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 of U3 snoRNA interacts by complementary base pairing with small subunit (ss) rRNA sequences within precursor (pre-) rRNA and through rearrangement and displacement mediates the formation of the universally conserved 5' end pseudoknot. We wondered how this conserved pseudoknot might be formed in the ss rRNAs of archaeal and bacterial organisms that lack 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 rRNA intermolecular interaction, we suggest that the box A-like 5' ETS sequence interacts through intramolecular complementary base pairing with the 5' end pseudoknot sequences within pre-rRNA; rearrangement of this structure mediates the formation of the conserved 5' end pseudoknot. 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 some bacterial or archaeal organisms lacking snoRNAs.