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E-GEOD-27365 - The activity of Rhodopseudomonas palustris p-coumaroyl-homoserine lactone-responsive transcription factor RpaR

Status
Released on 15 May 2011, last updated on 22 August 2013
Organism
Rhodopseudomonas palustris
Samples (6)
Protocols (4)
Description
The Rhodopseudomonas palustris transcriptional regulator RpaR responds to the RpaI-synthesized quorum-sensing signal p-coumaroyl-homoserine lactone (pC-HSL). Other characterized RpaR homologs respond to fatty acyl-HSLs. We show here that RpaR functions as a transcriptional activator, which binds directly to the rpaI promoter. We developed an RNAseq method that does not require a ribosome depletion step to define a set of transcripts regulated by pC-HSL and RpaR. The transcripts include several non-coding RNAs. A footprint analysis showed that purified His-tagged RpaR (His6-RpaR) binds to an inverted repeat element centered 48.5 base pairs upstream of the rpaI transcript start site, which we mapped by S1 nuclease protection and primer extension analyses. Although pC-HSL-RpaR bound to rpaI promoter DNA it did not bind to promoter regions of a number of RpaR-regulated genes not in the rpaI operon. This indicates that RpaR-control of these other genes is indirect. Because the RNAseq analysis allowed us to track transcript strand specificity we discovered that there is pC-HSL-RpaR-activated antisense transcription of rpaR. These data raise the possibility that this antisense RNA or other RpaR-activated non-coding RNAs mediate the indirect activation of genes in the RpaR-controlled regulon. The Rhodopseudomonas palustris p-Coumaroyl-HSL-RpaR regulon as defined by Not-so-random RNASeq. Three sets of comparisons: wt + vs - pC-HSL; wt vs rpaR mutant both + pC-HSL; rpaR + vs - pC-HSL.
Experiment type
RNA-seq of coding RNA 
Contacts
Somsak Phattarasukol <geo@ncbi.nlm.nih.gov>, Caroline S Harwood, E P Greenberg
Citation
Activity of the Rhodopseudomonas palustris p-coumaroyl-homoserine lactone-responsive transcription factor RpaR. Hirakawa H, Oda Y, Phattarasukol S, Armour CD, Castle JC, Raymond CK, Lappala CR, Schaefer AL, Harwood CS, Greenberg EP. , PMID:21378182
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
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