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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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Divergence in transporter usage. Cross-species expression profiles of (a) ATP-binding cassette (ABC) and (b) major facilitator superfamily (MFS) transporters are shown. Grey expression values denote a gene for which the species lacks an ortholog. (c) Change in cell density with addition of exogenous ergosterol at the fluconazole 50% inhibitory concentration across different mutant backgrounds. Sc.bpt1Δ is a gene knockout unrelated to fluconazole response and is included as a control. Error bars indicate one standard deviation. (d) Model for differential usage of transporters among Sc, Cg, and Kl.
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Figure 5: Divergence in transporter usage. Cross-species expression profiles of (a) ATP-binding cassette (ABC) and (b) major facilitator superfamily (MFS) transporters are shown. Grey expression values denote a gene for which the species lacks an ortholog. (c) Change in cell density with addition of exogenous ergosterol at the fluconazole 50% inhibitory concentration across different mutant backgrounds. Sc.bpt1Δ is a gene knockout unrelated to fluconazole response and is included as a control. Error bars indicate one standard deviation. (d) Model for differential usage of transporters among Sc, Cg, and Kl.

Mentions: A final pathway for which we observed striking expression divergence was multi-drug transport (Figure 4b; Additional file 1: Transport). Most genes in this pathway were covered by clusters 8, 11, 16 (Figure 5a, b). Multi-drug transporters are divided into two classes: ATP-binding cassette (ABC) and major facilitator superfamily (MFS) transporters [5]. We examined the expression patterns of these transporters and found at least two types of divergent behaviors. First, the fraction of differentially expressed Sc MFS transporters was low compared to Cg and Kl (Fisher exact test, one-tailed P = 0.025 and 0.020, respectively). Second, the timing of MFS gene expression differed, with Sc up-regulated late and Cg up-regulated early (Figure 5b). In SC, several ABC and MFS transporters have been shown to bind fluconazole as a substrate [20,42,43]. Of these, we found that the PDR5/10/15 family of ABC transporters was up-regulated in Cg and Sc but not Kl. Another fluconazole transporter, SNQ2, was up-regulated in Cg only.


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)

Divergence in transporter usage. Cross-species expression profiles of (a) ATP-binding cassette (ABC) and (b) major facilitator superfamily (MFS) transporters are shown. Grey expression values denote a gene for which the species lacks an ortholog. (c) Change in cell density with addition of exogenous ergosterol at the fluconazole 50% inhibitory concentration across different mutant backgrounds. Sc.bpt1Δ is a gene knockout unrelated to fluconazole response and is included as a control. Error bars indicate one standard deviation. (d) Model for differential usage of transporters among Sc, Cg, and Kl.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Divergence in transporter usage. Cross-species expression profiles of (a) ATP-binding cassette (ABC) and (b) major facilitator superfamily (MFS) transporters are shown. Grey expression values denote a gene for which the species lacks an ortholog. (c) Change in cell density with addition of exogenous ergosterol at the fluconazole 50% inhibitory concentration across different mutant backgrounds. Sc.bpt1Δ is a gene knockout unrelated to fluconazole response and is included as a control. Error bars indicate one standard deviation. (d) Model for differential usage of transporters among Sc, Cg, and Kl.
Mentions: A final pathway for which we observed striking expression divergence was multi-drug transport (Figure 4b; Additional file 1: Transport). Most genes in this pathway were covered by clusters 8, 11, 16 (Figure 5a, b). Multi-drug transporters are divided into two classes: ATP-binding cassette (ABC) and major facilitator superfamily (MFS) transporters [5]. We examined the expression patterns of these transporters and found at least two types of divergent behaviors. First, the fraction of differentially expressed Sc MFS transporters was low compared to Cg and Kl (Fisher exact test, one-tailed P = 0.025 and 0.020, respectively). Second, the timing of MFS gene expression differed, with Sc up-regulated late and Cg up-regulated early (Figure 5b). In SC, several ABC and MFS transporters have been shown to bind fluconazole as a substrate [20,42,43]. Of these, we found that the PDR5/10/15 family of ABC transporters was up-regulated in Cg and Sc but not Kl. Another fluconazole transporter, SNQ2, was up-regulated in Cg only.

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