Subcellular localization of the yeast proteome (original) (raw)
- Anuj Kumar1,
- Seema Agarwal1,
- John A. Heyman3,5,
- Sandra Matson1,
- Matthew Heidtman1,
- Stacy Piccirillo1,
- Lara Umansky1,
- Amar Drawid2,
- Ronald Jansen2,
- Yang Liu2,
- Kei-Hoi Cheung4,
- Perry Miller4,
- Mark Gerstein2,
- G. Shirleen Roeder1, and
- Michael Snyder1,2,6
- 1Department of Molecular, Cellular, and Developmental Biology, 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA;3Invitrogen Corporation, Carlsbad, California 92008, USA;4Center for Medical Informatics, Department of Anesthesiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
Abstract
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 ∼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 athttp://ygac.med.yale.edu.
Footnotes
↵5 Present address: Active Motif, 104 Avenue Franklin Roosevelt, Box-25, B-1330 Rixensart, Belgium.
↵6 Corresponding author.
E-MAIL michael.snyder{at}yale.edu; FAX (203) 432-6161.
Article and publication are at http://www.genesdev.org/cgi/doi/10.1101/gad.970902.
- Received December 18, 2001.
- Accepted February 1, 2002.
Cold Spring Harbor Laboratory Press