Abstract
Numerous factors direct eukaryotic ribosome biogenesis, and defects in a single ribosome assembly factor may be lethal or produce tissue-specific human ribosomopathies. Pre-ribosomal RNAs (pre-rRNAs) must be processed stepwise and at the correct subcellular locations to produce the mature rRNAs. Nop9 is a conserved small ribosomal subunit biogenesis factor, essential in yeast. Here we report a 2.1-Å crystal structure of Nop9 and a small-angle X-ray-scattering model of a Nop9:RNA complex that reveals a ‘C'-shaped fold formed from 11 Pumilio repeats. We show that Nop9 recognizes sequence and structural features of the 20S pre-rRNA near the cleavage site of the nuclease, Nob1. We further demonstrate that Nop9 inhibits Nob1 cleavage, the final processing step to produce mature small ribosomal subunit 18S rRNA. Together, our results suggest that Nop9 is critical for timely cleavage of the 20S pre-rRNA. Moreover, the Nop9 structure exemplifies a new class of Pumilio repeat proteins.
Highlights
Numerous factors direct eukaryotic ribosome biogenesis, and defects in a single ribosome assembly factor may be lethal or produce tissue-specific human ribosomopathies
We found that Nop[9] prefers uridine at position 16 in the 50 single-stranded region of the internal transcribed spacer 1 (ITS1) pre-ribosomal RNAs (rRNAs) and U–A or A–U base pairs at the base of the duplex region, suggesting that specific protein:RNA interaction may be focused in this region
Pre-rRNA processing is a multistep process that requires a series of cleavages by endo- and exonucleases to generate mature rRNA transcripts
Summary
Numerous factors direct eukaryotic ribosome biogenesis, and defects in a single ribosome assembly factor may be lethal or produce tissue-specific human ribosomopathies. Pre-ribosomal RNAs (pre-rRNAs) must be processed stepwise and at the correct subcellular locations to produce the mature rRNAs. Nop[9] is a conserved small ribosomal subunit biogenesis factor, essential in yeast. We further demonstrate that Nop[9] inhibits Nob[1] cleavage, the final processing step to produce mature small ribosomal subunit 18S rRNA. Distinct from classical PUFs, Puf-A/Puf[6] subfamily proteins are involved in large ribosomal subunit biogenesis, adopt an L-shaped structure comprising 11 PUM repeats and bind single- or double-stranded nucleic acids without apparent sequence specificity[12,21]. Our results suggest that Nop9’s essential role in SSU ribosome biogenesis is to prevent premature cleavage of the 20S pre-rRNA by Nob[1] in the nucleolus
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