Transcriptomics

Dataset Information

6

Identification of isobutanol response network of E. coli


ABSTRACT: Isobutanol has emerged as a potential biofuel due to recent metabolic engineering efforts. Here we used gene expression and transcription factor(TF)-gene interaction data, genetic knockouts, and Network Component Analysis (NCA) to map the isobutanol response network of Escherichia coli under aerobic conditions. A transcriptional response network consisting of 2004 genes/TFs and 2600 interactions was identified. Through further investigation ArcA, Fur, and PhoB were demonstrated to be important mediators of this response. In addition, the ethanol, n-butanol, and isobutanol response networks were compared in order to identify common and distinct toxicity features associated with these three alcohol based biofuels. E. coli was grown aerobically at 37C in minimal MOPS media with 0.2% glucose as the sole carbon source. At mid-log, the cultures were split in half with one half receiving a 1% isobutanol, 1% n-butanol, or 3% ethanol (vol/vol) treatment, while the other half remained unperturbed. After 10 minutes of continued growth cultures were harvested. Total RNA was purified using a Qiagen RNeasy midikit, and labeled indirectly with amino-allyl dUTP. Every experiment had a minimum of 4 biological replicates, each with 2 technical replicates (8 arrays/experiment). Normalized log10 expression ratios were obtained from lcDNA implemented with quality filtering (receptor.seas.ucla.edu/lcDNA; Hyduke DR, Rohlin L, Kao KC, Liao JC. 2003 A software package for cDNA microarray data normalization and assessing confidence intervals. OMICS 7(3):227-234.)

ORGANISM(S): Escherichia coli  

SUBMITTER: Mark P Brynildsen   James C Liao  Mark Brynildsen 

PROVIDER: E-GEOD-13444 | ArrayExpress | 2009-10-31

SECONDARY ACCESSION(S): GSE13444PRJNA110041

REPOSITORIES: GEO, ArrayExpress

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Publications

An integrated network approach identifies the isobutanol response network of Escherichia coli.

Brynildsen Mark P MP   Liao James C JC  

Molecular systems biology 20090616


Isobutanol has emerged as a potential biofuel due to recent metabolic engineering efforts. Here we used gene expression and transcription network connectivity data, genetic knockouts, and network component analysis (NCA) to map the initial isobutanol response network of Escherichia coli under aerobic conditions. NCA revealed profound perturbations to respiration. Further investigation showed ArcA as an important mediator of this response. Quinone/quinol malfunction was postulated to activate Arc  ...[more]

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