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Series GSE29424 Query DataSets for GSE29424
Status Public on May 24, 2011
Title Functional genomics study of endogenous free fatty acid overproduction in Escherichia coli
Platform organism Escherichia coli K-12
Sample organism Escherichia coli str. K-12 substr. MG1655
Experiment type Expression profiling by array
Summary Comparative analysis of changes in gene and protein expression and fatty acid profiles between Escherichia coli K-12 MG1655 ΔfadD ΔaraBAD expressing an acyl-acyl carrier protein thioesterase from Umbellularia californica (BTE) or a non-functional mutant thioesterase (BTE-H204A) to determine the functional basis for losses in cell viability, membrane integrity, or other stresses and metabolic perturbations that may be present. New hypotheses obtained from the study will assist in metabolic engineering efforts of improved strains exhibiting higher fatty acid yields and productivities.
 
Overall design Cultures of fatty acid overproducing (BTE-expressing) and negative control (non-functional BTE-H204A-expressing) strains of Escherichia coli K-12 MG1655 delta-fadD delta-araBAD (deficient in beta-oxidation and L-arabinose catabolism) were sampled under two different sets of media/induction/antibiotic conditions. These conditions were shake flasks at 37C, 250 rpm shaking, in EZ rich defined medium supplemented with 0.2% glucose and 0.01 mM biotin (EZglu), and in fermentors at 37C with controlled air sparging, agitation, and pH in EZ rich defined medium supplemented with 0.4% glycerol and 0.01 mM biotin (EZgly). Two strains were analyzed in the EZglu experiment, the background strain harboring either pTrc99A-BTE (fatty acid overproducing) or pTrc99A-BTE-H204A (control phenotype). Three strains were analyzed in the EZgly experiment, with the background strain haboring either pBAD35-BTE and pBAD33 (fatty acid overproducing), pBAD35-BTE and pBAD33-ACC (fatty acid overproducing, ACC are the 4 subunits of E. coli K-12 acetyl-CoA carboxylase expressed as an artificial operon accDABC in plasmid pBAD33), and pBAD35-BTE-H204A and pBAD33 (control phenotype). RNA was extracted from harvested cell pellets from biological triplicates (EZglu) or biological duplicates (EZgly) of each strain at three different sampling times as defined in each sample description. Due to a hybridization or scanning problem, biological duplicates rather than triplicates were analyzed at the mid-stationary phase sampling point in the EZglu experiment for the control strain harboring pTrc99A-BTE-H204A. Multiple technical replicates at either the hybridization or sample level were analyzed from the biological duplicates of the fermentor experiment. The form of technical replicate (sample or hybridization) is specified in each EZgly sample description.
 
Contributor(s) Lennen RM, Kruziki MA, Kumar K, Zinkel R, Burnum KE, Lipton MS, Hoover SW, Ranatunga DR, Wittkopp TM, Marner WD, Pfleger BF
Citation(s) 21948837
Submission date May 20, 2011
Last update date Jun 27, 2014
Contact name Rebecca Lennen
E-mail(s) lennen@wisc.edu
Organization name University of Wisconsin-Madison
Department Chemical and Biological Engineering
Street address 1415 Engineering Drive
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
 
Platforms (1)
GPL13634 UW-Escherichia_coli_K12-4x72k-v1.0 [090224_EcoK12_Zmob_expr]
Samples (42)
GSM727615 E_coli_RL08_pTrc99aBTEH204A-EZ_glucose_midlog-rep1
GSM727616 E_coli_RL08_pTrc99aBTEH204A-EZ_glucose_midlog-rep2
GSM727617 E_coli_RL08_pTrc99aBTEH204A-EZ_glucose_midlog-rep3
Relations
BioProject PRJNA141611

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE29424_RAW.tar 46.5 Mb (http)(custom) TAR (of PAIR)
Processed data included within Sample table
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