The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase

Nucleic Acids Res. 2010 Apr;38(7):2387-98. doi: 10.1093/nar/gkp1189. Epub 2010 Jan 4.


Nep1 (Emg1) is a highly conserved nucleolar protein with an essential function in ribosome biogenesis. A mutation in the human Nep1 homolog causes Bowen-Conradi syndrome-a severe developmental disorder. Structures of Nep1 revealed a dimer with a fold similar to the SPOUT-class of RNA-methyltransferases suggesting that Nep1 acts as a methyltransferase in ribosome biogenesis. The target for this putative methyltransferase activity has not been identified yet. We characterized the RNA-binding specificity of Methanocaldococcus jannaschii Nep1 by fluorescence- and NMR-spectroscopy as well as by yeast three-hybrid screening. Nep1 binds with high affinity to short RNA oligonucleotides corresponding to nt 910-921 of M. jannaschii 16S rRNA through a highly conserved basic surface cleft along the dimer interface. Nep1 only methylates RNAs containing a pseudouridine at a position corresponding to a previously identified hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) in eukaryotic 18S rRNAs. Analysis of the methylated nucleoside by MALDI-mass spectrometry, HPLC and NMR shows that the methyl group is transferred to the N1 of the pseudouridine. Thus, Nep1 is the first identified example of an N1-specific pseudouridine methyltransferase. This enzymatic activity is also conserved in human Nep1 suggesting that Nep1 is the methyltransferase in the biosynthesis of m1acp3-Psi in eukaryotic 18S rRNAs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Archaeal Proteins / chemistry*
  • Archaeal Proteins / metabolism
  • Base Sequence
  • Binding Sites
  • Consensus Sequence
  • Humans
  • Methanococcales / enzymology*
  • Methanococcales / genetics
  • Methylation
  • Methyltransferases / chemistry*
  • Methyltransferases / metabolism
  • Nuclear Magnetic Resonance, Biomolecular
  • Nuclear Proteins / chemistry*
  • Nuclear Proteins / metabolism
  • Pseudouridine / analogs & derivatives
  • Pseudouridine / analysis
  • Pseudouridine / metabolism*
  • RNA, Fungal / chemistry
  • RNA, Fungal / metabolism
  • RNA, Ribosomal / chemistry
  • RNA, Ribosomal / metabolism*
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / metabolism
  • Spectrometry, Fluorescence
  • Two-Hybrid System Techniques


  • Archaeal Proteins
  • Nuclear Proteins
  • RNA, Fungal
  • RNA, Ribosomal
  • RNA-Binding Proteins
  • 1-methylpseudouridine
  • Pseudouridine
  • EMG1 protein, human
  • Methyltransferases