A genetic interaction network containing approximately 1000 genes and approximately 4000 interactions was mapped by crossing mutations in 132 different query genes into a set of approximately 4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to identify components of the same pathway. The genetic network exhibited dense local neighborhoods; therefore, the position of a gene on a partially mapped network is predictive of other genetic interactions. Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.
Large-scale screening of genetic and chemical-genetic interactions was used to examine the assembly and regulation of -1,3-glucan in Saccharomyces cerevisiae. Using the set of deletion mutants in 0064ف nonessential genes, we scored synthetic interactions with genes encoding subunits of the -1,3-glucan synthase (FKS1, FKS2), the glucan synthesis regulator (SMI1/KNR4), and a -1,3-glucanosyltransferase (GAS1). In the resulting network, FKS1, FKS2, GAS1, and SMI1 are connected to 135 genes in 195 interactions, with 26 of these genes also interacting with CHS3 encoding chitin synthase III. A network core of 51 genes is multiply connected with 112 interactions. Thirty-two of these core genes are known to be involved in cell wall assembly and polarized growth, and 8 genes of unknown function are candidates for involvement in these processes. In parallel, we screened the yeast deletion mutant collection for altered sensitivity to the glucan synthase inhibitor, caspofungin. Deletions in 52 genes led to caspofungin hypersensitivity and those in 39 genes to resistance. Integration of the glucan interaction network with the caspofungin data indicates an overlapping set of genes involved in FKS2 regulation, compensatory chitin synthesis, protein mannosylation, and the PKC1-dependent cell integrity pathway. al. 2002). In addition to the Rho1p regulatory subunit, other proteins are required for normal levels of -1,3-cells, is responsible for cell shape and osmotic stability, and acts as a filter for large molecules. The cell wall glucan. The SMI1/KNR4 gene was cloned by complementation of a Hansenula mrakii K9 killer toxin (a glucan is composed mainly of -1,3 and -1,6-glucans, mannoproteins, and chitin, with the relative proportions of synthase inhibitor) resistant mutant (Hong et al. 1994). T HE cell wall is a major organelle that surroundsThe smi1⌬ mutant has a highly permeable cell wall and these constituents varying with growth conditions and shows both decreased glucan synthase activity and cell the cellular developmental program. -1,3-Glucan is the wall -1,3-glucan content (Hong et al. 1994; Martin et principal cell wall component, to which the other comal. 1999). Genetic and biochemical evidence suggests ponents are crosslinked (Smits et al. 1999; that Smi1p acts in the PKC1-SLT2 signaling cascade by 2002). Synthesis of -1,3-glucan occurs at the plasma modulating the kinase activity of Slt2p (Martin-Yken membrane. Glucan synthase is thought to contain a et al. 2002, 2003). catalytic subunit, encoded by the two homologous genes Cell wall composition changes during growth, bud-FKS1 and FKS2/GSC2 (Mazur et al. 1995), and a regulading, mating, and sporulation, and these dynamic protory subunit, the small GTPase Rho1p (Drgonova et cesses require remodeling of the crosslinking of -1, 3-al. 1996; Mazur and Baginsky 1996; Qadota et al.and -1,6-glucans to themselves and to other cell wall 1996). FKS1 and FKS2 encode a pair of integral membrane components. Gas1p, a GPI-anchored protein localized proteins wi...
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