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Integration of Posttranscriptional Gene Networks into Metabolic Adaptation and Biofilm Maturation in Candida albicans.

Verma-Gaur J, Qu Y, Harrison PF, Lo TL, Quenault T, Dagley MJ, Bellousoff M, Powell DR, Beilharz TH, Traven A - PLoS Genet. (2015)

Bottom Line: The extracellular matrix is critical for antifungal resistance and immune evasion, and yet of all biofilm maturation pathways extracellular matrix biogenesis is the least understood.We propose a model in which the hypoxic biofilm environment is sensed by regulators such as Ccr4 to orchestrate metabolic adaptation, as well as the regulation of extracellular matrix production by impacting on the expression of matrix-related cell wall genes.Therefore metabolic changes in biofilms might be intimately linked to a key biofilm maturation mechanism that ultimately results in untreatable fungal disease.

View Article: PubMed Central - PubMed

Affiliation: Infection and Immunity Program, Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.

ABSTRACT
The yeast Candida albicans is a human commensal and opportunistic pathogen. Although both commensalism and pathogenesis depend on metabolic adaptation, the regulatory pathways that mediate metabolic processes in C. albicans are incompletely defined. For example, metabolic change is a major feature that distinguishes community growth of C. albicans in biofilms compared to suspension cultures, but how metabolic adaptation is functionally interfaced with the structural and gene regulatory changes that drive biofilm maturation remains to be fully understood. We show here that the RNA binding protein Puf3 regulates a posttranscriptional mRNA network in C. albicans that impacts on mitochondrial biogenesis, and provide the first functional data suggesting evolutionary rewiring of posttranscriptional gene regulation between the model yeast Saccharomyces cerevisiae and C. albicans. A proportion of the Puf3 mRNA network is differentially expressed in biofilms, and by using a mutant in the mRNA deadenylase CCR4 (the enzyme recruited to mRNAs by Puf3 to control transcript stability) we show that posttranscriptional regulation is important for mitochondrial regulation in biofilms. Inactivation of CCR4 or dis-regulation of mitochondrial activity led to altered biofilm structure and over-production of extracellular matrix material. The extracellular matrix is critical for antifungal resistance and immune evasion, and yet of all biofilm maturation pathways extracellular matrix biogenesis is the least understood. We propose a model in which the hypoxic biofilm environment is sensed by regulators such as Ccr4 to orchestrate metabolic adaptation, as well as the regulation of extracellular matrix production by impacting on the expression of matrix-related cell wall genes. Therefore metabolic changes in biofilms might be intimately linked to a key biofilm maturation mechanism that ultimately results in untreatable fungal disease.

No MeSH data available.


Related in: MedlinePlus

The C. albicans Puf3 regulon and mitochondrial roles.(A) Venn diagram showing the number of mRNAs with a Puf3 binding motif in the 3′ UTRs in S. cerevisiae and C. albicans (only genes which contain orthologs in both species are depicted here). (B) Functional groupings of the Puf3 regulon in C. albicans. The data used to produce this chart is shown in S4 Dataset. (C) Growth of C. albicans wild type and puf3Δ/Δ mutant on plates supplied with glucose, glycerol or lactate. Ten-fold serial dilutions were made starting from OD600 = 0.5, and plates were photographed after 2 days of growth. (D) Mitochondria in the indicated strains were stained with MitoTracker and imaged as described in Materials and Methods. (E) C. albicans growth on plates was tested as in (C), in the presence or absence of CCCP. Growth was observed on glycerol plates where mitochondrial function is essential.
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pgen.1005590.g003: The C. albicans Puf3 regulon and mitochondrial roles.(A) Venn diagram showing the number of mRNAs with a Puf3 binding motif in the 3′ UTRs in S. cerevisiae and C. albicans (only genes which contain orthologs in both species are depicted here). (B) Functional groupings of the Puf3 regulon in C. albicans. The data used to produce this chart is shown in S4 Dataset. (C) Growth of C. albicans wild type and puf3Δ/Δ mutant on plates supplied with glucose, glycerol or lactate. Ten-fold serial dilutions were made starting from OD600 = 0.5, and plates were photographed after 2 days of growth. (D) Mitochondria in the indicated strains were stained with MitoTracker and imaged as described in Materials and Methods. (E) C. albicans growth on plates was tested as in (C), in the presence or absence of CCCP. Growth was observed on glycerol plates where mitochondrial function is essential.

Mentions: Armed with the 3′ UTR landscape for the C. albicans transcriptome, we identified a total of 555 putative Puf3 targets (S2 Dataset). For comparative purposes, we searched the S. cerevisiae genome in an equivalent manner and identified 671 genes with Puf3 binding sites in their 3′ UTR (S2 Dataset). In 3′ UTRs, the Puf3 motif occurs two or three times as often as random motifs of the same composition. However in the genomes as a whole Puf3-binding sequences are not more prevalent than random motifs of the same composition (2751 instances in S. cerevisiae, and 3463 instances in C. albicans). Of the 555 putative Puf3 targets in C. albicans, 432 (77.8%) have an ortholog in S. cerevisiae (S2 Dataset, Fig 3A). The number of genes where both species have the Puf3 motif is 198 (Fig 3A). This correlation is highly significant by Fisher’s Exact Test, as similar analysis with a random shuffling of the motif generally produces a value less than 3 in common. Therefore, the Puf3 motif is much more highly conserved than shuffled motifs. The 3′ UTR length of the shared mRNAs with the Puf3 motif is not conserved (S1 Fig, red dots). Furthermore, the position of the Puf3 binding site is not preserved relative to the stop codon or the polyadenylation site between the two species (Fig 2D and 2E).


Integration of Posttranscriptional Gene Networks into Metabolic Adaptation and Biofilm Maturation in Candida albicans.

Verma-Gaur J, Qu Y, Harrison PF, Lo TL, Quenault T, Dagley MJ, Bellousoff M, Powell DR, Beilharz TH, Traven A - PLoS Genet. (2015)

The C. albicans Puf3 regulon and mitochondrial roles.(A) Venn diagram showing the number of mRNAs with a Puf3 binding motif in the 3′ UTRs in S. cerevisiae and C. albicans (only genes which contain orthologs in both species are depicted here). (B) Functional groupings of the Puf3 regulon in C. albicans. The data used to produce this chart is shown in S4 Dataset. (C) Growth of C. albicans wild type and puf3Δ/Δ mutant on plates supplied with glucose, glycerol or lactate. Ten-fold serial dilutions were made starting from OD600 = 0.5, and plates were photographed after 2 days of growth. (D) Mitochondria in the indicated strains were stained with MitoTracker and imaged as described in Materials and Methods. (E) C. albicans growth on plates was tested as in (C), in the presence or absence of CCCP. Growth was observed on glycerol plates where mitochondrial function is essential.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4608769&req=5

pgen.1005590.g003: The C. albicans Puf3 regulon and mitochondrial roles.(A) Venn diagram showing the number of mRNAs with a Puf3 binding motif in the 3′ UTRs in S. cerevisiae and C. albicans (only genes which contain orthologs in both species are depicted here). (B) Functional groupings of the Puf3 regulon in C. albicans. The data used to produce this chart is shown in S4 Dataset. (C) Growth of C. albicans wild type and puf3Δ/Δ mutant on plates supplied with glucose, glycerol or lactate. Ten-fold serial dilutions were made starting from OD600 = 0.5, and plates were photographed after 2 days of growth. (D) Mitochondria in the indicated strains were stained with MitoTracker and imaged as described in Materials and Methods. (E) C. albicans growth on plates was tested as in (C), in the presence or absence of CCCP. Growth was observed on glycerol plates where mitochondrial function is essential.
Mentions: Armed with the 3′ UTR landscape for the C. albicans transcriptome, we identified a total of 555 putative Puf3 targets (S2 Dataset). For comparative purposes, we searched the S. cerevisiae genome in an equivalent manner and identified 671 genes with Puf3 binding sites in their 3′ UTR (S2 Dataset). In 3′ UTRs, the Puf3 motif occurs two or three times as often as random motifs of the same composition. However in the genomes as a whole Puf3-binding sequences are not more prevalent than random motifs of the same composition (2751 instances in S. cerevisiae, and 3463 instances in C. albicans). Of the 555 putative Puf3 targets in C. albicans, 432 (77.8%) have an ortholog in S. cerevisiae (S2 Dataset, Fig 3A). The number of genes where both species have the Puf3 motif is 198 (Fig 3A). This correlation is highly significant by Fisher’s Exact Test, as similar analysis with a random shuffling of the motif generally produces a value less than 3 in common. Therefore, the Puf3 motif is much more highly conserved than shuffled motifs. The 3′ UTR length of the shared mRNAs with the Puf3 motif is not conserved (S1 Fig, red dots). Furthermore, the position of the Puf3 binding site is not preserved relative to the stop codon or the polyadenylation site between the two species (Fig 2D and 2E).

Bottom Line: The extracellular matrix is critical for antifungal resistance and immune evasion, and yet of all biofilm maturation pathways extracellular matrix biogenesis is the least understood.We propose a model in which the hypoxic biofilm environment is sensed by regulators such as Ccr4 to orchestrate metabolic adaptation, as well as the regulation of extracellular matrix production by impacting on the expression of matrix-related cell wall genes.Therefore metabolic changes in biofilms might be intimately linked to a key biofilm maturation mechanism that ultimately results in untreatable fungal disease.

View Article: PubMed Central - PubMed

Affiliation: Infection and Immunity Program, Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.

ABSTRACT
The yeast Candida albicans is a human commensal and opportunistic pathogen. Although both commensalism and pathogenesis depend on metabolic adaptation, the regulatory pathways that mediate metabolic processes in C. albicans are incompletely defined. For example, metabolic change is a major feature that distinguishes community growth of C. albicans in biofilms compared to suspension cultures, but how metabolic adaptation is functionally interfaced with the structural and gene regulatory changes that drive biofilm maturation remains to be fully understood. We show here that the RNA binding protein Puf3 regulates a posttranscriptional mRNA network in C. albicans that impacts on mitochondrial biogenesis, and provide the first functional data suggesting evolutionary rewiring of posttranscriptional gene regulation between the model yeast Saccharomyces cerevisiae and C. albicans. A proportion of the Puf3 mRNA network is differentially expressed in biofilms, and by using a mutant in the mRNA deadenylase CCR4 (the enzyme recruited to mRNAs by Puf3 to control transcript stability) we show that posttranscriptional regulation is important for mitochondrial regulation in biofilms. Inactivation of CCR4 or dis-regulation of mitochondrial activity led to altered biofilm structure and over-production of extracellular matrix material. The extracellular matrix is critical for antifungal resistance and immune evasion, and yet of all biofilm maturation pathways extracellular matrix biogenesis is the least understood. We propose a model in which the hypoxic biofilm environment is sensed by regulators such as Ccr4 to orchestrate metabolic adaptation, as well as the regulation of extracellular matrix production by impacting on the expression of matrix-related cell wall genes. Therefore metabolic changes in biofilms might be intimately linked to a key biofilm maturation mechanism that ultimately results in untreatable fungal disease.

No MeSH data available.


Related in: MedlinePlus