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
FIG1 10M0.5 PGU1 02F44.7 FUS1 31M0.7
SST2 10M1.0 YOR296W 01?5.3 FUS3 21MNA
PRM1 10M0.6 SRL1 01F4.5 PRM2 11M0.5
PRM3 10M0.4 SRL3 02?1.9 PCL2 13?0.6
PRM6 10M0.8 CHS7 01F3.8 GIC2 11M/F1.4
BAR1 20M1.0 YNL208W 02?1.2 SVS1* 32?71.9
FUS2 20M0.6 YLR042C 02F14.9 MSB2 23F2.8
CIK1 10M0.6 YMR173W 01?7.2 YIL117C 11M/F1.2
PRM4 10M0.4 PHD1 01F2.2 TEC1* 42F1.1
AFR1 10M0.3 KSS1 01F8.2 YDR249C* 12?1.4
STE2 10M1.0 GSC2 01?1.9 GFA1 11?1.4
AGA1 30M0.4 TIP1 01?4.3
KAR4 20M0.5 FLO11 02FNA
SCW10 20M0.5 CLN1 02F2.7
ASG7 20M0.4 CWP1 01FNA
  • 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.