Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Total proteome analysis of engineered/adapted E.coli strains with glucose/xylose co-utilization ability

ABSTRACT: This project was about developing a bacterial strain that could consume a mixture of glucose and xylose simultaneously with higher ethanol productivity. In this study, an ethanologenic strain (SSK42) was made deficient in Carbon Catabolite Repression (CCR) by deleting the ptsG gene encoding EIIBCGlc component of PTS transport system. This strain (SCD00) was then evolved for several generations on xylose containing minimal media. A strain (SCD78) was finally obtained that, unlike its parent strain could consume glucose and xylose simultaneously. Then we performed proteomics analysis of evolved and un-evolved strain. The strain SSK42 was also considered for proteome analysis as a reference for analysis. The starting strain – SSK42, is the derivative of E.coli B.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Escherichia Coli

SUBMITTER: Chandra Dev

LAB HEAD: Syed Shams Yazdani

PROVIDER: PXD033577 | Pride | 2022-10-15

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Reference_database.fasta	Fasta
	SCD00_1_WP.mzML	Mzml
	SCD00_1_WP.mzid.gz	Mzid
	SCD00_1_WP.pdResult	Other
	SCD00_1_WP.pdResultView	Other

Items per page:

1 - 5 of 32

Publications

Adaptation on xylose improves glucose-xylose co-utilization and ethanol production in a carbon catabolite repression (CCR) compromised ethanologenic strain.

Dev Chandra C Jilani Syed Bilal SB Yazdani Syed Shams SS

Microbial cell factories 20220806 1

<h4>Background</h4>Sugar hydrolysates from lignocellulosic biomass are majorly composed of glucose and xylose that can be fermented to biofuels. Bacteria, despite having the natural ability to consume xylose are unable to consume it in presence of glucose due to a carbon catabolite repression (CCR) mechanism. This leads to overall reduced productivity as well as incomplete xylose utilization due to ethanol build-up from glucose utilization. In our effort to develop a strain for simultaneous ferm ...[more]

PMID: 35933385

Similar Datasets

Transcriptomic response of the xylose-selective strain derived from E. coli BL21(DE3) growing on xylose or glucose

Project description:Different genetic engineering strategies have been proposed to obtain E. coli strains that selectively consume xylose. In this study, a previously reported strategy for obtaining a xylose-selective strain in E. coli K12 was applied to E. coli BL21 (DE3). While this approach resulted in the expected xylose-selective phenotype, a low xylose consumption rate was recorded when the strain was grown on a mixture of xylose and glucose. To enhance xylose consumption, a variant of the transcriptional activator XylR was expressed. The resulting strain not only exhibited an improved capacity to consume xylose but also slightly recovered the ability to consume glucose. The aim of the microarray analysis was to identify the transcriptional changes associated with glucose assimilation in the BL21(DE3) derived xylose-selective strain.

2024-10-01 | GSE277741 | GEO

Expression data from parental and evolved Saccharomyces cerevisiae F12 cells in the presence of insoluble solids at high concentration and lignocellulose-derived inhibitors

Project description:Increasing yeast robustness against biomass-derived inhibitors and insoluble solids is essential for the realization of a bio-based economy. The xylose-fermenting Saccharomyces cereivisiae F12 strain was subjected to an adaptive laboratory evolution experiment in the presence of these stressors. The resulting evolved strain exhibit better fermentation performance in terms of xylose consumption and ethanol yields than the parental strain. The overexpression of genes related to cell wall integrity and the stress response, together with the downregulation of protein synthesis and iron transport and homeostasis were highlighted as the major biological processes responsible for the improved phenotype.

2022-01-11 | GSE159167 | GEO

Transcription profiling Saccharomyces cerevisiae xylose metabolism

Project description:In the present study transcriptome and proteome of recombinant, xylose-utilising S. cerevisiae grown in aerobic batch cultures on xylose were compared with glucose-grown cells both in glucose repressed and derepressed states. The aim was to study at genome-wide level how signalling and carbon catabolite repression differed in cells grown on either glucose or xylose. The more detailed knowledge about is xylose sensed as a fermentable carbon source, capable of catabolite repression like glucose, or is it rather recognised as a non-fermentable carbon source is important in achieving understanding for further engineering this yeast for more efficient anaerobic fermentation of xylose. Experiment Overall Design: Three aerobic batch fermentations were carried out both on 50 g l-1 glucose and on 50 g l-1 xylose to compare the yeast transcriptome and proteome of cells growing on xylose with that of glucose repressed and glucose derepressed cells. Samples of the xylose-grown cells were harvested at 72 h from the start of the xylose cultures with 32 g l-1 of residual xylose present. Samples of the glucose repressed cells were harvested at 5 h from the start of the glucose cultures with 37 g l-1 of residual glucose present. Samples of the glucose derepressed cells were harvested at 24 h from the start of the glucose cultures containing no glucose but 13 g l-1 of accumulated ethanol.

2008-10-26 | E-GEOD-12890 | biostudies-arrayexpress

All you can eat yeast: substitution of major hexose transporters by AtSWEET7 in Saccharomyces cerevisiae enables simultaneous utilization of multiple sugars

Project description:Yeast sugar transporters are highly evolved for optimized glucose transport, a major roadblock when it comes to utilizing non-glucose sugars in renewable feedstocks such as lignocellulosic biomass. The AtSWEET7p transporter has been identified for simultaneous transport of glucose and xylose, prevalent in plant cell wall hydrolysates. Here, we replaced endogenous hexose transporters with AtSWEET7 to construct an engineered Saccharomyces cerevisiae capable of multiple sugars with no glucose repression. The resulting strain (NKSW7-1) gained the capacity to simultaneously co-ferment glucose, xylose, mannose, and fructose in a synthetic medium, as well as the sugars in mixtures of bagasse hydrolysate and cane juice. Notably, the replacement of native sugar transporters by AtSWEET7 led to reprogramming of central carbon metabolism, activating glucose-repressed genes even in the presence of substantial amounts of glucose. Continuous culture experiments with the NKSW7-1 strain demonstrated feasibility of AtSWEET7 to disable glucose repression on other hexose or/and pentose sugar uptake. The broad transport capacity of AtSWEET7p can be utilized for achieving co-consumption of all sugars, especially in the case of emerging, underutilized, and renewable substrates.

2024-07-31 | GSE238127 | GEO

Transcriptomes of evolved Pseudomonas putida KT2440 on non-native sugars

Project description:Efficient utilization of lignocellulosic biomass-derived sugars is essential to improve the economics of biorefinery. While Pseudomonas putida is a promising microbial host, its usage is limited because this strain cannot utilize xylose or galactose as a sole carbon source. To address this issue, we heterologously introduced a xylose utilizing gene (xylD) from Caulobacter crescentus and a galactose operon (galETKM) from E. coli MG1655. To improve the utilization further, we evolved the engineered strains in minimal medium conditions. After the evolution, they acquired better fitnesses on the non-native sugars. To understand transcriptional changes after the evolution, the transcriptomes of few evolved isolates were analyzed.

2021-07-15 | GSE155767 | GEO

D-xylose catabolic pathways expressed in Herbaspirillum seropedicae

Project description:Herbaspirillum seropedicae are β-proteobacteria that establish as endophytes in various plants. They are able to consume diverse carbon sources, including hexoses and pentoses like D-xylose. D-xylose catabolism pathways have been described in some microorganisms, but databases of genes involved in these routes are limited. This is of special interest in biotechnology, considering that D-xylose is the second most abundant sugar in nature. Furthermore, it is found in some potential raw materials such as lignocellulosic biomass. In this work we present a study of D-xylose catabolism pathways in H. seropedicae strain Z69, using RNA-seq analysis and the subsequent study of phenotypes determined in targeted mutants in corresponding identified genes. G5B88_22805 gene, designated xylB, encodes a NAD+- dependent D-xylose dehydrogenase. Mutant Z69∆xylB was still able to grow on D-xylose, although at a reduced rate. This is due to expression of an L-arabinose dehydrogenase encoded by G5B88_05250 gene, and was thus able to use D-xylose as substrate. According to our results, H. seropedicae Z69 uses non-phosphorylative pathways to catabolize D-xylose. The lower portion of metabolism involves co-expression of two routes: Weimberg pathway that produces α-ketoglutarate and a novel pathway recently described that produces pyruvate and glycolate. This novel pathway seems to be essential since a mutant in the last step of this pathway, Z69∆G5B88_06410, was unable to grow on D‑xylose.

2021-03-01 | GSE162430 | GEO

Genomic and phenotypic characterization of a refactored xylose utilizing Saccharomyces cerevisiae for lignocellulosic biofuels/biochemicals production

Project description:To understand the mechanisms of enhanced xylose metabolism of XUSE, we reported transcriptome analysis of XUS (rationally engineered strain) and XUSE (evolved XUS strain) grown on xylose by performing RNA-sequencing. Compared with XUS, XUSE showed significantly different gene expression landscape with 463 up-regulated and 675 down-regulated genes (>2-fold, p-value<0.05). While the genes involved in non-oxidative pentose phosphate pathway, such as TKL1, TKL2 and TAL1, were down-regulated in XUSE, it shows the decreased transcriptional patterns of a number of genes encoding TCA cycle and respiratory enzymes. Also, the genes involved in the cellular metal ion regulation and sugar transporters showed significantly changed expression levels in XUSE. This study shows the gene expression landscape of XUSE revealing engineering strategies for the enhanced xylose metabolism in S. cerevisiae.

2018-12-26 | GSE116076 | GEO

iTRAQ experiment on Clostridium strain BOH3

Project description:This study uses iTRAQ based proteomics approach to understand the cellular metabolic machineries present within the Clostridium strain BOH3 (discovered by our group) which can simultaneously utilise both glucose (six carbon sugar) and xylose (five carbon sugar) to produce butanol and riboflavin.

2017-11-30 | PXD005239 | Pride

Project description:5 isolates evolved on xylose

| PRJNA782658 | ENA

Thermoanaerobacter sp. X514 in various carbon sources

Project description:The sugar metabolic mechanism on glucose, xylose, fructose and cellobiose as the sole or dual carbon source by Thermoanaerobacter sp. X514 was characterized by whole genome cDNA micorarrays. In this study, X514 cell grew in difeined medium supplement with different carbohydrates. Each sample was prepared harvested at early-, mid- and late-log phases respectively. Samples were used to acquire expression profiles of total 2322 unique genes, leading to metabolic mechanism construction.

2011-02-01 | E-GEOD-24458 | biostudies-arrayexpress

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