Site-Specific Pseudouridine Formation in Preribosomal RNA Is Guided by Small Nucleolar RNAs

Abstract

During the nucleolar maturation of eukaryotic ribosomal RNAs, many selected uridines are converted into pseudouridine by a thus far undefined mechanism. The nucleolus contains a large number of small RNAs (snoRNAs) that share two conserved sequence elements, box H and ACA. In this study, we demonstrate that site-specific pseudouridylation of rRNAs relies on short ribosomal signal sequences that are complementary to sequences in box H/ACA snoRNAs. Genetic depletion and reconstitution studies on yeast snR5 and snR36 snoRNAs demonstrate that box H/ACA snoRNAs function as guide RNAs in rRNA pseudouridylation. These results define a novel function for snoRNAs and further reinforce the idea that base pairing is the most common way to obtain specific substrate-"enzyme" interactions during rRNA maturation.

High-throughput sequencing reveals circular substrates for an archaeal RNA ligase

“…However, we stress that thermal protection of small non-coding RNAs does not alone explain the functional importance of RNA circularization, as e.g., circular pseudouridylation guides carrying H/ ACA motifs have not been reported to exist in archaea. The so called "H and ACA motifs" of these guides are obligatory found in single-stranded extremities of pseudouridylation guides, 32,33 thus likely disfavoring intramolecular ligation.…”

Pseudouridines in spliceosomal snRNAs

“…In the 1990s, though, a major breakthrough occurred when a large number of box H/ACA guide RNAs were found to direct rRNA pseudouridylation (Balakin et al, 1996;Ganot et al, 1997;Ni et al, 1997;Smith and Steitz, 1997;Yu et al, 2005). …”

“…5). In 1997, both the Fournier and the Kiss groups demonstrated experimentally that, indeed, rRNA pseudouridylation is guided by box H/ACA RNA (Ganot et al, 1997;Ni et al, 1997). In this RNA-guided scheme, the box H/ACA RNA folds into what is known as a "hairpin-hinge-hairpin-tail" structure, leaving an internal loop open in each hairpin.…”

“…Instead, they associate with proteins to form RNA-protein complexes known as box H/ACA RNPs ). Specifically, the box H/ACA RNPs are composed of a unique box H/ACA RNA and four core proteins [Cbf5 (dyskerin/ NAP57), Nhp2, Gar1, and Nop10] (Meier and Blobel, 1994;Balakin et al, 1996;Ganot et al, 1997;Ni et al, 1997;Yu et al, 2005;Grozdanov and Meier, 2009). Cbf5 is the enzymatic component of the RNP that catalyzes, upon positioning of the target uridine, the U-to-Ψ isomerization reaction (Zebarjadian et al, 1999;Grozdanov and Meier, 2009) (Fig.…”

“…About 15 years ago, though, several laboratories began to turn their attention to the mechanisms and functions of these modifications in spliceosomal snRNAs and rRNAs (Bachellerie et al, 1995;Cavaillé et al, 1996;KissLászló et al, 1996;Tycowski et al, 1996;Ganot et al, 1997;Ni et al, 1997;Smith and Steitz, 1997;Tycowski et al, 1998;Yu et al, 1998;Lowe and Eddy, 1999). Multiple effective assays and systems have since been developed for RNA modification research [reviewed in (Wu et al, 2011b)].…”