Comprehensive and quantitative analysis of yeast deletion mutants defective in apical and isotropic bud growth

Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
Current Genetics (Impact Factor: 1.71). 06/2009; 55(4):365-80. DOI: 10.1007/s00294-009-0251-0
Source: PubMed

ABSTRACT To obtain a comprehensive understanding of the budding phase transition, 4,711 Saccharomyces cerevisiae haploid nonessential gene deletion mutants were screened with the image processing program CalMorph, and 35 mutants with a round bud and 173 mutants with an elongated bud were statistically identified. We classified round and elongated bud mutants based on factors thought to affect the duration of the apical bud growth phase. Two round bud mutants (arc18 and sac6) were found to be defective in apical actin patch localization. Several elongated bud mutants demonstrated a delay of cell cycle progression at the apical growth phase, suggesting that these mutants have a defect in the control of cell cycle progression.

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    • ") and their mutants tend to have phenotypic defects that are detectable in standard growth conditions (e.g., elongated buds, flocculated colonies , aberrant cell wall involving morphologies and fitness defects) (Martin et al. 1996; Edgington et al. 1999; Asano et al. 2006; Breslow et al. 2008; Watanabe et al. 2009), reflecting their requirement for normal cell cycle progression. Consistent with these observations, the hub kinases were also significantly enriched for interactions with genes involved in cell cycle progression (11-fold, P < 10 À4 ) "
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    ABSTRACT: A combinatorial genetic perturbation strategy was applied to interrogate the yeast kinome on a genome-wide scale. We assessed the global effects of gene overexpression or gene deletion to map an integrated genetic interaction network of synthetic dosage lethal (SDL) and loss-of-function genetic interactions (GIs) for 92 kinases, producing a meta-network of 8700 GIs enriched for pathways known to be regulated by cognate kinases. Kinases most sensitive to dosage perturbations had constitutive cell cycle or cell polarity functions under standard growth conditions. Condition-specific screens confirmed that the spectrum of kinase dosage interactions can be expanded substantially in activating conditions. An integrated network composed of systematic SDL, negative and positive loss-of-function GIs, and literature-curated kinase-substrate interactions revealed kinase-dependent regulatory motifs predictive of novel gene-specific phenotypes. Our study provides a valuable resource to unravel novel functional relationships and pathways regulated by kinases and outlines a general strategy for deciphering mutant phenotypes from large-scale GI networks.
    Genome Research 02/2012; 22(4):791-801. DOI:10.1101/gr.129213.111 · 13.85 Impact Factor
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    • "reported an abnormal cell morphology in rpl27a, rpl2b, rps12 mutants (Watanabe et al., 2009), whereas others provided evidences of an altered cell shape after mutations in rpl27a (Nathan and Lindquist, 1995), rpl3 (Rosado et al., 2007), and rps7a (Ni and Snyder, 2001). Mutations in rps7a were also proven to induce alteration of cell morphology by Sopko and co-workers (Sopko et al., 2006). "
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    ABSTRACT: The yeast Saccharomyces cerevisiae, besides being an eukaryotic cell model, plays a fundamental role in the production of fermented foods. In the winemaking industry, yeast cell walls may be involved in numerous processes and contribute substantially to the final chemical and sensorial profiles of wines. Nonetheless, apart from mannoproteins, little is known on the protein components of the yeast cell wall and their changes during the fermentation of must into wine. In this work, we performed a dynamic analysis of the cell surface proteome (surfome) of an autochthonous wine yeast strain (previously selected as a wine fermentation starter) by shaving intact cells with trypsin and identifying tryptic peptides by means of nLC-ESI-LIT-MS/MS. Out of the 42 identified proteins, 16 and 14 were found to be specifically expressed in wine yeast surfome at the beginning and at the end of fermentation, respectively. The molecular functions of these specifically expressed proteins might help in explaining their roles in the cell wall as a response to the alcoholic fermentation-related stresses. Additionally, we provided the identification of 20 new potential cell wall related proteins. Globally, our results might provide new useful data for the selection and characterization of yeast strains to be used in the winemaking industry.
    Food Microbiology 09/2011; 28(6):1220-30. DOI:10.1016/ · 3.37 Impact Factor
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    • "In support of this, the knockdown of mammalian Arp4 (BAF53) increases chromosome territory size and deletion of Arp8 in yeast leads to an abnormally increased cell volume and irregular, elongated cell morphology compared with wild type together with unusually elongated buds (Hibbs et al, 2007; Watanabe et al, 2009). Although one cannot rule out more indirect effects at this point, these observations are consistent with a more general function of Arp4 and Arp8 in actin metabolism. "
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    ABSTRACT: Nuclear actin and actin-related proteins (Arps) are integral components of various chromatin-remodelling complexes. Actin in such nuclear assemblies does not form filaments but associates in defined complexes, for instance with Arp4 and Arp8 in the INO80 remodeller. To understand the relationship between nuclear actin and its associated Arps and to test the possibility that Arp4 and Arp8 help maintain actin in defined states, we structurally analysed Arp4 and Arp8 from Saccharomyces cerevisiae and tested their biochemical effects on actin assembly and disassembly. The solution structures of isolated Arp4 and Arp8 indicate them to be monomeric and the crystal structure of ATP-Arp4 reveals several differences to actin that explain why Arp4 does not form filaments itself. Remarkably, Arp4, assisted by Arp8, influences actin polymerization in vitro and is able to depolymerize actin filaments. Arp4 likely forms a complex with monomeric actin via the barbed end. Our data thus help explaining how nuclear actin is held in a discrete complex within the INO80 chromatin remodeller.
    The EMBO Journal 06/2011; 30(11):2153-66. DOI:10.1038/emboj.2011.118 · 10.75 Impact Factor
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