RNase R in Haloferax volcanii
Ribonucleases (RNases) are central to RNA metabolism, driving transcript processing, maturation, and degradation. In archaea, RNA degradation integrates bacterial and eukaryotic-like pathways, with most archaea relying on exosome complexes for RNA turnover. However, halophilic archaea, including Haloferax volcanii, lack exosome subunits and encode homologs of the bacterial RNase R instead. Previously reported to be essential and the primary 3'-5' exoribonuclease in this biological system, the precise function and substrate specificity of RNase R in H. volcanii remain unclear. To unravel its function and RNA substrates, we successfully generated an H. volcanii RNase R deletion strain (?rnr) and found that its absence had only mild effects on cellular adaptability. Using long-read RNA sequencing, we performed transcriptome-wide mapping of RNA degradation, end-processing, and rRNA maturation. While RNase R deletion had minimal effects on mRNA stability, it led to a substantial accumulation of late 16S rRNA precursors, suggesting a defined role in rRNA processing rather than general RNA turnover. These findings contrast with those observed for bacterial RNase R, which is more broadly involved in mRNA degradation.  Using full-length RNA sequencing, our study highlights the evolutionary divergence of ribonuclease function and uncovers unexpected nuances in archaeal RNA metabolism.