Similar Datasets
Project description:We report the genes regulated during citrate fermentation. Examination of 5 different time points during fermentation in Aspergillus niger H915-1.
2016-06-30 | E-GEOD-74544 | biostudies-arrayexpress
Project description:Despite a long and successful history of citrate production in Aspergillus niger, the molecular mechanism of citrate accumulation is only partially understood. In this study, we used comparative genomics and transcriptome analysis of citrate-producing strains-namely, A. niger H915-1 (citrate titer: 157 g L-1), A1 (117 g L-1), and L2 (76 g L-1)-to gain a genome-wide view of the mechanism of citrate accumulation. Compared with A. niger A1 and L2, A. niger H915-1 contained 92 mutated genes, including a succinate-semialdehyde dehydrogenase in the γ-aminobutyric acid shunt pathway and an aconitase family protein involved in citrate synthesis. Furthermore, transcriptome analysis of A. niger H915-1 revealed that the transcription levels of 479 genes changed between the cell growth stage (6 h) and the citrate synthesis stage (12 h, 24 h, 36 h, and 48 h). In the glycolysis pathway, triosephosphate isomerase was up-regulated, whereas pyruvate kinase was down-regulated. Two cytosol ATP-citrate lyases, which take part in the cycle of citrate synthesis, were up-regulated, and may coordinate with the alternative oxidases in the alternative respiratory pathway for energy balance. Finally, deletion of the oxaloacetate acetylhydrolase gene in H915-1 eliminated oxalate formation but neither influence on pH decrease nor difference in citrate production were observed.
| S-EPMC5247736 | biostudies-literature
Project description:Aspergillus niger is well known for its capability to produce citrate in high amounts but the detailed metabolic response causing citrate production has not been fully elucidated. Manganese is known to have an important effect as its limitation is a requirement to obtain high-level citrate formation. To identify the translational regulation causing citric acid overflow metabolism, transcriptome and proteome data from cultivations in manganese limitation and manganese excess conditions were analyzed. In addition to four already described main responses, two novel events were identified. The first metabolic response was down regulation of phosphoenolpyruvate carboxykinase (PEPCK) during manganese limited conditions, which was confirmed by in vivo experiments. Down regulation of the first step in the gluconeogenesis, while maintaining a high activity through glycolysis, promoted secretion of citrate into the medium as an alternative regulatory mechanism for adjusting the intracellular concentrations of TCA intermediates. The other novel observation was down regulation of two cation transporters at manganese limited conditions. It was hypothesized that lowered cation transport across the mitochondrial membrane reduced the ability of the cell to maintain homeostasis thereby favoring citric acid secretion. Finally, upregulation of an ABC transporter was measured, which was assumed to be a citrate permease.
2014-10-03 | GSE61985 | GEO
Project description:Generally, A. niger undergoes two steps consisting of seed stage and fermentation stage to synthesize malic acid. However, it remains unknown which metabolic pathways, regulators, and key genes respond to the transition from seed medium to fermentation medium. In this study, we obtained the total mRMA of a high L-malate-yielding strain A. niger RG0095 at seed stage and fermentation stage, respectively, and performed a global differential expression analysis.
2024-03-15 | GSE235528 | GEO
Project description:Desulfitobacterium hafniense DCB-2, a halo-respirer and versatile inorganic ion reducer, grows in hazardous waste contaminated environments. M-BM- Gene expression changes were determined when the strain was grown in the presence of high concentrations of Fe(+3), Se(+6), U(+6), or NO3(-) as alternative electron acceptors. (Thesis by Christina L. Harzman at Michigan State University, 2009) RNA was used to directly compare gene expression in control samples of pyruvate fermentation (20 mM) to fermentation in the presence inorganic electron acceptors or respiration-inducing conditions. M-BM- The inorganic electron acceptors added to media for fermentation were 1 mM selenate or 0.5 mM uranyl acetate. The respiration-inducing conditions were 50 mM ferric citrate (20 mM lactate carbon source) or 10 mM nitrate (20 mM lactate carbon source). Microarray hybridizations were performed with a dye swap and 3 biological replicates for a total of 6 slides per condition for comparison.
2012-11-29 | E-GEOD-33988 | biostudies-arrayexpress
Project description:Currently, there is no consensus regarding the mechanism underlying Aspergillus niger citrate biosynthesis and secretion. We hypothesise that depending on the experimental setup, extracellular citrate accumulation can have fundamentally different underlying transcriptomic landscapes. We show that varying the amount and type of supplement of an arginine auxotrophic A. niger strain results in transcriptional down-regulation of citrate metabolising enzymes in the condition in which more citrate is accumulated extracellularly. This contrasts with the transcriptional adaptations when increased citrate production is triggered by iron limitation. By combining gene expression data obtained from these two very distinct experimental setups with hidden Markov models and transporter homology approaches, we were able to compile a shortlist of the most likely citrate transporter candidates. Two candidates (An17g01710 and An09g06720m.01) were heterologously expressed in the yeast Saccharomyces cerevisiae, and one of the resultant mutants showed the ability to secrete citrate. Our findings provide steps in untangling the complex interplay of different mechanisms underlying A. niger citrate accumulation, and we demonstrate how a comparative transcriptomics approach complemented with further bioinformatics analyses can be used to pinpoint a fungal citrate exporter.
| S-EPMC6502548 | biostudies-literature
Project description:Aspergillus niger has an innate ability to secrete various organic acids, including citrate. The conditions required for A. niger citrate overproduction are well described, but the physiological reasons underlying extracellular citrate accumulation are not yet fully understood. One of the less understood culture conditions is the requirement of growth-limiting iron concentrations. While this has been attributed to iron-dependent citrate metabolizing enzymes, this straightforward relationship does not always hold true. Here, we show that an increase in citrate secretion under iron limited conditions is a physiological response consistent with a role of citrate as A. niger iron siderophore. We found that A. niger citrate secretion increases with decreasing amounts of iron added to the culture medium and, in contrast to previous findings, this response is independent of the nitrogen source. Differential transcriptomics analyses of the two A. niger mutants NW305 (gluconate non-producer) and NW186 (gluconate and oxalate non-producer) revealed up-regulation of the citrate biosynthesis gene citA under iron limited conditions compared to iron replete conditions. In addition, we show that A. niger can utilize Fe(III) citrate as iron source. Finally, we discuss our findings in the general context of the pH-dependency of A. niger organic acid production, offering an explanation, besides competition, for why A. niger organic acid production is a sequential process influenced by the external pH of the culture medium.
| S-EPMC5539119 | biostudies-literature
Project description:Aspergillus niger is well known for its capability to produce citrate in high amounts but the detailed metabolic response causing citrate production has not been fully elucidated. Manganese is known to have an important effect as its limitation is a requirement to obtain high-level citrate formation. To identify the translational regulation causing citric acid overflow metabolism, transcriptome and proteome data from cultivations in manganese limitation and manganese excess conditions were analyzed. In addition to four already described main responses, two novel events were identified. The first metabolic response was down regulation of phosphoenolpyruvate carboxykinase (PEPCK) during manganese limited conditions, which was confirmed by in vivo experiments. Down regulation of the first step in the gluconeogenesis, while maintaining a high activity through glycolysis, promoted secretion of citrate into the medium as an alternative regulatory mechanism for adjusting the intracellular concentrations of TCA intermediates. The other novel observation was down regulation of two cation transporters at manganese limited conditions. It was hypothesized that lowered cation transport across the mitochondrial membrane reduced the ability of the cell to maintain homeostasis thereby favoring citric acid secretion. Finally, upregulation of an ABC transporter was measured, which was assumed to be a citrate permease. 9 samples in total. Three conditions in triplicates
2014-10-03 | E-GEOD-61985 | biostudies-arrayexpress
Project description:BackgroundAs an attractive platform chemical, malic acid has been commonly used in the food, feed and pharmaceutical field. Microbial fermentation of biobased sources to produce malic acid has attracted great attention because it is sustainable and environment-friendly. However, most studies mainly focus on improving yield and ignore shortening fermentation time. A long fermentation period means high cost, and hinders the industrial applications of microbial fermentation. Stresses, especially oxidative stress generated during fermentation, inhibit microbial growth and production, and prolong fermentation period. Previous studies have shown that polypeptides could effectively relieve stresses, but the underlying mechanisms were poorly understood.ResultsIn this study, polypeptides (especially elastin peptide) addition improves the productivity of malic acid in A. niger, resulting in shortening of fermentation time from 120 to 108 h. Transcriptome and biochemical analyses demonstrated that both antioxidant enzyme-mediated oxidative stress defense system, such as superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX), and nonenzymatic antioxidant system, such as glutathione, were enhanced in the presence of elastin peptide, suggesting elastin peptide relieving oxidative stresses is involved in many pathways. In order to further investigate the relationship between oxidative stress defense and malic acid productivity, we overexpressed three enzymes (Sod1, CAT, Tps1) related to oxidation resistance in A. niger, respectively, and these resulting strains display varying degree of improvement in malic acid productivity. Especially, the strain overexpressing the Sod1 gene achieved a malate titer of 91.85 ± 2.58 g/L in 96 h, corresponding to a productivity of 0.96 g/L/h, which performs better than elastin peptide addition.ConclusionsOur investigation provides an excellent reference for alleviating the stress of the fungal fermentation process and improving fermentation efficiency.
| S-EPMC9801644 | biostudies-literature
Project description:the original data of black soldier fly larva mass fermentation with Bacillus subtilis and Aspergillus niger, analyzed by Chinese biotechnology company, published by Chinese Academy of Tropical Agricultural Sciences Environment and Plant Protection Institute for research only.
2023-10-25 | PXD037713 | JPOST Repository