Abstract
Pseudomonas aeruginosa KF702 (NBRC 110665) utilizes biphenyl as a sole source of carbon and degrades polychlorinated biphenyls (PCBs). Here, we report the 7,167,540-bp draft genome sequence of KF702, which contains 6,714 coding sequences and a 65.8 mol% G+C content. The strain possesses genes for biphenyl catabolism and other genes that mediate degradation of various aromatic compounds.
GENOME ANNOUNCEMENT
Polychlorinated biphenyls (PCBs) have been recognized as significant environmental pollutants for a long time. Biphenyl-utilizing bacteria cometabolize certain PCBs into chlorobenzoic acids through oxidation by biphenyl-catabolic enzymes. However, the biodegradabilities of PCBs are highly dependent on the chlorine substitutions, i.e., the number and position of substituted chlorines (1). It is also evident that the degradation capabilities of PCBs are different among the biphenyl-utilizing strains. The biphenyl catabolic bph genes were first cloned from P. pseudoalcaligenes KF707 (2). Since then, a number of PCB-degrading bacteria have been identified, including both Gram-negative and Gram-positive bacteria (3). Some strains possess very similar, if not identical, bph genes, while others possess diversified bph genes (4). The purpose of this study was to explore how bph genes are organized, transferred, and rearranged by sequencing the genomes of various PCB degraders isolated from the same site. We isolated 14 PCB-degrading bacterial strains (KF strains) including Pseudomonas aeruginosa KF702 from the same biphenyl-contaminated soil in Kitakyushu, Japan (4).
Whole-genome shotgun sequencing of P. aeruginosa KF702 was performed by the National Institute of Technology and Evaluation (NITE) using a combination of shotgun sequencing on a 454 Roche GS FLX+ system (Roche) and paired-end sequencing on a HiSeq sequencing system (Illumina). The Newbler software package (version 2.6, Roche) was used for the genome assembly. The draft genome was composed of 91 contigs (>701 bp), totaling 7,167,540 bases, with a G+C content of 65.8 mol%. The N50 contig size and the largest contig size were 210,619 bp and 464,066 bp, respectively.
Rapid genome annotation using the RAST annotation server (5) described 6,714 coding sequences (CDSs), 38 tRNA sequences, and three rRNA sequences. The coding sequences were classified into 573 subsystems, including cofactors, vitamins, prosthetic groups, and pigments (n = 335 CDSs); phages, prophages, transposable elements, and plasmids (n = 69 CDSs); iron acquisition and metabolism (n = 148 CDSs); motility and chemotaxis (n = 114 CDSs); nitrogen metabolism (n = 88 CDSs); metabolism of aromatic compounds (n = 164 CDSs); and carbohydrates (n = 540 CDSs). Comparison of P. aeruginosa KF702 with other Pseudomonas strains within the RAST server database identified P. aeruginosa 19BR (taxonomy identification no. 1051003.3) as its closest neighbor, with a score of 538, followed by P. aeruginosa LESB58 (taxonomy identification no. 557722.3) as the 27th closest neighbor, with a score of 242. P. aeruginosa 19BR is known as a multidrug- and polymyxin-resistant strain (6).
Functional annotations were compared with the Kyoto Encyclopedia of Genes and Genomes (KEGG) (7). Strain KF702 possessed the bph genes cluster very similar to those of P. pseudoalcaligenes KF707 (8), entire benzoate- and salicylate-degradative genes via the hydroxylation pathways, and some genes of the protocatechuate-gentisate and cyclohexanone degradation.
Nucleotide sequence accession numbers.
This draft genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession numbers BBQK01000001 to BBQK01000091.
ACKNOWLEDGMENT
This work was supported in part by a Beppu University research grant.
Footnotes
Citation Fujihara H, Yamazoe A, Hosoyama A, Suenaga H, Kimura N, Hirose J, Watanabe T, Futagami T, Goto M, Furukawa K. 2015. Draft genome sequence of Pseudomonas aeruginosa KF702 (NBRC 110665), a polychlorinated biphenyl-degrading bacterium isolated from biphenyl-contaminated soil. Genome Announc 3(3):e00517-15. doi:10.1128/genomeA.00517-15.
REFERENCES
- 1.Furukawa K. 1982. Microbial degradation of polychlorinated biphenyls, p 33–57. In Chakrabarty AM (ed), Biodegradation and detoxification of environmental pollutants. CRC Press, Boca Raton, FL. [Google Scholar]
- 2.Furukawa K, Miyazaki T. 1986. Cloning of a gene cluster encoding biphenyl and chlorobiphenyl degradation in Pseudomonas pseudoalcaligenes. J Bacteriol 166:392–398. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Furukawa K, Fujihara H. 2008. Microbial degradation of polychlorinated biphenyls: biochemical and molecular features. J Biosci Bioeng 105:433–449. doi: 10.1263/jbb.105.433. [DOI] [PubMed] [Google Scholar]
- 4.Furukawa K, Hayase N, Taira K, Tomizuka N. 1989. Molecular relationship of chromosomal genes encoding biphenyl/polychlorinated biphenyl catabolism: some soil bacteria possess a highly conserved bph operon. J Bacteriol 171:5467–5472. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Boyle B, Fernandez L, Laroche J, Kukavica-Ibrulj I, Mendes CM, Hancock RW, Levesque RC. 2012. Complete genome sequences of three Pseudomonas aeruginosa isolates with phenotypes of polymyxin B adaptation and inducible resistance. J Bacteriol 194:529–530. doi: 10.1128/JB.06246-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Ogata H, Goto S, Fujibuchi W, Kanehisa M. 1998. Computation with the KEGG pathway database. Biosystems 47:119–128. doi: 10.1016/S0303-2647(98)00017-3. [DOI] [PubMed] [Google Scholar]
- 8.Taira K, Hirose J, Hayashida S, Furukawa K. 1992. Analysis of bph operon from the polychlorinated biphenyl-degrading strain of Pseudomonas pseudoalcaligenes KF707. J Biol Chem 267:4844–4853. [PubMed] [Google Scholar]