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Table 3 Genes with class 2 (non-TATA box-containing) promoters in S. cerevisiae having orthologs which have TATA box in one or more other species of sensu stricto group.

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

    

Presence of TATA box

  

ORF

Gene name

Description

Minimal distance from consensusa

paradoxus

mikatae

kudriavtsevii

bayanus

Switch eventsb

Ancestral statec

YDL139C

SCM3

Suppressor of chromosome missegregation

1

+

-

-

-

  

YDR159W

SAC3

Component of nuclear pore

2

+

-

-

-

1

non-TATA

YGL091C

NBP35

 

1

+

-

-

-

1

non-TATA

YIR002C

MPH1

Helicase

1

+

-

-

-

1

non-TATA

YOL149W

DCP1

Decapping enzyme

1

+

-

-

-

1

non-TATA

YOR125C

CAT5

 

1

+

-

-

-

1

non-TATA

YLR011W

LOT6

 

1

+

GA

-

-

1

non-TATA

YOR154W

 

Hypothetical ORF

2

+

GA

-

-

1

non-TATA

YKL207W

 

Hypothetical ORF

1

+

GA

GA

GA

1

non-TATA

YDL005C

MED2

RNA Polymerase II transcriptional regulation mediator

4

-

+

-

-

1

non-TATA

YDL207W

GLE1

Polyadenylated-RNA-export factor

1

-

+

-

-

1

non-TATA

YDR459C

  

2

-

+

-

-

1

non-TATA

YER099C

PRS2

5-phospho-ribosyl-1(alpha)-pyrophosphate synthetase

2

-

+

-

-

1

non-TATA

YIL002C

INP51

Phosphatidylinositol 4,5-bisphosphate 5-phosphatase, synaptojanin-like protein

3

-

+

-

-

1

non-TATA

YNL125C

ESBP6

 

1

-

+

-

-

1

non-TATA

YOR201C

PET56

Ribose methyltransferase

1

-

+

-

-

1

non-TATA

YOR238W

 

Hypothetical ORF

5

-

+

-

-

1

non-TATA

YOR280C

FSH3

Serine hydrolase

1

-

+

-

-

1

non-TATA

YPL034W

 

Hypothetical ORF

2

-

+

-

-

1

non-TATA

YPL047W

SGF11

 

1

-

+

-

-

1

non-TATA

YPL096W

PNG1

De-N-glycosylation enzyme

2

-

+

-

-

1

non-TATA

YKL038W

RGT1

Transcriptional activator

4

-

+

GA

-

1

non-TATA

YDR422C

SIP1

Protein kinase complex component

1

-

+

-

GA

2

?

YOR211C

MGM1

 

3

-

+

-

GA

1

non-TATA

YPL112C

PEX25

 

2

-

+

GA

GA

1

non-TATA

YKL012W

PRP40

U1 snRNP protein involved in splicing

1

+

+

-

-

2

non-TATA

YGR134W

CAF130

CCR4 Associated Factor

1

+

+

-

GA

2

non-TATA

YBL074C

AAR2

Component of the U5 snRNP

1

-

-

+

-

1

non-TATA

YFR042W

  

2

-

-

+

-

1

non-TATA

YML065W

ORC1

Largest subunit of the origin recognition complex

4

-

-

+

-

1

non-TATA

YOR160W

MTR10

 

1

-

-

+

-

1

non-TATA

YOR228C

 

Hypothetical ORF

6

-

-

+

-

1

non-TATA

YPL091W

GLR1

 

1

-

-

+

-

1

non-TATA

YLR165C

PUS5

 

2

-

GA

+

-

1

non-TATA

YDR160W

SSY1

Component of the SPS plasma membrane amino acid sensor system (Ssy1p-Ptr3p-Ssy5p)

3

GA

-

+

GA

1

non-TATA

YBR108W

 

Hypothetical ORF

1

-

-

-

+

2

?

YHR105W

YPT35

Hypothetical ORF

2

-

-

-

+

1

?

YNL119W

NCS2

 

4

-

-

-

+

1

?

YKR053C

YSR3

Dihydrosphingosine 1-phosphate phosphatase

1

-

GA

GA

+

1

?

YOL020W

TAT2

Tryptophan permease

1

+

+

-

+

2

TATA

YMR169C

ALD3

 

1

-

+

GA

+

2

?

YMR170C

ALD2

 

1

-

-

+

+

1

TATA

YPR073C

LTP1

 

2

+

+

+

+

1

TATA

YDL054C

MCH1

 

5

+

+

+

+

1

TATA

Total

   

14

22

11

9

  
  1. a The minimal distance from TATA consensus is the minimal number of nucleotides different from the consensus sequence (TATA(A/T)A(A/T)(A/G)) in the octanucleotide of S. cerevisiae which is orthologous to the TATA box in the non-cerevisiae species. "Gap" indicates an alignment gap at the site of the TATA box; "GA" means that ORF was not conserved 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.
  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 '?').