title: Global analysis of protein phosphorylation in yeast.
abstract: Protein phosphorylation is estimated to affect 30% of the proteome and is a major regulatory mechanism that controls many basic cellular processes. Until recently, our biochemical understanding of protein phosphorylation on a global scale has been extremely limited; only one half of the yeast kinases have known in vivo substrates and the phosphorylating kinase is known for less than 160 phosphoproteins. Here we describe, with the use of proteome chip technology, the in vitro substrates recognized by most yeast protein kinases: we identified over 4,000 phosphorylation events involving 1,325 different proteins. These substrates represent a broad spectrum of different biochemical functions and cellular roles. Distinct sets of substrates were recognized by each protein kinase, including closely related kinases of the protein kinase A family and four cyclin-dependent kinases that vary only in their cyclin subunits. Although many substrates reside in the same cellular compartment or belong to the same functional category as their phosphorylating kinase, many others do not, indicating possible new roles for several kinases. Furthermore, integration of the phosphorylation results with protein-protein interaction and transcription factor binding data revealed novel regulatory modules. Our phosphorylation results have been assembled into a first-generation phosphorylation map for yeast. Because many yeast proteins and pathways are conserved, these results will provide insights into the mechanisms and roles of protein phosphorylation in many eukaryotes.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA.
authors.forename: Jason
authors.initials: J
authors.lastname: Ptacek
authors.forename: Geeta
authors.initials: G
authors.lastname: Devgan
authors.forename: Gregory
authors.initials: G
authors.lastname: Michaud
authors.forename: Heng
authors.initials: H
authors.lastname: Zhu
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zhu
authors.forename: Joseph
authors.initials: J
authors.lastname: Fasolo
authors.forename: Hong
authors.initials: H
authors.lastname: Guo
authors.forename: Ghil
authors.initials: G
authors.lastname: Jona
authors.forename: Ashton
authors.initials: A
authors.lastname: Breitkreutz
authors.forename: Richelle
authors.initials: R
authors.lastname: Sopko
authors.forename: Rhonda R
authors.initials: RR
authors.lastname: McCartney
authors.forename: Martin C
authors.initials: MC
authors.lastname: Schmidt
authors.forename: Najma
authors.initials: N
authors.lastname: Rachidi
authors.forename: Soo-Jung
authors.initials: SJ
authors.lastname: Lee
authors.forename: Angie S
authors.initials: AS
authors.lastname: Mah
authors.forename: Lihao
authors.initials: L
authors.lastname: Meng
authors.forename: Michael J R
authors.initials: MJ
authors.lastname: Stark
authors.forename: David F
authors.initials: DF
authors.lastname: Stern
authors.forename: Claudio
authors.initials: C
authors.lastname: De Virgilio
authors.forename: Mike
authors.initials: M
authors.lastname: Tyers
authors.forename: Brenda
authors.initials: B
authors.lastname: Andrews
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
authors.forename: Barry
authors.initials: B
authors.lastname: Schweitzer
authors.forename: Paul F
authors.initials: PF
authors.lastname: Predki
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
mesh_terms: D005057:Eukaryotic Cells / Q000378:metabolism; D005656:Fungal Proteins / Q000737:chemistry / Q000378:metabolism*; D010766:Phosphorylation; D040081:Protein Array Analysis; D011494:Protein Kinases / Q000145:classification / Q000378:metabolism*; D021381:Protein Transport; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics; D015203:Reproducibility of Results; D013379:Substrate Specificity; D015003:Yeasts / Q000201:enzymology / Q000378:metabolism*
chemical_list: D005656:Fungal Proteins; D020543:Proteome; D011494:Protein Kinases