Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis

Abstract

Genome-wide transcriptional profiling has important applications in evolutionary biology for assaying the extent of heterozygosity for alleles showing quantitative variation in gene expression in natural populations. We have used DNA microarray analysis to study the global pattern of transcription in a homothallic strain of Saccharomyces cerevisiae isolated from wine grapes in a Tuscan vineyard, along with the diploid progeny obtained after sporulation. The parental strain shows 2:2 segregation (heterozygosity) for three unlinked loci. One determines resistance to trifluoroleucine; another, resistance to copper sulfate; and the third is associated with a morphological phenotype observed as colonies with a ridged surface resembling a filigree. Global expression analysis of the progeny with the filigreed and smooth colony phenotypes revealed a greater than 2-fold difference in transcription for 378 genes (6% of the genome). A large number of the overexpressed genes function in pathways of amino acid biosynthesis (particularly methionine) and sulfur or nitrogen assimilation, whereas many of the underexpressed genes are amino acid permeases. These wholesale changes in amino acid metabolism segregate as a suite of traits resulting from a single gene or a small number of genes. We conclude that natural vineyard populations of S. cerevisiae can harbor alleles that cause massive alterations in the global patterns of gene expression. Hence, studies of expression variation in natural populations, without accompanying segregation analysis, may give a false picture of the number of segregating genes underlying the variation.

Figure 1

(A) Colony morphologies of the parental strain M28 and the smooth (S1, S2) and filigreed (F1, F2) segregants. The colonies range in size from 1.0 to 1.2 cm. (B) Convoluted surface of a filigreed colony. The diameter of the filament is approximately 0.2 mm.

Figure 2

Log-log scatterplot of fluorescence measured for mRNA labeled with either cyanine-3 or cyanine-5 fluorochrome in a competitive hybridization on a microarray containing 6218 ORFs. Spots with at least one fluorescence signal significantly above background are plotted for (A) F1 against S2 and (B) F1 against F2. Dark lines represent a 2-fold difference in expression; light lines represent a 5-fold difference in expression.

Figure 3

Relative expression levels of all genes overexpressed 3-fold or more in comparisons of F1 with S2 (front), F2 with S2 (rear), and F1 with the parental strain M28 (middle). The overexpressed genes are arranged in order of their mean expression level across all three comparisons.

Figure 4

Key steps related to the biosynthesis of methionine. The numbers are the relative levels of expression of the indicated genes.