Subcellular localization of the yeast proteome.

By Anuj Kumar, S. Agarwal, J. Heyman, S. Matson, M. Heidtman, Stacy Piccirillo, Lara Umansky, A. Drawid, R. Jansen, Yang Liu and 5 more. Genes & Development, 2002

746 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6623f116b5b5a53262556148e5d24858571854ba

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Citations in the corpus

Locating proteins in the cell using TargetP, SignalP and related tools (2007, background): “or simian virus V5 epitope to tag cDNAs and localize the resulting fusion proteins through fluorescence screening of the transfected yeast cell”
Comparing protein abundance and mRNA expression levels on a genomic scale (2003, positive): “(b,c) Additionally, we show that when looking at specific subsets (subcellular localization [52] or functional groups [34,35]) we can find both higher and lower correlations amongst these groups.”
Imaging mass spectrometry. (2007, background): “It has long been known that the proteins expressed within an organism are dependent on the organ, cell and sub-cellular location, and it has now been established that the spatial distribution of a biomolecule is intrinsically related to its role (Simpson et al., 2000; Kumar et al., 2002).”
Characterization of the human heart mitochondrial proteome (2003, background): “Recent high-throughput immunolocalization of 2,744 tagged gene products in yeas”
Ribosome assembly in eukaryotes. (2003, background): “g Column 9 indicates the results of protein localization by a systematic approach (Kumar et al., 2002).”
Mimicking cellular sorting improves prediction of subcellular localization. (2005, methodology): “Using experimental highthroughput methods for epitope and green fluorescent protein (GFP) tagging, two groups have recently reported localization data for most proteins in Saccharomyces cerevisiae (baker’s yeast).(6,7) So far, the majority of large-scale experimental efforts to predict localization ”
A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity (2003, background): “elegans may not be complete; for example, recent results estimated that 13% of yeast proteins are localized to the mitochondri”
Protein analysis on a proteomic scale (2003, background): “cerevisiae by immunolocalization of epitope-tagged gene product”
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae (2006, methodology): “We used previously published yeast protein localization data 5,6 , and yeast protein properties were obtained from the SGD (http:// www.yeastgenome.org/) and GO (http://www.geneontology.org) databases.”
Protein interaction networks from yeast to human. (2004, methodology): “These interaction data were complemented by several types of supporting data, including large-scale yeast protein localization data (using GFP-tagged yeast proteins [18 ,19]) and the quantitation of the expression levels of approximately 4500 affinitytagged yeast proteins through western blot analys”
FunSpec: a web-based cluster interpreter for yeast (2002, background): “…now mass stores of high-throughput biological data accumulating from experimental results such as synthetic lethal [13], protein interactions by yeast two hybrid [14,15] or mass spectrometry [16,17], immunolocalization [18], large-scale phenotypic analysis [19], and microarray analysis (eg., [8]).”
The Carnegie Protein Trap Library: A Versatile Tool for Drosophila Developmental Studies (2007, background): “Subcellular distribution of protein location: Previously, gene and protein trapping in yeast has been used to estimate the fraction of proteins that are localized to various cellular compartments (Ross-Macdonald et al. 1999; Kumar et al. 2002; Huh et al. 2003).”