1
|
Mehta V, Decan N, Ooi S, Gaudreau-Lapierre A, Copeland JW, Trinkle-Mulcahy L. SPECC1L binds the myosin phosphatase complex MYPT1/PP1β and can regulate its distribution between microtubules and filamentous actin. J Biol Chem 2023; 299:102893. [PMID: 36634848 PMCID: PMC9929477 DOI: 10.1016/j.jbc.2023.102893] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
The subcellular localization, activity , and substrate specificity of the serine/threonine protein phosphatase 1 catalytic subunit (PP1cat) is mediated through its dynamic association with regulatory subunits in holoenzyme complexes. While some functional overlap is observed for the three human PP1cat isoforms, they also show distinct targeting based on relative preferences for specific regulatory subunits. A well-known example is the preferential association of MYPT1 with PP1β in the myosin phosphatase complex. In smooth muscle, MYPT1/PP1β counteracts the muscle contraction induced by phosphorylation of the light chains of myosin by the myosin light chain kinase. This phosphatase complex is also found in nonmuscle cells, where it is targeted to both myosin and nonmyosin substrates and contributes to regulation of the balance of cytoskeletal structure and motility during cell migration and division. Although it remains unclear how MYPT1/PP1β traffics between microtubule- and actin-associated substrates, our identification of the microtubule- and actin-binding protein SPECC1L in both the PP1β and MYPT1 interactomes suggests that it is the missing link. Our validation of their association using coimmunoprecipitation and proximity biotinylation assays, together with the strong overlap that we observed for the SPECC1L and MYPT1 interactomes, confirmed that they exist in a stable complex in the cell. We further showed that SPECC1L binds MYPT1 directly and that it can impact the balance of the distribution of the MYPT1/PP1β complex between the microtubule and filamentous actin networks.
Collapse
Affiliation(s)
- Virja Mehta
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Nathalie Decan
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Sarah Ooi
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Antoine Gaudreau-Lapierre
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - John W. Copeland
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada
| | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada.
| |
Collapse
|
2
|
Venerando A, Bustos VH, Pinna LA, Cozza G. Editorial: Casein kinases in human diseases. Front Mol Biosci 2022; 9:1094922. [DOI: 10.3389/fmolb.2022.1094922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
|
3
|
Sun C, Zou H, Yang Z, Yang M, Chen X, Huang Y, Fan W, Yuan R. Proteomics and phosphoproteomics analysis of vitreous in idiopathic epiretinal membrane patients. Proteomics Clin Appl 2022; 16:e2100128. [PMID: 35510950 DOI: 10.1002/prca.202100128] [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: 12/11/2021] [Revised: 03/18/2022] [Accepted: 05/02/2022] [Indexed: 12/30/2022]
Abstract
PURPOSE The purpose of the present study was to characterize the idiopathic epiretinal membrane (iERM) through proteomics and phosphoproteomics analysis to facilitate the diagnosis and treatment of iERM. EXPERIMENTAL DESIGN The vitreous of 25 patients with an iERM and 15 patients with an idiopathic macular hole were analyzed by proteomic and phosphoproteomic analysis based on tandem mass tag. PRM was used to verify the differential proteins. RESULTS Proteomic analysis identified a total of 878 proteins, including 50 differential proteins. Tenascin-C, galectin-3-binding protein, glucose-6-phosphate isomerase, neuroserpin, collagen alpha-1(XI) chain, and collagen alpha-1(II) chain were verified to be upregulated in iERM by PRM. Phosphoproteomic analysis identified a total of 401 phosphorylation sites on 213 proteins, including 27 differential phosphorylation sites on 24 proteins. Mitogen-activated protein kinase-activated protein kinase (MAPKAPK)3 and MAPKAPK5 were predicted as the major kinases in the vitreous of iERM. Twenty-six of the differential proteins and phosphorylated proteins may be closely related to fibrosis in iERM. CONCLUSION AND CLINICAL RELEVANCE Our results indicated the potential biomarkers or therapeutic targets for iERM, provided key kinases that may be involved in iERM. Fibrosis plays an essential role in iERM, and further exploration of related differential proteins has important clinical significance.
Collapse
Affiliation(s)
- Chao Sun
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
| | - Huan Zou
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
| | - Zhouquan Yang
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
| | - Mei Yang
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
| | - Xiaofan Chen
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
| | - Yanming Huang
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
| | - Wei Fan
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
| | - Rongdi Yuan
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
| |
Collapse
|
4
|
Nipun VB, Amin KA. Recent Advances in Protein Kinase CK2, a Potential Therapeutic Target in Cancer. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022; 48:919-931. [DOI: 10.1134/s1068162022050144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- V. B. Nipun
- Cancer Research Center, Shantou University Medical Collage, Shantou, Guangdong, 515041, PR China
- Department of Chemistry, Faculty of Science, University of Imam Abdulrahman Bin Faisal university, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - K. A. Amin
- Department of Chemistry, Faculty of Science, University of Imam Abdulrahman Bin Faisal university, P.O. Box 1982, Dammam, 31441, Saudi Arabia
- Basic and Applied Scientific Research Center, Imam Abdulrahman Bin Faisal university, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| |
Collapse
|
5
|
Long Q, Feng L, Li Y, Zuo T, Chang L, Zhang Z, Xu P. Time-resolved quantitative phosphoproteomics reveals cellular responses induced by caffeine and coumarin. Toxicol Appl Pharmacol 2022; 449:116115. [PMID: 35691368 DOI: 10.1016/j.taap.2022.116115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022]
Abstract
Protein phosphorylation is a critical way that cells respond to external signals and environmental stresses. However, the patterns of cellular response to chemicals at different times were largely unknown. Here, we used quantitative phosphoproteomics to analyze the cellular response of kinases and signaling pathways, as well as pattern change of phosphorylated substrates in HepG2 cells that were exposed to caffeine and coumarin for 10 min and 24 h. Comparing the 10 min and 24 h groups, 33 kinases were co-responded and 32 signaling pathways were co-enriched in caffeine treated samples, while 48 kinases and 34 signaling pathways were co-identified in coumarin treated samples. Instead, the percentage of co-identified phosphorylated substrates only accounted for 4.31% and 9.57% between 10 min and 24 h in caffeine and coumarin treated samples, respectively. The results showed that specific chemical exposure led to a bunch of the same kinases and signaling pathways changed in HepG2 cells, while the phosphorylated substrates were different. In addition, it was found that insulin signaling pathway was significantly enriched by both the caffeine and coumarin treatment. The pattern changes in phosphorylation of protein substrates, kinases and signaling pathways with varied chemicals and different time course shed light on the potential mechanism of cellular responses to endless chemical stimulation.
Collapse
Affiliation(s)
- Qi Long
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Lijie Feng
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Yuan Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; School of Medicine, Guizhou University, Guiyang 550025, China
| | - Tao Zuo
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Zhenpeng Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China.
| | - Ping Xu
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; School of Medicine, Guizhou University, Guiyang 550025, China; School of Public Health, China Medical University, Shenyang 110122, China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding 071002, China.
| |
Collapse
|
6
|
Structural Insights into Protein Regulation by Phosphorylation and Substrate Recognition of Protein Kinases/Phosphatases. Life (Basel) 2021; 11:life11090957. [PMID: 34575106 PMCID: PMC8467178 DOI: 10.3390/life11090957] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/05/2021] [Accepted: 09/10/2021] [Indexed: 12/30/2022] Open
Abstract
Protein phosphorylation is one of the most widely observed and important post-translational modification (PTM) processes. Protein phosphorylation is regulated by protein kinases, each of which covalently attaches a phosphate group to an amino acid side chain on a serine (Ser), threonine (Thr), or tyrosine (Tyr) residue of a protein, and by protein phosphatases, each of which, conversely, removes a phosphate group from a phosphoprotein. These reversible enzyme activities provide a regulatory mechanism by activating or deactivating many diverse functions of proteins in various cellular processes. In this review, their structures and substrate recognition are described and summarized, focusing on Ser/Thr protein kinases and protein Ser/Thr phosphatases, and the regulation of protein structures by phosphorylation. The studies reviewed here and the resulting information could contribute to further structural, biochemical, and combined studies on the mechanisms of protein phosphorylation and to drug discovery approaches targeting protein kinases or protein phosphatases.
Collapse
|
7
|
From biomineralization to tumorogenesis-the expanding insight of the physiological and pathological roles of Fam20C. Biosci Rep 2021; 41:228577. [PMID: 33942849 PMCID: PMC8493443 DOI: 10.1042/bsr20210040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/20/2021] [Accepted: 04/30/2021] [Indexed: 01/23/2023] Open
Abstract
Fam20C is a Golgi kinase phosphorylating the majority of the secreted proteins. In this decade, the function of Fam20C has been largely disclosed in the loss-of function models. How the influence of the overexpressed Fam20C on cells or organs, and whether Fam20C was associated with tumorogensis still remain unknown. In the latest article in Bioscience Reports, a group from The Second Affiliated Hospital of Harbin Medical University established a correlation between the elevated Fam20C expression and the poor prognosis of multiple cancers (Biosci. Rep. (2021), 41(1) BSR20201920). In addition, they also proposed the potential mechanisms how the increased Fam20C expression played a detrimental role in tumor progression by suggesting that the up-regulated Fam20C level affected the infiltration of immune cells and the capability of cancer metastasis. To give an overview of the expanding knowledge of Fam20C involved in the physiological and pathological events, we first reviewed the history of Fam20C study in this commentary, then, evaluated the correlation of the elevated Fam20C expression to the prognosis of multiple cancers, and finally, interpreted the perspectives that the Fam20C gain-of-function model was also critical for cancer therapy.
Collapse
|
8
|
González-Coronel JM, Rodríguez-Alonso G, Guevara-García ÁA. A phylogenetic study of the members of the MAPK and MEK families across Viridiplantae. PLoS One 2021; 16:e0250584. [PMID: 33891654 PMCID: PMC8064577 DOI: 10.1371/journal.pone.0250584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/09/2021] [Indexed: 11/18/2022] Open
Abstract
Protein phosphorylation is regulated by the activity of enzymes generically known as kinases. One of those kinases is Mitogen-Activated Protein Kinases (MAPK), which operate through a phosphorylation cascade conformed by members from three related protein kinase families namely MAPK kinase kinase (MEKK), MAPK kinase (MEK), and MAPK; these three acts hierarchically. Establishing the evolution of these proteins in the plant kingdom is an interesting but complicated task because the current MAPK, MAPKK, and MAPKKK subfamilies arose from duplications and subsequent sub-functionalization during the early stage of the emergence of Viridiplantae. Here, an in silico genomic analysis was performed on 18 different plant species, which resulted in the identification of 96 genes not previously annotated as components of the MAPK (70) and MEK (26) families. Interestingly, a deeper analysis of the sequences encoded by such genes revealed the existence of putative domains not previously described as signatures of MAPK and MEK kinases. Additionally, our analysis also suggests the presence of conserved activation motifs besides the canonical TEY and TDY domains, which characterize the MAPK family.
Collapse
Affiliation(s)
- José Manuel González-Coronel
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Gustavo Rodríguez-Alonso
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Ángel Arturo Guevara-García
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| |
Collapse
|
9
|
Unremitting progresses for phosphoprotein synthesis. Curr Opin Chem Biol 2020; 58:96-111. [PMID: 32889414 DOI: 10.1016/j.cbpa.2020.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 02/03/2023]
Abstract
Phosphorylation, one of the important protein post-translational modifications, is involved in many essential cellular processes. Site-specifical and homogeneous phosphoproteins can be used as probes for elucidating the protein phosphorylation network and as potential therapeutics for interfering their involved biological events. However, the generation of phosphoproteins has been challenging owing to the limitation of chemical synthesis and protein expression systems. Despite the pioneering discoveries in phosphoprotein synthesis, over the past decade, great progresses in this field have also been made to promote the biofunctional exploration of protein phosphorylation largely. Therefore, in this review, we mainly summarize recent advances in phosphoprotein synthesis, which includes five sections: 1) synthesis of the nonhydrolyzable phosphorylated amino acid mimetic building blocks, 2) chemical total and semisynthesis strategy, 3) in-cell and in vitro genetic code expansion strategy, 4) the late-stage modification strategy, 5) nonoxygen phosphoprotein synthesis.
Collapse
|
10
|
Borgmann-Winter KE, Wang K, Bandyopadhyay S, Torshizi AD, Hahn CG, Hahn CG. The proteome and its dynamics: A missing piece for integrative multi-omics in schizophrenia. Schizophr Res 2020; 217:148-161. [PMID: 31416743 PMCID: PMC7500806 DOI: 10.1016/j.schres.2019.07.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/10/2019] [Accepted: 07/13/2019] [Indexed: 01/08/2023]
Abstract
The complex and heterogeneous pathophysiology of schizophrenia can be deconstructed by integration of large-scale datasets encompassing genes through behavioral phenotypes. Genome-wide datasets are now available for genetic, epigenetic and transcriptomic variations in schizophrenia, which are then analyzed by newly devised systems biology algorithms. A missing piece, however, is the inclusion of information on the proteome and its dynamics in schizophrenia. Proteomics has lagged behind omics of the genome, transcriptome and epigenome since analytic platforms were relatively less robust for proteins. There has been remarkable progress, however, in the instrumentation of liquid chromatography (LC) and mass spectrometry (MS) (LCMS), experimental paradigms and bioinformatics of the proteome. Here, we present a summary of methodological innovations of recent years in MS based proteomics and the power of new generation proteomics, review proteomics studies that have been conducted in schizophrenia to date, and propose how such data can be analyzed and integrated with other omics results. The function of a protein is determined by multiple molecular properties, i.e., subcellular localization, posttranslational modification (PTMs) and protein-protein interactions (PPIs). Incorporation of these properties poses additional challenges in proteomics and their integration with other omics; yet is a critical next step to close the loop of multi-omics integration. In sum, the recent advent of high-throughput proteome characterization technologies and novel mathematical approaches enable us to incorporate functional properties of the proteome to offer a comprehensive multi-omics based understanding of schizophrenia pathophysiology.
Collapse
Affiliation(s)
- Karin E. Borgmann-Winter
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104-3403,Department of Child and Adolescent Psychiatry and Behavioral Sciences, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Kai Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104,Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | | | - Abolfazl Doostparast Torshizi
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Chang-Gyu Hahn
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104-3403, United States of America.
| | - Chang-Gyu Hahn
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104-3403, United States of America.
| |
Collapse
|
11
|
Castillo J, Knol JC, Korver CM, Piersma SR, Pham TV, de Goeij-de Haas RR, van Pelt AMM, Jimenez CR, Jansen BJH. Human Testis Phosphoproteome Reveals Kinases as Potential Targets in Spermatogenesis and Testicular Cancer. Mol Cell Proteomics 2019; 18:S132-S144. [PMID: 30683686 PMCID: PMC6427237 DOI: 10.1074/mcp.ra118.001278] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Indexed: 12/25/2022] Open
Abstract
Spermatogenesis is a complex cell differentiation process that includes marked genetic, cellular, functional and structural changes. It requires tight regulation, because disturbances in any of the spermatogenic processes would lead to fertility deficiencies as well as disorders in offspring. To increase our knowledge of signal transduction during sperm development, we carried out a large-scale identification of the phosphorylation events that occur in the human male gonad. Metal oxide affinity chromatography using TiO2 combined with LC-MS/MS was conducted to profile the phosphoproteome of adult human testes with full spermatogenesis. A total of 8187 phosphopeptides derived from 2661 proteins were identified, resulting in the most complete report of human testicular phosphoproteins to date. Phosphorylation events were enriched in proteins functionally related to spermatogenesis, as well as to highly active processes in the male gonad, such as transcriptional and translational regulation, cytoskeleton organization, DNA packaging, cell cycle and apoptosis. Moreover, 174 phosphorylated kinases were identified. The most active human protein kinases in the testis were predicted both by the number of phosphopeptide spectra identified and the phosphorylation status of the kinase activation loop. The potential function of cyclin-dependent kinase 12 (CDK12) and p21-activated kinase 4 (PAK4) has been explored by in silico, protein-protein interaction analysis, immunodetection in testicular tissue, and a functional assay in a human embryonal carcinoma cell line. The colocalization of CDK12 with Golgi markers suggests a potential crucial role of this protein kinase during sperm formation. PAK4 has been found expressed in human spermatogonia, and a role in embryonal carcinoma cell response to apoptosis has been observed. Together, our protein discovery analysis confirms that phosphoregulation by protein kinases is highly active in sperm differentiation and opens a window to detailed characterization and validation of potential targets for the development of drugs modulating male fertility and tumor behavior.
Collapse
Affiliation(s)
- Judit Castillo
- Lead Pharma BV, Pivot Park, Kloosterstraat 9, 5349 AB Oss, The Netherlands;.
| | - Jaco C Knol
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Cindy M Korver
- Center for Reproductive Medicine, Research Institute Amsterdam Reproduction and Development, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Sander R Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Thang V Pham
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Richard R de Goeij-de Haas
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Ans M M van Pelt
- Center for Reproductive Medicine, Research Institute Amsterdam Reproduction and Development, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Connie R Jimenez
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Bastiaan J H Jansen
- Lead Pharma BV, Pivot Park, Kloosterstraat 9, 5349 AB Oss, The Netherlands;.
| |
Collapse
|
12
|
A rapid separation and characterization of mucins from mouse submandibular glands by supported molecular matrix electrophoresis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:76-81. [DOI: 10.1016/j.bbapap.2018.05.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/04/2018] [Accepted: 05/08/2018] [Indexed: 01/26/2023]
|
13
|
Dussaq AM, Kennell T, Eustace NJ, Anderson JC, Almeida JS, Willey CD. Kinomics toolbox-A web platform for analysis and viewing of kinomic peptide array data. PLoS One 2018; 13:e0202139. [PMID: 30130366 PMCID: PMC6103510 DOI: 10.1371/journal.pone.0202139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/27/2018] [Indexed: 12/14/2022] Open
Abstract
Kinomics is an emerging field of science that involves the study of global kinase activity. As kinases are essential players in virtually all cellular activities, kinomic testing can directly examine protein function, distinguishing kinomics from more remote, upstream components of the central dogma, such as genomics and transcriptomics. While there exist several different approaches for kinomic research, peptide microarrays are the most widely used and involve kinase activity assessment through measurement of phosphorylation of peptide substrates on the array. Unfortunately, bioinformatic tools for analyzing kinomic data are quite limited necessitating the development of accessible open access software in order to facilitate standardization and dissemination of kinomic data for scientific use. Here, we examine and present tools for data analysis for the popular PamChip® (PamGene International) kinomic peptide microarray. As a result, we propose (1) a procedural optimization of kinetic curve data capture, (2) new methods for background normalization, (3) guidelines for the detection of outliers during parameterization, and (4) a standardized data model to store array data at various analytical points. In order to utilize the new data model, we developed a series of tools to implement the new methods and to visualize the various data models. In the interest of accessibility, we developed this new toolbox as a series of JavaScript procedures that can be utilized as either server side resources (easily packaged as web services) or as client side scripts (web applications running in the browser). The aggregation of these tools within a Kinomics Toolbox provides an extensible web based analytic platform that researchers can engage directly and web programmers can extend. As a proof of concept, we developed three analytical tools, a technical reproducibility visualizer, an ANOVA based detector of differentially phosphorylated peptides, and a heatmap display with hierarchical clustering.
Collapse
Affiliation(s)
- Alex M. Dussaq
- Department of Radiation Oncology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Timothy Kennell
- Informatics Institute, Department of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Nicholas J. Eustace
- Department of Radiation Oncology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Joshua C. Anderson
- Department of Radiation Oncology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jonas S. Almeida
- Department of Biomedical Informatics, Stony Brook University School of Medicine, Stony Brook, New York, United States of America
| | - Christopher D. Willey
- Department of Radiation Oncology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
| |
Collapse
|
14
|
|
15
|
Franchin C, Borgo C, Cesaro L, Zaramella S, Vilardell J, Salvi M, Arrigoni G, Pinna LA. Re-evaluation of protein kinase CK2 pleiotropy: new insights provided by a phosphoproteomics analysis of CK2 knockout cells. Cell Mol Life Sci 2018; 75:2011-2026. [PMID: 29119230 PMCID: PMC11105740 DOI: 10.1007/s00018-017-2705-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/28/2017] [Accepted: 10/30/2017] [Indexed: 10/18/2022]
Abstract
CK2 denotes a ubiquitous and pleiotropic protein kinase whose holoenzyme is composed of two catalytic (α and/or α') and two regulatory β subunits. The CK2 consensus sequence, S/T-x-x-D/E/pS/pT is present in numerous phosphosites, but it is not clear how many of these are really generated by CK2. To gain information about this issue, advantage has been taken of C2C12 cells entirely deprived of both CK2 catalytic subunits by the CRISPR/Cas9 methodology. A comparative SILAC phosphoproteomics analysis reveals that, although about 30% of the quantified phosphosites do conform to the CK2 consensus, only one-third of these are substantially reduced in the CK2α/α'(-/-) cells, consistent with their generation by CK2. A parallel study with C2C12 cells deprived of the regulatory β subunit discloses a role of this subunit in determining CK2 targeting. We also find that phosphosites notoriously generated by CK2 are not fully abrogated in CK2α/α'(-/-) cells, while some phosphosites unrelated to CK2 are significantly altered. Collectively taken our data allow to conclude that the phosphoproteome generated by CK2 is not as ample and rigidly pre-determined as it was believed before. They also show that the lack of CK2 promotes phosphoproteomics perturbations attributable to kinases other than CK2.
Collapse
Affiliation(s)
- Cinzia Franchin
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, Padua, Italy
| | - Christian Borgo
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy
| | - Luca Cesaro
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, Padua, Italy
| | - Silvia Zaramella
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, Padua, Italy
| | - Jordi Vilardell
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy.
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy.
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, Padua, Italy.
| | - Lorenzo A Pinna
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy.
- CNR Institute of Neurosciences, Via U. Bassi 58/B, Padua, Italy.
| |
Collapse
|
16
|
Kumar TR. Fshb Knockout Mouse Model, Two Decades Later and Into the Future. Endocrinology 2018; 159:1941-1949. [PMID: 29579177 PMCID: PMC5888209 DOI: 10.1210/en.2018-00072] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/02/2018] [Indexed: 12/20/2022]
Abstract
In 1997, nearly 20 years ago, we reported the phenotypes of follicle-stimulating hormone (FSH) β (Fshb) null mice. Since then, these mice have been useful for various physiological and genetic studies in reproductive and skeletal biology. In a 2009 review titled "FSHβ Knockout Mouse Model: A Decade Ago and Into the Future," I summarized the need for and what led to the development of an FSH-deficient mouse model and its applications, including delineation of the emerging extragonadal roles of FSH in bone cells by using this genetic model. These studies opened up exciting avenues of research on osteoporosis and now extend into those on adiposity in postmenopausal women. Here, I summarize the progress made with this mouse model since 2009 with regard to FSH rerouting in vivo, deciphering the role of N-glycosylation on FSHβ, roles of FSH in somatic-germ cell interactions in gonads, and provide a road map that is anticipated to emerge in the near future. Undoubtedly, the next 10 years should be an even more exciting time to explore the fertile area of FSH biology and its implications for basic and clinical reproductive physiology research.
Collapse
Affiliation(s)
- T Rajendra Kumar
- Department of Obstetrics and Gynecology, Division of Reproductive Sciences, University of Colorado at Denver, Anschutz Medical Campus, Aurora, Colorado
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, University of Colorado at Denver, Anschutz Medical Campus, Aurora, Colorado
- Correspondence: T. Rajendra Kumar, PhD, Edgar L. and Patricia M. Makowski Professor, Department of Obstetrics and Gynecology, University of Colorado Anschutz Medical Campus, 12700 East 19th Avenue, RC-2 Complex, 15-3000B, Aurora, Colorado 80045. E-mail:
| |
Collapse
|
17
|
Bruegger JJ, Smith BC, Wynia-Smith SL, Marletta MA. Comparative and integrative metabolomics reveal that S-nitrosation inhibits physiologically relevant metabolic enzymes. J Biol Chem 2018; 293:6282-6296. [PMID: 29483187 DOI: 10.1074/jbc.m117.817700] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 02/21/2018] [Indexed: 12/16/2022] Open
Abstract
Cysteine S-nitrosation is a reversible post-translational modification mediated by nitric oxide (•NO)-derived agents. S-Nitrosation participates in cellular signaling and is associated with several diseases such as cancer, cardiovascular diseases, and neuronal disorders. Despite the physiological importance of this nonclassical •NO-signaling pathway, little is understood about how much S-nitrosation affects protein function. Moreover, identifying physiologically relevant targets of S-nitrosation is difficult because of the dynamics of transnitrosation and a limited understanding of the physiological mechanisms leading to selective protein S-nitrosation. To identify proteins whose activities are modulated by S-nitrosation, we performed a metabolomics study comparing WT and endothelial nitric-oxide synthase knockout mice. We integrated our results with those of a previous proteomics study that identified physiologically relevant S-nitrosated cysteines, and we found that the activity of at least 21 metabolic enzymes might be regulated by S-nitrosation. We cloned, expressed, and purified four of these enzymes and observed that S-nitrosation inhibits the metabolic enzymes 6-phosphogluconate dehydrogenase, Δ1-pyrroline-5-carboxylate dehydrogenase, catechol-O-methyltransferase, and d-3-phosphoglycerate dehydrogenase. Furthermore, using site-directed mutagenesis, we identified the predominant cysteine residue influencing the observed activity changes in each enzyme. In summary, using an integrated metabolomics approach, we have identified several physiologically relevant S-nitrosation targets, including metabolic enzymes, which are inhibited by this modification, and we have found the cysteines modified by S-nitrosation in each enzyme.
Collapse
Affiliation(s)
| | | | | | - Michael A Marletta
- From the QB3 Institute and .,Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-3220
| |
Collapse
|
18
|
Montenarh M, Götz C. Ecto-protein kinase CK2, the neglected form of CK2. Biomed Rep 2018; 8:307-313. [PMID: 29556379 DOI: 10.3892/br.2018.1069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 02/12/2018] [Indexed: 01/21/2023] Open
Abstract
Ecto-protein kinases, including protein kinase CK2 (former name, casein kinase 2), have been the focus of research for more than 30 years. At the beginning of the ecto-kinase research their identification was performed with substrates and inhibitors whose specificity under the current knowledge was rather limited. Since all currently known ecto-kinases, including ecto-CK2, have intracellular counterparts, one has to exclude that an ecto-localization originates from intracellular counterparts after cell damage. Protein kinase CK2 is involved in cellular key processes such as cell cycle progression, inhibition of apoptosis, DNA damage repair, differentiation and many other processes. CK2 is composed of two catalytic CK2α or CK2α' subunits and two non-catalytic CK2β subunits. Progress in the ecto-kinase and in particular ecto-CK2 studies was made with the use of transfected tagged CK2 subunits, which allowed to follow their individual transport and localization on the cell surface after transfection. Furthermore, immunofluorescence studies with antibodies against CK2 subunits as well as affinity chromatography with a binding partner of CK2 subunits have improved ecto-kinase research. The use of new and more specific inhibitors as well as of substrates, which do not cross the plasma membrane, have further improved the specificity for ecto-CK2. From the various substrates of ecto-CK2, it can be concluded that ecto-CK2 plays a role in Alzheimer disease, cell adhesion, platelet aggregation, immune response and cellular signalling. New tools and techniques, to study ecto-CK2 activity, are required to identify new substrates and thereby new functional implications for ecto-CK2.
Collapse
Affiliation(s)
- Mathias Montenarh
- Medical Biochemistry and Molecular Biology, Saarland University, D-66424 Homburg, Germany
| | - Claudia Götz
- Medical Biochemistry and Molecular Biology, Saarland University, D-66424 Homburg, Germany
| |
Collapse
|
19
|
Rossignoli G, Phillips RS, Astegno A, Menegazzi M, Voltattorni CB, Bertoldi M. Phosphorylation of pyridoxal 5'-phosphate enzymes: an intriguing and neglected topic. Amino Acids 2017; 50:205-215. [PMID: 29204749 DOI: 10.1007/s00726-017-2521-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 11/29/2017] [Indexed: 12/25/2022]
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes catalyze a wide range of reactions of amino acids and amines, with the exception of glycogen phosphorylase which exhibits peculiar both substrate preference and chemical mechanism. They represent about 4% of the gene products in eukaryotic cells. Although structure-function investigations regarding these enzymes are copious, their regulation by post-translational modifications is largely unknown. Protein phosphorylation is the most common post-translational modification fundamental in mediating diverse cellular functions. This review aims at summarizing the current knowledge on regulation of PLP enzymes by phosphorylation. Starting from the paradigmatic PLP-dependent glycogen phosphorylase, the first phosphoprotein discovered, we collect data in literature regarding functional phosphorylation events of eleven PLP enzymes belonging to different fold types and discuss the impact of the modification in affecting their activity and localization as well as the implications on the pathogenesis of diseases in which many of these enzymes are involved. The pivotal question is to correlate the structural consequences of phosphorylation among PLP enzymes of different folds with the functional modifications exerted in terms of activity or conformational changes or others. Although the literature shows that the phosphorylation of PLP enzymes plays important roles in mediating diverse cellular functions, our recapitulation of clue findings in the field makes clear that there is still much to be learnt. Besides mass spectrometry-based proteomic analyses, further biochemical and structural studies on purified native proteins are imperative to fully understand and predict how phosphorylation regulates PLP enzymes and to find the relationship between addition of a phosphate moiety and physiological response.
Collapse
Affiliation(s)
- Giada Rossignoli
- Department of Neuroscience, Biomedicine and Movement, University of Verona, Strada Le Grazie, 8, 37134, Verona, Italy
| | - Robert S Phillips
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Marta Menegazzi
- Department of Neuroscience, Biomedicine and Movement, University of Verona, Strada Le Grazie, 8, 37134, Verona, Italy
| | - Carla Borri Voltattorni
- Department of Neuroscience, Biomedicine and Movement, University of Verona, Strada Le Grazie, 8, 37134, Verona, Italy
| | - Mariarita Bertoldi
- Department of Neuroscience, Biomedicine and Movement, University of Verona, Strada Le Grazie, 8, 37134, Verona, Italy.
| |
Collapse
|
20
|
Bllaci L, Torsetnes SB, Wierzbicka C, Shinde S, Sellergren B, Rogowska-Wrzesinska A, Jensen ON. Phosphotyrosine Biased Enrichment of Tryptic Peptides from Cancer Cells by Combining pY-MIP and TiO2 Affinity Resins. Anal Chem 2017; 89:11332-11340. [DOI: 10.1021/acs.analchem.7b02091] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Loreta Bllaci
- Department
of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical
Sciences, University of Southern Denmark, DK-5230 Odense
M, Denmark
| | - Silje B. Torsetnes
- Department
of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical
Sciences, University of Southern Denmark, DK-5230 Odense
M, Denmark
| | - Celina Wierzbicka
- Department
of Biomedical Sciences, Malmö University, S-20506 Malmö, Sweden
| | - Sudhirkumar Shinde
- Department
of Biomedical Sciences, Malmö University, S-20506 Malmö, Sweden
| | - Börje Sellergren
- Department
of Biomedical Sciences, Malmö University, S-20506 Malmö, Sweden
| | - Adelina Rogowska-Wrzesinska
- Department
of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical
Sciences, University of Southern Denmark, DK-5230 Odense
M, Denmark
| | - Ole N. Jensen
- Department
of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical
Sciences, University of Southern Denmark, DK-5230 Odense
M, Denmark
| |
Collapse
|
21
|
Karasev DA, Veselova DA, Veselovsky AV, Sobolev BN, Zgoda VG, Archakov AI. Spatial features of proteins related to their phosphorylation and associated structural changes. Proteins 2017; 86:13-20. [DOI: 10.1002/prot.25397] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 09/13/2017] [Accepted: 10/04/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Dmitry A. Karasev
- Department of Bioinformatics; Institute of Biomedical Chemistry (IBMC); Moscow Russia
- Department of Biochemistry; Pirogov Russian National Research Medical University (RNRMU); Moscow Russia
| | - Darya A. Veselova
- Department of Bioinformatics; Institute of Biomedical Chemistry (IBMC); Moscow Russia
| | | | - Boris N. Sobolev
- Department of Bioinformatics; Institute of Biomedical Chemistry (IBMC); Moscow Russia
| | - Victor G. Zgoda
- Department of Bioinformatics; Institute of Biomedical Chemistry (IBMC); Moscow Russia
| | - Alexander I. Archakov
- Department of Bioinformatics; Institute of Biomedical Chemistry (IBMC); Moscow Russia
| |
Collapse
|
22
|
A Novel Phosphorylation Site-Kinase Network-Based Method for the Accurate Prediction of Kinase-Substrate Relationships. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1826496. [PMID: 29312990 PMCID: PMC5660750 DOI: 10.1155/2017/1826496] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/14/2017] [Accepted: 09/05/2017] [Indexed: 01/06/2023]
Abstract
Protein phosphorylation is catalyzed by kinases which regulate many aspects that control death, movement, and cell growth. Identification of the phosphorylation site-specific kinase-substrate relationships (ssKSRs) is important for understanding cellular dynamics and provides a fundamental basis for further disease-related research and drug design. Although several computational methods have been developed, most of these methods mainly use local sequence of phosphorylation sites and protein-protein interactions (PPIs) to construct the prediction model. While phosphorylation presents very complicated processes and is usually involved in various biological mechanisms, the aforementioned information is not sufficient for accurate prediction. In this study, we propose a new and powerful computational approach named KSRPred for ssKSRs prediction, by introducing a novel phosphorylation site-kinase network (pSKN) profiles that can efficiently incorporate the relationships between various protein kinases and phosphorylation sites. The experimental results show that the pSKN profiles can efficiently improve the prediction performance in collaboration with local sequence and PPI information. Furthermore, we compare our method with the existing ssKSRs prediction tools and the results demonstrate that KSRPred can significantly improve the prediction performance compared with existing tools.
Collapse
|