objective of many biological studies that aim at elucidating the complex signaling pathways that are involved in the progression and/or regression of a disease. The recent implementation of novel MS detection strategies has significantly advanced the capabilities for interrogating the complex cellular phosphoproteome. Simultaneously, the current advent of miniaturized technologies has clearly demonstrated the superior performance of microfluidic instrumentation for bioanalytical and biological applications that cope with speed, sensitivity and throughput-related demands. This review aims at providing an update on the latest developments regarding the interfacing of microfluidic devices with MS detection for exploring the challenging area of phosphoproteomics.
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Affiliation(s)
- Iulia M Lazar
- Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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Yates JR, Ruse CI, Nakorchevsky A. Proteomics by Mass Spectrometry: Approaches, Advances, and Applications. Annu Rev Biomed Eng 2009; 11:49-79. [DOI: 10.1146/annurev-bioeng-061008-124934] [Citation(s) in RCA: 798] [Impact Index Per Article: 53.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- John R. Yates
- Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037;
| | - Cristian I. Ruse
- Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037;
| | - Aleksey Nakorchevsky
- Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037;
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Rogers LD, Foster LJ. Phosphoproteomics--finally fulfilling the promise? MOLECULAR BIOSYSTEMS 2009; 5:1122-9. [PMID: 19756301 DOI: 10.1039/b905580k] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Networks of protein-protein and protein-metabolite interactions are commonly found in biological systems where signals must be passed from one location or component within a cell to another, such as from a receptor on the plasma membrane to a transcription factor in the nucleus. Regulation of such networks, or signal transduction pathways, is often achieved by transient, reversible modification of the components involved. Several types of post-translational modifications of proteins are employed in signal transduction including ubiquitylation of lysines and palmitoylation of cysteines, but by far the best appreciated and apparently the most important involves phosphorylation of serine, threonine and tyrosine residues. Whilst protein phosphorylation has long been recognized as functionally important, low stoichiometry has ultimately impeded global analyses (phosphoproteomics). Recent developments in the application of metal oxide chromatography and advanced mass spectrometric techniques have enabled phosphoproteomics to move beyond mere proof-of-principle experiments, to the stage where it can successfully address complex biological questions. Here we cover the development of phosphopeptide/protein analysis by mass spectrometry and the various techniques used to enrich phosphopeptides/proteins. We also speculate on the future of phosphoproteomic research, now that the goal of generating global phosphoproteomic datasets has been realized.
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Affiliation(s)
- Lindsay D Rogers
- Department of Biochemistry & Molecular Biology, Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
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Boersema PJ, Mohammed S, Heck AJR. Phosphopeptide fragmentation and analysis by mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:861-878. [PMID: 19504542 DOI: 10.1002/jms.1599] [Citation(s) in RCA: 284] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Reversible phosphorylation is a key event in many biological processes and is therefore a much studied phenomenon. The mass spectrometric (MS) analysis of phosphorylation is challenged by the substoichiometric levels of phosphorylation and the lability of the phosphate group in collision-induced dissociation (CID). Here, we review the fragmentation behaviour of phosphorylated peptides in MS and discuss several MS approaches that have been developed to improve and facilitate the analysis of phosphorylated peptides. CID of phosphopeptides typically results in spectra dominated by a neutral loss of the phosphate group. Several proposed mechanisms for this neutral loss and several factors affecting the extent at which this occurs are discussed. Approaches are described to interpret such neutral loss-dominated spectra to identify the phosphopeptide and localize the phosphorylation site. Methods using additional activation, such as MS(3) and multistage activation (MSA), have been designed to generate more sequence-informative fragments from the ion produced by the neutral loss. The characteristics and benefits of these methods are reviewed together with approaches using phosphopeptide derivatization or specific MS scan modes. Additionally, electron-driven dissociation methods by electron capture dissociation (ECD) or electron transfer dissociation (ETD) and their application in phosphopeptide analysis are evaluated. Finally, these techniques are put into perspective for their use in large-scale phosphoproteomics studies.
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Affiliation(s)
- Paul J Boersema
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJR, Mohammed S. Lys-N and Trypsin Cover Complementary Parts of the Phosphoproteome in a Refined SCX-Based Approach. Anal Chem 2009; 81:4493-501. [DOI: 10.1021/ac9004309] [Citation(s) in RCA: 224] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sharon Gauci
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and The Netherlands Proteomics Center
| | - Andreas O. Helbig
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and The Netherlands Proteomics Center
| | - Monique Slijper
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and The Netherlands Proteomics Center
| | - Jeroen Krijgsveld
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and The Netherlands Proteomics Center
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and The Netherlands Proteomics Center
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and The Netherlands Proteomics Center
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Taouatas N, Altelaar AFM, Drugan MM, Helbig AO, Mohammed S, Heck AJ. Strong Cation Exchange-based Fractionation of Lys-N-generated Peptides Facilitates the Targeted Analysis of Post-translational Modifications. Mol Cell Proteomics 2009; 8:190-200. [DOI: 10.1074/mcp.m800285-mcp200] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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