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ABSTRACT:
PROVIDER: PRJNA683095 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13213121_1.fastq.gz | Fastqsanger.gz | |||
| SRR13213121_2.fastq.gz | Fastqsanger.gz | |||
| SRR13213122_1.fastq.gz | Fastqsanger.gz | |||
| SRR13213122_2.fastq.gz | Fastqsanger.gz | |||
| SRR13213123_1.fastq.gz | Fastqsanger.gz |
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Project description:Flahaut2013 - Genome-scale metabolic model of L.lactis (MG1363)
Genome-scale metabolic model for Lactococcus lactis
MG1363 and its application to the analysis of flavor formation.
This model is described in the article:
Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation.
Flahaut NA, Wiersma A, van de Bunt B, Martens DE, Schaap PJ, Sijtsma L, Dos Santos VA, de Vos WM
Applied Microbiology and Biotechnology. 2013; 97(19):8729-8739
Abstract:
Lactococcus lactis subsp. cremoris MG1363 is a paradigm strain for lactococci used in industrial dairy fermentations. However, despite of its importance for process development, no genome-scale metabolic model has been reported thus far. Moreover, current models for other lactococci only focus on growth and sugar degradation. A metabolic model that includes nitrogen metabolism and flavor-forming pathways is instrumental for the understanding and designing new industrial applications of these lactic acid bacteria. A genome-scale, constraint-based model of the metabolism and transport in L. lactis MG1363, accounting for 518 genes, 754 reactions, and 650 metabolites, was developed and experimentally validated. Fifty-nine reactions are directly or indirectly involved in flavor formation. Flux Balance Analysis and Flux Variability Analysis were used to investigate flux distributions within the whole metabolic network. Anaerobic carbon-limited continuous cultures were used for estimating the energetic parameters. A thorough model-driven analysis showing a highly flexible nitrogen metabolism, e.g., branched-chain amino acid catabolism which coupled with the redox balance, is pivotal for the prediction of the formation of different flavor compounds. Furthermore, the model predicted the formation of volatile sulfur compounds as a result of the fermentation. These products were subsequently identified in the experimental fermentations carried out. Thus, the genome-scale metabolic model couples the carbon and nitrogen metabolism in L. lactis MG1363 with complete known catabolic pathways leading to flavor formation. The model provided valuable insights into the metabolic networks underlying flavor formation and has the potential to contribute to new developments in dairy industries and cheese-flavor research.
This model is hosted on BioModels Database
and identified by: MODEL1310300000
.
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.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
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2005-01-01 | MODEL1310300000 | BioModels
Project description:The aim of the study was to decipher metabolisms responsible (i) for the peculiar adaptation of L. plantarum during soy juice fermentation and (ii) for the release of aroma compounds, amino and short-chain fatty acid, and metabolites with health-promoting properties in soy yogurt. The strategy was the sequencing and annotation of a strain (L. plantarum CIRM-BIA777, PRJEB77707) able to degrade galacto- oligosaccharides, the sampling of soy yogurt, RNA-seq to identify differentially expressed genes of L. plantarum and corresponding metabolisms throughout the kinetics of fermentation. Acids and volatile compounds were also quantified.
2024-08-18 | E-MTAB-14345 | biostudies-arrayexpress
Project description:High-temperature fermentation of the Bacillus subtilis isolated from the black part of maotai Daqu. Studying on the gene expression profile using microarray for analyzing the connection between metabolites and the maotai flavor substances. 84 differential expressed genes were obtained, including 40 up-regulated genes and 44 down-regulated genes.The differentially expressed genes involved in the metabolic pathways were just only KBL (glycine C - acetyltransferase) and ripA (bifunctional 3, 4 - dihydroxy - 4-2 - butanone phosphate synthase), up-regulated 2.9 and 2.9 times respectively, and their catalytic reaction prodction of aminobutyric acid and dihydroxy ethyl ketone phosphate, respectively. They may be further derived into alcohol and ketone flavoring substances. However, a large number of differential expressed genes was related to sporulation, such as ybaN (polysaccharide deacetylase) and rapA (aspartic acid phosphatase), they were up-regulated 17.5 times and down-regulated 112.5 times. YbaN is closely related to the formation of spore cortex and high temperature group spore cortex obvious thickening by TEM. RapA is signaling molecules to restrain spore formation, its lower expression can promote the sporulation in group A. Formation and release of peptidoglycan and the DPA (2, 6 - Pyridinedicarboxylic acid) of spore cortex during theseveral rounds of low temperature to high temperature circulation fermentation may be the main source of furan and pyranand nitrogen heterocyclic compounds in maotai flavor substances . In this paper, the formation of high-temperature fermentation Bacillus subtilis spores is closely related to the generation of maotai flavor substances. There are total of eight samples. It divided two groups, set as group A (High temperature fermentation) and B (normal temperature fermentation, continuous 37C). There are four replicates for each group.
2016-07-18 | E-GEOD-71067 | biostudies-arrayexpress
Project description:This research work investigates the expression of the genes involved in flavor compound production in two hybrids between Saccharomyces cerevisiae and S. kudriavzevii under low (12°C) and moderate fermentation temperatures (28°C).
2015-09-05 | GSE30779 | GEO
Project description:High-temperature fermentation of the Bacillus subtilis isolated from the black part of maotai Daqu. Studying on the gene expression profile using microarray for analyzing the connection between metabolites and the maotai flavor substances. 84 differential expressed genes were obtained, including 40 up-regulated genes and 44 down-regulated genes.The differentially expressed genes involved in the metabolic pathways were just only KBL (glycine C - acetyltransferase) and ripA (bifunctional 3, 4 - dihydroxy - 4-2 - butanone phosphate synthase), up-regulated 2.9 and 2.9 times respectively, and their catalytic reaction prodction of aminobutyric acid and dihydroxy ethyl ketone phosphate, respectively. They may be further derived into alcohol and ketone flavoring substances. However, a large number of differential expressed genes was related to sporulation, such as ybaN (polysaccharide deacetylase) and rapA (aspartic acid phosphatase), they were up-regulated 17.5 times and down-regulated 112.5 times. YbaN is closely related to the formation of spore cortex and high temperature group spore cortex obvious thickening by TEM. RapA is signaling molecules to restrain spore formation, its lower expression can promote the sporulation in group A. Formation and release of peptidoglycan and the DPA (2, 6 - Pyridinedicarboxylic acid) of spore cortex during theseveral rounds of low temperature to high temperature circulation fermentation may be the main source of furan and pyranand nitrogen heterocyclic compounds in maotai flavor substances . In this paper, the formation of high-temperature fermentation Bacillus subtilis spores is closely related to the generation of maotai flavor substances.
2016-07-18 | GSE71067 | GEO