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T Kunisawa

Publications and source records attributed to T Kunisawa.

At least 19 recordsLinked to original sources
PubMed2001

Gene arrangements and phylogeny in the class Proteobacteria.

A simple method is presented for reconstructing phylogenetic trees on the basis of gene transposition. It is shown that differences in gene arrangements among genomes could allow us to determine whether a gene transposition event has occurred before or after species divergence from parsimonious considerations. The method is applied to evolutionary relationships among the bacterial class Proteobacteria, for which complete genomic sequences most densely accumulate and comprehensive gene order comparisons are possible. We were able to infer the emergence order of proteobacterial subclasses as epsilon-->beta-->gamma. This order is consistent with sequence-based inferences, which conversely confirms the usefulness of the approach presented here.

Aniline Compounds↗
PubMed2001

[Anesthetic management of two patients with insulinoma using propofol--in association with rapid radioimmunoassay for insulin].

We experienced anesthetic management of two patients with insulinoma in whom frequent hypoglycemic episodes with blood glucose levels of 39-42 mg.dl-1 had been observed. Each patient received epidural analgesia with a catheter inserted at the T 9/10 intervertebral space. Anesthesia was induced with propofol 80-100 mg and fentanyl 200 micrograms. Tracheal intubation was facilitated with vecuronium 6 mg. Anesthesia was maintained with continuous infusion of propofol and epidural anesthesia. Rapid measurements of immunoreactive insulin (IRI) were useful for localization of insulinoma during surgery. Perioperative plasma glucose levels could be maintained within normal ranges by continuous infusion of glucose. Rebound hyperglycemic episodes were not observed, and IRI was reduced after removal of the insulinoma. General anesthesia using propofol and epidural block is a useful choice for the anesthetic management of patients undergoing an operation for removal of an insulinoma.

Aged↗
PubMed1999

Gene order breakpoint evidence in animal mitochondrial phylogeny.

Multiple genome rearrangement methodology facilitates the inference of animal phylogeny from gene orders on the mitochondrial genome. The breakpoint distance is preferable to other, highly correlated but computationally more difficult, genomic distances when applied to these data. A number of theories of metazoan evolution are compared to phylogenies reconstructed by ancestral genome optimization, using a minimal total breakpoints criterion. The notion of unambiguously reconstructed segments is introduced as a way of extracting the invariant aspects of multiple solutions for a given ancestral genome; this enables a detailed reconstruction of the evolution of non-tRNA mitochondrial gene order.

Animals↗
PubMed1998

Comparison of synonymous codon distribution patterns of bacteriophage and host genomes.

Synonymous codon usage patterns of bacteriophage and host genomes were compared. Two indexes, G + C base composition of a gene (fgc) and fraction of translationally optimal codons of the gene (fop), were used in the comparison. Synonymous codon usage data of all the coding sequences on a genome are represented as a cloud of points in the plane of fop vs. fgc. The Escherichia coli coding sequences appear to exhibit two phases, "rising" and "flat" phases. Genes that are essential for survival and are thought to be native are located in the flat phase, while foreign-type genes from prophages and transposons are found in the rising phase with a slope of nearly unity in the fgc vs. fop plot. Synonymous codon distribution patterns of genes from temperate phages P4, P2, N15 and lambda are similar to the pattern of E. coli rising phase genes. In contrast, genes from the virulent phage T7 or T4, for which a phage-encoded DNA polymerase is identified, fall in a linear curve with a slope of nearly zero in the fop vs. fgc plane. These results may suggest that the G + C contents for T7, T4 and E. coli flat phase genes are subject to the directional mutation pressure and are determined by the DNA polymerase used in the replication. There is significant variation in the fop values of the phage genes, suggesting an adjustment to gene expression level. Similar analyses of codon distribution patterns were carried out for Haemophilus influenzae, Bacillus subtilis, Mycobacterium tuberculosis and their phages with complete genomic sequences available.

Bacillus subtilis↗
PubMed1996

Parametric genome rearrangement.

Algorithms inspired by comparative genomics calculate an edit distance between two linear orders based on elementary edit operations such as inversion, transposition and reciprocal translocation. All operations are generally assigned the same weight, simply by default, because no systematic empirical studies exist verifying whether algorithmic outputs involve realistic proportion of each. Nor do we have data on how weights should vary with the length of the inverted or transposed segment of the chromosome. In this paper, we present a rapid algorithm that allows each operation to take on a range of weights, producing an relatively tight upper bound on the distance between single-chromosome genomes, by means of a greedy search with look-ahead. The efficiency of this algorithm allows us to test random genomes for each parameter setting, to detect gene order similarity and to infer the parameter values most appropriate to the phylogenetic domain under study. We apply this method to genome segments in which the same gene order is conserved in Escherichia coli and Bacillus subtilis, as well as to the gene order in human versus Drosophila mitochondrial genomes. In both cases, we conclude that it is most appropriate to assign somewhat more than twice the weight to transpositions and inverted transpositions than to inversions. We also explore segment-length weighting for fungal mitochondrial gene orders.

Algorithms↗
PubMed1995

Identification and chromosomal distribution of DNA sequence segments conserved since divergence of Escherichia coli and Bacillus subtilis.

DNA sequence segments conserved since divergence of Escherichia coli and Bacillus subtilis were identified, using the GenBank sequence database. Chromosomal locations of the conserved segments were compared between the two bacteria, and the following three features were observed. (1) Although the two genomes are nearly identical in size, chromosomal arrangements of the conserved segments are considerably different from each other. (2) In many cases, chromosomal locations of a conserved segment in the two species have deviated from each other by a multiple of 60 degrees. (3) There are many instances in which a contiguous segment in one genome is split into two or more segments located at distinct positions in the other genome, and these split segments were found to tend to lie on the E. coli or B. subtilis genome separated by distances of multiples of 60 degrees. On the basis of these observations, genome organizations of the two bacteria were discussed in terms of genome doublings as well as random chromosomal rearrangements.

Bacillus subtilis↗
PubMed1992

Synonymous codon preferences in bacteriophage T4: a distinctive use of transfer RNAs from T4 and from its host Escherichia coli.

Codon usage data of bacteriophage T4 genes were compiled and synonymous codon preferences were investigated in comparison with tRNA availabilities in an infected cell. Since the genome of T4 is highly AT rich and its codon usage pattern is significantly different from that of its host Escherichia coli, certain codons of T4 genes need to be translated by appropriate host transfer RNAs present in minor amounts. To avoid this predicament, T4 phage seems to direct the synthesis of its own tRNA molecules and these phage tRNAs are suggested to supplement the host tRNA population with isoacceptors that are normally present in minor amounts. A positive correlation was found in that the frequency of E. coli optimal codons in T4 genes increases as the number of protein monomers per phage particle increases. A negative correlation was also found between the number of protein monomers per phage and the frequency of "T4 optimal codons", which are defined as those codons that are efficiently recognized by T4 tRNAs. From these observations it was proposed that tRNAs from the host are predominantly used for translation of highly expressed T4 genes while tRNAs from T4 tend to be used for translation of weakly expressed T4 genes. This distinctive tRNA-usage in T4 may be an optimization of translational efficiency, and an adjustment of T4-encoded tRNAs to the synonymous codon preferences, which are largely influenced by the high genomic AT-content, would have occurred during evolution.

Bacteriophage T4↗
PubMed1991

Identification of regulatory building blocks in Escherichia coli genome.

The nucleotide sequences of extragenic regions in the Escherichia coli genome are statistically analyzed. Sequence elements with high occurrence frequencies are identified; these elements are: (1) extragenic palindromic sequences, which are markedly distinguishable from the already identified repetitive extragenic palindromic sequences; (2) promoter sequences of purine biosynthetic genes; and (3) rho-independent terminator sequences. The repetitious occurrence and extensive sequence similarities suggest that these elements share common evolutionary origins. Copies of one sequence element would have become distributed to various positions on the genome during evolution and have been fixed at locations that provide a selective advantage. The extragenic regions of the E. coli genome seem to consist of various regulatory 'building blocks', similar to a protein which consists of modules or domains.

Base Sequence↗
PubMed1990

Computer-assisted analysis of chromosomal locations and transcriptional directions of Escherichia coli genes.

We present a computer-assisted method for locating and orienting nucleotide sequence segments on a large restriction map by comparing restriction fragment lengths. This method is based on the observation that long restriction fragments are rare and, therefore, the longest restriction fragments serve as effective discriminators. The method was applied to Escherichia coli genes, and chromosomal locations and transcriptional directions for more than 500 genes were determined.

Chromosome Mapping↗
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

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

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↗
PubMed1987

A possible mode of protein evolution. Role of the anti-sense strand in the generation of new proteins.

The possibility that a new functional protein may be generated during evolution by using the anti-sense strands of pre-existing genes is proposed. Sequence similarity between the anti-sense strand of one gene and the sense strand of another gene may provide evidence for this generation. The computer search for the "sense/anti-sense" strand similarities between nucleotide sequences for receptors and sequences available in a database was carried out. This type of similarity was found for various receptor genes, such as the low density lipoprotein receptor, lymphocyte receptor for IgE, asialoglycoprotein receptor (hepatic lectin), T-cell receptor, epidermal growth factor receptor, insulin receptor and estrogen receptor genes. Sequence similarities between the sense strands of receptor genes were also found. These results may suggest that the repertoire of proteins was increased by the utilization of the anti-sense or sense strands of pre-existing genes.

Amino Acid Sequence↗