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Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata. Genome Biol 9:R164

Equipe de Bioinformatique Génomique et Moléculaire, INSERM UMR S726, Université Paris 7, INTS, 6 rue Alexandre Cabanel, 75015 Paris, France.
Genome biology (Impact Factor: 10.47). 12/2008; 9(11):R164. DOI: 10.1186/gb-2008-9-11-r164
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ABSTRACT Recent technical and methodological advances have placed microbial models at the forefront of evolutionary and environmental genomics. To better understand the logic of genetic network evolution, we combined comparative transcriptomics, a differential clustering algorithm and promoter analyses in a study of the evolution of transcriptional networks responding to an antifungal agent in two yeast species: the free-living model organism Saccharomyces cerevisiae and the human pathogen Candida glabrata.
We found that although the gene expression patterns characterizing the response to drugs were remarkably conserved between the two species, part of the underlying regulatory networks differed. In particular, the roles of the oxidative stress response transcription factors ScYap1p (in S. cerevisiae) and Cgap1p (in C. glabrata) had diverged. The sets of genes whose benomyl response depends on these factors are significantly different. Also, the DNA motifs targeted by ScYap1p and Cgap1p are differently represented in the promoters of these genes, suggesting that the DNA binding properties of the two proteins are slightly different. Experimental assays of ScYap1p and Cgap1p activities in vivo were in accordance with this last observation.
Based on these results and recently published data, we suggest that the robustness of environmental stress responses among related species contrasts with the rapid evolution of regulatory sequences, and depends on both the coevolution of transcription factor binding properties and the versatility of regulatory associations within transcriptional networks.

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    • "In contrast to S. cerevisiae (DeRisi et al., 2000), however, no remarkable overexpression of CgPDR16 has been observed in transcriptome analyses using strains either containing gain-of-function CgPDR1 alleles (Vermitsky et al., 2006; Tsai et al., 2010; Caudle et al., 2011; Ferrari et al., 2011) or exposed to drugs (Lelandais et al., 2008). "
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    Yeast 08/2013; 30(10). DOI:10.1002/yea.2978 · 1.74 Impact Factor
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    • "Due to the S. cerevisiae arrays used, they were unable to examine more divergent species. In order to broaden these studies to more divergent yeasts, species-specific arrays must be used, as has been done, for example, for Candida glabrata[27]. Most importantly, due to the limited condition space of just a small number of treatments in these studies, conclusions about evolution of gene function and regulation have been difficult to generalize. "
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    • "The resulting gene expression profiles are then compared with various information, including orthology links, functional annotations from the gene ontology (GO) and the conservation of known cisregulatory elements in orthologous promoters. To do so, several methodologies have been published, including the direct comparison of gene expression profiles from orthologous genes [12] [13] [14] [15], the quantification of the coexpression conservation of clusters of genes [16] [17] or multispecies fuzzy clustering using orthology links as a constraint to optimize GO enrichment in the final clusters [18]. To our knowledge, the most impressive work of this kind has been performed by the laboratory of Aviv Regev and her collaborators (Dawn Anne Thompson, personal communication ). "
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