The GA motif: An RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs

Two different transcription termination control mechanisms, the T box and S box systems, are used to regulate transcription of many bacterial aminoacy l-tRNA synthetase, amino acid biosynthesis, and amino acid transport genes. Both of these regulatory mechanisms involve an untranslated mRNA leader re gion capable of adopting alternate structural conformations that result in transcription termination or transcription elongation into the downstream r egion. Comparative analyses revealed a small RNA secondary structural eleme nt, designated the GA motif, that is highly conserved in both T box and S b ox leader sequences. The motif consists of two short helices separated by a n asymmetric internal loop, with highly conserved GA dinucleotide sequences on either side of the internal loop. Site-directed mutagenesis of this mot if in model T and S box leader sequences indicated that it is essential for transcriptional regulation in both systems. This motif is similar to the b inding site of yeast ribosomal protein L30, the Snu13p binding sites found in U4 snRNA and box C/D snoRNAs, and two elements in 23S rRNA.