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. 2005 Dec 27;102(52):19015-20.
doi: 10.1073/pnas.0509436102. Epub 2005 Dec 19.

High-dimensional and large-scale phenotyping of yeast mutants

Yoshikazu Ohya  1 , Jun Sese, Masashi Yukawa, Fumi Sano, Yoichiro Nakatani, Taro L Saito, Ayaka Saka, Tomoyuki Fukuda, Satoru Ishihara, Satomi Oka, Genjiro Suzuki, Machika Watanabe, Aiko Hirata, Miwaka Ohtani, Hiroshi Sawai, Nicolas Fraysse, Jean-Paul Latgé, Jean M François, Markus Aebi, Seiji Tanaka, Sachiko Muramatsu, Hiroyuki Araki, Kintake Sonoike, Satoru Nogami, Shinichi Morishita
Affiliations

High-dimensional and large-scale phenotyping of yeast mutants

Yoshikazu Ohya et al. Proc Natl Acad Sci U S A. .

Abstract

One of the most powerful techniques for attributing functions to genes in uni- and multicellular organisms is comprehensive analysis of mutant traits. In this study, systematic and quantitative analyses of mutant traits are achieved in the budding yeast Saccharomyces cerevisiae by investigating morphological phenotypes. Analysis of fluorescent microscopic images of triple-stained cells makes it possible to treat morphological variations as quantitative traits. Deletion of nearly half of the yeast genes not essential for growth affects these morphological traits. Similar morphological phenotypes are caused by deletions of functionally related genes, enabling a functional assignment of a locus to a specific cellular pathway. The high-dimensional phenotypic analysis of defined yeast mutant strains provides another step toward attributing gene function to all of the genes in the yeast genome.

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Figures

Fig. 1.
Fig. 1.
Comprehensive analysis of morphological phenotypes in yeast. (A) Classification of parameters. A subset of parameters used to characterize individual cells is shown. Among all of the 501 parameters measured, 254 revealed statistically reliable data (see Supporting Text). Thresholded at a correlation coefficient value of 0.9, 175 of 254 parameters were considered to be independent (see Fig. 6, which is published as supporting information on the PNAS web site). (B) Data sets were obtained from 126 independent wild-type samples and compared with all data sets from the 4,718 mutant strains. As an example, the distribution of the average of outline length of cells with no bud and a single nucleus is shown. (C) Number of morphological mutants distinct from wild type at the P value for both sides indicated. Deletion strains whose morphological normality P is less than or equal to the threshold in at least one parameter are counted as morphological mutants (see Supporting Text for details). (D) Frequency of the number of parameters altered in the strains analyzed. The number of deletion strains in each category with the GO term “biological process unknown” assigned to the corresponding locus is shown in yellow.
Fig. 2.
Fig. 2.
Phenotypic analysis of mutant strains and correlation to cellular functions. (A) Polarisome mutants are enriched in the mutant class with altered bud morphology; 4,718 mutants were sorted by roundness of bud. Mutant strains that deviate from wild-type phenotype are shown in magenta or green. The positions of polarisome mutant strains and wild type are indicated with yellow and white lines, respectively. A round bud is a common feature for polarisome perturbation. (B) Cellular functions (as defined by GO terms) that are affected in subsets of mutant strains displaying specific morphological phenotypes. Mutant strains significantly different from wild-type cells are shown in green and magenta, respectively. Genes annotated to the GO term but that exhibit wild-type measurements are in black text. The relative positions of mutant strains with deletions in the loci given are indicated by yellow lines.
Fig. 3.
Fig. 3.
Enrichment of defined mutant classes within a defined set of morphological phenotypes. (A) Mutant strains affected in DNA metabolism and DNA-related functions are enriched in strains displaying a large bud size before mitosis. Distributions of the mutants with a large bud size before mitosis are shown in magenta. The pie chart on the right represents the ratio of mutants with defects in DNA-related function within the morphological group “large bud size before mitosis.” Genes associated with the GO term “DNA metabolism” and genes involved in DNA-related function are shown in yellow and red, respectively. The pie chart on the left represents the ratio of genes associated with the GO term “DNA metabolism” to total nonessential mutants. (B) Mutants affected in specific cellular functions are enriched in mutant class displaying the defined phenotype. The cellular function is given above each statistical analysis. The enrichment is observed at indicated probability by chance. (Left) The diagram of each analysis displays the frequency of the mutant strains assigned to the given cellular function. (Right) The diagram displays the frequency of such defined strains within strains with the indicated morphological phenotype.
Fig. 4.
Fig. 4.
Functional classification of morphological mutants. (A) The descriptive morphological phenotype of a set of 14 recombinational repair mutant strains (I) and 42 mutant strains with low glucan content (II) was defined and used as a query to identify mutant strains that display the appropriate phenotype. Nineteen (for query I) and 10 (for query II) candidate strains were identified. The locus deleted in these strains, the gene name, and the putative function (as given by the GO term) is given. A * indicates mutant strains used as a query. (B) Color-coded representation of the morphological phenotypes displayed by these mutant strains. Morphological difference from wild type is shown for each mutant such that the magnitude is indicated by the intensity of the colors displayed. The brightest colors represent a significant difference (P < 0.00001) for one side. Magenta and green indicate that the mutant has a significantly higher or lower value than that of the wild type, respectively. The numerals in the vertical axis represent the following morphological parameters: 1, C12-2_A1B; 2, A7-2_A1B; 3, C117_A1B; 4, C118_A1B; 5, DCV114_A1B; 6, C125_A1B; 7, D118_A1B; 8, CCV115_C; 9, C118_C; 10, DCV112_C; 11, D109_C; 12, D125_C; 13, CCV104_C; 14, DCV151_C; 15, C117_C; 16, DCV106_C; 17, D103_C; 18, A108; 19, DCV145_C; 20, DCV146_C; 21, A107_A1B; 22, C123; 23, D202; 24, D213; 25, D216; 26, A110; 27, A119; 28, D110_A1B; 29, D207; 30, C106_A1B; and 31, D214. A precise parameter description is shown in Fig. 5 and Table 1. (C and D) Scatter plots of indicated mutant phenotypes of each strain analyzed. The candidate strains identified by using the specified group phenotypes are highlighted. The phenotype of wild-type strains treated with hydroxyurea (HU) is shown in C. (D) The phenotype of wild-type and fks1-1144 mutant cells grown at the temperature indicated is shown.
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