The ribosome assembly factor Nep1 responsible for Bowen–Conradi syndrome is a pseudouridine-N1-specific methyltransferase

Abstract

Nucleotide modifications are widespread in functionally important classes of cellular RNA molecules including tRNAs, rRNAs and spliceosomal snRNAs ( 1). Presumably, the modifications are important for the proper folding, the stability and the function of these RNAs ( 2). The two most commonly observed modifications in rRNAs are 2′-O-methylations of ribose moieties and the conversion of uridine to pseudouridine but other modifications such as base methylations also exist. Clusters of modified rRNA nucleotides are found in functionally important domains such as rRNA regions associated with the peptidyltransferase center and the decoding center ( 3, 4). Numerous dedicated enzymes acting on one or several specific nucleotides are responsible for the introduction of ribose 2′-O-methyl groups and pseudouridines in prokaryotic rRNA ( 5, 6). In contrast, in eukaryotes and in archaea most 2′-O-methylations and all pseudouridinylations are catalyzed by small nucleolar ribonucleoprotein particles (snoRNPs) consisting of snoRNAs and associated proteins simultaneously with the processing of the 35S rRNA precursor. The snoRNAs act as guides for the snoRNPs to the specific modification sites by virtue of their sequence complementarity with the respective rRNA target sequences ( 7). C/D box snoRNAs in concert with the Nop1 methyltransferase introduce ribose 2′-O-methylations ( 8). H/ACA-box sno-RNAs together with pseudouridine kinase Cbf5 mediate the formation of pseudouridines [for a recent review, see ( 9)]. For other modifications, dedicated enzymes are required that modify specific nucleotides of the rRNA without the participation of snoRNPs ( 10). Examples include the universally conserved Dim1/Ksga methyltransferase responsible for the N6-dimethylations of A1781 and A1782 in 18S rRNA ( 11) and Bud23 catalyzing the N7-methylation of G1575 in 18S rRNA ( 12).