TABLE 3.
Known and potential targets of Rgt1a
| ORF | Gene name | Protein function or characteristic | Ratio of spot intensity of the mutant to that of the wild typeb
|
No. of Rgt1 sites/ no. of conserved sitesc | |||
|---|---|---|---|---|---|---|---|
| rgt1Δ Gal | RGT2-1 Gal | SNF3-1 Gal | snf3Δ rgt2Δ Glu | ||||
| YHR092C | HXT4 | Glucose transporter | ↑23.1 (↑10.5) | ↑2.4 | ↑10.6 | ↓0.2 | 5/2 |
| YDR345C | HXT3 | Glucose transporter | ↑13.3 (↑16.9) | ↑2.8 | ↑5.3 | ↓0.2 | 11/7 |
| YMR011W | HXT2 | Glucose transporter | ↑13.0 (NC) | ↑1.9 | ↑5.2 | ↓0.3 | 3/2 |
| YKR075C | Similarity to N terminus of Reg1 | ↑12.6 (↑2.1) | ↑2.0 | ↑8.1 | ↓0.2 | 7/5 | |
| YGL157W | Similarity to dihydroflavonol 4-reductase | ↑7.9 (↑6.6) | ↑2.5 | ↑4.6 | ↓0.1 | 2/1 | |
| YHR094C | HXT1 | Glucose transporter | ↑7.2 (↑51.4) | ↑2.4 | ↑3.8 | ↓0.1 | 11/4 |
| YOR047C | STD1 | Regulator of Rgt1 | ↑4.5 (↑3.5) | NC | ↑2.7 | ↓0.4 | 2/2 |
| YHR096C | HXT5 | Glucose transporter | ↑4.0 (NC) | NC | ↑2.1 | ↓0.3 | 4/0 |
| YGL209W | MIG2 | Glucose-dependent repressor | ↑3.4 (↑12.5) | ↑2.0 | ↑6.8 | NC | 9/4 |
| YNL234W | Heme-binding globin-like protein | ↑3.1 (NC) | NC | ↑1.8 | ↓0.5 | 2/1 | |
| YOR062C | Similarity to N terminus of Reg1 | ↑3.0 (↑5) | NC | ↑1.7 | ↓0.2 | 4/1 | |
| YNL065W | AQR1 | MFSg transporter; resistance to monocarboxylic acids | ↑2.6 (NC) | NC | ↑1.7 | NC | 5/4 |
| YLR109W | AHP1 | Alkyl hydroperoxide reductase; redox homeostasis | ↑2.5 (NC) | NC | ↑1.7 | ↓0.1 | 2/2 |
| YER037W | PHM8 | Involved in phosphate metabolism? | ↑2.4 (NC) | ↑2.2 | ↑2.3 | ↓0.2 | 1/1 |
| YOR338W | Uncharacterized ORF (SGD) | ↑2.2 (NC) | NC | NC | NC | 0 | |
| YKL036C | Dubious ORF (SGD) | ↑2.1 (A) | NC | NC | NC | 2 | |
| YCR005C | CIT2 | Peroxisomal citrate synthase | ↑2.1 (↑4) | ↑1.7 | NC | ↓0.5 | 3/2d |
| YER028C | MIG3 | Possible glucose-dependent repressor | ↑2.0 (↑4.6) | NC | NC | NC | 4/2 |
| YGL039W | Similarity to dihydroflavonol 4-reductase | ↑2.0 (NC) | NC | NC | ↓0.5 | 2/0 | |
| YKL035W | UGP1 | UDP-glucose pyrophosphorylase | ↑2.0 (NC) | NC | NC | NC | 1/0 |
| YOL016C | CMK2 | Calmodulin-dependent protein kinase | ↑2.0 (↑3.4) | ↑1.7 | NC | NC | 1/0 |
| YHR087W | Uncharacterized ORF (SGD) | ↑2.0 (NC) | NC | NC | ↓0.2 | 1/0 | |
| YMR316W | DIA1 | Regulation of invasive growth? | ↑1.9 (NC) | ↑1.7 | NC | NC | 3/0 |
| YER062C | HOR2 | Glycerol-1-phosphatase | ↑1.9 (NC) | NC | NC | ↓0.3 | 2/1 |
| YJL214W | HXT8 | Glucose transporter | ↑1.9 (↑1.8) | NC | ↑2.9 | NC | 5/0 |
| YBR105C | VID24 | Vacuolar protein targeting | ↑1.9 (↑2.6) | NC | NC | NC | 4/3 |
| YDR423C | CAD1 | Jun family of transcription factors | ↑1.9 (NC) | NC | NC | NC | 0 |
| YHR097C | Uncharacterized ORF (SGD) | ↑1.9 (NC) | NC | NC | ↓0.5 | 0 | |
| YOL046C | Dubious ORF (SGD) | ↑1.9 (A) | NC | NC | NC | 2 | |
| YBR067C | TIP1 | Cell wall mannoprotein | ↑1.9 (NC) | NC | NC | ↑3.8 | 5/1 |
| YDR277C | MTH1 | Regulator of Rgt1 | ↑1.8 (↑2.1) | NC | ↑2.0 | NC | 4/2 |
| YOL136C | PFK2 | 6-Phosphofructo-2-kinase; regulation of glycolysis | ↑1.8 (NC) | NC | ↑1.8 | NC | 2/2 |
| YFL054C | Glycerol transporter | ↑1.8 (↑3.5) | NC | ↑2.0 | NC | 3/2 | |
| YDR001C | NTH1 | Neutral trehalase; stress response | ↑1.8 (NC) | NC | NC | NC | 2/2 |
| YPL026C | SKS1 | Protein kinase; multicopy suppressor of snf3 | ↑1.8 (NC) | NC | NC | NC | 6/3e |
| YLR413W | Uncharacterized ORF (SGD) | ↑1.8 (NC) | NC | NC | NC | 1/0 | |
| YDL062W | Dubious ORF (SGD) | ↑1.8 (A) | NC | NC | NC | 1 | |
| YMR136W | GAT2 | GATA zinc finger toxin factor | ↑1.8 (NC) | NC | NC | NC | 2/1 |
| YFR016C | Uncharacterized ORF (SGD) | ↑1.8 (NC) | NC | NC | NC | 0 | |
| YKR098C | UBP11 | Ubiquitin-specific protease | ↑1.8 (NC) | NC | NC | NC | 4/3 |
| YKR076W | ECM4 | Cell wall organization | ↑1.8 (NC) | NC | NC | NC | 7/5f |
| YLR194C | Uncharacterized ORF (SGD) | ↑1.8 (↑1.8) | NC | NC | ↓0.3 | 1/0 | |
| YAL061W | Putative polyol dehydrogenase | ↑1.8 (↑1.7) | NC | NC | NC | 1/0 | |
Genes whose transcript levels were induced to increase at least 1.8-fold on galactose in a homozygous rgt1Δ/rgt1Δ strain (YM6440) in microarray hybridizations (averages of ratios of mutant spot intensities to wild-type intensities are shown). Boldface type indicates that the ORF or gene was a good candidate for an Rgt1 target (see the text).
The ratio of gene transcript levels, determined from hybridization of cellular RNA probes to DNA microarrays, of heterozygous RGT2-1 (YM6554) and SNF3-1 (YM6557) strains grown on galactose and a haploid snf3Δ rgt2Δ strain (YM6370) grown on glucose (Glu) to the gene transcript levels of wild-type (diploid and haploid) strains. The same data from the hybridization of RNA (from an rgt1Δ haploid strain [YM4509] compared to that in the wild type [YM4127] grown in rich 3% glycerol plus 3% lactate medium) to an oligonucleotide array (Affymetrix) are in parentheses. A, Affymetrix hybridization analysis software designated the transcript as being absent; NC, transcript levels that were not changed significantly in the mutant relative to those in the wild type. Symbols: ↑, increased transcript level (≥1.7-fold) in the mutant compared to that in the wild type; ↓, decreased transcript level (≤0.5-fold) in the mutant compared to that in the wild type.
Ratio of the number of potential Rgt1 binding sites (CGGANNA) (33) in the promoter to the number of these sites that are conserved in the orthologous promoters of other Saccharomyces species, as described in reference 14.
No Rgt1 binding sites lie in the 201 bp between CIT2 and YCR006C (classified as dubious in the SGD), but three potential Rgt1 binding sites lie within 1,200 bp upstream of the CIT2 ATG.
Only one Rgt1 binding site is in the intergenic region, but five additional sites lie in the upstream 558-bp ORF (YPL025C, a likely gene since a two-hybrid interaction has been reported between YPL025C and MIG1 [65]).
ECM4 and YKR075C are divergently transcribed and so share upstream sequences. These conserved potential Rgt1 binding sites are rather remote from the ECM4 ATG, and the closest three sites are not conserved, so it is doubtful that Rgt1 regulates ECM4 expression.
MFS, major facilitator superfamily.