Proteomic analysis of various stages of fermentation of pea isolate in presence of Aspergillus oryzae
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ABSTRACT:
ORGANISM(S): Cellular Organisms
SUBMITTER: Kishore Rajagopalan
PROVIDER: PXD038174 | JPOST Repository | Fri Mar 08 00:00:00 GMT 2024
REPOSITORIES: jPOST
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 0%20hr_S1_1.raw | Raw | |||
| 0%20hr_S1_2.raw | Raw | |||
| 0%20hr_S2_1.raw | Raw | |||
| 0%20hr_S2_2.raw | Raw | |||
| 12%20hr_S1_1.raw | Raw |
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Project description:Background Lactococcus lactis is recognised as a safe (GRAS) microorganism and has hence gained interest in numerous biotechnological approaches. As it is fastidious for several amino acids, optimization of processes which involve this organism requires a thorough understanding of its metabolic regulations during multisubstrate growth. Results Using glucose limited continuous cultivations, specific growth rate dependent metabolism of L. Lactis including utilization of amino acids was studied based on extracellular metabolome, global transcriptome and proteome analysis. A new growth medium was designed with reduced amino acid concentrations to increase precision of measurements of consumption of amino acids. Consumption patterns were calculated for all 20 amino acids and measured carbon balance showed good fit of the data at all growth rates studied. It was observed that metabolism of L. lactis became more efficient with rising specific growth rate in the range 0.10 – 0.60 h-1, indicated by 30% increase in biomass yield based on glucose consumption, 50% increase in efficiency of nitrogen use for biomass synthesis, and 40% reduction in energy spilling. The latter was realized by decrease in the overall product formation and higher efficiency of incorporation of amino acids into biomass. L. lactis global transcriptome and proteome profiles showed good correlation supporting the general idea of transcription level control of bacterial metabolism, but the data indicated that substrate transport systems together with lower part of glycolysis in L. lactis were presumably under allosteric control. Conclusions The current study demonstrates advantages of the usage of strictly controlled continuous cultivation methods combined with multi-omics approach for quantitative understanding of amino acid and energy metabolism of Lactococcus lactis which is a valuable new knowledge for development of balanced growth media, gene manipulations for desired product formation etc. Moreover, collected dataset is an excellent input for developing metabolic models.
2011-01-11 | GSE26536 | GEO
Project description:Background Lactococcus lactis is recognised as a safe (GRAS) microorganism and has hence gained interest in numerous biotechnological approaches. As it is fastidious for several amino acids, optimization of processes which involve this organism requires a thorough understanding of its metabolic regulations during multisubstrate growth. Results Using glucose limited continuous cultivations, specific growth rate dependent metabolism of L. Lactis including utilization of amino acids was studied based on extracellular metabolome, global transcriptome and proteome analysis. A new growth medium was designed with reduced amino acid concentrations to increase precision of measurements of consumption of amino acids. Consumption patterns were calculated for all 20 amino acids and measured carbon balance showed good fit of the data at all growth rates studied. It was observed that metabolism of L. lactis became more efficient with rising specific growth rate in the range 0.10 – 0.60 h-1, indicated by 30% increase in biomass yield based on glucose consumption, 50% increase in efficiency of nitrogen use for biomass synthesis, and 40% reduction in energy spilling. The latter was realized by decrease in the overall product formation and higher efficiency of incorporation of amino acids into biomass. L. lactis global transcriptome and proteome profiles showed good correlation supporting the general idea of transcription level control of bacterial metabolism, but the data indicated that substrate transport systems together with lower part of glycolysis in L. lactis were presumably under allosteric control. Conclusions The current study demonstrates advantages of the usage of strictly controlled continuous cultivation methods combined with multi-omics approach for quantitative understanding of amino acid and energy metabolism of Lactococcus lactis which is a valuable new knowledge for development of balanced growth media, gene manipulations for desired product formation etc. Moreover, collected dataset is an excellent input for developing metabolic models. For microarray analysis, steady state chemostat culture of L. lactis IL1403 was used as reference (? = 0.10 1/h). Subsequent quasi steady state points from A-stat experiment at specific growth rates 0.52 ± 0.03; 0.42 ± 0.02; 0.29 ± 0.01 1/h in biological duplicates and 0.17 1/h were compared to the reference sample.
2011-01-11 | E-GEOD-26536 | biostudies-arrayexpress
Project description:Seaweeds are attracting substantial interest as novel sources of sustainable food protein, as they are established sources of industrial hydrocolloids and have reasonable protein content. In this study we investigate the protein composition and quality of a seaweed protein extract (SPE) from Gigartina radula obtained as a side-stream from industrial carrageenan production. The SPE displayed low (<2%), but pH-dependent, aqueous solubility due to the harsh (heat and extreme pH) employed during extraction. Solubility was improved using buffer and detergent to facilitate proteomic characterization by quantitative LC-MS/MS. Proteomics revealed that the SPE was dominated by proteins related to light harvest and particularly rich in phycobiliproteins (44% relative molar abundance), where phycoerythrin was the most abundant (28%). Based on subcellular localization of identified proteins, the extraction method was evaluated as good for release of cellular protein. The SPE was found to be rich in essential amino acids (36-41%) and particularly in branched chain amino acids (22-24%) and thereby a potential source of nutritional food protein. Using bioinformatic prediction and structural modelling, we found that abundant proteins in the SPE contained high potential, novel emulsifier peptides with amphiphilic properties required to stabilize an oil/water interface. Based on this study, Gigartina could serve as a good candidate for extraction of sustainable and nutritious food protein and possibly be further processed to obtain a hydrolysate with good emulsifying properties for use in foods.
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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
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Project description:Ingestion of a diet with a restricted Methionine (MR) content results in robust activation of a set of browning genes in IWAT (inguinal white adipose tissue). So far, data were obtained using a mix of elemental amino acids as the dietary protein source, which was replaced in this experiment with casein. To reduce methionine content, casein was oxidized and methionine was added back to a concentration similar to the diets using elemental amino acids as protein source. Results show that mice reduce body weight and adiposity on MR containing oxidized casein similar to MR containing elemental amino acids. Similarly, energy expenditure, as well as food and water intake were increased. The RNAseq experiment was conducted to compare the effect of MR using these two protein sources on the IWAT transcriptome.
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Project description:Ingestion of a diet with a restricted Methionine (MR) content results in robust activation of hepatic stress pathways regulated by PERK, ATF4, and Nfe2l2. In addition, genes regulating hepatic lipogenesis are downregulated. So far, data were obtained using a mix of elemental amino acids as the dietary protein source, which was replaced in this experiment with casein. To reduce methionine content, casein was oxidized and methionine was added back to a concentration similar to the diets using elemental amino acids as protein source. Results show that mice reduce body weight and adiposity on MR containing oxidized casein similar to MR containing elemental amino acids. Similarly, energy expenditure, as well as food and water intake were increased. The RNAseq experiment was conducted to compare the effect of MR using these two protein sources on the hepatic transcriptome.
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