Ontology highlight
ABSTRACT:
PROVIDER: PRJNA659152 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12513293_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR12513294_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR12513295_subreads.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptome analysis and comparison of three Aspergillus aculeatus strains
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Project description:The filamentous fungus Trichoderma reesei is the main industrial cellulytic enzymes producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome sequencing, transcriptome) can shed light on the mechanisms of cellulase production and help identify genes linked to performance. Previously, our group published comparative genome sequencing of the lower and higher producer strains NG14 and RUT C30. In this follow-up work, we examined how these mutations affect phenotype at the level of the transcriptome and cultivation behavior. We performed kinetic transcriptome analysis of the NG14 and RUT C30 strains of early cellulase production induced by lactose using bioreactor cultivations close to industrial conditions. RUT C30 exhibited both earlier onset of cellulase production and higher steady-state productivity. A rather low number of genes were regulated, most of them being specific to the NG14 strains. Clustering of these genes highlighted similar behavior for some functional categories, and allowed to distinguish between induction-related genes and productivity-related genes. The lower number of genes regulated in RUT C30 could not formally be linked to the relief in catabolic repression that is characteristic of this strain. Cross-comparison of our transcriptome data with mutations previously identified revealed that most genes from our dataset have not been mutated. Interestingly, the few mutated genes belong to the same clusters, suggesting these clusters contain genes playing a role in strain performance. This is the first kinetic transcriptome study carried out in industry-relevant conditions with two related strains of T. reesei showing distinctive performances. Our study sheds some light on some of the events occurring in these strains following induction by lactose. The fact that few regulated genes have been affected by mutagenesis suggest that the induction mechanism is essentially intact and that there is room for further improvement of T. reesei. We also provide some potential target for further genetic improvement of these strains.
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Project description:Genome-wide comparative analysis of Aspergillus fumigatus strains
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Project description:Aspergillus flavus and A. oryzae represent two unique species predicted to have spent centuries in vastly different environments. A. flavus is an important opportunistic plant pathogen known for contaminating crops with the carcinogenic mycotoxin, aflatoxin and A. oryzae is a domesticated fungus used in food fermentations. Remarkably, the genomes of these two species are still nearly identical. We have used the recently sequenced genomes of A. oryzae RIB40 and A. flavus NRRL3357 along with array based comparative genome hybridization (CGH) as a tool to compare genomes across several strains of these two species. A comparison of three strains from each species by CGH revealed only 42 and 129 genes unique to A. flavus and A. oryzae, respectively. Further, only 709 genes were identified as being polymorphic between the species. Despite the high degree of similarity between these two species, correlation analysis among all data from the CGH arrays for all strains used in this study reveals a species split. However, this view of species demarcation becomes muddled when focused on only those genes for secondary metabolism.
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Project description:Background: Filamentous fungi produce large quantities of extracellular enzymes, such as cellulase and xylanase, to degrade polysaccharides derived from plant biomass. This process is controlled by a complex network of transcription factors (TFs). However, the regulatory mechanisms of cellulase and xylanase gene expression are poorly understood. Results: In this study, we reveal that the bZIP transcription factor Mthac-1 exerts dual regulatory effects on the production of cellulase and xylanase in the filamentous fungus Myceliophthora thermophila. The absence of Mthac-1 caused a reduction in cellulase and xylanase activities, as well as decreased protein secretion during the early phase of cultivation in Avicel medium, compared with the wild-type (WT) strain. However, in the middle and late stages, enzyme activities and protein secretion were noticeably enhanced by the deletion of Mthac-1. Additionally, the loss of Mthac-1 led to severe growth defects on sloid media containing various carbon sources, characterized by few hyphae branching and reduced conidiation. Real-time quantitative reverse transcription PCR (RT-qPCR) analysis showed that Mthac-1 dynamically regulates the expression of major cellulase genes. Furthermore, electrophoretic mobility shift assays (EMSAs) demonstrated that Mthac-1 directly binds to the promoter regions of the β-glucosidase gene bgl1 (MYCTH_66804), cellobiohydrolase gene cbh1 (MYCTH_109566), endoglucanase gene egl2 (MYCTH_86753), xylanase gene xyn1 (MYCTH_112050), and the crucial regulatory gene xyr1 (MYCTH_2310145), exhibiting higher binding affinity for xyn1 and xyr1. Notably, comparative transcriptomic analysis indicated that Mthac-1 also plays an important role in the expression of 26S proteasome-encoding genes under cellulolytic conditions. Conclusions: Mthac-1 functions as a dual regulator of cellulase and xylanase production by regulating the expression of major cellulase and xylanase genes, as well as the key transactivator gene Mtxyr1, via direct promoter binding. Our work provides new insights into the regulatory mechanisms underlying cellulase and xylanase gene expression and has potential applications in fungal strain engineering in biorefinery industries.
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