Studies on the secondary structure of 5.8 S rRNA from a thermophile, Thermomyces lanuginosus

The nucleotide sequence of ribosomal 5.8 S RNA from a thermophilic fungus, Thermomyces lanuginosus, was determined to be (formula: see text). The secondary structure was probed under a variety of ionic conditions using limited pancreatic and T1 ribonuclease digestion and rapid gel sequencing techniques. The results generally supported the "burp gun" model previously proposed for all 5.8 S rRNAs (Nazar, R. N., Sitz, T. O., and Busch, H. (1975) J. Biol. Chem. 250, 8591-8597) and were inconsistent with a recently suggested "cloverleaf" configuration (Luoma, G. A., and Marshall, A. G. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 4901-4905). Theoretical considerations of the overall stability also appear to favor the former estimate. As previously observed with other 5.8 S RNAs the sequence of T. lanuginosus RNA is strikingly homologous with other species; it differs in only 13 positions from that of yeast. When compared to yeast, the differences appear not to contribute to the stability of the secondary structure but probably lead to a more stable 5.8 S-25 S rRNA interaction in the large ribosomal subunit. A general comparison of T. lanuginosus 5.8 S RNA with all known 5.8 S RNA sequences indicates that, although modified nucleotides differ significantly between species, they are always located in four highly conserved regions of the 5.8 S molecule, probably contributing to the unique character of these very essential sequences.