Structural organization of ribosomal RNAs from Novikoff hepatoma. I. Characterization of fragmentation products from 40 S subunit.

The internal topography of rRNAs in situ was probed with RNase T1. Isolated polysomes were treated with RNase T1 to examine the unprotected regions of rRNAs contained in polysomes. The 40 S subunit yielded 23 cleavage products of 18 S rRNA, of which the fragments from three domains were isolated, characterized, and compared with the secondary structure of 18 S rRNA proposed by Chan et al. (Chan, Y.-L., Gutell, R., Noller, H.F., and Wool, I.G. (1984) J. Biol. Chem. 259, 224-230). There were two consistent fragments (1-71, 1-74) derived from the 5' domain, where two alternative sites were cleaved at a loop, indicating conformational flexibility of 40 S subunit. There was a fragment (1760-1874) consisting of the 3'-end portion derived from the 3'-minor domain where a single site was cleaved at a loop. These patterns of cleavages at the single-stranded regions are similar to those of bacterial 16 S rRNA. In contrast to the phylogenetic similarity of cleavages between 16 S rRNA and 18 S rRNA (Stiegler, P., Carbon, P., Zucker, M., Ebel, J. P., and Ehresmann, C. (1981) Nucleic Acids Res. 9, 2153-2172), a difference was found in one fragment (777-840) derived from the unassigned long insert of the central domain. Based on the determination of its cleavage sites, a secondary structure model is proposed, which conserves a phylogenetic consistency among yeast, Xenopus, rat, and rabbit.