title: Genome and proteome analysis of Pseudomonas chloritidismutans AW-1Tthat grows on n-decane with chlorate or oxygen as electron acceptor.
abstract: Growth of Pseudomonas chloritidismutans AW-1Ton C7 to C12 n-alkanes with oxygen or chlorate as electron acceptor was studied by genome and proteome analysis. Whole genome shotgun sequencing resulted in a 5 Mbp assembled sequence with a G + C content of 62.5%. The automatic annotation identified 4767 protein-encoding genes and a putative function could be assigned to almost 80% of the predicted proteins. The distinct phylogenetic position of P. chloritidismutans AW-1Twithin the Pseudomonas stutzeri cluster became clear by comparison of average nucleotide identity values of sequenced genomes. Analysis of the proteome of P. chloritidismutans AW-1Tshowed the versatility of this bacterium to adapt to aerobic and anaerobic growth conditions with acetate or n-decane as substrates. All enzymes involved in the alkane oxidation pathway were identified. An alkane monooxygenase was detected in n-decane-grown cells, but not in acetate-grown cells. The enzyme was found when grown in the presence of oxygen or chlorate, indicating that under both conditions an oxygenase-mediated pathway is employed for alkane degradation. Proteomic and biochemical data also showed that both chlorate reductase and chlorite dismutase are constitutively present, but most abundant under chlorate-reducing conditions.
authors.affiliation: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands.
authors.forename: Farrakh
authors.initials: F
authors.lastname: Mehboob
authors.affiliation: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands.
authors.forename: Margreet J
authors.initials: MJ
authors.lastname: Oosterkamp
authors.affiliation: Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands.
authors.forename: Jasper J
authors.initials: JJ
authors.lastname: Koehorst
authors.affiliation: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands.
authors.forename: Sumaira
authors.initials: S
authors.lastname: Farrakh
authors.affiliation: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands.
authors.forename: Teun
authors.initials: T
authors.lastname: Veuskens
authors.affiliation: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands.
authors.forename: Caroline M
authors.initials: CM
authors.lastname: Plugge
authors.affiliation: Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, Wageningen, 6703 HA, The Netherlands.
authors.forename: Sjef
authors.initials: S
authors.lastname: Boeren
authors.affiliation: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands.
authors.forename: Willem M
authors.initials: WM
authors.lastname: de Vos
authors.affiliation: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands.
authors.forename: Gosse
authors.initials: G
authors.lastname: Schraa
authors.affiliation: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands.|Centre of Biological Engineering, University of Minho, Braga, 4710-057, Portugal.
authors.forename: Alfons J M
authors.initials: AJ
authors.lastname: Stams
authors.affiliation: Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands. Peter.Schaap@wur.nl.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Schaap
mesh_terms: D000473:Alkanes / Q000378:metabolism*; D002704:Chlorates / Q000378:metabolism*; D042926:Cytochrome P-450 CYP4A / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D016680:Genome, Bacterial / Q000235:genetics; D016877:Oxidants; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics / Q000378:metabolism; D010100:Oxygen / Q000378:metabolism*; D010802:Phylogeny; D020543:Proteome / Q000378:metabolism; D040901:Proteomics; D044223:Pseudomonas stutzeri / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism*
chemical_list: D000473:Alkanes; D002704:Chlorates; D016877:Oxidants; D020543:Proteome; D010088:Oxidoreductases; C402794:chlorite dismutase; D042926:Cytochrome P-450 CYP4A; C021777:chlorate reductase; C012867:decane; D010100:Oxygen