RNase W, a conserved ribonuclease family with a novel active site

• Published in: Nucleic acids research 2024-11, Vol.52 (21), p.13386-13401
• Main Authors: Vayssières, Marlène, Jüttner, Michael, Haas, Karina, Ancelin, Aurélie, Marchfelder, Anita, Leulliot, Nicolas, Ferreira-Cerca, Sébastien, Blaud, Magali
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Archaeal Proteins - chemistry; Archaeal Proteins - genetics; Archaeal Proteins - metabolism; Catalytic Domain; Crystallography, X-Ray; Endoribonucleases - chemistry; Endoribonucleases - genetics; Endoribonucleases - metabolism; Escherichia coli - enzymology; Escherichia coli - genetics; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Life Sciences; Models, Molecular; Protein Domains; Pyrococcus furiosus - enzymology; Pyrococcus furiosus - genetics; Ribonucleases - chemistry; Ribonucleases - genetics; Ribonucleases - metabolism; RNA and RNA-protein complexes
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkae907

Ribosome biogenesis is a complex process requiring multiple precursor ribosomal RNA (rRNA) cleavage steps. In archaea, the full set of ribonucleases (RNases) involved in rRNA processing remains to be discovered. A previous study suggested that FAU-1, a conserved protein containing an RNase G/E-like protein domain fused to a domain of unknown function (DUF402), acts as an RNase in archaea. However, the molecular basis of this activity remained so far elusive. Here, we report two X-ray crystallographic structures of RNase G/E-like-DUF402 hybrid proteins from Pyrococcus furiosus and Sulfolobus acidocaldarius, at 2.1 and 2.0 Å, respectively. The structures highlight a structural homology with the 5' RNA recognition domain of Escherichia coli RNase E but no homology with other known catalytic nuclease domains. Surprisingly, we demonstrate that the C-terminal domain of this hybrid protein, annotated as a putative diphosphatase domain, harbors the RNase activity. Our functional analysis also supports a model by which the RNase G/E-like domain acts as a regulatory subunit of the RNase activity. Finally, in vivo experiments in Haloferax volcanii suggest that this RNase participates in the maturation of pre-16S rRNA. Together, our study defines a new RNase family, which we termed the RNase W family, as the first archaea-specific contributor to archaeal ribosome biogenesis.