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

doi:10.1016/j.isci.2022.104489

Time-resolved phosphoproteome and proteome analysis reveals kinase signaling on master transcription factors during myogenesis

iScience. 2022 May 30;25(6):104489. doi: 10.1016/j.isci.2022.104489. eCollection 2022 Jun 17.

Authors

Di Xiao^{1

2}, Marissa Caldow³, Hani Jieun Kim^{1

2}, Ronnie Blazev³, Rene Koopman³, Deborah Manandi¹, Benjamin L Parker³, Pengyi Yang^{1

2}

Affiliations

¹ Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia.
² Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia.
³ Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia.

Abstract

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.

Keywords: Developmental biology; cell biology; proteomics.