The CRM domain: An RNA binding module derived from an ancient ribosome-associated protein

Alice Barkan*, Larik Klipcan, Oren Ostersetzer, Tetsuya Kawamura, Yukari Asakura, Kenneth P. Watkins

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

88 Scopus citations

Abstract

The CRS1-YhbY domain (also called the CRM domain) is represented as a stand-alone protein in Archaea and Bacteria, and in a family of single- and multidomain proteins in plants. The function of this domain is unknown, but structural data and the presence of the domain in several proteins known to interact with RNA have led to the proposal that it binds RNA. Here we describe a phylogenetic analysis of the domain, its incorporation into diverse proteins in plants, and biochemical properties of a prokaryotic and eukaryotic representative of the domain family. We show that a bacterial member of the family, Escherichia coli YhbY, is associated with pre-50S ribosomal subunits, suggesting that YhbY functions in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. We show further that an isolated maize CRM domain has RNA binding activity in vitro, and that a small motif shared with KH RNA binding domains, a conserved "GxxG" loop, contributes to its RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. Published by Cold Spring Harbor Laboratory Press.

Original languageAmerican English
Pages (from-to)55-64
Number of pages10
JournalRNA
Volume13
Issue number1
DOIs
StatePublished - 2007
Externally publishedYes

Keywords

  • CRS1-YhbY
  • Group II intron
  • RNA binding domain
  • Ribosome assembly
  • UPF0044

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