The goal of this research is to determine the regulatory circuits in S. cerevisiae that control filamentation, a key morphogenetic even in pathogenic and non-pathogenic fungi. Our deletion library in the S. cerevisiae Sigma strain, when compared with the reference library in S288c, enables a comprehensive assessment of the genetic mechanisms leading to different filamentation and viability phenotypes for the same mutation in two different laboratory strains. This problem is the same one confronting human geneticists tackling the heritability of complex disease traits. The analysis of the filamentation/adhesion trait, which is important for the ability of fungi to adhere to medical devices, revealed that a m6A modification of mRNA, catalyzed by the IME4 gene, is a key post-trancriptional event that controls the decision to enter the filamentation or meiotic pathway. Experiments will determine the function of this m6A modification and whether the disappearance of the mark is due to demethylation or specific messenger degradation. The signal transduction pathway (the filamentation MAPK pathway, fMAPK) that activates filamentation genes in one strain (Sigma) is not required in the other (S288c), which has evolved polymorphisms that bypass the necessity for this pathway. The analysis of this alternative filamentation pathway will reveal the underlying network within which these polymorphisms develop. Of particular importance are two cis-acting non-coding RNAs, PWR1 and ICR1, that have been shown in Sigma to be a cis-acting toggle controlling the expression of the adjacent FLO11 gene, which is required for filamentation. Experiments are designed to determine whether these non-coding RNAs are involved in FLO11 expression in S288c, where a different set of trans- acting factors activate FLO11. These experiments will shed new light on the ubiquity of ncRNA regulation within a species. Our genome-wide comparison also identified conditionally essential genes, genes whose function is required for viability in one strain but not the other. The analysis of the genetic differences that lead to suppression of lethality has raised the possibility that extra-chromosomal elements (mitochondrial DNA) and dsRNA interact with chromosomal polymorphisms to cause variation. The discovery of these nucleo/cytoplasmic interactions adds an unanticipated dimension to the analysis of complex traits.

Public Health Relevance

Fungi, a major source of human disease, gain entry into the body mainly by adhering to indwelling medical devices such as catheters. This adhesion phenotype is complex, controlled by a network of interacting genes whose expression is regulated by nutrition, interaction, and non-coding RNAs. We have developed methods to identify the components of this network, which could identify new targets for anti-fungal agents.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM035010-30
Application #
8733704
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Reddy, Michael K
Project Start
1984-07-01
Project End
2017-05-31
Budget Start
2014-06-01
Budget End
2015-05-31
Support Year
30
Fiscal Year
2014
Total Cost
$552,833
Indirect Cost
$269,329
Name
Whitehead Institute for Biomedical Research
Department
Type
DUNS #
120989983
City
Cambridge
State
MA
Country
United States
Zip Code
02142
Vyas, Valmik K; Barrasa, M Inmaculada; Fink, Gerald R (2015) A Candida albicans CRISPR system permits genetic engineering of essential genes and gene families. Sci Adv 1:e1500248
Lam, Felix H; Ghaderi, Adel; Fink, Gerald R et al. (2014) Biofuels. Engineering alcohol tolerance in yeast. Science 346:71-5
Edwards, Matthew D; Symbor-Nagrabska, Anna; Dollard, Lindsey et al. (2014) Interactions between chromosomal and nonchromosomal elements reveal missing heritability. Proc Natl Acad Sci U S A 111:7719-22
Wang, Benjamin L; Ghaderi, Adel; Zhou, Hang et al. (2014) Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption. Nat Biotechnol 32:473-8
Schwartz, Schraga; Bernstein, Douglas A; Mumbach, Maxwell R et al. (2014) Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 159:148-62
Schwartz, Schraga; Agarwala, Sudeep D; Mumbach, Maxwell R et al. (2013) High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell 155:1409-21
Avalos, José L; Fink, Gerald R; Stephanopoulos, Gregory (2013) Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols. Nat Biotechnol 31:335-41
Bumgarner, Stacie L; Neuert, Gregor; Voight, Benjamin F et al. (2012) Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment. Mol Cell 45:470-82
Agarwala, Sudeep D; Blitzblau, Hannah G; Hochwagen, Andreas et al. (2012) RNA methylation by the MIS complex regulates a cell fate decision in yeast. PLoS Genet 8:e1002732
Ryan, Owen; Shapiro, Rebecca S; Kurat, Christoph F et al. (2012) Global gene deletion analysis exploring yeast filamentous growth. Science 337:1353-6

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