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...

Full description

Saved in:
Bibliographic Details
Published inProceedings of the National Academy of Sciences - PNAS Vol. 100; no. 26; pp. 15724 - 15729
Main Authors Warringer, J, Ericson, E, Fernandez, L, Nerman, O, Blomberg, A
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 23.12.2003
National Acad Sciences
Subjects
Biological Sciences
Cell growth
Correlations
Cytoskeleton - genetics
Endosomes - genetics
Gene Deletion
Gene expression regulation
Genes
Genetic screening
Genetics
Genome, Fungal
Genomics
Golgi Apparatus - genetics
knockout mutants
Phenotype
Phenotypes
Quantum efficiency
Saccharomyces cerevisiae
Saccharomyces cerevisiae - drug effects
Saccharomyces cerevisiae - genetics
Saccharomyces cerevisiae - growth & development
salinity
Salt
salt stress
Salts
Sodium Chloride - pharmacology
Yeast
Yeasts
Online AccessGet full text

Cover

More Information
Summary: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.
Bibliography:ObjectType-Article-2
SourceType-Scholarly Journals-1
ObjectType-Feature-1
content type line 23
ObjectType-Article-1
ObjectType-Feature-2
To whom correspondence should be addressed. E-mail: jonas.warringer@gmm.gu.se.
This paper was submitted directly (Track II) to the PNAS office.
Edited by Fred Sherman, University of Rochester School of Medicine and Dentistry, Rochester, NY, and approved September 12, 2003
Abbreviations: LPI, logarithmic (natural logarithm) phenotypic index; LSC, logarithmic (natural logarithm) strain coefficients; MIPS, Munich Information Center for Protein Sequences.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.2435976100