Construction and analysis of gene co-expression network in the pathogenic fungus Ustilago maydis.

Introduction: Biological systems respond to environmental disturbances and a wide range of compounds through complex gene interaction networks. The enormous growth of experimental information obtained using large-scale genomic techniques such as microarrays and RNA sequencing led to the construction of a wide variety of gene co-expression networks in recent years. These networks allow the discovery of clusters of co-expressed genes that potentially work in the same process linking them to biological processes often of interest to industrial, medicinal, and academic research. Methods: In this study, we built the gene co-expression network of Ustilago maydis from the gene expression data of 168 samples belonging to 19 series, which correspond to the GPL3681 platform deposited in the NCBI using WGCNA software. This network was analyzed to identify clusters of co-expressed genes, gene hubs and Gene Ontology terms. Additionally, we identified relevant modules through a hypergeometric approach based on a predicted set of transcription factors and virulence genes. Results and Discussion: We identified 13 modules in the gene co-expression network of U. maydis. The TFs enriched in the modules of interest belong to the superfamilies of Nucleic acid-binding proteins, Winged helix DNA-binding, and Zn2/Cys6 DNA-binding. On the other hand, the modules enriched with virulence genes were classified into diseases related to corn smut, Invasive candidiasis, among others. Finally, a large number of hypothetical, a large number of hypothetical genes were identified as highly co-expressed with virulence genes, making them possible experimental targets.

Identifying Genes Devoted to the Cell Death Process in the Gene Regulatory Network of Ustilago maydis.

Cell death is a process that can be divided into three morphological patterns: apoptosis, autophagy and necrosis. In fungi, cell death is induced in response to intracellular and extracellular perturbations, such as plant defense molecules, toxins and fungicides, among others. Ustilago maydis is a dimorphic fungus used as a model for pathogenic fungi of animals, including humans, and plants. Here, we reconstructed the transcriptional regulatory network of U. maydis, through homology inferences by using as templates the well-known gene regulatory networks (GRNs) of Saccharomyces cerevisiae, Aspergillus nidulans and Neurospora crassa. Based on this GRN, we identified transcription factors (TFs) as hubs and functional modules and calculated diverse topological metrics. In addition, we analyzed exhaustively the module related to cell death, with 60 TFs and 108 genes, where diverse cell proliferation, mating-type switching and meiosis, among other functions, were identified. To determine the role of some of these genes, we selected a set of 11 genes for expression analysis by qRT-PCR (sin3, rlm1, aif1, tdh3 [isoform A], tdh3 [isoform B], ald4, mca1, nuc1, tor1, ras1, and atg8) whose homologues in other fungi have been described as central in cell death. These genes were identified as downregulated at 72 h, in agreement with the beginning of the cell death process. Our results can serve as the basis for the study of transcriptional regulation, not only of the cell death process but also of all the cellular processes of U. maydis.

Cell death in Ustilago maydis: comparison with other fungi and the effect of metformin and curcumin on its chronological lifespan.

Ustilago maydis is a Basidiomycota fungus, in which very little is known about its mechanisms of cell survival and death. To date, only the role of metacaspase1, acetate and hydrogen peroxide as inducers of cell death has been investigated. In the present work, we analyzed the lifespan of U. maydis compared with other species like Sporisorium reilianum, Saccharomyces cerevisiae and Yarrowia lipolytica, and we observed that U. maydis has a minor lifespan. We probe the addition of low concentrations metformin and curcumin to the culture media, and we observed that both prolonged the lifespan of U. maydis, a result observed for the first time in a phytopathogen fungus. However, higher concentrations of curcumin were toxic for the cells, and interestingly induced the yeast-to-mycelium dimorphic transition. The positive effect of metformin and curcumin appears to be related to an inhibition of the mechanistic Target of Rapamycin (mTOR) pathway, increase expression of autophagy genes and reducing of reactive oxygen species. These data indicate that U. maydis may be a eukaryotic model organism to elucidate the molecular mechanism underlying apoptotic and necrosis pathways, and the lifespan increase caused by metformin and curcumin.

Autophagosomes accumulation in the vacuoles of the fungus Ustilago maydis and the role of proteases in their digestion.

In the present study we determined whether Ustilago maydis accumulates autophagosomes within vacuoles when the cells are exposed to nutritional stress conditions. We investigated whether proteinase B and proteinase A are involved in their degradation. To this effect, wild type and Δpep4 mutant were incubated in minimal medium lacking a carbon source. It was observed that after incubation in nutrient-deficient media, spherical bodies appeared within the Δpep4 mutant strains vacuoles. In addition, autophagosomes were accumulated in U. maydis WT cells incubated in the presence of the serine protease inhibitor PMSF and accumulation of large autophagosomes and electrodense structures in the Δpep4 mutant cell vacuoles took place. These results demonstrate that the homologues of both, the proteinase B and the protease A, are involved in the autophagosomes degradation process in U. maydis.

The pep4 gene encoding proteinase A is involved in dimorphism and pathogenesis of Ustilago maydis.

Vacuole proteases have important functions in different physiological processes in fungi. Taking this aspect into consideration, and as a continuation of our studies on the analysis of the proteolytic system of Ustilago maydis, a phytopathogenic member of the Basidiomycota, we have analysed the role of the pep4 gene encoding the vacuolar acid proteinase PrA in the pathogenesis and morphogenesis of the fungus. After confirmation of the location of the protease in the vacuole using fluorescent probes, we obtained deletion mutants of the gene in sexually compatible strains of U. maydis (FB1 and FB2), and analysed their phenotypes. It was observed that the yeast to mycelium dimorphic transition induced by a pH change in the medium, or the use of a fatty acid as sole carbon source, was severely reduced in Δpep4 mutants. In addition, the virulence of the mutants in maize seedlings was reduced, as revealed by the lower proportion of plants infected and the reduction in size of the tumours induced by the pathogen, when compared with wild-type strains. All of these phenotypic alterations were reversed by complementation of the mutant strains with the wild-type gene. These results provide evidence of the importance of the pep4 gene for the morphogenesis and virulence of U. maydis.