Reconstructing the regulatory kinase pathways of myogenesis from phosphopeptide data.
Multiple kinase activities are required for skeletal muscle differentiation. However, the mechanisms by which these kinase pathways converge to coordinate the myogenic process are unknown. Using multiple phosphoprotein and phosphopeptide enrichment techniques we obtained phosphopeptides from growing and differentiating C2C12 muscle cells and determined specific peptide sequences using LC-MS/MS. To place these phosphopeptides into a rational context, a bioinformatics approach was used. Phosphorylation sites were matched to known site-specific and to site non-specific kinase-substrate interactions, and then other substrates and upstream regulators of the implicated kinases were incorporated into a model network of protein-protein interactions. The model network implicated several kinases of known relevance to myogenesis including AKT, GSK3, CDK5, p38, DYRK, and MAPKAPK2 kinases. This combination of proteomics and bioinformatics technologies should offer great utility as the volume of protein-protein and kinase-substrate information continues to increase.
Puente
Lawrence G
LG
Ottawa Health Research Institute, Molecular Medicine Program, Ottawa Hospital, and Department of Cellular and Molecular Medicine, Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ontario K1H 8L6, Canada.
Voisin
Sébastien
S
Lee
Robin E C
RE
Megeney
Lynn A
LA
D000818:Animals; D002478:Cells, Cultured; D053858:Metabolic Networks and Pathways; D051379:Mice; D008954:Models, Biological; D024510:Muscle Development / Q000502:physiology*; D010748:Phosphopeptides / Q000032:analysis*; D010770:Phosphotransferases / Q000378:metabolism*; D025941:Protein Interaction Mapping; D017346:Protein Serine-Threonine Kinases / Q000378:metabolism; D011505:Protein-Tyrosine Kinases / Q000378:metabolism; D040901:Proteomics / Q000379:methods; D049490:Systems Biology; D000097603:Dyrk Kinases
D010748:Phosphopeptides; D010770:Phosphotransferases; D017346:Protein Serine-Threonine Kinases; D011505:Protein-Tyrosine Kinases; D000097603:Dyrk Kinases