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Investigation of Aspergillus fumigatus biofilm formation by various "omics" approaches.

Muszkieta L, Beauvais A, Pähtz V, Gibbons JG, Anton Leberre V, Beau R, Shibuya K, Rokas A, Francois JM, Kniemeyer O, Brakhage AA, Latgé JP - Front Microbiol (2013)

Bottom Line: In the lung, Aspergillus fumigatus usually forms a dense colony of filaments embedded in a polymeric extracellular matrix called biofilm (BF).This extracellular matrix embeds and glues hyphae together and protects the fungus from an outside hostile environment.Recent works have shown that the fungus in this aerial grown BF-like state exhibits reduced susceptibility to antifungal drugs and undergoes major metabolic changes that are thought to be associated to virulence.

View Article: PubMed Central - PubMed

Affiliation: Unité des Aspergillus, Institut Pasteur Paris Cedex, France.

ABSTRACT
In the lung, Aspergillus fumigatus usually forms a dense colony of filaments embedded in a polymeric extracellular matrix called biofilm (BF). This extracellular matrix embeds and glues hyphae together and protects the fungus from an outside hostile environment. This extracellular matrix is absent in fungal colonies grown under classical liquid shake conditions (PL), which were historically used to understand A. fumigatus pathobiology. Recent works have shown that the fungus in this aerial grown BF-like state exhibits reduced susceptibility to antifungal drugs and undergoes major metabolic changes that are thought to be associated to virulence. These differences in pathological and physiological characteristics between BF and liquid shake conditions suggest that the PL condition is a poor in vitro disease model. In the laboratory, A. fumigatus mycelium embedded by the extracellular matrix can be produced in vitro in aerial condition using an agar-based medium. To provide a global and accurate understanding of A. fumigatus in vitro BF growth, we utilized microarray, RNA-sequencing, and proteomic analysis to compare the global gene and protein expression profiles of A. fumigatus grown under BF and PL conditions. In this review, we will present the different signatures obtained with these three "omics" methods. We will discuss the advantages and limitations of each method and their complementarity.

No MeSH data available.


Related in: MedlinePlus

Differential expression of genes involved in glycolysis pathway and TCA cycle during biofilm growth.
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Figure 3: Differential expression of genes involved in glycolysis pathway and TCA cycle during biofilm growth.

Mentions: RNA-sequencing as compared to microarrays provides clear evidence that entire pathways are differentially expressed. For example, the glycolysis pathway responsible for the conversion of glucose to pyruvate was shown to be down regulated in the A. fumigatus BF in both transcriptomic methods. Whereas microarrays allowed the identification of only 5 down regulated genes of the glycolysis, the RNA-sequencing highlighted 17 down regulated genes out of 28 genes constituting the glycolysis pathway (Figure 3). Genes encoding enzymes of the tricarboxylic-acid cycle are also differentially expressed as revealed by both transcriptomic methods. Genes encoding enzymes responsible of the conversion of citrate to succinyl-CoA, the oxidative branch of the TCA cycle, were shown to be down regulated in RNA-sequencing whereas enzymes participating in the conversion of succinyl-CoA to oxaloacetate were shown to be up regulated. In line with this, the isocitrate lyase, which is involved in the conversion of isocitrate to glyoxylate and succinate was shown to be up regulated in both analyses. These results reflect that the fungus may not acquire energy by fermentation but by metabolizing acetyl-CoA using the glyoxylate cycle under BF conditions. NADH formed by this cycle can enter then in the respiratory chain pathway. Genes belonging to the mitochondrial complexes II, III, and V, controlling oxidative phosphorylation, were shown to be up regulated in the BF in the RNA-sequencing analysis. In Candida albicans, levels of isocitrate lyase and malate synthase are greatly increased upon contact with its human host and interestingly, isocitrate lyase has been shown to be key virulence factor (Lorenz and Fink, 2001). In contrast, isocitrate lyase of A. fumigatus is not essential for the development of invasive aspergillosis in a murine model (Schobel et al., 2007).


Investigation of Aspergillus fumigatus biofilm formation by various "omics" approaches.

Muszkieta L, Beauvais A, Pähtz V, Gibbons JG, Anton Leberre V, Beau R, Shibuya K, Rokas A, Francois JM, Kniemeyer O, Brakhage AA, Latgé JP - Front Microbiol (2013)

Differential expression of genes involved in glycolysis pathway and TCA cycle during biofilm growth.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3569664&req=5

Figure 3: Differential expression of genes involved in glycolysis pathway and TCA cycle during biofilm growth.
Mentions: RNA-sequencing as compared to microarrays provides clear evidence that entire pathways are differentially expressed. For example, the glycolysis pathway responsible for the conversion of glucose to pyruvate was shown to be down regulated in the A. fumigatus BF in both transcriptomic methods. Whereas microarrays allowed the identification of only 5 down regulated genes of the glycolysis, the RNA-sequencing highlighted 17 down regulated genes out of 28 genes constituting the glycolysis pathway (Figure 3). Genes encoding enzymes of the tricarboxylic-acid cycle are also differentially expressed as revealed by both transcriptomic methods. Genes encoding enzymes responsible of the conversion of citrate to succinyl-CoA, the oxidative branch of the TCA cycle, were shown to be down regulated in RNA-sequencing whereas enzymes participating in the conversion of succinyl-CoA to oxaloacetate were shown to be up regulated. In line with this, the isocitrate lyase, which is involved in the conversion of isocitrate to glyoxylate and succinate was shown to be up regulated in both analyses. These results reflect that the fungus may not acquire energy by fermentation but by metabolizing acetyl-CoA using the glyoxylate cycle under BF conditions. NADH formed by this cycle can enter then in the respiratory chain pathway. Genes belonging to the mitochondrial complexes II, III, and V, controlling oxidative phosphorylation, were shown to be up regulated in the BF in the RNA-sequencing analysis. In Candida albicans, levels of isocitrate lyase and malate synthase are greatly increased upon contact with its human host and interestingly, isocitrate lyase has been shown to be key virulence factor (Lorenz and Fink, 2001). In contrast, isocitrate lyase of A. fumigatus is not essential for the development of invasive aspergillosis in a murine model (Schobel et al., 2007).

Bottom Line: In the lung, Aspergillus fumigatus usually forms a dense colony of filaments embedded in a polymeric extracellular matrix called biofilm (BF).This extracellular matrix embeds and glues hyphae together and protects the fungus from an outside hostile environment.Recent works have shown that the fungus in this aerial grown BF-like state exhibits reduced susceptibility to antifungal drugs and undergoes major metabolic changes that are thought to be associated to virulence.

View Article: PubMed Central - PubMed

Affiliation: Unité des Aspergillus, Institut Pasteur Paris Cedex, France.

ABSTRACT
In the lung, Aspergillus fumigatus usually forms a dense colony of filaments embedded in a polymeric extracellular matrix called biofilm (BF). This extracellular matrix embeds and glues hyphae together and protects the fungus from an outside hostile environment. This extracellular matrix is absent in fungal colonies grown under classical liquid shake conditions (PL), which were historically used to understand A. fumigatus pathobiology. Recent works have shown that the fungus in this aerial grown BF-like state exhibits reduced susceptibility to antifungal drugs and undergoes major metabolic changes that are thought to be associated to virulence. These differences in pathological and physiological characteristics between BF and liquid shake conditions suggest that the PL condition is a poor in vitro disease model. In the laboratory, A. fumigatus mycelium embedded by the extracellular matrix can be produced in vitro in aerial condition using an agar-based medium. To provide a global and accurate understanding of A. fumigatus in vitro BF growth, we utilized microarray, RNA-sequencing, and proteomic analysis to compare the global gene and protein expression profiles of A. fumigatus grown under BF and PL conditions. In this review, we will present the different signatures obtained with these three "omics" methods. We will discuss the advantages and limitations of each method and their complementarity.

No MeSH data available.


Related in: MedlinePlus