Teiji Okayasu

Classification of eubacteria based on their complete genome: where does Mycoplasmataceae belong?

The amino acid compositions of 11 Gram–positive and 12 Gram–negative eubacteria were determined from their complete genomes. They were classified into two groups, ‘S–type’ represented by Staphylococcus aureus and ‘E–type’ represented by Escherichia coli, based on their patterns of amino acid compositions determined from the complete genome. These two groups were characterized by their concentrations of Arg, Ala and Lys. Mycoplasmas, which lack a cell wall, belonged to the ‘S–type’, while Gram–positive mycobacteria belonged to the ‘E–type’. Rickettsia prowazekii, Borrelia burgdorferi, Campylobacter jejuni and Helicobacter pylori, which are Gram–negative, belong to the ‘S–type’. The classification into two groups based on their amino acid compositions determined from the complete genome was independent of Gram staining. In addition, the amino acid composition based on the plasmid resembled that based on the parent complete genome.

Gene assembly consisting of small units with similar amino acid composition in the Saccharomyces cerevisiae genome

Amino acid compositions of all genes in Saccharomyces cerevisiae were determined using a computer analysis of the complete genome. The amino acid composition of an assembly of several genes or a single gene consisted of 3000–7000 amino acid residues forming a certain pattern of amino acid composition. This rule was independent not only of the gene size, but also of the gene position. Thus, the small units, consisting of 3000–7000 amino acid residues, showed a similar amino acid composition, and they formed all the genes in the complete genome.

An evaluation of evolutionary theories based on genomic structures in Saccharomyces cerevisiae and Encephalitozoon cuniculi

Codon usage patterns in 16 chromosomes coincided with each other in Saccharomyces cerevisiae, and the same result was obtained from Encephalitozoon cuniculi consisting of 11 chromosomes, although each chromosome function differs. In addition, preferential codon usage in the regenerated coding systems for Leu and Lys differed between Saccharomyces cerevisiae and Encephalitozoon cuniculi. These results cannot be explained by Darwin’s natural selection theory or by the neutral theory proposed against Darwin’s. Furthermore, the codon usage patterns were examined in both prokaryotes and eukaryotes. The use of G or C at the third codon position was much lower than T or A in Ureaplasma urealyticum, whereas inversely the use of G or C at the third codon position was much higher than T or A in Mycobacterium tuberculosis. Additionally, Candida albicans and Plasmodium falciparum also showed a very low usage of G or C at the third codon position. It is a difficult leap to speculate that the inverse codon usage change occurred over the genome during biological evolution. Thus, the present results strongly suggest that organisms were derived from different origins, indicating that the origin of life was plural, based on genomic structures.

Increase in Insulin Binding Affinity by Chloroquine in Cultured Rat Hepatoma Cells

Chloroquine increased the binding of 125I-labeled insulin to rat hepatoma cells (R-Y121B) at 4 degrees C. The effect of chloroquine on insulin binding was amplified at 23 degrees C, and a large increase in cell-associated radioactivity was observed. Scatchard analysis showed that chloroquine increased the affinity of insulin for cells at both 4 degrees C and 23 degrees C, and that this increase eventually caused the accumulation of insulin internalized by cells at 23 degrees C.

Concanavalin a Changes not only the Number of Insulin Binding Sites but also the Binding Affinity in Rat Hepatoma Cells in Culture

When rat hepatoma cells (R-Y121B) were first incubated with labeled insulin, followed by concanavalin A, at 500 micrograms/ml at 23 degrees C, the total cell-associated radioactivity increased. At 4 degrees C, however, this increase was not observed. Scatchard analysis revealed that concanavalin A increased insulin binding affinity. The bound insulin was internalized together with concanavalin A. When the cells were incubated with concanavalin A prior to insulin addition, however, the total cell-associated radioactivity decreased at both temperatures. This was caused by the masking of insulin binding sites by the lectin.

Normalization of Complete Genome Characteristics: Application to Evolution from Primitive Organisms to Homo sapiens.

Normalized nucleotide and amino acid contents of complete genome sequences can be visualized as radar charts. The shapes of these charts depict the characteristics of an organism’s genome. The normalized values calculated from the genome sequence theoretically exclude experimental errors. Further, because normalization is independent of both target size and kind, this procedure is applicable not only to single genes but also to whole genomes, which consist of a huge number of different genes. In this review, we discuss the applications of the normalization of the nucleotide and predicted amino acid contents of complete genomes to the investigation of genome structure and to evolutionary research from primitive organisms to Homo sapiens. Some of the results could never have been obtained from the analysis of individual nucleotide or amino acid sequences but were revealed only after the normalization of nucleotide and amino acid contents was applied to genome research. The discovery that genome structure was homogeneous was obtained only after normalization methods were applied to the nucleotide or predicted amino acid contents of genome sequences. Normalization procedures are also applicable to evolutionary research. Thus, normalization of the contents of whole genomes is a useful procedure that can help to characterize organisms.

Evidence for Natural Selection in Nucleotide Content Relationships Based on Complete Mitochondrial Genomes: Strong Effect of Guanine Content on Separation between Terrestrial and Aquatic Vertebrates

The complete vertebrate mitochondrial genome consists of 13 coding genes. We used this genome to investigate the existence of natural selection in vertebrate evolution. From the complete mitochondrial genomes, we predicted nucleotide contents and then separated these values into coding and non-coding regions. When nucleotide contents of a coding or non-coding region were plotted against the nucleotide content of the complete mitochondrial genomes, we obtained linear regression lines only between homonucleotides and their analogs. On every plot using G or A content purine, G content in aquatic vertebrates was higher than that in terrestrial vertebrates, while A content in aquatic vertebrates was lower than that in terrestrial vertebrates. Based on these relationships, vertebrates were separated into two groups, terrestrial and aquatic. However, using C or T content pyrimidine, clear separation between these two groups was not obtained. The hagfish (Eptatretus burgeri) was further separated from both terrestrial and aquatic vertebrates. Based on these results, nucleotide content relationships predicted from the complete vertebrate mitochondrial genomes reveal the existence of natural selection based on evolutionary separation between terrestrial and aquatic vertebrate groups. In addition, we propose that separation of the two groups might be linked to ammonia detoxification based on high G and low A contents, which encode Glu rich and Lys poor proteins.