Genome-wide maps of primary and processed start-sites of transcripts revealed mechanism controlling in vivo stoichiometry of protein complex in bacteria

Here a differential mRNA-sequencing (dRNA-Seq) strategy was employed to distinguish transcriptional start-sites (TSs) and post-transcriptional processed sites (PSs) of transcripts in the cellulolytic mesophile Clostridium cellulolyticum. PS-harboring genes usually encode heteromultimeric complexes such as flagella, ribosomes, F-type ATPases, and cellulosomes. Intriguingly, PSs located in intergenic reigons (iPSs) were appear to be associated with a particular set of operons that expressed as a complex ratio, in which stem-loops were often found at upstream and/or downstream of highly-expressed processed transcripts; among operons, the folding free energy (deltaG) of the stem-loops is negatively correlated with polarity in transcript level of the operon. Overall design: mRNA profiles of C. cellulolyticum H10 grown under three carbon sources in two RNA treatments were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000