Rate of promoter class turn-over in yeast evolution

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.

		Description	Presence of TATA box^a
ORF	Gene name		paradoxus	mikatae	kudriavtsevii	bayanus	Switch events^b	Ancestral state^c
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

^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.
^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.
^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 '?').

ISSN: 2730-7182