Evolution of Selective RNA Processing and Stabilization operons in cellulosome-harboring Clostridium spp.

In selective RNA processing and stabilization (SRPS) operons, the stoichiometry of encoded proteins is determined by their respective 3-end stem-loops (SLs), yet the evolution of this mechanism remains elusive. In cellulosomal operons of Clostridium spp., we show that the SLs and their associated genes form a monogamy companionship during the operon evolution. Based on {Delta}G of such SLs, we propose CoSLOE (Composite SL-based Operon Evolution) model with evolutionary ratio (ER) >1 or <1 for positive or negative selection of SRPS operons. In the composite SL-{Delta}G-based tree (CoSL-tree) of cellulosomal operons, when traversing from leafs to the root nodes, ERs reveal diversifying/positive selection towards a less efficient cellulosomal system, consistent with glycoside-hydrolase gene variation both in-operon and genome-wide. A similar pattern is followed by the ATPase operon and the majority of orthologous SRPS operons genome-wide, suggesting conservation among operons in such selection. Thus SRPS operons via their transcript-stabilizing non-coding elements are highlighting a link between operon stoichiometry and operon evolution.