title: A cluster of ribosome synthesis factors regulate pre-rRNA folding and 5.8S rRNA maturation by the Rat1 exonuclease.
abstract: The 5'-exonuclease Rat1 degrades pre-rRNA spacer fragments and processes the 5'-ends of the 5.8S and 25S rRNAs. UV crosslinking revealed multiple Rat1-binding sites across the pre-rRNA, consistent with its known functions. The major 5.8S 5'-end is generated by Rat1 digestion of the internal transcribed spacer 1 (ITS1) spacer from cleavage site A(3). Processing from A(3) requires the 'A(3)-cluster' proteins, including Cic1, Erb1, Nop7, Nop12 and Nop15, which show interdependent pre-rRNA binding. Surprisingly, A(3)-cluster factors were not crosslinked close to site A(3), but bound sites around the 5.8S 3'- and 25S 5'-regions, which are base paired in mature ribosomes, and in the ITS2 spacer that separates these rRNAs. In contrast, Nop4, a protein required for endonucleolytic cleavage in ITS1, binds the pre-rRNA near the 5'-end of 5.8S. ITS2 was reported to undergo structural remodelling. In vivo chemical probing indicates that A(3)-cluster binding is required for this reorganization, potentially regulating the timing of processing. We predict that Nop4 and the A(3) cluster establish long-range interactions between the 5.8S and 25S rRNAs, which are subsequently maintained by ribosomal protein binding.
authors.affiliation: Wellcome Trust Centre for Cell Biology and Centre for Systems Biology at Edinburgh, University of Edinburgh, Edinburgh, Scotland. sgrannem@staffmail.ed.ac.uk
authors.forename: Sander
authors.initials: S
authors.lastname: Granneman
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Petfalski
authors.forename: David
authors.initials: D
authors.lastname: Tollervey
mesh_terms: D001665:Binding Sites; D002352:Carrier Proteins / Q000235:genetics; D018360:Crystallography, X-Ray; D021903:DNA, Ribosomal Spacer; D005092:Exonucleases / Q000378:metabolism*; D005095:Exoribonucleases / Q000378:metabolism*; D015966:Gene Expression Regulation, Fungal; D008954:Models, Biological; D005810:Multigene Family; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012322:RNA Precursors / Q000235:genetics*; D012340:RNA, Ribosomal, 5.8S / Q000235:genetics*; D012269:Ribosomal Proteins / Q000235:genetics; D012270:Ribosomes / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*
chemical_list: D002352:Carrier Proteins; C437314:Cic1 protein, S cerevisiae; D021903:DNA, Ribosomal Spacer; C568702:Nop15 protein, S cerevisiae; D012322:RNA Precursors; D012340:RNA, Ribosomal, 5.8S; D012269:Ribosomal Proteins; D029701:Saccharomyces cerevisiae Proteins; C075577:RAT1 protein, S cerevisiae; D005092:Exonucleases; D005095:Exoribonucleases