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Sequence homologies of 27 bacterial ferredoxins were examined using a computer program that quantitatively evaluates extent of similarity as a correlation coefficient. The results of a similarity search among the sequences demonstrated that the basal sequence consists of a pair of extremely similar segments of 26 amino acids connected by a three-amino acid group. The segment pairs, which would have arisen from gene duplication, are termed the first and second units. Because of the gene duplication, the connector sequence appears to have been introduced as a structurally important chain reversal. Each of the two units contains four cysteine residues, which are inserted one by one among seven, two, two, three, and eight amino acid alignments, respectively. The bacterial ferredoxins were categorized with regard to basal constitution as follows: group 1, in which both units closely conform to the basal structure; group 2, in which the second unit is modified in a characteristic manner among members; group 3, in which the first unit is modified in a characteristic manner, while the conforming second unit is accompanied by a long accessory sequence; group 4, in which there are modifications before and/or after the units, of which the respective central domains remain nearly intact; and group 5, where only the former of two Fe:S cluster ligation sets of four cysteines is estimated to remain intact, whereas the latter set is extremely modified. It is noteworthy that throughout all bacterial ferredoxins, one of two cysteine sets never fails to be completely intact and, moreover, the connector of three amino acids also exists intact. Based on this grouping and on the correspondences among the groups, average correlation coefficients among all members were computed, and the respective evolutionary relationships were examined. The results supported the proposition that transposition had occurred in the Azotobacter-type ferredoxins of group 3.

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The cytoplasmic 80s ribosomal proteins from the cells of yeast Sachharomyces cerevisiae were analysed by SDS two-dimensional polyacrylamide gel electrophoresis. Seventyfour proteins were identified and consecutively numbered from 1 to 74. Upon oxidation of the 80s proteins with performic acid, ten proteins (no. 15, 20, 35, 40, 44, 46, 49, 51, 54 and 55) were dislocated on the gel without change of the total number of protein spots. Five proteins (no. 8, 14, 16, 36 and 74) were phosphorylated in vivo as seen in 32P-labelling experiments. The large and small subunits separated in low magnesium medium were analyzed by the above gel electrophoresis. At least forty-five and twenty-eight proteins were assumed to be in the large and small subunits, respectively. All proteins found in the 80s ribosomes, except for no. 3, were detected in either subunit without appearance of new spots. The acidic protein no. 3 seems to be lost during subunit dissociation.

The accurate and efficient translation of proteins is of fundamental importance to both bacteria and higher organisms. Most of our knowledge about the control of translational fidelity comes from studies of Escherichia coli. In particular, ram (ribosomal ambiguity) mutations in structural genes of E. coli ribosomal proteins S4 and S5 have been shown to increase translational error frequencies. We describe the first sequence Analyses of informational suppressors in Escherichia coli have elucidated the components involved in determining the fidelity of translation. In most instances, the factors identified have been either tRNAs or ribosomal proteins (31,69,84). Alterations in five different ribosomal proteins have been shown to influence translational accuracy. Mutations in the structural genes for S12 (30), S17 (8), and L6 (53) can cause an increase in accuracy, while mutations in the structural genes for L7/L12 (47), S4 (77), and S5 (13, 71) can decrease fidelity. Such mutations that affect S4 or S5 are known as ram (ribosomal ambiguity) mutations because they cause a general ambiguity of translation, suppressing nonsense as well as missense and frameshift mutations (3, 73). More recently, nonsense suppressor phenotypes have also been shown to be associated with mutations in elongation factor EF-Tu (85, 89).We and others have used a similar genetic approach to identify components of the eucaryotic protein synthesis machinery that control translational fidelity (2,21,25,54,65,88,91,95 sup45, SUP44, and SUP46 strains increase in vitro misreading of polyuridylate templates (25,62).Despite the suggestive biochemical evidence, the first two yeast omnipotent suppressor genes to be cloned and sequenced (SUP35+ and SUP45+) do not encode ribosomal proteins (10,11,17,18,38,54,57,95). The SUP45+ gene is predicted to encode a protein of molecular mass 49 kDa (10). Regions of weak similarity to several tRNA synthetases were found, but the function of the gene product is still not known. The SUP35+ gene is predicted to encode a protein of 76.5 kDa that shows a high degree of similarity to EF-la (45, 54, 95) but is not identical to any of the three biochemically characterized elongation factors from yeast cells. Neither SUP35+ nor SUP45+ appears likely to encode a ribosomal protein, since both predicted gene products are much larger than ribosomal proteins, and their codon usage patterns indicate that, unlike ribosomal protein genes, they are not highly expressed (10,54,95).Here, we describe the sequence of a third yeast omnipotent suppressor gene, sup44+. This suppressor does encode a ribosomal protein. Furthermore, the SUP44 protein shows substantial sequence similarity to the E. coli S5 ram protein. MATERIALS AND METHODSStrains and genetic methods. The following Saccharomyces cerevisiae strains were used: SL815-26B [et met8-J leu2-1 trpl-J (his5-2 and/or his3-J) Iys2-J ura3-52 SUP44] and SL-982 [ala ura3-521ura3-52 met8-J/met8-J leu2-111eu2-1 ade3-261+ his5-21+ his3-All+ tyr7-J1+ trpl-l1+]. Standard yeast genetic procedu...

Twenty proteins were isolated from the 30S ribosomal subunits of Bacillus subtilis and their amino acid compositions and amino-terminal amino acid sequences were determined. These results were compared with the data of Escherichia coli 30S ribosomal proteins and the structural correspondence of individual ribosomal proteins has been established between B. subtilis and E. coli. Post-translational modifications of amino-terminal amino acids of the ribosomal proteins which have been found in E. coli are almost absent in B. subtilis with the exception of acetylated forms of S9.

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