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Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering.

Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T - Genome Biol. (2010)

Bottom Line: The analysis suggests complementary strategies for coping with ergosterol depletion by azoles - Saccharomyces imports exogenous ergosterol, Candida exports fluconazole, while Kluyveromyces does neither, leading to extreme sensitivity.This approach revealed significant divergence among regulatory programs associated with fluconazole sensitivity.In future, such approaches might be used to survey a wider range of species, drug concentrations and stimuli to reveal conserved and divergent molecular response pathways.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

ABSTRACT

Background: Fungal infections are an emerging health risk, especially those involving yeast that are resistant to antifungal agents. To understand the range of mechanisms by which yeasts can respond to anti-fungals, we compared gene expression patterns across three evolutionarily distant species - Saccharomyces cerevisiae, Candida glabrata and Kluyveromyces lactis - over time following fluconazole exposure.

Results: Conserved and diverged expression patterns were identified using a novel soft clustering algorithm that concurrently clusters data from all species while incorporating sequence orthology. The analysis suggests complementary strategies for coping with ergosterol depletion by azoles - Saccharomyces imports exogenous ergosterol, Candida exports fluconazole, while Kluyveromyces does neither, leading to extreme sensitivity. In support of this hypothesis we find that only Saccharomyces becomes more azole resistant in ergosterol-supplemented media; that this depends on sterol importers Aus1 and Pdr11; and that transgenic expression of sterol importers in Kluyveromyces alleviates its drug sensitivity.

Conclusions: We have compared the dynamic transcriptional responses of three diverse yeast species to fluconazole treatment using a novel clustering algorithm. This approach revealed significant divergence among regulatory programs associated with fluconazole sensitivity. In future, such approaches might be used to survey a wider range of species, drug concentrations and stimuli to reveal conserved and divergent molecular response pathways.

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Pathway expression conservation and divergence. (a) Top conserved and (b) diverged pathway responses as revealed by the soft clustering approach. Each pathway is represented by a pie with four slices - green, yellow, red, and black - denoting the percentage of orthologs in that pathway for which all three species co-clustered, two species co-clustered, no two species co-clustered, and no species' orthologs were differentially expressed, respectively. Pathways were defined using GO biological process annotations. (c) Schematic of ergosterol biosynthesis, the most conserved pathway response. Interestingly, this pathway includes isoprenoid biosynthesis, for which the response was one of the most divergent. (d) mRNA expression responses of ergosterol pathway genes are shown in order of occurrence in the pathway. Expression levels of genes 3 to 8 (boxed, and red) corresponding to isoprenoid biosynthesis are strikingly divergent. The fluconazole target Erg11 is boxed. (e) Hierarchically clustered mRNA expression responses of methionine biosynthesis genes show extensive divergence across species. Grey expression values denote a gene for which the species lacks an ortholog.
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Figure 4: Pathway expression conservation and divergence. (a) Top conserved and (b) diverged pathway responses as revealed by the soft clustering approach. Each pathway is represented by a pie with four slices - green, yellow, red, and black - denoting the percentage of orthologs in that pathway for which all three species co-clustered, two species co-clustered, no two species co-clustered, and no species' orthologs were differentially expressed, respectively. Pathways were defined using GO biological process annotations. (c) Schematic of ergosterol biosynthesis, the most conserved pathway response. Interestingly, this pathway includes isoprenoid biosynthesis, for which the response was one of the most divergent. (d) mRNA expression responses of ergosterol pathway genes are shown in order of occurrence in the pathway. Expression levels of genes 3 to 8 (boxed, and red) corresponding to isoprenoid biosynthesis are strikingly divergent. The fluconazole target Erg11 is boxed. (e) Hierarchically clustered mRNA expression responses of methionine biosynthesis genes show extensive divergence across species. Grey expression values denote a gene for which the species lacks an ortholog.

Mentions: Next, we analyzed the soft clusters to identify pathways for which the fluconazole response is either highly conserved or strikingly divergent. For this purpose, differentially expressed pathways were identified using the GO Biological Process database [38] (Materials and methods). For each pathway, we computed the number of orthologous gene groups for which: 1, all three species were in the same cluster (full co-clustering); 2, two species were in the same cluster (partial co-clustering); or 3, no two species were in the same cluster (no co-clustering). The pathways with the highest percentage of orthologs with full co-clustering are shown in Figure 4a. The pathways with the highest percentage of orthologs that do not co-cluster are shown in Figure 4b. Clustering results for all pathways are given in Table S2 in Additional file 3.


Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering.

Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T - Genome Biol. (2010)

Pathway expression conservation and divergence. (a) Top conserved and (b) diverged pathway responses as revealed by the soft clustering approach. Each pathway is represented by a pie with four slices - green, yellow, red, and black - denoting the percentage of orthologs in that pathway for which all three species co-clustered, two species co-clustered, no two species co-clustered, and no species' orthologs were differentially expressed, respectively. Pathways were defined using GO biological process annotations. (c) Schematic of ergosterol biosynthesis, the most conserved pathway response. Interestingly, this pathway includes isoprenoid biosynthesis, for which the response was one of the most divergent. (d) mRNA expression responses of ergosterol pathway genes are shown in order of occurrence in the pathway. Expression levels of genes 3 to 8 (boxed, and red) corresponding to isoprenoid biosynthesis are strikingly divergent. The fluconazole target Erg11 is boxed. (e) Hierarchically clustered mRNA expression responses of methionine biosynthesis genes show extensive divergence across species. Grey expression values denote a gene for which the species lacks an ortholog.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2926788&req=5

Figure 4: Pathway expression conservation and divergence. (a) Top conserved and (b) diverged pathway responses as revealed by the soft clustering approach. Each pathway is represented by a pie with four slices - green, yellow, red, and black - denoting the percentage of orthologs in that pathway for which all three species co-clustered, two species co-clustered, no two species co-clustered, and no species' orthologs were differentially expressed, respectively. Pathways were defined using GO biological process annotations. (c) Schematic of ergosterol biosynthesis, the most conserved pathway response. Interestingly, this pathway includes isoprenoid biosynthesis, for which the response was one of the most divergent. (d) mRNA expression responses of ergosterol pathway genes are shown in order of occurrence in the pathway. Expression levels of genes 3 to 8 (boxed, and red) corresponding to isoprenoid biosynthesis are strikingly divergent. The fluconazole target Erg11 is boxed. (e) Hierarchically clustered mRNA expression responses of methionine biosynthesis genes show extensive divergence across species. Grey expression values denote a gene for which the species lacks an ortholog.
Mentions: Next, we analyzed the soft clusters to identify pathways for which the fluconazole response is either highly conserved or strikingly divergent. For this purpose, differentially expressed pathways were identified using the GO Biological Process database [38] (Materials and methods). For each pathway, we computed the number of orthologous gene groups for which: 1, all three species were in the same cluster (full co-clustering); 2, two species were in the same cluster (partial co-clustering); or 3, no two species were in the same cluster (no co-clustering). The pathways with the highest percentage of orthologs with full co-clustering are shown in Figure 4a. The pathways with the highest percentage of orthologs that do not co-cluster are shown in Figure 4b. Clustering results for all pathways are given in Table S2 in Additional file 3.

Bottom Line: The analysis suggests complementary strategies for coping with ergosterol depletion by azoles - Saccharomyces imports exogenous ergosterol, Candida exports fluconazole, while Kluyveromyces does neither, leading to extreme sensitivity.This approach revealed significant divergence among regulatory programs associated with fluconazole sensitivity.In future, such approaches might be used to survey a wider range of species, drug concentrations and stimuli to reveal conserved and divergent molecular response pathways.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

ABSTRACT

Background: Fungal infections are an emerging health risk, especially those involving yeast that are resistant to antifungal agents. To understand the range of mechanisms by which yeasts can respond to anti-fungals, we compared gene expression patterns across three evolutionarily distant species - Saccharomyces cerevisiae, Candida glabrata and Kluyveromyces lactis - over time following fluconazole exposure.

Results: Conserved and diverged expression patterns were identified using a novel soft clustering algorithm that concurrently clusters data from all species while incorporating sequence orthology. The analysis suggests complementary strategies for coping with ergosterol depletion by azoles - Saccharomyces imports exogenous ergosterol, Candida exports fluconazole, while Kluyveromyces does neither, leading to extreme sensitivity. In support of this hypothesis we find that only Saccharomyces becomes more azole resistant in ergosterol-supplemented media; that this depends on sterol importers Aus1 and Pdr11; and that transgenic expression of sterol importers in Kluyveromyces alleviates its drug sensitivity.

Conclusions: We have compared the dynamic transcriptional responses of three diverse yeast species to fluconazole treatment using a novel clustering algorithm. This approach revealed significant divergence among regulatory programs associated with fluconazole sensitivity. In future, such approaches might be used to survey a wider range of species, drug concentrations and stimuli to reveal conserved and divergent molecular response pathways.

Show MeSH
Related in: MedlinePlus