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The secondary structure models of 5S rRNA have been constructed from the primary structure of 352 5S rRNA species available at present. All the 5S rRNAs examined can take essentially the same secondary structure, however they reveal characteristic differences between eukaryotes, metabacteria (= archaebacteria) and eubacteria. These three types of models can be further subgrouped by minor but characteristic differences. A phylogenic tree of organisms has been constructed using these 5S rRNA sequences by the weighted pairing method (WPG method). The tree reveals that there exist several major groups of eubacteria which seem to have diverged into different directions in the early stages of bacterial evolution. After emergence of eubacteria, metabacteria and eukaryotes separated from each other from their common ancestor. In the eukaryotic evolution, red algae (Rhodophyta) emerged first, and thereafter, thraustocytrids-Proctista, Ascomycota, green plants (green algae and land plants), Basidiomycota, Chromophyta (brown algae, diatoms and golden-yellow algae), slime- and water molds, various protozoans, and animals emerged in this order.

Seventeen ribosomal proteins of Saccharomyces cerevisiae were isolated from small ribosomal subunits and disodium ethylenediaminetetraacetate treated 80S ribosomes by chromatography on a column of carboxymethylcellulose and/or by filtration through Sephacryl S-200. The isolated proteins are YS4, YS7, YS8, YS9, YS10, YS12, YS14, YS18, YS23, YS29, YL11, YL13, YL16, YL17, YL22, YL38, and YL40 [nomenclature according to Otaka & Osawa (1981) [Otaka, E., & Osawa, S. (1981) Mol. Gen. Genet. 181, 176-182]]. The purification procedures and the amino acid compositions of these proteins are presented. Amino-terminal amino acid sequences of YS4, YS6, YS11, YS15, YS16, YS22, YL10, and YL31 have been determined and compared with those from rat liver [Wittmann-Liebold, B., Geissler, A. W., Lin, A., & Wool, I. G. (1979) J. Supramol. Struct. 12, 425-433] and Halobacterium cutirubrum [Matheson, A. T., Möller, W., Amons, R., & Yaguchi, M. (1980) in Ribosomes: Structure, Function and Genetics (Chambliss, G., et al., Eds.) pp 297-332, University Park Press, Baltimore, MD; M. Yaguchi, unpublished experiments].

The rate of nucleotide substitution (k(nuc)) of 5s RNA was estimated to be (1.8 +/- 0.5) x 10(-10) per site per year by comparing the nucleotide sequences of human and Xenopus 5s RNA and using the geological time elapsed since the separation of mammals and amphibians. Similarly, k(nuc) of 5.8s rRNA was calculated to be 0.93 10(-1u) per site per year from the sequences of rat hepatoma cells and Saccbaromyces cerevisiae. For the comparison of these data with the amino acid substitution rate of known proteins, the k(nuc) values of 5s rRNA and 5.8s rRNA were converted to the rate of amino acid substitution (k(aa')). The k(aa') values in pauling units were 0.4 and 2 0.3, respectively. The average k(aa) of ribosomal proteins was also estimated to be 0.2 0.3 pauling from the N-terminal amino acid sequences of seventeen 30s ribosomal proteins of Bacillus stearothermopbilus and Eschericbia coli. Thus, the evolutionary rates of these ribosomal components studied here are similar to each other; they considerably slower than that of the known cellular proteins. Most, if not all, of the replacements in ribosomal proteins occurred between amino acids of a chemically similar nature.

The 40S ribonucleoprotein particle in Escherichia coli cells, accumulated in the presence of a low concentration of chloramphenicol, lacks at least four ribosomal structural protein components which are present in the mature 50S ribosomal subunit. The 40S ribonucleoprotein prepared by exposing the 50S ribosomal subunit to a concentrated lithium chloride solution may also be deficient in the same protein components.

Erythromycin combines with 50S ribosomal subunit of an erythromycin-sensitive Escherichia coli (strain Q13), while ribosomes from an erythromycin-resistant mutant from this strain have little affinity for the antibiotic. A protein component of the 50S subunit of the mutant strain is distinct from that of the parent Q13 strain.

Compositions of the ribosomal proteins of 60 bacterial strains belonging to the genus Escherichia and its related genera were examined by use of a column of carboxymethyl cellulose. The ribosomes were classified into seven groups and were further differentiated into several types (subgroups) according to their protein compositions. It was shown that ribosomal protein composition is a useful characteristic for studies of bacterial taxonomy.