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Diversity and catalytic potential of PAH-specific ring-hydroxylating dioxygenases from a hydrocarbon-contaminated soil

Authors
  • Martin, Florence1, 2
  • Malagnoux, Laure1, 2
  • Violet, Fabien1, 2
  • Jakoncic, Jean3
  • Jouanneau, Yves1, 2, 4
  • 1 CEA, DSV, Laboratoire de Chimie et Biologie des Métaux, Grenoble Cedex 9, 38054, France , Grenoble Cedex 9 (France)
  • 2 CNRS UMR 5249, Grenoble, France , Grenoble (France)
  • 3 Brookhaven National Laboratory, National Synchrotron Light Source, Upton, NY, USA , Upton (United States)
  • 4 UMR 5249 CNRS/UJF/CEA, LCBM/iRTSV, Grenoble Cedex 9, 38054, France , Grenoble Cedex 9 (France)
Type
Published Article
Journal
Applied Microbiology and Biotechnology
Publisher
Springer-Verlag
Publication Date
Aug 19, 2012
Volume
97
Issue
11
Pages
5125–5135
Identifiers
DOI: 10.1007/s00253-012-4335-2
Source
Springer Nature
Keywords
License
Yellow

Abstract

Ring-hydroxylating dioxygenases (RHDs) catalyze the initial oxidation step of a range of aromatic hydrocarbons including polycyclic aromatic hydrocarbons (PAHs). As such, they play a key role in the bacterial degradation of these pollutants in soil. Several polymerase chain reaction (PCR)-based methods have been implemented to assess the diversity of RHDs in soil, allowing limited sequence-based predictions on RHD function. In the present study, we developed a method for the isolation of PAH-specific RHD gene sequences of Gram-negative bacteria, and for analysis of their catalytic function. The genomic DNA of soil PAH degraders was labeled in situ by stable isotope probing, then used to PCR amplify sequences specifying the catalytic domain of RHDs. Sequences obtained fell into five clusters phylogenetically linked to RHDs from either Sphingomonadales or Burkholderiales. However, two clusters comprised sequences distantly related to known RHDs. Some of these sequences were cloned in-frame in place of the corresponding region of the phnAIa gene from Sphingomonas CHY-1 to generate hybrid genes, which were expressed in Escherichia. coli as chimerical enzyme complexes. Some of the RHD chimeras were found to be competent in the oxidation of two- and three-ring PAHs, but other appeared unstable. Our data are interpreted in structural terms based on 3D modeling of the catalytic subunit of hybrid RHDs. The strategy described herein might be useful for exploring the catalytic potential of the soil metagenome and recruit RHDs with new activities from uncultured soil bacteria.

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