Table 2.
New candidate Zap1 target genes identified by E1, E2, and E3 clustering.
| ORFa | Gene | Function | Fold induction | ZRE | |||||
| E1b | E2b | E3-1c | E3-2c | startd | scoree | sequencef | |||
| YBL029W | function unknown | 3.0 | 2.9 | 1.6 | 1.4 | -995 | 5.8 | CCCCTGCCGGT | |
| YBR072W* | HSP26* | small heat shock protein, protein folding | 40.5 | 2.0 | 3.3 | 3.5 | -451 | 5.3 | ACCTTGCCTGT |
| YDR077W* | SED1* | cell wall protein | 2.6 | 2.2 | 2.6 | 2.1 | -896 | 4.7 | CCCTTATAGGA |
| YGR088W* | CTT1* | catalase T, oxidative stress resistance | 17.1 | 3.7 | 1.9 | 1.7 | -337 | 5.7 | CCCTTACCGGT |
| YGR243W | FMP43 | mitochondrial protein, function unknown | 2.8 | 2.7 | 3.1 | 2.5 | -552 | 4.9 | TCCTCGAATGT |
| YHR214W-A | function unknown | 6.5 | 2.6 | 3.0 | 3.2 | -274 | 4.8 | ACCTCTGGTGT | |
| YIL045W | PIG2 | putative protein phosphatase regulatory subunit | 4.6 | 2.4 | 1.6 | 1.5 | -859 | 4.7 | ACCTTCCACGT |
| YJL048C* | UBX6* | UBX (ubiquitin regulatory X) domain-containing protein | 2.3 | 3.3 | 1.8 | 1.6 | -198 | 5.2 | TCCATTAAGGT |
| -39 | 5.9 | CCCTCAAAGGA | |||||||
| YKR046C | PET10 | lipid particle protein, unknown function | 2.9 | 3.0 | 1.7 | 1.7 | -929 | 4.8 | ATCTTGCAGGT |
| YLR136C* | TIS11* | tristetraproline homolog, control of mRNA stability | 2.6 | 4.1 | 5.6 | 3.7 | -821 | 4.9 | GCCCGTGAGGT |
| -768 | 6.3 | AACCTGCGGGT | |||||||
| -507 | 6.0 | GCCCAGAGGGT | |||||||
| YML028W | TSA1 | peroxiredoxin, oxidative stress resistance | 5.0 | 2.9 | 2.0 | 1.5 | -195 | 5.5 | GCCCGTCGGGT |
| -170 | 7.2 | TCCCTAAAGGA | |||||||
| YMR181C | function unknown | 5.9 | 2.2 | 2.6 | 2.7 | -237 | 5.1 | CCCTTCGAGGG | |
| YNL239W* | LAP3* | homocysteine thiolactonase | 2.1 | 4.7 | 2.9 | 2.9 | -947 | 4.8 | GCCTCCAATGT |
| YOL082W | ATG19 | autophagy and cytoplasm-to-vacuole (CVT) targeting pathway | 4.3 | 3.2 | 1.6 | 1.4 | -281 | 5.9 | ACCTTAAAAGT |
| -998 | 4.9 | ACCAACAGGGT | |||||||
| YOL155C* | cell wall protein | 11.8 | 3.5 | 2.3 | 2.9 | -361 | 6.3 | ACCGTGCAGGA | |
| YPL159C | PET20 | mitochondrial protein required for respiratory growth | 9.1 | 5.2 | 4.5 | 4.0 | -278 | 5.3 | GCCATTAAGGT |
| -180 | 5.6 | ACCCTTTGGGA | |||||||
a) Results for genes marked with asterisks were confirmed independently by S1 nuclease protection assay in Figure 2.
b) Expression ratios are the average of two independent microarray experiments (Lyons et. al. 2000).
c) Results from two independent microarray experiments (E3-1 and E3-2) are shown.
d) Numbers indicate the distance from the ATG initiation codon.
e) Score calculated for each sequence with a position-specific scoring matrix generated by RSAT.
f) ZREs shown in bold were tested for interaction with Zap1 as described in Figure 3A.