GSE27365
The activity of Rhodopseudomonas palustris p-coumaroyl-homoserine lactone-responsive transcription factor RpaR
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. Overall design: 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.