The Mrs1 splicing factor binds the bI3 group I intron at each of two tetraloop-receptor motifs

PLoS One. 2010 Feb 1;5(2):e8983. doi: 10.1371/journal.pone.0008983.


Most large ribozymes require protein cofactors in order to function efficiently. The yeast mitochondrial bI3 group I intron requires two proteins for efficient splicing, Mrs1 and the bI3 maturase. Mrs1 has evolved from DNA junction resolvases to function as an RNA cofactor for at least two group I introns; however, the RNA binding site and the mechanism by which Mrs1 facilitates splicing were unknown. Here we use high-throughput RNA structure analysis to show that Mrs1 binds a ubiquitous RNA tertiary structure motif, the GNRA tetraloop-receptor interaction, at two sites in the bI3 RNA. Mrs1 also interacts at similar tetraloop-receptor elements, as well as other structures, in the self-folding Azoarcus group I intron and in the RNase P enzyme. Thus, Mrs1 recognizes general features found in the tetraloop-receptor motif. Identification of the two Mrs1 binding sites now makes it possible to create a model of the complete six-component bI3 ribonucleoprotein. All protein cofactors bind at the periphery of the RNA such that every long-range RNA tertiary interaction is stabilized by protein binding, involving either Mrs1 or the bI3 maturase. This work emphasizes the strong evolutionary pressure to bolster RNA tertiary structure with RNA-binding interactions as seen in the ribosome, spliceosome, and other large RNA machines.

Publication types

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

MeSH terms

  • Azoarcus / genetics
  • Base Sequence
  • Binding Sites
  • Endoribonucleases / genetics*
  • Introns / genetics*
  • Mitochondrial Proteins / genetics
  • Mitochondrial Proteins / metabolism*
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Nucleotidyltransferases / genetics*
  • Protein Binding
  • Protein Conformation
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism
  • RNA, Fungal / chemistry
  • RNA, Fungal / genetics
  • RNA, Fungal / metabolism
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*
  • Ribonuclease P / genetics
  • Ribonucleoproteins / chemistry
  • Ribonucleoproteins / metabolism
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*


  • MRS1 protein, S cerevisiae
  • Mitochondrial Proteins
  • RNA, Bacterial
  • RNA, Fungal
  • RNA-Binding Proteins
  • Ribonucleoproteins
  • Saccharomyces cerevisiae Proteins
  • Nucleotidyltransferases
  • mRNA maturase
  • Endoribonucleases
  • Ribonuclease P