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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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Gene expression response to caspofungin treatment during infection.(A). Changes in expression levels for 248 C. albicans environmentally responsive genes are presented for caspofungin treated versus untreated cells at 24 hr postinfection (“Kidney,” S6 Data), in vitro in YPD at 30°C (“YPD,” from [30]), and in vitro in RPMI at 37°C (“RPMI,” S6 Data). These environmentally responsive genes are the same ones for which expression was measured during the time-course of infection depicted in Fig. 1. For comparison, the expression ratios of the same genes at 12 hr postinfection relative to the inoculum are shown (“12 hr/0 hr,” from Fig. 1). The data are presented in heat map format. Regions “1” and “2” are expanded on the right to make gene names legible. (B). Expression levels for 231 C. albicans transcription factor genes were measured for caspofungin treated versus untreated cells at 24 hr postinfection (“In vivo caspo-induced,” S6 Data) and in vitro in RPMI at 37°C (“In vitro caspo-induced,” S6 Data). Significantly up-regulated transcription factor genes are listed (≥2-fold change and p < 0.05). For comparison, the significantly down-regulated transcription factor genes at 12 hr postinfection are listed (“Early down-regulated,” S6 Data). All numerical data for this figure are in S7 Data.
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pbio.1002076.g008: Gene expression response to caspofungin treatment during infection.(A). Changes in expression levels for 248 C. albicans environmentally responsive genes are presented for caspofungin treated versus untreated cells at 24 hr postinfection (“Kidney,” S6 Data), in vitro in YPD at 30°C (“YPD,” from [30]), and in vitro in RPMI at 37°C (“RPMI,” S6 Data). These environmentally responsive genes are the same ones for which expression was measured during the time-course of infection depicted in Fig. 1. For comparison, the expression ratios of the same genes at 12 hr postinfection relative to the inoculum are shown (“12 hr/0 hr,” from Fig. 1). The data are presented in heat map format. Regions “1” and “2” are expanded on the right to make gene names legible. (B). Expression levels for 231 C. albicans transcription factor genes were measured for caspofungin treated versus untreated cells at 24 hr postinfection (“In vivo caspo-induced,” S6 Data) and in vitro in RPMI at 37°C (“In vitro caspo-induced,” S6 Data). Significantly up-regulated transcription factor genes are listed (≥2-fold change and p < 0.05). For comparison, the significantly down-regulated transcription factor genes at 12 hr postinfection are listed (“Early down-regulated,” S6 Data). All numerical data for this figure are in S7 Data.

Mentions: Caspofungin, a cell wall inhibitor, is an extremely effective antifungal drug [6]. The gene expression response to caspofungin treatment has been assayed during growth in vitro [28–30], but not under infection conditions. We reasoned that the response to caspofungin may be different in vivo. Therefore, we assayed expression of the 248 environmentally responsive genes 2 hr after caspofungin administration in mice that had already been infected for 24 hr. There was no detectable decline in fungal cell number after this brief treatment time, but an extensive gene expression response was manifested (S6 Data). A much broader set of genes was induced by caspofungin in vivo than had been detected through previous in vitro studies (Fig. 8A). Specifically, 44 of the genes assayed showed significantly increased RNA accumulation (≥2-fold, p < 0.05) after caspofungin treatment in vivo compared to untreated infection samples. Several induced genes specify cell wall or secreted proteins (ALS4, ALS9, GCA2, PGA13, PGA26, PGA31, PGA37, PHR2, PIR1, RBR2, SAP1, and SAP9), and others specify enzymes that function in glucose generation (PCK1, GPM2, and DAK2). Thus, the in vivo response suggests that the cell wall is restructured in response to the drug through an alteration of cell wall protein composition and an increase in β-glucan synthesis.


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)

Gene expression response to caspofungin treatment during infection.(A). Changes in expression levels for 248 C. albicans environmentally responsive genes are presented for caspofungin treated versus untreated cells at 24 hr postinfection (“Kidney,” S6 Data), in vitro in YPD at 30°C (“YPD,” from [30]), and in vitro in RPMI at 37°C (“RPMI,” S6 Data). These environmentally responsive genes are the same ones for which expression was measured during the time-course of infection depicted in Fig. 1. For comparison, the expression ratios of the same genes at 12 hr postinfection relative to the inoculum are shown (“12 hr/0 hr,” from Fig. 1). The data are presented in heat map format. Regions “1” and “2” are expanded on the right to make gene names legible. (B). Expression levels for 231 C. albicans transcription factor genes were measured for caspofungin treated versus untreated cells at 24 hr postinfection (“In vivo caspo-induced,” S6 Data) and in vitro in RPMI at 37°C (“In vitro caspo-induced,” S6 Data). Significantly up-regulated transcription factor genes are listed (≥2-fold change and p < 0.05). For comparison, the significantly down-regulated transcription factor genes at 12 hr postinfection are listed (“Early down-regulated,” S6 Data). All numerical data for this figure are in S7 Data.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4333574&req=5

pbio.1002076.g008: Gene expression response to caspofungin treatment during infection.(A). Changes in expression levels for 248 C. albicans environmentally responsive genes are presented for caspofungin treated versus untreated cells at 24 hr postinfection (“Kidney,” S6 Data), in vitro in YPD at 30°C (“YPD,” from [30]), and in vitro in RPMI at 37°C (“RPMI,” S6 Data). These environmentally responsive genes are the same ones for which expression was measured during the time-course of infection depicted in Fig. 1. For comparison, the expression ratios of the same genes at 12 hr postinfection relative to the inoculum are shown (“12 hr/0 hr,” from Fig. 1). The data are presented in heat map format. Regions “1” and “2” are expanded on the right to make gene names legible. (B). Expression levels for 231 C. albicans transcription factor genes were measured for caspofungin treated versus untreated cells at 24 hr postinfection (“In vivo caspo-induced,” S6 Data) and in vitro in RPMI at 37°C (“In vitro caspo-induced,” S6 Data). Significantly up-regulated transcription factor genes are listed (≥2-fold change and p < 0.05). For comparison, the significantly down-regulated transcription factor genes at 12 hr postinfection are listed (“Early down-regulated,” S6 Data). All numerical data for this figure are in S7 Data.
Mentions: Caspofungin, a cell wall inhibitor, is an extremely effective antifungal drug [6]. The gene expression response to caspofungin treatment has been assayed during growth in vitro [28–30], but not under infection conditions. We reasoned that the response to caspofungin may be different in vivo. Therefore, we assayed expression of the 248 environmentally responsive genes 2 hr after caspofungin administration in mice that had already been infected for 24 hr. There was no detectable decline in fungal cell number after this brief treatment time, but an extensive gene expression response was manifested (S6 Data). A much broader set of genes was induced by caspofungin in vivo than had been detected through previous in vitro studies (Fig. 8A). Specifically, 44 of the genes assayed showed significantly increased RNA accumulation (≥2-fold, p < 0.05) after caspofungin treatment in vivo compared to untreated infection samples. Several induced genes specify cell wall or secreted proteins (ALS4, ALS9, GCA2, PGA13, PGA26, PGA31, PGA37, PHR2, PIR1, RBR2, SAP1, and SAP9), and others specify enzymes that function in glucose generation (PCK1, GPM2, and DAK2). Thus, the in vivo response suggests that the cell wall is restructured in response to the drug through an alteration of cell wall protein composition and an increase in β-glucan synthesis.

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