Draft genome sequence of a caprolactam degrader bacterium: Pseudomonas taiwanensis strain SJ9

Abstract

Pseudomonas taiwanensis strain SJ9 is a caprolactam degrader, isolated from industrial wastewater in South Korea and considered to have the potential for caprolactam bioremediation. The genome of this strain is approximately 6.2 Mb (G + C content, 61.75%) with 6,010 protein-coding sequences (CDS), of which 46% are assigned to recognized functional genes. This draft genome of strain SJ9 will provide insights into the genetic basis of its caprolactam-degradation ability.

Keywords:
Pseudomonas taiwanensis; Bioremediation; Biodegradation; Caprolactam; Nylon

Introduction

Members of the genus Pseudomonas that have been isolated and characterized so far have mostly been found as innocuous environmental microorganisms. They have great potential for biotechnological applications owing to their metabolic versatility and adaptability.11 Ridgway HF, Safarik J, Phipps D, Carl P, Clark D. Identification and catabolic activity of well-derived gasoline-degrading bacteria from a contaminated aquifer. Appl Environ Microbiol. 1990;56:3565-3575.,22 Loh KC, Cao B. Paradigm in biodegradation using Pseudomonas putida – a review of proteomics studies. Enzyme Microb Technol. 2008;43:1-12.Pseudomonas spp. can thrive in diverse habitats and are known for their ability to colonize soil and participate in soil biochemical processes.33 Raaijmakers JM, Weller DM, Thomashow LS. Frequency of antibiotic-producing Pseudomonas spp. in natural environments. Appl Environ Microbiol. 1997;63:881-887.,44 Dowling DN, O'Gara F. Metabolites of Pseudomonas involved in the biocontrol of plant disease. Trends Biotechnol. 1994;12:133-141. The potential of Pseudomonas spp. for the degradation and bioremediation of a wide variety of chemicals, including natural and synthetic compounds such as caprolactam,55 Kulkarni RS, Kanekar PP. Bioremediation of epsilon-caprolactam from nylon-6 waste water by use of Pseudomonas aeruginosa MCM B-407. Curr Microbiol. 1998;37:191-194. naphthalene,66 Rossello-Mora RA, Lalucat J, Garcia-Valdes E. Comparative biochemical and genetic analysis of naphthalene degradation among Pseudomonas stutzeri strains. Appl Environ Microbiol. 1994;60:966-972. and toluene,77 Zylstra GJ, McCombie WR, Gibson DT, Finette BA. Toluene degradation by Pseudomonas putida F1: genetic organization of the tod operon. Appl Environ Microbiol. 1988;54:1498-1503. has attracted a great research interest. P. taiwanensis strain SJ9 was isolated from a wastewater sample collected from a sewage treatment plant in Daegu, South Korea. This work reports the draft genome of P. taiwanensis strain SJ9.

The genome of the strain SJ9 was sequenced using an Ion Torrent Personal Genome Machine (PGM) sequencer system.88 Rothberg JM, Hinz W, Rearick TM, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011;475:348-352. The sequence reads were assembled using Mimicking Intelligent Read Assembly (MIRA) 3.4.0 and CLC Genomics Workbench (version 6.0), with manual processing using SeqMan software to reduce the contig number. The best assembly results comprised 736 contigs (>400 bp). The draft genome consists of 6,253,055 bp covering almost whole of the predicted average genome, with a G + C content of 61.75%. The assembled contigs were submitted to the RAST annotation server (http://rast.nmpdr.org/) for subsystem classification and functional annotation.99 Aziz RK, Bartels D, Best AA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75. This analysis predicted 6,010 protein-coding sequences (CDS), of which 46% were assigned to recognized functional genes. Furthermore, 71 tRNA and 12 rRNA genes were also predicted.

The genome also harbored a complete gene cluster coding for caprolactam degrading enzymes such as 2,3-dehydroadipyl-CoA hydratase, acyl-CoA dehydrogenase, aldehyde dehydrogenase, and enoyl-CoA hydratase.1010 Buell CR, Joardar V, Lindeberg M, et al. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci USA. 2003;100:10181-10186.,1111 Silby MW, Cerdeno-Tarraga AM, Vernikos GS, et al. Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol. 2009;10:R51. This draft genome sequence of P. taiwanensis strain SJ9 will help improve the general understanding of the genetic basis of caprolactam degradation by Pseudomonas spp.

Nucleotide sequence accession numbers

The draft sequence of P. taiwanensis strain SJ9 obtained in this Whole Genome Shotgun project has been deposited at GenBank under the accession no. AXUP00000000. The version described in this paper is the first version, with accession no. AXUP01000000.

Acknowledgments

This study was sponsored by Agricultural Biotechnology Development Program, Ministry of Agriculture, Food and Rural Affairs.

References

  • 1
    Ridgway HF, Safarik J, Phipps D, Carl P, Clark D. Identification and catabolic activity of well-derived gasoline-degrading bacteria from a contaminated aquifer. Appl Environ Microbiol 1990;56:3565-3575.
  • 2
    Loh KC, Cao B. Paradigm in biodegradation using Pseudomonas putida – a review of proteomics studies. Enzyme Microb Technol 2008;43:1-12.
  • 3
    Raaijmakers JM, Weller DM, Thomashow LS. Frequency of antibiotic-producing Pseudomonas spp. in natural environments. Appl Environ Microbiol. 1997;63:881-887.
  • 4
    Dowling DN, O'Gara F. Metabolites of Pseudomonas involved in the biocontrol of plant disease. Trends Biotechnol. 1994;12:133-141.
  • 5
    Kulkarni RS, Kanekar PP. Bioremediation of epsilon-caprolactam from nylon-6 waste water by use of Pseudomonas aeruginosa MCM B-407. Curr Microbiol. 1998;37:191-194.
  • 6
    Rossello-Mora RA, Lalucat J, Garcia-Valdes E. Comparative biochemical and genetic analysis of naphthalene degradation among Pseudomonas stutzeri strains. Appl Environ Microbiol 1994;60:966-972.
  • 7
    Zylstra GJ, McCombie WR, Gibson DT, Finette BA. Toluene degradation by Pseudomonas putida F1: genetic organization of the tod operon. Appl Environ Microbiol 1988;54:1498-1503.
  • 8
    Rothberg JM, Hinz W, Rearick TM, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011;475:348-352.
  • 9
    Aziz RK, Bartels D, Best AA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008;9:75.
  • 10
    Buell CR, Joardar V, Lindeberg M, et al. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci USA 2003;100:10181-10186.
  • 11
    Silby MW, Cerdeno-Tarraga AM, Vernikos GS, et al. Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol 2009;10:R51.

Publication Dates

  • Publication in this collection
    Apr-Jun 2017

History

  • Received
    22 July 2015
  • Accepted
    15 Sept 2015
Sociedade Brasileira de Microbiologia USP - ICB III - Dep. de Microbiologia, Sociedade Brasileira de Microbiologia, Av. Prof. Lineu Prestes, 2415, Cidade Universitária, 05508-900 São Paulo, SP - Brasil, Ramal USP 7979, Tel. / Fax: (55 11) 3813-9647 ou 3037-7095 - São Paulo - SP - Brazil
E-mail: bjm@sbmicrobiologia.org.br