High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast

TY - JOUR

T1 - High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast

AU - Gnad, Florian

AU - de Godoy, Lyris M F

AU - Cox, Jürgen

AU - Neuhauser, Nadin

AU - Ren, Shubin

AU - Olsen, Jesper V

AU - Mann, Matthias

PY - 2009

Y1 - 2009

N2 - 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).

AB - 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).

U2 - 10.1002/pmic.200900144

DO - 10.1002/pmic.200900144

M3 - Journal article

C2 - 19795423

SN - 1615-9853

VL - 9

SP - 4642

EP - 4652

JO - Proteomics

JF - Proteomics

IS - 20

ER -