A phylogenetic analysis reveals an unusual sequence conservation within introns involved in RNA editing

Adenosine deaminases that act on RNA (ADARs) are RNA editing enzymes that c onvert adenosines to inosines within cellular and viral RNAs. Certain gluta mate receptor (gluR) pre-mRNAs are substrates for the enzymes in vivo. For example, at the R/G editing site of gluR-B, -C, and -D RNAs, ADARs change a n arginine codon (AGA) to a glycine codon (IGA) so that two protein isoform s can be synthesized from a single encoded mRNA; the highly related gluR-A sequence is not edited at this site. To gain insight into what features of an RNA substrate are important for accurate and efficient editing by an ADA R, we performed a phylogenetic analysis of sequences required for editing a t the R/G site. We observed highly conserved sequences that were shared by gluR-B, -C, and -D, but absent from gluR-A. Surprisingly, in contrast to re sults obtained in phylogenetic analyses of tRNA and rRNA, it was the bases in paired, helical regions whose identity was conserved, whereas bases in n onhelical regions varied, but maintained their nonhelical state. We specula te this pattern in part reflects constraints imposed by ADAR's unique speci ficity and gained support for our hypotheses with mutagenesis studies. Unex pectedly, we observed that some of the gluR introns were conserved beyond t he sequences required for editing. The similar to 600-nt intron 13 of gluR- C was particularly remarkable, showing >94% nucleotide identity between hum an and chicken, organisms estimated to have diverged 310 million years ago.