Kawai M

References (10)

Title : Complete genome sequence and expression profile of the commercial lytic enzyme producer Lysobacter enzymogenes M497-1 - Takami_2017_DNA.Res_24_169
Author(s) : Takami H , Toyoda A , Uchiyama I , Itoh T , Takaki Y , Arai W , Nishi S , Kawai M , Shin-Ya K , Ikeda H
Ref : DNA Research , 24 :169 , 2017
Abstract : Lysobacter enzymogenes M497-1 is a producer of commercialized achromopeptidase and is expected to harbour genes encoding various other antimicrobial enzymes. Here, we present the complete sequence of the genome of M497-1 and the expression profiles of the genes for various antimicrobial enzymes. Of the 117 peptidase-encoding genes found in the 6.1-Mb genome of M497-1, 15 genes (aside from the gene encoding the achromopeptidase) were expressed at a level higher than that of the average ribosomal protein genes in the 24-h culture. Thus, the strain was found more valuable than hitherto considered. In addition, M497-1 harbours 98 genes involved in the biosynthesis of various natural products, 16 of which are M497-1-specific across 4 Lysobacter species. A gene cluster starting at LEN_2603 through LEN_2673 among the 98 genes closely resembled the lysobactin biosynthesis gene cluster of Lysobacter sp. ATCC 53042. It is likely that M497-1 may produce lysobactin or related antibacterial compounds. Furthermore, comparative genomic analysis of M497-1 and four other Lysobacter species revealed that their core genome structure comprises 3,737 orthologous groups. Our findings are expected to advance further biotechnological application of Lysobacter spp. as a promising source of natural bioactive compounds.
ESTHER : Takami_2017_DNA.Res_24_169
PubMedSearch : Takami_2017_DNA.Res_24_169
PubMedID: 28065880
Gene_locus related to this paper: lysen-a0a1j1ebl3 , lysen-a0a1j1e5b0 , lysen-a0a0s2dfs0

Title : High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes - Kawai_2014_Front.Microbiol_5_80
Author(s) : Kawai M , Futagami T , Toyoda A , Takaki Y , Nishi S , Hori S , Arai W , Tsubouchi T , Morono Y , Uchiyama I , Ito T , Fujiyama A , Inagaki F , Takami H
Ref : Front Microbiol , 5 :80 , 2014
Abstract : Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere.
ESTHER : Kawai_2014_Front.Microbiol_5_80
PubMedSearch : Kawai_2014_Front.Microbiol_5_80
PubMedID: 24624126
Gene_locus related to this paper: 9zzzz-x0wci8 , 9zzzz-x1k9j7 , 9zzzz-x0se68 , 9zzzz-x0tpm6 , 9zzzz-x0tv89 , 9zzzz-x0ws69 , 9zzzz-x1tg33 , 9zzzz-x1anx0 , 9zzzz-x1m8t8 , 9zzzz-x1a5i7 , 9zzzz-x1k2t2 , 9zzzz-x0uzq5

Title : Decreased resting energy expenditure in patients with Duchenne muscular dystrophy - Shimizu-Fujiwara_2012_Brain.Dev_34_206
Author(s) : Shimizu-Fujiwara M , Komaki H , Nakagawa E , Mori-Yoshimura M , Oya Y , Fujisaki T , Tokita Y , Kubota N , Shimazaki R , Sato K , Ishikawa T , Goto K , Mochizuki H , Takanoha S , Ogata K , Kawai M , Konagaya M , Miyazaki T , Tatara K , Sugai K , Sasaki M
Ref : Brain Dev , 34 :206 , 2012
Abstract : BACKGROUND: Skeletal muscle metabolism is a major determinant of resting energy expenditure (REE). Although the severe muscle loss that characterizes Duchenne muscular dystrophy (DMD) may alter REE, this has not been extensively investigated. METHODS: We studied REE in 77 patients with DMD ranging in age from 10 to 37 years using a portable indirect calorimeter, together with several clinical parameters (age, height, body weight (BW), body mass index (BMI), vital capacity (VC), creatine kinase, creatinine, albumin, cholinesterase, prealbumin), and assessed their influence on REE. In addition, in 12 patients maintaining a stable body weight, the ratio of energy intake to REE was calculated and defined as an alternative index for the physical activity level (aPAL). RESULTS: REE (kcal/day, mean+/-SD) in DMD patients was 1123 (10-11 years), 1186+/-188 (12-14 years), 1146+/-214 (15-17 years), 1006+/-136 (18-29 years) and 1023+/-97 (>/=30 years), each of these values being significantly lower than the corresponding control (p<0.0001). VC (p<0.001) was the parameter most strongly associated with REE, followed by BMI (p<0.01) and BW (p<0.05). The calculated aPAL values were 1.61 (10-11 years), 1.19 (12-14 years), 1.16 (15-17 years), and 1.57 (18-29 years). CONCLUSION: The REE in DMD patients was significantly lower than the normal value in every age group, and strongly associated with VC. Both the low REE and PAL values during the early teens, resulting in a low energy requirement, might be related to the obesity that frequently occurs in this age group. In contrast, the high PAL value in the late stage of the disease, possibly due to the presence of respiratory failure, may lead to a high energy requirement, and thus become one of the risk factors for development of malnutrition.
ESTHER : Shimizu-Fujiwara_2012_Brain.Dev_34_206
PubMedSearch : Shimizu-Fujiwara_2012_Brain.Dev_34_206
PubMedID: 21632191

Title : Birth and death of genes linked to chromosomal inversion - Furuta_2011_Proc.Natl.Acad.Sci.U.S.A_108_1501
Author(s) : Furuta Y , Kawai M , Yahara K , Takahashi N , Handa N , Tsuru T , Oshima K , Yoshida M , Azuma T , Hattori M , Uchiyama I , Kobayashi I
Ref : Proc Natl Acad Sci U S A , 108 :1501 , 2011
Abstract : The birth and death of genes is central to adaptive evolution, yet the underlying genome dynamics remain elusive. The availability of closely related complete genome sequences helps to follow changes in gene contents and clarify their relationship to overall genome organization. Helicobacter pylori, bacteria in our stomach, are known for their extreme genome plasticity through mutation and recombination and will make a good target for such an analysis. In comparing their complete genome sequences, we found that gain and loss of genes (loci) for outer membrane proteins, which mediate host interaction, occurred at breakpoints of chromosomal inversions. Sequence comparison there revealed a unique mechanism of DNA duplication: DNA duplication associated with inversion. In this process, a DNA segment at one chromosomal locus is copied and inserted, in an inverted orientation, into a distant locus on the same chromosome, while the entire region between these two loci is also inverted. Recognition of this and three more inversion modes, which occur through reciprocal recombination between long or short sequence similarity or adjacent to a mobile element, allowed reconstruction of synteny evolution through inversion events in this species. These results will guide the interpretation of extensive DNA sequencing results for understanding long- and short-term genome evolution in various organisms and in cancer cells.
ESTHER : Furuta_2011_Proc.Natl.Acad.Sci.U.S.A_108_1501
PubMedSearch : Furuta_2011_Proc.Natl.Acad.Sci.U.S.A_108_1501
PubMedID: 21212362

Title : Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes - Kawai_2011_BMC.Microbiol_11_104
Author(s) : Kawai M , Furuta Y , Yahara K , Tsuru T , Oshima K , Handa N , Takahashi N , Yoshida M , Azuma T , Hattori M , Uchiyama I , Kobayashi I
Ref : BMC Microbiol , 11 :104 , 2011
Abstract : BACKGROUND: The genome of Helicobacter pylori, an oncogenic bacterium in the human stomach, rapidly evolves and shows wide geographical divergence. The high incidence of stomach cancer in East Asia might be related to bacterial genotype. We used newly developed comparative methods to follow the evolution of East Asian H. pylori genomes using 20 complete genome sequences from Japanese, Korean, Amerind, European, and West African strains.
RESULTS: A phylogenetic tree of concatenated well-defined core genes supported divergence of the East Asian lineage (hspEAsia; Japanese and Korean) from the European lineage ancestor, and then from the Amerind lineage ancestor. Phylogenetic profiling revealed a large difference in the repertoire of outer membrane proteins (including oipA, hopMN, babABC, sabAB and vacA-2) through gene loss, gain, and mutation. All known functions associated with molybdenum, a rare element essential to nearly all organisms that catalyzes two-electron-transfer oxidation-reduction reactions, appeared to be inactivated. Two pathways linking acetyl~CoA and acetate appeared intact in some Japanese strains. Phylogenetic analysis revealed greater divergence between the East Asian (hspEAsia) and the European (hpEurope) genomes in proteins in host interaction, specifically virulence factors (tipalpha), outer membrane proteins, and lipopolysaccharide synthesis (human Lewis antigen mimicry) enzymes. Divergence was also seen in proteins in electron transfer and translation fidelity (miaA, tilS), a DNA recombinase/exonuclease that recognizes genome identity (addA), and DNA/RNA hybrid nucleases (rnhAB). Positively selected amino acid changes between hspEAsia and hpEurope were mapped to products of cagA, vacA, homC (outer membrane protein), sotB (sugar transport), and a translation fidelity factor (miaA). Large divergence was seen in genes related to antibiotics: frxA (metronidazole resistance), def (peptide deformylase, drug target), and ftsA (actin-like, drug target).
CONCLUSIONS: These results demonstrate dramatic genome evolution within a species, especially in likely host interaction genes. The East Asian strains appear to differ greatly from the European strains in electron transfer and redox reactions. These findings also suggest a model of adaptive evolution through proteome diversification and selection through modulation of translational fidelity. The results define H. pylori East Asian lineages and provide essential information for understanding their pathogenesis and designing drugs and therapies that target them.
ESTHER : Kawai_2011_BMC.Microbiol_11_104
PubMedSearch : Kawai_2011_BMC.Microbiol_11_104
PubMedID: 21575176

Title : Cow's milk allergy presenting Hirschsprung's disease-mimicking symptoms - Kawai_2005_Pediatr.Surg.Int_21_850
Author(s) : Kawai M , Kubota A , Ida S , Yamamura Y , Yoshimura N , Takeuchi M , Nakayama M , Okuyama H , Oue T , Kawahara H , Okada A
Ref : Pediatr Surg Int , 21 :850 , 2005
Abstract : The authors present a neonatal case of allergic colitis, which manifested the difficulty of spontaneous defecation and irregular narrowing of distal rectum in contrast enema. Rectal suction biopsy showed positive acetylcholinesterase activity. These clinical, radiological and histological findings were indistinguishable from Hirschsprung's disease. Gastrointestinal symptoms were improved by the cessation of cow's milk formula. The present findings may impact on the less recognizable gastrointestinal manifestation of allergic colitis.
ESTHER : Kawai_2005_Pediatr.Surg.Int_21_850
PubMedSearch : Kawai_2005_Pediatr.Surg.Int_21_850
PubMedID: 16189674

Title : Haplotype structures of EPHX1 and their effects on the metabolism of carbamazepine-10,11-epoxide in Japanese epileptic patients - Nakajima_2005_Eur.J.Clin.Pharmacol_61_25
Author(s) : Nakajima Y , Saito Y , Shiseki K , Fukushima-Uesaka H , Hasegawa R , Ozawa S , Sugai K , Katoh M , Saitoh O , Ohnuma T , Kawai M , Ohtsuki T , Suzuki C , Minami N , Kimura H , Goto Y , Kamatani N , Kaniwa N , Sawada J
Ref : European Journal of Clinical Pharmacology , 61 :25 , 2005
Abstract : OBJECTIVE: Microsomal epoxide hydrolase (mEH) is an enzyme that detoxifies reactive epoxides and catalyzes the biotransformation of carbamazepine-10,11-epoxide (CBZ-epoxide) to carbamazepine-10,11-diol (CBZ-diol). Utilizing single nucleotide polymorphisms (SNPs) of the EPHX1 gene encoding mEH, we identified the haplotypes of EPHX1 blocks and investigated the association between the block haplotypes and CBZ-epoxide metabolism.
METHODS: SNPs of EPHX1 were analyzed by means of polymerase chain reaction amplification and DNA sequencing using DNA extracted from the blood leukocytes of 96 Japanese epileptic patients, including 58 carbamazepine-administered patients. The plasma concentrations of CBZ and its four metabolites were determined using high-performance liquid chromatography.
RESULTS: From sequencing all 9 exons and their surrounding introns, 29 SNPs were found in EPHX1. The SNPs were separated into three blocks on the basis of linkage disequilibrium, and the block haplotype combinations (diplotypes) were assigned. Using plasma CBZ-diol/CBZ-epoxide ratios (diol/epoxide ratios) indicative of the mEH activity, the effects of the diplotypes in each EPHX1 block were analyzed on CBZ-epoxide metabolism. In block 2, the diol/epoxide ratios increased significantly depending on the number of haplotype *2 bearing Y113H (P=0.0241). In block 3, the ratios decreased depending on the number of haplotype *2 bearing H139R (P=0.0351). Also, an increasing effect of a *1 subtype, *1c, was observed on the ratio. CONCLUSION: These results show that some EPHX1 haplotypes are associated with altered CBZ-epoxide metabolism. This is the first report on the haplotype structures of EPHX1 and their potential in vivo effects.
ESTHER : Nakajima_2005_Eur.J.Clin.Pharmacol_61_25
PubMedSearch : Nakajima_2005_Eur.J.Clin.Pharmacol_61_25
PubMedID: 15692831

Title : Five novel single nucleotide polymorphisms in the EPHX1 gene encoding microsomal epoxide hydrolase - Shiseki_2003_Drug.Metab.Pharmacokinet_18_150
Author(s) : Shiseki K , Itoda M , Saito Y , Nakajima Y , Maekawa K , Kimura H , Goto Y , Saitoh O , Katoh M , Ohnuma T , Kawai M , Sugai K , Ohtsuki T , Suzuki C , Minami N , Ozawa S , Sawada J
Ref : Drug Metab Pharmacokinet , 18 :150 , 2003
Abstract : Five novel single nucleotide polymorphisms (SNPs) were found in the EPHX1 gene from 96 Japanese epileptic patients. The detected SNPs were as follows: 1) SNP, MPJ6_EX1009; GENE NAME, EPHX1 ACCESSION NUMBER, NT_004525.12; LENGTH, 25 bases; 5'-CCTCACTTCAGTG/ACTGGGCTTTGCC-3'. 2) SNP, MPJ6_EX1013; GENE NAME, EPHX1; ACCESSION NUMBER, NT_004525.12; LENGTH, 25 bases; 5'-TCCGCAGCCAGGG/CAGGACGACAGCA-3'. 3) SNP, MPJ6_EX1026; GENE NAME, EPHX1; ACCESSION NUMBER, NT_004525.12; LENGTH, 25 bases; 5'-GTTCTCCCTGGAC/TGACCTGCTGACC-3'. 4) SNP, MPJ6_EX1028; GENE NAME, EPHX1; ACCESSION NUMBER, NT_004525.12; LENGTH, 25 bases; 5'-AGGCAGGGGGACG/AGCCAGTCTTGGG-3'. 5) SNP, MPJ6_EX1030; GENE NAME, EPHX1; ACCESSION NUMBER, NT_004525.12; LENGTH, 25 bases; 5'-TGAAAAGTGGGTG/AAGGTTCAAGTAC-3'. The frequencies were 0.016 for MPJ6_EX1028 (IVS8+54G>A) and 0.005 for the other SNPs. The SNP MPJ6_EX1013 (130G>C) results in an amino acid alteration (E44Q). The other three SNPs in the coding region, MPJ6_EX1009 (30G>A), MPJ6_EX1026 (1056C>T), and MPJ6_EX1030 (1239G>A) result in synonymous changes (V10V, D352D, and V413V, respectively).
ESTHER : Shiseki_2003_Drug.Metab.Pharmacokinet_18_150
PubMedSearch : Shiseki_2003_Drug.Metab.Pharmacokinet_18_150
PubMedID: 15618730
Gene_locus related to this paper: human-EPHX1

Title : Oscillations of receptor-operated cationic current and internal calcium in single guinea-pig ileal smooth muscle cells - Komori_1993_Pflugers.Arch_424_431
Author(s) : Komori S , Kawai M , Pacaud P , Ohashi H , Bolton TB
Ref : Pflugers Arch , 424 :431 , 1993
Abstract : In single cells isolated from guinea-pig ileal smooth muscle, held under voltage clamp at -40 mV or -50 mV by patch pipette in the whole-cell recording mode, carbachol (CCh) evoked an oscillatory inward cationic current. The frequency of current oscillations increased with increasing CCh concentration. CCh-evoked current oscillations were followed very closely by oscillations in intracellular free Ca2+ estimated from the Indo-1 signal, and were abolished by inclusion of EGTA in the pipette solution. Ryanodine and heparin, but not nifedipine, blocked the generation of current oscillations. CCh-evoked current oscillations were abolished upon withdrawal of extracellular calcium and restored upon its reintroduction. Inclusion of GTP[gamma S] in the pipette solution caused the generation of an oscillatory inward current, which was blocked by ryanodine. The present results are consistent with the hypothesis that CCh-evoked cationic current is gated by activation of a G protein and is steeply dependent on [Ca2+]i, fluctuations in the release of Ca2+ from stores during carbachol's action produce oscillations in [Ca2+]i which cause similar oscillations in the cationic current.
ESTHER : Komori_1993_Pflugers.Arch_424_431
PubMedSearch : Komori_1993_Pflugers.Arch_424_431
PubMedID: 8255727

Title : Voltage fluctuations at the frog sartorius motor endplate produced by a covalently attached activator - Cox_1979_J.Membr.Biol_51_145
Author(s) : Cox RN , Kawai M , Karlin A , Brandt PW
Ref : J Membr Biol , 51 :145 , 1979
Abstract : The depolarization that develops after covalent attachment of trimethylammonium benzoyl to the dithiothreitol-reduced frog sartorius acetylcholine receptor is accompanied by a small increase in voltage fluctuations. The amplitude of the elementary voltage event produced by the covalently attached activator is about 0.04 microV, almost an order of magnitude below the acetylcholine shot-effect amplitude in the control preparation, and about one-fourth the acetylcholine shot amplitude after disulfide-bond reduction. Spectral density plots of trimethylammonium-benzoyl noise can be analyzed in terms of two relaxation rates that bracket the single rate observed in response to acetylcholine.
ESTHER : Cox_1979_J.Membr.Biol_51_145
PubMedSearch : Cox_1979_J.Membr.Biol_51_145
PubMedID: 316828