Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa

Transcriptomic and genetic analysis reveals a Zn2Cys6 transcription factor specifically required for conidiation in submerged cultures of Thermothelomyces thermophilus

Filamentous fungi are important producers of enzymes and secondary metabolites. The industrial thermophilic species, Thermothelomyces thermophilus, is closely related to the model fungus, Neurospora crassa. A critical aspect of the filamentous fungal life cycle is the production of asexual spores (conidia), which are regulated by various stimuli, including nutrient availability. Several species of fungi, including T. thermophilus, produce conidia under submerged fermentation conditions, which can be detrimental to product yields. In this study, transcriptional profiling of T. thermophilus was used to map changes during asexual development in submerged cultures, which revealed commonalities of regulation between T. thermophilus and N. crassa. We further identified a transcription factor, res1, whose deletion resulted in a complete loss of conidia production under fermentation conditions, but which did not affect conidiation on plates. Under fermentation conditions, the ∆res1 deletion strain showed increased biomass production relative to the wild-type strain, indicating that the manipulation of res1 in T. thermophilus has the potential to increase productivity in industrial settings. Overexpression of res1 caused a severe growth defect and early conidia production on both plates and in submerged cultures, indicating res1 overexpression can bypass regulatory aspects associated with conidiation on plates. Using chromatin-immunoprecipitation sequencing, we identified 35 target genes of Res1, including known conidiation regulators identified in N. crassa, revealing common and divergent aspects of asexual reproduction in these two species.IMPORTANCEFilamentous fungi, such as Thermothelomyces thermophilus, are important industrial species and have been harnessed in the Biotechnology industry for the production of industrially relevant chemicals and proteins. However, under fermentation conditions, some filamentous fungi will undergo a switch from mycelial growth to asexual development. In this study, we use transcriptional profiling of asexual development in T. thermophilus and identify a transcription factor that specifically regulates the developmental switch to the production of unwanted asexual propagules under fermentation conditions, thus altering secreted protein production. Mutations in this transcription factor Res1 result in the loss of asexual development in submerged cultures but do not affect asexual sporulation when exposed to air. The identification of stage-specific developmental regulation of asexual spore production and comparative analyses of conidiation in filamentous ascomycete species have the potential to further manipulate these species for industrial advantage.

Transcription factor-dependent regulatory networks of sexual reproduction in Fusarium graminearum

Transcription factors (TFs) involved in sexual reproduction in filamentous fungi have been characterized. However, we have little understanding of how these TFs synergize within regulatory networks resulting in sexual development. We investigated 13 TFs in Fusarium graminearum, whose knockouts exhibited abortive or arrested phenotypes during sexual development to elucidate the transcriptional regulatory cascade underlying the development of the sexual fruiting bodies. A Bayesian network of the TFs was inferred based on transcriptomic data from key stages of sexual development. We evaluated in silico knockout impacts to the networks of the developmental phenotypes among the TFs and guided knockout transcriptomics experiments to properly assess regulatory roles of genes with same developmental phenotypes. Additional transcriptome data were collected for the TF knockouts guided by the stage at which their phenotypes appeared and by the cognate in silico prediction. Global TF networks revealed that TFs within the mating-type locus (MAT genes) trigger a transcriptional cascade involving TFs that affected early stages of sexual development. Notably, PNA1, whose knockout mutants produced exceptionally small protoperithecia, was shown to be an upstream activator for MAT genes and several TFs essential for ascospore production. In addition, knockout mutants of SUB1 produced excessive numbers of protoperithecia, wherein MAT genes and pheromone-related genes exhibited dysregulated expression. We conclude that PNA1 and SUB1 play central and suppressive roles in initiating sexual reproduction, respectively. This comprehensive investigation contributes to our understanding of the transcriptional framework governing the multicellular body plan during sexual reproduction in F. graminearum.IMPORTANCEUnderstanding transcriptional regulation of sexual development is crucial to the elucidation of the complex reproductive biology in Fusarium graminearum. We performed gene knockouts on 13 transcription factors (TFs), demonstrating knockout phenotypes affecting distinct stages of sexual development. Using transcriptomic data across stages of sexual development, we inferred a Bayesian network of these TFs that guided experiments to assess the robustness of gene interactions using a systems biology approach. We discovered that the mating-type locus (MAT genes) initiates a transcriptional cascade, with PNA1 identified as an upstream activator essential for early sexual development and ascospore production. Conversely, SUB1 was found to play a suppressive role, with knockout mutants exhibiting excessive protoperithecia due to abnormally high expression of MAT and pheromone-related genes. These findings highlight the central roles of PNA1 and SUB1 in regulating other gene activity related to sexual reproduction, contributing to a deeper understanding of the mechanisms of the multiple TFs that regulate sexual development.

Symmetric and asymmetric DNA N6-adenine methylation regulates different biological responses in Mucorales

DNA N6-adenine methylation (6mA) has recently gained importance as an epigenetic modification in eukaryotes. Its function in lineages with high levels, such as early-diverging fungi (EDF), is of particular interest. Here, we investigated the biological significance and evolutionary implications of 6mA in EDF, which exhibit divergent evolutionary patterns in 6mA usage. The analysis of two Mucorales species displaying extreme 6mA usage reveals that species with high 6mA levels show symmetric methylation enriched in highly expressed genes. In contrast, species with low 6mA levels show mostly asymmetric 6mA. Interestingly, transcriptomic regulation throughout development and in response to environmental cues is associated with changes in the 6mA landscape. Furthermore, we identify an EDF-specific methyltransferase, likely originated from endosymbiotic bacteria, as responsible for asymmetric methylation, while an MTA-70 methylation complex performs symmetric methylation. The distinct phenotypes observed in the corresponding mutants reinforced the critical role of both types of 6mA in EDF.

Method for assessing the content of molybdenum enzymes in the internal organs of fish

Molybdenum enzymes (Mo-enzymes) contain a molybdenum cofactor (MoCo) in the active site. These enzymes are potentially interesting for studying the survival mechanism of fish under hypoxic water conditions. This is because Mo-enzymes can synthesize nitric oxide from nitrates and nitrites, which are present in high concentrations under hypoxic water conditions. However, there is currently no method for assessing the Mo-enzymes content in the fish internal organs. Methods capable of determining Mo-enzymes content in the fish are of major importance. For this purpose, a method for quantitative determination of MoCo from plant tissues was modified. We demonstrated the Mo-enzyme content assessment by isolated MoCo from the fish's internal organs and the Neurospora crassa nit-1 extract containing inactive NADPH nitrate reductase. The Mo enzyme content was calculated using a calibration curve in nM of nitrites as a product of restored NADPH reductase activity after complementation with MoCo. Here we present a robust laboratory method which can be used to assess the content of Mo-enzymes in the internal organs of fish.•Mo-enzymes play a crucial role in detoxifying toxic compounds. Therefore, it is important to develop a method to accurately determine the amount of Mo-enzymes present. Notably, the method demonstrated the efficiency and accuracy as detected high content of Mo-enzymes in the liver and intestines (P < 0.0001). The obtained data on the distribution of Mo-enzymes in the internal organs of this species correspond to that of other vertebrates. Here, we present a rapid, sensitive, accurate and accessible method.•The developed method is simple and easy to use. Importantly, the protocol does not require complex manipulations, and the equipment used is available in most laboratories. The article provides step-by-step instructions for reproducing the method.

Unravelling the Function of the Sesquiterpene Cyclase STC3 in the Lifecycle of Botrytis cinerea

The genome sequencing of Botrytis cinerea supplies a general overview of the map of genes involved in secondary metabolite synthesis. B. cinerea genomic data reveals that this phytopathogenic fungus has seven sesquiterpene cyclase (Bcstc) genes that encode proteins involved in the farnesyl diphosphate cyclization. Three sesquiterpene cyclases (BcStc1, BcStc5 and BcStc7) are characterized, related to the biosynthesis of botrydial, abscisic acid and (+)-4-epi-eremophilenol, respectively. However, the role of the other four sesquiterpene cyclases (BcStc2, BcStc3, BcStc4 and BcStc6) remains unknown. BcStc3 is a well-conserved protein with homologues in many fungal species, and here, we undertake its functional characterization in the lifecycle of the fungus. A null mutant ΔBcstc3 and an overexpressed-Bcstc3 transformant (OvBcstc3) are generated, and both strains show the deregulation of those other sesquiterpene cyclase-encoding genes (Bcstc1, Bcstc5 and Bcstc7). These results suggest a co-regulation of the expression of the sesquiterpene cyclase gene family in B. cinerea. The phenotypic characterization of both transformants reveals that BcStc3 is involved in oxidative stress tolerance, the production of reactive oxygen species and virulence. The metabolomic analysis allows the isolation of characteristic polyketides and eremophilenols from the secondary metabolism of B. cinerea, although no sesquiterpenes different from those already described are identified.

The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics

Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.

Metagenomic analysis of mycobiome in wild and captivity Sumatran orangutans (Pongo abelii)

Objective

This study analyzes the mycobiome in wild and captive Sumatran orangutans.

Materials and Methods

Nine orangutan feces samples from the wild and nine from captivity were divided into three repeats from 11- to 15-year-olds in good health. The Illumina platform for analysis of ITS bioinformatics was used according to the Qiime2 and CCMetagen approaches.

Results

Wild Sumatran orangutans include 53% Ascomycota, 38% uncultured fungi, and 4% Basidiomycota. Orangutans in captivity are 57% Ascomycota, 26% uncultured fungi, and 2% Basidiomycota. Based on genus level, uncultured Neurospora (31%), Penicillium (10%), Aspergillus (3%), Fusarium (3%), Candida (2%), Cutaneotrichosporon (2%), and Limonomyces (2%) are found in wild orangutans. The most prevalent genus among captivity orangutans is Aspergillus (32%), followed by fungal sp. (11%), Lasiodiplodia (18%), Devriesia (2%), and Sordariomycetes (2%). According to the Chao1 diversity index and Shannon and Simpson, there was no significant difference between wild and captive Sumatran orangutans.

Conclusion

Neurospora is unique to wild Sumatran orangutans, although Aspergillus predominates in captive orangutans. We hypothesize that the gut mycobiome of wild orangutans will resemble that of orangutans in captivity. The excellent range of food sources in the forest does not result in the prevalence of fungi in the typical gut microbiome.