Genome-wide search for yeast RNase P substrates reveals role in maturation of intron-encoded box C/D small nucleolar RNAs

Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12218-23. doi: 10.1073/pnas.0801906105. Epub 2008 Aug 19.

Abstract

Ribonuclease P (RNase P) is an essential endonuclease responsible for the 5'-end maturation of precursor tRNAs. Bacterial RNase P also processes precursor 4.5S RNA, tmRNA, 30S preribosomal RNA, and several reported protein-coding RNAs. Eukaryotic nuclear RNase P is far more complex than in the bacterial form, employing multiple essential protein subunits in addition to the catalytic RNA subunit. RNomic studies have shown that RNase P binds other RNAs in addition to tRNAs, but no non-tRNA substrates have previously been identified. Additional substrates were identified by using a multipronged approach in the budding yeast Saccharomyces cerevisiae. First, RNase P-dependant changes in RNA abundance were examined on whole-genome microarrays by using strains containing temperature sensitive (TS) mutations in two of the essential RNase P subunits, Pop1p and Rpr1r. Second, RNase P was rapidly affinity-purified, and copurified RNAs were identified by using a genome-wide microarray. Third, to identify RNAs that do not change abundance when RNase P is depleted but accumulate as larger precursors, >80 potential small RNA substrates were probed directly by Northern blot analysis with RNA from the RNase P TS mutants. Numerous potential substrates were identified, of which we characterized the box C/D intron-encoded small nucleolar RNAs (snoRNAs), because these both copurify with RNase P and accumulate larger forms in the RNase P temperature-sensitive mutants. It was previously known that two pathways existed for excising these snoRNAs, one using the pre-mRNA splicing path and the other that was independent of splicing. RNase P appears to participate in the splicing-independent path for the box C/D intron-encoded snoRNAs.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Genome, Fungal*
  • Mutation
  • Oligonucleotide Array Sequence Analysis
  • RNA Splicing
  • RNA, Small Nucleolar / metabolism*
  • Ribonuclease P / genetics
  • Ribonuclease P / metabolism*
  • Saccharomyces cerevisiae / genetics

Substances

  • RNA, Small Nucleolar
  • Ribonuclease P

Associated data

  • GEO/GSE10514