Secondary structure of the large subunit ribosomal RNA from Escherichia coli, Zea mays chloroplast, and human and mouse mitochondrial ribosomes

Abstract

Short base-paired RNA fragments, and fragments containing intra-RNA cross-links, were isolated from E. coli 23S rRNA or 50S ribosomal subunits by two-dimensional gel electrophoresis. The interactions thus found were used as a first basis for constructing a secondary structure model of the 23S rRNA. Sequence comparison with the 23S rDNA from Z. mays chloroplasts, as well as with the 16S (large subunit) rDNA from human and mouse mitochondria, enabled the experimental model to be improved and extrapolated to give complete secondary structures of all four species. The structures are organized in well-defined domains, with over 450 compensating base changes between the two 23S species. Some ribosomal structural "'switches" were found, one involving 5S rRNA.

Structure and function of ribosomal RNA

“…The main effort has concentrated on the E. coli 16S and 23S rRNA, and three essentially similar secondary structure models were proposed for both molecules (16S RNA: Stiegler et al, 198 1a;Zwieb et al, 1981;and 23S RNA: Glotz et al, 1981;Branlant et al, 1981). In each case the structures were derived by a two-track approach, involving firstly the collection of experimental data from the E. coli RNA and secondly phylogenetic comparisons with ribosomal RNA sequences from other organisms (reviewed by Brimacombe et al, 1983;Woese et al, 1983;Noller, 1984).…”

“…Table 1), namely-in the case of the small subunit-for mammalian mitochondrial 12S RNA (e.g. Stiegler et al, 1981b;Zwieb et al, 1981) (Kuntzel & K6chel, 1981;Gray et al, 1984). In the case of the large subunit, models have been published for mammalian mitochondrial 16S RNA (e.g.…”

“…In the case of the large subunit, models have been published for mammalian mitochondrial 16S RNA (e.g. Glotz et al, 1981;Branlant et al, 1981) as well as for eukaryotic 26S RNA (Veldman et al, 1981) and 28S RNA (e.g. Michot et al, 1984;Hadjiolov et al, 1984).…”

“…After partial digestion, the cross-linked products are isolated by two-dimensional electrophoresis and the cross-link sites determined by classical fingerprinting techniques. The early studies Glotz et al, 1981) only led to the identification of secondary structural cross-links, but, by using different partial digestion conditions, a number of tertiary as well as secondary intra-RNA cross-links have now been localized in both 50S (Stiege et al, 1982(Stiege et al, , 1983 tRNA has also been used as a target for crosslinking studies. In one series of experiments, Prince et al (1982) showed that the hypermodified uridine at the 5'-anticodon position of tRNAval or tRNASer is cross-linked to C-1400 in the E. coli 16S RNA sequence.…”

Sequence of the 3′‐terminal domain of mouse 18 S rRNA

“…Due both to its known location at subunit interface and to direct experimental evidence [6,13,14], the 3'-te rminal domain of small subunit rRNA appears to be more directly involved in these functions. A more precise knowledge of its role should be gained from comparative RNA sequence analysis which has proved valuable for establishing secondary structure models for prokaryotic rRNAs [15][16][17]. Among eukaryotes, yeast [ 18] and Xenopus [ 19] are the only complete 18 S rRNA sequences published so far; their comparison has revealed extensive stretches of high homology interspersed with heterologous tracts while conserved sequences with prokaryotes are clearly restricted to the 3'-terminal region of the molecule.…”