TABLE 3.

Comparative promoter analysis for conserved Ste12 and Tec1 binding sites in four closely related Saccharomyces speciesa

Genes with only conserved PREsbGenes with only conserved TCScGenes with both PREs and TCSd
GeneNo. of PREsNo. of TCSPathwayExpression ratioGeneNo. of PREsNo. of TCSPathwayExpression ratioGeneNo. of PREsNo. of TCSPathwayExpression ratio
FIG110M0.5PGU102F44.7FUS131M0.7
SST210M1.0YOR296W01?5.3FUS321MNA
PRM110M0.6SRL101F4.5PRM211M0.5
PRM310M0.4SRL302?1.9PCL213?0.6
PRM610M0.8CHS701F3.8GIC211M/F1.4
BAR120M1.0YNL208W02?1.2SVS1*32?71.9
FUS220M0.6YLR042C02F14.9MSB223F2.8
CIK110M0.6YMR173W01?7.2YIL117C11M/F1.2
PRM410M0.4PHD101F2.2TEC1*42F1.1
AFR110M0.3KSS101F8.2YDR249C*12?1.4
STE210M1.0GSC201?1.9GFA111?1.4
AGA130M0.4TIP101?4.3
KAR420M0.5FLO1102FNA
SCW1020M0.5CLN102F2.7
ASG720M0.4CWP101FNA
  • a Microarray data of dig1 dig2 versus wild-type were used to identify Ste12-regulated genes (21). Genes that were upregulated at least twofold in dig1 dig2 versus wild type were included in this study. Ty1 genes were excluded from the list. In addition, FLO11, CLN1, CWP1, and TEC1 were added as they are shown to be regulated by the filamentation pathway and Ste12/Tec1 in other studies (31, 47). The 1,000-bp upstream sequences of each gene from all four Saccharomyces species were extracted (23) and compared to determine potential conserved Ste12 PREs (TGAAACR) and TCS sites (CATTCY). Functional assignments to either the mating (M) or filamentation (F) pathway are based on functional studies and/or transcriptional patterns (27, 31, 36, 45, 47). Ratios of their expression in fus3 mutants treated with 50 nM α-factor versus wild type treated with 50 nM α-factor are from Hughes et al. (21). NA, not available; ?, not determined.

  • b See Fig. S1 in the supplemental material.

  • c See Fig. S2 in the supplemental material.

  • d See Fig. S3 in the supplemental material. Among the genes with both PREs and TCS, TEC1 contains an FRE, which is indicated with an asterisk. In addition, YDR249C and SVS1 also have a potential FRE with 11 bp and 4 bp between the PRE and TCS, respectively. GFA1 promoter contains a PRE and a TCS with 28-bp spacing.