3.4. GSEA of DE genes by gcr2
DE genes in the gcr2 mutant were subjected to GSEA using Gene
Ontology (GO) biological process (Table 4). On both glucose and xylose
conditions, genes associated with translation, nucleotide biosynthesis,
lipid biosynthesis, and one-carbon metabolism were up-regulated, and
genes associated with protein transport were down-regulated. However,
the direction of the transcriptional changes by gcr2 in two gene
sets (sugar metabolism and oxidation-reduction) and their genes were
opposites depending on the type of substrates; they were up-regulated on
xylose but down-regulated on glucose (Fig. 3). For example, ALD3 ,
encoding aldehyde dehydrogenase, is known to be induced in response to
stress; it was induced by gcr2 under xylose conditions but
repressed under glucose conditions. Because Gcr2 is a native
transcriptional activator for glucose metabolism, the heterologous
xylose metabolism might interfere with the native metabolic regulation
and cause some discrepancies in the direction of transcriptional
regulation mediated by Gcr2.