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Activation and alliance of regulatory pathways in C. albicans during mammalian infection.

Xu W, Solis NV, Ehrlich RL, Woolford CA, Filler SG, Mitchell AP - PLoS Biol. (2015)

Bottom Line: Gene expression dynamics have provided foundational insight into almost all biological processes.Perturbation with the cell wall inhibitor caspofungin also has distinct gene expression impact in vivo and in vitro.Our findings support the principle that virulence is a property that is manifested only in the distinct environment in which host-pathogen interaction occurs.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

ABSTRACT
Gene expression dynamics have provided foundational insight into almost all biological processes. Here, we analyze expression of environmentally responsive genes and transcription factor genes to infer signals and pathways that drive pathogen gene regulation during invasive Candida albicans infection of a mammalian host. Environmentally responsive gene expression shows that there are early and late phases of infection. The early phase includes induction of zinc and iron limitation genes, genes that respond to transcription factor Rim101, and genes characteristic of invasive hyphal cells. The late phase includes responses related to phagocytosis by macrophages. Transcription factor gene expression also reflects early and late phases. Transcription factor genes that are required for virulence or proliferation in vivo are enriched among highly expressed transcription factor genes. Mutants defective in six transcription factor genes, three previously studied in detail (Rim101, Efg1, Zap1) and three less extensively studied (Rob1, Rpn4, Sut1), are profiled during infection. Most of these mutants have distinct gene expression profiles during infection as compared to in vitro growth. Infection profiles suggest that Sut1 acts in the same pathway as Zap1, and we verify that functional relationship with the finding that overexpression of either ZAP1 or the Zap1-dependent zinc transporter gene ZRT2 restores pathogenicity to a sut1 mutant. Perturbation with the cell wall inhibitor caspofungin also has distinct gene expression impact in vivo and in vitro. Unexpectedly, caspofungin induces many of the same genes that are repressed early during infection, a phenomenon that we suggest may contribute to drug efficacy. The pathogen response circuitry is tailored uniquely during infection, with many relevant regulatory relationships that are not evident during growth in vitro. Our findings support the principle that virulence is a property that is manifested only in the distinct environment in which host-pathogen interaction occurs.

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Rim101-dependent gene regulation during invasive infection.RNA levels for 148 C. albicans environmental response genes were determined by nanoString at 24 hr postinfection for the rim101 mutant and complemented strains (S5 Data). (A). Expression ratios are plotted for each gene in rim101Δ/Δ versus wild type (X axis) and rim101Δ/Δ versus complemented strain (Y axis). Three genes (red data points) have significantly different expression ratios in the two comparisons. (B). Expression ratios are presented for all genes significantly down-regulated in the rim101Δ/Δ strain relative to the complemented strain during kidney infection (blue bars; ≥2-fold change and p-value < 0.05). The expression ratios for the same genes in the same strains during intra-abdominal candidiasis (IAC) infection (red bars; reported in [12]) or during in vitro growth in Spider medium (green bars) are displayed. Complete data are in S5 Data. (C). Expression ratios are presented for all genes significantly up-regulated in the rim101Δ/Δ strain relative to the complemented strain during kidney infection (blue bars; ≥2-fold change and p-value < 0.05), during abdominal infection (red bars; reported in [12]) or during in vitro growth in Spider medium (green bars) are displayed. Complete data are in S5 Data. All numerical data for this figure are in S7 Data.
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pbio.1002076.g005: Rim101-dependent gene regulation during invasive infection.RNA levels for 148 C. albicans environmental response genes were determined by nanoString at 24 hr postinfection for the rim101 mutant and complemented strains (S5 Data). (A). Expression ratios are plotted for each gene in rim101Δ/Δ versus wild type (X axis) and rim101Δ/Δ versus complemented strain (Y axis). Three genes (red data points) have significantly different expression ratios in the two comparisons. (B). Expression ratios are presented for all genes significantly down-regulated in the rim101Δ/Δ strain relative to the complemented strain during kidney infection (blue bars; ≥2-fold change and p-value < 0.05). The expression ratios for the same genes in the same strains during intra-abdominal candidiasis (IAC) infection (red bars; reported in [12]) or during in vitro growth in Spider medium (green bars) are displayed. Complete data are in S5 Data. (C). Expression ratios are presented for all genes significantly up-regulated in the rim101Δ/Δ strain relative to the complemented strain during kidney infection (blue bars; ≥2-fold change and p-value < 0.05), during abdominal infection (red bars; reported in [12]) or during in vitro growth in Spider medium (green bars) are displayed. Complete data are in S5 Data. All numerical data for this figure are in S7 Data.

Mentions: We sought to understand regulatory relationships during infection, and we began this analysis with the transcription factor Rim101. We chose RIM101 because it is the most highly expressed transcription factor gene at 48 hr postinfection; its RNA levels comprise over 3% of the total RNA levels for all 231 transcription factor genes (S4 Data). Rim101 clearly functions during infection: early up-regulated genes correlate with known Rim101-dependent genes, and prior studies show that it is required for virulence in the mouse disseminated infection model, where it promotes both hyphal formation and proliferation [19]. In order to define the gene expression basis for the rim101Δ/Δ mutant virulence defect, we assayed expression of 148 environmentally responsive genes by the rim101Δ/Δ mutant and rim101Δ/Δ+pRIM101 complemented strain at 24 hr postinfection (S5 Data). The rim101Δ/Δ mutant presented significantly reduced accumulation of 33 RNAs (≥2-fold change and p < 0.05, including RIM101 itself), and increased expression of 14 RNAs, compared to the wild-type strain (S5 Data). RNA accumulation in the complemented strain closely mirrored that of the wild type (Fig. 5A). Specifically, RNA accumulation levels were restored by the complementing RIM101 allele for all genes except GAP2, PHR1, and HYR1 (p < 0.05). In the complemented strain, expression of GAP2 and PHR1 trended toward the wild-type level, thus suggesting that these few gene expression differences from the wild type are the result of reduced gene dosage of RIM101 alleles in the complemented strain compared to the wild type, as documented previously for these strains [19].


Activation and alliance of regulatory pathways in C. albicans during mammalian infection.

Xu W, Solis NV, Ehrlich RL, Woolford CA, Filler SG, Mitchell AP - PLoS Biol. (2015)

Rim101-dependent gene regulation during invasive infection.RNA levels for 148 C. albicans environmental response genes were determined by nanoString at 24 hr postinfection for the rim101 mutant and complemented strains (S5 Data). (A). Expression ratios are plotted for each gene in rim101Δ/Δ versus wild type (X axis) and rim101Δ/Δ versus complemented strain (Y axis). Three genes (red data points) have significantly different expression ratios in the two comparisons. (B). Expression ratios are presented for all genes significantly down-regulated in the rim101Δ/Δ strain relative to the complemented strain during kidney infection (blue bars; ≥2-fold change and p-value < 0.05). The expression ratios for the same genes in the same strains during intra-abdominal candidiasis (IAC) infection (red bars; reported in [12]) or during in vitro growth in Spider medium (green bars) are displayed. Complete data are in S5 Data. (C). Expression ratios are presented for all genes significantly up-regulated in the rim101Δ/Δ strain relative to the complemented strain during kidney infection (blue bars; ≥2-fold change and p-value < 0.05), during abdominal infection (red bars; reported in [12]) or during in vitro growth in Spider medium (green bars) are displayed. Complete data are in S5 Data. All numerical data for this figure are in S7 Data.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4333574&req=5

pbio.1002076.g005: Rim101-dependent gene regulation during invasive infection.RNA levels for 148 C. albicans environmental response genes were determined by nanoString at 24 hr postinfection for the rim101 mutant and complemented strains (S5 Data). (A). Expression ratios are plotted for each gene in rim101Δ/Δ versus wild type (X axis) and rim101Δ/Δ versus complemented strain (Y axis). Three genes (red data points) have significantly different expression ratios in the two comparisons. (B). Expression ratios are presented for all genes significantly down-regulated in the rim101Δ/Δ strain relative to the complemented strain during kidney infection (blue bars; ≥2-fold change and p-value < 0.05). The expression ratios for the same genes in the same strains during intra-abdominal candidiasis (IAC) infection (red bars; reported in [12]) or during in vitro growth in Spider medium (green bars) are displayed. Complete data are in S5 Data. (C). Expression ratios are presented for all genes significantly up-regulated in the rim101Δ/Δ strain relative to the complemented strain during kidney infection (blue bars; ≥2-fold change and p-value < 0.05), during abdominal infection (red bars; reported in [12]) or during in vitro growth in Spider medium (green bars) are displayed. Complete data are in S5 Data. All numerical data for this figure are in S7 Data.
Mentions: We sought to understand regulatory relationships during infection, and we began this analysis with the transcription factor Rim101. We chose RIM101 because it is the most highly expressed transcription factor gene at 48 hr postinfection; its RNA levels comprise over 3% of the total RNA levels for all 231 transcription factor genes (S4 Data). Rim101 clearly functions during infection: early up-regulated genes correlate with known Rim101-dependent genes, and prior studies show that it is required for virulence in the mouse disseminated infection model, where it promotes both hyphal formation and proliferation [19]. In order to define the gene expression basis for the rim101Δ/Δ mutant virulence defect, we assayed expression of 148 environmentally responsive genes by the rim101Δ/Δ mutant and rim101Δ/Δ+pRIM101 complemented strain at 24 hr postinfection (S5 Data). The rim101Δ/Δ mutant presented significantly reduced accumulation of 33 RNAs (≥2-fold change and p < 0.05, including RIM101 itself), and increased expression of 14 RNAs, compared to the wild-type strain (S5 Data). RNA accumulation in the complemented strain closely mirrored that of the wild type (Fig. 5A). Specifically, RNA accumulation levels were restored by the complementing RIM101 allele for all genes except GAP2, PHR1, and HYR1 (p < 0.05). In the complemented strain, expression of GAP2 and PHR1 trended toward the wild-type level, thus suggesting that these few gene expression differences from the wild type are the result of reduced gene dosage of RIM101 alleles in the complemented strain compared to the wild type, as documented previously for these strains [19].

Bottom Line: Gene expression dynamics have provided foundational insight into almost all biological processes.Perturbation with the cell wall inhibitor caspofungin also has distinct gene expression impact in vivo and in vitro.Our findings support the principle that virulence is a property that is manifested only in the distinct environment in which host-pathogen interaction occurs.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

ABSTRACT
Gene expression dynamics have provided foundational insight into almost all biological processes. Here, we analyze expression of environmentally responsive genes and transcription factor genes to infer signals and pathways that drive pathogen gene regulation during invasive Candida albicans infection of a mammalian host. Environmentally responsive gene expression shows that there are early and late phases of infection. The early phase includes induction of zinc and iron limitation genes, genes that respond to transcription factor Rim101, and genes characteristic of invasive hyphal cells. The late phase includes responses related to phagocytosis by macrophages. Transcription factor gene expression also reflects early and late phases. Transcription factor genes that are required for virulence or proliferation in vivo are enriched among highly expressed transcription factor genes. Mutants defective in six transcription factor genes, three previously studied in detail (Rim101, Efg1, Zap1) and three less extensively studied (Rob1, Rpn4, Sut1), are profiled during infection. Most of these mutants have distinct gene expression profiles during infection as compared to in vitro growth. Infection profiles suggest that Sut1 acts in the same pathway as Zap1, and we verify that functional relationship with the finding that overexpression of either ZAP1 or the Zap1-dependent zinc transporter gene ZRT2 restores pathogenicity to a sut1 mutant. Perturbation with the cell wall inhibitor caspofungin also has distinct gene expression impact in vivo and in vitro. Unexpectedly, caspofungin induces many of the same genes that are repressed early during infection, a phenomenon that we suggest may contribute to drug efficacy. The pathogen response circuitry is tailored uniquely during infection, with many relevant regulatory relationships that are not evident during growth in vitro. Our findings support the principle that virulence is a property that is manifested only in the distinct environment in which host-pathogen interaction occurs.

Show MeSH
Related in: MedlinePlus