Appearance and Evolution of γ-Hexachlorocyclohexane-Degrading Bacteria

Nagata, Yasunobu; Tabata, Michiro; Ohhata, Satoshi; Tsuda, Masashi

doi:10.1007/978-4-431-54520-0_2

Cited by 2 publications

(3 citation statements)

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“…MI1205 and Sphingomonas sp. MM-1) suggested the independent acquisition of HCH degradation in each of the four strains ( Nagata et al 2014 ). The expanding number of genomes available for HCH-degrading strains allows us to test the relative contribution of these two modes of evolution more broadly in lin pathway evolution.…”

Section: Resultsmentioning

confidence: 99%

“…In the case of the lin system, however, we can identify some of the mechanisms involved and their continuing effects. Various methods of horizontal transfer have been responsible for the initial recruitment of the upstream lin genes to strains already possessing a downstream component ( Nagata et al 2014 ) and this work implicates an ICE in the acquisition of linB . An initial association of IS 6100 with some of the lin genes has spread such that the entire pathway (at least for the strains isolated from the Czech Republic) is now associated with IS 6100 elements.…”

Section: Discussionmentioning

confidence: 96%

“…The increasing involvement of IS 6100 with the lin genes may indicate the beginning of a second phase in the evolution of the pathway ( Figure 7 ). The first phase of evolution, the initial formation of the pathway, is proposed to have occurred with the recruitment of the upstream genes (through various means) into an ancestral strain containing the downstream genes that make up core sphingomonad functions ( Nagata et al 2014 ). The current phase appears to involve a consolidation of the pathway, in which we see an increase in IS 6100 activity that expands IS 6100 association to genes that were initially transferred through other means ( e.g.…”

Section: Discussionmentioning

confidence: 99%

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Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains

Pearce

Oakeshott

Pandey

2015

G3 Genes|Genomes|Genetics

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Hexachlorocyclohexane (HCH), a synthetic organochloride, was first used as a broad-acre insecticide in the 1940s, and many HCH-degrading bacterial strains have been isolated from around the globe during the last 20 years. To date, the same degradation pathway (the lin pathway) has been implicated in all strains characterized, although the pathway has only been characterized intensively in two strains and for only a single HCH isomer. To further elucidate the evolution of the lin pathway, we have biochemically and genetically characterized three HCH-degrading strains from the Czech Republic and compared the genomes of these and seven other HCH-degrading bacterial strains. The three new strains each yielded a distinct set of metabolites during their degradation of HCH isomers. Variable assembly of the pathway is a common feature across the 10 genomes, eight of which (including all three Czech strains) were either missing key lin genes or containing duplicate copies of upstream lin genes (linA-F). The analysis also confirmed the important role of horizontal transfer mediated by insertion sequence IS6100 in the acquisition of the pathway, with a stronger association of IS6100 to the lin genes in the new strains. In one strain, a linA variant was identified that likely caused a novel degradation phenotype involving a shift in isomer preference. This study identifies a number of strains that are in the early stages of lin pathway acquisition and shows that the state of the pathway can explain the degradation patterns observed.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 96%

Section: Discussionmentioning

confidence: 99%

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Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains

Pearce

Oakeshott

Pandey

2015

G3 Genes|Genomes|Genetics

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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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Appearance and Evolution of γ-Hexachlorocyclohexane-Degrading Bacteria

Cited by 2 publications

References 70 publications

Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains

Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains

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

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