Modeling the Thermoproteaceae RNase P RNA

RNA Biol. 2012 Sep;9(9):1155-60. doi: 10.4161/rna.21502. Epub 2012 Sep 1.

Abstract

The RNA component of the RNase P complex is found throughout most branches of the tree of life and is principally responsible for removing the 5' leader sequence from pre-tRNA transcripts during tRNA maturation. RNase P RNA has a number of universal core features, however variations in sequence and structure found in homologs across the tree of life require multiple Rfam covariance search models to detect accurately. We describe a new Rfam search model to enable efficient detection of the diminutive archaeal Type T RNase P RNAs, which are missed by existing Rfam models. Using the new model, we establish effective score detection thresholds, and detect four new RNase P RNA genes in recently completed genomes from the crenarchaeal family Thermoproteaceae.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Archaeal Proteins / chemistry
  • Archaeal Proteins / genetics
  • Archaeal Proteins / metabolism*
  • Models, Molecular*
  • RNA Processing, Post-Transcriptional / physiology
  • RNA, Archaeal / chemistry
  • RNA, Archaeal / genetics
  • RNA, Archaeal / metabolism*
  • RNA, Transfer / genetics
  • RNA, Transfer / metabolism
  • Ribonuclease P / chemistry
  • Ribonuclease P / genetics
  • Ribonuclease P / metabolism*
  • Thermoproteaceae / chemistry
  • Thermoproteaceae / genetics
  • Thermoproteaceae / metabolism*

Substances

  • Archaeal Proteins
  • RNA, Archaeal
  • RNA, Transfer
  • Ribonuclease P