Abstract
Author SummaryConserved metabolic machineries direct energy production and investment in most life forms. However, variation in the transcriptional regulation of the genes that encode this machinery has been observed and shown to contribute to phenotypic differences between species. Here, we show that the regulatory circuits governing the expression of central metabolic components (in this case the ribosomes) in different yeast species have an unexpected level of evolutionary plasticity. Most transcription factors involved in the regulation of expression of ribosomal genes have in fact been reused in new ways during the evolutionary time separating S. cerevisiae and C. albicans to generate global changes in transcriptional network structures and new ribosomal regulatory complexes.
Highlights
A conserved metabolic machinery forms the common basis of all cells; variation in the regulation of the genes that encode this machinery produces fundamental phenotypic differences between species
A Crf1 ortholog could not be identified in the C. albicans clade, consistent with the recent appearance of this ribosomal protein (RP) co-repressor in the fungal lineage and its strain-specific role in the budding yeast [35,41]
We set out to determine the binding locations of tagged Cbf1, Hmo1, Rap1, Tbf1, Fhl1, and Ifh1 by chromatin immunoprecipitation (ChIP)-CHIP in haploid S. cerevisiae and diploid C. albicans strains (Table S1) with full-genome tiling arrays (20 and 17 probes/kb, respectively), and selected targets were validated by ChIP-Quantitative PCR (qPCR) (Datasets S1 and S2 and Figure S2)
Summary
A conserved metabolic machinery forms the common basis of all cells; variation in the regulation of the genes that encode this machinery produces fundamental phenotypic differences between species. Several groups have linked phenotypic traits to changes in the expression of conserved gene in diverse metazoans like Darwin finches, sticklebacks, and flies [1,2,3,4,5,6]. This differential gene expression can be obtained by varying the structure of cellular transcriptional regulatory networks (TRNs), and many types of modifications can drive changes in gene regulation. Changing the chromatin status of a gene by varying its nucleosome occupancy, its gene neighborhood, or its chromosome position can have impacts on its expression level [20,21]. Several studies have highlighted gene expression differences between species [26,27,28], but the flexibility of the regulatory network that drives these transcriptional changes still needs to be studied
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