Conserved core structure in the internal transcribed spacer 1 of the Schizosaccharomyces pombe precursor ribosomal RNA

The structure of the internal transcribed spacer 1 (ITS1) in Schizosaccharo myces pombe was examined with respect to phylogenetically conserved feature s in yeasts as well as the binding of transacting factors that potentially play a role in ribosomal maturation. Computer analyses and probes for nucle ase protection indicate a compact, more highly organized structure than pre viously proposed in Saccharomyces cerevisiae, with distinct structural feat ures which can be recognized in S. cerevisiae. These include a central exte nded hairpin structure as well as smaller hairpins immediately adjacent to the maturing termini. Comparisons with ITS sequences in more diverse organi sms indicate that the same features also can be recognized. This is especia lly clear in organisms which contain very short sequences in which the puta tive structures are much less ambiguous. Again nuclease protection analyses in one of these, Verticillium albo-atrum, confirm a central hairpin with a dditional hairpins linked to the maturing termini. Protein binding and gel retardation; studies with the S. pombe ITS1 further indicate that, as obser ved in the 3' external transcripted spacer (ETS) region, the extended hairp in is not only the site of intermediate RNA cleavage during rRNA processing , but also a site for specific interactions with one or more soluble factor s. Taken together with other analyses on transcribed spacer regions, the pr esent data provide evidence that the spacer regions act not only to organiz e the maturing terminal sequences but also may serve to organize specific s oluble factors, possibly acting in a manner which is analogous with that of the free small nucleolar ribonucleo protein particles (snoRNPs). (C) 1998 Academic Press.