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

Abstract

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.

Structure and function of ribosomal RNA

“…Michot et al, 1984;Hadjiolov et al, 1984). The equivalence of eukaryotic 5.8S RNA to the 5'-terminal region of prokaryotic 23S RNA has already been mentioned in the previous section, and the interaction between 5.8S RNA and the 5'-region of the 26S or 28S RNA is now well-documented (Vaughn et al, 1984;Walker et al, 1983;see Brimacombe et al, 1983, for review). Evidence is also accumulating for an interaction of 5.8S RNA with the 3'-end of the 26S or 28S RNA (Kelly & Cox, 1981;Georgiev et al, 1984), but the precise nature of this putative interaction is not yet clear; although there is strong evidence that the extreme 5'-and 3'-ends of prokaryotic 23S RNA interact with one another (helix 1, Fig.…”

An unusual genetic code in nuclear genes of Tetrahymena.

“…Indeed, Jukes (4) (24,25). Similarly, histones H3, H2B, and H2A of Tetrahymena are the most divergent (17,26) as are their 5.8S ribosomal (27) and tRNAs (28). Literal use of these "molecular clocks" can suggest that ciliates diverged from all other organisms before life originated on earth (24).…”

Multigene‐based phylogeny analyses of the controversial family Condylostomatidae (Ciliophora, Heterotrichea)

“…The secondary structures of variable regions 2 and 4 of SSU rDNA were predicted based on the modes of the eukaryotic SSU rRNA presented in Strüder‐Kypke, Wright, Fokin, and Lynn () and Wuyts et al (), respectively. The sequences of ITS2 region were constrained according to the rules suggested by Vaughn, Sperbeck, Ransey, and Lawrence (), Miao et al () and Gao, Katz, and Song (). The structures were edited with RNA VIZ 2.0 (Rijk & Wachter, ) to produce acceptable illustrations.…”