Transcriptomic analysis of the exit from dormancy of Aspergillus fumigatus conidia

Lamarre, Claude; Sokol, Sergueï; Debeaupuis, J P; Henry, Christine; Lacroix, Céline; Glaser, Philippe; Coppée, Jean‐Yves; François, Jean; Latgé, Jean‐Paul

doi:10.1186/1471-2164-9-417

Cited by 122 publications

(129 citation statements)

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“…Upon harvesting, the fungal colony from the BF culture was immediately frozen in liquid nitrogen and ground into a fine powder with a mortar and pestle. We extracted total RNA using a previously described phenol-chloroform protocol (30). RNA samples were then treated with DNase and further purified using the Qiagen RNeasy minikit, following manufacturer's instructions (20,24).…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2012

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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.

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Section: Methodsmentioning

confidence: 99%

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

et al. 2012

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“…Tubulin was used as a loading control. (3,27,33,34). It has also been suggested that germination results in a shift from a maintenance fermentative metabolism to respiration (27).…”

Section: Cap655041)mentioning

confidence: 99%

“…(3,27,33,34). It has also been suggested that germination results in a shift from a maintenance fermentative metabolism to respiration (27). Inhibitors of the respiratory chain severely delay germination of A. fumigatus conidia, and active mitochondria are found very early in germination (47).…”

Section: Cap655041)mentioning

confidence: 99%

“…In microarray analysis of A. nidulans conidial germination, citA mRNA has been detected in ungerminated and germinated spores (3 and 5 h) while mcsA expression was not detected (deposited data of reference 3). Hybridization to A. fumigatus macroarrays of PCR fragments from approximately one-third of the genes showed that citrate synthase mRNA was present in resting spores and also increased during the first 30 min following germination, while methylcitrate synthase RNA, although detected before germination, was not present in the mRNA population at 30 min (27). We have detected mitochondrial localized CitA-GFP in both ungerminated conidia as well as 5 h after germination and found that germination of citA⌬ conidia was significantly delayed.…”

Section: Cap655041)mentioning

confidence: 99%

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Metabolic and Developmental Effects Resulting from Deletion of thecitAGene Encoding Citrate Synthase in Aspergillus nidulans

Murray

Hynes

2010

Eukaryot Cell

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Citrate synthase is a central activity in carbon metabolism. It is required for the tricarboxylic acid (TCA) cycle, respiration, and the glyoxylate cycle. In Saccharomyces cerevisiae and Arabidopsis thaliana, there are mitochondrial and peroxisomal isoforms encoded by separate genes, while in Aspergillus nidulans, a single gene, citA, encodes a protein with predicted mitochondrial and peroxisomal targeting sequences (PTS). Deletion of citA results in poor growth on glucose but not on derepressing carbon sources, including those requiring the glyoxylate cycle. Growth on glucose is restored by a mutation in the creA carbon catabolite repressor gene. Methylcitrate synthase, required for propionyl-coenzyme A (CoA) metabolism, has previously been shown to have citrate synthase activity. We have been unable to construct the mcsA⌬ citA⌬ double mutant, and the expression of mcsA is subject to CreA-mediated carbon repression. Therefore, McsA can substitute for the loss of CitA activity. Deletion of citA does not affect conidiation or sexual development but results in delayed conidial germination as well as a complete loss of ascospores in fruiting bodies, which can be attributed to loss of meiosis. These defects are suppressed by the creA204 mutation, indicating that McsA activity can substitute for the loss of CitA. A mutation of the putative PTS1-encoding sequence in citA had no effect on carbon source utilization or development but did result in slower colony extension arising from single conidia or ascospores. CitA-green fluorescent protein (GFP) studies showed mitochondrial localization in conidia, ascospores, and hyphae. Peroxisomal localization was not detected. However, a very low and variable detection of punctate GFP fluorescence was sometimes observed in conidia germinated for 5 h when the mitochondrial targeting sequence was deleted.There has been increased interest in primary carbon metabolism in fungi in recent years. There are two main reasons for this. As fungal pathogens establish infection they must adapt their utilization of carbon sources to the substrates present in the new environment of the host cells (reviewed in reference 6). With many of the fungal genomes available, the number of genes encoding enzymes and transporters potentially involved in central metabolism has become apparent and is greater than might have been anticipated (for example, see reference 16). Deciphering this complexity requires not only genome-wide studies but also detailed studies of individual genes encoding these proteins in order to determine their regulation and the cellular localization of the proteins, as well as their roles in metabolism and development. Here we report molecular genetic analysis of the citA gene encoding citrate synthase (EC 4.1.3.7), a central enzyme of carbon metabolism, in the filamentous ascomycete Aspergillus nidulans.Citrate synthase is required for the formation of citrate from acetyl-coenzyme A (CoA) and oxaloacetate in the tricarboxylic acid (TCA) cycle and is therefore necessary for respirat...

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“…This also raised the question of the existence of other molecules that could be associated with osmoprotection during the fungal biological cycle. GB was an obvious candidate to study since (i) it is an osmoprotectant in plants and bacteria and (ii) a transcriptomic study of the conidial germination of A. fumigatus showed that a gene orthologous to the bacterial choline oxidase gene was one of the most upregulated genes in the early steps of conidial germination (10).…”

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Pathway of Glycine Betaine Biosynthesis in Aspergillus fumigatus

et al. 2013

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Transcriptomic analysis of the exit from dormancy of Aspergillus fumigatus conidia

Cited by 122 publications

References 52 publications

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

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

Metabolic and Developmental Effects Resulting from Deletion of thecitAGene Encoding Citrate Synthase in Aspergillus nidulans

Pathway of Glycine Betaine Biosynthesis in Aspergillus fumigatus

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