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 264

modification also appears to be important for pre-rRNA processing and rRNA
maturation. Namely, depletion of the yeast H/ACA snoRNA snR35, which guides Y
modification on the hypermodified 1-methyl-3-(3-amino-3-carboxypropyl) Y 1191
residue (M 1 acp 3 Y1191) in 18S rRNA (Brand et al. 1978 ), leads to defective process-
ing of pre-rRNA and a reduction in mature 18S rRNA species (Liang et al. 2009 ) .
Why modification of this residue can have such a substantial effect on 18S rRNA
maturation remains unclear. It seems likely that individual Y modi fi cations at
specific sites on rRNA may affect rRNA maturation by possibly imposing confor-
mational changes on pre-rRNA close to regions where cleavage steps occur. An
additional H/ACA snoRNA, snR30 (U17 in humans), is also implicated in process-
ing of rRNA (Morrissey and Tollervey 1993 ). It has been demonstrated that the
ability of this H/ACA snoRNA to bind pre-rRNA is critical for rRNA processing,
although it still remains unclear whether this specific H/ACA snoRNA participates
in rRNA pseudouridylation.
In light of the fact that rRNA pseudouridylation affects rRNA processing and
maturation, it is not surprising that pseudouridylation of rRNA also impinges on the
production of mature cytoplasmic ribosome subunits. In particular, a point mutation
in Cbf5 at a critical aspartate, D95A, which abolishes rRNA pseudouridylation,
severely impairs the production of ribosome subunits (Zebarjadian et al. 1999 ) . In
addition, depletion of six Y residues within the PTC significantly alters ribosome
profiles in yeast: they contain fewer polysomes and display an altered 60S/80S ratio
compared to wild-type strains, both of which correlate with a reduction in transla-
tion activity (King et al. 2003 ). Collectively, these studies imply that Y residues
and/or clusters of specific Y modifications in functionally important regions of
rRNA play a critical role in ribosome biogenesis and that, when disrupted,
significantly reduce overall rates of protein synthesis.

13.4.2 How Does Pseudouridylation of rRNA Control Gene

Expression?

The contribution of distinct Y residues towards regulating translation has mostly been
investigated in yeast by means of genetic deletion of single H/ACA snoRNAs that
guide modification at a specific uridine residue (Baudin-Baillieu et al. 2009 ; Ganot
et al. 1997 ; Liang et al. 2009 ). Interestingly, these studies demonstrate that in most
cases, loss of individual rRNA modifications have no overall effect on global rates of
protein synthesis; however, combined loss of a number of modifications within specific
regions of the ribosome can significantly diminish overall rates of protein synthesis
(Liang et al. 2009 ). Particularly, loss of Y modifications in the decoding center of the
SSU results in reduced overall translation levels (Liang et al. 2009 ) . For example,
combined loss of the hypermodified M 1 acp 3 Y1191 at the P-site and Y1187 at the
A-site (obtained by depletion of H/ACA snoRNAs snR35 and snR36, respectively)
significantly decreases in vivo incorporation rates of ( 35 S) methionine into total pro-
tein (25 % decrease), as compared to depletion of individual modifications (7 %