Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds

Miyazaki, Ryo; Bertelli, Claire; Benaglio, Paola; Canton, Jonas; Coi, Nicoló De; Gharib, Walid H.; Gjoksi, Bebeka; Goesmann, Alexander; Greub, Gilbert; Harshman, Keith; Linke, Burkhard; Mikulic, Josip; Mueller, Linda; Nicolas, Damien; Robinson-Rechavi, Marc; Rivolta, Carlo; Roggo, Clémence; Roy, Shantanu; Sentchilo, Vladimir; Siebenthal, Alexandra Von; Falquet, Laurent; Meer, Jan Roelof van der

doi:10.1111/1462-2920.12498

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Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds

Miyazaki, Ryo Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan - Department of Fundamental Microbiology, University of Lausanne, Switzerland
Bertelli, Claire Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland - Swiss Institute for Bioinformatics (SIB), Lausanne, Switzerland
Benaglio, Paola Departments of Medical Genetics, University of Lausanne, Switzerland
Canton, Jonas Master in Molecular Life Sciences, University of Lausanne, Switzerland
Coi, Nicoló De Master in Molecular Life Sciences, University of Lausanne, Switzerland
Gharib, Walid H. Department of Ecology and Evolution, University of Lausanne, Switzerland
Gjoksi, Bebeka Master in Molecular Life Sciences, University of Lausanne, Switzerland
Goesmann, Alexander Bioinformatics and Systems Biology, Justus-Liebig-University, Gießen, Germany
Greub, Gilbert Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
Harshman, Keith Lausanne Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne, Switzerland
Linke, Burkhard Bioinformatics and Systems Biology, Justus-Liebig-University, Gießen, Germany
Mikulic, Josip Master in Molecular Life Sciences, University of Lausanne, Switzerland
Mueller, Linda Master in Molecular Life Sciences, University of Lausanne, Switzerland
Nicolas, Damien Master in Molecular Life Sciences, University of Lausanne, Switzerland
Robinson-Rechavi, Marc Swiss Institute for Bioinformatics (SIB), Lausanne, Switzerland - Department of Ecology and Evolution, University of Lausanne, Switzerland
Rivolta, Carlo Departments of Medical Genetics, University of Lausanne, Switzerland
Roggo, Clémence Master in Molecular Life Sciences, University of Lausanne, Switzerland
Roy, Shantanu Department of Fundamental Microbiology, University of Lausanne, Switzerland
Sentchilo, Vladimir Department of Fundamental Microbiology, University of Lausanne, Switzerland
Siebenthal, Alexandra Von Master in Molecular Life Sciences, University of Lausanne, Switzerland
Falquet, Laurent Swiss Institute for Bioinformatics (SIB), Lausanne, Switzerland
Meer, Jan Roelof van der Department of Fundamental Microbiology, University of Lausanne, Switzerland

28.05.2014

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Environmental Microbiology. - 2015, vol. 17, no. 1, p. 91-104

English Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least eight genomic islands [prophages and integrative conjugative elements (ICEs)], which were absent in closely related pseudomonads. We confirm that two ICEs are identical copies of the 103 kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed that it is composed of a variable and a ‘core’ region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220 kb region and a prophage that drastically change the host metabolic capacity and survivability.

Faculty

Faculté des sciences et de médecine

Department

Département de Biologie

Language