The overall goal of the proposed research is to acquire a set of mutations covering the entire surface of conserved proteins already known to have important cellular functions in yeast. After characterization, these mutations will be used to find interacting genes and proteins using a variety of genetic techniques, including isolation and analysis of pseudo-revertants, unlinked non-complementing mutants, and mutations displaying synthetic lethality. We expect to find different genetic interactions with mutations linking different regions of a protein's surface, and it is for this reason that we plan to start with a """"""""synoptic"""""""" set of mutations made with a recent modification of a new technology, the charged-to-alanine scan. Genetic studies of mutations in the interacting genes will be supplemented with limited biochemical investigations aimed at characterizing the interactions of normal and mutant gene products. We hope in the end to make the finding of interacting genes and proteins by genetic methods as reliable and routine as mutagenesis has become. These technologies will be developed and applied to several specific projects: First, we will construct and characterize a synoptic set of new tubulin mutants of yeast. Second, we will identify genetically genes encoding ligands to the actin and tubulin cytoskeletons starting with a synoptic set of alanine-scanning mutants covering actin (already in hand) and the tubulins. Third, we will carry out homolog-scanning hybrid mutagenesis between pairs of genes encoding small GTP-binding proteins in yeast (e.g. the products of the YPTI and SEC4 genes) in order to try to identify, in complementation tests using these hybrids, the sub-domains of these highly similar proteins that determine their specificity for a particular function in protein secretion. Fourth, we will construct mutations with scorable non-lethal or conditional-lethal phenotypes within specificity-determining subdomains of the aforementioned GTP-binding proteins and use these to identify genetically genes encoding protein ligands to particular GTP-binding proteins.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Method to Extend Research in Time (MERIT) Award (R37)
Project #
5R37GM046406-10
Application #
6179367
Study Section
Special Emphasis Panel (NSS)
Program Officer
Deatherage, James F
Project Start
1991-07-01
Project End
2001-06-30
Budget Start
2000-07-01
Budget End
2001-06-30
Support Year
10
Fiscal Year
2000
Total Cost
$682,907
Indirect Cost
Name
Stanford University
Department
Genetics
Type
Schools of Medicine
DUNS #
800771545
City
Stanford
State
CA
Country
United States
Zip Code
94305
Gibney, Patrick A; Schieler, Ariel; Chen, Jonathan C et al. (2018) Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast. Mol Biol Cell 29:897-910
Hackett, Sean R; Zanotelli, Vito R T; Xu, Wenxin et al. (2016) Systems-level analysis of mechanisms regulating yeast metabolic flux. Science 354:
Reavey, Caitlin T; Hickman, Mark J; Dobi, Krista C et al. (2015) Analysis of Polygenic Mutants Suggests a Role for Mediator in Regulating Transcriptional Activation Distance in Saccharomyces cerevisiae. Genetics 201:599-612
Møller, Henrik D; Parsons, Lance; Jørgensen, Tue S et al. (2015) Extrachromosomal circular DNA is common in yeast. Proc Natl Acad Sci U S A 112:E3114-22
Gibney, Patrick A; Schieler, Ariel; Chen, Jonathan C et al. (2015) Characterizing the in vivo role of trehalose in Saccharomyces cerevisiae using the AGT1 transporter. Proc Natl Acad Sci U S A 112:6116-21
McIsaac, R Scott; Gibney, Patrick A; Chandran, Sunil S et al. (2014) Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae. Nucleic Acids Res 42:e48
Lang, Gregory I; Rice, Daniel P; Hickman, Mark J et al. (2013) Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature 500:571-4
Gibney, Patrick A; Lu, Charles; Caudy, Amy A et al. (2013) Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes. Proc Natl Acad Sci U S A 110:E4393-402
McIsaac, R Scott; Silverman, Sanford J; Parsons, Lance et al. (2013) Visualization and analysis of mRNA molecules using fluorescence in situ hybridization in Saccharomyces cerevisiae. J Vis Exp :e50382
Gibney, Patrick A; Hickman, Mark J; Bradley, Patrick H et al. (2013) Phylogenetic portrait of the Saccharomyces cerevisiae functional genome. G3 (Bethesda) 3:1335-40

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