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Mol. Cell. Biol. doi:10.1128/MCB.01574-07
Copyright (c) 2008, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Different Mechanisms for Pseudouridine Formation in Yeast 5S and 5.8S Ribosomal RNAs

Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003 USA; Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 1X5 Canada

^* To whom correspondence should be addressed. Email: wdecatur{at}biochem.umass.edu.

	Abstract

Selection of sites for pseudouridylation in eukaryotic cytoplasmic ribosomal RNA (rRNA) occurs by base-pairing with specific guide sequences within the RNA components of box H/ACA small nucleolar ribonucleoproteins (snoRNPs). 44 of the 46 pseudouridines (s) in the cytoplasmic rRNA of Saccharomyces cerevisiae have been assigned to guide snoRNAs. Here, we examine the mechanism of formation in 5S and 5.8S rRNA in which the unassigned s occur. We show that while formation of in 5.8S rRNA is associated with snoRNP activity, pseudouridylation of 5S rRNA is not. The position of in 5.8S rRNA is guided by snoRNA snR43 using conserved sequence elements that also function to guide pseudouridylation elsewhere in the large subunit ribosomal RNA; an internal stem-loop that is not part of typical yeast snoRNAs is also conserved in snR43. The multisubstrate synthase Pus7 catalyzes formation of the in 5S rRNA at a site that conforms to the 7-nt consensus sequence present in other substrates of Pus7. The different mechanisms involved in 5S and 5.8S rRNA pseudouridylation, as well as the multi-specificities of the individual trans-factors concerned, suggest possible roles in linking ribosome production to other processes, such as splicing and transfer RNA synthesis.