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Series GSE7265 Query DataSets for GSE7265
Status Public on Mar 17, 2007
Title Time series analysis of glucose-lactose diauxie: involvement of stringent response
Organism Escherichia coli
Experiment type Expression profiling by array
Summary Guanosine 3 ,5 -bispyrophosphate (ppGpp), also known as ‘‘magic spot,’’ has been shown to bind prokaryotic RNA polymerase to down-regulate ribosome production and increase transcription of amino acid biosynthesis genes during the stringent response to amino acid starvation. Because many environmental growth perturbations cause ppGpp to accumulate, we hypothesize ppGpp to have an overarching role in regulating the genetic program that coordinates transitions between logarithmic growth (feast) and growth arrest (famine). We used the classic glucose-lactose diauxie as an experimental system to investigate the temporal changes in transcription that accompany growth arrest and recovery in wildtype Escherichia coli and in mutants that lack RelA (ppGpp synthetase) and other global regulators, i.e., RpoS and Crp. When cultured on a mixture of glucose and lactose, E. coli grows preferentially on glucose until it is exhausted, resulting in growth arrest while the cells adjust to growth on lactose, i.e., diauxie. Diauxie was delayed in the relA mutant and was accompanied by a 15% decrease in the number of carbon sources used and a 3-fold overall decrease in the induction of RpoS and Crp regulon genes. Thus the data significantly expand the previously known role of ppGpp and support a model wherein the ppGpp-dependent redistribution of RNA polymerase across the genome is the driving force behind control of the stringent response, general stress response, and starvation-induced carbon scavenging. Our conceptual model of diauxie describes these global control circuits as dynamic, interconnected, and dependent upon ppGpp for the efficient temporal coordination of gene expression that programs the cell for transitions between feast and famine.
 
Overall design E. coli MG1655 and isogenic mutants were cultured in a 2 l Biostat B fermentor (B. Braun Biotech International) containing 1 liter of Morpholinepropanesulfonic acid (MOPS) minimal medium with 0.5 g/l of glucose and 1.5 g/l of lactose. The temperature was maintained at 37 ºC and pH was kept constant at 7.2 by the addition of 2 M NaOH. The dissolved oxygen level was maintained above 20% of saturation by adjusting the agitation speeds in the range of 270-500 rpm with fixed 1 l/min air flow.
 
Contributor(s) Traxler MF, Chang D, Conway T, Grissom J
Citation(s) 16467149
Submission date Mar 14, 2007
Last update date Mar 16, 2012
Contact name Joe Grissom
E-mail(s) jgrissom@ou.edu
Phone 405-325-4906
URL http://www.ou.edu/microarray/
Organization name University of Oklahoma
Department Advanced Center for Genome Technology
Lab Conway Lab
Street address 101 David L. Boren Blvd
City Norman
State/province OK
ZIP/Postal code 73019
Country USA
 
Platforms (1)
GPL4995 ConwayLab_Ecoli_6041 features_v1
Samples (136)
GSM175161 WT_tp1_hyb1: 780 min post-inoculation
GSM175162 WT_tp1_hyb2: 780 min post-inoculation
GSM175163 WT_tp1_hyb3: 780 min post-inoculation
Relations
BioProject PRJNA98023

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
GSE7265_RAW.tar 68.4 Mb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table

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