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Ezaki S, Makise K, Shinozaki B, Odo T, Asano T, Terai H, Yamashita T, Miki S, Wang Z. Localization and interaction effects in ultrathin epitaxial NbN superconducting films. J Phys Condens Matter 2012; 24:475702. [PMID: 23111056 DOI: 10.1088/0953-8984/24/47/475702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
For epitaxial NbN films with thickness d, 2.0 nm ≤ d ≤ 20.5 nm, we observed a sharp superconducting transition, for which the transition temperature T(c) monotonically decreased with increasing 1/d. Regarding the suppression of T(c), the sheet resistance R(sq) dependence of T(c) closely fitted the Finkel'stein formula from localization theory, with a reasonable value of the electron mean free path comparable to atomic distance, which was used as a fitting parameter. On the other hand, the critical sheet resistance R(c), at which the superconducting-insulator transition was expected, was approximately one-third of the universal value R(q) = h/4e(2) suggested by the dirty boson model for self-duality. It is concluded that T(c) depression in the present NbN system is determined by localization theory but not the dirty boson model.
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Affiliation(s)
- S Ezaki
- Department of Physics, Kyushu University, Fukuoka 810-8560, Japan
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Higashibata H, Fujiwara S, Ezaki S, Takagi M, Fukui K, Imanaka T. Effect of polyamines on histone-induced DNA compaction of hyperthermophilic archaea. J Biosci Bioeng 2005; 89:103-6. [PMID: 16232710 DOI: 10.1016/s1389-1723(00)88061-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/1999] [Accepted: 10/25/1999] [Indexed: 11/28/2022]
Abstract
The effect of polyamines on histone-mediated DNA compaction was examined in vitro with archaeal histone HpkA from Pyrococcus kodakaraensis KOD1. An agarose gel mobility-shift experiment indicated that histone-bound DNA (compacted DNA) was further compacted by addition of a polyamine (putrescine, spermidine, or spermine) or its acetylated form (N-acetylputrescine, N1-acetylspermidine, N8-acetylspermidine, or N1-acetylspermine) when the mixture was incubated at above 75 degrees C. Spermine was most effective in compaction enhancement among all the polyamines tested. A high concentration of potassium ion (1.0 M) did not stabilize the compacted form of DNA even though double-stranded DNA was stably maintained against thermal denaturation at elevated temperatures under this condition. It appears likely that multivalent polyamines have a nucleosome maintenance function in hyperthermophilic archaea in high-temperature environments.
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Affiliation(s)
- H Higashibata
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Ezaki S, Miyaoku K, Nishi K, Tanaka T, Fujiwara S, Takagi M, Atomi H, Imanaka T. Gene analysis and enzymatic properties of thermostable beta-glycosidase from Pyrococcus kodakaraensis KOD1. J Biosci Bioeng 2005; 88:130-5. [PMID: 16232586 DOI: 10.1016/s1389-1723(99)80190-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/1999] [Accepted: 05/06/1999] [Indexed: 11/19/2022]
Abstract
A beta-glycosidase with broad substrate specificity was identified from a hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1. The gene encoding beta-glycosidase (Pk-gly) consists of 1449 nucleotides corresponding to a polypeptide of 483 amino acids. The protein showed similarity with other beta-glycosidases from family-1 glycosyl hydrolases, in particular, it showed high identity to beta-mannosidase from P. furiosus (55.7%), beta-glycosidase from Sulfolobus solfataricus (42.7%) and beta-glucosidase from P. furiosus (41.9%). The cloned gene was expressed in Escherichia coli and the recombinant protein was purified. The beta-glycosidase showed optimal activity at pH 6.5 and at an extremely high temperature of 100 degrees C, and had a half-life of 18 h at 90 degrees C. The beta-glycosidase hydrolyzed various pNp-beta-glycopyranosides, with kcat K(m) values in the order of pNp-beta-glucopyranoside = pNp-beta-mannopyranoside > pNp-beta-galactopyranoside > pNp-beta-xylopyranoside. pNp-beta-mannopyranoside was the substrate exhibiting the lowest K(m) value [0.254 mM] with a kcat K(m) ratio comparable to that of pNp-beta-glucopyranoside. This substrate specificity was distinct from previously reported beta-glycosidases. We observed that the region in PK-Gly corresponding to the fifth alpha-helix and beta-strand region of beta-glycosidase from S. solfataricus, which constitutes a large portion of the channel for substrate incorporation, displayed a chimeric structure, with the N-terminal region similar to beta-glycosidases and the C-terminal region similar to beta-mannosidases. An exo-type hydrolytic activity and transglycosylation activity were also observed towards cellooligomers.
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Affiliation(s)
- S Ezaki
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
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Rashid N, Kikuchi H, Ezaki S, Atomi H, Imanaka T. Isolation and characterization of psychrotrophs from subterranean environments. J Biosci Bioeng 2005; 87:746-51. [PMID: 16232548 DOI: 10.1016/s1389-1723(99)80147-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/1999] [Accepted: 03/03/1999] [Indexed: 11/22/2022]
Abstract
Subterranean environments are potential sources for the isolation of novel microorganisms. Water and soil samples were collected at depths ranging from 10 to 1800 meters below the surface, and screening was carried out with aerobic rich and anaerobic minimal media. Two psychrotrophic and three chemoautotrophic strains were isolated. One of the psychrotrophic isolates, designated SN16A, grew at temperatures between -5 and 37 degrees C with optimal growth between 25 and 30 degrees C. The other psychrotroph, designated KB700A, grew between -10 and 30 degrees C. Little difference in growth rate could be observed between 20 and 30 degrees C; however, this strain did not grow at 37 degrees C. KB700A utilized CO2 chemoautotrophically at 30 degrees C, using hydrogen as an energy source. Both strains were characterized biochemically. The complete 16S rRNA sequence of KB700A was 98.7% homologous with that of Pseudomonas marginalis. However, the 16S rRNA of SN16A showed only 95.4% identity at maximum-with the corresponding gene of Arthrobacter globiformis-suggesting that this strain may belong to a novel genus. Both strains exhibited the ability to produce hydrolytic enzymes on plate assays. Our results suggest that subterranean environments are promising sources for the isolation of psychrotrophic microorganisms.
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Affiliation(s)
- N Rashid
- Core Research for Evolutional Science and Technology (CREST), Hon-cho, Kawaguchi, Saitama 332-0012, Japan
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Sakai M, Ezaki S, Suzuki N, Kurane R. Isolation and characterization of a novel polychlorinated biphenyl-degrading bacterium, Paenibacillus sp. KBC101. Appl Microbiol Biotechnol 2005; 68:111-6. [PMID: 15678306 DOI: 10.1007/s00253-004-1848-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2004] [Revised: 11/09/2004] [Accepted: 11/11/2004] [Indexed: 11/26/2022]
Abstract
The biphenyl-utilizing bacterial strain KBC101 has been newly isolated from soil. Biphenyl-grown cells of KBC101 efficiently degraded di- to nonachlorobiphenyls. The isolate was identified as Paenibacillus sp. with respect to its 16S rDNA sequence and fatty acid profiles, as well as various biological and physiological characteristics. In the case of highly chlorinated biphenyl (polychlorinated biphenyl; PCB) congeners, the degradation activities of this strain were superior to those of the previously reported strong PCB degrader, Rhodococcus sp. RHA1. Recalcitrant coplanar PCBs, such as 3,4,3',4'-CB, were also efficiently degraded by strain KBC101 cells. This is the first report of a representative of the genus Paenibacillus capable of degrading PCBs. In addition to growth on biphenyl, strain KBC101 could grow on dibenzofuran, xanthene, benzophenone, anthrone, phenanthrene, naphthalene, fluorene, fluoranthene, and chrysene as sole sources of carbon and energy. Paenibacillus sp. strain KBC101 presented heterogeneous degradation profiles toward various aromatic compounds.
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Affiliation(s)
- M Sakai
- Biotechnology Research Centre, Kubota Corporation, Koyodai 5-6, Ryuugasaki City, 301-0852, Ibaraki, Japan
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Nakamura T, Ezaki S, Takasaki J, Itabashi K, Ogawa Y. Leukemoid reaction and chronic lung disease in infants with very low birth weight. J Matern Fetal Neonatal Med 2002; 11:396-9. [PMID: 12389655 DOI: 10.1080/jmf.11.6.396.399] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVES To analyze the relationship between the leukemoid reaction and chronic lung disease in very-low-birth-weight (VLBW) infants. METHODS Neonates born weighing less than 1500 g without evidence of congenital anomalies and admitted to our hospital from October 1985 to December 1999 comprised our study. Leukemoid reaction was defined as a peripheral white blood cell (WBC) count of > or = 50 x 10(3)/microl. The infants who demonstrated a leukemoid reaction formed the study group, while the remainder formed the control group. The relationship between neonatal variables and WBC counts was studied. RESULTS Fourteen of the 486 infants demonstrated WBC counts of > or = 50 x 10(3)/microl, with an incidence of 2.9%. Univariate analysis demonstrated a significant association between a leukemoid reaction and chronic lung disease following intrauterine infection. CONCLUSION A leukemoid reaction was observed in 2.9% of VLBW infants in our neonatal intensive care unit. A significant association was demonstrated between the leukemoid reaction and chronic lung disease following intrauterine infection.
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Affiliation(s)
- T Nakamura
- Center for Maternal, Fetal and Neonatal Medicine, Saitama Medical Center, Saitama Medical School, Kawagoe, Japan
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Abstract
We have previously reported that a psychrotrophic bacterium, Pseudomonas sp. strain KB700A, which displays sigmoidal growth even at -5 degrees C, produced a lipase. A genomic DNA library of strain KB700A was introduced into Escherichia coli TG1, and screening on tributyrin-containing agar plates led to the isolation of the lipase gene. Sequence analysis revealed an open reading frame (KB-lip) consisting of 1,422 nucleotides that encoded a protein (KB-Lip) of 474 amino acids with a molecular mass of 49,924 Da. KB-Lip showed 90% identity with the lipase from Pseudomonas fluorescens and was found to be a member of Subfamily I.3 lipase. Gene expression and purification of the recombinant protein were performed. KB-Lip displayed high lipase activity in the presence of Ca2+. Addition of EDTA completely abolished lipase activity, indicating that KB-Lip was a Ca2+-dependent lipase. Addition of Mn2+ and Sr2+ also led to enhancement of lipase activity but to a much lower extent than that produced by Ca2+. The optimal pH of KB-Lip was 8 to 8.5. The addition of detergents enhanced the enzyme activity. When p-nitrophenyl esters and triglyceride substrates of various chain-lengths were examined, the lipase displayed highest activity towards C10 acyl groups. We also determined the positional specificity and found that the activity was 20-fold higher toward the 1(3) position than toward the 2 position. The optimal temperature for KB-Lip was 35 degrees C, lower than that for any previously reported Subfamily I.3 lipase. The enzyme was also thermolabile compared to these lipases. Furthermore, KB-Lip displayed higher levels of activity at low temperatures than did other enzymes from Subfamily I.3, indicating that KB-Lip has evolved to function in cold environments, in accordance with the temperature range for growth of its psychrotrophic host, strain KB700A.
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Affiliation(s)
- N Rashid
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
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Affiliation(s)
- H Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 606-8501, Japan
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Matsuda T, Fujikawa M, Haruki M, Tang XF, Ezaki S, Imanaka T, Morikawa M, Kanaya S. Interaction of TIP26 from a hyperthermophilic archaeon with TFB/TBP/DNA ternary complex. Extremophiles 2001; 5:177-82. [PMID: 11453461 DOI: 10.1007/s007920100193] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Interactions of TBP-interacting protein (TIP26), TBP, and TFB from a hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 with TATA-DNA were examined by electrophoretic mobility shift assay. Tk-TFB formed a ternary complex with Tk-TBP and TATA-DNA. Tk-TIP26 did not inhibit the formation of this ternary complex, but interacted with it to form a TIP26/TFB/TBP/DNA quaternary complex. This interaction is rather weak, and a large excess of Tk-TIP26 over Tk-TBP is required to fully convert the TFB/TBP/DNA ternary complex to the quaternary complex. However, determination of the concentration of Tk-TIP26 and Tk-TBP in KOD1 cells by Western blotting analysis indicated that the concentration of Tk-TIP26 is approximately ten times that of Tk-TBP, suggesting that the quaternary complex might also form in vivo.
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Affiliation(s)
- T Matsuda
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Japan
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Tang XF, Ezaki S, Atomi H, Imanaka T. Anthranilate synthase without an LLES motif from a hyperthermophilic archaeon is inhibited by tryptophan. Biochem Biophys Res Commun 2001; 281:858-65. [PMID: 11237738 DOI: 10.1006/bbrc.2001.4428] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tk-trpE and Tk-trpG, the genes that encode the two subunits of anthranilate synthase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1, have been expressed independently in Escherichia coli. The anthranilate synthase complex (Tk-AS complex) was obtained by heat-treatment of the mixture of cell-free extracts containing each recombinant protein, Tk-TrpE (alpha subunit) and Tk-TrpG (beta subunit), at 85 degrees C for 10 min. Further purification of Tk-AS complex was carried out by anion-exchange chromatography followed by gel-filtration. Molecular mass estimations from gel-filtration chromatography indicated that Tk-AS complex was a heterodimer (alphabeta). The complex displayed both ammonia- and glutamine-dependent anthranilate synthase activities, and could not utilize asparagine as an ammonia donor. The optimal pH was pH 10.0 and the optimal temperature was 85 degrees C in both cases. Mg2+ was necessary for the anthranilate synthase activity. At 75 degrees C, the K(m) values of chorismate for ammonia- and glutamine-dependent activities were 13.8 and 3.4 microM, respectively. The K(m) value of Mg2+ was 20.5 microM. The K(m) values of glutamine and NH4Cl were 88 microM and 5.6 mM, respectively. Although Tk-TrpE displayed 47.6% similarity with TrpE of Salmonella typhimurium, conserved amino acid residues proven to be essential for inhibition of enzyme activity by L-tryptophan were not present in Tk-TrpE. Namely, residues corresponding to Glu39, Met293, and Cys465 in the enzyme from S. typhimurium were replaced by Arg28, Thr221, and Ala384 in Tk-TrpE. Nevertheless, significant inhibition by L-tryptophan was observed, with K(i) values of 5.25 and 74 microM for ammonia and glutamine-dependent activities, respectively. The inhibition was competitive with respect to chorismate. The results suggest that the amino acid residues involved in the feedback inhibition by L-tryptophan in the case of Tk-AS complex are distinct from previously reported anthranilate synthases.
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Affiliation(s)
- X F Tang
- Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Kyoto, Yoshida-Honmachi, Sakyo-ku, 606-8501, Japan
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Abstract
Pyridoxal 5'-phosphate-dependent tryptophan synthase catalyzes the last two reactions of tryptophan biosynthesis, and is comprised of two distinct subunits, alpha and beta. TktrpA and TktrpB, which encode the alpha subunit and beta subunit of tryptophan synthase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1, were independently expressed in Escherichia coli and their protein products were purified. Tryptophan synthase complex (Tk-TS complex), obtained by heat treatment of a mixture of the cell-free extracts containing each subunit, was also purified. Gel-filtration chromatography revealed that Tk-TrpA was a monomer (alpha), Tk-TrpB was a dimer (beta2), and Tk-TS complex was a tetramer (alpha2 beta2). The Tk-TS complex catalyzed the overall alphabeta reaction with a specific activity of 110 micromol Trp per micromol active site per min under its optimal conditions (80 degrees C, pH 8.5). Individual activity of the alpha and beta reactions of the Tk-TS complex were 8.5 micromol indole per micromol active site per min (70 degrees C, pH 7.0) and 119 micromol Trp per micromol active site per min (90 degrees C, pH 7.0), respectively. The low activity of the alpha reaction of the Tk-TS complex indicated that turnover of the beta reaction, namely the consumption of indole, was necessary for efficient progression of the alpha reaction. The alpha and beta reaction activities of independently purified Tk-TrpA and Tk-TrpB were 10-fold lower than the respective activities detected from the Tk-TS complex, indicating that during heat treatment, each subunit was necessary for the other to obtain a proper conformation for high enzyme activity. Tk-TrpA showed only trace activities at all temperatures examined (40-85 degrees C). Tk-TrpB also displayed low levels of activity at temperatures below 70 degrees C. However, Tk-TrpB activity increased at temperatures above 70 degrees C, and eventually at 100 degrees C, reached an equivalent level of activity with the beta reaction activity of Tk-TS complex. Taking into account the results of circular dichroism analyses of the three enzymes, a model is proposed which explains the relationship between structure and activity of the alpha and beta subunits with changes in temperature. This is the first report of an archaeal tryptophan synthase, and the first biochemical analysis of a thermostable tryptophan synthase at high temperature.
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Affiliation(s)
- X F Tang
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto, Japan
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Abstract
A gene encoding DNA ligase (lig(Tk)) from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1, has been cloned and sequenced, and its protein product has been characterized. lig(Tk) consists of 1,686 bp, corresponding to a polypeptide of 562 amino acids with a predicted molecular mass of 64,079 Da. Sequence comparison with previously reported DNA ligases and the presence of conserved motifs suggested that Lig(Tk) was an ATP-dependent DNA ligase. Phylogenetic analysis indicated that Lig(Tk) was closely related to the ATP-dependent DNA ligase from Methanobacterium thermoautotrophicum DeltaH, a moderate thermophilic archaeon, along with putative DNA ligases from Euryarchaeota and Crenarchaeota. We expressed lig(Tk) in Escherichia coli and purified the recombinant protein. Recombinant Lig(Tk) was monomeric, as is the case for other DNA ligases. The protein displayed DNA ligase activity in the presence of ATP and Mg(2+). The optimum pH of Lig(Tk) was 8.0, the optimum concentration of Mg(2+), which was indispensable for the enzyme activity, was 14 to 18 mM, and the optimum concentration of K(+) was 10 to 30 mM. Lig(Tk) did not display single-stranded DNA ligase activity. At enzyme concentrations of 200 nM, we observed significant DNA ligase activity even at 100 degrees C. Unexpectedly, Lig(Tk) displayed a relatively small, but significant, DNA ligase activity when NAD(+) was added as the cofactor. Treatment of NAD(+) with hexokinase did not affect this activity, excluding the possibility of contaminant ATP in the NAD(+) solution. This unique cofactor specificity was also supported by the observation of adenylation of Lig(Tk) with NAD(+). This is the first biochemical study of a DNA ligase from a hyperthermophilic archaeon.
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Affiliation(s)
- M Nakatani
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
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Tang X, Ezaki S, Fujiwara S, Takagi M, Atomi H, Imanaka T. The tryptophan biosynthesis gene cluster trpCDEGFBA from Pyrococcus kodakaraensis KOD1 is regulated at the transcriptional level and expressed as a single mRNA. Mol Gen Genet 1999; 262:815-21. [PMID: 10628865 DOI: 10.1007/s004380051145] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The entire gene cluster encoding enzymes involved in biosynthesis of L-tryptophan in the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 has been cloned and sequenced. Seven ORFs, which encode indole-3-glycerol phosphate synthase (trpC), anthranilate phosphoribosyltransferase (trpD), the two subunits of anthranilate synthase (trpEG), phosphoribosyl anthranilate isomerase (trpF) and the two subunits of tryptophan synthase (trpAB), were identified. The gene order is trpCDEGFBA, covering a region of 6045 bp. In order to confirm the function of the gene products, we expressed the first gene, Pk-trpC, in Escherichia coli. The protein product was purified, and was found to show the expected indole-3-glycerol phosphate synthase activity, with a temperature optimum of 85 degrees C. We could clearly identify a single mRNA transcript by Northern analysis using probes in the central and 3'-regions of the gene cluster, indicating that the gene cluster is transcribed as an operon. A significant increase in trp mRNA level was observed in cells grown in medium depleted of L-tryptophan, compared to cells grown in medium supplemented with L-tryptophan, indicating that expression of the gene cluster is regulated at the transcriptional level.
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Affiliation(s)
- X Tang
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Japan
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Maeda N, Kitano K, Fukui T, Ezaki S, Atomi H, Miki K, Imanaka T. Ribulose bisphosphate carboxylase/oxygenase from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 is composed solely of large subunits and forms a pentagonal structure. J Mol Biol 1999; 293:57-66. [PMID: 10512715 DOI: 10.1006/jmbi.1999.3145] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We previously reported the presence of a highly active, carboxylase-specific ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in a hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1. In this study, structural analysis of Pk -Rubisco has been performed. Phylogenetic analysis of Rubiscos indicated that archaeal Rubiscos, including Pk -Rubisco, were distinct from previously reported type I and type II enzymes in terms of primary structure. In order to investigate the existence of small subunits in native Pk -Rubisco, immunoprecipitation and native-PAGE experiments were performed. No specific protein other than the expected large subunit of Pk -Rubisco was detected when the cell-free extracts of P. kodakaraensis KOD1 were immunoprecipitated with polyclonal antibodies against the recombinant enzyme. Furthermore, native and recombinant Pk -Rubiscos exhibited identical mobilities on native-PAGE. These results indicated that native Pk -Rubisco consisted solely of large subunits. Electron micrographs of purified recombinant Pk -Rubisco displayed pentagonal ring-like assemblies of the molecules. Crystals of Pk -Rubisco obtained from ammonium sulfate solutions diffracted X-rays beyond 2.8 A resolution. The self-rotation function of the diffraction data showed the existence of 5-fold and 2-fold axes, which are located perpendicularly to each other. These results, along with the molecular mass of Pk -Rubisco estimated from gel filtration, strongly suggest that Pk -Rubisco is a decamer composed only of large subunits, with pentagonal ring-like structure. This is the first report of a decameric assembly of Rubisco, which is thought to belong to neither type I nor type II Rubiscos.
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Affiliation(s)
- N Maeda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Yoshida-Honmachi, Sakyo-ku, 606-8501, Japan
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Nagahisa K, Ezaki S, Fujiwara S, Imanaka T, Takagi M. Sequence and transcriptional studies of five clustered flagellin genes from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1. FEMS Microbiol Lett 1999; 178:183-90. [PMID: 10483738 DOI: 10.1111/j.1574-6968.1999.tb13776.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Five clustered genes (flaB1, flaB2, flaB3, flaB4 and flaB5) for multiple subunits of flagellar filaments from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 were cloned and sequenced. Deduced amino acid sequences were aligned and it was revealed that five flagellin genes are homologous especially in the N-terminal hydrophobic region which might be important for interaction among flagellin subunits. Phylogenetic analysis was performed among archaeal flagellins from methanogens, an extreme halophile and our hyperthermophile, indicating that KOD1 flagellins were grouped together with methanogenic counterparts and were distinguishable from halophilic flagellins. Northern analysis of transcripts from flagellin genes from P. kodakaraensis KOD1 revealed that four major transcripts (0.98, 3.7, 5.4 and 9.2 kb) initiating from immediately upstream of flaB1 encode different combinations of five flagellins.
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Affiliation(s)
- K Nagahisa
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan
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Ezaki S, Maeda N, Kishimoto T, Atomi H, Imanaka T. Presence of a structurally novel type ribulose-bisphosphate carboxylase/oxygenase in the hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1. J Biol Chem 1999; 274:5078-82. [PMID: 9988755 DOI: 10.1074/jbc.274.8.5078] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have characterized the gene encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) of the hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1. The gene encoded a protein consisting of 444 amino acid residues, corresponding in size to the large subunit of previously reported Rubiscos. Rubisco of P. kodakaraensis KOD1 (Pk-Rubisco) showed only 51.4% similarity with the large subunit of type I Rubisco from spinach and 47.3% with that of type II Rubisco from Rhodospirillum rubrum, suggesting that the enzyme was not a member of either type. Active site residues identified from type I and type II Rubiscos were conserved. We expressed the gene in Escherichia coli, and we obtained a soluble protein with the expected molecular mass and N-terminal amino acid sequence. Purification of the recombinant protein revealed that Pk-Rubisco was an L8 type homo-octamer. Pk-Rubisco showed highest specific activity of 19.8 x 10(3) nmol of CO2 fixed per min/mg, and a tau value of 310 at 90 degreesC, both higher than any previously characterized Rubisco. The optimum pH was 8.3, and the enzyme possessed extreme thermostability, with a half-life of 15 h at 80 degreesC. Northern blot analysis demonstrated that the gene was transcribed in P. kodakaraensis KOD1. Furthermore, Western blot analysis with cell-free extract of P. kodakaraensis KOD1 clearly indicated the presence of Pk-Rubisco in the native host cells.
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Affiliation(s)
- S Ezaki
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
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Hirata Y, Igarashi K, Ezaki S, Atomi H, Imanaka T. High-level production of erythritol by strain 618A-01 isolated from pollen. J Biosci Bioeng 1999; 87:630-5. [PMID: 16232530 DOI: 10.1016/s1389-1723(99)80126-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/1998] [Accepted: 01/26/1999] [Indexed: 11/16/2022]
Abstract
We have isolated a microorganism (strain 618A-01) from pollen which has the ability to produce erythritol when grown in the presence of glucose as the carbon source. When cultivated in a medium consisting of 20% glucose and 1% dried bouillon in a shake flask, 75 g/l erythritol was produced after 950 h, corresponding to a 37.5% yield against glucose consumption. No other polyols, including glycerol, were detected in the medium. Positive-ion fast atom bombardment mass spectrometry and 1H- and 13C-NMR analyses confirmed that the fermentation product was erythritol. Scanning electron microscopic analysis clearly demonstrated that the cells grown on YPD medium at 30 degrees C showed yeast-like morphology, while they appeared like hyphae at 37 degrees C. The complete 18S rRNA sequence of the isolate was determined, which showed high identity (99.5%) with the genus Ustilago of the phylum Basidiomycota. The data strongly suggest that strain 618A-01 belongs to the class Ustilaginomycetes. The culture conditions for the production of erythritol by the isolate were examined. The use of medium containing 1% tryptone, 0.5% yeast extract and 0.5% NaCl yielded the highest cell growth and erythritol productivity among the media tested. Continuous glucose feeding at 6-7% to the fermentor further increased the production of erythritol, and we obtained a maximal 100 g/l erythritol after 530 h, with a 39.3% yield.
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Affiliation(s)
- Y Hirata
- Biochemical Laboratory, Saraya Co., 24-12 Tamate-cho, Kashiwara 582-0028 Japan
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18
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Furusho J, Yamaguchi K, Ikura Y, Kogure T, Suzuki M, Konishi S, Simizu G, Nakayama Y, Itoh K, Sakamoto Y, Ishikawa A, Ezaki S, Nawata J, Kumagai K. Patient background of the Pokemon phenomenon: questionnaire studies in multiple pediatric clinics. Acta Paediatr Jpn 1998; 40:550-4. [PMID: 9893288 DOI: 10.1111/j.1442-200x.1998.tb01988.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Many children in Japan developed various neuropsychological problems, including seizures, while watching the program Pocket Monster, televised on 16 December 1997. To examine the basis for this incident, we have performed a survey of volunteering children and their parents who visited our pediatric clinics for other reasons from 8 January to 28 February 1998. Children and their parents filled out questionnaires. Among the total of 662 children surveyed, the great majority (603, 91.1%) was found to have watched the Pocket Monster program and 30 individuals (5.0% of viewers) complained of variable degrees of neuropsychological abnormalities. These included seizures (two cases), headache (nine cases), nausea (eight cases), blurred vision (four cases), vertigo (two cases), dysthymia (two cases) and vomiting (one case). Nearly half (14) of these children developed symptoms during or immediately after watching the program, while the remainder did so later. Representative cases are reported and other statistical aspects are discussed.
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Affiliation(s)
- J Furusho
- Department of Pediatrics, School of Medicine, Showa University, Tokyo, Japan
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19
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Higuchi T, Mikuniya T, Osoegawa K, Ezaki S, Sumichika H, Mizui Y, Shoji T, Kishihara K, Muta S, Kuhara S. Streptomyces ATP nucleotide 3'-pyrophosphokinase-gene cloning and sequence analysis. Biosci Biotechnol Biochem 1994; 58:2182-7. [PMID: 7765711 DOI: 10.1271/bbb.58.2182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Streptomyces ATP nucleotide 3'-pyrophosphokinase is an extracellular enzyme that transfers 5'-beta, gamma-pyrophosphoryl groups of ATP to a variety of nucleotides at the 3'-OH site. The enzyme gene was cloned from partially Sau3AI-digested chromosomal DNA of S. morookaensis in S. lividans TK24/pIJ699 and then in E. coli JM83/pUC12. Some transformants produced the active enzyme. The gene was sequenced by the dideoxynucleotide termination procedure. Its GC content was 72%. Its putative promoter regions, showing little homology to that of the Streptomyces consensus type, were pointed out. No sequence homology was found between the pyrophosphokinase and any other known genes including those of the most mechanistically similar bacterial stringent factor and related proteins. Northern hybridization analysis showed that the gene is constitutionally polycistronic and expressed under transcriptional control. Nuclease S1 mapping indicated that the gene transcription starts from its translation initiation site.
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Affiliation(s)
- T Higuchi
- Laboratory of Molecular Gene Technics, Graduate School of Genetic Resources Technology, Kyushu University, Fukuoka, Japan
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Ueno Y, Watanabe M, Yajima T, Ezaki S, Takaishi H, Inoue N, Iwao Y, Ishii H, Ishikawa H, Aiso S, Hibi T. Expression of interleukin-7 protein and mRNA in colonic epithelial cells. Pathophysiology 1994. [DOI: 10.1016/0928-4680(94)90557-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Hamada S, Ezaki S, Hayashi K, Toko K, Yamafuji K. Electric current precedes emergence of a lateral root in higher plants. Plant Physiol 1992; 100:614-9. [PMID: 16653036 PMCID: PMC1075602 DOI: 10.1104/pp.100.2.614] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Stable electrochemical patterns appear spontaneously around roots of higher plants and are closely related to growth. An electric potential pattern accompanied by lateral root emergence was measured along the surface of the primary root of adzuki bean (Phaseolus angularis) over 21 h using a microelectrode manipulated by a newly developed apparatus. The electric potential became lower at the point where a lateral root emerged. This change preceded the emergence of the lateral root by about 10 h. A theory is presented for calculating two-dimensional patterns of electric potential and electric current density around the primary root (and a lateral root) using only data on the one-dimensional electric potential measured near the surface of the primary root. The development of the lateral root inside the primary root is associated with the influx of electric current of about 0.7 muA.cm(-2) at the surface.
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Affiliation(s)
- S Hamada
- Department of Electronics, Faculty of Engineering, Kyushu University 36, Fukuoka 812, Japan
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Abstract
An apparatus for measuring simultaneously the surface electrical potentials along epicotyl was developed to study the largely bending situation by gravity. Potentials increased on the upper side and decreased on the lower side after the horizontal placement. The time course of electrical changes consisted of two components which correspond to growth movements observed during gravitropism.
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Affiliation(s)
- K Imagawa
- Department of Electronics, Faculty of Engineering, Kyushu University 36, Fukuoka 812, Japan
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Souda M, Toko K, Hayashi K, Fujiyoshi T, Ezaki S, Yamafuji K. Relationship between Growth and Electric Oscillations in Bean Roots. Plant Physiol 1990; 93:532-6. [PMID: 16667498 PMCID: PMC1062545 DOI: 10.1104/pp.93.2.532] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Extracellular and intracellular electric potentials in bean roots are known to show electric oscillations along the longitudinal axis with a period of several minutes. The relationship between growth and the electric oscillations was studied using roots of adzuki (Phaseolus chrysanthos). We measured surface electric potentials with a multielectrode apparatus while simultaneously measuring elongation using a CCD camera and monitor. Roots having an electric oscillation grew faster than roots with no oscillation. Furthermore, elongation rate was higher in roots with higher oscillation frequency. Oscillation frequency had a strong dependence on temperature; i.e. Q(10) was estimated at 1.7. These results suggest a correlation between electric oscillation and elongation.
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Affiliation(s)
- M Souda
- Department of Electronics, Faculty of Engineering, Kyushu University 36, Fukuoka 812, Japan
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Toko K, Tsukiji M, Ezaki S, Yamafuji K. Current-voltage characteristics and self-sustained oscillations in dioleyl phosphate-millipore membranes. Biophys Chem 1984; 20:39-59. [PMID: 17005149 DOI: 10.1016/0301-4622(84)80004-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/1983] [Revised: 01/30/1984] [Accepted: 02/01/1984] [Indexed: 10/18/2022]
Abstract
For an artificial membrane prepared by infiltrating dioleyl phosphate (DOPH) into pores of a Millipore filter, we propose a theoretical model for explaining observed data on electric behavior, such as d.c. current-voltage characteristics and self-sustained oscillations of the electric potential. The model consists of a simple electric circuit composed of electric resistances and capacitances as given functions of internal variables which represent conformational states of DOPH molecules and salt concentration inside the pore concerned. The kinetic equations for these variables are the same as those presented previously for describing a phase transition of DOPH. except for a slight modification taking account of effects of salt accumulation inside the pore. The present theory can describe well the I-V hysteresis and various features of spike-like oscillations with long periods of up to a few hours in the absence of external force and also short-period oscillations with periods of the order of 1 s under pressure difference.
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Affiliation(s)
- K Toko
- Department of Electronics, Faculty of Engineering, Kyushu University 36, Fukuoka 812, Japan
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Ezaki S. [Pharmacological studies of tectoridin and tectorigenin]. Nihon Yakurigaku Zasshi 1968; 64:186-198. [PMID: 5749289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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