Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by <named-content content-type="genus-species">Sphingobium chlorophenolicum</named-content>

ABSTRACT Pentachlorophenol (PCP) is a highly toxic pesticide that was first introduced in the 1930s. The alphaproteobacterium Sphingobium chlorophenolicum, which was isolated from PCP-contaminated sediment, has assembled a metabolic pathway capable of completely degrading PCP. This pathway produces...

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Autores principales:	Jake J. Flood, Shelley D. Copley
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	RNA-seq Sphingobium chlorophenolicum Tn-seq benzoquinone biodegradation hydroquinone Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/894ad69ede9c4c42928a0b18cda0b251
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spelling	oai:doaj.org-article:894ad69ede9c4c42928a0b18cda0b2512021-12-02T18:15:43ZGenome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by <named-content content-type="genus-species">Sphingobium chlorophenolicum</named-content>10.1128/mSystems.00275-182379-5077https://doaj.org/article/894ad69ede9c4c42928a0b18cda0b2512018-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00275-18https://doaj.org/toc/2379-5077ABSTRACT Pentachlorophenol (PCP) is a highly toxic pesticide that was first introduced in the 1930s. The alphaproteobacterium Sphingobium chlorophenolicum, which was isolated from PCP-contaminated sediment, has assembled a metabolic pathway capable of completely degrading PCP. This pathway produces four toxic intermediates, including a chlorinated benzoquinone that is a potent alkylating agent and three chlorinated hydroquinones that react with O2 to produce reactive oxygen species (ROS). RNA-seq analysis revealed that PCP causes a global stress response that resembles responses to proton motive force uncoupling and membrane disruption, while surprisingly, little of the response resembles the responses expected to be produced by the PCP degradation intermediates. Tn-seq was used to identify genes important for fitness in the presence of PCP. By comparing the genes that are important for fitness in wild-type S. chlorophenolicum and a non-PCP-degrading mutant, we identified genes that are important only when the PCP degradation intermediates are produced. These include genes encoding two enzymes that are likely to be involved in protection against ROS. In addition to these enzymes, the endogenous levels of other enzymes that protect cells from oxidative stress appear to mitigate the toxic effects of the chlorinated benzoquinone and hydroquinone metabolites of PCP. The combination of RNA-seq and Tn-seq results identify important mechanisms for defense against the toxicity of PCP. IMPORTANCE Phenolic compounds such as pentachlorophenol (PCP), triclosan, and 2,4-dichlorophenoxyacetic acid (2,4-D) represent a common class of anthropogenic biocides. Despite the novelty of these compounds, many can be degraded by microbes isolated from contaminated sites. However, degradation of this class of chemicals often generates toxic intermediates, which may contribute to their recalcitrance to biodegradation. We have addressed the stresses associated with degradation of PCP by Sphingobium chlorophenolicum by examining the transcriptional response after PCP exposure and identifying genes necessary for growth during both exposure to and degradation of PCP. This work identifies some of the mechanisms that protect cells from this toxic compound and facilitate its degradation. This information could be used to engineer strains capable of improved biodegradation of PCP or similar phenolic pollutants.Jake J. FloodShelley D. CopleyAmerican Society for MicrobiologyarticleRNA-seqSphingobium chlorophenolicumTn-seqbenzoquinonebiodegradationhydroquinoneMicrobiologyQR1-502ENmSystems, Vol 3, Iss 6 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	RNA-seq Sphingobium chlorophenolicum Tn-seq benzoquinone biodegradation hydroquinone Microbiology QR1-502
spellingShingle	RNA-seq Sphingobium chlorophenolicum Tn-seq benzoquinone biodegradation hydroquinone Microbiology QR1-502 Jake J. Flood Shelley D. Copley Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by <named-content content-type="genus-species">Sphingobium chlorophenolicum</named-content>
description	ABSTRACT Pentachlorophenol (PCP) is a highly toxic pesticide that was first introduced in the 1930s. The alphaproteobacterium Sphingobium chlorophenolicum, which was isolated from PCP-contaminated sediment, has assembled a metabolic pathway capable of completely degrading PCP. This pathway produces four toxic intermediates, including a chlorinated benzoquinone that is a potent alkylating agent and three chlorinated hydroquinones that react with O2 to produce reactive oxygen species (ROS). RNA-seq analysis revealed that PCP causes a global stress response that resembles responses to proton motive force uncoupling and membrane disruption, while surprisingly, little of the response resembles the responses expected to be produced by the PCP degradation intermediates. Tn-seq was used to identify genes important for fitness in the presence of PCP. By comparing the genes that are important for fitness in wild-type S. chlorophenolicum and a non-PCP-degrading mutant, we identified genes that are important only when the PCP degradation intermediates are produced. These include genes encoding two enzymes that are likely to be involved in protection against ROS. In addition to these enzymes, the endogenous levels of other enzymes that protect cells from oxidative stress appear to mitigate the toxic effects of the chlorinated benzoquinone and hydroquinone metabolites of PCP. The combination of RNA-seq and Tn-seq results identify important mechanisms for defense against the toxicity of PCP. IMPORTANCE Phenolic compounds such as pentachlorophenol (PCP), triclosan, and 2,4-dichlorophenoxyacetic acid (2,4-D) represent a common class of anthropogenic biocides. Despite the novelty of these compounds, many can be degraded by microbes isolated from contaminated sites. However, degradation of this class of chemicals often generates toxic intermediates, which may contribute to their recalcitrance to biodegradation. We have addressed the stresses associated with degradation of PCP by Sphingobium chlorophenolicum by examining the transcriptional response after PCP exposure and identifying genes necessary for growth during both exposure to and degradation of PCP. This work identifies some of the mechanisms that protect cells from this toxic compound and facilitate its degradation. This information could be used to engineer strains capable of improved biodegradation of PCP or similar phenolic pollutants.
format	article
author	Jake J. Flood Shelley D. Copley
author_facet	Jake J. Flood Shelley D. Copley
author_sort	Jake J. Flood
title	Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by <named-content content-type="genus-species">Sphingobium chlorophenolicum</named-content>
title_short	Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by <named-content content-type="genus-species">Sphingobium chlorophenolicum</named-content>
title_full	Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by <named-content content-type="genus-species">Sphingobium chlorophenolicum</named-content>
title_fullStr	Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by <named-content content-type="genus-species">Sphingobium chlorophenolicum</named-content>
title_full_unstemmed	Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by <named-content content-type="genus-species">Sphingobium chlorophenolicum</named-content>
title_sort	genome-wide analysis of transcriptional changes and genes that contribute to fitness during degradation of the anthropogenic pollutant pentachlorophenol by <named-content content-type="genus-species">sphingobium chlorophenolicum</named-content>
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/894ad69ede9c4c42928a0b18cda0b251
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Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by <named-content content-type="genus-species">Sphingobium chlorophenolicum</named-content>

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