Summary auto-generated
This mini-review summarizes the first 50 microarray studies examining global gene expression in filamentous fungi species, covering over 20 species across multiple research areas. Metabolic studies revealed substantial differences between filamentous fungi and yeast in transcriptional regulation of primary metabolic pathways, particularly regarding glucose repression and anaerobic metabolism. Secondary metabolite studies identified genes for both useful and harmful metabolites, including aflatoxin and fumonisin biosynthesis. Developmental studies using species like Neurospora crassa and Sordaria macrospora identified genes controlling conidial germination, fruiting body formation, circadian rhythms, and light-responsive processes. Pathogenesis research investigated both plant and animal fungal pathogens, revealing genes involved in appressorium formation, host adaptation, and virulence factors through both in vitro and in planta studies. Symbiosis research focused on ectomycorrhizal associations, identifying fungal and plant genes regulating nutrient exchange. Industrial application studies examined biomass-degrading enzyme expression and heterologous protein secretion. Microarray platforms varied, primarily using PCR-amplified ESTs and cDNA arrays, with most studies including validation through Northern blotting or real-time quantitative PCR.
Key findings
- Filamentous fungi show striking differences from yeast in glucose repression and primary metabolism regulation, with reduced glycolytic gene up-regulation under anaerobic conditions and partial TCA cycle response to glucose starvation
- Microarray studies identified novel secondary metabolite biosynthesis genes and clusters, including the antitumor compound terrequinone A and genes involved in aflatoxin and fumonisin production
- Pathogenic filamentous fungi express specific virulence genes during host infection, with some genes pre-existing in dormant spores and others showing 500-fold higher expression during in planta infection
- Circadian clock-controlled genes in Neurospora show temperature and light responsiveness mediated by the FRQ/WCC oscillator, with potential evolutionary conservation across diverse organisms
- Ectomycorrhizal symbiosis involves coordinated fungal and plant gene expression changes, including upregulation of hexose transporters and electron transport chain genes in fungal partners
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Abstract
Microarray studies have examined global gene expression in over 20 species of filamentous fungi encompassing a wide variety of research areas. The majority have addressed aspects of metabolism or pathogenicity. Metabolic studies have revealed important differences in the transcriptional regulation of genes for primary metabolic pathways between filamentous fungi and yeast. Transcriptional profiles for genes involved in secondary metabolism have also been established. Genes required for the biosynthesis of both useful and detrimental secondary metabolites have been identified. Due to the economic, ecological and medical implications, it is not surprising that many studies have used microarray analysis to examine gene expression in pathogenic filamentous fungi. Genes involved in various stages of pathogenicity have been identified, including those thought to be important for adaptation to the host environment. While most of the studies have simulated pathogenic conditions in vitro, a small number have also reported fungal gene expression within their plant hosts. This review summarizes the first 50 microarray studies in filamentous fungi and highlights areas for future investigation.