Time-resolved phosphoproteome and proteome analysis reveals kinase signaling on master transcription factors during myogenesis
Di Xiao,
Marissa Caldow,
Hani Jieun Kim,
Ronnie Blazev,
Rene Koopman,
Deborah Manandi,
Benjamin L. Parker,
Pengyi Yang
Affiliations
Di Xiao
Computational Systems Biology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia; Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
Marissa Caldow
Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
Hani Jieun Kim
Computational Systems Biology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia; Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
Ronnie Blazev
Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
Rene Koopman
Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
Deborah Manandi
Computational Systems Biology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
Benjamin L. Parker
Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia; Corresponding author
Pengyi Yang
Computational Systems Biology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia; Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia; Corresponding author
Summary: Myogenesis is governed by signaling networks that are tightly regulated in a time-dependent manner. Although different protein kinases have been identified, knowledge of the global signaling networks and their downstream substrates during myogenesis remains incomplete. Here, we map the myogenic differentiation of C2C12 cells using phosphoproteomics and proteomics. From these data, we infer global kinase activity and predict the substrates that are involved in myogenesis. We found that multiple mitogen-activated protein kinases (MAPKs) mark the initial wave of signaling cascades. Further phosphoproteomic and proteomic profiling with MAPK1/3 and MAPK8/9 specific inhibitions unveil their shared and distinctive roles in myogenesis. Lastly, we identified and validated the transcription factor nuclear factor 1 X-type (NFIX) as a novel MAPK1/3 substrate and demonstrated the functional impact of NFIX phosphorylation on myogenesis. Altogether, these data characterize the dynamics, interactions, and downstream control of kinase signaling networks during myogenesis on a global scale.
