Subcellular localization of the yeast proteome.
Protein localization data are a valuable information resource helpful in elucidating eukaryotic protein function. Here, we report the first proteome-scale analysis of protein localization within any eukaryote. Using directed topoisomerase I-mediated cloning strategies and genome-wide transposon mutagenesis, we have epitope-tagged 60% of the Saccharomyces cerevisiae proteome. By high-throughput immunolocalization of tagged gene products, we have determined the subcellular localization of 2744 yeast proteins. Extrapolating these data through a computational algorithm employing Bayesian formalism, we define the yeast localizome (the subcellular distribution of all 6100 yeast proteins). We estimate the yeast proteome to encompass approximately 5100 soluble proteins and >1000 transmembrane proteins. Our results indicate that 47% of yeast proteins are cytoplasmic, 13% mitochondrial, 13% exocytic (including proteins of the endoplasmic reticulum and secretory vesicles), and 27% nuclear/nucleolar. A subset of nuclear proteins was further analyzed by immunolocalization using surface-spread preparations of meiotic chromosomes. Of these proteins, 38% were found associated with chromosomal DNA. As determined from phenotypic analyses of nuclear proteins, 34% are essential for spore viability--a percentage nearly twice as great as that observed for the proteome as a whole. In total, this study presents experimentally derived localization data for 955 proteins of previously unknown function: nearly half of all functionally uncharacterized proteins in yeast. To facilitate access to these data, we provide a searchable database featuring 2900 fluorescent micrographs at http://ygac.med.yale.edu.
Kumar
Anuj
A
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.
Agarwal
Seema
S
Heyman
John A
JA
Matson
Sandra
S
Heidtman
Matthew
M
Piccirillo
Stacy
S
Umansky
Lara
L
Drawid
Amar
A
Jansen
Ronald
R
Liu
Yang
Y
Cheung
Kei-Hoi
KH
Miller
Perry
P
Gerstein
Mark
M
Roeder
G Shirleen
GS
Snyder
Michael
M
D000465:Algorithms; D002467:Cell Nucleus / Q000378:metabolism; D002875:Chromosomes / Q000378:metabolism; D003593:Cytoplasm / Q000378:metabolism; D019992:Databases as Topic; D000939:Epitopes; D016681:Genome, Fungal; D008856:Microscopy, Fluorescence; D008928:Mitochondria / Q000378:metabolism; D008957:Models, Genetic; D016296:Mutagenesis; D010641:Phenotype; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D012984:Software
D000939:Epitopes