Persinoti, G. F. | bioRxiv Science

bioRxiv2018

Whole genome analysis illustrates global clonal population structure of the ubiquitous dermatophyte pathogen Trichophyton rubrum

Dermatophytes include fungal species that infect humans, as well as those which also infect other animals or only grow in the environment. The dermatophyte species Trichophyton rubrum is a frequent cause of skin infection in immunocompetent individuals. While members of the T. rubrum species complex have been further categorized based on various morphologies, the population structure and ability to undergo sexual reproduction are not well understood. In this study, we analyze a large set of T. rubrum and Trichophyton interdigitale isolates to examine mating types, evidence of mating, and genetic variation. We find that nearly all isolates of T. rubrum are of a single mating type, and that incubation with T. rubrum morphotype megninii isolates of the other mating type failed to induce sexual development. While the region around the mating type locus is characterized by a higher frequency of SNPs compared to other genomic regions, we find that the population is remarkably clonal, with highly conserved gene content, low levels of variation, and little evidence of recombination These results support a model of recent transition to asexual growth when this species specialized to growth on human hosts.\n\nData access: Genome sequence data is available in NCBI under the Umbrella BioProject PRJNA186851.

genetics↗

bioRxiv2018

Comparative RNA-seq based transcriptomic analysis of Aspergillus nidulans recombinant strains overproducing heterologous glycoside hydrolases

Filamentous fungi are important cellular factories for the production and secretion of homologous and heterologous enzymes such as carbohydrate-active enzymes. However, the regulation of protein secretion in these microorganisms requires more profound studies since the enzyme levels produced are usually below the levels required by industry for profitable processes. Genomic and transcriptomic approaches have been used to understand the overexpression and production of heterologous enzymes and their capacity to induce different cellular biological processes. To investigate this regulation, Aspergillus nidulans recombinant strains were analyzed by transcriptomics. We designed three A. nidulans recombinant strains producing the following heterologous proteins: alpha-arabinofuranosidase (AbfA), beta-glucosidase (BglC) and thermophilic mannanase (Tp-Man5). The heterologous genes abfA and bglC were highly expressed, while tp-man5 mRNA levels were low and similar to those of a reference gene. There was an indirect relationship between mRNA and protein secretion levels, suggesting that transcription is not a bottleneck for target gene expression in this system. Despite the distinct features of the recombinant proteins, 30 differentially expressed genes were common to all the recombinant strains, suggesting that these genes represent a general response to the expression of heterologous genes. We also showed that the early activation of the canonical unfolded protein response (UPR) pathway by hacA alternative splicing was normalized after 8h, except in the strain expressing BglC, suggesting either no accumulation of the BglC misfolded form or the presence of an alternative endoplasmic reticulum (ER) stress and UPR pathway. Finally, to focus our analysis on the secretion pathway, a set of 374 genes was further evaluated. Seventeen genes were common to all the recombinant strains, suggesting again that these genes represent a general response of A. nidulans cells to the overexpression of recombinant genes, even thermophilic genes. Additionally, we reported the possible genetic interactions of these 17 genes based on coexpression network calculations. Interestingly, protein improvements are nongeneric, and improvements in the production of one target protein are not necessarily transferable to another one. Thus, this study may provide genetic and cellular background and targets for genetic manipulation to improve protein secretion by A. nidulans.

microbiology↗