Rate of promoter class turn-over in yeast evolution.
BACKGROUND
Phylogenetic conservation at the DNA level is routinely used as evidence of molecular function, under the assumption that locations and sequences of functional DNA segments remain invariant in evolution. In particular, short DNA segments participating in initiation and regulation of transcription are often conserved between related species. However, transcription of a gene can evolve, and this evolution may involve changes of even such conservative DNA segments. Genes of yeast Saccharomyces have promoters of two classes, class 1 (TATA-containing) and class 2 (non-TATA-containing).


RESULTS
Comparison of upstream non-coding regions of orthologous genes from the five species of Saccharomyces sensu stricto group shows that among 212 genes which very likely have class 1 promoters in S. cerevisiae, 17 probably have class 2 promoters in one or more other species. Conversely, among 322 genes which very likely have class 2 promoters in S. cerevisiae, 44 probably have class 1 promoters in one or more other species. Also, for at least 2 genes from the set of 212 S. cerevisiae genes with class 1 promoters, the locations of the TATA consensus sequences are substantially different between the species.


CONCLUSIONS
Our results indicate that, in the course of yeast evolution, a promoter switches its class with the probability at least approximately 0.1 per time required for the accumulation of one nucleotide substitution at a non-coding site. Thus, key sequences involved in initiation of transcription evolve with substantial rates in yeast.
Bazykin
Georgii A
GA
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA. gbazykin@princeton.edu
Kondrashov
Alexey S
AS
D001483:Base Sequence; D019143:Evolution, Molecular; D005800:Genes, Fungal; D008969:Molecular Sequence Data; D010802:Phylogeny; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012440:Saccharomyces / Q000145:classification / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity