High-resolution yeast phenomics resolves different physiological features in the saline response

We present a methodology for gene functional prediction based on extraction of physiologically relevant growth variables from all viable haploid yeast knockout mutants. This quantitative phenomics approach, here applied to saline cultivation, identified marginal but functionally important phenotypes and allowed the precise determination of time to adapt to an environmental challenge, rate of growth, and efficiency of growth. We identified ≈500 salt-sensitive gene deletions, the majority of which were previously uncharacterized and displayed salt sensitivity for only one of the three physiological features. We also report a high correlation to protein–protein interaction data; in particular, several salt-sensitive subcellular networks indicating functional modules were revealed. In contrast, no correlation was found between gene dispensability and gene expression. It is proposed that high-resolution phenomics will be instrumental in systemwide descriptions of intragenomic functional networks.

[1]  S. Hohmann.  Osmotic Stress Signaling and Osmoadaptation in Yeasts , 2002, Microbiology and Molecular Biology Reviews.

[2]  Y. Dong,et al.  Systematic functional analysis of the Caenorhabditis elegans genome using RNAi , 2003, Nature.

[3]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[4]  M. Resnick,et al.  Genes required for ionizing radiation resistance in yeast , 2001, Nature Genetics.

[5]  M. Cyert,et al.  Genetic analysis of calmodulin and its targets in Saccharomyces cerevisiae. , 2001, Annual review of genetics.

[6]  Ronald W. Davis,et al.  A genome-wide screen in Saccharomyces cerevisiae for genes affecting UV radiation sensitivity , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[7]  T. G. Watson,et al.  Effects of sodium chloride on steady-state growth and metabolism of Saccharomyces cerevisiae. , 1970, Journal of general microbiology.

[8]  Anders Blomberg,et al.  Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae , 2003, Yeast.

[9]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[10]  W. J. Dickinson,et al.  Marginal fitness contributions of nonessential genes in yeast. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[11]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[12]  M. Snyder,et al.  A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. , 2001, Molecular biology of the cell.

[13]  Gary D Bader,et al.  Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants , 2001, Science.

[14]  K. Siegers,et al.  A novel protein complex promoting formation of functional α‐ and γ‐tubulin , 1998, The EMBO journal.

[15]  R. Gerlai.  Phenomics: fiction or the future? , 2002, Trends in Neurosciences.

[16]  Daniel R. Richards,et al.  Dissecting the architecture of a quantitative trait locus in yeast , 2002, Nature.

[17]  Elizabeth A. Winzeler,et al.  Genomic profiling of drug sensitivities via induced haploinsufficiency , 1999, Nature Genetics.

[18]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[19]  M. Aigle,et al.  Rvs161p and Sphingolipids Are Required for Actin Repolarization following Salt Stress , 2002, Eukaryotic Cell.

[20]  A. Mitchell,et al.  The Transcription Factor Rim101p Governs Ion Tolerance and Cell Differentiation by Direct Repression of the Regulatory Genes NRG1 and SMP1 in Saccharomyces cerevisiae , 2003, Molecular and Cellular Biology.

[21]  T. Ito,et al.  Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Kei-Hoi Cheung,et al.  Large-scale analysis of the yeast genome by transposon tagging and gene disruption , 1999, Nature.

[23]  Seth Sadis,et al.  Complementary whole-genome technologies reveal the cellular response to proteasome inhibition by PS-341 , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[24]  C. Glover.  On the physiological role of casein kinase II in Saccharomyces cerevisiae. , 1998, Progress in nucleic acid research and molecular biology.

[25]  E. Lander,et al.  Remodeling of yeast genome expression in response to environmental changes. , 2001, Molecular biology of the cell.

[26]  Elizabeth A. Winzeler,et al.  Large-scale mutagenesis and functional genomics in yeast , 2002, Functional & Integrative Genomics.

[27]  M. Johnston,et al.  A chemical genomics approach toward understanding the global functions of the target of rapamycin protein (TOR). , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[28]  D. Hawthorne,et al.  OSMOTIC-REMEDIAL MUTANTS. A NEW CLASSIFICATION FOR NUTRITIONAL MUTANTS IN YEAST. , 1964, Genetics.

[29]  Ronald W. Davis,et al.  Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.

[30]  Ronald W. Davis,et al.  Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents , 2002, Proceedings of the National Academy of Sciences of the United States of America.