Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PSY3642_to_PSY3639_SC_aerobic

ABSTRACT: We designed and experimentally validated an in silico gene deletion strategy for engineering endogenous one-carbon (C1) metabolism in yeast. Specifically, a Flux Balance Analysis (FBA) model predicted that five genes ALT2, FDH1, FDH2, FUM1, and ZWF1, when deleted in combination, would cause Saccharomyces cerevisiae to overproduce and secrete formic acid under aerobic growth conditions. Once constructed, the quintuple mutant strain showed the predicted increase in formic acid secretion relative to a formate dehydrogenase mutant (fdh1 fdh2 ), while formic acid secretion in wild-type yeast was undetectable. Gene expression and physiological data generated post hoc identified a mitochondrial deficiency phenotype in the engineered strain and regulatory events that suggest a role for multisite modulation—the coordinated expression of multiple pathway enzymes—in controlling yeast C1 metabolism. Together, these results demonstrate that FBA-based modeling strategies can be useful tools for non-fermentative pathway design and discovery in eukaryotic microbes. In addition, the results indicate that seemingly unrelated mutations can be combined to modulate flux through biochemical reactions that interact at a systems level across subcellular compartments. Samples were processed in biological triplicate with one sample processed with dye orientations reversed to minimize the effects of incorporation bias.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Caleb Kennedy

PROVIDER: E-GEOD-12240 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

PSY3642_to_PSY3639_SC_aerobic

Project description:We designed and experimentally validated an in silico gene deletion strategy for engineering endogenous one-carbon (C1) metabolism in yeast. Specifically, a Flux Balance Analysis (FBA) model predicted that five genes ALT2, FDH1, FDH2, FUM1, and ZWF1, when deleted in combination, would cause Saccharomyces cerevisiae to overproduce and secrete formic acid under aerobic growth conditions. Once constructed, the quintuple mutant strain showed the predicted increase in formic acid secretion relative to a formate dehydrogenase mutant (fdh1 fdh2 ), while formic acid secretion in wild-type yeast was undetectable. Gene expression and physiological data generated post hoc identified a mitochondrial deficiency phenotype in the engineered strain and regulatory events that suggest a role for multisite modulation—the coordinated expression of multiple pathway enzymes—in controlling yeast C1 metabolism. Together, these results demonstrate that FBA-based modeling strategies can be useful tools for non-fermentative pathway design and discovery in eukaryotic microbes. In addition, the results indicate that seemingly unrelated mutations can be combined to modulate flux through biochemical reactions that interact at a systems level across subcellular compartments.

2009-07-24 | GSE12240 | GEO

S. cerevisiae engineered chassis for dicarboxylic acid production

Project description:Chassis strain suitable for producing multiple compounds is a central concept in synthetic biology. Design of a chassis using computational, first-principle, models is particularly attractive due to the predictability and control it offers, including against phenotype reversal due to adaptive mutations. Yet, the theory of model-based chassis design has not been put to experimental test. Here, we report two Saccharomyces cerevisiae chassis strains for dicarboxylic acid production based on genome-scale metabolic modelling. The chassis strain, harboring gene knockouts in serine biosynthesis and in pentose-phosphate pathway, is geared for higher flux towards three target products - succinate, fumarate and malate - but does not appreciably secrete any. Introducing modular product-specific mutations resulted in improved secretion of the corresponding acid as predicted by the model. Adaptive laboratory evolution of the chassis-derived producer cells further improved production for succinate and fumarate attesting to the evolutionary robustness of the underlying growth-product coupling. In the case of malate, which exhibited decreased production during evolution, the multi-omics analysis revealed flux bypass at peroxisomal malate dehydrogenase not accounted in the model. Transcriptomics, proteomics and metabolomics analysis showed overall concordance with the flux re-routing predicted by the model. Together, our results provide experimental evidence for model-based design of microbial chassis and have implications for computer-aided design of microbial cell factories.

2021-07-20 | PXD020611 | Pride

L. lactis NZ9000 (pNZbcaP-H6) Vs. L. lactis NZ9000 (pNZ8048)

2011-07-20 | GSE30776 | GEO

Comparative RNA-Seq of Cupriavidus necator H16, formerly Ralstonia eutropha H16, grown in minimal media with 3-hydroxypropionic acid (3-HP) or fructose as sole carbon source.

Project description:3-hydroxypropionic acid (3-HP) is a promising platform chemical with various industrial applications. Several metabolic routes to produce 3-HP from organic substrates such as sugars or glycerol have been implemented in yeast, enterobacterial species and other microorganisms. In this work, we investigated 3-HP metabolism of the well-studied ‘Knallgas bacterium’ Cupriavidus necator, a potential C1-chassis for the production of 3-HP and other fatty acid derivatives from CO2 and H2. When testing C. necator for its tolerance towards 3-HP, it was noted that it could utilise the compound as the sole source of carbon and energy.

2019-03-31 | E-MTAB-7701 | biostudies-arrayexpress

Metabolic engineering of oleaginous yeast in lipogenic phase enhances production of nervonic acid

Project description:Insufficient biosynthesis efficiency can be a major obstacle to engineer oleaginous yeasts to overproduce very long-chain fatty acids (VLCFAs) during the lipogenic phase. Taking nervonic acid (NA, C24:1) as an example, we overcame the bottleneck to overproduce NA in engineered Rhodosporidium toruloides by improving the biosynthesis of VLCFAs during the lipogenic phase. First, evaluating the catalytic preferences of three plant-derived ketoacyl-CoA synthases rationally guided reconstructing efficient NA biosynthetic pathway in R. toruloides. More importantly, a genome-wide transcriptional analysis endowed clues to strengthen the fatty acid elongation (FAE) module and identify/use lipogenic phase-activated promoter, collectively addressing the stagnation of NA accumulation during the lipogenic phase. The best-designed strain exhibited a high NA content (major component in total fatty acid [TFA], 46.3%) and produced a titer of 44.2 g/L in a 5 L bioreactor. The strategy developed here provides an engineering framework to establish the microbial process of producing valuable VLCFAs in oleaginous yeasts.

2023-09-14 | GSE241709 | GEO

RNA-Seq of wild type yeast and several knockout strains in different chemically defined media

Project description:This experiment investigates yeast pathways involved in the secretion of metabolites that enable the growth of lactic acid bacteria. Wild-type Saccharomyces cerevisiae (S90) in different defined media, as well as four mutant yeasts with selective gene deletions, were forwarded to RNA-seq to characterise global differences in transcriptomes and identify genes/pathways with altered gene expression levels.

2017-12-01 | E-MTAB-4651 | biostudies-arrayexpress

Model-guided development of evolutionarily stable yeast chassis for dicarboxylic acids production

Project description:<p>Chassis strain suitable for producing multiple compounds is a central concept in synthetic biology. Design of a chassis using computational, first-principle, models is particularly attractive due to the predictability and control it offers, including against phenotype reversal due to adaptive mutations. Yet, the theory of model-based chassis design has rarely been put to rigorous experimental test and assessed at multiomics level. Here, we report two <em>Saccharomyces cerevisiae</em> chassis strains for dicarboxylic acid production based on genome-scale metabolic modelling. The chassis strain, harbouring gene knockouts in serine biosynthesis and in pentose-phosphate pathway, is geared for higher flux towards three target products - succinate, fumarate and malate - but does not appreciably secrete any. Introducing modular product-specific mutations resulted in improved secretion of the corresponding acid as predicted by the model. Adaptive laboratory evolution of the chassis-derived producer cells further improved production for succinate and fumarate attesting to the evolutionary robustness of the underlying growth-product coupling. In the case of malate, which exhibited decreased production during evolution, the multiomics analysis revealed flux bypass at peroxisomal malate dehydrogenase that was not accounted in the model. Integration of transcriptomics, proteomics and metabolomics data showed overall concordance with the flux re-routing predicted by the model. Together, our results provide experimental evidence for model-based design of microbial chassis and have implications for computer-aided design of microbial cell factories.</p>

2021-07-19 | MTBLS2007 | MetaboLights

Integrating Extracellular Flux Measurements and Genome-Scale Modeling Reveals Novel Differences between Brown and White Adipocytes

Project description:This study predicted flux differences between brown and white adipocytes by integrating the results of extracellular flux analyzers, such as the Seahorse Analyzer, with metabolic modeling. The microarrays of the individuals' preadipocytes were used to support the predictions. These are the same individuals who were assayed by microarray in GSE68544.

2017-12-18 | GSE100003 | GEO

L. lactis NZ9000 (pNZbcaP-H6) Vs. L. lactis NZ9000 (pNZ8048)

Project description:Our transcriptome data shows that the two-component system CesSR, which senses cell envelope stresses of different origins, is one of the major players when L. lactis is forced to overproduce the endogenous membrane protein BcaP, a branched-chain amino acid permease. Two-condition experiment: nisin induced overproduction of BcaP vs. control. Biological replicates: 2 controls, 2 overproduction cultures; independently grown and harvested; dye swaped on the second array.

2011-07-19 | E-GEOD-30776 | biostudies-arrayexpress

Absolute proteome quantification in the gas-fermenting acetogen Clostridium autoethanogenum

Project description:Microbes that can recycle one-carbon (C1) greenhouse gases into fuels and chemicals are vital for the biosustainability of future industries. Acetogens are the most efficient known microbes for fixing carbon oxides CO2 and CO. Understanding proteome allocation is important for metabolic engineering as it dictates metabolic fitness. Here, we use absolute proteomics to quantify intracellular concentrations for >1,000 proteins in the model-acetogen Clostridium autoethanogenum grown on three gas mixtures. We detect prioritisation of proteome allocation for C1 fixation and significant expression of proteins involved in the production of acetate and ethanol as well as proteins with unclear functions. The data also revealed which isoenzymes are important. Integration of proteomic and metabolic flux data demonstrated that enzymes catalyse high fluxes with high concentrations and high in vivo catalytic rates. We show that flux throughput was dominantly controlled through enzyme catalytic rates rather than concentrations. Our work serves as a reference dataset and advances systems-level understanding and engineering of acetogens.

2022-05-22 | PXD025732 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data