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Draft Genome Sequence of the Deep-Sea Bacterium Moritella sp. JT01 and Identification of Biotechnologically Relevant Genes

Abstract

Deep-sea bacteria can produce various biotechnologically relevant enzymes due to their adaptations to high pressures and low temperatures. To identify such enzymes, we have sequenced the genome of the polycaprolactone-degrading bacterium Moritella sp. JT01, isolated from sediment samples from Japan Trench (6957 m depth), using a Illumina HiSeq2000 sequencer (12.1 million paired-end reads) and CLC Genomics Workbench (version 6.5.1) for the assembly, resulting in a 4.83-Mb genome (42 scaffolds). The genome was annotated using Rapid Annotation using Subsystem Technology (RAST), Protein Homology/analogY Recognition Engine V 2.0 (PHYRE2), and BLAST2Go, revealing 4439 protein coding sequences and 101 RNAs. Gene products with industrial relevance, such as lipases (three) and esterases (four), were identified and are related to bacterium’s ability to degrade polycaprolactone. The annotation revealed proteins related to deep-sea survival, such as cold-shock proteins (six) and desaturases (three). The presence of secondary metabolite biosynthetic gene clusters suggests that this bacterium could produce nonribosomal peptides, polyunsaturated fatty acids, and bacteriocins. To demonstrate the potential of this genome, a lipase was cloned an introduced into Escherichia coli. The lipase was purified and characterized, showing activity over a wide temperature range (over 50% at 20–60 °C) and pH range (over 80% at pH 6.3 to 9). This enzyme has tolerance to the surfactant action of sodium dodecyl sulfate and shows 30% increased activity when subjected to a working pressure of 200 MPa. The genomic characterization of Moritella sp. JT01 reveals traits associated with survival in the deep-sea and their potential uses in biotechnology, as exemplified by the characterized lipase.

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Acknowledgments

CAPES (Brazil, Process CAPES/JSPS 02/13), FAPESC (Brazil, Process 3422/2012), and CNPq-INCT-Mar COI (Brazil, Process 565062/2010-7) supported this work. We also thank CAPES for scholarship support provided to A.O.S.L (Process 08740/14-3), CNPq for scholarship provided to E.J.O. (Process 381573/2015-0), A.O.S.L (Process 311010/2015-6), and Santa Catarina State Govern for R.C.F. scholarships.

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Correspondence to André Oliveira de Souza Lima.

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Freitas, R.C., Odisi, E.J., Kato, C. et al. Draft Genome Sequence of the Deep-Sea Bacterium Moritella sp. JT01 and Identification of Biotechnologically Relevant Genes. Mar Biotechnol 19, 480–487 (2017). https://doi.org/10.1007/s10126-017-9767-3

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Keywords

  • Genomic
  • Heterologous expression
  • Bioprospecting
  • Marine bacteria
  • Lipase