title: Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time sequencing.
abstract: Pseudomonas pseudoalcaligenes CECT5344 tolerates cyanide and is also able to utilize cyanide and cyano-derivatives as a nitrogen source under alkaline conditions. The strain is considered as candidate for bioremediation of habitats contaminated with cyanide-containing liquid wastes. Information on the genome sequence of the strain CECT5344 became available previously. The P. pseudoalcaligenes CECT5344 genome was now resequenced by applying the single molecule, real-time (SMRT(®)) sequencing technique developed by Pacific Biosciences. The complete and finished genome sequence of the strain consists of a 4,696,984 bp chromosome featuring a GC-content of 62.34%. Comparative analyses between the new and previous versions of the P. pseudoalcaligenes CECT5344 genome sequence revealed additional regions in the new sequence that were missed in the older version. These additional regions mostly represent mobile genetic elements. Moreover, five additional genes predicted to play a role in sulfoxide reduction are present in the newly established genome sequence. The P. pseudoalcaligenes CECT5344 genome sequence is highly related to the genome sequences of different Pseudomonas mendocina strains. Approximately, 70% of all genes are shared between P. pseudoalcaligenes and P. mendocina. In contrast to P. mendocina, putative pathogenicity genes were not identified in the P. pseudoalcaligenes CECT5344 genome. P. pseudoalcaligenes CECT5344 possesses unique genes for nitrilases and mercury resistance proteins that are of importance for survival in habitats contaminated with cyano- and mercury compounds. As an additional feature of the SMRT sequencing technology, the methylome of P. pseudoalcaligenes was established. Six sequence motifs featuring methylated adenine residues (m6A) were identified in the genome. The genome encodes several methyltransferases, some of which may be considered for methylation of the m6A motifs identified. The complete genome sequence of the strain CECT5344 now provides the basis for exploitation of genetic features for biotechnological purposes.
authors.affiliation: Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, D-33615 Bielefeld, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Wibberg
authors.affiliation: Faculty of Technology, Center for Biotechnology (CeBiTec), Bielefeld University, D-33615 Bielefeld, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Bremges
authors.affiliation: Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, D-33615 Bielefeld, Germany.
authors.forename: Tanja
authors.initials: T
authors.lastname: Dammann-Kalinowski
authors.affiliation: Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, D-33615 Bielefeld, Germany.
authors.forename: Irena
authors.initials: I
authors.lastname: Maus
authors.affiliation: Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain.
authors.forename: M Isabel
authors.initials: MI
authors.lastname: Igeño
authors.affiliation: Pacific Biosciences Germany GmbH, Germany.
authors.forename: Ralph
authors.initials: R
authors.lastname: Vogelsang
authors.affiliation: Pacific Biosciences Germany GmbH, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: König
authors.affiliation: Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain.
authors.forename: Víctor M
authors.initials: VM
authors.lastname: Luque-Almagro
authors.affiliation: Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain.
authors.forename: M Dolores
authors.initials: MD
authors.lastname: Roldán
authors.affiliation: Faculty of Technology, Center for Biotechnology (CeBiTec), Bielefeld University, D-33615 Bielefeld, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Sczyrba
authors.affiliation: Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain.
authors.forename: Conrado
authors.initials: C
authors.lastname: Moreno-Vivián
authors.affiliation: Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, Avenida de la Universidad SN, E-10071Cáceres, Spain.
authors.forename: Rafael
authors.initials: R
authors.lastname: Blasco
authors.affiliation: Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, D-33615 Bielefeld, Germany.
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
authors.affiliation: Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, D-33615 Bielefeld, Germany. Electronic address: aschluet@cebitec.uni-bielefeld.de.
authors.forename: Andreas
authors.initials: A
authors.lastname: Schlüter
mesh_terms: D003486:Cyanides / Q000378:metabolism*; D019175:DNA Methylation; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D044205:Pseudomonas pseudoalcaligenes / Q000235:genetics* / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D003486:Cyanides; D004269:DNA, Bacterial
keywords: Bioremediation; Core genome; Mercury resistance; Methylome; Nitrilase; Restriction/modification system