Microaerobic fermentation alters lactose metabolism in Escherichia coli
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ABSTRACT:
PROVIDER: PRJNA559739 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9948680_1.fastq.gz | Fastqsanger.gz | |||
| SRR9948680_2.fastq.gz | Fastqsanger.gz | |||
| SRR9948681_1.fastq.gz | Fastqsanger.gz | |||
| SRR9948681_2.fastq.gz | Fastqsanger.gz | |||
| SRR9948682_1.fastq.gz | Fastqsanger.gz |
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Project description:We report the effect of oxygenation state in lactose grown escherichia coli producing recombinant proteins. To shed more light on the mechanistic correlation between the uptake of lactose and dissolved oxygen, a comprehensive study has been undertaken with the E. coli BL21 (DE3) strain. Differences in consumption pattern of lactose, metabolites, biomass and product formation due to aerobiosis have been investigated. Transcriptomic profiling of metabolic changes due to aerobic process and microaerobic process during protein formation phase has been studied and the results provide a deeper understanding of protein production in E. coli BL21 (DE3) strains with lactose based promoter expression systems.This study also provides a scientific understanding of escherichia coli metabolism upon oxygen fluctuations.
2020-05-18 | GSE135698 | GEO
Project description:The engineering of Saccharomyces cerevisiae strains for lactose utilization has been attempted with the intent of developing high productivity processes for alcoholic fermentation of cheese whey. A recombinant S. cerevisiae flocculent strain that efficiently ferments lactose to ethanol was previously obtained by evolutionary engineering of an original recombinant that displayed poor lactose fermentation performance. In this study, we compared the transcriptomes of the original and the evolved recombinant strains (T1 and T1-E, respectively) growing in lactose, using cDNA microarrays. Microarray data revealed 173 genes whose expression levels differed more than 1.5-fold. About half of these genes were related to RNA mediated transposition. We also found genes involved in DNA repair and recombination mechanisms, response to stress, chromatin remodelling, cell cycle control, mitosis regulation, glycolysis and alcoholic fermentation. These transcriptomic data are in agreement with some of the previously identified physiological and molecular differences between the recombinants, and point to further hypotheses to explain those differences.
2008-11-01 | GSE12433 | GEO
Project description:Lactose (1,4-0-M-CM-^_-d-galactopyranosyl-d-glucose), a by-product from cheese manufacture or whey processing industries, is known to induce the formation of plant biomass hydrolyzing enzymes needed for the biorefinery industry in the fungus Trichoderma reesei, but the reason for this induction and the underlying mechanism are not fully understood. Here, we used systems analysis of the Trichoderma reesei transcriptome during utilization of lactose. We found that the respective CAZome encoded glycosyl hydrolases specifically tailored for the attack of monocotyledon xyloglucan. In addition, genes for a high number of putative transporters of the major facilitator superfamily were also induced. Systematic knock out of them identified a gene whose knock-out completely impaired lactose utilization and cellulase induction in Trichoderma reesei. These data shed new light on the mechanism by which Trichoderma reesei metabolizes lactose and illuminate the key role of M-CM-^_-D-galactosides in habitat specificity of this fungus. We used two biological replicas of Trichoderma reesei growing on lactose, glucose and glycerol
2013-06-30 | E-GEOD-39276 | biostudies-arrayexpress
Project description:Lactose (1,4-0-ß-d-galactopyranosyl-d-glucose), a by-product from cheese manufacture or whey processing industries, is known to induce the formation of plant biomass hydrolyzing enzymes needed for the biorefinery industry in the fungus Trichoderma reesei, but the reason for this induction and the underlying mechanism are not fully understood. Here, we used systems analysis of the Trichoderma reesei transcriptome during utilization of lactose. We found that the respective CAZome encoded glycosyl hydrolases specifically tailored for the attack of monocotyledon xyloglucan. In addition, genes for a high number of putative transporters of the major facilitator superfamily were also induced. Systematic knock out of them identified a gene whose knock-out completely impaired lactose utilization and cellulase induction in Trichoderma reesei. These data shed new light on the mechanism by which Trichoderma reesei metabolizes lactose and illuminate the key role of ß-D-galactosides in habitat specificity of this fungus.
2013-06-30 | GSE39276 | GEO
Project description:The engineering of Saccharomyces cerevisiae strains for lactose utilization has been attempted with the intent of developing high productivity processes for alcoholic fermentation of cheese whey. A recombinant S. cerevisiae flocculent strain that efficiently ferments lactose to ethanol was previously obtained by evolutionary engineering of an original recombinant that displayed poor lactose fermentation performance. In this study, we compared the transcriptomes of the original and the evolved recombinant strains (T1 and T1-E, respectively) growing in lactose, using cDNA microarrays. Microarray data revealed 173 genes whose expression levels differed more than 1.5-fold. About half of these genes were related to RNA mediated transposition. We also found genes involved in DNA repair and recombination mechanisms, response to stress, chromatin remodelling, cell cycle control, mitosis regulation, glycolysis and alcoholic fermentation. These transcriptomic data are in agreement with some of the previously identified physiological and molecular differences between the recombinants, and point to further hypotheses to explain those differences. Four samples, each corresponding to independent biological cultivations of the two strains (T1 and T1-E), were analysed. To reduce the bias due to unequal incorporation or differences in quantum efficiency of the two dyes, RNA samples from a second independent experiment were labeled by opposite dye to the first experiment (method called dye switch), and this procedure was repeated 4 times, leading to 4 independent intensity values for each gene (spots) on the microarray. This experimental design minimizes the intrinsic biological noise between identical culture conditions and the technical variations inherent to the DNA microarray technology.
2008-10-31 | E-GEOD-12433 | biostudies-arrayexpress
Project description:The present study aims to explore chemostat-based transcriptome analysis of mixed cultures by investigating interactions between the yeast S. cerevisiae and the lactic acid bacterium L. bulgaricus . S. cerevisiae and L. bulgaricus are both frequently encountered in kefir, a fermented dairy product. In the context of this study, this binary culture serves as a model for the many traditional food and beverage fermentation processes in which yeasts and lactic acid bacteria occur together. The design of the cultivation conditions was based on the observation that L. bulgaricus, but not S. cerevisiae, can use lactose as a carbon source for growth and that S. cerevisiae, but not L. bulgaricus, can grow on galactose that is released upon hydrolysis of lactose by the bacterial β-galactosidase. Mixed populations of yeasts and lactic acid bacteria occur in many dairy, food and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir fermentations, were studied during anaerobic growth on lactose. By combining physiological and transcriptome analysis of the two strains in the co-cultures, five mechanisms of interaction were identified. 1. L. bulgaricus hydrolyses lactose, which cannot be metabolized by S. cerevisiae, to galactose and glucose. Subsequently, galactose, which cannot be metabolized by L. bulgaricus, is excreted and provides a carbon source for yeast. 2. In pure cultures, L. bulgaricus only grows at increased CO2 concentrations. In anaerobic mixed cultures, the yeast provides this CO2 via alcoholic fermentation. 3. Analysis of amino acid consumption from the defined medium indicated that S. cerevisiae supplied alanine to the bacteria. 4. A mild but significant low-iron response in the yeast transcriptome, identified by DNA microarray analysis, was consistent with the chelation of iron by the lactate produced by L. bulgaricus. 5. Transcriptome analysis of L. bulgaricus in mixed cultures showed an overrepresentation of transcripts involved in lipids metabolism suggesting either a competition of the two microorganisms for fatty acids, or a response to the ethanol produced by S. cerevisiae.
2013-04-01 | GSE45623 | GEO
Project description:The present study aims to explore chemostat-based transcriptome analysis of mixed cultures by investigating interactions between the yeast S. cerevisiae and the lactic acid bacterium Lb. bulgaricus . S. cerevisiae and Lb. bulgaricus are both frequently encountered in kefir, a fermented dairy product (25). In the context of this study, this binary culture serves as a model for the many traditional food and beverage fermentation processes in which yeasts and lactic acid bacteria occur together (19,26-30). The design of the cultivation conditions was based on the observation that Lb. bulgaricus, but not S. cerevisiae, can use lactose as a carbon source for growth and that S. cerevisiae, but not Lb. bulgaricus, can grow on galactose that is released upon hydrolysis of lactose by the bacterial M-NM-2-galactosidase. Mixed populations of yeasts and lactic acid bacteria occur in many dairy, food and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir fermentations, were studied during anaerobic growth on lactose. By combining physiological and transcriptome analysis of the two strains in the co-cultures, five mechanisms of interaction were identified. 1. Lb. bulgaricus hydrolyses lactose, which cannot be metabolized by S. cerevisiae, to galactose and glucose. Subsequently, galactose, which cannot be metabolized by Lb. bulgaricus, is excreted and provides a carbon source for yeast. 2. In pure cultures, Lb. bulgaricus only grows at increased CO2 concentrations. In anaerobic mixed cultures, the yeast provides this CO2 via alcoholic fermentation. 3. Analysis of amino acid consumption from the defined medium indicated that S. cerevisiae supplied alanine to the bacteria. 4. A mild but significant low-iron response in the yeast transcriptome, identified by DNA microarray analysis, was consistent with the chelation of iron by the lactate produced by Lb. bulgaricus. 5. Transcriptome analysis of Lb. bulgaricus in mixed cultures showed an overrepresentation of transcripts involved in lipids metabolism suggesting either a competition of the two microorganisms for fatty acids, or a response to the ethanol produced by S. cerevisiae. To our knowledge, this is the first transcriptome study of a cross-kingdom binary mixed culture that analyses responses of both microorganisms. This study demonstrates that chemostat-based transcriptome analysis is a powerful tool to investigated microbial interaction in mixed populations. To investigate the impact of of co-cultivation with Lb. bulgaricus on S. cerevisiae, a DNA microarray-based transcriptome analysis of S. cerevisiae's response was performed on anaerobic, lactose-limited chemostat cultures grown in the presence and absence of L. bulgaricus.
2013-08-22 | E-GEOD-45776 | biostudies-arrayexpress
Project description:Purpose: High γ-aminobutyric acid (GABA)-producing Levilactobacillus brevis strain NPS-QW 145 along with Streptococcus thermophilus (one of the two starter bacteria used to make yogurt for its proteolytic activity) to enhance GABA production in milk. But a mechanistic understanding on how Levilactobacillus brevis cooperated with S. thermophilus to stimulate GABA production has been lacking. Method: Metatranscriptomic analyses combined with peptidomics were carried out to unravel the casein and lactose utilization patterns during milk fermentation with the co-culture. Results: We found particular peptides hydrolyzed by S. thermophilus 1275 were transported and biodegraded with peptidase in Lb. brevis 145 to meet the growth needs of the latter. In addition, amino acid synthesis and metabolism in Lb. brevis 145 were also activated to further support its growth. Glucose, as a result of lactose hydrolysis by S. thermophilus 1275, but not available lactose in milk, was outcompeted by Lb. brevis 145 as a main carbon source for glycolysis to produce ATP.In the stationary phase, under the acidic condition due to accumulation of lactic acid produced by S. thermophilus 1275, genes expression involved in pyridoxal phosphate (coenzyme of glutamic acid decarboxylase) metabolism and glutamic acid decarboxylase (Gad) in Lb. brevis 145 were induced for GABA production.
2020-09-16 | GSE157976 | GEO
Project description:All organisms have evolved elaborate physiological pathways that regulate growth, proliferation, metabolism, and stress response. These pathways must be properly coordinated to elicit the appropriate response to an ever-changing environment. While individual pathways have been well studied in a variety of model systems, there remains much to uncover about how they are integrated to produce global changes in a cell. Past work from our lab, focused on engineering the budding yeast Saccharomyces cerevisiae for fermentation of the non-native pentose sugar xylose, discovered that hyperactivation of the RAS/Protein Kinase A (PKA) pathway was needed for rapid anaerobic xylose fermentation. Interestingly, the mechanism of PKA hyperactivation has a dramatic impact on growth and metabolism on xylose; deletion of the RAS inhibitor IRA2 permits rapid growth and fermentation, while deletion of the PKA regulatory subunit BCY1 allows for fermentation without growth on xylose. To understand how a single deletion in the PKA pathway can decouple growth and metabolism, we performed transcriptomic analysis of these strains, predicting that altered PKA activity would impact global gene expression and identify pathways important for growth and metabolism coordination. Notably, we found enriched differential expression of lipid metabolism genes, targets of the phospholipid biosynthetic gene transcription factor Ino4, and genes containing the Aft1/2 consensus motif. These results suggested that dysfunctional lipid homeostasis may be responsible for decoupling growth and metabolism in the bcy1∆ strain. In parallel work, we also directly evolved the bcy1∆ strain to grow anaerobically on xylose and found point mutations in TPK1, OPI1, RIM8, and TOA1 permitted growth. Interestingly, Opi1 is the inhibitor of Ino4, further supporting the role of lipid homeostasis in growth and metabolism coordination. This work shows that a single genetic change can have dramatic impacts on multiple aspects of cellular physiology.
2023-05-01 | GSE220465 | GEO
Project description:We have examined and compared the transcriptome of T. reesei growing on wheat straw and lactose as carbon sources under otherwise similar conditions. Gene expression on wheat straw exceeded that on lactose, and 1619 genes were found to be only induced on wheat straw but not on lactose. They comprised 30 % of the CAZome, but were also enriched in genes associated with phospholipid metabolism, DNA synthesis and repair and iron homeostatis. Two thirds of the CAZome was expressed both on wheat straw as well as on lactose, but 60 % of it at least >2-fold higher on the former. Major wheat straw specific genes comprised xylanases, chitinases and M-CM-^_-mannosidases. Interestingly, the latter two CAZyme families were significantly higher expressed in a strain in which xyr1 encoding the major regulator of cellulase and hemicellulase biosynthesis is non-functional, demonstrating that XYR1 is a repressor of these genes. We used two biological replicas of four T. reesei strains growing on glucose, lactose, and on wheat straw
2013-09-17 | E-GEOD-46155 | biostudies-arrayexpress