PubMed Health⌕ Search

Biomedical subjects

R Kikuno

Publications and source records attributed to R Kikuno.

At least 37 records · Page 2Linked to original sources
PubMed1998

Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.

In this paper, we report the sequences of 100 cDNA clones newly determined from a set of size-fractionated human brain cDNA libraries and predict the coding sequences of the corresponding genes, named KIAA0819 to KIAA0918. These cDNA clones were selected on the basis of their coding potentials of large proteins (50 kDa and more) by using in vitro transcription/translation assays. The sequence data showed that the average sizes of the inserts and corresponding open reading frames are 4.4 kb and 2.5 kb (831 amino acid residues), respectively. Homology and motif/domain searches against the public databases indicated that the predicted coding sequences of 83 genes were similar to those of known genes, 59% of which (49 genes) were categorized as coding for proteins functionally related to cell signaling/communication, cell structure/motility and nucleic acid management. The chromosomal locations and the expression profiles of all the genes were also examined. For 54 clones including brain-specific ones, the mRNA levels were further examined among 8 brain regions (amygdala, corpus callosum, cerebellum, caudate nucleus, hippocampus, substantia nigra, subthalamic nucleus, and thalamus), spinal cord, and fetal brain.

Amino Acid Sequence↗
PubMed1998

Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.

In our series of projects for accumulating sequence information on the coding sequences of unidentified human genes, we have newly determined the sequences of 100 cDNA clones from a set of size-fractionated human brain cDNA libraries, and predicted the coding sequences of the corresponding genes, named KIAA0711 to KIAA0810. These cDNA clones were selected according to their coding potentials of large proteins (50 kDa and more) in vitro. The average sizes of the inserts and corresponding open reading frames were 4.3 kb and 2.6 kb (869 amino acid residues), respectively. Sequence analyses against the public databases indicated that the predicted coding sequences of 78 genes were similar to those of known genes, 64% of which (50 genes) were categorized as proteins functionally related to cell signaling/communication, cell structure/motility and nucleic acid management. As additional information concerning genes characterized in this study, the chromosomal locations of the clones were determined by using human-rodent hybrid panels and the expression profiles among 10 human tissues were examined by reverse transcription-coupled polymerase chain reaction which was substantially improved by enzyme-linked immunosorbent assay.

Brain Chemistry↗
PubMed1998

Beta-carotene hydroxylase gene from the cyanobacterium Synechocystis sp. PCC6803.

The ORF sll1468 of Synechocystis sp. PCC6803 was identified as a gene for beta-carotene hydroxylase by functional complementation in a beta-carotene-producing Escherichia coli. The gene product of ORF sll1468 added hydroxyl groups to the beta-ionone rings of beta-carotene (beta, beta-carotene) to form zeaxanthin (beta, beta-carotene-3,3'-diol). This newly identified beta-carotene hydroxylase does not show overall amino acid sequence similarity to the known beta-carotene hydroxylases. However, it showed significant sequence similarity to beta-carotene ketolases of marine bacteria and a green alga.

Amino Acid Sequence↗
PubMed1997

Cloning and crystal structure of hematopoietic prostaglandin D synthase.

Hematopoietic prostaglandin (PG) D synthase is the key enzyme for production of the D and J series of prostanoids in the immune system and mast cells. We isolated a cDNA for the rat enzyme, crystallized the recombinant enzyme, and determined the three-dimensional structure of the enzyme complexed with glutathione at 2.3 A resolution. The enzyme is the first member of the sigma class glutathione S-transferase (GST) from vertebrates and possesses a prominent cleft as the active site, which is never seen among other members of the GST family. The unique 3-D architecture of the cleft leads to the putative substrate binding mode and its catalytic mechanism, responsible for the specific isomerization from PGH2 to PGD2.

Animals↗
PubMed1997

Molecular cloning and expression of the Caenorhabditis elegans klp-3, an ortholog of C terminus motor kinesins Kar3 and ncd.

Common to all eukaryotes, kinesins are cytoskeletal motor proteins that mediate intracellular transport on microtubule tracks, using ATP hydrolysis. A Caenorhabditis elegans cDNA clone corresponding to the klp-3 gene, encoding a novel kinesin, was isolated, and mapped on LGII. Northern blot analysis using the klp-3 cDNA probe reveals a 1.9 kb mRNA that is transcribed at a low level during development. Temporal and spatial expression of the klp-3::lacZ fusion gene is limited to the marginal cells in the pharynx, and a group of muscle cells in the posterior gut region. The nucleotide sequence of klp-3 has been deduced from the cDNA and nematode genome sequencing consortium data. Conceptual translation of the klp-3 gene reveals a kinesin-like protein with its conserved motor domain containing the ATP binding and microtubule binding sites located in the C terminus. KLP-3 shares extensive homology with the yeast Kar3 and Drosophila ncd kinesins, which have previously been shown to mediate chromosomal movement and segregation during meiosis and mitosis. Overexpression of the klp-3 gene partially rescues the lethal phenotype of the maternal lethal him-14 ts(it44) mutants at non-permissive temperatures, and reduces the incidence of males caused by non-disjunction of the X-chromosome. Similarly, expression of a klp-3 antisense RNA, under the control of a heat shock promoter, causes embryonic arrest, dead eggs and polyploid cells in transgenic lines, suggesting a critical role for the klp-3 function in chromosome segregation. Further analysis of the klp-3 gene in C. elegans may elucidate diverse functions of the C terminus mitotic motor proteins during development.

Amino Acid Sequence↗
PubMed1997

Cloning of human and mouse cDNAs encoding novel zinc finger proteins expressed in cerebellum and hippocampus.

We identified a novel gene, kf-1, highly expressed in the normal cerebellum but not in the cerebral cortex, the expression of which could have been augmented in the cerebral cortex of a sporadic Alzheimer's disease patient. We cloned human and mouse entire kf-1 cDNAs encoding conserved 79 kDa proteins containing a zinc-binding RING-H2 finger motif at the carboxy-terminus as found in acetylcholine receptor-associated protein (RAPsyn). The 3'-untranslated regions are highly conserved between human and mouse as to constitute a common mRNA secondary structure. In situ hybridization analysis of mouse brain sections revealed strong kf-1 expression in the cerebellum and hippocampus. We propose that KF-1 is involved in membranous protein-sorting apparatus similarly to RAPsyn. We mapped the human kf-1 gene to 2p11.2.

Alzheimer Disease↗
PubMed1997

Molecular evolution of the photolyase-blue-light photoreceptor family.

The photolyase-blue-light photoreceptor family is composed of cyclobutane pyrimidine dimer (CPD) photolyases, (6-4) photolyases, and blue-light photoreceptors. CPD photolyase and (6-4) photolyase are involved in photoreactivation for CPD and (6-4) photoproducts, respectively. CPD photolyase is classified into two subclasses, class I and II, based on amino acid sequence similarity. Blue-light photoreceptors are essential light detectors for the early development of plants. The amino acid sequence of the receptor is similar to those of the photolyases, although the receptor does not show the activity of photoreactivation. To investigate the functional divergence of the family, the amino acid sequences of the proteins were aligned. The alignment suggested that the recognition mechanisms of the cofactors and the substrate of class I CPD photolyases (class I photolyases) are different from those of class II CPD photolyases (class II photolyases). We reconstructed the phylogenetic trees based on the alignment by the NJ method and the ML method. The phylogenetic analysis suggested that the ancestral gene of the family had encoded CPD photolyase and that the gene duplication of the ancestral proteins had occurred at least eight times before the divergence between eubacteria and eukaryotes.

Amino Acid Sequence↗
PubMed1994

Molecular cloning and characterization of OB-cadherin, a new member of cadherin family expressed in osteoblasts.

The preferential screening of cDNA libraries derived from the mouse osteoblastic cell line MC3T3-E1 has yielded a cDNA clone encoding 796 amino acids including the typical 24-residue-long signal sequence. The predicted amino acid sequence revealed that this protein constitutes a new member of the cadherin family. We propose the name OB-cadherin (OB for osteoblast) for this new protein. RNA analyses revealed that the OB-cadherin gene is selectively expressed in osteoblastic cell lines, precursor cell lines of osteoblasts, and primary osteoblastic cells from calvaria, as well as in lung, testis, and brain tissues at low levels. Transfection of OB-cadherin cDNA into L cells resulted in the acquisition of the Ca(2+)-dependent adhesive property. Two different forms of the human OB-cadherin cDNA were subsequently cloned; one is a counterpart of mouse OB-cadherin gene, and the other encodes a protein with a truncated cytoplasmic domain. The results suggest that the newly found OB-cadherin might have an important role in bone formation.

Amino Acid Sequence↗
PubMed1994

Cloning and characterization of OSF-3, a new member of the MER5 family, expressed in mouse osteoblastic cells.

A cDNA library prepared from the mouse osteoblastic cell line, MC3T3-E1, was screened for the presence of specifically expressed genes by employing subtraction hybridization/differential screening methods. A cDNA clone was identified and sequenced, encoding a protein designated as osteoblast specific factor 3 (OSF-3) comprising 199 amino acids. RNA dot blot analysis indicated weak OSF-3 expression in thymus, spleen, brain, lung, testis, and heart, and high expression in kidney and liver. A homology search of an amino acid sequence database revealed a strong relationship of OSF-3 to the MER5 (gene preferentially expression in murine erythroleukemia cells) protein and human pag (proliferation associated gene) product. This indicates that OSF-3 plays an intrinsic role in the proliferation and/or differentiation of bone cells.

Amino Acid Sequence↗
PubMed1993

Osteoblast-specific factor 2: cloning of a putative bone adhesion protein with homology with the insect protein fasciclin I.

A cDNA library prepared from the mouse osteoblastic cell line MC3T3-E1 was screened for the presence of specifically expressed genes by employing a combined subtraction hybridization/differential screening approach. A cDNA was identified and sequenced which encodes a protein designated osteoblast-specific factor 2 (OSF-2) comprising 811 amino acids. OSF-2 has a typical signal sequence, followed by a cysteine-rich domain, a fourfold repeated domain and a C-terminal domain. The protein lacks a typical transmembrane region. The fourfold repeated domain of OSF-2 shows homology with the insect protein fasciclin I. RNA analyses revealed that OSF-2 is expressed in bone and to a lesser extent in lung, but not in other tissues. Mouse OSF-2 cDNA was subsequently used as a probe to clone the human counterpart. Mouse and human OSF-2 show a high amino acid sequence conservation except for the signal sequence and two regions in the C-terminal domain in which 'in-frame' insertions or deletions are observed, implying alternative splicing events. On the basis of the amino acid sequence homology with fasciclin I, we suggest that OSF-2 functions as a homophilic adhesion molecule in bone formation.

3T3 Cells↗
PubMed1992

[Newly developed MRSA medium].

We have developed a new selective medium, tentatively named MR(SA)2, for rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) from clinical specimens. MR(SA)2 medium contained modified Müller-Hinton agar supplemented with 75 g of NaCl, 10 g of mannit, 20 mg of bromcresol purple, 20 g of egg-yolk, 4 mg of oxacillin, and 12.5 mg of ceftisoxime per 1,000 ml. There were no differences between the growth of MRSA strains on this medium at 30 C and that of 37 C. This medium can detect the egg-yolk reaction instead of the coagulase reaction. By single streaking of a test material on the surfaces of MR(SA)2 agar, MRSAs can easily be distinguished from methicillin-resistant coagulase-negative staphylococci (MR-CNS), other bacteria and fungi from their colony morphologies in a quantitative manner. A few MRSA strains would not form colonies on this medium because of their susceptibilities to ceftisoxime, but this may not inpede its use, since most MRSA strains isolated from clinical materials showed resistance to ceftisoxime. From the above results, the MR(SA)2 medium may be suitable for rapid detection of MRSA and MR-CNS.

Ceftizoxime↗
PubMed1992

[Proposal for the nosocomial infection control of methicillin-resistant Staphylococcus aureus (MRSA)].

To determine the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in hospital environments, quantitative isolation of MRSA from environmental and human specimens was performed. It was found that as many as 6 x 10(4) colony forming units (CFU)/100cm2 of MRSA and also methicillin-resistant coagulase-negative Staphylococcus (MRCNS) were isolated from 1) 25-100% of the bed-mattresses tested in 10 out of 11 (90%) hospitals, and also 2) bed sheets for patients, floors of patient wards, laundry, bath-room, toilet and laundry storage-room. And seven and eight palms of 20 patients were contaminated with MRCNS and MRSA, respectively, and MRCNS contamination was revealed in six of medical staffs. These results indicate that hospital environments, especially the mattresses and hospital floors are highly contaminated with MRCNS and MRSA, and sanitation and cleanliness of mattresses and floors are necessary to prevent the dissemination of both MRCNS and MRSA in hospital.

Cross Infection↗
PubMed1990

Isolation of mouse and human cDNA clones encoding a protein expressed specifically in osteoblasts and brain tissues.

Using the differential hybridization screening method between osteoblastic and fibroblastic cells, a cDNA clone coding for an osteoblast specific protein, named OSF-1, consisting of 168 amino acid residues including a possible 32 amino acid long leader sequence, was isolated from murine osteoblastic cell line MC3T3-E1. The OSF-1 gene was shown by Northern blotting analysis to be expressed in mouse calvarial osteoblast-enriched cells and in mouse brain tissues, but not in thymus, spleen, kidney, liver, lung, testis or heart. The human counterpart was also found in cDNA libraries from human osteosarcoma cell line MG63 and normal brain tissues. DNA sequence analysis revealed four amino acid sequence differences between the mouse and human, of which only one is located in the mature protein. This extremely high sequence conservation suggests that OSF-1 plays a fundamental role in bone and brain functions.

Animals↗
PubMed1987

Structure of human alpha 2-plasmin inhibitor deduced from the cDNA sequence.

We have isolated three cDNA clones for human alpha 2-plasmin inhibitor (alpha 2-PI). Two clones are from human hepatoma cell line, Hep G2, and cover the entire protein coding region plus the 3'-flanking region up to the poly(A) sequence, and the other clone is from human liver and contains the carboxyl-terminal half. The total length of the cDNAs is 2.29 kb, corresponding to more than 95% of the full-length mRNA. alpha 2-PI seems to consist of 452 amino acid residues plus 39 amino acid residues for the signal peptide. The amino acid sequence shows 23 to 28% homology to those of five other protease inhibitors, plasminogen activator inhibitor (PAI), protein C inhibitor (PCI), alpha 1-antitrypsin (alpha 1-AT), antithrombin III (AT III), and alpha 1-antichymotrypsin (alpha 1-AC). alpha 2-PI seems to be the most distantly related among these inhibitors. Comparison of the phylogenetic trees of proteases and their inhibitors indicates that four proteases, namely elastase (or trypsin), chymotrypsin, plasminogen activator, and thrombin, may have evolved concurrently with the corresponding inhibitors. However, alpha 2-PI and PCI seem to have evolved asynchronously from their substrates. The data suggest that alpha 2-PI may originally have inhibited some protease other than plasmin, and protein C may have had an inhibitor different from the present one early in its evolutionary history.

Amino Acid Sequence↗
PubMed1985

Sequence homologies among mitochondrial DNA-coded URF2, URF4 and URF5.

Amino acid sequences coded for by 13 different genes of mammalian mitochondrial DNA (mtDNA) including 8 unassigned open reading frames (URFs) were compared in pairs. It was found that significant homologies exist among the amino acid sequences of the three URFs (URF2, URF4 and URF5) with a probability of occurrence of less than 10(-5). This result strongly suggests that the 3 URFs evolved from a single ancestral gene by a series of gene duplications. A phylogenetic tree based on the alignment of the URF sequences from mammals, an insect, a fungus and protozoa revealed a very remote divergence of the 3 URFs, going back to a time before separations of animal/protozoa and animal/fungus.

Amino Acid Sequence↗
PubMed1985

Close structural resemblance between putative polymerase of a Drosophila transposable genetic element 17.6 and pol gene product of Moloney murine leukaemia virus.

We have made a computer-assisted search for homology among polymerases or putative polymerases of various viruses and a transposable element, the Drosophila copia-like element 17.6. The search revealed that the putative polymerase (second open reading frame) of the copia-like element 17.6 bears close resemblance in overall structural organization to the pol gene product of Moloney murine leukaemia virus (M-MuLV): they show significant homology to each other at both the N- and C-terminal portions, suggesting that the 17.6 putative polymerase carries two enzymatic activities, related to reverse transcriptase and DNA endonuclease. The putative polymerase of cauliflower mosaic virus (CaMV) shows striking homology with the putative polymerase of 17.6 over almost its entire length, but it lacks the DNA endonuclease-related sequence. Furthermore, it was shown that the N-terminal ends of the M-MuLV pol product and the CaMV and 17.6 putative polymerases exhibit strong sequence homology with the gag-specific protease (p15) of Rous sarcoma virus (RSV) as well as the amino acid sequence predicted from the gag/pol spacer sequence of human adult T-cell leukaemia virus (HTLV). These p15-related sequences contain a highly conserved stretch of amino acids which show a close similarity with sequences around the active site amino acids Asp-Thr-Gly of the acid protease family, suggesting that they have an activity similar to acid protease. On the basis of the alignment of reverse transcriptase-related sequences, a dendrogram representing phylogenetic relationships among all the viruses compared together with 17.6 was constructed and its evolutionary implication is discussed.

Amino Acid Sequence↗
PubMed1985

Evolution of influenza virus genes.

The nucleotide sequences of the eight different influenza A virus segments (genes) were compared among 14 different subtypes. These comparisons demonstrate the presence of molecular clocks in the viral genes; they accumulated both silent and amino acid-changing substitutions at approximately constant rates with respect to time during evolution. In addition, comparison of the rates of evolution among the eight viral genes, excluding the P2 gene, revealed a rapid and roughly equal rate of silent substitution for different genes. The P2 gene exception is explained as the result of recombination (reassortment) between distantly related strains. The rate of amino acid-changing substitution differs greatly from gene to gene. The rate of silent substitution was estimated to be 1.1 X 10(-2)/site/year on the average--that is, about 2 X 10(6) times higher than eukaryotic gene equivalents, which is remarkable. Strain A/USSR/90/77 was shown to evolve with a rate that is similar to those of other strains but to behave as if replication was frozen during a certain period (Nakajima et al. 1978). The frozen period was estimated to be 25 yr on the basis of the molecular clock. A similar analysis revealed another example of frozen replication--in this case, apparently for a period of about 9 yr--in a duck strain, A/duck/Ontario/77.

Amino Acid Sequence↗