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Nucleic Acids Research, 1984, Vol. 12, No. 19 7479-7502
© 1984

MOLECULAR BIOLOGY

A universal model for the secondary structure of S.8S ribosomal RNA molecules, their contact sites with 28S ribosomal RNAs, and their prokaryotic equivalent

Jack C. Vaughn, Sally J. Sperbeck, W.Jay Ramsey and Charles B. Lawrence

Department of Zoology, Miami University Oxford, OH 45056, USA Department of Cell Biology, Baylor College Medicine Houston, TX 77030, USA

Received August 14, 1984. Accepted September 4, 1984.

The phylogenetic approach (ref. 1) has been utilized in construction of a universal 5.8S rRNA secondary structure model, in which about 65% of the residues exist in paired structures. Conserved nucleotides primarily occupy unpaired regions. Multiple compensating base changes are demonstrated to be present in each of the five postulated helices, thereby forming a major basis for their proof. The results of chemical and enzymatic probing of 5.8S rRNAs (ref. 13, 32) are fully consistent with, and support, our model. This model differs in several ways from recently proposed 5.8S rRNA models (ref. 3, 4), which are discussed. Each of the helices in our model has been extended to the corresponding bacterial, chloroplast and mitochondrial sequences, which are demonstrated to be positionally conserved by alignment with their eukaryotic counterparts. This extension is also made for the base paired 5.8S/28S contact points, and their prokaryotic and organelle counterparts. The demonstrated identity of secondary structure in these diverse molecules strongly suggests that they perform equivalent functions in prokaryotic and eukaryotic ribosomes.


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M. Gottschling and J. Plotner
Secondary structure models of the nuclear internal transcribed spacer regions and 5.8S rRNA in Calciodinelloideae (Peridiniaceae) and other dinoflagellates
Nucleic Acids Res., January 13, 2004; 32(1): 307 - 315.
[Abstract] [Full Text] [PDF]


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