High-throughput detection of RNA processing in bacteria

• DOI: 10.1186/s12864-018-4538-8
• Publication Date: 2018-04-03T22:24:21Z
• Authors: Erin E. Gill; Luisa S. Chan; Geoffrey L. Winsor; Neil Dobson; Raymond Lo; Shannan J. Ho Sui; Bhavjinder K. Dhi...; Patrick K. Taylor; Raunak Shrestha; Cory Spencer; Robert E. W. Hancock; Peter J. Unrau; Fiona S. L. Brinkman
• Keywords: Nucleases; Sequence Analysis, RNA; pRNA-Seq; Chromosome Mapping; High-Throughput Nucleotide Sequencing; 612; QH426-470; Gene regulation; RNA, Bacterial; RNA processing; dRNA-Seq; Pseudomonas aeruginosa; Genetics; RNA-Seq; Gene expression; RNA Processing, Post-Transcriptional; Transcription Initiation Site; Promoter Regions, Genetic; Transcription; TP248.13-248.65; Genome, Bacterial; Biotechnology; Research Article

Understanding the RNA processing of an organism's transcriptome is essential but challenging step in understanding its biology. Here we investigate with unprecedented detail Pseudomonas aeruginosa PAO1, a medically important and innately multi-drug resistant bacterium. We systematically mapped cleavage dephosphorylation sites that result 5′-monophosphate terminated (pRNA) using monophosphate RNA-Seq (pRNA-Seq). Transcriptional start (TSS) were also differential (dRNA-Seq) both datasets compared to conventional performed variety growth conditions. The pRNA-Seq library revealed known tRNA, rRNA transfer-messenger (tmRNA) sites, together previously uncharacterized events found disproportionately near 5′ ends transcripts associated basic bacterial functions such as oxidative phosphorylation purine metabolism. majority (97%) processed mRNAs cleaved at precise codon positions within defined sequence motifs indicative distinct endonucleolytic activities. most abundant these corresponded closely E. coli RNase E site established vitro. Using dRNA-Seq library, operon analysis predicted 3159 potential TSS. A correlation uncovered 105 antiparallel pairs TSS separated by 18 bp from each other centered on single palindromic TAT(A/T)ATA (likely − 10 promoter elements), suggesting that, consistent previous vitro experimentation, can initiate transcription bi-directionally may thus provide novel form transcriptional regulation. allowed us confirm expression small non-coding RNAs (ncRNAs), many which are differentially expressed swarming biofilm formation This study uses pRNA-Seq, method provides genome-wide survey processing, bacterium discover extensive transcript not appreciated. have gained insight into maturation turnover well NOTE: All data has been submitted NCBI read archive. Accession numbers follows: [NCBI archive: SRX156386, SRX157659, SRX157660, SRX157661, SRX157683 SRX158075]. viewable Jbrowse www.pseudomonas.com .