The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons
Abstract
Bacteria are key in the biodegradation of polycyclic aromatic hydrocarbons (PAH), which are widespread environmental pollutants. At least six genotypes of PAH degraders are distinguishable via phylogenies of the ring-hydroxylating dioxygenase (RHD) that initiates bacterial PAH metabolism. A given RHD genotype can be possessed by a variety of bacterial genera, suggesting horizontal gene transfer (HGT) is an important process for dissemination of PAH-degrading genes. But, mechanisms of HGT for most RHD genotypes are unknown. Here, we report in silico and functional analyses of the phenanthrene-degrading bacterium Delftia sp. Cs1-4, a representative of the phnAFK2 RHD group. The phnAFK2 genotype predominates PAH degrader communities in some soils and sediments, but, until now, their genomic biology has not been explored. In the present study, genes for the entire phenanthrene catabolic pathway were discovered on a novel ca. 232 kb genomic island (GEI), now termed the phn island. This GEI had characteristics of an integrative and conjugative element with a mobilization/stabilization system similar to that of SXT/R391-type GEI. But, it could not be grouped with any known GEI, and was the first member of a new GEI class. The island also carried genes predicted to encode: synthesis of quorum sensing signal molecules, fattymore »
- Authors:
-
- University of Wisconsin, Madison, WI (United States)
- Publication Date:
- Research Org.:
- Univ. of Wisconsin, Madison, WI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); Univ. of Wisconsin–Madison; National Science Foundation (NSF)
- OSTI Identifier:
- 1628054
- Grant/Contract Number:
- AC02-05CH11231; MCB0920664; CSP795673
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 3; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; polynuclear aromatic hydrocarbons; phenanthrene; biodegradation; horizontal gene transfer; genomic island; Delftia; bioremediation; genomics
Citation Formats
Hickey, William J., Chen, Shicheng, and Zhao, Jiangchao. The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons. United States: N. p., 2012.
Web. doi:10.3389/fmicb.2012.00125.
Hickey, William J., Chen, Shicheng, & Zhao, Jiangchao. The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons. United States. https://doi.org/10.3389/fmicb.2012.00125
Hickey, William J., Chen, Shicheng, and Zhao, Jiangchao. Wed .
"The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons". United States. https://doi.org/10.3389/fmicb.2012.00125. https://www.osti.gov/servlets/purl/1628054.
@article{osti_1628054,
title = {The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons},
author = {Hickey, William J. and Chen, Shicheng and Zhao, Jiangchao},
abstractNote = {Bacteria are key in the biodegradation of polycyclic aromatic hydrocarbons (PAH), which are widespread environmental pollutants. At least six genotypes of PAH degraders are distinguishable via phylogenies of the ring-hydroxylating dioxygenase (RHD) that initiates bacterial PAH metabolism. A given RHD genotype can be possessed by a variety of bacterial genera, suggesting horizontal gene transfer (HGT) is an important process for dissemination of PAH-degrading genes. But, mechanisms of HGT for most RHD genotypes are unknown. Here, we report in silico and functional analyses of the phenanthrene-degrading bacterium Delftia sp. Cs1-4, a representative of the phnAFK2 RHD group. The phnAFK2 genotype predominates PAH degrader communities in some soils and sediments, but, until now, their genomic biology has not been explored. In the present study, genes for the entire phenanthrene catabolic pathway were discovered on a novel ca. 232 kb genomic island (GEI), now termed the phn island. This GEI had characteristics of an integrative and conjugative element with a mobilization/stabilization system similar to that of SXT/R391-type GEI. But, it could not be grouped with any known GEI, and was the first member of a new GEI class. The island also carried genes predicted to encode: synthesis of quorum sensing signal molecules, fatty acid/polyhydroxyalkanoate biosynthesis, a type IV secretory system, a PRTRC system, DNA mobilization functions and >50 hypothetical proteins. The 50% G + C content of the phn gene cluster differed significantly from the 66.7% G + C level of the island as a whole and the strain Cs1-4 chromosome, indicating a divergent phylogenetic origin for the phn genes. Collectively, these studies added new insights into the genetic elements affecting the PAH biodegradation capacity of microbial communities specifically, and the potential vehicles of HGT in general.},
doi = {10.3389/fmicb.2012.00125},
journal = {Frontiers in Microbiology},
number = ,
volume = 3,
place = {United States},
year = {Wed Apr 04 00:00:00 EDT 2012},
month = {Wed Apr 04 00:00:00 EDT 2012}
}
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