A phylogenetic view of bacterial ribonucleases

Abstract

A phylogenetic analysis of bacterial genomes shows them to comprise persistent genes, the "paleome" (Greek: palaios, ancient, reminiscent of the origin of life), associated with genes permitting development of life in a particular niche, the "cenome" (from koinos, common, a radical often used in ecology). Most ribonucleases belong to the former, demonstrating their central position in core life processes. These enzymes appear to have often (but not always) evolved through consistent scenarios, generally grouping bacteria into well-defined clades. The evolution of phosphorylases (which salvage energy) is particularly revealing, resulting in diverse complex structures whose function is to degrade RNA. The degradosome of the gamma-Proteobacteria is a paradigm of such complex structures that emphasizes the essential role of energy in degradative processes. The A+T-rich Firmicutes behave in a highly original manner, where many ribonucleases and related proteins coevolve as a group. The recent identification of novel activities in these organisms, stresses the (underestimated) importance of degradation of very short RNAs, as well as 5'-3' degradative processes in Bacteria.