FORMATION OF THE 5' END PSEUDOKNOT IN SMALL-SUBUNIT RIBOSOMAL-RNA - INVOLVEMENT OF U3-LIKE SEQUENCES

Hughes (1996, J Mol Biol 259:645-654) proposed that the box A region o f U3 snoRNA interacts by complementary base pairing with small subunit (ss) rRNA sequences within precursor (pre-) rRNA and through rearrang ement and displacement mediates the formation of the universally conse rved 5' end pseudoknot. We wondered how this conserved pseudoknot migh t be formed in the ss rRNAs of archaeal and bacterial organisms that l ack a U3 RNA. In examining the 5' external transcribed spacer (5' ETS) region in pre-rRNA transcripts from some of these organisms, we noted the presence of U3 box A-like sequences. By analogy with the U3-ss rR NA intermolecular interaction, we suggest that the box A-like 5' ETS s equence interacts through intramolecular complementary base pairing wi th the 5' end pseudoknot sequences within pre-rRNA; rearrangement of t his structure mediates the formation of the conserved 5' end pseudokno t. If correct, this means that some of the pre-rRNA maturation-folding functions provided in trans by snoRNAs in eukaryotic organisms may be provided in cis by the spacer sequences in pre-rRNA transcripts in so me bacterial or archaeal organisms lacking snoRNAs.