Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Escherichia coli strain:BW25113

ABSTRACT: Genome sequencing data of evolved strains from ALE experiments

PROVIDER: PRJDB6152 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DRR099820_1.fastq.gz	Fastqsanger.gz
	DRR099820_2.fastq.gz	Fastqsanger.gz
	DRR099821_1.fastq.gz	Fastqsanger.gz
	DRR099821_2.fastq.gz	Fastqsanger.gz
	DRR099822_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Autotrophic adaptive laboratory evolution of the acetogen Clostridium autoethanogenum delivers the gas-fermenting strain LAbrini with superior growth, products, and robustness

Project description:Microbes able to convert gaseous one-carbon (C1) waste feedstocks are increasingly important to transition to the sustainable production of renewable chemicals and fuels. Acetogens are interesting biocatalysts since gas fermentation using Clostridium autoethanogenum has been commercialised. However, most acetogen strains need complex nutrients, display slow growth, and are not robust for bioreactor fermentations. In this work, we used three different and independent adaptive laboratory evolution (ALE) strategies to evolve the wild-type C. autoethanogenum to grow faster, without yeast extract and to be robust in operating continuous bioreactor cultures. Multiple evolved strains with improved phenotypes were isolated on minimal media with one strain, named “LAbrini”, exhibiting superior performance regarding the maximum specific growth rate, product profile, and robustness in continuous cultures. Whole-genome sequencing of the evolved strains identified 25 mutations. Of particular interest are two genes that acquired seven different mutations across the three ALE strategies, potentially as a result of convergent evolution. Reverse genetic engineering of mutations in potentially sporulation-related genes CLAU_3129 (spo0A) and CLAU_1957 recovered all three superior features of our ALE strains through triggering significant proteomic rearrangements. This work provides a robust C. autoethanogenum strain “LAbrini” to accelerate phenotyping and genetic engineering and to better understand acetogen metabolism.

2024-06-12 | GSE225123 | GEO

Escherichia coli BW25113

Project description:Evolved pQGS sequencing in E. coli

| PRJNA472665 | ENA

Complete Genome Sequence of Escherichia coli BW25113.

Project description:Escherichia coli BW25113 is the parent strain of the Keio collection comprising nearly 4,000 single-gene deletion mutants. We report the complete 4,631,469-bp genome sequence of this strain and the key variations from the type strain E. coli MG1655.

| S-EPMC4200154 | biostudies-literature

Autotrophic adaptive laboratory evolution of the acetogen Clostridium autoethanogenum delivers the gas-fermenting strain LAbrini with superior growth, products, and robustness

2024-06-12 | PXD047330 | Pride

Escherichia coli strain 8624 and Escherichia coli strain VS94 with signaling molecules

Project description:These E. coli strains were grown with various signaling molecules and the expression profiles were determined. Keywords: addition of quorum and host hormone signals

2007-09-20 | GSE7439 | GEO

Characterization of an Entner-Doudoroff pathway-activated Escherichia coli

Project description:We obtained pfkAB-deleted E. coli K-12 MG1655 strain that can thrive on glucose minimal medium with adaptive laboratory evolution (pfk_ALE-1 strain). Functional analysis of the mutations detected in the pfk_ALE-1 strain was conducted to elucidate the molecular mechanisms underlying the effects of these mutations. We performed transcriptome analysis with RNA-seq to investigate the transcriptomic effects of mutations involved in the glycolytic pathway and global transcriptional regulation. Transcriptomic analysis revealed the expression levels of 4,497 genes on the chromosome of MG1655 and ALE-1 strains.

2022-11-16 | GSE199153 | GEO

Escherichia coli BW25113

Project description:Experimentally evolved lines of Escherichia coli in the brwon winged green bug Plautia stali

| PRJDB5544 | ENA

Expression data from laboratory evolution of Escherichia coli on lactate or glycerol

Project description:Laboratory adaptive evolution experiments were conducted using serial passage of E. coli in M9 minimal medium supplemented with either 2 g/L of lactate for 60 days or 2 g/L of glycerol for 44 days. 7 parallel evolution strains were generated for growth on lactate and 7 parallel evolution strains were generated for growth on glycerol. Affymetrix arrays were used to study the time-course change in gene expression from unevolved E. coli (day 0) to a midpoint evolved strain (day 20) and evolutionary endpoints

2011-10-22 | GSE33147 | GEO

Genome-wide maps of CRP(T168P)-binding change in Escherichia coli W

Project description:Using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolved cells under the selective condition toward the acquisition of genotypes that optimally reallocated cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we determined that spontaneous mutations in the conserved regions of proteins involved in global transcriptional regulation altered the expression of several genes associated with central carbon metabolism. Our study provides a new perspective on adaptive laboratory evolution (ALE) using synthetic biosensors, thereby supporting future efforts in metabolic pathway optimization.

2021-08-23 | GSE162594 | GEO

Transcriptome profiling in an Escherichia coli strain collection

Project description:In order to understand the impact of genetic variants on transcription and ultimately in changes in observed phenotypes we have measured transcript levels in an Escherichia coli strains collection, for which genetic and phenotypic data has also been measured.

2022-03-01 | GSE126081 | 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