The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons

Hickey, William J.; Chen, Shicheng; Zhao, Jiangchao

doi:10.3389/fmicb.2012.00125

Title: The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons

Journal Article · Wed Apr 04 00:00:00 EDT 2012 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2012.00125· OSTI ID:1628054

Hickey, William J. ^[1]; Chen, Shicheng ^[1]; Zhao, Jiangchao ^[1]

University of Wisconsin, Madison, WI (United States)

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 phn_AFK2RHD group. The phn_AFK2 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.

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Research Organization:: Univ. of Wisconsin, Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); Univ. of Wisconsin–Madison; National Science Foundation (NSF)

Grant/Contract Number:: AC02-05CH11231; MCB0920664; CSP795673

OSTI ID:: 1628054

Journal Information:: Frontiers in Microbiology, Vol. 3; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
polynuclear aromatic hydrocarbons
phenanthrene
biodegradation
horizontal gene transfer
genomic island
Delftia
bioremediation
genomics

Title: The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons

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