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Chapter 5.1.1 : Genomic Features and Genome-Wide Analyses of Dioxin-Like Compound Degraders

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Genomic Features and Genome-Wide Analyses of Dioxin-Like Compound Degraders, Page 1 of 2

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Abstract:

A large number of microorganisms capable of degrading xenobiotic aromatic compounds has been isolated, and applications of them for bioremediation to remove the contamination by these compounds have been studied. Recently, genome sequences of dioxin-like compound-degrading bacteria have been determined, including degraders of biphenyl, dibenzofuran, dibenzo-p-dioxin, and their chlorinated derivatives such as Burkholderia xenovorans LB400, Rhodococcus jostii RHA1, and Sphingomonas wittichii RW1. Their key enzymes and pathways to metabolize these compounds have been elucidated, and molecular mechanisms to regulate their expression have been analyzed in detail. Some of their degradative genes are located on mobile genetic elements, such as a large plasmid and an integrative and conjugative element, which could have an important role for distribution of their degradative genes. Comparisons of crystal structures of the degrading enzymes showed their putative evolutional relationships. Genome-wide analyses including transcriptome, proteome, and mutagenesis have revealed how the degraders expressed their degradative genes, how they survived in different environments, and what the key environmental factors to express their degrading ability. Combination of phytoremediation and bioaugmentation treatments was shown to be efficient for decontamination. These aspects could be essential to improve decontamination by bioremediation.

Citation: Shintani M, Kimbara K. 2016. Genomic Features and Genome-Wide Analyses of Dioxin-Like Compound Degraders, p 5.1.1-1-5.1.1-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.1
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FIGURE 1

Proposed metabolic pathways for dioxin-like compounds, biphenyl, dibenzofuran, and dibenzo--dioxin. The intermediate product in brackets is unstable and spontaneously converted to the lower compound. CAT and HPD indicates catechol and 2-hydroxypenta-2,4-dienoic acid, respectively. doi: 10.1128/9781555818821.ch5.1.1.f1

Citation: Shintani M, Kimbara K. 2016. Genomic Features and Genome-Wide Analyses of Dioxin-Like Compound Degraders, p 5.1.1-1-5.1.1-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.1
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Tables

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TABLE 1

Dioxin-like compound-degraders whose genome sequences were determined

Citation: Shintani M, Kimbara K. 2016. Genomic Features and Genome-Wide Analyses of Dioxin-Like Compound Degraders, p 5.1.1-1-5.1.1-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.1
Generic image for table
TABLE 2

(Putative) mobile genetic elements carrying degradative genes for dioxin-like compounds

Citation: Shintani M, Kimbara K. 2016. Genomic Features and Genome-Wide Analyses of Dioxin-Like Compound Degraders, p 5.1.1-1-5.1.1-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.1

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