High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.
Protein phosphorylation is a fundamental regulatory mechanism that affects many cell signaling processes. Using high-accuracy MS and stable isotope labeling in cell culture-labeling, we provide a global view of the Saccharomyces cerevisiae phosphoproteome, containing 3620 phosphorylation sites mapped to 1118 proteins, representatively covering the yeast kinome and a multitude of transcription factors. We show that a single false discovery rate for all peptide identifications significantly overestimates occurrence of rare modifications, such as tyrosine phosphorylation in yeast. The identified phosphorylation sites are predominantly located on irregularly structured and accessible protein regions. We found high evolutionary conservation of phosphorylated proteins and a large overlap of significantly over-represented motifs with the human phosphoproteome. Nevertheless, phosphorylation events at the site level were not highly conserved between yeast and higher eukaryotes, which points to metazoan-specific kinase and substrate families. We constructed a yeast-specific phosphorylation sites predictor on the basis of a support vector machine, which - together with the yeast phosphorylation data - is integrated into the PHOSIDA database (www.phosida.com).
Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Martinsried, Germany.
Florian
F
Gnad
Lyris M F
LM
de Godoy
Jürgen
J
Cox
Nadin
N
Neuhauser
Shubin
S
Ren
Jesper V
JV
Olsen
Matthias
M
Mann
D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D019143:Evolution, Molecular; D006801:Humans; D010766:Phosphorylation; D020543:Proteome / Q000032:analysis* / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000737:chemistry*; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis* / Q000235:genetics
D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins