Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa

Abstract

Fungal fruiting body size and form are influenced by the ecology of the species, including diverse environmental stimuli. Accordingly, nutritional resources available to the fungus during development can be vital to successful production of fruiting bodies. To investigate the effect of nutrition, perithecial development of N. crassa was induced on two different media, a chemically sparsely nutritive Synthetic Crossing Medium (SCM) and a natural Carrot Agar (CA). Protoperithecia were collected before crossing, and perithecia were collected at 2, 24, 48, 72, 96, 120, and at full maturity 144 hours after crossing. No differences in fruiting body morphology were observed between the two media at any time point. A circuit of microarray hybridizations comparing cDNA from all neighboring stages was performed. For a majority of differentially expressed genes, expression was higher in SCM than in CA, and expression of core metabolic genes was particularly affected. Effects of nutrition were highest in magnitude before crossing, lowering in magnitude during early perithecial development. Interestingly, metabolic effects of the media were also large in magnitude during late perithecial development, at which stage the lower expression in CA presumably reflected the continued intake of diverse complex initial compounds, diminishing the need for expression of anabolic pathways. However, for genes with key regulatory roles in sexual development, including pheromone precursor ccg-4 and poi2, expression patterns were similar between treatments. When possible, a common nutritional environment is ideal for comparing transcriptional profiles between different fungi. Nevertheless, the observed consistency of the developmental program across media, despite considerable metabolic differentiation is reassuring. This result facilitates comparative studies that will require different nutritional resources for sexual development in different fungi.

Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa

“…LOX estimates and RPKMs (see Table S3 in the supplemental material) (29) from the current transcriptomic experiment were compared to a previous investigation of perithecial development using microarray analysis (22), in which more than 900 genes were measured across a completely independent experiment using the same time points of development. Observed expression patterns were generally conserved between the two experiments, especially for genes detected with high fold changes in expression as measured by microarray analysis (45).…”

“…However, the sexual growth of N. crassa arises as a consequence of a communion of cells of different nuclear types; the heterokaryotic reproductive cells develop into sterile paraphyses within the perithecium or undergo karyogamy and a short diploid phase prior to the production of haploid ascospores. This heterokaryosis has made it challenging to study sexual differentiation using traditional methods based on genetic screens for mutants (13,14), and genome-wide assays so far have yielded only limited information about the genetics underlying the production of multicellular sexual reproduction structures such as perithecia (13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23).…”

Sex-linked transcriptional divergence in the hermaphrodite fungusNeurospora tetrasperma

“…Following data treatment and mapping of microarray probes to gene identifiers, a total of 6159 and 4048 genes were identified as expressed when tissue was grown on crossing and vegetative growth medium, respectively. The higher number of genes expressed in sexual/female tissue can be attributed to the increased complexity of transcription across N. crassa sexual development [29] in comparison with vegetative/male development [43]. In our samples, in particular, the sexual tissues constitute both hyphae and protoperithecia of different stages of maturity.…”

Simple Genetic Tools to Study Fruiting Body Development in Fungi

“…Fruiting body mutants are now available for many fungi other than P. anserina, including Sordaria macrospora [27], N. crassa [28], A. nidulans [29] and Coprinopsis cinerea (formely Coprinus cinereus) [30,31] and could be analyzed using similar methods. They are complementary to the now more widespread large scale analyses of transcriptomes during fruiting body development as performed in the ascomycetes Fusarium graminearum and Fusarium verticilloides [32][33][34], N. crassa [35,36], S. macrospora [37], Pyronema confluens [38], Tuber melanosporum [39][40][41], Cordyceps militaris [42] and Ophiocordyceps sinensis [43], as well as in the basidiomycetes C. cinerea [44], Moniliophthora perniciosa [45], Agrocybe aegerita [46], Lentinula edodes [47,48], Auricularia polytricha [49] and Ganoderma lucidum [50].…”