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Series GSE3105 Query DataSets for GSE3105
Status Public on Aug 31, 2005
Title Effect of small RNA RyhB on global iron use in Escherichia coli
Platform organism Escherichia coli K-12
Sample organism Escherichia coli
Experiment type Expression profiling by array
Summary RyhB is a non-coding RNA regulated by the Fur repressor. It has previously been shown to cause the rapid degradation of a number of mRNAs that encode proteins that utilize iron. Here we examine the effect of ectopic RyhB production on global gene expression by microarray analysis. Many of the previously identified targets were found, as well as other mRNAs encoding iron-binding proteins, bringing the total number of regulated operons to at least 18, encoding 56 genes. The two major operons involved in Fe-S cluster assembly showed different behavior; the isc operon appears to be a direct target of RyhB action, while the suf operon does not. This is consistent with previous findings suggesting that the suf genes but not the isc genes are important for Fe-S cluster synthesis under iron-limiting conditions, presumably for essential iron-binding proteins. In addition, we observed repression of Fur-regulated genes upon RyhB expression, interpreted as due to intracellular iron-sparing resulting from reduced synthesis of iron-binding proteins. Our results demonstrate the broad effects of a single non-coding RNA on iron homeostasis.
Keywords: RNA degradation, iron stavation, RyhB small RNA, iron-using proteins
Overall design Derivatives of MG1655 carrying either pBAD-ryhB or the control vector pNM12 were used in all experiments.
The strains used contain the (delta)ara714 allele to prevent catabolism of arabinose and the (delta)ryhB::cat allele to restrict RyhB expression to the inducible pBAD-ryhB vector.
Overnight bacterial cultures were incubated in LB media with ampicillin at a final concentration of 50 ug/mL at 37oC and diluted 1000-fold into 50 mL of fresh LB-ampicillin media at 37oC with agitation. To induce RyhB expression, cultures carrying the pBAD-ryhB construct were grown to an O.D.600 of 0.5 and arabinose was added to the culture at a final concentration of 0.1%. In some experiments, 50 uM FeSO4 was added to the new culture after dilution from overnight culture. Total RNA was extracted from cells at the indicated time using the hot phenol procedure.
Contributor(s) Massé E, Vanderpool CK, Gottesman S
Citation(s) 16199566
Submission date Aug 10, 2005
Last update date Mar 16, 2012
Contact name Eric Masse
Organization name Universite de Sherbrooke
Department Biochemistry
Lab Eric Masse
Street address 3001 12e Avenue
City Sherbrooke
State/province Quebec
ZIP/Postal code J1H 5N4
Country Canada
Platforms (1)
GPL199 [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array
Samples (12)
GSM67647 wild-type pBAD-ryhB#1 + arabinose
GSM67648 wild-type pBAD-ryhB #2 + arabinose
GSM67651 wild-type pNM12#1 +arabinose
BioProject PRJNA93109

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