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Nakasone K, Nishimori M, Kiuchi K, Shinohara M, Fukuzawa K, Takami T, Nakamura T, Sonoda Y, Takahara H, Yamamoto K, Suzuki Y, Tani K, Iwai H, Nakanishi Y, Hirata K. Prediction of difficulty in cryoballoon ablation with a 3D deep learning model using polygonal mesh representation. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Cryoballoon ablation (CBA) is a useful treatment for pulmonary vein isolation (PVI). Some cases, however, are difficult to treat and may require multiple freezing procedures and/or touch-up ablation. Although several predictors of CBA difficulty have been reported, no report has been able to assess the spatial location and morphology of the left atrium (LA) and pulmonary veins (PVs). A polygonal mesh is a collection of vertices, edges, and faces that defines the shape of a polyhedral object, and is able to represent a spatial location with a small amount of information. We hypothesized that a deep learning model that learns mesh representation datasets could more accurately detect the CBA difficulty and that we could establish a novel evaluation method in CBA.
Purpose
The aim of this study was to create a model to predict CBA difficulty with a 3D deep learning model using polygonal mesh representation.
Methods and results
All the 140 patients who underwent CBA for drug-resistant atrial fibrillation between January 2015 and January 2022 were included. A 28-mm cryoballoon (Arctic Front Advance, Medtronic) was used in all cases. We defined CBA difficulty as requiring a touch-up ablation procedure to create complete PVI. We converted the volume data in DICOM format of the computed tomography images of PVs and LA to obj file format (shown in Figure 1), which supports the definition of the geometry for object surfaces using polygonal meshes. Next, we developed a deep learning model that could learn polygonal meshes and classify whether the CBA required touch-up ablation or not. Only a training dataset is used to train the deep learning model, and finally, a test dataset is used to evaluate the model metrics. The accuracy, area under the ROC curve, recall, precision, and f1-score of the deep learning model using the test dataset was 86.5%, 87.7%, 66.7%, 75.0%, 70.6%, respectively.
Conclusions
We developed a 3D deep learning model that can detect a difficulty in CBA using polygonal mesh representation. By predicting difficult cases in advance, we will be able to develop strategies to increase the success rate.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - K Tani
- Kobe University , Kobe , Japan
| | - H Iwai
- Kobe University , Kobe , Japan
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Nakasone K, Fukuzawa K, Kiuchi K, Takami M, Takemoto M, Sakai J, Nakamura T, Yatomi A, Sonoda Y, Takahara H, Yamamoto K, Suzuki Y, Tani K, Hirata K. VT recurrence and predictors in patients with VT inducibility at the end of VT ablation. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.0663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
A successful Radiofrequency (RF) ablation of ventricular tachycardia (VT) can prevent VT recurrence. It has been reported that VT non-inducibility at the end of RF ablation is associated with less likely VT recurrence in ischemic cardiomyopathy (ICM) and non-ICM (NCIM). However, it is not clear whether we should use VT non-inducibility as routine end point in RF ablation of VT.
Purpose
The aim of this study was to evaluate VT recurrence in patients who couldn't be achieved VT non-inducibility at the end of RF ablation and the factors attributed to VT recurrence in ICM and NICM patients.
Methods
Between January 2009 and April 2020, 84 consecutive patients (ICM: 34, NICM: 50) underwent RF ablation for drug-resistant VT in our hospital. VT non-inducibility was defined as any ventricular tachy-arrhythmia, including clinical VT, non-clinical VT, and VF, was not induced by programed stimuli at the end of session. Non-inducibility was achieved in 37 patients but it was not achieved in 47 patients (ICM: 18, NICM: 29). To evaluate the validity of “non-inducibility” as an end point of VT ablation, 47 patients (male: 40, mean age: 66±15 years) in whom non-inducibility of any ventricular tachyarrhythmia was not achieved were studied. The primary endpoint was recurrence of any sustained VT and VF during follow up period (mean follow-up period was 1.4 (range, 0.0, 2.0) years.)
Results
Mean left ventricular ejection fraction (LVEF) was 36±13%. Epicardial ablation was required in 8 patients. 32 patients had electrical storm at the time of ablation. Among them, 21 patients had VT recurrence and 26 patients had non-VT recurrence during follow-up period. VT recurrence rate was significantly lower in patients with LVEF≥35% than those with LVEF<35% (HR=0.31, 95% CI 1.25–9.92). Multivariate survival analysis identified LVEF≥35% (HR=0.34, 95% CI 0.10–0.98) and ablation of VT isthmus (HR=0.18, 95% CI 0.02–0.78) as independent predictors of non-VT recurrence.
Conclusions
Even if non-inducibility of any ventricular tachyarrhythmia wasn't achieved at the end of ablation, the patients with LVEF≥35% or who had ablated of VT isthmus might prevent VT recurrence. The validity of non-inducibility of any ventricular tachyarrhythmia should be evaluated in each patient's background.
Funding Acknowledgement
Type of funding sources: Public hospital(s). Main funding source(s): Abbott, Medtronic
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Affiliation(s)
| | | | | | | | | | - J Sakai
- Kobe University, Kobe, Japan
| | | | | | | | | | | | | | - K Tani
- Kobe University, Kobe, Japan
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Kurata A, Sugiura M, Kokoda K, Tsujimoto H, Numata T, Kato C, Nakasone K, Kishimoto N. Taxonomy of actinomycetes in the deep-sea Calyptogena communities and characterization of the antibacterial compound produced by Actinomadura sp. DS-MS-114. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1342563] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Atsushi Kurata
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Japan
| | - Miwa Sugiura
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Japan
| | - Kento Kokoda
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Japan
| | - Hiroaki Tsujimoto
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Japan
| | - Tetsuya Numata
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Japan
| | - Chiaki Kato
- Department of Marine Biodiversity Research, Japan Agency For Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Kaoru Nakasone
- Department of Biotechnology and Chemistry, Faculty of Engineering, Kindai University, Higashi-Hiroshima City, Japan
| | - Noriaki Kishimoto
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Japan
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Haruna T, Funasako M, Nakasone K. P1700Self-adjustment to atrial fibrillation in patients with persistent atrial fibrillation determines the suitability of aggressive sinus maintenance therapy. Europace 2017. [DOI: 10.1093/ehjci/eux161.010] [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: 11/12/2022] Open
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Haruna T, Funasako M, Nakasone K. P1701Cardiac MRI can potentially differentiate atrial fibrillation-induced cardiomyopathy from pre-existing left ventricular dysfunction complicated by atrial fibrillation. Europace 2017. [DOI: 10.1093/ehjci/eux161.011] [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: 11/13/2022] Open
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Kurata A, Yamaura Y, Tanaka T, Kato C, Nakasone K, Kishimoto N. Antifungal peptidic compound from the deep-sea bacterium Aneurinibacillus sp. YR247. World J Microbiol Biotechnol 2017; 33:73. [PMID: 28299556 PMCID: PMC5352791 DOI: 10.1007/s11274-017-2239-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 03/05/2017] [Indexed: 12/04/2022]
Abstract
Aneurinibacillus: sp. YR247 was newly isolated from the deep-sea sediment inside the Calyptogena community at a depth of 1171 m in Sagami Bay. The strain exhibited antifungal activity against the filamentous fungus Aspergillus brasiliensis NBRC9455. A crude extract prepared from the YR247 cells by ethanol extraction exhibited broad antimicrobial activities. The antifungal compound is stable at 4-70 °C and pH 2.0-12.0. After treatment with proteinase K, the antifungal activity was not detected, indicating that the antifungal compound of strain YR247 is a peptidic compound. Electrospray ionization mass spectrometry of the purified antifungal compound indicated that the peptidic compound has an average molecular weight of 1167.9. The molecular weight of the antifungal compound from strain YR247 is different from those of antimicrobial peptides produced by the related Aneurinibacillus and Bacillus bacteria. The antifungal peptidic compound from the deep-sea bacterium Aneurinibacillus sp. YR247 may be useful as a biocontrol agent.
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Affiliation(s)
- Atsushi Kurata
- Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara City, Nara, 631-8505, Japan.
| | - Yuto Yamaura
- Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara City, Nara, 631-8505, Japan
| | - Takumi Tanaka
- Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara City, Nara, 631-8505, Japan
| | - Chiaki Kato
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, 237-0061, Japan
| | - Kaoru Nakasone
- Faculty of Engineering, Kindai University, 1 Takaya Umenobe, Higashi-Hiroshima City, Hiroshima, 739-2116, Japan
| | - Noriaki Kishimoto
- Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara City, Nara, 631-8505, Japan
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Wakai S, Abe A, Fujii S, Nakasone K, Sambongi Y. Pyrophosphate hydrolysis in the extremely halophilic archaeon Haloarcula japonica is catalyzed by a single enzyme with a broad ionic strength range. Extremophiles 2017; 21:471-477. [DOI: 10.1007/s00792-017-0917-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/27/2017] [Indexed: 11/30/2022]
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Yamada O, Machida M, Hosoyama A, Goto M, Takahashi T, Futagami T, Yamagata Y, Takeuchi M, Kobayashi T, Koike H, Abe K, Asai K, Arita M, Fujita N, Fukuda K, Higa KI, Horikawa H, Ishikawa T, Jinno K, Kato Y, Kirimura K, Mizutani O, Nakasone K, Sano M, Shiraishi Y, Tsukahara M, Gomi K. Genome sequence of Aspergillus luchuensis NBRC 4314. DNA Res 2016; 23:507-515. [PMID: 27651094 PMCID: PMC5144674 DOI: 10.1093/dnares/dsw032] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/02/2016] [Indexed: 12/03/2022] Open
Abstract
Awamori is a traditional distilled beverage made from steamed Thai-Indica rice in Okinawa, Japan. For brewing the liquor, two microbes, local kuro (black) koji mold Aspergillus luchuensis and awamori yeast Saccharomyces cerevisiae are involved. In contrast, that yeasts are used for ethanol fermentation throughout the world, a characteristic of Japanese fermentation industries is the use of Aspergillus molds as a source of enzymes for the maceration and saccharification of raw materials. Here we report the draft genome of a kuro (black) koji mold, A. luchuensis NBRC 4314 (RIB 2604). The total length of nonredundant sequences was nearly 34.7 Mb, comprising approximately 2,300 contigs with 16 telomere-like sequences. In total, 11,691 genes were predicted to encode proteins. Most of the housekeeping genes, such as transcription factors and N-and O-glycosylation system, were conserved with respect to Aspergillus niger and Aspergillus oryzae An alternative oxidase and acid-stable α-amylase regarding citric acid production and fermentation at a low pH as well as a unique glutamic peptidase were also found in the genome. Furthermore, key biosynthetic gene clusters of ochratoxin A and fumonisin B were absent when compared with A. niger genome, showing the safety of A. luchuensis for food and beverage production. This genome information will facilitate not only comparative genomics with industrial kuro-koji molds, but also molecular breeding of the molds in improvements of awamori fermentation.
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Affiliation(s)
- Osamu Yamada
- National Research Institute of Brewing, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | - Masayuki Machida
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, AIST, Tsukuba, Ibaraki 305-8566, Japan
| | - Akira Hosoyama
- National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066, Japan
| | - Masatoshi Goto
- Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Toru Takahashi
- National Research Institute of Brewing, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | - Taiki Futagami
- Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Youhei Yamagata
- Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-0054, Japan
| | - Michio Takeuchi
- Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-0054, Japan
| | | | - Hideaki Koike
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, AIST, Tsukuba, Ibaraki 305-8566, Japan
| | - Keietsu Abe
- Tohoku University, Aoba-ku, Sendai 981-8555, Japan
| | - Kiyoshi Asai
- Computational Biology Research Center, AIST, Koto-ku, Tokyo 135-0064, Japan
| | - Masanori Arita
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Nobuyuki Fujita
- National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066, Japan
| | - Kazuro Fukuda
- Asahi Breweries, LTD, Sumida-ku, Tokyo 130-8602, Japan
| | - Ken-Ichi Higa
- Industrial Technology Center, Okinawa Prefectural Government, Uruma, Okinawa 904-2234, Japan
| | - Hiroshi Horikawa
- National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066, Japan
| | | | - Koji Jinno
- National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066, Japan
| | - Yumiko Kato
- National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066, Japan
| | - Kohtaro Kirimura
- Department of Applied Chemistry, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Osamu Mizutani
- National Research Institute of Brewing, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | - Kaoru Nakasone
- Kinki University Faculty of Engineering, Higashi-hiroshima, Hiroshima 739-2116, Japan
| | - Motoaki Sano
- Kanazawa Institute of Technology, Nonoichi, Ishikawa 921-8501, Japan
| | - Yohei Shiraishi
- National Research Institute of Brewing, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | | | - Katsuya Gomi
- Tohoku University, Aoba-ku, Sendai 981-8555, Japan
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Satahira K, Nakasone K, Ihara T. Sterilization Effects of HO<sub>2</sub>/O<sub>2</sub><sup>-</sup> Radicals Produced by H<sub>2</sub>O-O<sub>2</sub> Plasma. J PHOTOPOLYM SCI TEC 2016. [DOI: 10.2494/photopolymer.29.433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Sato H, Nakasone K, Yoshida T, Kato C, Maruyama T. Increases of heat shock proteins and their mRNAs at high hydrostatic pressure in a deep-sea piezophilic bacterium, Shewanella violacea. Extremophiles 2015; 19:751-62. [PMID: 25982740 DOI: 10.1007/s00792-015-0751-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 04/26/2015] [Indexed: 11/30/2022]
Abstract
When non-extremophiles encounter extreme environmental conditions, which are natural for the extremophiles, stress reactions, e.g., expression of heat shock proteins (HSPs), are thought to be induced for survival. To understand how the extremophiles live in such extreme environments, we studied the effects of high hydrostatic pressure on cellular contents of HSPs and their mRNAs during growth in a piezophilic bacterium, Shewanella violacea. HSPs increased at high hydrostatic pressures even when optimal for growth. The mRNAs and proteins of these HSPs significantly increased at higher hydrostatic pressure in S. violacea. In the non-piezophilic Escherichia coli, however, their mRNAs decreased, while their proteins did not change. Several transcriptional start sites (TSSs) for HSP genes were determined by the primer extension method and some of them showed hydrostatic pressure-dependent increase of the mRNAs. A major refolding target of one of the HSPs, chaperonin, at high hydrostatic pressure was shown to be RplB, a subunit of the 50S ribosome. These results suggested that in S. violacea, HSPs play essential roles, e.g., maintaining protein complex machinery including ribosomes, in the growth and viability at high hydrostatic pressure, and that, in their expression, the transcription is under the control of σ(32).
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Affiliation(s)
- Hiroshi Sato
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midoriku, Yokohama, 226-8501, Japan
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Kawano H, Nakasone K, Abe F, Kato C, Yoshida Y, Usami R, Horikoshi K. Protein–DNA Interactions under High-Pressure Conditions, Studied by Capillary Narrow-Tube Electrophoresis. Biosci Biotechnol Biochem 2014; 69:1415-7. [PMID: 16041150 DOI: 10.1271/bbb.69.1415] [Citation(s) in RCA: 3] [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: 11/08/2022]
Abstract
The method of electrophoretic mobility shift assay under high-pressure conditions was improved using a high-pressure electrophoresis apparatus with capillary narrow-tube gel. It was found that the protein-DNA complex in the gel was stained as a high-resolution spot with ethidium bromide. Using this method, it was found that the behavior under high-pressure conditions of the protein-DNA complex composed of NtrC protein and its target promoter DNA is important for the pressure-regulated transcription process, and it was confirmed that the complex was dissociated above a pressure of 70 MPa.
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Affiliation(s)
- Hiroaki Kawano
- Extremobiosphere Research Center (XBR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
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Yatsunami R, Ando A, Yang Y, Takaichi S, Kohno M, Matsumura Y, Ikeda H, Fukui T, Nakasone K, Fujita N, Sekine M, Takashina T, Nakamura S. Identification of carotenoids from the extremely halophilic archaeon Haloarcula japonica. Front Microbiol 2014; 5:100. [PMID: 24672517 PMCID: PMC3956123 DOI: 10.3389/fmicb.2014.00100] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 02/25/2014] [Indexed: 12/20/2022] Open
Abstract
The carotenoids produced by extremely halophilic archaeon Haloarcula japonica were extracted and identified by their chemical, chromatographic, and spectroscopic characteristics (UV-Vis and mass spectrometry). The composition (mol%) was 68.1% bacterioruberin, 22.5% monoanhydrobacterioruberin, 9.3% bisanhydrobacterioruberin, <0.1% isopentenyldehydrorhodopin, and trace amounts of lycopene and phytoene. The in vitro scavenging capacity of a carotenoid, bacterioruberin, extracted from Haloarcula japonica cells against 1,1-diphenyl-2-picrylhydrazyl (DPPH) radicals was evaluated. The antioxidant capacity of bacterioruberin was much higher than that of β -carotene.
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Affiliation(s)
- Rie Yatsunami
- Department of Bioengineering, Tokyo Institute of Technology Yokohama, Japan
| | - Ai Ando
- Department of Bioengineering, Tokyo Institute of Technology Yokohama, Japan
| | - Ying Yang
- Department of Bioengineering, Tokyo Institute of Technology Yokohama, Japan
| | | | - Masahiro Kohno
- Department of Bioengineering, Tokyo Institute of Technology Yokohama, Japan
| | - Yuriko Matsumura
- Department of Bioengineering, Tokyo Institute of Technology Yokohama, Japan
| | - Hiroshi Ikeda
- Department of Bioengineering, Tokyo Institute of Technology Yokohama, Japan
| | - Toshiaki Fukui
- Department of Bioengineering, Tokyo Institute of Technology Yokohama, Japan
| | - Kaoru Nakasone
- Department of Biotechnology and Chemistry, Kinki University Hiroshima, Japan
| | - Nobuyuki Fujita
- Biotechnology Field, National Institute of Technology and Evaluation Tokyo, Japan
| | - Mitsuo Sekine
- Biotechnology Field, National Institute of Technology and Evaluation Tokyo, Japan
| | | | - Satoshi Nakamura
- Department of Bioengineering, Tokyo Institute of Technology Yokohama, Japan
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Wakai S, Kidokoro SI, Masaki K, Nakasone K, Sambongi Y. Constant enthalpy change value during pyrophosphate hydrolysis within the physiological limits of NaCl. J Biol Chem 2013; 288:29247-51. [PMID: 23965994 DOI: 10.1074/jbc.m113.502963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A decrease in water activity was thought to result in smaller enthalpy change values during PPi hydrolysis, indicating the importance of solvation for the reaction. However, the physiological significance of this phenomenon is unknown. Here, we combined biochemistry and calorimetry to solve this problem using NaCl, a physiologically occurring water activity-reducing reagent. The pyrophosphatase activities of extremely halophilic Haloarcula japonica, which can grow at ∼4 M NaCl, and non-halophilic Escherichia coli and Saccharomyces cerevisiae were maximal at 2.0 and 0.1 M NaCl, respectively. Thus, halophilic and non-halophilic pyrophosphatases exhibit distinct maximal activities at different NaCl concentration ranges. Upon calorimetry, the same exothermic enthalpy change of -35 kJ/mol was obtained for the halophile and non-halophiles at 1.5-4.0 and 0.1-2.0 M NaCl, respectively. These results show that solvation changes caused by up to 4.0 M NaCl (water activity of ∼0.84) do not affect the enthalpy change in PPi hydrolysis. It has been postulated that PPi is an ATP analog, having a so-called high energy phosphate bond, and that the hydrolysis of both compounds is enthalpically driven. Therefore, our results indicate that the hydrolysis of high energy phosphate compounds, which are responsible for biological energy conversion, is enthalpically driven within the physiological limits of NaCl.
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Affiliation(s)
- Satoshi Wakai
- From the Graduate School of Biosphere Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
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Minegishi H, Kamekura M, Kitajima-Ihara T, Nakasone K, Echigo A, Shimane Y, Usami R, Itoh T, Ihara K. Gene orders in the upstream of 16S rRNA genes divide genera of the family Halobacteriaceae into two groups. Int J Syst Evol Microbiol 2012; 62:188-195. [DOI: 10.1099/ijs.0.031708-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In many prokaryotic species, 16S rRNA genes are present in multiple copies, and their sequences in general do not differ significantly owing to concerted evolution. At the time of writing, the genus Haloarcula of the family Halobacteriaceae comprises nine species with validly published names, all of which possess two to four highly heterogeneous 16S rRNA genes. Existence of multiple heterogeneous 16S rRNA genes makes it difficult to reconstruct a biological phylogenetic tree using their sequence data. If the orthologous gene is able to be discriminated from paralogous genes, a tree reconstructed from orthologous genes will reflect a simple biological phylogenetic relationship. At present, however, we have no means to distinguish the orthologous rRNA operon from paralogous ones in the members of the family Halobacteriaceae. In this study, we found that the dihydroorotate oxidase gene, pyrD, was present in the immediate upstream of one 16S rRNA gene in each of ten strains of the family Halobacteriaceae whose genome sequences have been determined, and the direction of the pyrD gene was opposite to that of the 16S rRNA genes. In two other strains whose genome sequences have been determined, the pyrD gene was present in far separated positions. We designed PCR primer sets to amplify DNA fragments encompassing a region from the conserved region of the pyrD gene to a conserved region of the tRNA-Ala gene or the 23S rRNA gene to determine the 16S rRNA gene sequences preceded by the pyrD gene, and to see if the pyrD gene is conserved in the immediate upstream of rRNA operon(s) in the type strains of the type species of 28 genera of the family Halobacteriaceae. Seventeen type strains, including the ten strains mentioned above, gave amplified DNA fragments of approximately 4000 bp, while eleven type strains, including the two strains mentioned above, did not give any PCR products. These eleven strains are members of the Clade I haloarchaea, originally defined by Walsh et al. (2004) and expanded by Minegishi et al. (2010). Analysis of contig sequences of three strains belonging to the Clade I haloarchaea also revealed the absence of the pyrD gene in the immediate upstream of any 16S rRNA genes. It may be scientifically sound to hypothesize that during the evolution of members of the family Halobacteriaceae, a pyrD gene transposition event happened in one group and this was followed by subsequent speciation processes in each group, yielding species/genera of the Clade I group and ‘the rest’ of the present family Halobacteriaceae.
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Affiliation(s)
- Hiroaki Minegishi
- Bio-Nano Electronics Research Center, Toyo University, Kawagoe, Saitama, Japan
| | | | | | - Kaoru Nakasone
- Department of Chemistry and Environmental Technology, School of Engineering, Kinki University, Higashi-Hiroshima, Hiroshima, Japan
| | - Akinobu Echigo
- Faculty of Science and Engineering, Toyo University, Kawagoe, Saitama, Japan
- Bio-Nano Electronics Research Center, Toyo University, Kawagoe, Saitama, Japan
| | - Yasuhiro Shimane
- Graduate School of Interdisciplinary New Science, Toyo University, Kawagoe, Saitama, Japan
| | - Ron Usami
- Graduate School of Interdisciplinary New Science, Toyo University, Kawagoe, Saitama, Japan
- Faculty of Science and Engineering, Toyo University, Kawagoe, Saitama, Japan
- Bio-Nano Electronics Research Center, Toyo University, Kawagoe, Saitama, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama, Japan
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Nagoya, Aichi, Japan
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Kawamoto J, Sato T, Nakasone K, Kato C, Mihara H, Esaki N, Kurihara T. Favourable effects of eicosapentaenoic acid on the late step of the cell division in a piezophilic bacterium, Shewanella violacea DSS12, at high-hydrostatic pressures. Environ Microbiol 2011; 13:2293-8. [PMID: 21518217 DOI: 10.1111/j.1462-2920.2011.02487.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Shewanella violacea DSS12, a deep-sea bacterium, produces eicosapentaenoic acid (EPA) as a component of membrane phospholipids. Although various isolates from the deep sea, such as Photobacterium profundum SS9, Colwellia psychrerythraea 34H and various Shewanella strains, produce EPA- or docosahexaenoic acid-containing phospholipids, the physiological role of these polyunsaturated fatty acids remains unclear. In this article, we illustrate the physiological importance of EPA for high-pressure adaptation in strain DSS12 with the help of an EPA-deficient mutant (DSS12(pfaA)). DSS12(pfaA) showed significant growth retardation at 30 MPa, but not at 0.1 MPa. We also found that DSS12(pfaA) grown at 30 MPa forms filamentous cells. When an EPA-containing phospholipid (sn-1-oleoly-sn-2-eicosapentaenoyl phosphatidylethanolamine) was supplemented, the growth retardation and the morphological defect of DSS12(pfaA) were suppressed, indicating that the externally added EPA-containing phospholipid compensated for the loss of endogenous EPA. In contrast, the addition of an oleic acid-containing phospholipid (sn-1,2-dioleoyl phosphatidylethanolamine) did not affect the growth and the morphology of the cells. Immunofluorescent microscopic analysis with anti-FtsZ antibody revealed a number of Z-rings and separated nucleoids in DSS12(pfaA) grown at 30 MPa. These results demonstrate the physiological importance of EPA for the later step of Z-ring formation of S. violacea DSS12 under high-pressure conditions.
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Affiliation(s)
- Jun Kawamoto
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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Murakami C, Ohmae E, Tate SI, Gekko K, Nakasone K, Kato C. Comparative study on dihydrofolate reductases from Shewanella species living in deep-sea and ambient atmospheric-pressure environments. Extremophiles 2010; 15:165-75. [PMID: 21181485 DOI: 10.1007/s00792-010-0345-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 12/01/2010] [Indexed: 10/18/2022]
Abstract
To examine whether dihydrofolate reductase (DHFR) from deep-sea bacteria has undergone molecular evolution to adapt to high-pressure environments, we cloned eight DHFRs from Shewanella species living in deep-sea and ambient atmospheric-pressure environments, and subsequently purified six proteins to compare their structures, stabilities, and functions. The DHFRs showed 74-90% identity in primary structure to DHFR from S. violacea, but only 55% identity to DHFR from Escherichia coli (ecDHFR). Far-ultraviolet circular dichroism and fluorescence spectra suggested that the secondary and tertiary structures of these DHFRs were similar. In addition, no significant differences were found in structural stability as monitored by urea-induced unfolding and the kinetic parameters, K(m) and k(cat); although the DHFRs from Shewanella species were less stable and more active (2- to 4-fold increases in k(cat)/K(m)) than ecDHFR. Interestingly, the pressure effects on enzyme activity revealed that DHFRs from ambient-atmospheric species are not necessarily incompatible with high pressure, and DHFRs from deep-sea species are not necessarily tolerant of high pressure. These results suggest that the DHFR molecule itself has not evolved to adapt to high-pressure environments, but rather, those Shewanella species with enzymes capable of retaining functional activity under high pressure migrated into the deep-sea.
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Affiliation(s)
- Chiho Murakami
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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Aono E, Baba T, Ara T, Nishi T, Nakamichi T, Inamoto E, Toyonaga H, Hasegawa M, Takai Y, Okumura Y, Baba M, Tomita M, Kato C, Oshima T, Nakasone K, Mori H. Complete genome sequence and comparative analysis of Shewanella violacea, a psychrophilic and piezophilic bacterium from deep sea floor sediments. Mol Biosyst 2010. [PMID: 20458400 DOI: 10.1039/c000396d.] [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] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Remineralization of organic matter in deep-sea sediments is important in oceanic biogeochemical cycles, and bacteria play a major role in this process. Shewanella violacea DSS12 is a psychrophilic and piezophilic gamma-proteobacterium that was isolated from the surface layer of deep sea sediment at a depth of 5110 m. Here, we report the complete genome sequence of S. violacea and comparative analysis with the genome of S. oneidensis MR-1, isolated from sediments of a freshwater lake. Unlike S. oneidensis, this deep-sea Shewanella possesses very few terminal reductases for anaerobic respiration and no c-type cytochromes or outer membrane proteins involved in respiratory Fe(iii) reduction, which is characteristic of most Shewanella species. Instead, the S. violacea genome contains more terminal oxidases for aerobic respiration and a much greater number of putative secreted proteases and polysaccharases, in particular, for hydrolysis of collagen, cellulose and chitin, than are encoded in S. oneidensis. Transporters and assimilatory reductases for nitrate and nitrite, and nitric oxide-detoxifying mechanisms (flavohemoglobin and flavorubredoxin) are found in S. violacea. Comparative analysis of the S. violacea genome revealed the respiratory adaptation of this bacterium to aerobiosis, leading to predominantly aerobic oxidation of organic matter in surface sediments, as well as its ability to efficiently use diverse organic matter and to assimilate inorganic nitrogen as a survival strategy in the nutrient-poor deep-sea floor.
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Affiliation(s)
- Eiji Aono
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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Aono E, Baba T, Ara T, Nishi T, Nakamichi T, Inamoto E, Toyonaga H, Hasegawa M, Takai Y, Okumura Y, Baba M, Tomita M, Kato C, Oshima T, Nakasone K, Mori H. Complete genome sequence and comparative analysis of Shewanella violacea, a psychrophilic and piezophilic bacterium from deep sea floor sediments. Mol Biosyst 2010; 6:1216-26. [PMID: 20458400 DOI: 10.1039/c000396d] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Remineralization of organic matter in deep-sea sediments is important in oceanic biogeochemical cycles, and bacteria play a major role in this process. Shewanella violacea DSS12 is a psychrophilic and piezophilic gamma-proteobacterium that was isolated from the surface layer of deep sea sediment at a depth of 5110 m. Here, we report the complete genome sequence of S. violacea and comparative analysis with the genome of S. oneidensis MR-1, isolated from sediments of a freshwater lake. Unlike S. oneidensis, this deep-sea Shewanella possesses very few terminal reductases for anaerobic respiration and no c-type cytochromes or outer membrane proteins involved in respiratory Fe(iii) reduction, which is characteristic of most Shewanella species. Instead, the S. violacea genome contains more terminal oxidases for aerobic respiration and a much greater number of putative secreted proteases and polysaccharases, in particular, for hydrolysis of collagen, cellulose and chitin, than are encoded in S. oneidensis. Transporters and assimilatory reductases for nitrate and nitrite, and nitric oxide-detoxifying mechanisms (flavohemoglobin and flavorubredoxin) are found in S. violacea. Comparative analysis of the S. violacea genome revealed the respiratory adaptation of this bacterium to aerobiosis, leading to predominantly aerobic oxidation of organic matter in surface sediments, as well as its ability to efficiently use diverse organic matter and to assimilate inorganic nitrogen as a survival strategy in the nutrient-poor deep-sea floor.
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Affiliation(s)
- Eiji Aono
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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Murakami C, Ohmae E, Tate SI, Gekko K, Nakasone K, Kato C. Cloning and characterization of dihydrofolate reductases from deep-sea bacteria. J Biochem 2009; 147:591-9. [DOI: 10.1093/jb/mvp206] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Tamegai H, Chikuma S, Ishii M, Nakasone K, Kato C. ThenarQPgenes for a two-component regulatory system from the deep-sea bacteriumShewanella violaceaDSS12. ACTA ACUST UNITED AC 2009; 19:308-12. [PMID: 17852338 DOI: 10.1080/10425170701605856] [Citation(s) in RCA: 4] [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: 10/22/2022]
Abstract
Shewanella violacea DSS12 is facultative piezophile isolated from the deep-sea. The expression of cydDC genes (required for d-type cytochrome maturation) of the organism is regulated by hydrostatic pressure. In this study, we analyzed the nucleotide sequence upstream of cydDC in detail and found that there are putative binding sites for the NarL protein which is part of a two-component regulatory system also containing the sensor protein NarX. Furthermore, we identified the narQP genes (homologues of narXL) from S. violacea DSS12 and demonstrated the heterologous expression of narP in Escherichia coli. These results will be helpful in examining pressure regulation of gene expression in S. violacea at the molecular level.
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Affiliation(s)
- Hideyuki Tamegai
- Department of Chemistry, College of Humanities and Sciences, Nihon University, Tokyo, Japan.
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Kawano H, Suzaki Y, Fukuchi J, Nakasone K, Abe F, Kato C, Yoshida Y, Usami R, Horikoshi K. Cloning and Overproduction of therpoZGene Encoding an RNA Polymerase ω Subunit from a Deep-sea PiezophilicShewanella violaceaStrain DSS12. ACTA ACUST UNITED AC 2009; 15:118-22. [PMID: 15346766 DOI: 10.1080/1042517042000208626] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We have cloned the rpoZ gene, encoding RNA polymerase omega protein, by PCR approach from the deep-sea piezophilic and psychrophilic bacterium, Shewanella violacea strain DSS12. The cloned gene, 285bp in length, was found to encode a protein consisting of 94 amino acid residues with a molecular mass of 10,327 Da. Significant homology was evident comparing the RpoZ protein of S. violacea with that of Shewanella oneidensis (69% identity), Vibrio cholerae (65% identity), Escherichia coli K-12 (64% identity) and Haemophilus influenzae (61% identity). From the Northern blot analysis, S. violacea rpoZ gene was expressed constitutively under pressure conditions of 0.1, 30 and 50MPa. We constructed expression plasmid to overproduce the RpoZ protein and transformed into E. coli JM109 as a host of overproduction. Upon induction, the recombinant protein encoded by plasmid pQrpoZ was overexpressed and purified using Ni2+ affinity column.
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Affiliation(s)
- Hiroaki Kawano
- The Deepstar Group, Japan Marine Science and Technology Center, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
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Yu F, Okamto S, Nakasone K, Adachi K, Matsuda S, Harada H, Misawa N, Utsumi R. Molecular cloning and functional characterization of alpha-humulene synthase, a possible key enzyme of zerumbone biosynthesis in shampoo ginger (Zingiber zerumbet Smith). Planta 2008; 227:1291-9. [PMID: 18273640 DOI: 10.1007/s00425-008-0700-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2007] [Accepted: 01/24/2008] [Indexed: 05/25/2023]
Abstract
Shampoo ginger (Zingiber zerumbet Smith) has a high content and large variety of terpenoids in the essential oil of its rhizome. Here, we report on the isolation of a cDNA clone (ZSS1) encoding alpha-humulene synthase, a possible key enzyme of zerumbone biosynthesis. This clone contains an open reading frame of 1,644 bp and is predicted to encode a protein of 548 amino acids with a calculated molecular mass of 64.5 kDa. The deduced amino acid sequence shows 34-63% identity with known sesquiterpene synthases of other angiosperm species. Based on exon-intron organization, ZSS1 is classified as the terpene synthase-III (TPS-III) subfamily. When expressed in Escherichia coli, the recombinant enzyme catalyzed the formation of a major product, alpha-humulene (95%) and a minor by-product, beta-caryophyllene (5%). Introduction of ZSS1 and the foreign mevalonate pathway involved in FPP synthesis into E. coli results in in vivo production of alpha-humulene. Transcript of ZSS1 was detected almost exclusively in rhizomes and was up-regulated in both leaves and rhizomes after treatment with methyl jasmonate (MeJA), suggesting its ecological function in shampoo ginger.
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Affiliation(s)
- Fengnian Yu
- Department of Bioscience, Graduate School of Agriculture, Kinki University, 3327-204 Nakamachi, Nara, 631-8505, Japan
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Ogawa K, Sonoyama T, Takeda T, Ichiki SI, Nakamura S, Kobayashi Y, Uchiyama S, Nakasone K, Takayama SIJ, Mita H, Yamamoto Y, Sambongi Y. Roles of a short connecting disulfide bond in the stability and function of psychrophilic Shewanella violacea cytochrome c (5). Extremophiles 2007; 11:797-807. [PMID: 17657404 DOI: 10.1007/s00792-007-0099-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [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: 05/31/2007] [Accepted: 06/15/2007] [Indexed: 10/23/2022]
Abstract
Cys-59 and Cys-62, forming a disulfide bond in the four-residue loop of Shewanella violacea cytochrome c (5) (SV cytc (5)), contribute to protein stability but not to redox function. These Cys residues were substituted with Ala in SV cytc (5), and the structural and functional properties of the resulting C59A/C62A variant were determined and compared with those of the wild-type. The variant had similar features to those of the wild-type in absorption, circular dichroic, and paramagnetic (1)H NMR spectra. In addition, the redox potentials of the wild-type and variant were essentially the same, indicating that removal of the disulfide bond from SV cytc (5) does not affect the redox function generated in the vicinity of heme. However, calorimetric analysis of the wild-type and variant showed that the mutations caused a drastic decrease in the protein stability through enthalpy, but not entropy. Four residues are encompassed by the SV cytc (5) disulfide bond, which is the shortest one that has been proved to affect protein stability. The protein stability of SV cytc (5) can be controlled without changing the redox function, providing a new strategy for regulating the stability and function of cytochrome c.
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Affiliation(s)
- Keiko Ogawa
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
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Koga K, Ikegami A, Nakasone K, Murayama R, Akanuma G, Natori Y, Nanamiya H, Kawamura F. Construction of Bacillus subtilis strains carrying the transcriptional bgaB fusion with the promoter region of each rrn operon and their differential transcription during spore development. J GEN APPL MICROBIOL 2006; 52:119-24. [PMID: 16778356 DOI: 10.2323/jgam.52.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Keiko Koga
- Laboratory of Molecular Genetics and Frontier Project 'Life's Adaptation Strategies to Environmental Changes', College of Science, Rikkyo University, Japan
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Kawano H, Nakasone K, Abe F, Kato C, Yoshida Y, Usami R, Horikoshi K. Identification of rpoBC genes encoding for beta and beta' subunits of RNA polymerase in a deep-sea piezophilic bacterium, Shewanella violacea strain DSS12. Biosci Biotechnol Biochem 2005; 69:575-82. [PMID: 15784987 DOI: 10.1271/bbb.69.575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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: 11/08/2022]
Abstract
RNA polymerase from cells of the deep-sea bacterium Shewanella violacea DSS12 was purified using three chromatographic steps. An in vitro transcription assay indicated that the purified enzyme was sigma(70) containing RNA polymerase. The enzyme activity was inhibited in the presence of rifampicin when the sensitive domain was targeted. The rpoBC genes encoding for the beta and beta' subunits of RNA polymerase were cloned and their nucleotide sequences determined. Expression plasmids, designated pQSVB and pQSVC, to overproduce these proteins were constructed, and the proteins were purified using a Ni(2+) affinity column. In vitro reconstitution using all proteins for the holoenzyme (alpha, beta, beta', sigma(70)) was carried out and the activity of the recombinant RNA polymerase was detected.
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Affiliation(s)
- Hiroaki Kawano
- Extremobiosphere Research Center (XBR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.
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Kawano H, Abe F, Nakasone K, Kato C, Yoshida Y, Usami R, Horikoshi K. Cloning and characterization of the rpoE gene encoding an RNA polymerase sigmaE factor from the deep-sea piezophilic Shewanella violacea strain DSS12. ACTA ACUST UNITED AC 2005; 16:69-74. [PMID: 16040350 DOI: 10.1080/10425170400024482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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: 10/26/2022]
Abstract
The rpoE gene encoding an RNA polymerase sigmaE subunit was isolated from a gamma-phage library of the deep-sea piezophilic and psychrophilic bacterium Shewanella violacea strain DSS12. Structual analysis showed that the gene organization of the fragment containing S. violacearpoE was the l-aspartate oxidase-coding gene, rpoE, rseA, rseB and rseC in that order, the same as in the case of Photobacterium profundum SS9 and Escherichia coli K-12. The cloned gene, 576 bp in length, was found to encode a protein consisting of 192 amino acid residues with a molecular mass of 21,806 Da. Amino acid alignment of the RpoE protein showed that the functional domains responsible for DNA recognition, DNA melting, core binding, and RseA interaction were highly conserved. We purified hexahistidine-fused RpoE protein by constructing an overexpression plasmid. Core-binding analysis revealed that the cloned RpoE protein has the ability to bind with core RNA polymerase as a sigma factor.
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Affiliation(s)
- Hiroaki Kawano
- Extremobiosphere Research Center (XBR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan.
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Tamegai H, Kawano H, Ishii A, Chikuma S, Nakasone K, Kato C. Pressure-regulated biosynthesis of cytochrome bd in piezo- and psychrophilic deep-sea bacterium Shewanella violacea DSS12. Extremophiles 2005; 9:247-53. [PMID: 15844013 DOI: 10.1007/s00792-005-0439-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [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: 12/28/2004] [Accepted: 02/04/2005] [Indexed: 10/25/2022]
Abstract
The genes of cytochrome bd-encoding cydAB were identified from a deep-sea bacterium Shewanella violacea DSS12. These showed significant homologies with known cydAB gene sequences from various organisms. Additionally, highly conserved regions that are important for the enzymatic function were also conserved in cydA of S. violacea. Based on the results, transcriptional analysis of cydAB operon and cydDC operon (required for assembly of cytochrome bd) of S. violacea in microaerobic condition was performed under the growth condition of various pressures. The gene of cydA was expressed even under the condition of atmospheric pressure and its expression was enhanced with pressurization. On the other hand, the expression of cydC was strongly depressed under the condition of atmospheric pressure compared with the case under high pressure. It appeared spectrophotometrically that loss of cytochrome bd in S. violacea under atmospheric pressure shown in previous study is caused mainly by the loss of cydDC. Further, under the growth condition of atmospheric pressure, either less amount or no d-type cytochrome was expressed compared with the case of high-pressure condition even if the organism was grown under alkaline condition or in the presence of uncoupler, which are the inducible condition of d-type cytochrome in Escherichia coli. These results suggested that the significant amount of d-type cytochrome expression is specific event under the growth condition of high pressure.
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Affiliation(s)
- Hideyuki Tamegai
- Department of Chemistry, College of Humanities and Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan.
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Ishii A, Oshima T, Sato T, Nakasone K, Mori H, Kato C. Analysis of hydrostatic pressure effects on transcription in Escherichia coli by DNA microarray procedure. Extremophiles 2004; 9:65-73. [PMID: 15340867 DOI: 10.1007/s00792-004-0414-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [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: 05/14/2004] [Accepted: 07/01/2004] [Indexed: 11/29/2022]
Abstract
Hydrostatic pressure is a well-known physical stimulus, but its effects on cell physiology have not been clarified. To investigate pressure effects on Escherichia coli, we carried out DNA microarray analysis of the entire E. coli genome. The microarray results showed pleiotropic effects on gene expression. In particular, heat- and cold-stress responses were induced simultaneously by the elevated pressure. Upon temperature stress (including both temperature up- and down-shifts) and other environmental stresses, gene expression adjusts to adapt to such environmental changes through regulations by several DNA-binding proteins. An E. coli mutant, which deleted the hns gene encoding one of the regulator proteins, exhibited great pressure sensitivity. The result suggested that the H-NS protein was a possible transcriptional regulator for adaptation of the high-pressure stress.
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Affiliation(s)
- Akihiro Ishii
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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Kawano H, Nakasone K, Matsumoto M, Yoshida Y, Usami R, Kato C, Abe F. Differential pressure resistance in the activity of RNA polymerase isolated from Shewanella violacea and Escherichia coli. Extremophiles 2004; 8:367-75. [PMID: 15241657 DOI: 10.1007/s00792-004-0397-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2004] [Accepted: 04/20/2004] [Indexed: 12/01/2022]
Abstract
RNA polymerase was purified from the piezophile Shewanella violacea DSS12, and the transcriptional activity after pressure treatment was compared with that of the mesophile Escherichia coli. Application of pressure at 100 MPa for 30 min reduced the E. coli RNA polymerase activity to 60% of the activity at atmospheric pressure, whereas the S. violacea RNA polymerase maintained full activity, indicating that the S. violacea RNA polymerase is more stable than its E. coli counterpart. This result was supported by the analysis of the strength of subunit interactions of the enzyme from both species, using a high-pressure electrophoresis apparatus, which showed that a pressure of 140 MPa caused dissociation of E. coli RNA polymerase but not that of S. violacea RNA polymerase. On the other hand, the core enzyme of S. violacea RNA polymerase, which lacked the sigma70 factor, was dissociated at 140 MPa. These results suggest that the sigma70 factor is required for stabilization of S. violacea RNA polymerase under high-pressure conditions. In this paper, we provide in vitro evidence for piezoadaptation at the transcriptional level, using purified RNA polymerase from cells of S. violacea and E. coli.
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Affiliation(s)
- Hiroaki Kawano
- The DEEPSTAR Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
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Ohmae E, Kubota K, Nakasone K, Kato C, Gekko K. Pressure-dependent Activity of Dihydrofolate Reductase from a Deep-sea BacteriumShewanella violaceaStrain DSS12. CHEM LETT 2004. [DOI: 10.1246/cl.2004.798] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Kawano H, Ikegami A, Nakasone K, Kato C, Usami R, Horikoshi K. Reconstitution and characterization of NtrC protein in a deep-sea piezophilic bacterium, Shewanella violacea strain DSS12. Biosci Biotechnol Biochem 2003; 67:1983-5. [PMID: 14519985 DOI: 10.1271/bbb.67.1983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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: 11/08/2022]
Abstract
NtrC protein of piezophilic Shewanella violacea was overexpressed and purified, to confirm the protein-DNA interaction. An electrophoretic mobility shift assay demonstrated that the NtrC recognizes the sequence for NtrC binding within the region upstream of the glnA operon. Western blot analysis also showed that the NtrC is expressed at a higher level under high-pressure conditions than under atmospheric pressure conditions.
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Affiliation(s)
- Hiroaki Kawano
- Department of Applied Chemistry, Faculty of Engineering, Toyo University, Kawagoe, Saitama, Japan
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Ishii A, Nakasone K, Sato T, Wachi M, Sugai M, Nagai K, Kato C. Isolation and characterization of the dcw cluster from the piezophilic deep-sea bacterium Shewanella violacea. J Biochem 2002; 132:183-8. [PMID: 12153713 DOI: 10.1093/oxfordjournals.jbchem.a003208] [Citation(s) in RCA: 12] [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: 11/12/2022] Open
Abstract
The dcw cluster of genes involved in cell division and cell wall synthesis from the piezophilic deep-sea bacterium Shewanella violacea was isolated and characterized. It comprises 15 open reading frames, of which the organization is mraZ-mraW-ftsL-ftsI-murE-murF-mraY-murD-ftsW-murG-murC-ftsQ-ftsA-ftsZ-envA, in that order. To analyze transcription upstream from the ftsZ gene, Northern blot and primer extension analyses were performed. The results showed that gene expression is not pressure dependent. Western blot analysis showed that the FtsZ protein is equally expressed under several pressure conditions in the range of atmospheric (0.1 MPa) to high (50 MPa) pressures. Using immunofluorescence microscopy, the FtsZ ring was observed in the center of cells at pressure conditions of 0.1 to 50 MPa. These results imply that the FtsZ protein function is not affected by elevated pressure in this piezophilic bacterium.
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Affiliation(s)
- Akihiro Ishii
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
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Nakasone K, Ikegami A, Kawano H, Kato C, Usami R, Horikoshi K. Transcriptional regulation under pressure conditions by RNA polymerase sigma54 factor with a two-component regulatory system in Shewanella violacea. Extremophiles 2002; 6:89-95. [PMID: 12013439 DOI: 10.1007/s00792-001-0247-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [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: 10/27/2022]
Abstract
Deep-sea bacteria have unique systems for gene and protein expression controlled by hydrostatic pressure. One of the sigma factors, sigma54, was found to play an important role in pressure-regulated transcription in a deep-sea piezophilic bacterium, Shewanella violacea. A glutamine synthetase gene (glnA) has been targeted as a model for the pressure-regulated promoter to investigate transcriptional regulation by the sigma54 factor. Recognition sites for sigma54 and sigma70 factors were observed at an upstream region of the glnA, and NtrC-binding sites were also identified at the same region. Primer extension analyses revealed that the transcription initiation sites of both promoters were determined and that transcription from the sigma54 site was regulated by elevated pressure. The sigma54 promoter is known to be activated by a two-component signal transduction system, the NtrB-NtrC phosphorylation relay. Our results suggested that this system might be regulated by deep-sea conditions and that the gene expression controlled by the sigma54 promoter was actually regulated by pressure. We propose a possible model of the molecular mechanisms for pressure-regulated transcription.
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Affiliation(s)
- Kaoru Nakasone
- Department of Chemistry and Environmental Technology, School of Engineering, Kinki University, Higashi-Hiroshima, Japan
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Nakasone K, Yamada M, Qureshi MH, Kato C, Horikoshi K. Piezoresponse of the cyo-operon coding for quinol oxidase subunits in a deep-sea piezophilic bacterium, Shewanella violacea. Biosci Biotechnol Biochem 2001; 65:690-3. [PMID: 11330692 DOI: 10.1271/bbb.65.690] [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: 11/08/2022]
Abstract
We have isolated the genes for quinol oxidase from a deep-sea piezophilic bacterium, Shewanella violacea. Analysis of the deduced amino acid sequences of the cyo subunits showed that this oxidase has high similarity to Escherichia coli bo-type quinol oxidase. Northern blot analysis showed that these genes are expressed at a high level when the bacterium is grown at elevated pressure. Upstream in the cyo-operon, a sigma54-binding motif and an octamer sequence unit were found, suggesting that these elements may play a role in regulation of expression of the cyo-operon in response to changes in pressure.
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Affiliation(s)
- K Nakasone
- The DEEPSTAR Group, Japan Marine Science and Technology Center, Yokosuka.
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Nakasone K, Ikegami A, Kato C, Horikoshi K. Isolation of the rpoD gene encoding the principal sigma factor of the deep-sea piezophilic bacterium Shewanella violacea strain DSS12 and its overexpression in Escherichia coli. Biosci Biotechnol Biochem 2001; 65:190-3. [PMID: 11272828 DOI: 10.1271/bbb.65.190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [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: 11/08/2022]
Abstract
The gene encoding the principal a factor (rpoD) of the piezophilic bacterium Shewanella violacea was cloned and sequenced. The rpoD gene was found to encode a polypeptide consisting of 614 amino acid residues, showing 75.6 and 64.3% identity to those of Escherichia coli and Pseudomonas putida, respectively. Comparison with E. coli sigma70 and P. putida sigma70 showed that significant similarity exists in four conserved regions known to be required for promoter recognition and core binding. Using an expression plasmid harboring the rpoD gene, the S. violacea sigma70 factor was overexpressed in E. coli and successfully purified to near homogeneity.
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Affiliation(s)
- K Nakasone
- The DEEP STAR Group, Japan Marine Science and Technology Center, Kanagawa, Japan.
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Nakasone K, Ikegami A, Fujii S, Kato C, Horikoshi K. Isolation and piezoresponse of the rpoA gene encoding the RNA polymerase alpha subunit from the deep-sea piezophilic bacterium Shewanella violacea. FEMS Microbiol Lett 2000; 193:261-8. [PMID: 11111034 DOI: 10.1111/j.1574-6968.2000.tb09434.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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: 11/29/2022] Open
Abstract
The rpoA gene encoding the alpha subunit of RNA polymerase from the deep-sea piezophilic bacterium Shewanella violacea DSS12 was cloned and sequenced. The rpoA gene was found to encode a polypeptide consisting of 329 amino acids with a molecular mass of 36238 Da. S. violacea alpha protein was expressed in a ts Escherichia coli mutant, to confirm whether the rpoA gene is functional. It complemented this mutation, indicating a chimeric RNA polymerase is assembled at the non-permissive temperature. Recombinant alpha protein was overexpressed using an expression plasmid harboring the rpoA gene and purified to near homogeneity. Primer extension analysis revealed that two transcriptional initiation sites are recognized by sigma(70) RNA polymerase. It also indicated that pressure response (piezoresponse) in the alpha operon occurred at the transcriptional level, suggesting some positive regulators may interact with the transcriptional apparatus and regulate the expression of the operon at different pressure conditions.
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Affiliation(s)
- K Nakasone
- The DEEP STAR Group, Japan Marine Science and Technology Center, Yokosuka, Kanagawa, Japan.
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Takami H, Nakasone K, Takaki Y, Maeno G, Sasaki R, Masui N, Fuji F, Hirama C, Nakamura Y, Ogasawara N, Kuhara S, Horikoshi K. Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucleic Acids Res 2000; 28:4317-31. [PMID: 11058132 PMCID: PMC113120 DOI: 10.1093/nar/28.21.4317] [Citation(s) in RCA: 429] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The 4 202 353 bp genome of the alkaliphilic bacterium Bacillus halodurans C-125 contains 4066 predicted protein coding sequences (CDSs), 2141 (52.7%) of which have functional assignments, 1182 (29%) of which are conserved CDSs with unknown function and 743 (18. 3%) of which have no match to any protein database. Among the total CDSs, 8.8% match sequences of proteins found only in Bacillus subtilis and 66.7% are widely conserved in comparison with the proteins of various organisms, including B.subtilis. The B. halodurans genome contains 112 transposase genes, indicating that transposases have played an important evolutionary role in horizontal gene transfer and also in internal genetic rearrangement in the genome. Strain C-125 lacks some of the necessary genes for competence, such as comS, srfA and rapC, supporting the fact that competence has not been demonstrated experimentally in C-125. There is no paralog of tupA, encoding teichuronopeptide, which contributes to alkaliphily, in the C-125 genome and an ortholog of tupA cannot be found in the B.subtilis genome. Out of 11 sigma factors which belong to the extracytoplasmic function family, 10 are unique to B. halodurans, suggesting that they may have a role in the special mechanism of adaptation to an alkaline environment.
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Affiliation(s)
- H Takami
- Japan Marine Science and Technology Center, Deep-Sea Microorganisms Research Group, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan.
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Yamaguchi T, Hayashi T, Takami H, Nakasone K, Ohnishi M, Nakayama K, Yamada S, Komatsuzawa H, Sugai M. Phage conversion of exfoliative toxin A production in Staphylococcus aureus. Mol Microbiol 2000; 38:694-705. [PMID: 11115106 DOI: 10.1046/j.1365-2958.2000.02169.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.1] [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: 11/20/2022]
Abstract
The staphylococcal exfoliative toxins (ETs) are extracellular proteins that cause splitting of human skin at the epidermal layer during infection in infants. Two antigenically distinct toxins possessing identical activity have been isolated from Staphylococcus aureus, ETA and ETB. The gene for ETA (eta) is located on the chromosome, whereas that for ETB is located on a large plasmid. The observation that relatively few clinical isolates produce ETA suggests that the eta gene is acquired by horizontal gene transfer. In this study, we isolated a temperate phage (phiETA) that encodes ETA and determined the complete nucleotide sequence of the phiETA genome. phiETA has a head with a hexagonal outline and a non-contractile and flexible tail. The genome of phiETA is a circularly permuted linear double-stranded DNA, and the genome size is 43 081 bp. Sixty-six open reading frames (ORFs) were identified on the phiETA genome, including eta, which was found to be located very close to a putative attachment site (attP). phiETA converted ETA non-producing strains into ETA producers. Southern blot analysis of chromosomal DNA from clinical isolates suggested that phiETA or related phages are responsible for the acquisition of eta genes in S. aureus.
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Affiliation(s)
- T Yamaguchi
- Department of Microbiology, Hiroshima University Faculty of Dentistry, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8553, Japan
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Ikegami A, Nakasone K, Kato C, Nakamura Y, Yoshikawa I, Usami R, Horikoshi K. Glutamine synthetase gene expression at elevated hydrostatic pressure in a deep-sea piezophilic Shewanella violacea. FEMS Microbiol Lett 2000; 192:91-5. [PMID: 11040434 DOI: 10.1111/j.1574-6968.2000.tb09364.x] [Citation(s) in RCA: 15] [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: 11/29/2022] Open
Abstract
A glutamine synthetase gene (glnA) was isolated from a deep-sea piezophilic bacterium, Shewanella violacea strain DSS12. A 7.5-kb SacI fragment containing the complete glnA gene was cloned and sequenced. The glnA gene was found to encode a protein consisting of 469 amino acid residues, showing 75.0% identity to the glutamine synthetase of Escherichia coli. Primer extension analyses revealed two transcription initiation sites in glnA and expression from each site was positively regulated by pressure. Putative promoters recognized by sigma(70) and sigma(54) were identified in the region upstream of glnA. An electrophoretic mobility shift assay demonstrated that S. violacea sigma(54) specifically binds to the promoter region of glnA, suggesting that sigma(54) may play an important role in pressure-regulated transcription in this piezophilic bacterium.
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Affiliation(s)
- A Ikegami
- The DEEPSTAR Group, Japan Marine Science and Technology Center, Yokosuka, Japan
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Nakasone K, Masui N, Takaki Y, Sasaki R, Maeno G, Sakiyama T, Hirama C, Fuji F, Takami H. Characterization and comparative study of the rrn operons of alkaliphilic Bacillus halodurans C-125. Extremophiles 2000; 4:209-14. [PMID: 10972189 DOI: 10.1007/pl00010713] [Citation(s) in RCA: 10] [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: 10/25/2022]
Abstract
The ribosomal RNA operons (rrn) of alkaliphilic Bacillus halodurans C-125 were characterized and compared with those of B. subtilis. We isolated clones containing rrn operons from a lambda phage library of the C-125 chromosome, and the complete nucleotide sequence of each was determined. Eight rrn operons were identified by PFGE analysis of the C-125 chromosome digested with I-CeuI. The transcriptional orientation of the rrn operons mapped on the chromosome by Southern hybridization analysis was the same as the direction of replication of the chromosome. These operons were designated as rrnA-H, starting from the oriC locus in clockwise rotation. Sequence and structural analyses of these operons suggested that six of the rrn operons in the C-125 chromosome, rrnA, rrnB, rrnC-rrnD, rrnE, and rrnH, correspond to rrnO, rrnA, rrnJ-rrnW, rrnI, and rrnD in B. subtilis, whereas the other rrn operons (rrnF and rrnG) were specifically observed in C-125. The rrn loci were positioned from 0 degrees to 90 degrees on the physical map, with the oriC locus assigned the position zero degrees. Two ORFs annotated as tnpA and ykfC, whose gene products are likely to act as transposases, were found downstream of these six operons. Comparative analysis of the 16S-23S and 23S-5S ITS (internally transcribed sequence) regions of B. halodurans C-125 and those of B. subtilis revealed that the ITS regions in C-125 were much longer than those in B. subtilis. There was no substantial difference in the length of potential promoter sequences in B. halodurans and B. subtilis.
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Affiliation(s)
- K Nakasone
- Deep-sea Microorganisms Research Group, Japan Marine Science and Technology Center, Yokosuka.
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Yamada M, Nakasone K, Tamegai H, Kato C, Usami R, Horikoshi K. Pressure regulation of soluble cytochromes c in a deep-Sea piezophilic bacterium, Shewanella violacea. J Bacteriol 2000; 182:2945-52. [PMID: 10781566 PMCID: PMC102006 DOI: 10.1128/jb.182.10.2945-2952.2000] [Citation(s) in RCA: 43] [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: 11/20/2022] Open
Abstract
Two c-type cytochromes from the soluble fraction of a deep-sea moderately piezophilic bacterium, Shewanella violacea, were purified and characterized, and the genes coding for these cytochromes were cloned and sequenced. One of the cytochromes, designated cytochrome c(A), was found to have a molecular mass of approximately 8.3 kDa, and it contained one heme c per molecule. The other, designated cytochrome c(B), was found to have a molecular mass of approximately 23 kDa, and it contained two heme c molecules per protein molecule. The amount of cytochrome c(B) expressed in cells grown at high hydrostatic pressure (50 MPa) was less than that in cells grown at atmospheric pressure, whereas cytochrome c(A) was constitutively expressed under all pressure conditions examined. The results of Northern blotting analysis were consistent with the above-mentioned observations and suggested that the pressure regulation of cytochrome c(B) gene expression occurred at the transcriptional level. These results suggest that the components of the respiratory chain of moderately piezophilic S. violacea could be exchanged according to the growth pressure conditions.
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Affiliation(s)
- M Yamada
- The DEEPSTAR Group, Japan Marine Science and Technology Center, Yokosuka 237-0061, Japan
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Ikegami A, Nakasone K, Fujita M, Fujii S, Kato C, Usami R, Horikoshi K. Cloning and characterization of the gene encoding RNA polymerase sigma factor sigma(54) of deep-sea piezophilic Shewanella violacea. Biochim Biophys Acta 2000; 1491:315-20. [PMID: 10760597 DOI: 10.1016/s0167-4781(00)00035-x] [Citation(s) in RCA: 12] [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] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have recently reported that a sigma(54)-like factor recognizes a DNA element, designated as region A, upstream of a pressure-regulated operon in piezophilic Shewanella violacea strain DSS12 (Nakasone et al., FEMS Microbiology Lett. 176 (1999) 351-356). In this study, we isolated and characterized the rpoN gene of this piezophilic bacterium. The rpoN gene was found to encode a putative protein consisting of 492 amino acid residues with a predicted molecular mass of 55359 Da. Significant homology was evident comparing the rpoN sequence of S. violacea with that of Escherichia coli (62.8% identity), Vibrio anguillarum (61.7% identity) and Pseudomonas putida (57.0% identity). The DNA-binding domain at the C-terminus of sigma(54) is well conserved in the case of the S. violacea rpoN gene product and the helix-turn-helix motif and the RpoN box are also present. In addition, the conserved glutamine-rich domain is present at the N-terminus. sigma(54) in S. violacea was expressed at a relatively constant level under various growth conditions as determined by both primer extension and Western blotting analyses. By means of a recombinant plasmid, a hexahistidine-tagged derivative of the sigma(54) from strain DSS12 was overexpressed in Escherichia coli and purified to near homogeneity. An electrophoretic mobility shift assay demonstrated that the purified sigma(54) protein specifically recognizes region A in the above-mentioned pressure-regulated operon.
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Affiliation(s)
- A Ikegami
- Department of Applied Chemistry, Faculty of Engineering, Toyo University, 2100 Kujirai, Kawagoe, Saitama, Japan
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Ikegami A, Nakasone K, Kato C, Usami R, Horikoshi K. Structural analysis of the ntrBC genes of deep-sea piezophilic Shewanella violacea. Biosci Biotechnol Biochem 2000; 64:915-8. [PMID: 10830521 DOI: 10.1271/bbb.64.915] [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: 11/08/2022]
Abstract
The ntrBC genes coding for the bacterial signal-transducing protein NtrB and the bacterial enhancer-binding protein NtrC of deep-sea piezophilic Shewanella violacea were cloned and their nucleotide sequences were analyzed. The conserved regions of NtrB and those of NtrC are well conserved in the case of the ntrBC products of S. violacea.
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Affiliation(s)
- A Ikegami
- Department of Applied Chemistry, Faculty of Engineering, Toyo University, Saitama, Japan
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Fujii S, Nakasone K, Horikoshi K. Cloning of two cold shock genes, cspA and cspG, from the deep-sea psychrophilic bacterium Shewanella violacea strain DSS12. FEMS Microbiol Lett 1999; 178:123-8. [PMID: 10483731 DOI: 10.1111/j.1574-6968.1999.tb13767.x] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
We cloned and characterized two cold shock inducible genes from the deep-sea psychrophilic bacterium Shewanella violacea strain DSS12. The cloned genes, designated cspA and cspG, encode proteins each consisting of 70 amino acid residues which show 62 and 67% sequence identity with Escherichia coli CspA and CspG, respectively. AT-rich UP elements were found immediately upstream of the promoter region and the cspA and cspG mRNA contained unusually long 5' untranslated regions like that in the E. coli cspA, cspB, cspG and cspI genes. Following a temperature downshift to 4 degrees C or -1 degree C, the levels of cspA and cspG mRNA increased and the level of expression of cspG was greater than that of cspA both before and after cold shock. These results suggest that CspA and CspG may function as RNA chaperones, the mRNAs encoded by these two genes may be regulated post-transcriptionally and they may function as regulators of other cold shock inducible genes like in E. coli.
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Affiliation(s)
- S Fujii
- DEEPSTAR Group, Japan Marine Science and Technology Center, Yokosuka, Japan.
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Takami H, Takaki Y, Nakasone K, Sakiyama T, Maeno G, Sasaki R, Hirama C, Fuji F, Masui N. Genetic analysis of the chromosome of alkaliphilic Bacillus halodurans C-125. Extremophiles 1999; 3:227-33. [PMID: 10484179 DOI: 10.1007/s007920050120] [Citation(s) in RCA: 15] [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: 10/28/2022]
Abstract
Seventeen Sse8387I linking clones isolated from the chromosome of Bacillus halodurans C-125 for the purpose of constructing a physical map were sequenced and analyzed by comparison with the BSORF database and the nonredundant protein databank. The orientations of Sse8387I or AscI linking clones serving to join adjacent fragments were determined by southern blot analysis using specific DNA probes. One-third of the open reading frames (ORFs) identified in the Sse8387I linking clones showed no significant similarity to any protein so far reported. The ORFs showing significant similarities to those of Bacillus subtilis were mapped in the chromosome of strain C-125, and the locations of the putative genes on the map were not well conserved between B. halodurans C-125 and B. subtilis.
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Affiliation(s)
- H Takami
- Deep-sea Microorganisms Research Group, Japan Marine Science and Technology Center, Natsushima, Yokosuka, Japan.
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Nakasone K, Ikegami A, Kato C, Usami R, Horikoshi K. Analysis ofcis-elements upstream of the pressure-regulated operon in the deep-sea barophilic bacteriumShewanella violaceastrain DSS12. FEMS Microbiol Lett 1999. [DOI: 10.1111/j.1574-6968.1999.tb13683.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Takami H, Masui N, Nakasone K, Horikoshi K. Replication origin region of the chromosome of alkaliphilic Bacillus halodurans C-125. Biosci Biotechnol Biochem 1999; 63:1134-7. [PMID: 10427704 DOI: 10.1271/bbb.63.1134] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An 18.5-kb DNA fragment containing the oriC region of the chromosome of the alkaliphilic Bacillus halodurans C-125 was obtained by PCR and sequenced. Sixteen open reading frames (ORFs) were identified in this region. A sequencing similarity search using the BSORF database found that ORF1 to 13 all had significant similarities to gene products of Bacillus subtilis. Three other ORFs (ORF14-16) of unknown function were positioned down-stream of gyrB instead of rrnO, which is found in the same region in the case of B. subtilis. The ORF organization from gidA to gyrA was the same as that of B. subtilis. The gene organization and the location of the DnaA-box region were also similar to those of the chromosomes of other bacteria, such as Escherichia coli and Pseudomonas putida. There were two DnaA-box clusters (Box-region C and R) with a consensus sequence TTATCCACA on both sides of the dnaA gene but another DnaA box cluster (Box-region L) which is found in the region between thdF and jag in B. subtilis was not found in the corresponding region in the case of alkaliphilic Bacillus halodurans C-125.
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Affiliation(s)
- H Takami
- Deep-sea Microorganisms Research Group, Japan Marine Science and Technology Center, Kanagawa, Japan.
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Takami H, Takaki Y, Nakasone K, Hirama C, Inoue A, Horikoshi K. Sequence analysis of a 32-kb region including the major ribosomal protein gene clusters from alkaliphilic Bacillus sp. strain C-125. Biosci Biotechnol Biochem 1999; 63:452-5. [PMID: 10192928 DOI: 10.1271/bbb.63.452] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Forty-one open reading frames (ORFs) were identified in a 32-kb DNA fragment of alkaliphilic Bacillus sp. C-125. A similarity search using the BSORF database found 37 ORFs with significant sequence similarity to B. subtilis RNA polymerase subunits, elongation factor G, elongation factor Tu, and ribosomal proteins. Each ORF product showed more than 70% identity to those of B. subtilis. Gene organization in the region of str, S10, spc, and the alpha cluster was highly conserved among three strains, C-125, B. subtilis, and B. stearothermophilus.
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Affiliation(s)
- H Takami
- Deep-sea Microorganisms Research Group, Japan Marine Science and Technology Center, Kanagawa, Japan.
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