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Krycer JR, Yugi K, Hirayama A, Fazakerley DJ, Quek LE, Scalzo R, Ohno S, Hodson MP, Ikeda S, Shoji F, Suzuki K, Domanova W, Parker BL, Nelson ME, Humphrey SJ, Turner N, Hoehn KL, Cooney GJ, Soga T, Kuroda S, James DE. Dynamic Metabolomics Reveals that Insulin Primes the Adipocyte for Glucose Metabolism. Cell Rep 2018; 21:3536-3547. [PMID: 29262332 DOI: 10.1016/j.celrep.2017.11.085] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/06/2017] [Accepted: 11/22/2017] [Indexed: 01/13/2023] Open
Abstract
Insulin triggers an extensive signaling cascade to coordinate adipocyte glucose metabolism. It is considered that the major role of insulin is to provide anabolic substrates by activating GLUT4-dependent glucose uptake. However, insulin stimulates phosphorylation of many metabolic proteins. To examine the implications of this on glucose metabolism, we performed dynamic tracer metabolomics in cultured adipocytes treated with insulin. Temporal analysis of metabolite concentrations and tracer labeling revealed rapid and distinct changes in glucose metabolism, favoring specific glycolytic branch points and pyruvate anaplerosis. Integrating dynamic metabolomics and phosphoproteomics data revealed that insulin-dependent phosphorylation of anabolic enzymes occurred prior to substrate accumulation. Indeed, glycogen synthesis was activated independently of glucose supply. We refer to this phenomenon as metabolic priming, whereby insulin signaling creates a demand-driven system to "pull" glucose into specific anabolic pathways. This complements the supply-driven regulation of anabolism by substrate accumulation and highlights an additional role for insulin action in adipocyte glucose metabolism.
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Affiliation(s)
- James R Krycer
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Katsuyuki Yugi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; YCI Laboratory for Trans-Omics, Young Chief Investigator Program, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; PRESTO, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; AMED-CREST, AMED, 1-7-1 Otemachi, Chiyoda-Ku, Tokyo 100-0004, Japan
| | - Daniel J Fazakerley
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Lake-Ee Quek
- Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia; School of Mathematics and Statistics, The University of Sydney, Sydney NSW 2006, Australia
| | - Richard Scalzo
- Centre for Translational Data Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Satoshi Ohno
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mark P Hodson
- Metabolomics Australia Queensland Node, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia; School of Pharmacy, Faculty of Health and Behavioural Sciences, University of Queensland, Brisbane, QLD 4072, Australia; Metabolomics Research Laboratory, Victor Chang Innovation Centre, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Satsuki Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Futaba Shoji
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Kumi Suzuki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Westa Domanova
- Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia; School of Physics, University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin L Parker
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Marin E Nelson
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Sean J Humphrey
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Nigel Turner
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Kyle L Hoehn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Gregory J Cooney
- Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia; Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; AMED-CREST, AMED, 1-7-1 Otemachi, Chiyoda-Ku, Tokyo 100-0004, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan; CREST, Japan Science and Technology Agency, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - David E James
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia; Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia.
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Domanova W, Krycer J, Chaudhuri R, Yang P, Vafaee F, Fazakerley D, Humphrey S, James D, Kuncic Z. Unraveling Kinase Activation Dynamics Using Kinase-Substrate Relationships from Temporal Large-Scale Phosphoproteomics Studies. PLoS One 2016; 11:e0157763. [PMID: 27336693 PMCID: PMC4918924 DOI: 10.1371/journal.pone.0157763] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/03/2016] [Indexed: 01/04/2023] Open
Abstract
In response to stimuli, biological processes are tightly controlled by dynamic cellular signaling mechanisms. Reversible protein phosphorylation occurs on rapid time-scales (milliseconds to seconds), making it an ideal carrier of these signals. Advances in mass spectrometry-based proteomics have led to the identification of many tens of thousands of phosphorylation sites, yet for the majority of these the kinase is unknown and the underlying network topology of signaling networks therefore remains obscured. Identifying kinase substrate relationships (KSRs) is therefore an important goal in cell signaling research. Existing consensus sequence motif based prediction algorithms do not consider the biological context of KSRs, and are therefore insensitive to many other mechanisms guiding kinase-substrate recognition in cellular contexts. Here, we use temporal information to identify biologically relevant KSRs from Large-scale In Vivo Experiments (KSR-LIVE) in a data-dependent and automated fashion. First, we used available phosphorylation databases to construct a repository of existing experimentally-predicted KSRs. For each kinase in this database, we used time-resolved phosphoproteomics data to examine how its substrates changed in phosphorylation over time. Although substrates for a particular kinase clustered together, they often exhibited a different temporal pattern to the phosphorylation of the kinase. Therefore, although phosphorylation regulates kinase activity, our findings imply that substrate phosphorylation likely serve as a better proxy for kinase activity than kinase phosphorylation. KSR-LIVE can thereby infer which kinases are regulated within a biological context. Moreover, KSR-LIVE can also be used to automatically generate positive training sets for the subsequent prediction of novel KSRs using machine learning approaches. We demonstrate that this approach can distinguish between Akt and Rps6kb1, two kinases that share the same linear consensus motif, and provide evidence suggesting IRS-1 S265 as a novel Akt site. KSR-LIVE is an open-access algorithm that allows users to dissect phosphorylation signaling within a specific biological context, with the potential to be included in the standard analysis workflow for studying temporal high-throughput signal transduction data.
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Affiliation(s)
- Westa Domanova
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Physics, The University of Sydney, Sydney, NSW 2006, Australia
| | - James Krycer
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Rima Chaudhuri
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Pengyi Yang
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC 27709, United States of America
| | - Fatemeh Vafaee
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - Daniel Fazakerley
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Sean Humphrey
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, 82152, Germany
| | - David James
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Zdenka Kuncic
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Physics, The University of Sydney, Sydney, NSW 2006, Australia
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Wilkins K, Hassan M, Francescatto M, Jespersen J, Parra RG, Cuypers B, DeBlasio D, Junge A, Jigisha A, Rahman F, Laenen G, Willems S, Thorrez L, Moreau Y, Raju N, Chothani SP, Ramakrishnan C, Sekijima M, Gromiha MM, Slator PJ, Burroughs NJ, Szałaj P, Tang Z, Michalski P, Luo O, Li X, Ruan Y, Plewczynski D, Fiscon G, Weitschek E, Ciccozzi M, Bertolazzi P, Felici G, Cuypers B, Meysman P, Vanaerschot M, Berg M, Imamura H, Dujardin JC, Laukens K, Domanova W, Krycer JR, Chaudhuri R, Yang P, Vafaee F, Fazakerley DJ, Humphrey SJ, James DE, Kuncic Z. Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015. BMC Bioinformatics 2016; 17 Suppl 3:95. [PMID: 26986007 PMCID: PMC4895264 DOI: 10.1186/s12859-016-0901-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A Systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic
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