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Biomedical subjects

J Otsuka

Publications and source records attributed to J Otsuka.

At least 19 recordsLinked to original sources
PubMed1992

Evolution of metabolic pathways by chance assembly of enzyme proteins generated from sense and antisense strands of pre-existing genes.

In order to get an insight into the evolutionary aspect of metabolic pathways, especially of the ubiquitous glycolytic pathway, we have carried out an extensive search of sense-sense and sense-antisense similarities for enzyme proteins in the glycolytic pathway, the pentose phosphate cycle, alcohol and lactate fermentation pathways and the TCA cycle. This investigation of amino acid sequences reveals a curious pattern of similarity relations; no similarity can be found between the enzyme proteins in a section of the glycolytic pathway where the glyceraldehyde-3-phosphate or even glycerol-3-phosphate is converted into the pyruvate while many examples of sense-sense and sense-antisense similarities are found even between enzyme proteins in distant blocks, e.g. between the proteins in the TCA cycle and those in the pentose phosphate cycle, as well as between the functionally associated proteins in each of these blocks. Complementary to this characteristic pattern of amino acid sequence similarity, the search for similarities of nucleotide sequences also finds that the similarities of glycolytic enzyme genes, some sense-sense and others sense-antisense similarities, are concentrated on the nucleotide sequences of prokaryotic 16S or eukaryotic 18S ribosomal RNA gene with its flanks, although some of the copy sequences are also found in transfer RNA genes as well as in 23S or 26S ribosomal RNA gene. These results strongly suggest that the metabolic pathways have been developed by the chance assembly of enzyme proteins generated from the sense and antisense strands of pre-existing genes, e.g. the fermentation pathways and pentose phosphate cycle by the proteins from the genes of enzymes in the glycolytic pathway and the TCA cycle from all these successively increased genes, ascribing the origin of metabolic enzyme genes to the close relation between the glycolytic enzyme protein genes and the RNA gene cluster.

Animals↗
PubMed1992

Structure model of core proteins in photosystem I inferred from the comparison with those in photosystem II and bacteria; an application of principal component analysis to detect the similar regions between distantly related families of proteins.

A principal component analysis based on the physico-chemical properties of amino acid residues is developed to assign similar regions between distantly related families of proteins, taking account of the species diversities in respective families. The most important advantage of this analysis should be that it reflects different physico-chemical properties and thus can predict more detailed structural properties, including the transmembrane helices, than the hydropathy analysis. Its first application reconfirms the similarity between the core proteins of photosynthetic reaction center in purple bacteria and those of photosystem II, indicating that the low percentage of identical amino acid residues estimated previously between them is due to much allowance for amino acid substitutions in purple bacteria. The application of this analysis to the core proteins of photosystem I reveals that any of these proteins includes two domains, each showing high similarity to the amino acid sequences of core proteins in photosystem II and purple bacteria. A core structure model of A1 and A2 proteins folded into four layers of sheets of transmembrane helices is proposed to provide a molecular basis for the electron pathway suggested by spectroscopic experiments as well as for the interaction sites with plastocyanin, 9 kDa protein and LHC proteins.

Amino Acid Sequence↗
PubMed1992

Effects of estrogen and progesterone on the development of the mammary gland and the associated blood vessels in ovariectomized mice.

Effects of estrogen and progesterone on the first abdomino-inguinal mammary gland and the associated blood vessels in ovariectomized mice were investigated morphometrically, and light and electron microscopically. Although there were no significant differences in the area of the fat pad of the mammary gland among the experimental groups, the area of the mammary parenchyma and diameters of the blood vessels supplying the mammary gland, i.e., A. et V. circumflexa ilium profunda and A. et V. epigastrica caudalis superficialis, reached the maximal value in ovariectomized mice treated with estradiol (E) + progesterone (P). Similarly, the blood capillaries around buds and ducts of the mammary gland were most densely distributed in E + P treated mice. In the adipose tissues of the mammary stroma in intact mice, fat cells were of multilocular type in the peripheral regions around the main vessel, and of unilocular type in the other part. In E and E + P treated mice, however, fat cells were mostly of unilocular type. These findings suggest that the formation of mammary fat tissues may occur in advance of that of the mammary parenchyma. By TEM, epithelial cells of the mammary parenchyma contained a large number of mitochondria and ribosomes, well-developed Golgi apparatus and rER, and large lipid droplets. Endothelial cells of blood capillaries displayed numerous pinocytotic vesicles, longer marginal folds and microvillous processes. Each organelle in these two cell types increased in number or developed to a greater degree in E + P treated mice than the other experimental groups.(ABSTRACT TRUNCATED AT 250 WORDS)

Adipose Tissue↗
PubMed1992

Pregnancy and lactation affect the microvasculature of the mammary gland in mice.

Microvascular changes in the mammary gland in mice during pregnancy and lactation were investigated by scanning electron microscopy (SEM) with a corrosion cast method, transmission electron microscopy (TEM) and morphometry. By SEM, duct-associated capillary plexuses were sparsely distributed to branch into adipocytes during virgin period. With advance in pregnancy, both branches from the capillary plexuses and branches from the vessels surrounding adipocytes extended further to form capillary networks. The basket-like architecture was completed by day 18 of pregnancy. These findings may indicate that angiogenesis occurs frequently during this period. During lactation, the basket-like architecture still remained and the capillaries surrounding alveoli meandered. After weaning, the regression of microvasculature followed the degeneration of alveoli. By TEM and morphometry, the density of pinocytotic vesicles (PVs) (number of PVs per microns 2 of endothelium cytoplasm) increased twofold from day 18 of pregnancy to day 5 of lactation, furthermore increased threefold from days 10 to 20 of lactation, and subsequently decreased after weaning. Marginal folds and microvillous processes gradually increased in length with advance in pregnancy, reached the maximum from days 5 to 15 of lactation, and thereafter decreased. In addition, the capillaries with thinner walls were in close contact with alveoli during the late stage of pregnancy and during lactation. Furthermore, the alveolar epithelial cells had well-developed basal infoldings during lactation. These findings suggest that the capillaries play an important role in transporting materials necessary for milk production.

Animals↗
PubMed1992

Fine structure of the parotid gland in the crest-tailed marsupial-rat (Dasyuroides byrnei).

The parotid gland of Dasyuroides byrnei was examined by light microscopy, and transmission and scanning electron microscopy. The acini were composed predominantly of seromucous cells with a few mucous cells. The seromucous cells were light or dark cells containing acidophilic spherical granules of moderate to high electron density and had well-developed cytoplasmic organelles-ordinary mitochondria and large mitochondria with tubular cristae, RER with vesicular or tubular elements, and Golgi apparatus with lamellae, vesicles and vacuoles. The mucous cells had basophilic amorphous granules of low electron density, like those of ordinary mucous cells. The intercalated ducts were composed of simple cuboidal light cells having a few electron-dense granules. The striated ducts consisted of tall columnar light cells containing numerous vesicles and mitochondria with tubular cristae, the same as found in acinar seromucous cells.

Animals↗
PubMed1991

Principal component analysis to detect the similarity of distantly related proteins; its application to cytochromes c, c1 and f.

A new method has been developed for detecting the similarity between distantly related families of proteins. The amino acid sequences of each family of proteins are vertically aligned by a homologous alignment method and the physico-chemical properties of the amino acid residues at the corresponding site are evaluated simultaneously, by method of the principal component analysis. Taking into account the species diversity of each family of proteins, we assign the similar regions between the different families of proteins by the overlapping degree of the standard deviations around the mean values of the first principal component. To investigate the homologous relationship between the electron transport proteins in photosynthetic and O2 respiratory systems, this method has been applied to 70 species of mitochondrial cytochrome c, 4 species of cytochrome c1 and 7 species of cytochrome f. This analysis reveals that both cytochrome f and cytochrome c1 have large regions which are similar to those of cytochrome c. Assuming that these similar regions have the same stereochemical structures as those in cytochrome c, we can predict the outlines of the tertiary structures of cytochrome c1 and cytochrome f, respectively, each able to interact with its electron acceptor, cytochrome c and plastocyanin.

Amino Acid Sequence↗
PubMed1991

A protein secondary structure database (PSS).

A protein secondary structure database (PSS) has been designed to correlate the Protein Sequence Database of the PIR-International with the atomic coordinates and bond connectivities database of the Protein Data Bank in the Brookhaven National Laboratory. The present database includes secondary structures determined by X-ray diffraction analysis, but not predicted structures. The database currently contains data from both the Protein Sequence Database and the Protein Data Bank Database, and will encompass the NMR database in the future. The main characteristics of the database are as follows: (1) the secondary structures, sites, regions and domains of structural interest are displayed together with protein primary structures; and (2) the secondary structure of a desired length of peptide fragment is displayed upon request, as are the peptide fragment(s) that correspond to a defined secondary structure. This database also has software to indicate amino acid pairs having hydrogen bonds and to count the occurrence frequency of each pair as well as the conformational parameters widely used in semi-empirical methods of secondary structure prediction.

Amino Acid Sequence↗
PubMed1990

Discrimination between adaptive and neutral amino acid substitutions in vertebrate hemoglobins.

A discriminant analysis on the basis of the physicochemical properties of amino acid residues is developed to investigate the accumulation pattern of amino acid substitutions in a family of proteins. The application of this analysis to vertebrate hemoglobins reveals the following new results. (1) The major components of teleost fish and amphibian hemoglobins showing the Root effect are sharply discriminated from mammalian hemoglobins in several regions of the alpha and beta chains, whereas shark, minor components of teleost fish and amphibian, reptile, and bird hemoglobins showing no Root effect exhibit a gradual change to mammalian hemoglobin in a straightforward way. This result suggests at least two lines of molecular evolution in vertebrate hemoglobins. (2) The nonadult hemoglobin chains are allocated to the latter line, i.e., tadpole, zeta, and pi chains are similar to shark and trout I chains, and epsilon and gamma chains are similar to some of the reptile chains. (3) In any case, most of the amino acid residues causing the discrimination are located near the sites that carry the amino acid residues conserved well throughout all classes of vertebrates, suggesting that modifications adapting to the respective living conditions or respiratory organs have taken place effectively near the amino acid residues essential for the manifestation of cooperative oxygen binding. (4) The amino acid residues at other sites are changed from one to another species even within the same class, showing a constant substitution rate as a whole. These amino acid substitutions may be nearly neutral, being under a weak functional constraint. The number of sites allowing such neutral substitutions is rather small, less than one-half of all the sites in the adult hemoglobins of bird and mammal, whereas it amounts to two-thirds in teleost fish hemoglobins.

Amino Acid Sequence↗
PubMed1990

Fine structure of the mandibular gland in crest-tailed marsupial-rat (Dasyuroides byrnei).

The mandibular glands of Dasyuroides byrnei were examined by light microscopy, and transmission and scanning electron microscopy. The secretory units consisted of numerous seromucous acini and a few seromucous demilunes. The seromucous acini were almost always capped by demilunes. The acinar seromucous cells contained faintly basophilic, light, coarse, bipatite secretory granules with matrix of low and moderate densities. The demilunar cells were dark compared with acinar seromucous cells and contained acidophilic secretory granules with a fibrillogranular matrix of moderate density. Preacinar cells with a seromucous nature were occasionally present at the junction between the acinus and intercalated duct. These cells had numerous basophilic granules, which were similar to those of acinar seromucous cells. The intercalated ducts consisted of simple cuboidal light cells that had a few small electron-dense granules. The striated ducts were composed of tall columnar light cells containing numerous vesicles, but no secretory granules. The mandibular acini of D. byrnei were composed of two cell types having a seromucous nature, unlike those of the opossum and many other mammals.

Animals↗
PubMed1990

Escherichia coli K12 genomic database.

We have compiled the genomic nucleic acid sequence data of Escherichia coli K12 available from the existing major data collections and from the literature. The collected data are structured as a database for easy access and analysis. The sequence segments in the database are ordered by genetic map position. Sequence redundancy has been completely removed by combining overlapping sequences; therefore, our sequence data are amenable to statistical analysis. We have specified with a plus or minus (+ or -) on which of the two DNA strands the segment exists. The database currently contains a total of 954,392 bp, which corresponds to about 20% of the entire genome size. The sequence data are available on request.

Base Sequence↗
PubMed1989

Fine structure of the mandibular gland in volcano rabbit.

The mandibular glands of 6 male and 6 female volcano rabbits were examined by means of light and transmission electron microscopy. The acinar cells of the glands were seromucous in nature, and contained faintly basophilic granules. The cells were classified into the light cells containing granules of low or moderate densities and the clear cells having polygonal granules of low density. The preacinar cells were occasionally observed at the site between acinus and intercalated duct. These cells had many weakly basophilic granules which contained fine granular materials of moderate density. The intercalated ducts were composed of light cells containing cored granules. The striated duct cells consisted of light cells and dark cells. Both of them contained a few vacuoles and vesicles, but no secretory granules. No sex-and age-related differences were observed in the mandibular gland of the volcano rabbit. The mandibular gland of the volcano rabbit was similar to the rabbit mandibular gland rather than the pika mandibular gland morphologically.

Animals↗
PubMed1989

Rapid evolutionary repair of base mispairings in stem regions of eukaryotic 5S rRNA.

An extensive set of 216 eukaryotic 5S rRNA sequences are compared and the previous observations, that (i) invariable base positions are located primarily in loop regions and (ii) stem regions are more variable but the number of mispairings is kept small, are confirmed. On the basis of a comparison of the contemporary sequences, evolutionary processes of base substitutions in stem regions are discussed. It is found that there is no evident selective pressure to keep a particular kind of base pair in stem regions and individual bases may change freely as long as mispairings are kept few. It is also found that the secondary structure of 5S rRNA has been maintained stable by an equilibrium between base pair formation- and destruction-substitutions and that the low occurrence of mispairings in stem regions is attributable to a high value (ca. 90) of the equilibrium constant. The present analyses suggest a structure-function relationship of the eukaryotic 5S rRNA; stem regions structurally help loop regions to interact well with other ribosomal components and therefore, there is a marked selection pressure to maintain the secondary structure under the evolutionary noise of mutation.

Animals↗
PubMed1988

A study on the quaternary structure change of hemoglobin in the ligation process.

In order to inquire into the molecular mechanism underlying the cooperative ligand binding to hemoglobin (Hb), conformational interaction at the interfaces between subunits are investigated on the basis of the atomic coordinates of human deoxy and human carbonmonoxy Hbs. Hypothetical intermediate structures are used, each of which is obtained from the procedure where one or more subunits in deoxy Hb are replaced by the corresponding CO-liganded subunits in carbonmonoxy Hb using the method of superimposition of two sets of atomic coordinates. When either alpha or beta subunit is substituted with the corresponding subunit in carbonmonoxy Hb, serious steric hindrances are produced between alpha 1FG4(92)Arg and beta 2C3(37)Trp or between alpha 1C6(41)Thr and beta 2FG4(97)His, all of which belong to the allosteric core affected directly by ligand binding. These steric hindrances become more serious when both alpha 1(alpha 2) and beta 2(beta 1) subunits are substituted. Therefore the change in the relative distance between iron atom and porphyrin by ligation results in strain in the C-terminal residues as an effect of the steric hindrance between the FG and C segments. However, no steric hindrance can be seen between subunits when the subunits in carbonmonoxy Hb are substituted with the corresponding subunits in deoxy Hb. The nature of the quaternary structural change from liganded to deoxy Hb seems to be different from that from deoxy to liganded Hb.

Calorimetry↗
PubMed1988

Regulation in the synthesis of Escherichia coli RNA polymerase proposed from sequence analysis.

A computer analysis of the operons containing Escherichia coli RNA polymerase subunits was carried out to obtain information about the regulation in the synthesis of these subunits, identifying intercistronic promoter and terminator sequences and searching for ribosome-binding sites and possible secondary structures of the corresponding mRNAs. This investigation showed an extensive secondary structure of beta-mRNA, which provides a molecular basis for the mechanism of the phenomenologically known post-transcriptional regulation in the synthesis of beta subunit. Since a similar secondary structure was also recognized in the mRNA corresponding to the upstream part of alpha subunit gene, it is proposed that the synthesis of alpha subunit is autogenously regulated by RNA polymerase itself, probably at the translational level, in the same way as in the synthesis of beta subunit. This regulation not only guarantees the suppression of overproduction of RNA polymerase subunits but also throws light on the problem of how the syntheses of RNA polymerase and ribosome respond similarly to the shift of nutrients and temperature, but differently to the starvation for amino acids.

Base Sequence↗
PubMed1988

Periodic distribution of homologous genes or gene segments on the Escherichia coli K12 genome.

A computer search for homologous relationships among Escherichia coli proteins has been carried out with the use of databases. Homologous genes or gene segments thus identified at the amino acid sequence level have a tendency to lie on the genome separated by distances of multiples of 7 min. This relatively regular pattern of gene distribution on the E. coli genome is interpreted as reflecting the early history of multiple genome doublings. Evolutionary advantages of duplications of the total genome are discussed in relation to the acquisition of new multistep pathways such as the Krebs cycle and to the generation of a variety of proteins in existence today.

Base Sequence↗
PubMed1987

Accumulation pattern of amino acid substitutions in protein evolution.

A simple method for the evolutionary analysis of amino acid sequence data is presented and used to examine whether the number of variable sites (NVS) of a protein is constant during its evolution. The NVSs for hemoglobin and for mitochondrial cytochrome c are each found to be almost constant, and the ratio between the NVSs is close to the ratio between the unit evolutionary periods. This indicates that the substitution rate per variable site is almost uniform for these proteins, as the neutral theory claims. An advantage of the present analysis is that it can be done without knowledge of paleontological divergence times and can be extended to bacterial proteins such as bacterial c-type cytochromes. It is suggested that the NVS of cytochrome c has been almost constant even over the long period (ca. 3.0 billion years) of bacterial evolution but that at least two different substitution rates are necessary to describe the accumulated changes in the sequence. This "two clock" interpretation is consistent with fossil evidence for the appearance times of photosynthetic bacteria and eukaryotes.

Amino Acid Sequence↗
PubMed1987

Theoretical analysis of single-round transcription experiments on trp leader region.

A kinetic model is proposed to reproduce the time courses of the concentration change in paused leader RNA, terminated leader RNA, and readthrough RNA in the single-round transcription experiments on trp leader region of Escherichia coli and its mutants, L132, L75, and L75L135 (Winkler, M. E., and C. Yanofsky, 1981, Biochemistry, 20:3738-3744; Fisher, R., and C. Yanofsky, 1983, J. Biol. Chem., 258:9208-9212). This model fits the experimental results well and also captures the essential aspects of the processes of transcriptional pausing and termination. In the wild type template, under optimal conditions, it is found that the transcription rate at the pause and attenuation sites is of the same order of magnitude, 10,000-fold lower than the transcription rate at the other sites, and the high termination level at the attenuation site is attributable to a higher dissociation rate. This analysis also provides a clue as to how the template base change, various concentrations of ribonucleoside triphosphates, and the presence or absence of L-factor affect the transcription and dissociation rates to yield different termination levels at the pause or attenuation site. It also discusses the molecular mechanism of the transcriptional pausing and termination.

DNA-Directed RNA Polymerases↗