The “Fifth” RNA Nucleotide: A Role for Ribosomal RNA Pseudouridylation in Control of Gene Expression at the Translational Level - Biophysical Approaches to Translational Control of Gene Expression - page 257

13.3.1.3 Orphan H/ACA SnoRNAs

In addition to the H/ACA snoRNAs implicated in the modification of rRNA, recent
genomic surveys have also identified a large number of “orphan” H/ACA snoRNA
genes, so-called because their putative target residues have not been identified
(Huttenhofer et al. 2001 ; Vitali et al. 2003 ). While it still remains to be determined
if orphan H/ACA snoRNAs are implicated in RNA pseudouridylation, a recent
study in yeast demonstrated that pseudouridylation of spliceosomal snRNA by H/
ACA scaRNAs can be induced at sites of imperfect sequence identity (Wu et al.
2011 ). This finding opens the possibility that orphan H/ACA snoRNAs (in addition
to H/ACA snoRNAs with assigned target residues) may contribute to the modification
of specific uridine residues by imperfect sequence complementarity. It can also be
envisioned that noncanonical substrate RNAs, such as mRNAs, may be targets of
H/ACA snoRNPs containing orphan H/ACA snoRNAs. Orphan H/ACA snoRNAs
may also have additional substrates/roles that are not implicated in RNA
modifications, as recent computational analyses suggest that several orphan H/ACA
snoRNAs may function as long precursor forms of microRNAs (miRNAs) (Scott
et al. 2009 ). However, whether orphan H/ACA snoRNAs are precursors of func-
tional miRNAs in vivo remains to be explored.
Overall, it is clear that H/ACA snoRNAs are highly specialized RNA elements
that modulate pseudouridylation at specific sites on rRNA. Concurrent to research
centered on investigating the RNA component of the H/ACA snoRNP, several struc-
tural and functional insights into the protein components of this complex have
already greatly aided our current understanding of rRNA pseudouridylation in
eukaryotic cells and will be discussed in the following sections.

13.3.2 H/ACA SnoRNP Complex Protein Components

13.3.2.1 Cbf5 (Dyskerin in Mammals)

Cbf5 was originally identified in yeast as an essential centromere-binding protein
based on its sequence homology to microtubule-binding components (Jiang et al.
1993 ) and was later demonstrated to be the Y synthase responsible for catalyzing
the pseudouridylation of rRNA (Lafontaine et al. 1998 ; Watkins et al. 1998 ) . In line
with findings in the bacterial truB Y synthase, an aspartate at amino acid position
95 of Cbf5 is essential for its pseudouridylation activity (Zebarjadian et al. 1999 ) .
Several biochemical analyses in eukaryotes reveal that Cbf5 associates with three
core binding partners, Nhp2 (NHP2 in humans), Nop10 (NOP10 in humans), and
Gar1 (hGAR1 in humans), which altogether constitute the protein component of the
box H/ACA snoRNP (Henras et al. 2004 ; Pogacic et al. 2000 ; Watkins et al. 1998 ;
Yang et al. 2000 ). Importantly, the presence of a conserved RNA-binding domain
(PUA domain) within Cbf5 is critical for its ability to bind H/ACA snoRNAs
(Fig. 13.3 ) (Li and Ye 2006 ; Rashid et al. 2006 ) and additional studies suggest an