Biomedical subjects

Kohji Yamamoto

Publications and source records attributed to Kohji Yamamoto.

At least 19 recordsLinked to original sources

PubMed2006

Genes encoding small heat shock proteins of the silkworm, Bombyx mori.

Small heat shock protein (sHSP) is a family of ubiquitous polypeptides involved in a variety of physiological phenomena. From the silkworm, Bombyx mori, we isolated and sequenced the following cDNAs encoding sHSPs: shsp19.9, shsp20.1, shsp20.4, shsp20.8, shsp21.4, and shsp23.7. shsp21.4 was nearly twice as large in size as other shsps. The deduced amino acid sequence of sHSP21.4 was similar to that of Drosophila melanogaster CG14207-PA. Other sHSPs were highly similar to each other and, in a phylogenetic tree, formed a cluster including Plodia interpunctella alphaCP25. It was speculated that shsp21.4 has at least one intron in genome while other shsps do not. The transcripts of all shsps were subtle, but were constitutively detected in various tissues. Heat shock triggered a substantial increase in the transcripts other than shsp21.4. The B. mori sHSPs are perhaps classified into at least two groups: sHSP21.4 and others.

Animals↗

PubMed2006

Steroid hormone profiles of urban and tidal rivers using LC/MS/MS equipped with electrospray ionization and atmospheric pressure photoionization sources.

A highly sensitive and uncomplicated method of analyzing steroidal hormones in river and estuarine water samples was developed using a liquid chromatography tandem mass spectrometer equipped with an electrospray ionization (ESI) source and atmospheric pressure photoionization (APPI) source. Steroidal hormones included not only estrogen but also androgen and conjugates of these two. APPI displayed greater sensitivity than ESI for most of the unconjugated steroids examined, with very high sensitivity for testosterone and 4-androstene-3,17-dione in particular. For conjugated hormones, in contrast, ESI was more effective. The method developed was applied to the determination of hormones in the rivers of Osaka City and their estuaries, where the hormones detected were affected by the effluent from municipal wastewater treatment plants (WWTPs), and hormone concentration values were comparable to those reported in previous studies of such effluent. Because of the two-way flow and stagnancy of streams and watercourses, continuous input of steroidal hormones from WWTPs seems to bring about local accumulation. Levels of androgen were 1 order of magnitude lower than those of estrogen. Estrone, estrone 3-sulfate, and 4-androstene-3,17-dione were detected in almost all water samples, with maxima of 51, 5.1, and 6.4 ng L(-1), respectively.

Atmospheric Pressure↗

PubMed2006

Proteome analysis of silk gland proteins from the silkworm, Bombyx mori.

The silk gland of Bombyx mori is an organ specialized for the synthesis and secretion of silk proteins. We report here the resolution of silk gland proteins by 2-DE and the identification of many of those proteins. This was accomplished by dissecting the glands into several sections, with each exhibiting more than 400 protein spots by 2-DE, of which 100 spots were excised and characterized by in-gel digestion followed by PMF. Ninety-three proteins were tentatively identified. These were then categorized into groups involved in silk protein secretion, transport, lipid metabolism, defense, etc. Western blotting of a 2-DE gel using an antibody of the carotenoid binding protein confirmed the presence of this protein in the silk gland. Proteins including fibroin L-chain and P25 were found as multiple isoforms, some of which contained differential amounts of phosphate residues as analyzed by on-probe dephosphorylation. The current analysis contributes to our understanding of proteins expressed by the silk gland not only of the model lepidopteran B. mori, but also to proteins from other silk-producing insects such as Philosamia cynthia ricini.

Animals↗

PubMed2006

The intrinsic ATPase activity of Mycobacterium tuberculosis DnaA promotes rapid oligomerization of DnaA on oriC.

Oligomerization of the initiator protein, DnaA, on the origin of replication (oriC) is crucial for initiation of DNA replication. Studies in Escherichia coli (Gram-negative) have revealed that binding of DnaA to ATP, but not hydrolysis of ATP, is sufficient to promote DnaA binding, oligomerization and DNA strand separation. To begin understanding the initial events involved in the initiation of DNA replication in Mycobacterium tuberculosis (Gram-positive), we investigated interactions of M. tuberculosis DnaA (DnaA(TB)) with oriC using surface plasmon resonance in the presence of ATP and ADP. We provide evidence that, in contrast to what is observed in E. coli, ATPase activity of DnaA(TB) promoted rapid oligomerization on oriC. In support, we found that a recombinant mutant DnaA(TB) proficient in binding to ATP, but deficient in ATPase activity, did not oligomerize as rapidly. The corresponding mutation in the dnaA gene of M. tuberculosis resulted in non-viability, presumably due to a defect in oriC-DnaA interactions. Dimethy sulphate (DMS) footprinting experiments revealed that DnaA(TB) bound to DnaA boxes similarly with ATP or ADP. DnaA(TB) binding to individual DnaA boxes revealed that rapid oligomerization on oriC is triggered only after the initial interaction of DnaA with individual DnaA boxes. We propose that ATPase activity enables the DnaA protomers on oriC to rapidly form oligomeric complexes competent for replication initiation.

Adenosine Triphosphatases↗

PubMed2006

Silkworm midgut proteins interacting with a hemolymph protease inhibitor, CI-8.

CI-8 is the chymotrypsin inhibitor in hemolymph from the silkworm, Bombyx mori. It occurs in the midgut at the spinning stage of larva, but little information on the mechanism of its uptake in the midgut is available. We found that two polypeptides interacting with CI-8 are in the midgut membrane, and we purified them using a biotinylated CI-8, viz., p29 and p60, having molecular sizes of 29 kDa and 60 kDa respectively. The structures of p29 and p60 were examined by N-terminal amino acid sequencing and peptide mass mapping, including tryptic digestion. p29 was highly similar to the matured 19G1-30K lipoprotein from hemolymph, but p60 was novel. Purified p29 was recognized by anti-19G1-30K antibody, and was confirmed to be similar to 19G1-30K. The antibody also neutralized the CI-8 binding ability of p29 in the midgut membrane. p29 and p60 are perhaps proteinaceous factors involved in the uptake of CI-8 into the midgut through the membrane.

Amino Acid Sequence↗

PubMed2005

Molecular and biochemical characterization of manganese-containing superoxide dismutase from the silkworm, Bombyx mori.

Superoxide dismutase (SOD) is responsible for the removal of superoxide anion from living organisms. In this study, cDNA encoding the manganese-containing SOD (MnSOD) from the silkworm, Bombyx mori, was isolated by reverse transcriptase-polymerase chain reaction and sequenced. The deduced amino acid sequence of the MnSOD revealed 62% identity to that of the Drosophila melanogaster; both were close to each other in a phylogenetic tree. The MnSOD was overproduced in Escherichia coli and purified. The internal structure of the recombinant MnSOD was confirmed by peptide mass fingerprinting method. The recombinant MnSOD facilitating the reduction reaction of superoxide anion retained 75% of its original activity after incubation at pH 4-11 for 24 h at 4 degrees C. Its activity was never affected by incubation at pH 7 for 30 min below 50 degrees C.

Amino Acid Sequence↗

PubMed2005

Terahertz time-domain spectroscopy of amino acids and polypeptides.

Frequency-dependent absorption coefficients and refractive indices of amino acids (glycine and l-alanine) and polypeptides (polyglycine and poly-l-alanine) in the wavenumber region from 7 to 55 cm(-1) were measured by terahertz time-domain spectroscopy. A vibrational band was observed at 45.5 cm(-1) for polyglycine, which was assigned as an interchain mode. The reduced absorption cross sections of the amino acids and polypeptides show power-law behavior. The exponents are different between the monomers and polymers, and those of the two polypeptides suggest that the time dependences of the total dipole moments are similar in the timescale of subpico- to picoseconds.

Alanine↗

PubMed2005

Cloning, expression and characterization of theta-class glutathione S-transferase from the silkworm, Bombyx mori.

This study focused on glutathione S-transferase (GST), one of the detoxification enzymes, from the silkworm, Bombyx mori (GSTT1). A cDNA encoding a putative GST was amplified by reverse transcriptase-polymerase chain reaction and sequenced. The deduced amino acid sequence revealed 59%, 57% and 56% identities to theta-class GSTs of Musca domestica, Anopheles gambiae and Drosophila melanogaster, respectively. GSTT1 was also estimated to be close to those GSTs in a phylogenetic tree. Recombinant GST (rGSTT1) was functionally overexpressed in Escherichia coli in a soluble form, purified to homogeneity, and characterized. The pH-optimum of rGSTT1 was broad from pH 4 to 9 and rGSTT1 retained more than 75% of its original activity after incubation at pH 5-11. Incubation for 30 min at temperatures below 50 degrees C also affected the activity insignificantly. The Michaelis constant for 1-chloro-2,4-dinitrobenzene was 0.48 mM.

Amino Acid Sequence↗

PubMed2005

Catalase from the silkworm, Bombyx mori: gene sequence, distribution, and overexpression.

Living organisms require mechanisms regulating reactive oxygen species (ROS) such as hydrogen peroxide and superoxide anion. Catalase is one of the regulatory enzymes and facilitates the degradation of hydrogen peroxide to oxygen and water. Biochemical information on an insect catalase is, however, insufficient. Using mRNA from fat body of the silkworm, Bombyx mori, a cDNA encoding a putative catalase was amplified by reverse transcriptase-polymerase chain reaction and sequenced. The deduced amino acid sequence comprised 507 residues with more than seventy residues forming a scaffold for a heme cofactor conserved. The sequence showed 71% and 66% identities to those of the Drosophila melanogaster and Apis mellifera catalases, respectively; the catalase from B. mori was estimated to be phylogenetically close to that from A. mellifera. The transcripts of the gene and the catalase activity were distributed in diverse tissues of B. mori, suggesting its ubiquitous nature. Using the gene, a recombinant catalase (rCAT) was functionally overexpressed in a soluble form using Escherichia coli, purified to homogeneity, and characterized. The pH-optimum of rCAT was broad around pH 8.0. More than 80% of the original rCAT activity was retained after incubation in the following conditions: at pH 8-11 and 4 degrees C for 24 h; at pH 7 and temperatures below 50 degrees C for 30 min. The Michaelis constant for hydrogen peroxide was evaluated to be 28 mM at pH 6.5 and 30 degrees C. rCAT was suggested to be a member of the typical catalase family.

Adipose Tissue↗

PubMed2005

Integration of molecular and classical linkage groups of the silkworm, Bombyx mori (n = 28).

Previously published linkage groups (LGs) composed of molecular markers were assigned to classical LGs in the silkworm, Bombyx mori (n = 28). Four markers from the classical linkage map, og, w-1, Lp, and Pfl, were assigned to the molecular linkage maps using sequence tagged sites. In addition, linkage analysis was carried out using BF1 progeny between wild-type and mutant stocks carrying morphological phenotypic markers. As a result, the counterparts for 26 of 28 molecular LGs were identified with their counterparts of the classical LGs. Two visible markers, Sel and Xan, representing different classical LGs, were found to be linked.

Animals↗

PubMed2005

Proteomic studies of isoforms of the P25 component of Bombyx mori fibroin.

It is recognized that P25 is one of three polypeptide components of the fibroin synthesized in the larval silk gland (SG) of silkworm, having two glycosylated isoforms. In the present study, however, eight P25 isoforms were separated by proteomics, including two-dimensional gel electrophoresis of whole SG proteins, and were identified by the peptide mass fingerprinting method. Four of the eight isoforms were identified as Bombyx mandarina P25s, although the SG of Bombyx mori has never been considered to contain the P25 from B. mandarina. It is suggested that this diversity of P25 isoforms depends on phosphorylation modification in addition to glycosylation.

Amino Acid Sequence↗

PubMed2005

Superoxide dismutase from the silkworm, Bombyx mori: sequence, distribution, and overexpression.

Superoxide dismutase (SOD) is an enzyme facilitating the removal of superoxide anions from living organisms. This study focused on SOD from the silkworm, Bombyx mori (bmSOD). cDNA encoding bmSOD was amplified by reverse transcriptase-polymerase chain reaction. The deduced amino acid sequence of bmSOD indicated that the residues forming the Cu/Zn binding site are conserved and that the sequence is in 60% identity to that of the Drosophila melanogaster. B. mori SOD was also close to the D. melanogaster SOD in a phylogenetic tree. The bmSOD mRNA and the enzyme activity were widely distributed in diverse tissues. bmSOD functionally overexpressed in Escherichia coli in a soluble form was purified, and its stability was examined. bmSOD at 4 degrees C retained almost all of its original activity after incubation at pH 4-11 for 24 h. Incubation (pH 7) for 30 min at temperatures below 40 degrees C also affected activity insignificantly.

Amino Acid Sequence↗

PubMed2004

Overexpression in Escherichia coli and purification of recombinant CI-b1, a Kunitz-type chymotrypsin inhibitor of silkworm.

Present research provided an efficient approach to obtain large quantities of active recombinant CI-b1, a Kunitz-type chymotrypsin inhibitor of silkworm, Bombyx mori. The cDNA encoding mature CI-b1 was cloned into pDEST17 vector. Recombinant protein with hexa-histidine tag attached to the N-terminal of CI-b1 was expressed in Escherichia coli Origami B cells. It can be purified to homogeneity via the gel filtration chromatography on a Sephacryl S-200 column followed the affinity chromatography on a Ni-NTA column. The two sequential purification procedures yielded 4.3mg purified (His)(6)-tagged CI-b1 from 200ml of culture medium. Studies on (His)(6)-tagged CI-b1 revealed that three disulfide bonds were formed in the recombinant CI-b1 and the inhibitory properties of recombinant CI-b1 against alpha-chymotrypsin were similar to those of native CI-b1. Recombinant CI-b1 immobilized on Ni-NTA resin was used to detect the interactions occurring between the CI-b1 and its target factors.

Animals↗

PubMed2004

Proteomic studies of lipopolysaccharide-induced polypeptides in the silkworm, Bombyx mori.

Silkworm larvae at the 5th instar were injected with lipopolysaccharide from Escherichia coli and inducible polypeptides were examined within a pI range of 3-10 and a size range of 14-97 kDa by proteomics, including peptide mass fingerprinting. No polypeptides were induced in the midgut. FB1 and H1-4 polypeptides were significantly induced in fat body and hemolymph, respectively. FB1 and H1 were estimated to be antitrypsin and serpin-2 proteinase inhibitors respectively. H2 and H3 were novel polypeptides. H4 was estimated to be attacin antibacterial polypeptide with high coverage of sequence. The amounts of all the induced polypeptides decreased at 48 h after the injection.

Animals↗

PubMed2004

Utility of dry gel from two-dimensional electrophoresis for peptide mass fingerprinting analysis of silkworm proteins.

We compared the use of wet and dry two-dimensional electrophoresis (2-DE) gels for in-gel tryptic digestion and subsequent analysis by mass spectrometry, first using bovine serum albumin (BSA) as a model protein and then using unknown proteins from an extract of the silkworm midgut. The gel was either dried at 80 degrees C or left wet. Upon analysis of BSA, there was little difference in peptide recovery from 2-DE or in mass spectrum between the dry and the wet gels. The midgut extract was resolved into more than 1,100 protein spots by 2-DE, and 40 of these spots were sampled for further analysis. For all of the 40 proteins, the results obtained from dry and wet gels were quite similar in mass spectra and protein identification, although the relative amounts of peptides from tryptic digestion ranged from 45 to 146%. Based on these results, we confirmed the utility of dry electrophoretic gels for proteomics of insect extracts.

Animals↗

PubMed2004

In vivo and in vitro interactions of the Bombyx mori chymotrypsin inhibitor b1 with Escherichia coli.

Various chymotrypsin inhibitors occur in the hemolymph of silkworm larvae. Interaction of chymotrypsin inhibitor b1 (CI-b1) with Escherichia coli was examined from the viewpoint of action against invading bacteria. Injection of dead E. coli cells into larva reduced the CI-b1 content of the hemolymph, suggesting in vivo binding of CI-b1 to the outer membrane of the cell. Results from incubation of E. coli in cell-free hemolymph in the presence or absence of lipopolysaccharide indicated that CI-b1 is the only CI bound to E. coli and that it interacts with lipopolysaccharide. CI-b1 formed a complex with lipopolysaccharide in vitro; the value of the dissociation constant was relatively large. Inhibitory activity of CI-b1 changed insignificantly in mixture with lipopolysaccharide. CI-b1 affected the growth of E. coli but never worked lethally. CI-b1 is speculated to be a mediator that scavenges intruding bacteria rather than a direct anti-bacterial factor. This is the first report confirming that CI-b1 is a lipopolysaccharide binding protein.

Animals↗

PubMed2004

Stem durability testing of interdental brush.

The purpose of the present study was to determine the ability of interdental brush to withstand repeated use and to relate this property to clinically observed fractures of such brushes. The stem durability test was conducted according to ISO (International Standards Organization) standard by using a bending at 90 degrees under a 500-g controlled load (ISO/TC106/SC7/ WG3). Two sizes (ss, m) of each of the five commercially available interdental brushes (D, B, P, I, S) were used. The cycle number at the time of fracture was noted for all interdental brushes. The fractured surfaces of the stem wire following the stem durability test were also observed under a scanning electron microscope. The specimens, when ranked in decreasing order of the number of cycles at which fracture occurred, were D-m, D-ss, B-ss, B-m > P-m, P-ss, I-ss, I-m, S-m, S-ss (P < 0.05). L-type interdental brushes (P-m, P-ss, I-ss, I-m, S-m, and S-ss) showed significantly decreased fracture resistance when compared with straight-type interdental brushes (D-m, D-ss, B-ss, B-m). In all cases, the fracture was found to be of ductile nature.

Dental Devices, Home Care↗

PubMed2003

Genomic structure and expression analysis of the gene encoding a silkworm basic Kunitz-type chymotrypsin inhibitor.

Kunitz-type chymotrypsin inhibitor CIb1 of silkworm Bombyx mori is a basic peptide consisting of 62 amino acid residues. To elucidate the mechanisms of transcriptional regulation of CIb1 gene expression, we cloned it for genomic structure analysis. CIb1 cDNA was used as a probe to screen a BAC sub-library. One positive clone containing the upstream sequences was isolated and the sequence result showed that CIb1 gene consists of three exons spaced by two introns. In the 5'-flanking region, consensus TATA and CCAAT boxes were identified. Other binding sites for transcription factors such as NF-kappaB, GATA, C/EBP, COUP-TF/HNF-4, RORalpha1, SRY, and HOXA3 were also detected. Southern blot analysis suggested a single copy of CIb1 gene in the silkworm genome. Northern blot analysis indicated that the expression of CIb1 gene is transcriptionally regulated during development and is apparently tissue-specific. The CIb1 mRNA was detected in fat body, ovary, trachea, and skin. We furthermore investigated the CIb1 expression profiles after LPS and E. coli injection. The fluctuations of CIb1 transcript in challenged larvae confirm our proposal that CIb1 is an immune responsible gene. According to our data, we discussed the transcriptional factors putatively responsible for the physiological role of CIb1 in the silkworm hemolymph.

Animals↗