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Oba S, Suzuki T, Maeda R, Omori T, Fuse H. Characterization and genetic analyses of a carbazole-degrading gram-positive marine isolate, Janibacter sp. strain OC11. Biosci Biotechnol Biochem 2014; 78:1094-101. [DOI: 10.1080/09168451.2014.917260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
Strain OC11 was isolated from seawater sampled at the coast of Chiba, Japan, in artificial seawater medium with carbazole (CAR) as the sole carbon source. Its 16S ribosomal RNA gene sequence suggested that strain OC11 belongs to the genus Janibacter. The CAR-degradation genes (car genes) of strain OC11 were PCR amplified, using degenerate primers designed based on the car gene sequences of other CAR-degrading bacteria. Complete nucleotide sequences encoding six complete open reading frames were determined, and the first known ferredoxin reductase gene (carAd) was found from a CAR-degrading bacterium isolated from the marine environment. An experiment using a mutant strain suggested that the car genes of strain OC11 are functional in CAR degradation. Southern hybridization indicated that strain OC11 had one car gene cluster in vivo. RT-PCR revealed that transcription of carOC11 constitutes an operon.
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Affiliation(s)
- Shintaro Oba
- Graduate School of Engineering and Science, Shibaura Institute of Technology, Saitama, Japan
| | - Toshihiro Suzuki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Rintaro Maeda
- Graduate School of Applied Chemistry, Shibaura Institute of Technology, Saitama, Japan
| | - Toshio Omori
- Department of Bioscience and Engineering, Shibaura Institute of Technology, Saitama, Japan
| | - Hiroyuki Fuse
- Department of Bioscience and Engineering, Shibaura Institute of Technology, Saitama, Japan
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Specific Interactions between the Ferredoxin and Terminal Oxygenase Components of a Class IIB Rieske Nonheme Iron Oxygenase, Carbazole 1,9a-Dioxygenase. J Mol Biol 2009; 392:436-51. [DOI: 10.1016/j.jmb.2009.07.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Revised: 07/07/2009] [Accepted: 07/08/2009] [Indexed: 11/21/2022]
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Umeda T, Katsuki J, Usami Y, Inoue K, Noguchi H, Fujimoto Z, Ashikawa Y, Yamane H, Nojiri H. Crystallization and preliminary X-ray diffraction studies of a novel ferredoxin involved in the dioxygenation of carbazole by Novosphingobium sp. KA1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:632-635. [PMID: 18607094 PMCID: PMC2443972 DOI: 10.1107/s1744309108016278] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Accepted: 05/29/2008] [Indexed: 05/26/2023]
Abstract
Novosphingobium sp. KA1 uses carbazole 1,9a-dioxygenase (CARDO) as the first dioxygenase in its carbazole-degradation pathway. The CARDO of KA1 contains a terminal oxygenase component and two electron-transfer components: ferredoxin and ferredoxin reductase. In contrast to the CARDO systems of other species, the ferredoxin component of KA1 is a putidaredoxin-type protein. This novel ferredoxin was crystallized at 293 K by the hanging-drop vapour-diffusion method using PEG MME 550 as the precipitant under anaerobic conditions. The crystals belong to space group C222(1) and diffraction data were collected to a resolution of 1.9 A (the diffraction limit was 1.6 A).
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Affiliation(s)
- Takashi Umeda
- Biotechnology Research Center, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Junichi Katsuki
- Biotechnology Research Center, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yusuke Usami
- Biotechnology Research Center, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kengo Inoue
- Biotechnology Research Center, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Haruko Noguchi
- Biotechnology Research Center, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Zui Fujimoto
- Protein Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Yuji Ashikawa
- Molecular Signaling Research Team, Structural Physiology Research Group, RIKEN Harima Institute SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hisakazu Yamane
- Biotechnology Research Center, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Professional Programme for Agricultural Bioinformatics, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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