Global Transcriptome Changes Underlying Colony Growth in the Opportunistic Human Pathogen Aspergillus fumigatus

Abstract

Aspergillus fumigatus is the most common and deadly pulmonary fungal infection worldwide. In the lung, the fungus usually forms a dense colony of filaments embedded in a polymeric extracellular matrix. To identify candidate genes involved in this biofilm (BF) growth, we used RNA-Seq to compare the transcriptomes of BF and liquid plankton (PL) growth. Sequencing and mapping of tens of millions sequence reads against the A. fumigatus transcriptome identified 3,728 differentially regulated genes in the two conditions. Although many of these genes, including the ones coding for transcription factors, stress response, the ribosome, and the translation machinery, likely reflect the different growth demands in the two conditions, our experiment also identified hundreds of candidate genes for the observed differences in morphology and pathobiology between BF and PL. We found an overrepresentation of upregulated genes in transport, secondary metabolism, and cell wall and surface functions. Furthermore, upregulated genes showed significant spatial structure across the A. fumigatus genome; they were more likely to occur in subtelomeric regions and colocalized in 27 genomic neighborhoods, many of which overlapped with known or candidate secondary metabolism gene clusters. We also identified 1,164 genes that were downregulated. This gene set was not spatially structured across the genome and was overrepresented in genes participating in primary metabolic functions, including carbon and amino acid metabolism. These results add valuable insight into the genetics of biofilm formation in A. fumigatus and other filamentous fungi and identify many relevant, in the context of biofilm biology, candidate genes for downstream functional experiments.

Extracellular DNA Release Acts as an Antifungal Resistance Mechanism in Mature Aspergillus fumigatus Biofilms

“…Moreover, biochemical inhibition of chitinase activity significantly affected eDNA release. It was also reported in an A. fumigatus biofilm study using microarray analysis that class IV chitinase mRNA was upregulated ϳ5-fold in 48-h biofilms (53), whereas Gibbons and colleagues did not identify this expression, but they explained this difference by the potential production of pseurotin A, a potent inhibitor of chitinases (54). Given that chitinases are markers of autolysis, this process is a possible mechanism for eDNA release.…”

α1,3 Glucans Are Dispensable in Aspergillus fumigatus

“…Reasons for these repeated failures remain unknown, but they could be due to the large size of the genes (Ͼ8 kb), their in vivo three-dimensional conformation, or the presence of one of these AGS genes (AGS1) in the subtelomeric region of a chromosome (chromosome 3), which is always difficult to manipulate genetically (11). Nevertheless, the lack of a growth phenotype in a triple AGS mutant totally devoid of ␣1,3 glucans showed definitively that the ␣1,3 glucans that are the major cell wall component are fully dispensable for A. fumigatus vegetative growth.…”

Transcriptional Changes in the Transition from Vegetative Cells to Asexual Development in the Model Fungus Aspergillus nidulans

“…It has been shown that the transcriptional control of each metabolic cluster and thus the concentration of the secondary metabolite linked to their activity depends on mechanisms exerted on various cluster functions, such as oxidoreduction, transcriptional regulation, or transport (13,74,76). Thus, we decided to study the genomic flanking regions of specific PKS-or NRPS-coding genes shown in Fig.…”

“…Thus, this powerful technique arises as an efficient tool for transcriptomic analyses in the genus Aspergillus, as shown in 2010 by Wang and coworkers (11), who published the first RNA-seq-based transcriptomic study of this genus. In these last 2 years, the RNA-seq-based studies involving Aspergillus species analyzed the temperature effect on secondary metabolite synthesis, biofilm formation, the response to lignocellulose, or domestication in A. fumigatus, A. flavus, A. niger, or A. oryzae, respectively (11)(12)(13)(14)(15).…”