Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Independent component analysis of E. coli’s transcriptome reveals the cellular processes which respond to heterologous gene expression

ABSTRACT: Heterologous gene expression to expand the native genetic capability of E. coli is the backbone of protein expression and metabolic engineering. The goal of this study was to determine how the identity of the heterologous gene expressed affected the host cell transcriptome. We generated a library of E. coli expressing 46 heterologous genes through an identical rhamnose inducible expression system and perform high throughput RNAseq as well as independent component analysis to elucidate the major variances in the transcriptome. We find that the major variations during heterologous gene expression can be divided into 5 main cellular responses: Fear vs greed, metal homeostasis, respiration, protein folding and amino acid and nucleotide metabolism.

ORGANISM(S): Escherichia coli

PROVIDER: GSE133607 | GEO | 2021/04/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

High throughput ribosome profiling of E. coli expressing a library of heterologous proteins

Project description:Heterologous gene expression to expand the native genetic capability of E. coli is the backbone of protein expression and metabolic engineering. The goal of this study was to determine how the identity of the heterologous gene expressed affected the host cell transcriptome. We generated a library of E. coli expressing 46 heterologous genes through an identical rhamnose inducible expression system and perform high throughput ribosome profiling.

2022-07-07 | GSE134324 | GEO

Adaptive laboratory evolution with heterologous pgi

Project description:We used RNA-seq to profile E. coli K-12 MG1655 strains subjected to adaptive laboratory evolution after knockout of endogenous glucose-6-phosphate isomerase (pgi) and subsequent expression of heterologous version of the pgi gene from Pseudomonas aeruginosa and Bacillus megaterium.

2023-02-09 | GSE224989 | GEO

Maximizing Heterologous Expression of Engineered Type I Polyketide Synthases: Investigating Codon Optimization Strategies

Project description:Type I polyketide synthases (T1PKSs) hold an enormous potential as a rational production platform for the biosynthesis of speciality chemicals. However, despite the great progress in this field, the heterologous expression of PKSs remains a major challenge. One of the first measures to improve heterologous gene expression can be codon optimization. Although controversial, choosing the wrong codon optimization strategy can have detrimental effects on protein and product levels. In this study, we analyzed 11 different codon variants of an engineered T1PKS and investigated in a systematic approach their influence on heterologous expression in Corynebacterium glutamicum, Escherichia coli, and Pseudomonas putida. Our best performing codon variants exhibited a minimum 50-fold increase in PKS protein levels, which also enables the production of an unnatural polyketide in each of the hosts. Furthermore, we developed a free online tool (https://basebuddy.lbl.gov) that offers transparent and highly customizable codon optimization with up-to-date codon usage tables. Here, we not only highlight the significance of codon optimization but also establish the groundwork for high-throughput assembly and characterization of PKS pathways in alternative hosts.

2023-09-01 | PXD042749 | Pride

Optimization of a heterologous pathway for protocatechuate catabolism in Escherichia coli

Project description:Optimization of a heterologous pathway for protocatechuate catabolism in Escherichia coli

2017-05-30 | MSV000081122 | MassIVE

Heterologous expression and detection of Apratoxins in E. coli

Project description:The apratoxin gene cluster was recovered from fosmid DNA library. The gene set responsible for the biosynthesis of the polyketide backbone was introduced in E. coli BAP strain and expressed at 30C for 24 hours. Two sets of control and experimental samples with culture broth pH adjusted at 8 and 12 respectively was extracted with ethyl acetate and dried.

2016-07-28 | ST000446 | MetabolomicsWorkbench

Expression profiling of E. coli expressing the heterologous sigma70 factor (rpoD) of Lactobacillus plantarum

Project description:Time course experiment to analyze transcriptional changes to the E. coli transcriptome due to overexpressing the heterologous sigma70 factor (RpoD) of Lactobacillus plantarum. A plasmid control strain (pControl) and the sigma70 overexpression strain (pLPLσ) were cultivated in parallel and after induction of RpoD expression samples for transcriptional profiling were taken in exponential, transition and stationary phase.

2015-03-18 | GSE66995 | GEO

Transcriptional profiling to elucidate processes regulated by 2',3'-cyclic nucleotide monophosphates in Escherichia coli

Project description:The impact of 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) on global gene expression in E. coli was investigated by heterologous expression of a 2',3'-cyclic nucleotide phosphodiesterase (CNPase), which reduces intracellular 2',3'-cNMP levels.

2021-05-23 | GSE114871 | GEO

Independent component analysis of E. coli’s transcriptome reveals the cellular processes which respond to heterologous gene expression

Project description:Independent component analysis of E. coli’s transcriptome reveals the cellular processes which respond to heterologous gene expression

| PRJNA552039 | ENA

Heterologous Expression of MBP-AtABC1K6-His in E. coli

Project description:Heterologous E. coli expression of AtABC1K6 tagged with maltose binding protein (MBP) and 6xHis tags revealed a spontaneous cleavage event of the recombinant protein during purification. Resulting bands were resolved on SDS-PAGE and excised for MS/MS identification. Mass spec-based identification of the individual bands determined the cleavage event as ocurring after Lysine-443. The results demonstrate that the resulting ca. 80 kD band, showing kinase activity, comprises the AtABC1K6-6xHis fragment lacking the first 71 residues of AtABC1K6.

2022-03-02 | PXD030384 | Pride

L-rhamnose globally changes the transcriptome of planktonic and biofilm Escherichia coli cells and modulates biofilm growth

Project description:L-rhamnose, a naturally abundant sugar, plays diverse biological roles in bacteria, influencing biofilm formation and pathogenesis. This study investigates the global impact of L-rhamnose on the transcriptome and biofilm formation of PHL628 E. coli under various experimental conditions. We compared growth in planktonic and biofilm states in rich (LB) and minimal (M9) media at 28 °C and 37 °C, with varying concentrations of L-rhamnose or D-glucose as a control. Our results reveal that L-rhamnose significantly affects growth kinetics and biofilm formation, particularly reducing biofilm growth in rich media at 37 °C. Transcriptomic analysis through RNA-seq showed that L-rhamnose modulates gene expression differently depending on the temperature and media conditions, promoting a planktonic state by upregulating genes involved in rhamnose transport and metabolism and downregulating genes related to adhesion and biofilm formation. These findings highlight the nuanced role of L-rhamnose in bacterial adaptation and survival, providing insights for potential applications in controlling biofilm-associated infections and industrial biofilm management.

2024-09-17 | GSE274311 | GEO

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