title: Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.
abstract: 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.
authors.affiliation: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan; Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland.
authors.forename: Ryo
authors.initials: R
authors.lastname: Miyazaki
authors.forename: Claire
authors.initials: C
authors.lastname: Bertelli
authors.forename: Paola
authors.initials: P
authors.lastname: Benaglio
authors.forename: Jonas
authors.initials: J
authors.lastname: Canton
authors.forename: Nicoló
authors.initials: N
authors.lastname: De Coi
authors.forename: Walid H
authors.initials: WH
authors.lastname: Gharib
authors.forename: Bebeka
authors.initials: B
authors.lastname: Gjoksi
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.forename: Gilbert
authors.initials: G
authors.lastname: Greub
authors.forename: Keith
authors.initials: K
authors.lastname: Harshman
authors.forename: Burkhard
authors.initials: B
authors.lastname: Linke
authors.forename: Josip
authors.initials: J
authors.lastname: Mikulic
authors.forename: Linda
authors.initials: L
authors.lastname: Mueller
authors.forename: Damien
authors.initials: D
authors.lastname: Nicolas
authors.forename: Marc
authors.initials: M
authors.lastname: Robinson-Rechavi
authors.forename: Carlo
authors.initials: C
authors.lastname: Rivolta
authors.forename: Clémence
authors.initials: C
authors.lastname: Roggo
authors.forename: Shantanu
authors.initials: S
authors.lastname: Roy
authors.forename: Vladimir
authors.initials: V
authors.lastname: Sentchilo
authors.forename: Alexandra Von
authors.initials: AV
authors.lastname: Siebenthal
authors.forename: Laurent
authors.initials: L
authors.lastname: Falquet
authors.forename: Jan Roelof
authors.initials: JR
authors.lastname: van der Meer
mesh_terms: D002723:Chlorobenzoates / Q000378:metabolism; D002876:Chromosomes, Bacterial; D016680:Genome, Bacterial; D044404:Genomic Islands; D023281:Genomics; D006841:Hydrocarbons, Aromatic / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D039002:Prophages / Q000235:genetics; D011549:Pseudomonas / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D011550:Pseudomonas aeruginosa / Q000235:genetics
chemical_list: D002723:Chlorobenzoates; D006841:Hydrocarbons, Aromatic