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K Ikeo

Publications and source records attributed to K Ikeo.

36 records · Page 2Linked to original sources
PubMed1997

Ascidian tyrosinase gene: its unique structure and expression in the developing brain.

Tadpole larvae of ascidians have two sensory pigment cells in the brain. One is the otolith cell that functions as a gravity receptor, the other pigment cell is part of a primitive photosensory structure termed the ocellus. These sensory cells, like vertebrate pigment cells, contain membrane-bounded melanin granules and are considered to reflect a crucial position in the evolutionary process of this cell type. To investigate the molecular changes accompanying the evolution of pigment cells, we have isolated from Halocynthia roretzi a gene encoding tyrosinase, a key enzyme in melanin biosynthesis. The cDNA has an open reading frame (ORF) of 596 amino acids, which is 36-39% identical in amino acid sequence to vertebrate tyrosinases. In addition, the sequence analysis of both cDNA and genomic clones reveals an unusual organization of the tyrosinase gene, an extraordinary 3' untranslated region of the transcripts with significant homology to the coding sequence, and a single short intron in the sequence encoding a cytoplasmic domain. Expression of the gene is detected first in two pigment precursor cells positioned in the neural plate of early neurulae, and later in two melanin-containing pigment cells within the brain of late tailbud embryos. Its expression pattern correlates well with the appearance of tyrosinase enzyme activity in the developing brain. These results provide the first description of pigment cell differentiation at the molecular level in the ascidian embryo, and also will contribute to a better understanding of the evolution of chordate pigment cells.

Amino Acid Sequence↗
PubMed1997

Evolutionary motif and its biological and structural significance.

We developed a method for multiple alignment of protein sequences. The main feature of this method is that it takes the evolutionary relationships of the proteins in question into account repeatedly for execution, until the relationships and alignment results are in agreement. We then applied this method to the data of the international DNA sequence databases, which are the most comprehensive and updated DNA databases in the world, in order to estimate the "evolutionary motif" by extensive use of a supercomputer. Though a few problems needed to be solved, we could estimate the length of the motifs in the range of 20 to 200 amino acids, with about 60 the most frequent length. We then discussed their biological and structural significance. We believe that we are now in a position to analyze DNA and protein not only in vivo and in vitro but also in silico.

Amino Acid Sequence↗
PubMed1997

Constrained evolution with respect to gene overlap of hepatitis B virus.

With the aim of elucidating the evolution of a hepadnavirus family, we constructed molecular phylogenetic trees for 27 strains of hepatitis B virus (HBV) using both the unweighted pair-grouping and neighbor-joining methods. All five gene regions, P, C, S, X, and preS, were used to construct the phylogenetic trees. Using the phylogenetic trees obtained, we classified these strains into five major groups in which the strains were closely related to each other. Our classification reinforced our previous view that genetic classification is not always compatible with conventional classification determined by serological subtypes. Moreover, constraints on the evolutionary process of HBV were analyzed for amino-acid-altering (nonsynonymous) and silent (synonymous) substitutions, because two-thirds of the open reading frame (ORF), P, contains alternating overlapping ORFs. In our unique analysis of this interesting gene structure of HBV, the most frequent synonymous substitutions were observed in the nonoverlapped parts of the P and C genes. On the other hand, the number of synonymous substitutions per nucleotide site for the S gene was quite low and appeared a strongly constrained evolution. Because the P gene overlaps the S gene in a different frame, the low rate of synonymous substitution for the S gene can be explained by the evolutionary constraints which are imposed on the overlapping gene region. In other words, synonymous substitutions in the S gene can cause amino acid changes in its overlapping region in a different frame. Thus, the evolution of HBV is constrained evolutionarily by the overlapping genes. We propose calling this mode of viral evolution "constrained evolution." The evolution of HBV represents a typical constrained evolution.

Amino Acid Sequence↗
PubMed1996

Evolutionary relationship of hepatitis C, pesti-, flavi-, plantviruses, and newly discovered GB hepatitis agents.

Two flavivirus-like viruses, GB virus-A (GBV-A) and GB virus-B (GBV-B), were recently identified in the GB hepatitis agent, and are distinct from the hepatitis A to E viruses. The putative helicase domain of GBV-A and GBV-B was found to have amino acid sequence homology with hepatitis C virus (HCV), and distantly, is also related to pestiviruses, flaviviruses, and plant viruses. A phylogenetic tree construction showed that GBVs and HCV are closely related, and they are clustered with pestiviruses, flaviviruses and plant viruses in that order.

Amino Acid Sequence↗
PubMed1996

Hepatitis C virus types 7, 8 and 9 should be classified as type 6 subtypes.

Tokita et al. reported the identification of hepatitis C virus type 7, 8 and 9 in Southeast Asia, based on the unweighed pair-group method with the arithmetic mean, a method that may not be appropriate when the nucleotide substitution rate is not constant over time. To determine more accurately the relationship of these proposed types 7, 8, and 9 with other types, a more appropriate approach, the neighbor-joining method, was applied to re-evaluate the phylogenetic relationship. A total of 660 HCV sequences, including the reported sequences, were collected from DNA databases. For every region, the nucleotide substitution rate was estimated by the 6-parameter method, and phylogenetic trees were constructed using the neighbor-joining method. The results of this analysis indicate that the newly proposed HCV types 7, 8 and 9 should be classified as type 6 subtypes. HCV type 6 appears to be diversified.

Evolution, Chemical↗
PubMed1996

Large-scale search for genes on which positive selection may operate.

We conducted a systematic search for the candidate genes on which positive selection may operate, on the premise that for such genes the number of nonsynonymous substitution is expected to be larger than that of synonymous substitutions when the nucleotide sequences of genes under investigation are compared with each other. By obtaining 3,595 groups of homologous sequences from the DDBJ, EMBL, and GenBank DNA sequence databases, we found that 17 gene groups can be the candidates for the genes on which positive selection may operate. Thus, such genes are found to occupy only about 0.5% of the vast number of gene groups so far available. Interestingly enough 9 out of the 17 gene groups were the surface antigens of parasites or viruses.

Amino Acid Sequence↗
PubMed1995

Different evolutionary histories of kringle and protease domains in serine proteases: a typical example of domain evolution.

With the aim of elucidating the evolutionary processes of the kringle and protease domains in serine proteases which are involved with the system of blood coagulation and fibrinolysis, we constructed phylogenetic trees for the kringle and protease domains, separately, by use of amino acid sequence data. The phylogenetic trees constructed clearly showed that the topologies were different between the kringle and protease domains. Because both domains are coded by single peptides of serine proteases, this strongly suggests that the kringle and protease domains must have undergone different evolutionary processes. Thus, these observations imply that serine proteases evolve in a way such that each domain is a unit of evolution, exemplifying a typical mode of domain evolution. A possible relationship between the domain evolution and the exon shuffling theory is also discussed from the viewpoint of gene evolution.

Amino Acid Sequence↗
PubMed1995

Relationships between serotypes and genotypes of hepatitis B virus: genetic classification of HBV by use of surface genes.

Hepatitis B virus (HBV) surface antigen (HBsAg), which is encoded by the HBV S gene, is conventionally classified into 4 serological subtypes, adw, adr, ayw and ayr. To determine the relationship between the HBsAg seroreactivity and the nucleotide sequence diversity of the HBV S gene, the nucleotide sequences of S genes for HBV isolates reported so far were aligned with each other. The numbers of nucleotide substitutions were then estimated by the 6-parameter method, and a phylogenetic tree was constructed by the unweighted paired grouping method with arithmetic mean (UPGMA) and the neighboring-joining (NJ) method. The phylogenetic trees constructed showed that all isolates were grouped into 4 genotypes (gyw, gdw-1, gdw-2, and gdr). More importantly, the genotypes did not necessarily correspond to the conventional serotypes. In particular, serotype 'adw' can be any of genotypes gdw-1, gdw-2, or gdr. Thus, genotyping by S genes gives more accurate information about genetic variation of HBV.

Amino Acid Sequence↗
PubMed1994

Molecular evolution of serine protease and its inhibitor with special reference to domain evolution.

The evolution of serine protease and its inhibitor are discussed with special reference to domain evolution. It is now known that most proteins are composed of more than one functional domain. Because serine proteases such as urokinase and plasminogen are made of various functional domains, these proteins are typical examples of the so-called mosaic proteins. When Kringle domains in serine proteases and a Kunitz-type protease inhibitor domain in the amyloid beta precursor protein in Alzheimer's disease patients were examined by the molecular evolutionary analysis, the phylogenetic trees constructed showed that these functional domains had undergone dynamic changes in the evolutionary process. In particular, these domains are evolutionarily movable. Thus, it is concluded that various functional domains evolved independently of each other and that they have been shuffled to create the existent mosaic proteins. This conclusion leads us to the reasonable speculation that those functional domains must have been minigenes possibly at the time of primordial life or the origin of life. We call these minigenes 'ancestral minigenes'. Every effort should be made to answer the question about the minimum set of ancestral minigenes that must have existed and must have been needed for maintaining life forms. The DNA sequence database is useful for making attempts to answer such difficult but significant questions.

Alzheimer Disease↗
PubMed1994

Evolution of pathogenic viruses with special reference to the rates of synonymous and nonsynonymous substitutions.

For pathogenic viruses such as human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), human influenza A virus, and human T-cell leukemia virus type I (HTLV-I), the evolutionary features were briefly reviewed with special reference to the rates of synonymous and nonsynonymous substitutions. In particular, these rates were discussed in connection with the neutral theory of molecular evolution. It was common to all the five pathogenic viruses that the rate of synonymous substitution was higher than that of nonsynonymous substitution particularly when the entire gene regions were compared between different isolates. This suggests that the viral proteins are quite conservative to functional and structural changes even though most of these viral genomes are evolving at a speed extraordinarily higher than their host genomes. Thus, this feature is consistent with the neutral theory. However, it is also pointed out that positive selection may be operating on some specific sites such as antigenic sites in order for the pathogenic viruses to escape from the host immune system.

Base Sequence↗
PubMed1993

Cloning of human, mouse and fission yeast recombination genes homologous to RAD51 and recA.

Rad51, of Saccharomyces cerevisiae, is a homologue of recA of Escherichia coli and plays crucial roles in both mitotic and meiotic recombination and in repair of double-strand breaks of DNA. We have cloned genes from human, mouse and fission yeast that are homologous to rad51. The 339 amino acid proteins predicted for the two mammalian genes are almost identical and are highly homologous (83%) with the yeast proteins. The mouse gene is transcribed at a high level in thymus, spleen, testis and ovary and at a lower level in brain and other tissues. The rad51 homologues fail to complement the DNA repair defect of rad51 mutants of S. cerevisiae. The mouse gene is located in the F1 region of chromosome 2 and the human gene maps to chromosome 15.

Amino Acid Sequence↗
PubMed1992

Phosphorylation of a surface receptor bound urokinase-type plasminogen activator in a human metastatic carcinomatous cell line.

The 32P-labeled urokinase (uPA) bound to surface receptors of Detroit 562 cells was immunoprecipitated by anti-uPA antibody. Amino acid analysis showed that tyrosines and serines were the acceptors. Inhibition of protein kinases greatly reduced the 32P incorporation, suggesting that the respective cellular src gene product and protein kinase C were involved in the phosphorylations. Proteins purified on chromatographic columns contained two forms of uPA, a high (HMW) and a low (LMW) molecular weight. Tyrosine-phosphorylation occurs in the HMW and A-chain. Such modifications might modulate the extracellular activities of uPA.

1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine↗
PubMed1992

Evolutionary origin of a Kunitz-type trypsin inhibitor domain inserted in the amyloid beta precursor protein of Alzheimer's disease.

The Kunitz-type protease inhibitor is one of the serine protease inhibitors. It is found in blood, saliva, and all tissues in mammals. Recently, a Kunitz-type sequence was found in the protein sequence of the amyloid beta precursor protein (beta APP). It is known that beta APP accumulates in the neuritic plaques and cerebrovascular deposits of patients with Alzheimer's disease. Collagen type VI in chicken also has an insertion of a Kunitz-type sequence. To elucidate the evolutionary origin of these insertion sequences, we constructed a phylogenetic tree by use of all the available sequences of Kunitz-type inhibitors. The tree shows that the ancestral gene of the Kunitz-type inhibitor appeared about 500 million years ago. Thereafter, this gene duplicated itself many times, and some of the duplicates were inserted into other protein-coding genes. During this process, the Kunitz-type sequence in the present beta APP gene diverged from its ancestral gene about 270 million years ago and was inserted into the gene soon after duplication. Although the function of the insertion sequences is unknown, our molecular evolutionary analysis shows that these insertion sequences in beta APP have an evolutionarily close relationship with the inter-alpha-trypsin inhibitor or trypstatin, which inhibits the activity of tryptase, a novel membrane-bound serine protease in human T4+ lymphocytes.

Alzheimer Disease↗
PubMed1991

Evolutionary origin of numerous kringles in human and simian apolipoprotein(a).

Human apolipoprotein(a) has a great size heterogeneity and consists of 38 kringle domains in the amino terminal and a serine protease domain in the carboxyl terminal. All but one kringle of apolipoprotein(a) are homologous to the fourth kringle of plasminogen. However, the 38th kringle resembles the fifth kringle of plasminogen and its seems to have been deleted in simian species. The phylogenetic trees suggest that an ancestral apolipoprotein(a) may have started with a duplicate of a plasminogen type protein. It also implies that deletion of the three kringles in the amino terminus followed, and that one of the remaining two kringles was duplicated in both human and simian species and the other was processed by a deletion in simian species after species separation. Thus, the number of kringles in other mammals not yet studied may vary considerably from species to species.

Animals↗
PubMed1991

Mutation pattern of human immunodeficiency virus gene.

Human immunodeficiency viruses (HIVs) show extensive genetic variation. This feature is the fundamental cause of pathogenicity of HIVs and thwarts efforts to develop effective vaccines. To understand the mutation mechanism of these viruses, we analysed nucleotide sequences of env and gag genes of the viruses by use of molecular evolutionary methods and estimated the direction and frequency of nucleotide substitutions. Results obtained showed that the frequency of changes between A and G was extremely high and the mutation pattern of HIVs was distinct from those of nuclear genes of their host cells. This distinction may be caused by the characteristics of the reverse transcription of HIVs. The mutation pattern obtained would be helpful to construct effective antiviral drugs.

Base Sequence↗
PubMed1990

Local function of urokinase receptor at the adhesion contact sites of a metastatic tumor cell.

The local activity of urokinase and its receptor associated with a cloned cell (C5) obtained from the cloning of Detroit 562 was investigated. The cellular binding sites, similar structure to adhesion plaques, were visualized by fluorescein labeled urokinase and the number was determined to be 300 per cell. The binding sites for radioiodinated urokinase were found to be 30 thousand per cell. Thus, about as many as 100 receptor molecules per site was estimated to be associated with the cellular membrane domains. Immunofluorescence studies demonstrated that the receptors were colocalized with a set of adhesion and cytoskeletal proteins such as vinculin, alpha-actinin and actin; localizing at the adhesion sites. These proteins soluble in 9 M urea were able to be reconstituted by dialyzing out the urea against low ionic buffer solution. It was demonstrated that vinculin and actin were co-associated. Since cell bound urokinase revealed fibrinolytic activity, it was suggested that the focal adhesions of the migrating cells would facilitate proteolytic action when cells move across the matrix architectures.

Actinin↗
PubMed1990

Evolutionary origin of human and simian immunodeficiency viruses.

From what viruses the human immunodeficiency viruses (HIVs) originated is an extremely controversial question. To address this question, we have analyzed nucleotide sequences of simian immunodeficiency viruses (SIVs) and HIVs by using the techniques for understanding molecular evolution. In particular, we compared the nucleotide sequences of whole genomes, gene region by gene region, between a given pair of viruses, including four types of SIVs--isolated from mandrills (Papio sphinx), African green monkeys (Cercopithecus aethiops), sooty mangabeys (Cercocebus atys), and rhesus macaques (Macaca mulatta)--as well as HIVs. Phylogenetic trees for all gene regions examined showed that the present HIVs may have emerged as different variants of SIVs of Old World monkeys, possibly from recombination between viruses related to SIVs.

Biological Evolution↗