Transcriptomics

Dataset Information

29

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


ABSTRACT: 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.

INSTRUMENT(S): Illumina Genome Analyzer II (Rhodopseudomonas palustris)

ORGANISM(S): Rhodopseudomonas palustris  

SUBMITTER: Somsak Phattarasukol 

PROVIDER: GSE27365 | GEO | 2011-05-15

SECONDARY ACCESSION(S): PRJNA137023

REPOSITORIES: GEO

Similar Datasets

2011-05-15 | E-GEOD-27365 | ArrayExpress
2008-07-25 | GSE10642 | GEO
2010-05-25 | E-GEOD-10642 | ArrayExpress
2008-05-07 | E-GEOD-6221 | ArrayExpress
2010-08-15 | E-GEOD-6742 | ArrayExpress
| GSE29310 | GEO
2012-12-12 | PXD000025 | Pride
2014-05-06 | E-GEOD-29310 | ArrayExpress
2014-02-04 | E-GEOD-51825 | ArrayExpress
2012-09-01 | E-GEOD-39025 | ArrayExpress