Functional analyses of bacterial NanoRNase B proteins reveals defining features of this enzyme family

A combination of exoribonucleases and endoribonucleases degrades RNA polymers to recycle nucleoside monophosphates. A byproduct of these reactions is the accumulation of short RNAs, 2-5 nucleotides in length. Characteristic enzymes, generally referred to as nanoRNases, specifically process short RNAs. Genes encoding nanoRNases are essential in some bacteria; therefore, it is assumed that the accumulation of short RNAs is detrimental to cells. However, the substrate preferences and enzymatic mechanisms of the known categories of nanoRNase enzymes have not been equally investigated. The NrnB category of nanoRNases has been particularly understudied. In this study, we identified bacterial NrnB homologs and discovered they can be grouped into three classes of proteins, which can be identified by their characteristic sequence features. Purified representatives of these classes of proteins revealed that they all process RNA substrates from the 3'-terminus. The presence of sequence features at the C-terminus was shown to be diagnostic for general exoribonuclease activity against long RNA substrates, whereas the absence of these C-terminal elements was correlated with proteins that preferentially acted against shorter RNA substrates. Together, these data define members of the overall NrnB family of nanoRNase proteins and identify some of their key features.