Complete Genome Sequence of a γ-Hexachlorocyclohexane Degrader,
            <i>Sphingobium</i>
            sp. Strain TKS, Isolated from a γ-Hexachlorocyclohexane-Degrading Microbial Community

Tabata, Michro; Ohhata, Satoshi; Kawasumi, Toru; Nikawadori, Yuki; Kishida, Ken; Sato, Takuya; Ohtsubo, Yoshiyuki; Tsuda, Masashi; Nagata, Yasunobu

doi:10.1128/genomea.00247-16

Cited by 10 publications

(10 citation statements)

References 9 publications

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“…The GenoFinisher and AceFileViewer programmes were used to finish the sequencing completion 35 . More detailed information for these procedures have been published elsewhere 23 , 25 , 26 . Sequencing gap regions were amplified by PCR using KOD FX (TOYOBO) or Ex Taq (TaKaRa) by using the total DNA of the respective strains as templates, and the resultant DNA fragments were sequenced using primers for PCR amplification.…”

Section: Methodsmentioning

confidence: 99%

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Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide

Tabata

Ohhata

Nikawadori

et al. 2016

DNA Res

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γ-Hexachlorocyclohexane (γ-HCH) is a recalcitrant man-made chlorinated pesticide. Here, the complete genome sequences of four γ-HCH-degrading sphingomonad strains, which are most unlikely to have been derived from one ancestral γ-HCH degrader, were compared. Together with several experimental data, we showed that (i) all the four strains carry almost identical linA to linE genes for the conversion of γ-HCH to maleylacetate (designated “specific” lin genes), (ii) considerably different genes are used for the metabolism of maleylacetate in one of the four strains, and (iii) the linKLMN genes for the putative ABC transporter necessary for γ-HCH utilization exhibit structural divergence, which reflects the phylogenetic relationship of their hosts. Replicon organization and location of the lin genes in the four genomes are significantly different with one another, and that most of the specific lin genes are located on multiple sphingomonad-unique plasmids. Copies of IS6100, the most abundant insertion sequence in the four strains, are often located in close proximity to the specific lin genes. Analysis of the footprints of target duplication upon IS6100 transposition and the experimental detection of IS6100 transposition strongly suggested that the IS6100 transposition has caused dynamic genome rearrangements and the diversification of lin-flanking regions in the four strains.

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Section: Methodsmentioning

confidence: 99%

“…MI1205, 24 , 25 and Sphingobium sp. TKS, 26 were determined. On the basis of our comparison of the complete genome sequences of these three strains and UT26, in association with several supporting experimental data, the evolution of γ-HCH-degrading bacterial strains is discussed.…”

Section: Introductionmentioning

confidence: 99%

Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide

Tabata

Ohhata

Nikawadori

et al. 2016

DNA Res

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“…To verify this hypothesis, pBBR_Pu_adhX for the expression of the adhX UT26 gene was introduced into three sphingomonad strains, Sphingobium sp. TKS [30], Sphingobium sp. MI1205 [31] and Sphingomonas sp.…”

Section: Identical or Almost Identical Adhx Orthologues Are Distributmentioning

confidence: 99%

Expression of an alcohol dehydrogenase gene in a heterotrophic bacterium induces carbon dioxide-dependent high-yield growth under oligotrophic conditions

et al. 2020

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Sphingobium japonicum strain UT26, whose γ-hexachlorocyclohexane-degrading ability has been studied in detail, is a typical aerobic and heterotrophic bacterium that needs organic carbon sources for its growth, and cannot grow on a minimal salt agar medium prepared without adding any organic carbon sources. Here, we isolated a mutant of UT26 with the ability to grow to visible state on such an oligotrophic medium from a transposon-induced mutant library. This high-yield growth under oligotrophic conditions (HYGO) phenotype was CO2-dependent and accompanied with CO2 incorporation. In the HYGO mutant, a transposon was inserted just upstream of the putative Zn-dependent alcohol dehydrogenase (ADH) gene (adhX) so that the adhX gene was constitutively expressed, probably by the transposon-derived promoter. The adhX-deletion mutant (UT26DAX) harbouring a plasmid carrying the adhX gene under the control of a constitutive promoter exhibited the HYGO phenotype. Moreover, the HYGO mutants spontaneously emerged among the UT26-derived hypermutator strain cells, and adhX was highly expressed in these HYGO mutants, while no HYGO mutant appeared among UT26DAX-derived hypermutator strain cells, indicating the necessity of adhX for the HYGO phenotype. His-tagged AdhX that was expressed in Escherichia coli and purified to homogeneity showed ADH activity towards methanol and other alcohols. Mutagenesis analysis of the adhX gene indicated a correlation between the ADH activity and the HYGO phenotype. These results demonstrated that the constitutive expression of an adhX-encoding protein with ADH activity in UT26 leads to the CO2-dependent HYGO phenotype. Identical or nearly identical adhX orthologues were found in other sphingomonad strains, and most of them were located on plasmids, suggesting that the adhX-mediated HYGO phenotype may be an important adaptation strategy to oligotrophic environments among sphingomonads.

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“…Primary comparison of the genome sequences of sphingomonad strains including degraders of highly recalcitrant compounds supports the idea that sphingomonads are a versatile group because of the plasticity of their genomes (Nagata et al ., ; Aylward et al ., ). It is strongly suggested that plasmid‐mediated gene transfer and chromosome‐plasmid recombination, together with prophage and transposon‐mediated rearrangements, play prominent roles in the genome evolution of sphingomonads (Copley et al ., ; Nagata et al ., ; Tabata et al ., ,b,c; Hegedus et al ., ). In some cases, the gene organizations seem to be edited by using insertion sequences.…”

Section: Sphingomonads a Bacterial Group Containing Various Strains mentioning

confidence: 99%

“…MM‐1 from India (Tabata et al ., ; Tabata et al ., ), Sphingobium sp. TKS from Kyushu, Japan (Tabata et al ., ), and Sphingobium indicum B90A (Verma et al ., ). The genome organizations of these five lindane‐degrading strains are summarized in Table .…”

Section: Genomes Of Lindane‐degrading Sphingomonad Strainsmentioning

confidence: 99%

Lessons from the genomes of lindane‐degrading sphingomonads

Nagata

Kato

Ohtsubo

et al. 2019

Environ Microbiol Rep

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Summary Bacterial strains capable of degrading man‐made xenobiotic compounds are good materials to study bacterial evolution towards new metabolic functions. Lindane (γ‐hexachlorocyclohexane, γ‐HCH, or γ‐BHC) is an especially good target compound for the purpose, because it is relatively recalcitrant but can be degraded by a limited range of bacterial strains. A comparison of the complete genome sequences of lindane‐degrading sphingomonad strains clearly demonstrated that (i) lindane‐degrading strains emerged from a number of different ancestral hosts that have recruited lin genes encoding enzymes that are able to channel lindane to central metabolites, (ii) in sphingomonads lin genes have been acquired by horizontal gene transfer mediated by different plasmids and in which IS6100 plays a role in recruitment and distribution of genes, and (iii) IS6100 plays a role in dynamic genome rearrangements providing genetic diversity to different strains and ability to evolve to other states. Lindane‐degrading bacteria whose genomes change so easily and quickly are also fascinating starting materials for tracing the bacterial evolution process experimentally in a relatively short time period. As the origin of the specific lin genes remains a mystery, such genes will be useful probes for exploring the cryptic ‘gene pool’ available to bacteria.

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Complete Genome Sequence of a γ-Hexachlorocyclohexane Degrader, Sphingobium sp. Strain TKS, Isolated from a γ-Hexachlorocyclohexane-Degrading Microbial Community

Cited by 10 publications

References 9 publications

Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide

Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide

Expression of an alcohol dehydrogenase gene in a heterotrophic bacterium induces carbon dioxide-dependent high-yield growth under oligotrophic conditions

Lessons from the genomes of lindane‐degrading sphingomonads

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