Identification of genes responsible for biosynthesis of kojic acid in Aspergillus oryzae
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ABSTRACT:
ORGANISM(S): Aspergillus oryzae
PROVIDER: GSE43280 | GEO | 2013/12/07
SECONDARY ACCESSION(S): PRJNA185809
REPOSITORIES: GEO
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Project description:Kojic acid is produced in large amounts by Aspergillus oryzae as a secondary metabolite and is widely used in the cosmetic industry. Glucose can be converted to kojic acid, perhaps by only a few steps, but no genes for the conversion have thus far been revealed. Using a DNA microarray, gene expression proM-oM-,M-^Ales under three pairs of conditions signiM-oM-,M-^Acantly affecting kojic acid production were compared. All genes were ranked using an index parameter reM-oM-,M-^Becting both high amounts of transcription and a high induction ratio under producing conditions. After disruption of nine candidate genes selected from the top of the list, two genes of unknown function were found to be responsible for kojic acid biosynthesis, one having an oxidoreductase motif and the other a transporter motif. These two genes are closely associated in the genome, showing typical characteristics of genes involved in secondary metabolism. Analysis in two-color microarray experiments used total RNA isolated from A. oryzae mycelia in three pairs of kojic acid producing to non(less)-producing conditions. The pairs of culture conditions were: 4 d to 2d; 7d to 4d; nitrate(-) to nitrate(+) in kojic acid producing medium.
2013-12-07 | E-GEOD-43280 | biostudies-arrayexpress
Project description:Identification of genes responsible for biosynthesis of kojic acid in Aspergillus oryzae
| PRJNA185809 | ENA
Project description:Environmental conditions are quite effective during propagation and industrial application of Baker’s yeast (Saccharomyces cerevisiae). The change of temperature is one of the most important conditions which affects the dough-leaving capacity of yeast cells. Accordingly, heat changes play an essential role in the commercial and economic impact of the yeast. Recent technologies in genomics have been used for analysis of global gene expression profiles such as microarray and RNA sequencing to solve the problems related with industrial application of yeast. Hereby, the aim of this study is to explore the effects of heat stresses on global gene expression profiles and to identify the candidate genes for the heat stress response in commercial baker’s yeast by using microarray technology and comparative statistical data analyses. Data from all hybridizations and array normalization were analyzed using the GeneSpringGX 12.1 (Agilent) and the R 2.15.2 program language. In the analysis of this dataset, all required statistical methods are performed comparatively in each step and the best performed ones are used in further computations. Hence, as the first step of the analyses, different background normalization algorithms such as MAS5.0, RMA, MBEI and GC-RMA were applied and the algorithm which gives the most accurate findings was chosen for the normalization procedure. As a result, expression values, computed from CEL files, were processed by Robust Multiarray Analysis (RMA) which is the selected procedure for the normalization of the systematic differences between samples. In order to determine differentially expressed genes under heat stress treatments, two different methods, namely, the fold-change and the hypothesis testing approaches are executed. In the fold-change method, various cut-off values are implemented while different multiple testing procedures are performed for the hypothesis testing. Under the heat shock and temperature-shift stress conditions, up/down regulated differentially expressed probes were functionally categorized into the different groups via the cluster analyses. Transcriptome changes under the heat shock and temperature-shift stress treatments show that the number of differentially up-regulated genes among the heat shock proteins (HSPs) and transcription factors (TFs) changed significantly. Consequently, the identification of thousands of genes related with heat stress treatments via microarray technology and comparative statistical analysis resulted in the creation of big picture which provides the understanding of the importance for the baker’s yeast industrial applications.
2017-01-30 | E-MTAB-3459 | biostudies-arrayexpress
Project description:Mycovirus-induced secondary metabolism in Magnaporthe oryzae
| PRJDB9423 | ENA
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:ε-poly-L-lysine (ε-PL) is a high value, widely used natural antimicrobial peptide additive for foods and cosmetic products that is mainly produced by S. albulus. In previous work, we developed the high-yield industrial strain S. albulus WG-608 through successive rounds of engineering. Here, we use integrated physiological, transcriptomic, and proteomics association analysis to resolve the complex mechanisms underlying high ε-PL production by comparing WG-608 with the progenitor strain M-Z18. Our results show that key genes in the glycolysis, glyoxylate, and L-lysine biosynthesis pathways are differentially upregulated in WG-608, while genes in the biosynthetic pathways for fatty acids, various branched amino acids, and secondary metabolite by-products are downregulated. This regulatory pattern results in the introduction of more carbon atoms into L-lysine biosynthesis and ε-PL production. Furthermore, transcriptional and translational upregulation of genes involved in the tricarboxylic acid cycle, oxidative phosphorylation, and pentose phosphate pathway also increase the pools of available NADH, ATP, and NADPH. In addition, significant changes in the regulation of DNA replication, transcription, and translation, two component systems, and quorum sensing may facilitate the adaptability to environmental pressure, thus further regulating the ε-PL biosynthesis. This study enables comprehensive understanding of the biosynthetic mechanisms of ε-PL in S. albulus WG-608, while providing a theoretical foundation development of advanced Streptomycetaceae microbial cell factories.
2023-07-20 | PXD036099 | Pride
Project description:Rice blast caused by Magnaporthe oryzae is the most devastating disease of cultivated rice. Several protein kinase cascades have been known to be essential to pathogenesis or important for response to stress, mycelial growth and conidiation in M. oryzae. However, phosphoproteins and their phosphorylation sites (p-sites) in this important fungal pathogen remain largely to be identified. In this study, 8087 phosphopeptides corresponding to 9825 p-sites from 1147 phosphoproteins were identified in mycelia of M. oryzae under a false discovery rate of < 0.55% at the peptide level. Notably, 33 previously reported pathogenesis-related proteins were included in the phosphoproteins at the mascot delta score 10. Further analyses of 581 motif-containing phosphoproteins that met more stringent criteria revealed that the phosphoproteins shared 19 distinct phosphorylation motifs, including the motif RxxpSP that was newly identified in this study but is widely distributed in diverse organisms. These phosphoproteins were mapped into 81 biological pathways. A total of 82 acidic motif-containing phosphoproteins were identified. Surprisingly, none of them except one were mapped to any of the metabolic pathways. Furthermore, a prediction disclosed a total of 174 kinase-substrate specific interactions in mycelia of M. oryzae. This study also detected phosphorylation of the tyrosine phosphatase Pmp1 and 7 other proteins upstream of Pmk1, but not Pmk1 and its downstream transcription factors. These results prompted a necessary revision of Pmk1 MAPK cascade, in which dephosphorylation of Pmk1 by Pmp1 in mycelia may block the activation of downstream targets.
2017-07-17 | PXD002364 | Pride
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. We transferred A. oryzae cells from normoxic to hypoxic conditions for 6 h, and then back to normoxic conditions to examine the effect of hypoxia on gene expression. Total RNA was prepared for DNA microarray analysis from the cells after 1, 3, and 6 h of exposure to hypoxia, followed by 1, 3, and 6 h of reoxygenation.
2011-07-30 | E-GEOD-31046 | biostudies-arrayexpress
Project description:Ethylene is a gaseous plant hormone that regulates plant growth and development. Broad reprogramming of gene expression is required for ethylene responses. The primary ethylene transcription factor (TF) ETHYLENE INSENSITIVE3 (EIN3) drives expression of secondary TFs including the ETHYLENE RESPONSE DNA-BINDING FACTORS (EDFs), but the role of the EDFs within the ethylene genome regulatory network is not understood. Here, we describe an investigation into the function of the EDFs in ethylene signalling and hormonal cross-regulation. We determined the target genes and binding dynamics of EDFs 1, 2, 3 during an ethylene response and the effects of edf1234 quadruple mutation on gene expression. The EDFs and EIN3 shared a large proportion of their target genes but had different functions. The EDFs were associated with repression of target genes, but this was superseded by activation when EIN3 bound the same genes. Genes important in other hormone signalling pathways, in particular abscisic acid (ABA), were targets of the EDFs. This demonstrates how ethylene engages hormonal cross-regulation to repress genes in competing signalling pathways and prioritize itself.
2023-04-06 | GSE182617 | GEO
Project description:The aim of this experiment was to understand secondary cell wall formation as it is a major constituent of wood and plant fibres. To identify potential novel genes involved in this process, data has been generated from Arabidopsis stem, leaf and hypocotyl tissue undergoing varying amounts of secondary cell wall synthesis.
2006-01-01 | E-MEXP-265 | biostudies-arrayexpress