Laser Raman evidence for new cloverleaf secondary structures for eukaryotic 5.8S RNA and prokaryotic 5S RNA.

Abstract

Neither of the two previously proposed secondary structures for eukaryotic 5.8S RNA is consistent with the present laser Raman results. A new, highly stable "cloverleaf" secondary structure not only fits the Raman data but also accounts for previously determined enzymatic partial cleavage patterns, base sequence and pairing homologies, and GC and A'U base pair numbers and ratios. The new cloverleaf model also conserves several structural features (constant loops, bulges, and stems) consistent with known 5.8S RNA functions. Finally, we propose a similar new cloverleaf secondary structure for Escherichia coli 5S RNA, consonant with many known properties of prokaryotic 5S RNA. 5S RNA and 5.8S RNA belong to a class of small RNA molecules (including tRNA) that function in protein synthesis. The structure and function of the smaller tRNA is now understood largely because (i) tRNAPhe has been successfully crystallized and its three-dimensional structure has been determined (1, 2), and (ii) tRNA function is present in part in the free cytoplasm. In contrast, 5S RNA and 5.8S RNA are intimately bound to the ribosome. Their three-dimensional crystal structures have not yet been reported, and conclusions based on low-field hydrogen-bonded proton nuclear magnetic resonance spectra have been severely limited by poor resolution (3, 4). Less-direct structural information from other techniques has been reviewed (5), and more recent results are now discussed.Pene et al. (6) demonstrated that 5.8S RNA is strongly hydrogen-bonded to the 28S RNA of the large ribosomal subunit of eukaryotes. This interaction is between the 3' end of the 5.8S RNA molecule and a complementary segment of the 288 RNA and is stabilized by the presence of a G-C-rich loop near the 3' end of the 5.8S RNA (7). Moreover, all 5.8S RNA nucleotide sequences determined to date contain a sequence of bases that is complementary to the T4/CG-loop of tRNA (8-10). These facts suggest that 5.8S RNA in eukaryotes binds tRNA at the ribosome during transcription.In addition, the following facts connect the structure and function of eukaryotic 5.8S RNA to prokaryotic 5S RNA. First, yeast 5.8S RNA can bind the same ribosomal proteins (EL-18 and EL-25) that Escherichia coli 5S RNA binds most strongly, and this 5.8S RNA-E. colh protein complex exhibits GTPase and ATPase activities similar to those for the homologous 5S RNA-protein complex (11). Second, all prokaryotic 5S RNA molecules contain the complement of the TXCG-loop of tRNA and can bind the tetranucleotide UUCG (5). Third, both the prokaryotic 5S RNA sequence and the eukaryotic 5.8S RNA sequence are contained in the large ribosomal RNA transcription units (12). Therefore, because eukaryotic 5.8S RNA and prokaryotic 5S RNA appear to have similar origin and function, their secondary structures should be similar.Raman spectroscopy has proved to be a sensitive probe ofThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in a...

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