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Series GSE4556 Query DataSets for GSE4556
Status Public on Oct 01, 2006
Title pH and Anaerobiosis Coregulate Metabolism, Multidrug Transporters, and Envelope Composition in Escherichia coli K-12
Platform organism Escherichia coli K-12
Sample organism Escherichia coli
Experiment type Expression profiling by array
Summary In Escherichia coli, pH-dependent gene expression varies with oxygen level. Anaerobic pH-dependent expression ratios were analyzed and compared to the published analysis of aerated cultures (Maurer et al, 2005). E. coli K-12 strain W3110 was cultured in closed tubes containing LBK broth buffered at pH 5.7, pH 7.0, and pH 8.5. Gene expression profiles were obtained by cDNA hybridization to Affymetrix arrays.
pH-dependent expression was seen for 1,394 genes, of which 1,002 show no pH dependence under aeration. Four intergenic regions containing regulatory sRNAs were up-regulated by acid anaerobically (ryeA, csrB, gadY, rybC) and one sRNA (ryhA) by acid with aeration. Acid and anaerobiosis co-regulated the gad regulon; drug transporters (mdtEF, mdtL); catabolism of sugar derivatives whose fermentation minimized acid production; and all hydrogenases (hya, hyb, hyc, hyf, hyp). The hydrogenases however were up-regulated at high pH under aeration (observed by real-time PCR). Acid with anaerobiosis down-regulated penicillin-binding proteins (dacACD, mreBC) and ribosome biosynthesis. Ribosome down-regulation may be caused by restriction of anaerobic metabolism at low pH. A core group of 236 genes showed similar pH response with or without aeration. Core genes up-regulated by acid included fimbriae (fimAC), periplasmic chaperones (hdeAB), cyclopropane fatty acid synthase (cfa), the “constitutive” Na+/H+ antiporter (nhaB), and over thirty unidentified proteins. Core genes at high pH included maltodextrin transport (lamB, malEFGKMPQT), ATP synthase, and DNA repair (recA and mutL).
Overall, pH and anaerobiosis co-regulated metabolism and transport so as to maximize alternative catabolic options while minimizing acidification or alkalinization of the cytoplasm.
Keywords: Steady State
 
Overall design Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH during growth without aeration. The experiment was designed for direct comparison with the pH profile under aerobic conditions reported previously (GSE4511). Non-aerated overnight cultures were diluted 1:1000 and incubated in closed tubes containing potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.7, pH 7.0, and pH 8.5. Tubes were incubated at37°C with slow rotation (8 rpm) to an optical density at 600 nm of 0.2. For each of the three pH conditions, RNA was isolated from five independent cultures. Labeled cDNA was hybridized to Affymetrix antisense arrays according to standard procedures. To analyze the expression levels, Dchip software was used to generate model-based expression indices normalized to sample pH 7 replicate 1. ANOVA was used to identify genes with sitnificant expression differences among the three pH classes (p = 0.001). For genes showing significant differences, the Log2 expression ratios were determined for each pair of pH classes, and significance was determined by Tukey's test (p = 0.001).
 
Contributor(s) Hayes ET, Wilks JC, Yohannes E, Tate DP, Radmacher M, BonDurant SS, Slonczewski JL
Citation(s) 17026754
Submission date Mar 27, 2006
Last update date Mar 16, 2012
Contact name Joan Lyn Slonczewski
E-mail(s) slonczewski@kenyon.edu
Phone 740-427-5397
URL http://biology.kenyon.edu/slonc/slonc.htm
Organization name Kenyon College
Department Biology Dept
Street address 202 N. College Rd
City Gambier
State/province OH
ZIP/Postal code 43022
Country USA
 
Platforms (1)
GPL199 [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array
Samples (15)
GSM101766 Anaerobic pH 5.7 rep1
GSM101767 Anaerobic pH 5.7 rep2
GSM101768 Anaerobic pH 5.7 rep3
Relations
BioProject PRJNA94479

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE4556_RAW.tar 30.7 Mb (http)(custom) TAR (of CEL, EXP)
GSE4556_supp_1.xls 4.9 Mb (ftp)(http) XLS
GSE4556_supp_2.xls 8.7 Mb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data provided as supplementary file

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