Predicting Selective RNA Processing and Stabilization Operons in spp.

In selective RNA processing and stabilization (SRPS) operons, stem-loops (SLs) located at the 3'-UTR region of selected genes can control the stability of the corresponding transcripts and determine the stoichiometry of the operon. Here, for such operons, we developed a computational approach named SLOFE (stem-loop free energy) that identifies the SRPS operons and predicts their transcript- and protein-level stoichiometry at the whole-genome scale using only the genome sequence the minimum free energy (Δ) of specific SLs in the intergenic regions within operons. As validated by the experimental approach of differential RNA-Seq, SLOFE identifies genome-wide SRPS operons in with 80% accuracy and reveals that the SRPS mechanism contributes to diverse cellular activities. Moreover, in the identified SRPS operons, SLOFE predicts the transcript- and protein-level stoichiometry, including those encoding cellulosome complexes, ATP synthases, ABC transporter family proteins, and ribosomal proteins. Its accuracy exceeds those of existing approaches in , , , and . The ability to identify genome-wide SRPS operons and predict their stoichiometry DNA sequence should facilitate studying the function and evolution of SRPS operons in bacteria.