The known function of the DEXH/D-box protein Prp43p is the removal of the U2, U5, and U6 snRNPs from the postsplicing lariat-intron ribonucleoprotein complex. We demonstrate that affinity-purified Prp43p-associated material includes the expected spliceosomal components; however, we also identify several preribosomal complexes that are specifically purified with Prp43p. Conditional prp43 mutant alleles confer a 35S pre-rRNA processing defect, with subsequent depletion of 27S and 20S precursors. Upon a shift to a nonpermissive temperature, both large and small-ribosomal-subunit proteins accumulate in the nucleolus of prp43 mutants. Pulse-chase analysis demonstrates delayed kinetics of 35S, 27S, and 20S pre-rRNA processing with turnover of these intermediates. Microarray analysis of pre-mRNA splicing defects in prp43 mutants shows a very mild effect, similar to that of nonessential pre-mRNA splicing factors. Prp43p is the first DEXH/D-box protein shown to function in both RNA polymerase I and polymerase II transcript metabolism. Its essential function is in its newly characterized role in ribosome biogenesis of both ribosomal subunits, positioning Prp43p to regulate both pre-mRNA splicing and ribosome biogenesis.DEXH/D-box proteins comprise a family of RNA helicase and RNA helicase-like proteins that function in almost all aspects of eukaryotic gene expression. Included in these processes is RNA transcription (30, 49), pre-mRNA splicing (reviewed in reference 35), mRNA export (21, 34, 38), translation initiation (40), RNA interference (29, 41), RNA turnover (1), viral replication (31), and ribosome biogenesis (reviewed in references 13 and 44). Among this class of RNA helicases are the DEAD-box proteins and the DEAH-box proteins, which differ by subtle sequence variations in one or more of the motifs that define these proteins (reviewed in reference 42). In addition to an RNA-unwinding activity demonstrated by some of these enzymes, others exhibit an "RNPase" function that serves to displace proteins from or otherwise rearrange ribonucleoproteins (10,20). Although the specific function and mechanism of most DEXH/D-box proteins are unknown, the processes in which many of these enzymes function have been studied in great detail.The eukaryotic pre-mRNA splicing reaction is an ATP-intensive process in which at least eight DEXH/D-box proteins function (35). The genes for all eight Saccharomyces cerevisiae spliceosomal DEXH/D-box proteins are essential, although two have been shown to be dispensable in concert with bypass suppressor mutations (6, 23). DEXH/D-box proteins are required for virtually every known step of the pre-mRNA splicing reaction and are thought to monitor and modify RNA-RNA interactions and RNA-protein interactions in the highly dynamic process.Among the trans-acting spliceosomal RNA helicase-like proteins is Prp43p, which was originally identified in a PCR-based screen for RNA helicase genes in yeast (2, 9). It has been shown to be a bona fide RNA-dependent ATPase, although no RNA-unwinding activity h...
The enzymatic processing of cellular RNA molecules requires selective recognition of unique chemical and topological features. The unusual 2′,5′-phosphodiester linkages in RNA lariats produced by the spliceosome must be hydrolyzed by the intron debranching enzyme (Dbr1) before they can be metabolized or processed into essential cellular factors, such as snoRNA and miRNA. Dbr1 is also involved in the propagation of retrotransposons and retroviruses, although the precise role played by the enzyme in these processes is poorly understood. Here, we report the first structures of Dbr1 alone and in complex with several synthetic RNA compounds that mimic the branchpoint in lariat RNA. The structures, together with functional data on Dbr1 variants, reveal the molecular basis for 2′,5′-phosphodiester recognition and explain why the enzyme lacks activity toward 3′,5′-phosphodiester linkages. The findings illuminate structure/function relationships in a unique enzyme that is central to eukaryotic RNA metabolism and set the stage for the rational design of inhibitors that may represent novel therapeutic agents to treat retroviral infections and neurodegenerative disease.
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