Stable Expression of the Chlorocatechol Dioxygenase Gene from<i>Ralstonia eutropha</i>NH9 in Hybrid Poplar Cells

Ohmiya, Yasunori; Ono, Toshiro; Taniguchi, Toru; Itahana, N.; Ogawa, Naoto; Miyashita, Kiyotaka; Ohmiya, Kunio; Sakka, Kazuo; Kimura, Takeshi

doi:10.1271/bbb.80848

Cited by 3 publications

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References 9 publications

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“…BR60), 3-CB is known to be converted to 5-chloroprotocatechuate or protocatechuate by the products of the cbaABC genes and further metabolized via protocatechuate meta -ring fission pathway (Nakatsu et al, 1997). Several critical features of the ability of strain NH9 to degrade 3-CB have been characterized by analyses of the substrate specificity and application of chlorocatechol 1,2-dioxygenase (CbnA) (Liu et al, 2005; Ohmiya et al, 2009), and by biochemical and structural analyses of CbnR, a LysR-type transcriptional regulator controlling the expression of the cbnABCD genes (Moriuchi et al, 2017; Koentjoro et al, 2018). While these studies have been beneficial for gaining knowledge on both basic and applied aspects of the degradation ability of NH9 or its enzymes, genomic analysis of NH9 would provide further insights into the genes involved in the catabolism of aromatic compounds by this strain.…”

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confidence: 99%

Complete Genome Sequence of 3-Chlorobenzoate-Degrading Bacterium Cupriavidus necator NH9 and Reclassification of the Strains of the Genera Cupriavidus and Ralstonia Based on Phylogenetic and Whole-Genome Sequence Analyses

et al. 2019

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Cupriavidus necator NH9, a 3-chlorobenzoate (3-CB)-degrading bacterium, was isolated from soil in Japan. In this study, the complete genome sequence of NH9 was obtained via PacBio long-read sequencing to better understand the genetic components contributing to the strain's ability to degrade aromatic compounds, including 3-CB. The genome of NH9 comprised two circular chromosomes (4.3 and 3.4 Mb) and two circular plasmids (427 and 77 kb) containing 7,290 coding sequences, 15 rRNA and 68 tRNA genes. Kyoto Encyclopedia of Genes and Genomes pathway analysis of the protein-coding sequences in NH9 revealed a capacity to completely degrade benzoate, 2-, 3-, or 4-hydroxybenzoate, 2,3-, 2,5-, or 3,4-dihydroxybenzoate, benzoylformate, and benzonitrile. To validate the identification of NH9, phylogenetic analyses (16S rRNA sequence-based tree and multilocus sequence analysis) and whole-genome sequence analyses (average nucleotide identity, percentage of conserved proteins, and tetra-nucleotide analyses) were performed, confirming that NH9 is a C . necator strain. Over the course of our investigation, we noticed inconsistencies in the classification of several strains that were supposed to belong to the two closely-related genera Cupriavidus and Ralstonia . As a result of whole-genome sequence analysis of 46 Cupriavidus strains and 104 Ralstonia strains, we propose that the taxonomic classification of 41 of the 150 strains should be changed. Our results provide a clear delineation of the two genera based on genome sequences, thus allowing taxonomic identification of strains belonging to these two genera.

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Section: Introductionmentioning

confidence: 99%

Complete Genome Sequence of 3-Chlorobenzoate-Degrading Bacterium Cupriavidus necator NH9 and Reclassification of the Strains of the Genera Cupriavidus and Ralstonia Based on Phylogenetic and Whole-Genome Sequence Analyses

et al. 2019

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Growth, physiological and molecular traits in Salicaceae trees investigated for phytoremediation of heavy metals and organics

et al. 2011

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Worldwide, there are many large areas moderately contaminated with heavy metals and/or organics that have not been remediated due to the high cost and technical drawbacks of currently available technologies. Methods with a good potential for coping with these limitations are emerging from phytoremediation techniques, using, for example, specific amendments and/or plants selected from various candidates proven in several investigations to be reasonably efficient in extracting heavy metals from soil or water, or in co-metabolizing organics with bacteria flourishing or inoculated in their rhizospheres. Populus and Salix spp., two genera belonging to the Salicaceae family, include genotypes that can be considered among the candidates for this phytoremediation approach. This review shows the recent improvements in analytical tools based on the identification of useful genetic diversity associated with classical growth, physiological and biochemical traits, and the importance of plant genotype selection for enhancing phytoremediation efficiency. Particularly interesting are studies on the application of the phytoremediation of heavy metals and of chlorinated organics, in which microorganisms selected for their degradation capabilities were bioaugmented in the rhizosphere of Salicaceae planted at a high density for biomass and bioenergy production.

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Main trends in the genetic transformation of Populus species

Kutsokon

2011

Cytol. Genet.

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Stable Expression of the Chlorocatechol Dioxygenase Gene fromRalstonia eutrophaNH9 in Hybrid Poplar Cells

Cited by 3 publications

References 9 publications

Complete Genome Sequence of 3-Chlorobenzoate-Degrading Bacterium Cupriavidus necator NH9 and Reclassification of the Strains of the Genera Cupriavidus and Ralstonia Based on Phylogenetic and Whole-Genome Sequence Analyses

Complete Genome Sequence of 3-Chlorobenzoate-Degrading Bacterium Cupriavidus necator NH9 and Reclassification of the Strains of the Genera Cupriavidus and Ralstonia Based on Phylogenetic and Whole-Genome Sequence Analyses

Growth, physiological and molecular traits in Salicaceae trees investigated for phytoremediation of heavy metals and organics

Main trends in the genetic transformation of Populus species

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