Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae

doi:10.1073/pnas.0634629100

Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomycescerevisiae

^*Proteomics, Torrey Mesa Research Institute, 3115 Merryfield Row, San Diego, CA 92121; ^‡Genomics Institute, Novartis Research Foundation, 10675 John J. Hopkins Drive, San Diego, CA 92121; and ^¶Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037

Edited by Patrick O. Brown, Stanford University School of Medicine, Stanford, CA, and approved January 17, 2003 (received for review August 1, 2002)

Abstract

The mRNA and protein expression in Saccharomyces cerevisiae cultured in rich or minimal media was analyzed by oligonucleotide arrays and quantitative multidimensional protein identification technology. The overall correlation between mRNA and protein expression was weakly positive with a Spearman rank correlation coefficient of 0.45 for 678 loci. To place the data sets in a proper biological context, a clustering approach based on protein pathways and protein complexes was implemented. Protein expression levels were transcriptionally controlled for not only single loci but for entire protein pathways (e.g., Met, Arg, and Leu biosynthetic pathways). In contrast, the protein expression of loci in several protein complexes (e.g., SPT, COPI, and ribosome) was posttranscriptionally controlled. The coupling of the methods described provided insight into the biology of S. cerevisiae and a clustering strategy by which future studies should be based.

Footnotes

↵ † To whom correspondence should be addressed. E-mail: michael.washburn{at}syngenta.com.
↵ § Present address: Kalypsys, Inc., 11099 North Torrey Pines Road, Suite 200, La Jolla, CA 92037.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations:

YEPD,

yeast extract/peptone/dextrose;

MudPIT,

multidimensional protein identification technology;

ACN,

acetonitrile;

HFBA,

heptafluorobutyric acid;

CAI,

codon adaptation index