The box C/D sRNP dimeric architecture is conserved across domain Archaea

RNA. 2012 Aug;18(8):1527-40. doi: 10.1261/rna.033134.112. Epub 2012 Jun 29.

Abstract

Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze RNA-guided 2'-O-ribose methylation in two of the three domains of life. Recent structural studies have led to a controversy over whether box C/D sRNPs functionally assemble as monomeric or dimeric macromolecules. The archaeal box C/D sRNP from Methanococcus jannaschii (Mj) has been shown by glycerol gradient sedimentation, gel filtration chromatography, native gel analysis, and single-particle electron microscopy (EM) to adopt a di-sRNP architecture, containing four copies of each box C/D core protein and two copies of the Mj sR8 sRNA. Subsequently, investigators used a two-stranded artificial guide sRNA, CD45, to assemble a box C/D sRNP from Sulfolobus solfataricus with a short RNA methylation substrate, yielding a crystal structure of a mono-sRNP. To more closely examine box C/D sRNP architecture, we investigate the role of the omnipresent sRNA loop as a structural determinant of sRNP assembly. We show through sRNA mutagenesis, native gel electrophoresis, and single-particle EM that a di-sRNP is the near exclusive architecture obtained when reconstituting box C/D sRNPs with natural or artificial sRNAs containing an internal loop. Our results span three distantly related archaeal species--Sulfolobus solfataricus, Pyrococcus abyssi, and Archaeoglobus fulgidus--indicating that the di-sRNP architecture is broadly conserved across the entire archaeal domain.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Archaea / classification
  • Archaea / genetics
  • Archaea / metabolism*
  • Archaeal Proteins / chemistry*
  • Archaeal Proteins / genetics
  • Archaeal Proteins / metabolism*
  • Base Sequence
  • Methylation
  • Molecular Sequence Data
  • Mutagenesis
  • Protein Binding
  • Protein Conformation
  • Protein Multimerization
  • RNA, Archaeal / genetics
  • RNA, Archaeal / metabolism*
  • RNA, Small Nucleolar / genetics
  • RNA, Small Nucleolar / metabolism*
  • Ribonucleoproteins, Small Nucleolar / chemistry*
  • Ribonucleoproteins, Small Nucleolar / genetics
  • Ribonucleoproteins, Small Nucleolar / metabolism*

Substances

  • Archaeal Proteins
  • RNA, Archaeal
  • RNA, Small Nucleolar
  • Ribonucleoproteins, Small Nucleolar