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Hidetoshi Okuyama - One of the best experts on this subject based on the ideXlab platform.

  • The rpoH gene encoding heat shock sigma factor σ32 of Psychrophilic Bacterium Colwellia maris
    Extremophiles : life under extreme conditions, 2005
    Co-Authors: Seiji Yamauchi, Hidetoshi Okuyama, Yoshitaka Nishiyama, Hidenori Hayashi
    Abstract:

    The rpoH gene encoding a heat shock sigma factor, σ32, was cloned from the Psychrophilic Bacterium Colwellia maris. The deduced amino acid sequence of σ32 from C. maris is more than 60% homologous to that of σ32 from mesophilic bacteria. The RpoH box, a 9-amino-acid sequence region (QRKLFFNLR) specific to σ32, and two downstream box sequences complementary to a part of 16S rRNA were identified. Primer extension analysis showed that the C. maris rpoH is expressed from only one σ70-type promoter. Northern blot analysis showed that the level of rpoH mRNA was clearly increased at 20°C, a temperature that induces heat shock in this organism. In the presence of an inhibitor of transcriptional initiation, the degradation of rpoH mRNA was much slower at 20°C than at 10°C. Thus, increased stability of the rpoH mRNA might be responsible for the rpoH mRNA accumulation. The predicted secondary structure of the 5′-region of C. maris rpoH mRNA was different from the conserved patterns reported for most mesophilic bacteria, and the base pairing of the downstream boxes appeared to be less stable than that of Escherichia coli rpoH mRNA. Thus, essential features that ensure the HSP expression at a relatively low temperature are embedded in the rpoH gene of psychrophiles.

  • Gene structure and transcriptional regulation of dnaK and dnaJ genes from a Psychrophilic Bacterium, Colwellia maris
    Extremophiles, 2004
    Co-Authors: Seiji Yamauchi, Hidetoshi Okuyama, Yoshitaka Nishiyama, Hidenori Hayashi
    Abstract:

    The dnaK and dnaJ genes, encoding heat shock proteins, were cloned from a Psychrophilic Bacterium, Colwellia maris . Significant homology was evident comparing DnaK and DnaJ of the psychrophilile with the counterparts of mesophilic and thermophilic bacteria. In the DnaJ protein, three conserved regions of the Hsp40 family were observed. A putative promoter similar to the σ^32 consensus sequence was found upstream of the dnaK gene. The G+C content in the 5′-untranslated region of the dnaK gene was much lower than that in the corresponding region of mesophilic bacteria. Northern-blot analysis and primer-extension analysis showed that both genes were transcribed separately as monocistronic mRNAs. Following several temperature upshifts from 10 to 26°C, maximum induction of the dnaK and dnaJ mRNAs was detected at 20°C, suggesting that this temperature induces the heat shock response in this Bacterium. In addition, the level of the induction of the dnaJ gene was much lower than that of the dnaK gene. These findings together revealed several specific features of the heat shock response at a relatively low temperature in psychrophiles.

  • Gene structure and transcriptional regulation specific to the groESL operon from the Psychrophilic Bacterium Colwellia maris.
    Archives of microbiology, 2003
    Co-Authors: Seiji Yamauchi, Hidetoshi Okuyama, Eugene Hayato Morita, Hidenori Hayashi
    Abstract:

    The groESL operon of a Psychrophilic Bacterium, Colwellia maris, was cloned and sequenced. The operon contains two ORFs of 291 bp and 1,650 bp separated by 210 bp. Northern blot analysis suggested that the groESL operon was transcribed as a bicistronic mRNA, and that the amount of mRNA markedly increased after the temperature was raised from 10 °C to 20 °C. Although the optimum temperatures for GroESL function are different in Psychrophilic, mesophilic, and thermophilic bacteria, the deduced amino acid sequences of C. maris GroES and GroEL showed remarkably high similarity with those of GroES and GroEL from mesophilic and thermophilic bacteria. A putative promoter similar to the Escherichia coli σ32 consensus sequence was identified. One specific feature of C. maris groESL was that in the putative untranslated region the G+C content was about 24 mol%, which is much lower than that of mesophilic bacteria such as E. coli. The low G+C content may be important for maintaining transcription at low temperatures.

  • Assignment of Pseudomonas sp. strain E-3 to Pseudomonas psychrophila sp. nov., a new facultatively Psychrophilic Bacterium.
    Extremophiles : life under extreme conditions, 2001
    Co-Authors: Isao Yumoto, Yoshinobu Nodasaka, Hidetoshi Matsuyama, Teruo Kusano, Tomohiro Shingyo, Hidetoshi Okuyama
    Abstract:

    A facultatively Psychrophilic Bacterium, previously described as Pseudomonas sp. strain E-3, has been reassigned by phenotypic characterization, chemotaxonomic analysis, DNA–DNA hybridization, and 16S rRNA gene phylogenetic analysis. The organism was a gram-negative, aerobic, straight rod with polar flagella. It was catalase positive and oxidase positive, able to grow at –1°C but not at 40°C, and produced acid from D-glucose under aerobic conditions. The major isoprenoid quinone was ubiquinone-9, and the DNA G+C content was 57.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the Bacterium is a member of the genus Pseudomonas and was closest to Pseudomonas fragi. Determination of the DNA–DNA relatedness between strain E-3 and P. fragi revealed too low a level of homology (47.9%–51.3%) to identify them as the same species. On the basis of phenotypic characteristics, phylogenetic analysis, and DNA–DNA relatedness data, it is concluded that strain E-3 represents an individual species. Accordingly, the name Pseudomonas psychrophila is proposed. The type strain is E-3T (=JCM 10889).

  • Purification and Characterization of a Catalase from the Facultatively Psychrophilic Bacterium Vibrio rumoiensis S-1T Exhibiting High Catalase Activity
    Journal of bacteriology, 2000
    Co-Authors: Isao Yumoto, Hidetoshi Matsuyama, Hidetoshi Okuyama, Hideaki Iwata, Nobutoshi Ichise, Daisen Ichihashi, Anita Istokovics, Kosei Kawasaki
    Abstract:

    Catalase from the facultatively Psychrophilic Bacterium Vibrio rumoiensis S-1T, which was isolated from an environment exposed to H2O2 and exhibited high catalase activity, was purified and characterized, and its localization in the cell was determined. Its molecular mass was 230 kDa, and the molecule consisted of four identical subunits. The enzyme, which was not apparently reduced by dithionite, showed a Soret peak at 406 nm in a resting state. The catalytic activity was 527,500 U · mg of protein−1 under standard reaction conditions at 40°C, 1.5 and 4.3 times faster, respectively, than those of the Micrococcus luteus and bovine catalases examined under the same reaction conditions, and showed a broad optimum pH range (pH 6 to 10). The catalase from strain S-1T is located not only in the cytoplasmic space but also in the periplasmic space. There is little difference in the activation energy for the activity between strain S-1T catalase and M. luteus and bovine liver catalases. The thermoinstability of the activity of the former catalase were significantly higher than those of the latter catalases. The thermoinstability suggests that the catalase from strain S-1T should be categorized as a Psychrophilic enzyme. Although the catalase from strain S-1T is classified as a mammal type catalase, it exhibits the unique enzymatic properties of high intensity of enzymatic activity and thermoinstability. The results obtained suggest that these unique properties of the enzyme are in accordance with the environmental conditions under which the microorganism lives.

Rosa Margesin - One of the best experts on this subject based on the ideXlab platform.

  • pedobacter ruber sp nov a Psychrophilic Bacterium isolated from soil
    International Journal of Systematic and Evolutionary Microbiology, 2013
    Co-Authors: Rosa Margesin, Dechao Zhang
    Abstract:

    A Gram-staining-negative, red-pigmented, Psychrophilic, non-motile and rod-shaped bacterial strain, designated W1T, was isolated from soil and subjected to a polyphasic taxonomic investigation. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain W1T grouped with members of the genus Pedobacter and formed a distinct cluster with the type strain of Pedobacter composti (97.8 % 16S rRNA gene sequence similarity). Levels of 16S rRNA gene sequence similarity between strain W1T and the type strains of all other recognized species of the genus Pedobacter available at the time of writing were <97.0 %. The predominant cellular fatty acids (≥10 %) of strain W1T were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and anteiso-C15 : 0. The only menaquinone was MK-7. The genomic DNA G+C content was 39.0 mol% (HPLC). Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain W1T is a representative of a novel species of the genus Pedobacter , for which we propose the name Pedobacter ruber sp. nov. The type strain is W1T ( = DSM 24536T = LMG 26240T).

  • Sphingomonas alpina sp. nov., a Psychrophilic Bacterium isolated from alpine soil
    International Journal of Systematic and Evolutionary Microbiology, 2012
    Co-Authors: Rosa Margesin, Dechao Zhang, Hans-jürgen Busse
    Abstract:

    An aerobic, Gram-negative-staining, motile, Psychrophilic Bacterium, designated strain S8-3T, was isolated from alpine soil. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S8-3T was related to the genus Sphingomonas and had highest 16S rRNA gene sequence similarity with Sphingomonas oligophenolica S213T (98.0 %). 16S RNA gene sequence similarity between strain S8-3T and Sphingomonas paucimobilis ATCC 29837T (the type species of the genus Sphingomonas ) was 93.0 %. Strain S8-3T contained Q-10 as the ubiquinone and C18 : 1ω7c (65.0 %) and C14 : 0 2-OH (13.4 %) as the dominant fatty acids (>10 %). The major polyamines were the triamine sym-homospermidine and spermidine. The polar lipid profile contained sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The DNA G+C content was 64.1 mol%. Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain S8-3T is a representative of a novel species of the genus Sphingomonas , for which the name Sphingomonas alpina sp. nov. is proposed. The type strain is S8-3T ( = DSM 22537T = LMG 26055T).

  • Arthrobacter cryoconiti sp. nov., a Psychrophilic Bacterium isolated from alpine glacier cryoconite
    International Journal of Systematic and Evolutionary Microbiology, 2012
    Co-Authors: Rosa Margesin, Dechao Zhang, Peter Schumann, Hong-can Liu, Yu-guang Zhou, Mersiha Redzic, Franz Schinner
    Abstract:

    A Gram-stain-positive, aerobic, non-motile, Psychrophilic Bacterium, designated strain Cr6-08T, was isolated from alpine glacier cryoconite. Growth of strain Cr6-08T occurred at 1–25 °C. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain Cr6-08T is most closely related to members of the genus Arthrobacter. Strain Cr6-08T possessed chemotaxonomic properties consistent with those of the genus Arthrobacter, such as peptidoglycan type A3α (l-Lys–l-Ala4), MK-9(H2) as major menaquinone and anteiso- and iso-branched compounds (anteiso-C15 : 0 and iso-C15 : 0) as major cellular fatty acids. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown glycolipid and three unknown polar lipids. The genomic DNA G+C content of strain Cr6-08T was 57.3 mol%. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain Cr6-08T is considered to represent a novel species of the genus Arthrobacter, for which the name Arthrobacter cryoconiti sp. nov. is proposed. The type strain is Cr6-08T ( = DSM 23324T  = LMG 26052T  = CGMCC 1.10698T).

  • sphingopyxis bauzanensis sp nov a Psychrophilic Bacterium isolated from soil
    International Journal of Systematic and Evolutionary Microbiology, 2010
    Co-Authors: Dechao Zhang, Hong-can Liu, Yu-hua Xin, Yu-guang Zhou, Franz Schinner, Rosa Margesin
    Abstract:

    Strain BZ30T was isolated from hydrocarbon-contaminated soil. The Gram-negative, aerobic Bacterium was Psychrophilic and able to grow at temperatures ranging from 1 to 30 °C. The predominant cellular fatty acids of strain BZ30T were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) (37.4 %), C18 : 1 ω7c (19.6 %), C16 : 0 (8.2 %), C14 : 0 2-OH (8.0 %) and C16 : 0 2-OH (5.0 %). The predominant ubiquinone was Q-10. Major polar lipids were sphingoglycolipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Spermidine was the major polyamine. The genomic DNA G+C content was 64.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain BZ30T belonged to the family Sphingomonadaceae of the α-4 group of the phylum Proteobacteria, and was related to the members of the genus Sphingopyxis, sharing the highest sequence similarities with the type strains of Sphingopyxis chilensis (98.3 %), S. witflariensis (98.2 %), S. taejonensis (97.4 %) and S. ginsengisoli (97.2 %). On the basis of the phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain BZ30T represents a novel species of the genus Sphingopyxis, for which the name Sphingopyxis bauzanensis is proposed. The type strain is BZ30T (=DSM 22271T =CGMCC 1.8959T =CIP 110136T).

  • Arthrobacter alpinus sp. nov., a Psychrophilic Bacterium isolated from alpine soil.
    International Journal of Systematic and Evolutionary Microbiology, 2010
    Co-Authors: Dechao Zhang, Peter Schumann, Hong-can Liu, Yu-hua Xin, Yu-guang Zhou, Franz Schinner, Rosa Margesin
    Abstract:

    An aerobic, Gram-reaction-positive, non-motile, Psychrophilic Bacterium, designated strain S6-3(T), was isolated from alpine soil. Cells exhibited a rod-coccus growth cycle and produced a yellow pigment. Growth occurred at 1-25 degrees C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S6-3(T) was related to members of the genus Arthrobacter, sharing highest sequence similarities with the type strains of Arthrobacter psychrolactophilus (97.9 %) and Arthrobacter stackebrandtii (97.6 %). Strain S6-3(T) had MK-9(H(2)) as the major menaquinone and anteiso-C(15 : 0) as the major fatty acid. The cell-wall peptidoglycan was of type A3alpha l-Lys-l-Thr-Ala(3). The predominant cell-wall sugars were galactose and rhamnose. The genomic DNA G+C content of strain S6-3(T) was 61.9 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain S6-3(T) is considered to represent a novel species of the genus Arthrobacter, for which the name Arthrobacter alpinus sp. nov. is proposed. The type strain is S6-3(T) (=DSM 22274(T) =CGMCC 1.8950(T)).

Dechao Zhang - One of the best experts on this subject based on the ideXlab platform.

  • pedobacter ruber sp nov a Psychrophilic Bacterium isolated from soil
    International Journal of Systematic and Evolutionary Microbiology, 2013
    Co-Authors: Rosa Margesin, Dechao Zhang
    Abstract:

    A Gram-staining-negative, red-pigmented, Psychrophilic, non-motile and rod-shaped bacterial strain, designated W1T, was isolated from soil and subjected to a polyphasic taxonomic investigation. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain W1T grouped with members of the genus Pedobacter and formed a distinct cluster with the type strain of Pedobacter composti (97.8 % 16S rRNA gene sequence similarity). Levels of 16S rRNA gene sequence similarity between strain W1T and the type strains of all other recognized species of the genus Pedobacter available at the time of writing were <97.0 %. The predominant cellular fatty acids (≥10 %) of strain W1T were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and anteiso-C15 : 0. The only menaquinone was MK-7. The genomic DNA G+C content was 39.0 mol% (HPLC). Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain W1T is a representative of a novel species of the genus Pedobacter , for which we propose the name Pedobacter ruber sp. nov. The type strain is W1T ( = DSM 24536T = LMG 26240T).

  • Sphingomonas alpina sp. nov., a Psychrophilic Bacterium isolated from alpine soil
    International Journal of Systematic and Evolutionary Microbiology, 2012
    Co-Authors: Rosa Margesin, Dechao Zhang, Hans-jürgen Busse
    Abstract:

    An aerobic, Gram-negative-staining, motile, Psychrophilic Bacterium, designated strain S8-3T, was isolated from alpine soil. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S8-3T was related to the genus Sphingomonas and had highest 16S rRNA gene sequence similarity with Sphingomonas oligophenolica S213T (98.0 %). 16S RNA gene sequence similarity between strain S8-3T and Sphingomonas paucimobilis ATCC 29837T (the type species of the genus Sphingomonas ) was 93.0 %. Strain S8-3T contained Q-10 as the ubiquinone and C18 : 1ω7c (65.0 %) and C14 : 0 2-OH (13.4 %) as the dominant fatty acids (>10 %). The major polyamines were the triamine sym-homospermidine and spermidine. The polar lipid profile contained sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The DNA G+C content was 64.1 mol%. Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain S8-3T is a representative of a novel species of the genus Sphingomonas , for which the name Sphingomonas alpina sp. nov. is proposed. The type strain is S8-3T ( = DSM 22537T = LMG 26055T).

  • Arthrobacter cryoconiti sp. nov., a Psychrophilic Bacterium isolated from alpine glacier cryoconite
    International Journal of Systematic and Evolutionary Microbiology, 2012
    Co-Authors: Rosa Margesin, Dechao Zhang, Peter Schumann, Hong-can Liu, Yu-guang Zhou, Mersiha Redzic, Franz Schinner
    Abstract:

    A Gram-stain-positive, aerobic, non-motile, Psychrophilic Bacterium, designated strain Cr6-08T, was isolated from alpine glacier cryoconite. Growth of strain Cr6-08T occurred at 1–25 °C. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain Cr6-08T is most closely related to members of the genus Arthrobacter. Strain Cr6-08T possessed chemotaxonomic properties consistent with those of the genus Arthrobacter, such as peptidoglycan type A3α (l-Lys–l-Ala4), MK-9(H2) as major menaquinone and anteiso- and iso-branched compounds (anteiso-C15 : 0 and iso-C15 : 0) as major cellular fatty acids. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown glycolipid and three unknown polar lipids. The genomic DNA G+C content of strain Cr6-08T was 57.3 mol%. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain Cr6-08T is considered to represent a novel species of the genus Arthrobacter, for which the name Arthrobacter cryoconiti sp. nov. is proposed. The type strain is Cr6-08T ( = DSM 23324T  = LMG 26052T  = CGMCC 1.10698T).

  • sphingopyxis bauzanensis sp nov a Psychrophilic Bacterium isolated from soil
    International Journal of Systematic and Evolutionary Microbiology, 2010
    Co-Authors: Dechao Zhang, Hong-can Liu, Yu-hua Xin, Yu-guang Zhou, Franz Schinner, Rosa Margesin
    Abstract:

    Strain BZ30T was isolated from hydrocarbon-contaminated soil. The Gram-negative, aerobic Bacterium was Psychrophilic and able to grow at temperatures ranging from 1 to 30 °C. The predominant cellular fatty acids of strain BZ30T were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) (37.4 %), C18 : 1 ω7c (19.6 %), C16 : 0 (8.2 %), C14 : 0 2-OH (8.0 %) and C16 : 0 2-OH (5.0 %). The predominant ubiquinone was Q-10. Major polar lipids were sphingoglycolipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Spermidine was the major polyamine. The genomic DNA G+C content was 64.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain BZ30T belonged to the family Sphingomonadaceae of the α-4 group of the phylum Proteobacteria, and was related to the members of the genus Sphingopyxis, sharing the highest sequence similarities with the type strains of Sphingopyxis chilensis (98.3 %), S. witflariensis (98.2 %), S. taejonensis (97.4 %) and S. ginsengisoli (97.2 %). On the basis of the phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain BZ30T represents a novel species of the genus Sphingopyxis, for which the name Sphingopyxis bauzanensis is proposed. The type strain is BZ30T (=DSM 22271T =CGMCC 1.8959T =CIP 110136T).

  • Arthrobacter alpinus sp. nov., a Psychrophilic Bacterium isolated from alpine soil.
    International Journal of Systematic and Evolutionary Microbiology, 2010
    Co-Authors: Dechao Zhang, Peter Schumann, Hong-can Liu, Yu-hua Xin, Yu-guang Zhou, Franz Schinner, Rosa Margesin
    Abstract:

    An aerobic, Gram-reaction-positive, non-motile, Psychrophilic Bacterium, designated strain S6-3(T), was isolated from alpine soil. Cells exhibited a rod-coccus growth cycle and produced a yellow pigment. Growth occurred at 1-25 degrees C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S6-3(T) was related to members of the genus Arthrobacter, sharing highest sequence similarities with the type strains of Arthrobacter psychrolactophilus (97.9 %) and Arthrobacter stackebrandtii (97.6 %). Strain S6-3(T) had MK-9(H(2)) as the major menaquinone and anteiso-C(15 : 0) as the major fatty acid. The cell-wall peptidoglycan was of type A3alpha l-Lys-l-Thr-Ala(3). The predominant cell-wall sugars were galactose and rhamnose. The genomic DNA G+C content of strain S6-3(T) was 61.9 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain S6-3(T) is considered to represent a novel species of the genus Arthrobacter, for which the name Arthrobacter alpinus sp. nov. is proposed. The type strain is S6-3(T) (=DSM 22274(T) =CGMCC 1.8950(T)).

Isao Yumoto - One of the best experts on this subject based on the ideXlab platform.

  • psychromonas marina sp nov a novel halophilic facultatively Psychrophilic Bacterium isolated from the coast of the okhotsk sea
    International Journal of Systematic and Evolutionary Microbiology, 2002
    Co-Authors: Kosei Kawasaki, Megumi Hishinuma, Yuichi Nogi, Yoshinobu Nodasaka, Hidetoshi Matsuyama, Isao Yumoto
    Abstract:

    A facultatively Psychrophilic Bacterium, strain 4-22T, was isolated from a cold current off the Monbetsu coast of the Okhotsk Sea in Hokkaido, Japan. The isolate was a rod-shaped facultative anaerobe that reduced nitrate to nitrite and hydrolysed starch, DNA and alginic acid, but not chitin or gelatin. The isolate grew at 0 degrees C, but not at 26 degrees C; the optimum growth temperature was 14-16 degrees C. NaCl was required for growth. The DNA G+C content was 43.5 mol%. The whole-cell fatty acids consisted of significant amounts of an unsaturated fatty acid, C16:1, and a saturated fatty acid, C16:0. A polyunsaturated fatty acid, docosahexaenoic acid (C22:6), was also detected (1.6%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 4-22T was closely related to Psychromonas antarctica (95.7% similarity). DNA-DNA hybridization revealed a relatedness of 31% between strain 4-22T and P. antarctica. Based on physiological and biochemical characteristics and the phylogenetic position as determined by 16S rRNA gene analysis and DNA-DNA relatedness, it is concluded that the isolate represents a novel species, for which the name Psychromonas marina sp. nov. is proposed. The type strain is 4-22T (= JCM 10501T = IAM 14899T = NCIMB 13792T).

  • Assignment of Pseudomonas sp. strain E-3 to Pseudomonas psychrophila sp. nov., a new facultatively Psychrophilic Bacterium.
    Extremophiles : life under extreme conditions, 2001
    Co-Authors: Isao Yumoto, Yoshinobu Nodasaka, Hidetoshi Matsuyama, Teruo Kusano, Tomohiro Shingyo, Hidetoshi Okuyama
    Abstract:

    A facultatively Psychrophilic Bacterium, previously described as Pseudomonas sp. strain E-3, has been reassigned by phenotypic characterization, chemotaxonomic analysis, DNA–DNA hybridization, and 16S rRNA gene phylogenetic analysis. The organism was a gram-negative, aerobic, straight rod with polar flagella. It was catalase positive and oxidase positive, able to grow at –1°C but not at 40°C, and produced acid from D-glucose under aerobic conditions. The major isoprenoid quinone was ubiquinone-9, and the DNA G+C content was 57.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the Bacterium is a member of the genus Pseudomonas and was closest to Pseudomonas fragi. Determination of the DNA–DNA relatedness between strain E-3 and P. fragi revealed too low a level of homology (47.9%–51.3%) to identify them as the same species. On the basis of phenotypic characteristics, phylogenetic analysis, and DNA–DNA relatedness data, it is concluded that strain E-3 represents an individual species. Accordingly, the name Pseudomonas psychrophila is proposed. The type strain is E-3T (=JCM 10889).

  • Purification and Characterization of a Catalase from the Facultatively Psychrophilic Bacterium Vibrio rumoiensis S-1T Exhibiting High Catalase Activity
    Journal of bacteriology, 2000
    Co-Authors: Isao Yumoto, Hidetoshi Matsuyama, Hidetoshi Okuyama, Hideaki Iwata, Nobutoshi Ichise, Daisen Ichihashi, Anita Istokovics, Kosei Kawasaki
    Abstract:

    Catalase from the facultatively Psychrophilic Bacterium Vibrio rumoiensis S-1T, which was isolated from an environment exposed to H2O2 and exhibited high catalase activity, was purified and characterized, and its localization in the cell was determined. Its molecular mass was 230 kDa, and the molecule consisted of four identical subunits. The enzyme, which was not apparently reduced by dithionite, showed a Soret peak at 406 nm in a resting state. The catalytic activity was 527,500 U · mg of protein−1 under standard reaction conditions at 40°C, 1.5 and 4.3 times faster, respectively, than those of the Micrococcus luteus and bovine catalases examined under the same reaction conditions, and showed a broad optimum pH range (pH 6 to 10). The catalase from strain S-1T is located not only in the cytoplasmic space but also in the periplasmic space. There is little difference in the activation energy for the activity between strain S-1T catalase and M. luteus and bovine liver catalases. The thermoinstability of the activity of the former catalase were significantly higher than those of the latter catalases. The thermoinstability suggests that the catalase from strain S-1T should be categorized as a Psychrophilic enzyme. Although the catalase from strain S-1T is classified as a mammal type catalase, it exhibits the unique enzymatic properties of high intensity of enzymatic activity and thermoinstability. The results obtained suggest that these unique properties of the enzyme are in accordance with the environmental conditions under which the microorganism lives.

  • Characterization of a facultatively Psychrophilic Bacterium, vibrio rumoiensis sp. nov., that exhibits high catalase activity
    Applied and environmental microbiology, 1999
    Co-Authors: Isao Yumoto, Hidetoshi Matsuyama, Hidetoshi Okuyama, Hideaki Iwata, Tomoo Sawabe, Keisuke Ueno, Nobutoshi Ichise, Kosei Kawasaki
    Abstract:

    A novel facultatively Psychrophilic Bacterium, strain S-1, which exhibits extraordinarily high catalase activity was isolated from the drain pool of a fish product processing plant that uses H2O2 as a bleaching and microbicidal agent. The catalase activity of the isolate was 1 or 2 orders of magnitude higher than those of CoryneBacterium glutamicum, Staphylococcus aureus, Pseudomonas fluorescens, and five other species tested in this study. The strain seemed to possess only one kind of catalase, according to the results of polyacrylamide gel electrophoresis of the cell extract. The optimum temperature for catalase activity was about 30°C, which was about 20°C lower than that for bovine catalase activity. Electron microscopic observation revealed that the surface of the microorganism was covered by blebs. Although the isolate was nonflagellated, its taxonomic position on the basis of physiological and biochemical characteristics and analysis of 16S rRNA sequence and DNA-DNA relatedness data indicated that strain S-1 is a new species belonging to the genus Vibrio. Accordingly, we propose the name Vibrio rumoiensis. The type strain is S-1 (FERM P-14531).

  • Assignment of Vibrio sp. strain ABE-1 to Colwellia maris sp. nov., a new Psychrophilic Bacterium.
    International Journal of Systematic Bacteriology, 1998
    Co-Authors: Isao Yumoto, Kosei Kawasaki, Hidetoshi Matsuyama, Hideaki Iwata, Hidetoshi Okuyama
    Abstract:

    A Psychrophilic Bacterium, previously described as Vibrio sp. strain ABE-1T, has been reassigned by phenotypic characterization, chemotaxonomic analysis and 16S rRNA phylogenetic analysis. The organism was curved rods and it could reduce nitrate to nitrite and hydrolyse gelatin and DNA, but not chitin. NaCI was required for growth. This strain was susceptible to the vibriostatic compound 0/129. The major isoprenoid quinone was ubiquinone-8 and the DNA G+C content was 39·4 mol%. The whole-cell fatty acids comprised saturated and monounsaturated fatty acids with 10–18 C atoms; saturated and monounsaturated C16 fatty acids were predominant. Strain ABE-1Tcontained the unique trans-unsaturated fatty acid, 9-trans-hexadecenoic acid. Although strain ABE-1Thas been identified as a Vibrio species, the strain did not ferment glucose. Phylogenetic analysis based on 16S rRNA sequencing indicated that strain ABE-1Twas more closely related to Colwellia species than to Vibrio species. However, strain ABE-1Tdiffered from other reported Colwellia species in terms of phylogenetic position, some phenotypic characteristics, chemotaxonomic analysis and relatedness by DNA-DNA hybridization. Accordingly, the name Colwellia maris is proposed. The type strain is ABE-1T(= JCM 10085T).

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  • Purification and characterization of a cold-adapted isocitrate lyase and expression analysis of the cold-inducible isocitrate lyase gene from the Psychrophilic Bacterium Colwellia psychrerythraea
    Extremophiles : life under extreme conditions, 2002
    Co-Authors: Seiya Watanabe, Naoto Yamaoka, Noriyuki Fukunaga, Yasuhiro Takada
    Abstract:

    Isocitrate lyase (ICL) from Colwellia psychrerythraea, a Psychrophilic Bacterium, was purified and characterized. The subunit molecular mass was 64 kDa, which is larger than that of other bacterial ICLs. The optimal temperature for its activity was 25°C, the value of Km for the substrate (DL-isocitrate) was minimum at 15°C, and the catalytic efficiency (kcat/Km) value was maximum at 20°C. Furthermore, the enzyme was remarkably thermolabile and completely inactivated by incubation for 2 min at 30°C. These features indicate that ICL from this Bacterium is a typical cold-adapted enzyme. A partial amino acid sequence of the C. psychrerythraea ICL was very similar to that of the closely related psychrophile Colwellia maris. Expression of the gene encoding the C. psychrerythraea ICL was found to be induced by low temperatures and by acetate in the medium. The cold adaptation of the catalytic properties of ICL and the stimulated expression of its gene at low temperatures strongly suggest that this enzyme is important for the growth of this Bacterium in a cold environment.

  • The cold-inducible icl gene encoding thermolabile isocitrate lyase of a Psychrophilic Bacterium, Colwellia maris.
    Microbiology (Reading England), 2002
    Co-Authors: Seiya Watanabe, Yasuhiro Takada, Naoto Yamaoka, Noriyuki Fukunaga
    Abstract:

    The gene encoding isocitrate lyase (ICL; EC 4.1.3.1) of a Psychrophilic Bacterium, Colwellia maris, was cloned and sequenced. The ORF of the gene (icl) was 1584 bp long, and the predicted gene product consisted of 528 aa (molecular mass 58150 Da) and showed low homology with the corresponding enzymes from other organisms. The analyses of amino acid content and primary structure of the C. maris ICL suggested that it possessed many features of a cold-adapted enzyme. Primer extension and Northern blot analyses revealed that two species of the icl mRNAs with differential lengths of 5'-untranslated regions (TS1 and TS2) were present, of which the 5' end (TS1 and TS2 sites) were G and A, located at 130 and 39 bases upstream of the translation start codon, respectively. The levels of TS1 and TS2 mRNAs were increased by both acetate and low temperature. The induction of icl expression by low temperature took place in the C. maris cells grown on succinate as the carbon source but not acetate. Furthermore, a similar manner of inductions was also found in the levels of the translation and the enzyme activity in cell-free extract. These results suggest that the icl gene, encoding thermolabile isocitrate lyase, of C. maris is important for acetate utilization and cold adaptation.

  • cis-Acting Elements Responsible for Low-Temperature-Inducible Expression of the Gene Coding for the Thermolabile Isocitrate Dehydrogenase Isozyme of a Psychrophilic Bacterium, Vibrio sp. Strain ABE-1
    Journal of bacteriology, 1999
    Co-Authors: Takehiko Sahara, Yasuhiro Takada, Masahiro Suzuki, Jun-ichiro Tsuruha, Noriyuki Fukunaga
    Abstract:

    Transcriptional control of the low-temperature-inducible icdII gene, encoding the thermolabile isocitrate dehydrogenase of a Psychrophilic Bacterium, Vibrio sp. strain ABE-1, was found to be mediated in part by a transcriptional silencer locating at nucleotide positions −560 to −526 upstream from the transcription start site of icdII. Deletion of the silencer resulted in a 20-fold-increased level of expression of the gene at low temperature (15°C) but not at high temperature (37°C). In addition, a CCAAT sequence located 2 bases upstream of the −35 region was found to be essential for the low-temperature-inducible expression of the gene. By deletion of this sequence, low-temperature-dependent expression of the gene was completely abolished. The ability of the icdII promoter to control the expression of other genes was confirmed by using a fusion gene containing the icdII promoter region and the promoterless icdI open reading frame, which encodes the non-cold-inducible isocitrate dehydrogenase isozyme of Vibrio sp. strain ABE-1. Escherichia coli transformants harboring icdII acquired an ability to grow rapidly at low temperature.

  • Genes encoding two isocitrate dehydrogenase isozymes of a Psychrophilic Bacterium, Vibrio sp. strain ABE-1.
    Journal of bacteriology, 1993
    Co-Authors: Atsushi Ishii, Yasuhiro Takada, Takehiko Sahara, Shoji Sasaki, Masahiro Suzuki, Noriyuki Fukunaga
    Abstract:

    The genes coding for two structurally different isocitrate dehydrogenase isozymes (IDH-I and IDH-II) of a Psychrophilic Bacterium, Vibrio sp. strain ABE-1, were cloned and sequenced. Open reading frames of the genes (icdI and icdII) are 1,248 and 2,229 bp in length, respectively. The amino acid sequences predicted from the open reading frames of icdI and icdII corresponded to the N-terminal amino acid sequences of the purified IDH-I and IDH-II, respectively. No homology was found between the deduced amino acid sequences of the isozymes; however, the IDH-I, a dimeric enzyme, had a high amino acid sequence identity (74.3%) to the Escherichia coli IDH. The deduced amino acid sequence of the IDH-II, a monomeric enzyme, was not related to any known sequence. However, the IDH-II had an amino acid sequence homologous to that of a cyanogen bromide-cleaved peptide containing a putative active-site methionyl residue of the monomeric IDH of Azotobacter vinelandii. The two genes (icdlI and icdII) were found to be tandemly located in the same orientation. Northern (RNA) blot analyses showed that the two genes are transcribed independently. Primer extension experiments located single transcriptional start sites 39 and 96 bp upstream of the start codons of icdI and icdII, respectively. The amount of icdI transcript but not icdII increased when Vibrio sp. strain ABE-1 cells were cultured in acetate minimal medium. Images