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The CRM domain is a recently recognized RNA binding domain found in three group II intron splicing factors in chloroplasts, in a bacterial protein that associates with ribosome precursors, and in a family of uncharacterized proteins in plants. To elucidate the functional repertoire of proteins with CRM domains, we studied CFM2 (for CRM Family Member 2), which harbors four CRM domains. RNA coimmunoprecipitation assays showed that CFM2 in maize (Zea mays) chloroplasts is associated with the group I intron in pre-trnL-UAA and group II introns in the ndhA and ycf3 pre-mRNAs. T-DNA insertions in the Arabidopsis thaliana ortholog condition a defective-seed phenotype (strong allele) or chlorophyll-deficient seedlings with impaired splicing of the trnL group I intron and the ndhA, ycf3-int1, and clpP-int2 group II introns (weak alleles). CFM2 and two previously described CRM proteins are bound simultaneously to the ndhA and ycf3-int1 introns and act in a nonredundant fashion to promote their splicing. With these findings, CRM domain proteins are implicated in the activities of three classes of catalytic RNA: group I introns, group II introns, and 23S rRNA.
INTRODUCTION
Catalytic ribonucleoprotein particles (RNPs) are at the core of several fundamental cellular processes, including protein synthesis, tRNA processing, and RNA splicing. In some catalytic RNPs, RNA subunits harbor the catalytic activity and proteins serve to enhance the assembly or stability of the catalytically active RNA structure (Weeks, 1997; Ban et al., 2000; Hsieh et al., 2004; Pyle and Lambowitz, 2006). The chloroplast RNA splicing and ribosome maturation (CRM) domain is found in four characterized proteins that assemble with catalytic RNA and was named to reflect the functions of these proteins: CRS1, CAF1, and CAF2, each harboring several CRM domains, are required for the splicing of different group II intron subsets in land plant chloroplasts and are bound to those introns in vivo (Till et al., 2001; Ostheimer et al., 2003); Escherichia coli YhbY is a standalone CRM domain that associates with assembling 50S ribosomal subunits (Barkan et al., 2007). Structural (Ostheimer et al., 2002) and biochemical (Barkan et al., 2007) data showed CRM domains to be RNA binding domains, and one multidomain CRMprotein, CRS1, has been shown to bind RNA in a sequencespecific fashion (Ostersetzer et al., 2005). The Arabidopsis thaliana and rice (Oryza...