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Comparative genome analysis of P seudomonas knackmussii B 13, the first bacterium known to degrade chloroaromatic compounds
Author(s) -
Miyazaki Ryo,
Bertelli Claire,
Benaglio Paola,
Canton Jonas,
De Coi Nicoló,
Gharib Walid H.,
Gjoksi Bebeka,
Goesmann Alexander,
Greub Gilbert,
Harshman Keith,
Linke Burkhard,
Mikulic Josip,
Mueller Linda,
Nicolas Damien,
RobinsonRechavi Marc,
Rivolta Carlo,
Roggo Clémence,
Roy Shantanu,
Sentchilo Vladimir,
Siebenthal Alexandra Von,
Falquet Laurent,
Meer Jan Roelof
Publication year - 2015
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/1462-2920.12498
Subject(s) - biology , genome , bacteria , computational biology , genetics , microbiology and biotechnology , gene
Summary P seudomonas knackmussii B 13 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 B 13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B 13 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 B 13 is closest to P seudomonas denitrificans and P seudomonas aeruginosa . The B 13 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 ICE clc that carries the genes for chlorocatechol metabolism. Comparison of ICE clc 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 B 13 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.