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18S rRNA processing requires base pairings of snR30 H/ACA snoRNA to eukaryote-specific 18S sequences.

Fayet-Lebaron E, Atzorn V, Henry Y, Kiss T - EMBO J. (2009)

Bottom Line: Here, we provide biochemical and genetic evidence demonstrating that during pre-rRNA processing, two evolutionarily conserved sequence elements in the 3'-hairpin of snR30 base-pair with short pre-rRNA sequences located in the eukaryote-specific internal region of 18S rRNA.The newly discovered snR30-18S base-pairing interactions are essential for 18S rRNA production and they constitute a complex snoRNA target RNA transient structure that is novel to H/ACA RNAs.We also demonstrate that besides the 18S recognition motifs, the distal part of the 3'-hairpin of snR30 contains an additional snoRNA element that is essential for 18S rRNA processing and that functions most likely as a snoRNP protein-binding site.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, IFR109 CNRS, Université Paul Sabatier, Toulouse, France.

ABSTRACT
The H/ACA RNAs represent an abundant, evolutionarily conserved and functionally diverse class of non-coding RNAs. Many H/ACA RNAs direct pseudouridylation of rRNAs and snRNAs, while members of the rapidly growing group of 'orphan' H/ACA RNAs participate in pre-rRNA processing, telomere synthesis and probably, in other nuclear processes. The yeast snR30 'orphan' H/ACA snoRNA has long been known to function in the nucleolytic processing of 18S rRNA, but its molecular role remained unknown. Here, we provide biochemical and genetic evidence demonstrating that during pre-rRNA processing, two evolutionarily conserved sequence elements in the 3'-hairpin of snR30 base-pair with short pre-rRNA sequences located in the eukaryote-specific internal region of 18S rRNA. The newly discovered snR30-18S base-pairing interactions are essential for 18S rRNA production and they constitute a complex snoRNA target RNA transient structure that is novel to H/ACA RNAs. We also demonstrate that besides the 18S recognition motifs, the distal part of the 3'-hairpin of snR30 contains an additional snoRNA element that is essential for 18S rRNA processing and that functions most likely as a snoRNP protein-binding site.

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A proposed interaction of snR30/U17 with 18S rRNA. (A) A consensus structure for the 3′-terminal hairpins of snR30/U17 snoRNAs. The conserved m1, m2 and box ACA sequences are shown. The bracketed base-pairing interactions are not conserved. (B) Putative base-pairing interactions of snR30/U17 snoRNAs with cognate 18S/17S rRNAs. The m1 and m2 motifs selecting ribosomal rm1 and rm2 sequences are boxed. For sequences of human, S. cerevisiae, S. pombe and T. thermophila snR30/U17 snoRNAs, see Atzorn et al (2004) and references therein. T. brucei snR30 has been reported by Barth et al (2005). Sequences of human (U13369), S. cerevisiae (J01353), S. pombe (X58056), T. thermophila (M10938) and T. brucei (AJ009142) 18S/17S rRNAs are from the GenBank. (C) A schematic representation of the predicted interaction of the 3′-hairpin of snR30/U17 snoRNAs with 18S/17S rRNA sequences. (D) A schematic two-dimensional structure of yeast 18S rRNA. A central domain of 18S that is missing from E. coli 16S rRNA is unfolded (Gutell, 1993). Positions of the rm1 and rm2 sequences are indicated.
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f3: A proposed interaction of snR30/U17 with 18S rRNA. (A) A consensus structure for the 3′-terminal hairpins of snR30/U17 snoRNAs. The conserved m1, m2 and box ACA sequences are shown. The bracketed base-pairing interactions are not conserved. (B) Putative base-pairing interactions of snR30/U17 snoRNAs with cognate 18S/17S rRNAs. The m1 and m2 motifs selecting ribosomal rm1 and rm2 sequences are boxed. For sequences of human, S. cerevisiae, S. pombe and T. thermophila snR30/U17 snoRNAs, see Atzorn et al (2004) and references therein. T. brucei snR30 has been reported by Barth et al (2005). Sequences of human (U13369), S. cerevisiae (J01353), S. pombe (X58056), T. thermophila (M10938) and T. brucei (AJ009142) 18S/17S rRNAs are from the GenBank. (C) A schematic representation of the predicted interaction of the 3′-hairpin of snR30/U17 snoRNAs with 18S/17S rRNA sequences. (D) A schematic two-dimensional structure of yeast 18S rRNA. A central domain of 18S that is missing from E. coli 16S rRNA is unfolded (Gutell, 1993). Positions of the rm1 and rm2 sequences are indicated.

Mentions: We have previously demonstrated that the 3′-hairpin of snR30 contains two evolutionarily conserved sequence motifs, m1 and m2, that are essential for 18S production (Atzorn et al, 2004). A consensus secondary structure accommodating the 3′-hairpins of all known snR30 (U17) snoRNAs is shown in Figure 3A. The unpaired m1 and m2 sequences are located on the opposite strands of an internal loop that is highly reminiscent of the pseudouridylation loop of H/ACA modification guide RNAs. Therefore, we hypothesized that similarly to the antisense elements of pseudouridylation guide RNAs, the m1 and m2 sequences of snR30 function as pre-rRNA-docking sites which base-pair with ribosomal target sequences located between the C646 and A1246 residues of 18S rRNA.


18S rRNA processing requires base pairings of snR30 H/ACA snoRNA to eukaryote-specific 18S sequences.

Fayet-Lebaron E, Atzorn V, Henry Y, Kiss T - EMBO J. (2009)

A proposed interaction of snR30/U17 with 18S rRNA. (A) A consensus structure for the 3′-terminal hairpins of snR30/U17 snoRNAs. The conserved m1, m2 and box ACA sequences are shown. The bracketed base-pairing interactions are not conserved. (B) Putative base-pairing interactions of snR30/U17 snoRNAs with cognate 18S/17S rRNAs. The m1 and m2 motifs selecting ribosomal rm1 and rm2 sequences are boxed. For sequences of human, S. cerevisiae, S. pombe and T. thermophila snR30/U17 snoRNAs, see Atzorn et al (2004) and references therein. T. brucei snR30 has been reported by Barth et al (2005). Sequences of human (U13369), S. cerevisiae (J01353), S. pombe (X58056), T. thermophila (M10938) and T. brucei (AJ009142) 18S/17S rRNAs are from the GenBank. (C) A schematic representation of the predicted interaction of the 3′-hairpin of snR30/U17 snoRNAs with 18S/17S rRNA sequences. (D) A schematic two-dimensional structure of yeast 18S rRNA. A central domain of 18S that is missing from E. coli 16S rRNA is unfolded (Gutell, 1993). Positions of the rm1 and rm2 sequences are indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2664660&req=5

f3: A proposed interaction of snR30/U17 with 18S rRNA. (A) A consensus structure for the 3′-terminal hairpins of snR30/U17 snoRNAs. The conserved m1, m2 and box ACA sequences are shown. The bracketed base-pairing interactions are not conserved. (B) Putative base-pairing interactions of snR30/U17 snoRNAs with cognate 18S/17S rRNAs. The m1 and m2 motifs selecting ribosomal rm1 and rm2 sequences are boxed. For sequences of human, S. cerevisiae, S. pombe and T. thermophila snR30/U17 snoRNAs, see Atzorn et al (2004) and references therein. T. brucei snR30 has been reported by Barth et al (2005). Sequences of human (U13369), S. cerevisiae (J01353), S. pombe (X58056), T. thermophila (M10938) and T. brucei (AJ009142) 18S/17S rRNAs are from the GenBank. (C) A schematic representation of the predicted interaction of the 3′-hairpin of snR30/U17 snoRNAs with 18S/17S rRNA sequences. (D) A schematic two-dimensional structure of yeast 18S rRNA. A central domain of 18S that is missing from E. coli 16S rRNA is unfolded (Gutell, 1993). Positions of the rm1 and rm2 sequences are indicated.
Mentions: We have previously demonstrated that the 3′-hairpin of snR30 contains two evolutionarily conserved sequence motifs, m1 and m2, that are essential for 18S production (Atzorn et al, 2004). A consensus secondary structure accommodating the 3′-hairpins of all known snR30 (U17) snoRNAs is shown in Figure 3A. The unpaired m1 and m2 sequences are located on the opposite strands of an internal loop that is highly reminiscent of the pseudouridylation loop of H/ACA modification guide RNAs. Therefore, we hypothesized that similarly to the antisense elements of pseudouridylation guide RNAs, the m1 and m2 sequences of snR30 function as pre-rRNA-docking sites which base-pair with ribosomal target sequences located between the C646 and A1246 residues of 18S rRNA.

Bottom Line: Here, we provide biochemical and genetic evidence demonstrating that during pre-rRNA processing, two evolutionarily conserved sequence elements in the 3'-hairpin of snR30 base-pair with short pre-rRNA sequences located in the eukaryote-specific internal region of 18S rRNA.The newly discovered snR30-18S base-pairing interactions are essential for 18S rRNA production and they constitute a complex snoRNA target RNA transient structure that is novel to H/ACA RNAs.We also demonstrate that besides the 18S recognition motifs, the distal part of the 3'-hairpin of snR30 contains an additional snoRNA element that is essential for 18S rRNA processing and that functions most likely as a snoRNP protein-binding site.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, IFR109 CNRS, Université Paul Sabatier, Toulouse, France.

ABSTRACT
The H/ACA RNAs represent an abundant, evolutionarily conserved and functionally diverse class of non-coding RNAs. Many H/ACA RNAs direct pseudouridylation of rRNAs and snRNAs, while members of the rapidly growing group of 'orphan' H/ACA RNAs participate in pre-rRNA processing, telomere synthesis and probably, in other nuclear processes. The yeast snR30 'orphan' H/ACA snoRNA has long been known to function in the nucleolytic processing of 18S rRNA, but its molecular role remained unknown. Here, we provide biochemical and genetic evidence demonstrating that during pre-rRNA processing, two evolutionarily conserved sequence elements in the 3'-hairpin of snR30 base-pair with short pre-rRNA sequences located in the eukaryote-specific internal region of 18S rRNA. The newly discovered snR30-18S base-pairing interactions are essential for 18S rRNA production and they constitute a complex snoRNA target RNA transient structure that is novel to H/ACA RNAs. We also demonstrate that besides the 18S recognition motifs, the distal part of the 3'-hairpin of snR30 contains an additional snoRNA element that is essential for 18S rRNA processing and that functions most likely as a snoRNP protein-binding site.

Show MeSH