Archaeal β-CASP ribonucleases of the aCPSF1 family are orthologs of the eukaryal CPSF-73 factor

Bacterial RNase J and eukaryal cleavage and polyadenylation specificity factor (CPSF-73) are members of the β-CASP family of ribonucleases involved in mRNA processing and degradation. Here we report an in-depth phylogenomic analysis that delineates aRNase J and archaeal CPSF (aCPSF) as distinct orthologous groups and establishes their repartition in 110 archaeal genomes. The aCPSF1 subgroup, which has been inherited vertically and is strictly conserved, is characterized by an N-terminal extension with two K homology (KH) domains and a C-terminal motif involved in dimerization of the holoenzyme. Pab-aCPSF1 (Pyrococcus abyssi homolog) has an endoribonucleolytic activity that preferentially cleaves at single-stranded CA dinucleotides and a 5′–3′ exoribonucleolytic activity that acts on 5′ monophosphate substrates. These activities are the same as described for the eukaryotic cleavage and polyadenylation factor, CPSF-73, when engaged in the CPSF complex. The N-terminal KH domains are important for endoribonucleolytic cleavage at certain specific sites and the formation of stable high molecular weight ribonucleoprotein complexes. Dimerization of Pab-aCPSF is important for exoribonucleolytic activity and RNA binding. Altogether, our results suggest that aCPSF1 performs an essential function and that an enzyme with similar activities was present in the last common ancestor of Archaea and Eukarya.