Evidence of DNA methylation in Aspergillus oryzae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA534472 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8949990_1.fastq.gz | Fastqsanger.gz | |||
| SRR8949990_2.fastq.gz | Fastqsanger.gz | |||
| SRR8949991_1.fastq.gz | Fastqsanger.gz | |||
| SRR8949991_2.fastq.gz | Fastqsanger.gz | |||
| SRR8949992_1.fastq.gz | Fastqsanger.gz |
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Project description:DNA methylation is an important epigenetic modification widespread in eukaryotes and bacteria. However, genomic methylation levels show a dramatic diversity throughout the evolution of life, varying even between closely-related species and strains. In Aspergillus, a genus of filamentous fungi, the existence of DNA methylation has been controversial with previous studies reporting different conclusions using different species and detection methods. Here, we report DNA methylation analysis of Aspergillus oryzae, an important species in the Japanese fermentation industry, and a close relative of the pathogen Aspergillus flavus whose DNA methylation has been denied by the recent previous study using bisulfite sequencing. In this study, we conduct bisulfite-seq and RNA-seq of A. oryzae using three biological replicates from each of liquid and solid culture conditions. The statistical analysis of these data reveals thousands of highly-confident methylated cytosines (mCs), while the re-analysis of data from A. flavus detects few mCs being consistent with the previous study. Based on the comparative genome analysis of A. oryzae and A. flavus, we find that a substantial fraction of mCs are observed in syntenic segments including the aflatoxin biosynthesis gene cluster. Together, our results are the first evidence of DNA methylation in A. oryzae, providing a new example of the evolutionary diversity of DNA methylation as well as a new insight into its industrial applications.
2025-04-01 | GSE130260 | GEO
Project description:DNA methylation is an important epigenetic modification widespread in eukaryotes and bacteria. However, genomic methylation levels show a dramatic diversity throughout the evolution of life, varying even between closely-related species and strains. In Aspergillus, a genus of filamentous fungi, the existence of DNA methylation has been controversial with previous studies reporting different conclusions using different species and detection methods. Here, we report DNA methylation analysis of Aspergillus oryzae, an important species in the Japanese fermentation industry, and a close relative of the pathogen Aspergillus flavus whose DNA methylation has been denied by the recent previous study using bisulfite sequencing. In this study, we conduct bisulfite-seq and RNA-seq of A. oryzae using three biological replicates from each of liquid and solid culture conditions. The statistical analysis of these data reveals thousands of highly-confident methylated cytosines (mCs), while the re-analysis of data from A. flavus detects few mCs being consistent with the previous study. Based on the comparative genome analysis of A. oryzae and A. flavus, we find that a substantial fraction of mCs are observed in syntenic segments including the aflatoxin biosynthesis gene cluster. Together, our results are the first evidence of DNA methylation in A. oryzae, providing a new example of the evolutionary diversity of DNA methylation as well as a new insight into its industrial applications.
2025-04-01 | GSE130259 | GEO
Project description:Evidence of DNA methylation in Aspergillus oryzae [RNA-seq]
| PRJNA534476 | ENA
Project description:Evidence of DNA methylation in Aspergillus oryzae [bisulfite-seq]
| PRJNA534475 | ENA
Project description:The filamentous fungus Aspergillus oryzae is an important microbial cell factory for industrial production of useful enzymes, such as α-amylase. In order to optimize the industrial enzyme production process, there is a need to understand fundamental processes underlying protein production, here under how protein production links to metabolism through global regulatory structures. In this study, two α-amylase-producing strains of A. oryzae, a wild type strain and a transformant strain containing additional copies of the α-amylase gene, were characterized at a systematic level. Based on integrated analysis of ome-data together with genome-scale metabolic network and flux calculation, we identified key genes, key enzymes, key proteins, and key metabolites involved in the processes of protein synthesis and secretion, nucleotide metabolism, and amino acid metabolism that can be the potential targets for improving industrial protein production. Keywords: Two Aspergillus oryzae strains and two different carbon sources
2012-02-12 | GSE22566 | GEO
Project description:The filamentous fungus Aspergillus oryzae is an important microbial cell factory for industrial production of useful enzymes, such as α-amylase. In order to optimize the industrial enzyme production process, there is a need to understand fundamental processes underlying protein production, here under how protein production links to metabolism through global regulatory structures. In this study, two α-amylase-producing strains of A. oryzae, a wild type strain and a transformant strain containing additional copies of the α-amylase gene, were characterized at a systematic level. Based on integrated analysis of ome-data together with genome-scale metabolic network and flux calculation, we identified key genes, key enzymes, key proteins, and key metabolites involved in the processes of protein synthesis and secretion, nucleotide metabolism, and amino acid metabolism that can be the potential targets for improving industrial protein production. Keywords: Two Aspergillus oryzae strains and two different carbon sources Two carbon sources (glucose, maltose) with three biological replicates for A. oryzae strain A1560 and strain CF1.1
2012-02-12 | E-GEOD-22566 | biostudies-arrayexpress
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: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.
2010-02-02 | GSE18851 | GEO
Project description:Hypoxia imposes stress on filamentous fungi that require oxygen to proliferate. Global transcription analysis of Aspergillus oryzae grown under hypoxic conditions found that the expression of about 50% of 4,244 affected genes was either induced or repressed more than 2-fold. A comparison of these genes with the hypoxically-regulated genes of A. nidulans (Masuo et al., Mol. Gen. Genet. 2010, 284:415-424) based on their predicted amino acid sequences classified them as bi-directional best hit (BBH), one-way best hit (extra homolog: EH) and no-hit (non-syntenic genes: NSG) genes. Clustering analysis of the BBH genes indicated that A. oryzae and A. nidulans down-regulated global translation and transcription under hypoxic conditions, respectively. Under hypoxic conditions, both fungi up-regulated genes for alcohol fermentation and the γ-aminobutyrate shunt of the tricarboxylate cycle, whereas A. oryzae up-regulated the glyoxylate pathway, indicating that both fungi eliminate NADH accumulation under hypoxic conditions. The A. oryzae NS genes included specific genes for secondary and nitric oxide metabolism under hypoxic conditions. This comparative transcriptomic analysis discovered common and strain-specific responses to hypoxia in hypoxic Aspergillus species.
2011-07-31 | GSE31046 | GEO
Project description:The full genome sequencing of the filamentous fungi Aspergillus nidulans, Aspergillus niger and Aspergillus oryzae has opened the possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are presenting an Affymetrix GeneChip developed for transcriptome analysis of any of the three above-mentioned aspergilli. Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose-and xylose media has been performed, and used to validate the performance of the micro array. By doing gene comparisons of all three species, and cross-analysing this with the expression data, 23 genes, including the xylose transcriptional activator XlnR, have been identified to be a conserved response across the Aspergillus sp. Promoter analysis of the upregulated genes in all three species suggest the XlnR-binding site to be 5’-GGNTAAA-3’. We are thus presenting a validated tool for transcription analysis of three Aspergillus species and a methodology for comparative transcriptomics. Keywords: Physiological response
2008-02-15 | GSE9277 | GEO