401
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Kucharova V, Wiker HG. Proteogenomics in microbiology: taking the right turn at the junction of genomics and proteomics. Proteomics 2014; 14:2360-675. [PMID: 25263021 DOI: 10.1002/pmic.201400168] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/18/2014] [Accepted: 09/23/2014] [Indexed: 12/14/2022]
Abstract
High-accuracy and high-throughput proteomic methods have completely changed the way we can identify and characterize proteins. MS-based proteomics can now provide a unique supplement to genomic data and add a new level of information to the interpretation of genomic sequences. Proteomics-driven genome annotation has become especially relevant in microbiology where genomes are sequenced on a daily basis and limitations of an in silico driven annotation process are well recognized. In this review paper, we outline different strategies on how one can design a proteogenomic experiment, for example on genome-sequenced (synonymous proteogenomics) versus unsequenced organisms (ortho-proteogenomics) or with the aid of other "omic" data such as RNA-seq. We touch upon many challenges that are encountered during a typical proteogenomic study, mostly concerning bioinformatics methods and downstream data analysis, but also related to creation and use of sequence databases. A large list of proteogenomic case studies of different microorganisms is provided to illustrate the mapping of MS/MS-derived peptide spectra to genomic DNA sequences. These investigations have led to accurate determination of translational initiation sites, pointed out eventual read-throughs or programmed frameshifts, detected signal peptide processing or other protein maturation events, removed questionable annotation assignments, and provided evidence for predicted hypothetical proteins.
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Affiliation(s)
- Veronika Kucharova
- Department of Clinical Science, The Gade Research Group for Infection and Immunity, University of Bergen, Norway
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402
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Batth TS, Francavilla C, Olsen JV. Off-Line High-pH Reversed-Phase Fractionation for In-Depth Phosphoproteomics. J Proteome Res 2014; 13:6176-86. [DOI: 10.1021/pr500893m] [Citation(s) in RCA: 216] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Tanveer S. Batth
- Proteomics
Program, Novo
Nordisk Foundation Center for Protein Research, Faculty of Health
and Medical Science, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Chiara Francavilla
- Proteomics
Program, Novo
Nordisk Foundation Center for Protein Research, Faculty of Health
and Medical Science, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Jesper V. Olsen
- Proteomics
Program, Novo
Nordisk Foundation Center for Protein Research, Faculty of Health
and Medical Science, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
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403
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Tape C, Worboys JD, Sinclair J, Gourlay R, Vogt J, McMahon KM, Trost M, Lauffenburger DA, Lamont DJ, Jørgensen C. Reproducible automated phosphopeptide enrichment using magnetic TiO2 and Ti-IMAC. Anal Chem 2014; 86:10296-302. [PMID: 25233145 PMCID: PMC4206527 DOI: 10.1021/ac5025842] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 09/18/2014] [Indexed: 12/28/2022]
Abstract
Reproducible, comprehensive phosphopeptide enrichment is essential for studying phosphorylation-regulated processes. Here, we describe the application of hyper-porous magnetic TiO2 and Ti-IMAC microspheres for uniform automated phosphopeptide enrichment. Combining magnetic microspheres with a magnetic particle-handling robot enables rapid (45 min), reproducible (r2 ≥ 0.80) and high-fidelity (>90% purity) phosphopeptide purification in a 96-well format. Automated phosphopeptide enrichment demonstrates reproducible synthetic phosphopeptide recovery across 2 orders of magnitude, "well-to-well" quantitative reproducibility indistinguishable to internal SILAC standards, and robust "plate-to-plate" reproducibility across 5 days of independent enrichments. As a result, automated phosphopeptide enrichment enables statistical analysis of label-free phosphoproteomic samples in a high-throughput manner. This technique uses commercially available, off-the-shelf components and can be easily adopted by any laboratory interested in phosphoproteomic analysis. We provide a free downloadable automated phosphopeptide enrichment program to facilitate uniform interlaboratory collaboration and exchange of phosphoproteomic data sets.
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Affiliation(s)
- Christopher
J. Tape
- The
Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jonathan D. Worboys
- The
Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
| | - John Sinclair
- The
Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
| | - Robert Gourlay
- FingerPrints
Proteomics Facility, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Janis Vogt
- FingerPrints
Proteomics Facility, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Kelly M. McMahon
- Cancer
Research UK Manchester Institute, The University
of Manchester, Wilmslow
Road, Manchester M20 4BX, United Kingdom
| | - Matthias Trost
- FingerPrints
Proteomics Facility, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Douglas A. Lauffenburger
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Douglas J. Lamont
- FingerPrints
Proteomics Facility, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Claus Jørgensen
- The
Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
- Cancer
Research UK Manchester Institute, The University
of Manchester, Wilmslow
Road, Manchester M20 4BX, United Kingdom
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404
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Li X, Wang W, Chen J. From pathways to networks: connecting dots by establishing protein-protein interaction networks in signaling pathways using affinity purification and mass spectrometry. Proteomics 2014; 15:188-202. [PMID: 25137225 DOI: 10.1002/pmic.201400147] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 07/28/2014] [Accepted: 08/13/2014] [Indexed: 12/27/2022]
Abstract
Signal transductions are the basis of biological activities in all living organisms. Studying the signaling pathways, especially under physiological conditions, has become one of the most important facets of modern biological research. During the last decade, MS has been used extensively in biological research and is proven to be effective in addressing important biological questions. Here, we review the current progress in the understanding of signaling networks using MS approaches. We will focus on studies of protein-protein interactions that use affinity purification followed by MS approach. We discuss obstacles to affinity purification, data processing, functional validation, and identification of transient interactions and provide potential solutions for pathway-specific proteomics analysis, which we hope one day will lead to a comprehensive understanding of signaling networks in humans.
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Affiliation(s)
- Xu Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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405
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Palmeri A, Ferrè F, Helmer-Citterich M. Exploiting holistic approaches to model specificity in protein phosphorylation. Front Genet 2014; 5:315. [PMID: 25324856 PMCID: PMC4179730 DOI: 10.3389/fgene.2014.00315] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/21/2014] [Indexed: 12/27/2022] Open
Abstract
Phosphate plays a chemically unique role in shaping cellular signaling of all current living systems, especially eukaryotes. Protein phosphorylation has been studied at several levels, from the near-site context, both in sequence and structure, to the crowded cellular environment, and ultimately to the systems-level perspective. Despite the tremendous advances in mass spectrometry and efforts dedicated to the development of ad hoc highly sophisticated methods, phosphorylation site inference and associated kinase identification are still unresolved problems in kinome biology. The sequence and structure of the substrate near-site context are not sufficient alone to model the in vivo phosphorylation rules, and they should be integrated with orthogonal information in all possible applications. Here we provide an overview of the different contexts that contribute to protein phosphorylation, discussing their potential impact in phosphorylation site annotation and in predicting kinase-substrate specificity.
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Affiliation(s)
- Antonio Palmeri
- Department of Biology, Centre for Molecular Bioinformatics, University of Rome Tor Vergata Rome, Italy
| | - Fabrizio Ferrè
- Department of Biology, Centre for Molecular Bioinformatics, University of Rome Tor Vergata Rome, Italy
| | - Manuela Helmer-Citterich
- Department of Biology, Centre for Molecular Bioinformatics, University of Rome Tor Vergata Rome, Italy
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406
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Hendriks IA, D'Souza RCJ, Yang B, Verlaan-de Vries M, Mann M, Vertegaal ACO. Uncovering global SUMOylation signaling networks in a site-specific manner. Nat Struct Mol Biol 2014; 21:927-36. [PMID: 25218447 PMCID: PMC4259010 DOI: 10.1038/nsmb.2890] [Citation(s) in RCA: 358] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 08/19/2014] [Indexed: 12/28/2022]
Abstract
SUMOylation is a reversible post-translational modification essential for genome stability. Using high-resolution mass spectrometry, we have studied global SUMOylation in human cells and in a site-specific manner, identifying a total of over 4,300 SUMOylation sites in over 1,600 proteins. Moreover, for the first time in excess of 1,000 SUMOylation sites were identified under standard growth conditions. SUMOylation dynamics were quantitatively studied in response to SUMO protease inhibition, proteasome inhibition and heat shock. A considerable amount of SUMOylated lysines have previously been reported to be ubiquitylated, acetylated or methylated, indicating crosstalk between SUMO and other post-translational modifications. We identified 70 phosphorylation and 4 acetylation events in close proximity to SUMOylation sites, and provide evidence for acetylation-dependent SUMOylation of endogenous histone H3. SUMOylation regulates target proteins involved in all nuclear processes including transcription, DNA repair, chromatin remodeling, pre-mRNA splicing and ribosome assembly.
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Affiliation(s)
- Ivo A Hendriks
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Rochelle C J D'Souza
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Bing Yang
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Matty Verlaan-de Vries
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Alfred C O Vertegaal
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
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407
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Venne AS, Zahedi RP. The potential of fractional diagonal chromatography strategies for the enrichment of post-translational modifications. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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408
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Weidner C, Fischer C, Sauer S. PHOXTRACK-a tool for interpreting comprehensive datasets of post-translational modifications of proteins. ACTA ACUST UNITED AC 2014; 30:3410-1. [PMID: 25152232 DOI: 10.1093/bioinformatics/btu572] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
UNLABELLED We introduce PHOXTRACK (PHOsphosite-X-TRacing Analysis of Causal Kinases), a user-friendly freely available software tool for analyzing large datasets of post-translational modifications of proteins, such as phosphorylation, which are commonly gained by mass spectrometry detection. In contrast to other currently applied data analysis approaches, PHOXTRACK uses full sets of quantitative proteomics data and applies non-parametric statistics to calculate whether defined kinase-specific sets of phosphosite sequences indicate statistically significant concordant differences between various biological conditions. PHOXTRACK is an efficient tool for extracting post-translational information of comprehensive proteomics datasets to decipher key regulatory proteins and to infer biologically relevant molecular pathways. AVAILABILITY PHOXTRACK will be maintained over the next years and is freely available as an online tool for non-commercial use at http://phoxtrack.molgen.mpg.de. Users will also find a tutorial at this Web site and can additionally give feedback at https://groups.google.com/d/forum/phoxtrack-discuss.
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Affiliation(s)
- Christopher Weidner
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Cornelius Fischer
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Sascha Sauer
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
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409
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Sharma K, D'Souza RCJ, Tyanova S, Schaab C, Wiśniewski JR, Cox J, Mann M. Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling. Cell Rep 2014; 8:1583-94. [PMID: 25159151 DOI: 10.1016/j.celrep.2014.07.036] [Citation(s) in RCA: 717] [Impact Index Per Article: 71.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 05/30/2014] [Accepted: 07/22/2014] [Indexed: 11/17/2022] Open
Abstract
Regulatory protein phosphorylation controls normal and pathophysiological signaling in eukaryotic cells. Despite great advances in mass-spectrometry-based proteomics, the extent, localization, and site-specific stoichiometry of this posttranslational modification (PTM) are unknown. Here, we develop a stringent experimental and computational workflow, capable of mapping more than 50,000 distinct phosphorylated peptides in a single human cancer cell line. We detected more than three-quarters of cellular proteins as phosphoproteins and determined very high stoichiometries in mitosis or growth factor signaling by label-free quantitation. The proportion of phospho-Tyr drastically decreases as coverage of the phosphoproteome increases, whereas Ser/Thr sites saturate only for technical reasons. Tyrosine phosphorylation is maintained at especially low stoichiometric levels in the absence of specific signaling events. Unexpectedly, it is enriched on higher-abundance proteins, and this correlates with the substrate KM values of tyrosine kinases. Our data suggest that P-Tyr should be considered a functionally separate PTM of eukaryotic proteomes.
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Affiliation(s)
- Kirti Sharma
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Rochelle C J D'Souza
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Stefka Tyanova
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christoph Schaab
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Jacek R Wiśniewski
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Jürgen Cox
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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410
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van Els CACM, Corbière V, Smits K, van Gaans-van den Brink JAM, Poelen MCM, Mascart F, Meiring HD, Locht C. Toward Understanding the Essence of Post-Translational Modifications for the Mycobacterium tuberculosis Immunoproteome. Front Immunol 2014; 5:361. [PMID: 25157249 PMCID: PMC4127798 DOI: 10.3389/fimmu.2014.00361] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 07/14/2014] [Indexed: 11/20/2022] Open
Abstract
CD4+ T cells are prominent effector cells in controlling Mycobacterium tuberculosis (Mtb) infection but may also contribute to immunopathology. Studies probing the CD4+ T cell response from individuals latently infected with Mtb or patients with active tuberculosis using either small or proteome-wide antigen screens so far revealed a multi-antigenic, yet mostly invariable repertoire of immunogenic Mtb proteins. Recent developments in mass spectrometry-based proteomics have highlighted the occurrence of numerous types of post-translational modifications (PTMs) in proteomes of prokaryotes, including Mtb. The well-known PTMs in Mtb are glycosylation, lipidation, or phosphorylation, known regulators of protein function or compartmentalization. Other PTMs include methylation, acetylation, and pupylation, involved in protein stability. While all PTMs add variability to the Mtb proteome, relatively little is understood about their role in the anti-Mtb immune responses. Here, we review Mtb protein PTMs and methods to assess their role in protective immunity against Mtb.
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Affiliation(s)
- Cécile A C M van Els
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment , Bilthoven , Netherlands
| | - Véronique Corbière
- Laboratory for Vaccinology and Mucosal Immunity, Université Libre de Bruxelles (U.L.B.) , Brussels , Belgium
| | - Kaat Smits
- Laboratory for Vaccinology and Mucosal Immunity, Université Libre de Bruxelles (U.L.B.) , Brussels , Belgium
| | | | - Martien C M Poelen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment , Bilthoven , Netherlands
| | - Francoise Mascart
- Laboratory for Vaccinology and Mucosal Immunity, Université Libre de Bruxelles (U.L.B.) , Brussels , Belgium ; Immunobiology Clinic, Hôpital Erasme, Université Libre de Bruxelles (U.L.B.) , Brussels , Belgium
| | - Hugo D Meiring
- Institute for Translational Vaccinology , Bilthoven , Netherlands
| | - Camille Locht
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille , Lille , France ; INSERM U1019 , Lille , France ; CNRS UMR8204 , Lille , France ; Université Lille Nord de France , Lille , France
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411
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Helm D, Vissers JPC, Hughes CJ, Hahne H, Ruprecht B, Pachl F, Grzyb A, Richardson K, Wildgoose J, Maier SK, Marx H, Wilhelm M, Becher I, Lemeer S, Bantscheff M, Langridge JI, Kuster B. Ion mobility tandem mass spectrometry enhances performance of bottom-up proteomics. Mol Cell Proteomics 2014; 13:3709-15. [PMID: 25106551 DOI: 10.1074/mcp.m114.041038] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
One of the limiting factors in determining the sensitivity of tandem mass spectrometry using hybrid quadrupole orthogonal acceleration time-of-flight instruments is the duty cycle of the orthogonal ion injection system. As a consequence, only a fraction of the generated fragment ion beam is collected by the time-of-flight analyzer. Here we describe a method utilizing postfragmentation ion mobility spectrometry of peptide fragment ions in conjunction with mobility time synchronized orthogonal ion injection leading to a substantially improved duty cycle and a concomitant improvement in sensitivity of up to 10-fold for bottom-up proteomic experiments. This enabled the identification of 7500 human proteins within 1 day and 8600 phosphorylation sites within 5 h of LC-MS/MS time. The method also proved powerful for multiplexed quantification experiments using tandem mass tags exemplified by the chemoproteomic interaction analysis of histone deacetylases with Trichostatin A.
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Affiliation(s)
- Dominic Helm
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | | | | | - Hannes Hahne
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Benjamin Ruprecht
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Fiona Pachl
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | | | | | | | - Stefan K Maier
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Harald Marx
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Mathias Wilhelm
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | | | - Simone Lemeer
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | | | | | - Bernhard Kuster
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany; ‖Center for Integrated Protein Science Munich, Germany
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412
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Subramonian D, Raghunayakula S, Olsen JV, Beningo KA, Paschen W, Zhang XD. Analysis of changes in SUMO-2/3 modification during breast cancer progression and metastasis. J Proteome Res 2014; 13:3905-18. [PMID: 25072996 DOI: 10.1021/pr500119a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
SUMOylation is an essential posttranslational modification and regulates many cellular processes. Dysregulation of SUMOylation plays a critical role in metastasis, yet how its perturbation affects this lethal process of cancer is not well understood. We found that SUMO-2/3 modification is greatly up-regulated in metastatic breast cancer cells compared with nonmetastatic control cells. To identify proteins differentially modified by SUMO-2/3 between metastatic and nonmetastatic cells, we established a method in which endogenous SUMO-2/3 conjugates are labeled by stable isotope labeling by amino acids in cell culture (SILAC), immunopurified by SUMO-2/3 monoclonal antibodies and epitope-peptide elution, and analyzed by quantitative mass spectrometry. We identified 66 putative SUMO-2/3-conjugated proteins, of which 15 proteins show a significant increase/decrease in SUMO-2/3 modification in metastatic cells. Targets with altered SUMOylation are involved in cell cycle, migration, inflammation, glycolysis, gene expression, and SUMO/ubiquitin pathways, suggesting that perturbations of SUMO-2/3 modification might contribute to metastasis by affecting these processes. Consistent with this, up-regulation of PML SUMO-2/3 modification corresponds to an increased number of PML nuclear bodies (PML-NBs) in metastatic cells, whereas up-regulation of global SUMO-2/3 modification promotes 3D cell migration. Our findings provide a foundation for further investigating the effects of SUMOylation on breast cancer progression and metastasis.
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Affiliation(s)
- Divya Subramonian
- Department of Biological Sciences, Wayne State University , 5047 Gullen Mall, Detroit, Michigan 48202, United States
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413
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In vivo quantitative phosphoproteomic profiling identifies novel regulators of castration-resistant prostate cancer growth. Oncogene 2014; 34:2764-76. [PMID: 25065596 DOI: 10.1038/onc.2014.206] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 04/21/2014] [Accepted: 05/28/2014] [Indexed: 12/13/2022]
Abstract
Prostate cancer remains a leading cause of cancer-related mortality worldwide owing to our inability to treat effectively castration-resistant tumors. To understand the signaling mechanisms sustaining castration-resistant growth, we implemented a mass spectrometry-based quantitative proteomic approach and use it to compare protein phosphorylation in orthotopic xenograft tumors grown in either intact or castrated mice. This investigation identified changes in phosphorylation of signaling proteins such as MEK, LYN, PRAS40, YAP1 and PAK2, indicating the concomitant activation of several oncogenic pathways in castration-resistant tumors, a notion that was confirmed by tumor transcriptome analysis. Further analysis demonstrated that the activation of mTORC1, PAK2 and the increased levels of YAP1 in castration-resistant tumors can be explained by the loss of androgen inhibitory actions. The analysis of clinical samples demonstrated elevated levels of PAK2 and YAP1 in castration-resistant tumors, whereas knockdown experiments in androgen-independent cells demonstrated that both YAP1 and PAK2 regulate cell colony formation and cell invasion activity. PAK2 also influenced cell proliferation and mitotic timing. Interestingly, these phenotypic changes occur in the absence of obvious alterations in the activity of AKT, MAPK or mTORC1 pathways, suggesting that PAK2 and YAP1 may represent novel targets for the treatment of castration-resistant prostate cancer. Pharmacologic inhibitors of PAK2 (PF-3758309) and YAP1 (Verteporfin) were able to inhibit the growth of androgen-independent PC3 xenografts. This work demonstrates the power of applying high-resolution mass spectrometry in the proteomic profiling of tumors grown in vivo for the identification of novel and clinically relevant regulatory proteins.
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414
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Bigeard J, Rayapuram N, Pflieger D, Hirt H. Phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. Proteomics 2014; 14:2127-40. [PMID: 24889195 DOI: 10.1002/pmic.201400073] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/28/2014] [Accepted: 05/26/2014] [Indexed: 12/25/2022]
Abstract
In eukaryotes, most of the DNA is located in the nucleus where it is organized with histone proteins in a higher order structure as chromatin. Chromatin and chromatin-associated proteins contribute to DNA-related processes such as replication and transcription as well as epigenetic regulation. Protein functions are often regulated by PTMs among which phosphorylation is one of the most abundant PTM. Phosphorylation of proteins affects important properties, such as enzyme activity, protein stability, or subcellular localization. We here describe the main specificities of protein phosphorylation in plants and review the current knowledge on phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. We also outline some future challenges to further elucidate protein phosphorylation and chromatin regulation.
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Affiliation(s)
- Jean Bigeard
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA/CNRS/Université d'Evry Val d'Essonne/Saclay Plant Sciences, Evry, France
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415
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van de Waterbeemd M, Lössl P, Gautier V, Marino F, Yamashita M, Conti E, Scholten A, Heck AJR. Simultane Untersuchung kinetischer, ortsspezifischer und struktureller Aspekte enzymatischer Proteinphosphorylierungen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404637] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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416
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van de Waterbeemd M, Lössl P, Gautier V, Marino F, Yamashita M, Conti E, Scholten A, Heck AJR. Simultaneous assessment of kinetic, site-specific, and structural aspects of enzymatic protein phosphorylation. Angew Chem Int Ed Engl 2014; 53:9660-4. [PMID: 25044833 DOI: 10.1002/anie.201404637] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Indexed: 12/27/2022]
Abstract
Protein phosphorylation is a widespread process forming the mechanistic basis of cellular signaling. Up to now, different aspects, for example, site-specificity, kinetics, role of co-factors, and structure-function relationships have been typically investigated by multiple techniques that are incompatible with one another. The approach introduced here maximizes the amount of information gained on protein (complex) phosphorylation while minimizing sample handling. Using high-resolution native mass spectrometry on intact protein (assemblies) up to 150 kDa we track the sequential incorporation of phosphate groups and map their localization by peptide LC-MS/MS. On two model systems, the protein kinase G and the interplay between Aurora kinase A and Bora, we demonstrate the simultaneous monitoring of various aspects of the phosphorylation process, namely the effect of different cofactors on PKG autophosphorylation and the interaction of AurA and Bora as both an enzyme-substrate pair and physical binding partners.
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Affiliation(s)
- Michiel van de Waterbeemd
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Center, Utrecht University, Padualaan 8, 3584 CH Utrecht (The Netherlands)
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417
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Breker M, Schuldiner M. The emergence of proteome-wide technologies: systematic analysis of proteins comes of age. Nat Rev Mol Cell Biol 2014; 15:453-64. [PMID: 24938631 DOI: 10.1038/nrm3821] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During the lifetime of a cell proteins can change their localization, alter their abundance and undergo modifications, all of which cannot be assayed by tracking mRNAs alone. Methods to study proteomes directly are coming of age, thereby opening new perspectives on the role of post-translational regulation in stabilizing the cellular milieu. Proteomics has undergone a revolution, and novel technologies for the systematic analysis of proteins have emerged. These methods can expand our ability to acquire information from single proteins to proteomes, from static to dynamic measures and from the population level to the level of single cells. Such approaches promise that proteomes will soon be studied at a similar level of dynamic resolution as has been the norm for transcriptomes.
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Affiliation(s)
- Michal Breker
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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418
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Pejaver V, Hsu WL, Xin F, Dunker AK, Uversky VN, Radivojac P. The structural and functional signatures of proteins that undergo multiple events of post-translational modification. Protein Sci 2014; 23:1077-93. [PMID: 24888500 DOI: 10.1002/pro.2494] [Citation(s) in RCA: 265] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/26/2014] [Accepted: 05/27/2014] [Indexed: 12/24/2022]
Abstract
UNLABELLED The structural, functional, and mechanistic characterization of several types of post-translational modifications (PTMs) is well-documented. PTMs, however, may interact or interfere with one another when regulating protein function. Yet, characterization of the structural and functional signatures of their crosstalk has been hindered by the scarcity of data. To this end, we developed a unified sequence-based predictor of 23 types of PTM sites that, we believe, is a useful tool in guiding biological experiments and data interpretation. We then used experimentally determined and predicted PTM sites to investigate two particular cases of potential PTM crosstalk in eukaryotes. First, we identified proteins statistically enriched in multiple types of PTM sites and found that they show preferences toward intrinsically disordered regions as well as functional roles in transcriptional, posttranscriptional, and developmental processes. Second, we observed that target sites modified by more than one type of PTM, referred to as shared PTM sites, show even stronger preferences toward disordered regions than their single-PTM counterparts; we explain this by the need for these regions to accommodate multiple partners. Finally, we investigated the influence of single and shared PTMs on differential regulation of protein-protein interactions. We provide evidence that molecular recognition features (MoRFs) show significant preferences for PTM sites, particularly shared PTM sites, implicating PTMs in the modulation of this specific type of macromolecular recognition. We conclude that intrinsic disorder is a strong structural prerequisite for complex PTM-based regulation, particularly in context-dependent protein-protein interactions related to transcriptional and developmental processes. AVAILABILITY www.modpred.org.
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Affiliation(s)
- Vikas Pejaver
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana, 47405
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419
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Baeza J, Dowell JA, Smallegan MJ, Fan J, Amador-Noguez D, Khan Z, Denu JM. Stoichiometry of site-specific lysine acetylation in an entire proteome. J Biol Chem 2014; 289:21326-38. [PMID: 24917678 DOI: 10.1074/jbc.m114.581843] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Acetylation of lysine ϵ-amino groups influences many cellular processes and has been mapped to thousands of sites across many organisms. Stoichiometric information of acetylation is essential to accurately interpret biological significance. Here, we developed and employed a novel method for directly quantifying stoichiometry of site-specific acetylation in the entire proteome of Escherichia coli. By coupling isotopic labeling and a novel pairing algorithm, our approach performs an in silico enrichment of acetyl peptides, circumventing the need for immunoenrichment. We investigated the function of the sole NAD(+)-dependent protein deacetylase, CobB, on both site-specific and global acetylation. We quantified 2206 peptides from 899 proteins and observed a wide distribution of acetyl stoichiometry, ranging from less than 1% up to 98%. Bioinformatic analysis revealed that metabolic enzymes, which either utilize or generate acetyl-CoA, and proteins involved in transcriptional and translational processes displayed the highest degree of acetylation. Loss of CobB led to increased global acetylation at low stoichiometry sites and induced site-specific changes at high stoichiometry sites, and biochemical analysis revealed altered acetyl-CoA metabolism. Thus, this study demonstrates that sirtuin deacetylase deficiency leads to both site-specific and global changes in protein acetylation stoichiometry, affecting central metabolism.
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Affiliation(s)
- Josue Baeza
- From the Department of Biomolecular Chemistry, the Wisconsin Institute for Discovery, and
| | | | | | - Jing Fan
- the Wisconsin Institute for Discovery, and
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53715 and
| | - Zia Khan
- the Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, College Park, Maryland 20742
| | - John M Denu
- From the Department of Biomolecular Chemistry, the Wisconsin Institute for Discovery, and
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420
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Franci G, Ciotta A, Altucci L. The Jumonji family: past, present and future of histone demethylases in cancer. Biomol Concepts 2014; 5:209-24. [DOI: 10.1515/bmc-2014-0010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/15/2014] [Indexed: 01/04/2023] Open
Abstract
AbstractThe first Jumonji gene was cloned in 1995 by Takeuchi et al. [Takeuchi T, Yamazaki Y, Katoh-Fukui Y, Tsuchiya R, Kondo S, Motoyama J, Higashinakagawa T. Gene trap capture of a novel mouse gene, jumonji, required for neural tube formation. Genes Dev 1995; 9: 1211–22.]. Several genes sharing similar biological features have since been discovered, and are currently grouped into the JMJ family. Interestingly, their deregulation has been associated with cardiac disease, obesity, neurological disorders and cancer. One of the mechanisms underlying their function is gene expression modulation via histone post-translational modifications (PTMs). Increasing evidence of Jumonji deregulation in tumours such as colon, prostate, haematological and breast cancer is continually emerging, hence the need to acquire a better understanding. The Genesapiens.org database of patient arrays allows target expression levels to be investigated in a wide range of cancers, corroborating and extending the role of the JMJ family. Here, we provide an overview of the expression profile and regulation of JMJ family members in cancer, examining the most recent literature in the light of analyses drawn from this database.
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Affiliation(s)
- Gianluigi Franci
- 1Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università degli Studi di Napoli, Vico L. De Crecchio 7, I-80138 Napoli, Italy
| | - Alfonso Ciotta
- 1Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università degli Studi di Napoli, Vico L. De Crecchio 7, I-80138 Napoli, Italy
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421
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Chen YA, Eschrich SA. Computational methods and opportunities for phosphorylation network medicine. Transl Cancer Res 2014; 3:266-278. [PMID: 25530950 PMCID: PMC4271781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein phosphorylation, one of the most ubiquitous post-translational modifications (PTM) of proteins, is known to play an essential role in cell signaling and regulation. With the increasing understanding of the complexity and redundancy of cell signaling, there is a growing recognition that targeting the entire network or system could be a necessary and advantageous strategy for treating cancer. Protein kinases, the proteins that add a phosphate group to the substrate proteins during phosphorylation events, have become one of the largest groups of 'druggable' targets in cancer therapeutics in recent years. Kinase inhibitors are being regularly used in clinics for cancer treatment. This therapeutic paradigm shift in cancer research is partly due to the generation and availability of high-dimensional proteomics data. Generation of this data, in turn, is enabled by increased use of mass-spectrometry (MS)-based or other high-throughput proteomics platforms as well as companion public databases and computational tools. This review briefly summarizes the current state and progress on phosphoproteomics identification, quantification, and platform related characteristics. We review existing database resources, computational tools, methods for phosphorylation network inference, and ultimately demonstrate the connection to therapeutics. Finally, many research opportunities exist for bioinformaticians or biostatisticians based on developments and limitations of the current and emerging technologies.
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Affiliation(s)
- Yian Ann Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, 12902 Magnolia Drive Tampa, FL 33612, USA
| | - Steven A Eschrich
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, 12902 Magnolia Drive Tampa, FL 33612, USA
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422
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Viktorsson K, Lewensohn R, Zhivotovsky B. Systems biology approaches to develop innovative strategies for lung cancer therapy. Cell Death Dis 2014; 5:e1260. [PMID: 24874732 PMCID: PMC4047893 DOI: 10.1038/cddis.2014.28] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Accepted: 12/17/2013] [Indexed: 02/06/2023]
Abstract
Lung cancer (LC) is a number one killer of cancer-related death among men and women worldwide. Major advances have been made in the diagnosis, staging and use of surgery for LC, but systemic chemotherapy and radiotherapy alone or in combination with some targeted agents remains the core treatment of advanced LC. Unfortunately, in spite of improved diagnosis, surgical methods and new treatments, mortality is still extremely high among LC patients. To understand the precise functioning of signaling pathways associated with resistance to current treatments in LC, as well as to identify novel treatment regimens, a holistic approach to analyze signaling networks should be applied. Here, we describe systems biology-based approaches to generate biomarkers and novel therapeutic targets in LC, as well as how this may contribute to personalized treatment for this malignancy.
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Affiliation(s)
- K Viktorsson
- Department of Oncology–Pathology, Karolinska Biomics Center, Karolinska Institutet, Stockholm SE-171 76, Sweden
| | - R Lewensohn
- Department of Oncology–Pathology, Karolinska Biomics Center, Karolinska Institutet, Stockholm SE-171 76, Sweden
| | - B Zhivotovsky
- Institute of Environmental Medicine, Division of Toxicology, Karolinska Institutet, Box 210, Stockholm SE-171 77, Sweden
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow 117192, Russia
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423
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Guan D, Shao J, Zhao Z, Wang P, Qin J, Deng Y, Boheler KR, Wang J, Yan B. PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data. Nucleic Acids Res 2014; 42:W130-6. [PMID: 24875471 PMCID: PMC4086064 DOI: 10.1093/nar/gku471] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interactions among transcriptional factors (TFs), cofactors and other proteins or enzymes can affect transcriptional regulatory capabilities of eukaryotic organisms. Post-translational modifications (PTMs) cooperate with TFs and epigenetic alterations to constitute a hierarchical complexity in transcriptional gene regulation. While clearly implicated in biological processes, our understanding of these complex regulatory mechanisms is still limited and incomplete. Various online software have been proposed for uncovering transcriptional and epigenetic regulatory networks, however, there is a lack of effective web-based software capable of constructing underlying interactive organizations between post-translational and transcriptional regulatory components. Here, we present an open web server, post-translational hierarchical gene regulatory network (PTHGRN) to unravel relationships among PTMs, TFs, epigenetic modifications and gene expression. PTHGRN utilizes a graphical Gaussian model with partial least squares regression-based methodology, and is able to integrate protein–protein interactions, ChIP-seq and gene expression data and to capture essential regulation features behind high-throughput data. The server provides an integrative platform for users to analyze ready-to-use public high-throughput Omics resources or upload their own data for systems biology study. Users can choose various parameters in the method, build network topologies of interests and dissect their associations with biological functions. Application of the software to stem cell and breast cancer demonstrates that it is an effective tool for understanding regulatory mechanisms in biological complex systems. PTHGRN web server is publically available at web site http://www.byanbioinfo.org/pthgrn.
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Affiliation(s)
- Daogang Guan
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Jiaofang Shao
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Panwen Wang
- Department of Biochemistry and HKU-SIRI, The University of Hong Kong, Hong Kong SAR, China
| | - Jing Qin
- Department of Biochemistry and HKU-SIRI, The University of Hong Kong, Hong Kong SAR, China
| | - Youping Deng
- Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, Illinois 60612, USA
| | - Kenneth R Boheler
- Stem Cell & Regenerative Medicine Consortium, LKS Faculty of Medicine and Department of Physiology, The University of Hong Kong, Hong Kong SAR, China
| | - Junwen Wang
- Department of Biochemistry and HKU-SIRI, The University of Hong Kong, Hong Kong SAR, China Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Bin Yan
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China Stem Cell & Regenerative Medicine Consortium, LKS Faculty of Medicine and Department of Physiology, The University of Hong Kong, Hong Kong SAR, China
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424
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Abstract
So-called 'in-depth proteomics' and its applied separation methodology to improve the proteome coverage depth has become an important issue in mass spectrometric-based proteomics and system-wide cell biology studies. Employing a bottom-up approach and a variety of separation techniques, it allows for identification of proteins with low copy numbers and enables researchers to correlate the number of expressed genes in a cell with the proteome. Here we describe recent advances in this field with emphasis on peptide and protein separation technologies. The discussion is focused both on single injection analyses employing long reversed phase liquid chromatography separations of peptides ('single shot proteomics') and on the combination of orthogonal protein and peptide separation methods to achieve maximum protein coverage. Owing to these improvements, in-depth proteomics has now fully entered the field and is being implemented in an increasing number of laboratories.
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Affiliation(s)
- Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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425
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Marino F, Cristobal A, Binai NA, Bache N, Heck AJR, Mohammed S. Characterization and usage of the EASY-spray technology as part of an online 2D SCX-RP ultra-high pressure system. Analyst 2014; 139:6520-8. [DOI: 10.1039/c4an01568a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The EASY-spray technology can now be implemented as a simple online 2D SCX-RP ultra-high pressure system, which allows one to reach deep proteome coverages.
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Affiliation(s)
- Fabio Marino
- Biomolecular Mass Spectrometry and Proteomics
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
- University of Utrecht
- 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre
| | - Alba Cristobal
- Biomolecular Mass Spectrometry and Proteomics
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
- University of Utrecht
- 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre
| | - Nadine A. Binai
- Biomolecular Mass Spectrometry and Proteomics
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
- University of Utrecht
- 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre
| | | | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
- University of Utrecht
- 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
- University of Utrecht
- 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre
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