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. 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