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E Otaka

Publications and source records attributed to E Otaka.

At least 19 recordsLinked to original sources
PubMed1995

The evolutionary relationships between homologs of ribosomal YL8 protein and YL8-like proteins.

We previously reported the sequence of YL8A, one of the two genes encoding yeast ribosomal protein YL8. With the aim of conducting an evolutionary study we have cloned and sequenced a second gene, YL8B. The disruption of both genes is lethal. Unlike other duplicated ribosomal protein genes, each open reading frame is interrupted by two introns containing long conserved sequences. A comparison of nucleotide and amino-acid sequences reveals that the duplication of the YL8 gene must have occurred very recently. Alignment and phylogenetic analysis of the amino-acid sequences of YL8-related proteins from various species show the existence not only of YL8 ribosomal proteins but also of a family of YL8-like proteins. These are present in at least three species of yeast and seem to be functionally distinct from ribosomal proteins.

Amino Acid Sequence↗
PubMed1992

Yeast ribosomal proteins: XIV. Complete nucleotide sequences of the two genes encoding Saccharomyces cerevisiae YL16.

We isolated and sequenced YL16A and YL16B encoding ribosomal protein YL16 of Saccharomyces cerevisiae. The two nucleotide sequences within coding regions retain 91.1% identity, and their predicted sequences of 176 amino acids show 93.8% identity. Out of the ribosomal protein sequences from various organisms currently available, no counterpart to YL16 could be found.

Amino Acid Sequence↗
PubMed1992

Yeast ribosomal proteins: XIII. Saccharomyces cerevisiae YL8A gene, interrupted with two introns, encodes a homolog of mammalian L7.

We isolated and sequenced a gene, YL8A, encoding ribosomal protein YL8 of Saccharomyces cerevisiae. It is one of the two duplicated genes encoding YL8 and is located on chromosome VII while the other is on chromosome XVI. The haploid strains carrying disrupted YL8A grew more slowly than the parent strain. The open reading frame is interrupted with two introns. The predicted amino acid sequence reveals that yeast YL8 is a homolog of mammalian ribosomal protein L7, E.coli L30 and others.

Amino Acid Sequence↗
PubMed1991

Yeast ribosomal proteins: XII. YS11 of Saccharomyces cerevisiae is a homologue to E. coli S4 according to the gene analysis.

We isolated and sequenced a gene, YS11A, encoding ribosomal protein YS11 of Saccharomyces cerevisiae. YS11A is one of two functional copies of the YS11 gene, located on chromosome XVI and transcribed in a lower amount than the other copy which is located on chromosome II. The disruption of YS11A has no effect on the growth of yeast. The 5'-flanking region contains a similar sequence to consensus UASrpg and the T-rich region. The open reading frame is interrupted with an intron located near the 5'-end. The predicted amino acid sequence reveals that yeast YS11 is a homologue to E. coli S4, one of the ram proteins, three chloroplast S4s and others out of the ribosomal protein sequences currently available.

Amino Acid Sequence↗
PubMed1990

Yeast ribosomal proteins: XI. Molecular analysis of two genes encoding YL41, an extremely small and basic ribosomal protein, from Saccharomyces cerevisiae.

Two genes encoding ribosomal protein YL41 were cloned from Saccharomyces cerevisiae chromosomal DNA. Both genes contain an uninterrupted region of only 75 nucleotides coding for a protein of 3.3 kD. Within the coding regions the nucleotide sequences are virtually identical, whereas in both the 5'- and 3'-flanking regions the two genes differ significantly from each other. The deduced protein shows an arginine and lysine content of 68 percent, i.e., 17 out of 25 residues, and the basic residues are evenly distributed over the molecule. When compared to the ribosomal protein sequences currently available no counterpart to YL41 could be found in prokaryotes and it seems likely that YL41 is a eukaryote-specific ribosomal protein.

Amino Acid Sequence↗
PubMed1990

Sequence and functional similarity between a yeast ribosomal protein and the Escherichia coli S5 ram protein.

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 of a ribosomal protein gene that affects translational ambiguity in a eucaryote. We show that the yeast omnipotent suppressor SUP44 encodes the yeast ribosomal protein S4. The gene exists as a single copy without an intron. The SUP44 protein is 26% identical (54% similar) to the well-characterized E. coli S5 ram protein. SUP44 is also 59% identical (78% similar) to mouse protein LLrep3, whose function was previously unknown (D.L. Heller, K.M. Gianda, and L. Leinwand, Mol. Cell. Biol. 8:2797-2803, 1988). The SUP44 suppressor mutation occurs near a region of the protein that corresponds to the known positions of alterations in E. coli S5 ram mutations. This is the first ribosomal protein whose function and sequence have been shown to be conserved between procaryotes and eucaryotes.

Amino Acid Sequence↗
PubMed1990

Examination of protein sequence homologies. VII. The complementary molecular coevolution of ribosomal proteins equivalent to Escherichia coli L7/L12 and L10.

Recently reported P1, P2 and metabacteria line sequences of transposition-type 'A' proteins, equivalent to Escherichia coli ribosomal protein L7/L12, were examined using a correlation method which evaluates the sequence similarity quantitatively. As the sequences could be aligned along the alignment previously constructed for 25 various 'A' proteins, the inclusive alignment further supports the previous claims concerning the rule of "preservation units" and the transpositional regeneration for metabacterial and eukaryotic 'A' proteins. Yeasts contain multispecies of P1 and P2 line genes and their P1 line sequences show low correlation coefficient values compared to other P1 line sequences, indicating a great evolutionary distance between lower and higher eukaryotes. Five sequences of protein P0 from metabacteria, yeast, and human, of which about 20 residues at the C termini are homologous with those of their own transposition-type 'A' proteins, were similarly examined. The N-terminal three-quarters of the sequences align naturally and the first two-thirds of the alignment could involve the E. coli L10 (EL10) sequence. An alignment of the remaining sequences at the C termini was established, relying on the well-matching sequence similarities between the metabacteria 'A' protein and their P0 protein sequences. Finally, the C-terminal halves of P0 protein sequences corresponded with almost overall sequences of the transposition-type 'A' proteins. The gene fusion of a protein might have resulted in the formation of the P0 proteins. A coupling of this gene fusion and the transposition of prototype 'A' proteins may have given rise to the complementary molecular transformations required for the development toward higher organism cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1989

Examination of protein sequence homologies: V. New perspectives on evolution between bacterial and chloroplast-type ferredoxins inferred from sequence evidence.

Sequence homologies among 34 chloroplast-type ferredoxins were examined using a computer program that quantitatively evaluates the extent of sequence similarity as a correlation coefficient. The resultant alignment contains six gaps representing insertions or deletions of some residues, all of which are located such that they precisely preserve the domains of structural fragments as determined by crystallographic data on Spirulina platensis ferredoxin. In the search for any total correlation between the chloroplast-type and 27 bacterial ferredoxins, 1891 comparison matrices prepared for possible combinations indicated that the bacterial basal sequence of 55 residues has been conserved evolutionarily in the chloroplast-type sequences corresponding to residue positions 36-90 of Spirulina platensis ferredoxin. In addition, the bacterial "connector sequence" region was found to be conserved. These findings strongly suggest that the bacterial and chloroplast-type ferredoxins descended from a common ancestor, and branched off after the bacterial gene duplication, whereas the chloroplast-type ferredoxins originally were generated by duplicating the already duplicated bacterial gene, i.e., by "double-duplication."

Amino Acid Sequence↗
PubMed1989

Structural comparison of 26S rRNA-binding ribosomal protein L25 from two different yeast strains and the equivalent proteins from three eubacteria and two chloroplasts.

The sequences of Saccharomyces carlsbergensis ribosomal protein (r-protein) SL25* and its equivalents from Candida utilis (CL25), Escherichia coli (EL23), Bacillus stearothermophilus (BL23), Mycoplasma capricolum (ML23), Marchantia polymorpha chloroplasts (McpL23), and Nicotiana tabacum chloroplasts (NcpL23) were examined using a computer program that evaluates the extent of sequence similarity by calculating correlation coefficients for each pair of residues in two proteins from a number of physical properties of individual amino acids. Comparison matrices demonstrate that the prokaryotic sequences (including McpL23 and NcpL23) can be aligned unambiguously by introducing small internal deletions/insertions at three specific positions. A similar comparison brought to light a clear evolutionary relationship between the prokaryotic and the yeast proteins despite the fact that visual inspection of these sequences revealed only limited similarity. The alignment deduced from this comparison shows the two yeast r-proteins to have acquired a long (50-60 amino acids) N-terminal extension as well as a 13-amino acid-long deletion near the C-terminus. The significance of these findings in terms of the evolution of r-proteins in general and the biological function of various parts of the SL25 protein in particular is discussed.

Amino Acid Sequence↗
PubMed1989

Examination of protein sequence homologies. VI. The evolution of Escherichia coli L7/L12 equivalent ribosomal proteins ('A' proteins), and the tertiary structure.

Sequence homologies among 23 complete and two partial sequences of ribosomal 'A' proteins from eukaryotes, metabacteria, eubacteria and chloroplasts, equivalent to Escherichia coli L7/L12, were examined using a correlation method that evaluates sequence similarity quantitatively. Examination of 325 comparison matrices prepared for possible combinations of the sequences indicates that 'A' protein sequences can be classified into two types: one is the "prototype" from eubacteria and chloroplasts, and the other is the "transposition type" from eukaryotes and metabacteria, which must have resulted from the internal transposition of the prototype sequence. The transposition type of eukaryotes can further be classified into P1 and P2 lines. Sequences of the P1 line are closer to those of metabacteria than to those of the P2 line. Eleven gaps, as deletion or insertion sites of amino acid residues, are necessary for an alignment of all the sequences. According to the crystallographic data for the C-terminal fragment (CTF) from E. coli L7, all the gaps involved in the CTF are located between segments that correspond to structural and functional elements such as alpha helix, beta strand, turning loop or hinge part. The existence of specific "preservation units" in these molecules is suggested. In contrast, the transposition site is located at the center of an alpha helix element that is involved in a folding domain, indicating that the transposition event was extremely drastic.

Amino Acid Sequence↗
PubMed1987

Examination of protein sequence homologies: IV. Twenty-seven bacterial ferredoxins.

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.

Amino Acid Sequence↗
PubMed1986

Examination of protein sequence homologies: III. Ribosomal protein YS25 from Saccharomyces cerevisiae and its counterparts from Schizosaccharomyces pombe, rat liver, and Escherichia coli.

The sequences of the ribosomal proteins YS25, SP-S28, RL-S21, and Ec-S6, from Saccharomyces cerevisiae, Schizosaccharomyces pombe, rat liver, and Escherichia coli, respectively, have been examined using a computer program that searches for homologous tertiary structures. Matrices of comparisons among the eukaryotic sequences show that they match each other sequentially without any internal gaps. The average values of the correlation coefficients obtained from the comparison matrices are higher for the first halves of the sequences than for the latter halves. This result suggests that the first halves of the sequences may represent a more important domain than the latter halves. The comparison matrices between the eukaryotic and bacterial sequences of ribosomal proteins, however, do not show sequentially arranged homology, though there are six well-matching segments arranged in different orders in the two types of sequences. This implies that the eukaryotic sequences of the ribosomal protein were reconstituted by two internal transpositions and six deletions of 4-12 residues each from the ancestral sequence during the divergence between bacterial and eukaryotic genes. These findings may give insight into structural and quantitative studies of evolutionary divergence between eukaryotes and prokaryotes.

Amino Acid Sequence↗
PubMed1986

In vivo phosphorylation of Saccharomyces cerevisiae ribosomal protein S10 by cyclic-AMP-dependent protein kinase.

Using wild-type Saccharomyces cerevisiae strains and mutants which are defective in the regulatory subunit of cyclic-AMP-dependent protein kinase (bcy1) and phosphoprotein phosphatase activity (ppd1), we demonstrated that a cyclic-AMP-dependent protein kinase phosphorylated the S. cerevisiae ribosomal protein S10 in vivo. S10 was not dephosphorylated in bcy1 or ppd1 mutants after heat shock. The phosphorylated forms of S10 were diminished during the stationary phase in bcy1 and ppd1 mutants as well as in wild-type cells.

Cell Cycle↗
PubMed1985

Primary structures of ribosomal protein YS25 from Saccharomyces cerevisiae and its counterparts from Schizosaccharomyces pombe and rat liver.

Protein YS25 and its counterparts, SP-S28 and rat S21 [nomenclature according to Sherton, C. C., & Wool, I. G. (1972) J. Biol. Chem. 247, 4460-4467], from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and rat liver cytoplasmic ribosomes, respectively, were sequenced by a combination of various enzymatic digestions and/or chemical cleavage. Proteins YS25 and SP-S28 consist of 87 amino acid residues, and rat S21 consists of 83. The amino termini are all N alpha-acetylated. The amino-terminal halves of the protein molecules are highly conserved (73-85% homologies) in contrast to the carboxy-terminal parts. Overall, rat S21 is 54% homologous to YS25 and 57% to SP-S28, despite a 76% homology between YS25 and SP-S28. Direct comparison with the available prokaryotic ribosomal protein sequences did not reveal any significant homology.

Amino Acid Sequence↗
PubMed1984

Immunological evidence for structural homology between Drosophila melanogaster (S14), rabbit liver (S12), Saccharomyces cerevisiae (S25), Bacillus subtilis (S6), and Escherichia coli (S6) ribosomal proteins.

Specific antibodies directed against Drosophila melanogaster acidic ribosomal protein S14 were used in a comparative study of eucaryotic and procaryotic ribosomes by immunoblotting and enzyme-linked immunosorbent assays. Common antigenic determinants and, thus, structural homology were found between D. melanogaster, Saccharomyces cerevisiae (S25), rabbit liver (S12), Bacillus subtilis (S6), and Escherichia coli (S6) ribosomes.

Animals↗
PubMed1983

Yeast ribosomal proteins: VII. Cytoplasmic ribosomal proteins from Schizosaccharomyces pombe.

The cytoplasmic ribosomal proteins from a fission yeast Schizosaccharomyces pombe were analysed by two-dimensional polyacrylamide gel electrophoresis. Seventy-three protein species were identified in the 80S ribosome, and named SP-S1 to SP-S33 and SP-L1 to SP-L40 in the small and large subunits, respectively. Many of these proteins could be correlated to those of Saccharomyces cerevisiae on the basis of their electrophoretic mobilities. Eleven proteins were isolated from the 80S ribosome, and their amino acid compositions were determined. Of these, SP-S6, SP-L1, SP-L12, SP-L15, SP-L17, SP-L27, SP-L36 and SP-L40c and d were sequenced from their amino-termini. SP-S28 and SP-L2 appear to have their amino-termini blocked. These results were compared with the data available for the S. cerevisiae and rat liver ribosomal proteins. The S. cerevisiae counterparts of the eight proteins mentioned above were found to be YS4, YL1, YL10, YL14, YL35, YL40 and YL44c and d, respectively. The rat liver counterparts of SP-S6, SP-L1, SP-L27 and SP-L40c and d were the rat S6, L4, L37 and P2, respectively. Comparison of the partial sequences of these ribosomal proteins suggests that these two yeasts are relatively far apart, phylogenetically.

Amino Acid Sequence↗
PubMed1982

Isolation of seventeen proteins and amino-terminal amino acid sequences of eight proteins from cytoplasmic ribosomes of yeast.

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].

Amino Acid Sequence↗