Abstract
BackgroundPhylogenetic 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).ResultsComparison 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.ConclusionOur results indicate that, in the course of yeast evolution, a promoter switches its class with the probability at least ~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.
Highlights
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
Class 1 and class 2 promoters in S. cerevisiae genes In order to study evolutionary switches of the promoter class, we first need to determine the class of individual genes
Let us start from considering S. cerevisiae genes where, in contrast to other yeast species, this task is facilitated by the available data on gene expression
Summary
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. Transcription of a gene can evolve, and this evolution may involve changes of even such conservative DNA segments. Functionally important DNA segments are not always strictly conserved, and can evolve due to a variety of factors, including positive selection [8,9,10,11]. This evolution leads to intraspecies polymorphism, often having significant impacts on function and fitness (reviewed in [12]), and to interspecies divergence. The known cases of such divergence usually involve presence of a functional (page number not for citation purposes)
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