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Table 1 Genes with class 1 (functional TATA box-containing) promoters in S. cerevisiae having orthologs which lack a TATA box in one or more other species of sensu stricto group.

From: Rate of promoter class turn-over in yeast evolution

   Description Presence of TATA boxa   
ORF Gene name   paradoxus mikatae kudriavtsevii bayanus Switch eventsb Ancestral statec
YLR109W AHP1 Thiol-specific peroxiredoxin + + + - (2) 1 ?
YPL221W BOP1 Unknown function + + + - (2) 1 ?
YBR298C MAL31 Maltose permease + + + - (5) 1 ?
YBR147W   Hypothetical ORF + + - (2) + 1 TATA
YCL035C GRX1 Oxidoreductase + + - (2) + 1 TATA
YDR005C MAF1 Mod5 protein sorting, negative effector of Pol III synthesis. + GA - (2) + 1 TATA
YPR193C HPA2 Tetrameric histone acetyltransferase + + - (2) + 1 TATA
YDR533C HSP31 Possible chaperone and cysteine protease + + - (3) + 1 TATA
YMR315W   Hypothetical ORF + + - (3) GA 1 ?
YDR282C   Hypothetical ORF + - (2) - (4) + 2 ?
YKL216W URA1 Catalyzes the conversion of dihydroorotic acid to orotic acid + - (2) + + 1 TATA
YNR033W ABZ1 Para-aminobenzoate (PABA) synthase + - (2) + + 1 TATA
YOR186W   Hypothetical ORF + - (2) + + 1 TATA
YOL143C RIB4 Catalyzes synthesis of riboflavin GA - (3) + + 1 TATA
YPR119W CLB2 Involved in mitotic induction + - (2) GA + ? ?
YLR346C   Unknown function - (gap) GA + + 1 TATA
YPL269W KAR9 Karyogamy protein - (gap) - (gap) - (gap) - (gap) 1 non-TATA
Total    2 7 8 4   
  1. a For non-conserved TATA boxes, the minimal number of nucleotides different from the consensus sequence of TATA box (TATA(A/T)A(A/T)(A/G)) is shown in parentheses. "Gap" indicates an alignment gap at the site of the TATA box; "GA" means that ORF was not present in the given species.
  2. b Parsimonious number of switch events in sensu stricto group; i.e., the minimum number of mutations within sensu stricto group necessary to produce this pattern. The number of events is unknown for ORF YPR119W due to lack of data for S. kudriavtsevii.
  3. c Inferred state in last common ancestor. In cases when more than one equally parsimonious ancestral state was possible, it could not be inferred reliably (marked as '?').
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BMC Ecology and Evolution

ISSN: 2730-7182

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