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Archaeal fibrillarin (aFib) is a well-characterized  S -adenosyl methionine (SAM)-dependent RNA 2′- O -methyltransferase that is known to act in a large C/D ribonucleoprotein (RNP) complex together with Nop5 and L7Ae proteins and a box C/D guide RNA. In the reaction, the guide RNA serves to direct the methylation reaction to a specific site in tRNA or rRNA by sequence complementarity. Here we show that a  Pyrococcus abyssi  aFib–Nop5 heterodimer can alone perform SAM-dependent 2′- O -methylation of 16S and 23S ribosomal RNAs in vitro independently of L7Ae and C/D guide RNAs. Using tritium-labeling, mass spectrometry, and reverse transcription analysis, we identified three in vitro 2′- O -methylated positions in the 16S rRNA of  P. abyssi , positions lying outside of previously reported pyrococcal C/D RNP methylation sites. This newly discovered stand-alone activity of aFib–Nop5 may provide an example of an ancestral activity retained in enzymes that were recruited to larger complexes during evolution.

Archaeal fibrillarin–Nop5 heterodimer 2′-O-methylates RNA independently of the C/D guide RNP particle