Aspergillus oryzae RIB40
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR003832_1.fastq.gz | Fastqsanger.gz | |||
| DRR003832_2.fastq.gz | Fastqsanger.gz | |||
| DRR003833_1.fastq.gz | Fastqsanger.gz | |||
| DRR003833_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Aspergillus oryzae RIB40 Genome sequencing and assembly
| PRJNA277168 | ENA
Project description:Aspergillus oryzae RIB40 grown in YPD, AF6 and EG:JM media
2022-07-18 | MSV000089904 | GNPS
Project description:Industrial lignocellulolytic side streams are considered an attractive carbon source for the cultivation of biotechnologically important fungi, although the presence of toxic pretreatment by-products is a major challenge yet to be overcome. Aspergillus oryzae is a filamentous fungus with a large secretion capacity, high tolerance for toxins, and a wide substrate variety, making it a promising candidate for side stream utilization. In the present study, the cellular detoxification of furfural, 5-hydroxymethylfurfural (HMF), levulinic acid, ferulic acid and vanillin was studied at the transcriptome level. A. oryzae RIB40 was grown in the presence of different inhibitors commonly found in the lignocellulolytic side streams and RNA sequencing was utilized to investigate the different transcriptomic changes in response to the inhibitors. The main cause of the transcriptomic response in all conditions was the xenobiotic-induced formation of reactive oxygen species (ROS). Apart from levulinic acid, all conditions showed strong initial suppression of metabolic pathways relating to cell proliferation, ribosomal functions and protein folding and sorting in the endoplasmic reticulum. Genes associated with cellular detoxification, namely NAD(P)H-dependent oxidoreductases and efflux transporters, such as the ATP-Binding Cassette (ABC) transporters and major facilitator superfamily (MFS) transporters showed strong upregulation upon exposure to xenobiotics. The results obtained provide important insights into the stress response of A. oryzae to the xenobiotic compounds and their cellular detoxification. Aldehydic inhibitors, especially HMF, caused stronger and more severe stress response in A. oryzae RIB40. Additionally, we identified several promising target genes for future strain engineering.
2025-06-18 | GSE296876 | GEO
Project description:Time-course mRNA-Seq analysis of Aspergillus oryzae RIB40 and the faaA disruptant grown in the presence of 1% Triton X-100
| PRJDB8293 | ENA
Project description:The Aspergillus oryzae, an important filamentous fungus used in food fermentation and enzyme industry, has been revealed to own prominent features in its genomic compositions by genome sequencing and various other tools. However, the functional complexity of the A. oryzae transcriptome has not yet been fully elucidated. Here, we applied direct high-throughput paired-end RNA sequencing (RNA-Seq) to the transcriptome of A. oryzae under four different culture conditions and confirmed most of the annotated genes. Moreover, with high resolution and sensitivity afforded by RNA-Seq, we were able to identify a substantial number of novel transcripts, new exons, untranslated regions, alternative upstream initiation codons (uATGs) and upstream open reading frames (uORFs), which serves a remarkable insight into the A. oryzae transcriptome. We also were able to assess the alternative mRNA isoforms in A. oryzae and found a large number of genes undergoing alternative splicing. Many genes or pathways that might involve in higher levels of protein production in solid-state culture than in liquid culture were identified by comparing gene expression levels between different cultures. Our analysis indicated that the transcriptome of A. oryzae was much more complex than previously anticipated and the results might provide a blueprint for further study of A. oryzae transcriptome. mRNA expression of Aspergillus oryzae in 4 different culture conditions was determined by method of RNA-Seq using short reads from high throughput sequencing technology.
2010-02-02 | E-GEOD-18851 | biostudies-arrayexpress
Project description:Expression data from Aspergillus oryzae grown under hypoxic condition.
| PRJNA144865 | ENA
Project description:In this study, we focused on chemically defined inducers or substrates to drive expression of cellulases, hemicellulases and accessory enzymes in the model filamentous fungus Aspergillus oryzae. Cellohexaose (O-CHE), mannohexaose (O-MHE), xylopentaose (O-XPE), arabinoheptaose (O-AHP), 1,3:1,4-M-NM-2-glucohexaose (O-BGHEXA), 63-M-NM-1-D-glucosyl-maltotriosyl-maltotriose (O-GMH), 61-M-NM-1-D-galactosyl-mannotriose (O-GM3), xyloglucan (X3Glc4-borohydride reduced; O-X3G4R), turanose (TYR) and sophorose (SOP) were used to induce the plant polysaccharide degradation machinery of A. oryzae. The strain used in this study was the A. oryzae sequenced strain RIB40, obtained from IBT culture collection at Technical University of Denmark. To obtain a global view of the A. oryzae transcriptome activated for plant biomass conversion, mRNA from growth after 2 h on 10 different carbohydrate active enzyme inducers (di- and M-bM-^@M-^Soligo saccharides) was subjected to custom-designed Agilent microarray analysis.
2013-07-15 | E-GEOD-48864 | biostudies-arrayexpress
Project description:Expression analysis of Aspergillus oryzae grown on different carbon sources
| PRJNA212019 | ENA
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.
2010-04-10 | GSE15650 | GEO