Specialized box C/D snoRNPs act as antisense guides to target RNA base acetylation

Abstract

Box C/D snoRNAs are known to guide site-specific ribose methylation of ribosomal RNA. Here, we demonstrate a novel and unexpected role for box C/D snoRNAs in guiding 18S rRNA acetylation in yeast. Our results demonstrate, for the first time, that the acetylation of two cytosine residues in 18S rRNA catalyzed by Kre33 is guided by two orphan box C/D snoRNAs–snR4 and snR45 –not known to be involved in methylation in yeast. We identified Kre33 binding sites on these snoRNAs as well as on the 18S rRNA, and demonstrate that both snR4 and snR45 establish extended bipartite complementarity around the cytosines targeted for acetylation, similar to pseudouridylation pocket formation by the H/ACA snoRNPs. We show that base pairing between these snoRNAs and 18S rRNA requires the putative helicase activity of Kre33, which is also needed to aid early pre-rRNA processing. Compared to yeast, the number of orphan box C/D snoRNAs in higher eukaryotes is much larger and we hypothesize that several of these may be involved in base-modifications.

The emerging role of RNA modifications in the regulation of mRNA stability

“…Knocking out N-acetyltransferase 10 (NAT10) reduces the level of ac 4 C modification on RNA, indicating that NAT10 is a primary ac 4 C writer protein (RNA cytosine acetyltransferase) 101 . In yeast, orphan box C/D snoRNAs specifically guide Kre33 (a yeast homolog of human NAT10) to ac 4 C target sites in rRNA 102 , similar to the way that Ψ is guided by the H/ ACA snoRNAs 85,86 . However, it remains unknown whether human NAT10 also uses box C/D snoRNAs to generate ac 4 C on its target RNAs.…”

A single N1- methyladenosine on the large ribosomal subunit rRNA impacts locally its structure and the translation of key metabolic enzymes

“…Ribosomal RNAs are universally modified and rRNA modifications often cluster in functionally important areas of the ribosome 21,45 . The complete chemical modification repertoire of yeast rRNAs and the cellular machinery responsible for it have recently been described 21,27 placing us in a position to address the putative roles of these chemical modifications in ribosome structure, function and regulation. Here, we have addressed the involvement in translation of a conserved m 1 A modification on the large ribosomal subunit and showed it is important to maintain locally the structure of the subunit with repercussions on the translation of specific transcripts encoding key metabolic enzymes.…”

“…Besides snoRNA-dependent rRNA modifications distinct rRNA base residues are modified by single enzymes 21,22 . The 18S rRNAs of Saccharomyces cerevisiae contain seven base modifications, four base methylations (mN), two base acetylation and one amino-carboxypropylation [23][24][25][26][27] . The complete set of base modified residues has been reported recently (2 m 1 A, 2 m 5 C and 2 m 3 U m 1 acp 3 Ѱ) [28][29][30][31] .…”

Small nucleolar RNAs: continuing identification of novel members and increasing diversity of their molecular mechanisms of action

“…Sharma et al [49] revealed a mechanism by which two orphan yeast box C/D snoRNAs, snR4 and snR45, catalyze the acetylation of two cytosine residues of the 18S rRNA. Both snoRNAs use bipartite complementarity to the 18S rRNA to expose the cytosine to be modified, a mechanism reminiscent of canonical pseudouridylation by box H/ ACA snoRNAs, and the associated enzyme carrying out the acetylation was shown to be Kre33 ( Figure 4E).…”