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Complete genome sequence and comparative analysis of Streptomyces seoulensis, a pioneer strain of nickel superoxide dismutase

  • Jihoon Shin
  • Shinae Park
  • Jung-Shin Lee
  • Eun-Jin Lee
  • Hong-Duk YounEmail author
Research Article

Abstract

Background

Streptomyces seoulensis has contributed to the discovery and initiation of extensive research into nickel superoxide dismutase (NiSOD), a unique type of superoxide dismutase found in actinomycetes. Still so far, there is no information about whole genome sequence of this strain.

Objective

To investigate complete genome sequence and perform bioinformatic analyses for genomic functions related with nickel-associated genes.

Methods

DNA was extracted using the Wizard Genomic DNA Purification Kit then sequenced using a Pacific Biosciences SMRT cell 8Pac V3 DNA Polymerase Binding Kit P6 with the PacBiov2 RSII platform. We assembled the PacBio long-reads with the HGAP3 pipeline.

Results

We obtained complete genome sequence of S. seoulensis, which comprises a 6,339,363 bp linear chromosome. While analyzing the genome to annotate the genomic function, we discovered the nickel-associated genes. We observed that the sodN gene encoding for NiSOD is located adjacent to the sodX gene, which encodes for the nickel-type superoxide dismutase maturation protease. In addition, several nickel-associated genes and gene clusters-nickel-responsive regulator, nickel uptake transporter, nickel–iron [NiFe]-hydrogenase and other putative genes were also detected. Strain specific genes were discovered through a comparative analysis of S. coelicolor and S. griseus. Further bioinformatic analyses revealed that this strain encodes at least 22 putative biosynthetic gene clusters, thereby implying that S. seoulensis has the potential to produce novel bioactive compounds.

Conclusion

We annotated the genome and determined nickel-associated genes and gene clusters and discovered biosynthetic gene clusters for secondary metabolites implying that S. seoulensis produces novel types of bioactive compounds.

Keywords

Streptomyces seoulensis Complete genome sequence Nickel superoxide dismutase 

Notes

Acknowledgements

This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIP) [National Creative Research Laboratory Program (2012R1A3A2048767 to H.-D.Y)] and by Education and Research Encouragement Fund of Seoul National University Hospital.

Supplementary material

13258_2019_878_MOESM1_ESM.pdf (44 kb)
Fig. S1 Phylogenetic analysis of NiSOD and hydrogenase genes. (A) Phylogenetic tree showing the similarity of S. seoulensis sodN with other sodN genes from 38 related bacterial strains. The sodN sequences of closely related species were obtained from the NCBI GenBank database. The phylogenetic tree was generated using the Neighbor-Joining method. The S. seoulensis sodN gene is indicated by an arrow. (B) Phylogenetic analysis of hydrogenase encoding genes with known sequences from other Streptomyces species. Left: hypA, Right: hypB
13258_2019_878_MOESM2_ESM.pdf (12 kb)
Fig. S2 Comparative analysis of genome alignment with MAUVE
13258_2019_878_MOESM3_ESM.pdf (187 kb)
Fig. S3 Comparison of putative biosynthetic gene clusters for secondary metabolites in S. seoulensis with S. coelicolor A3(2) and S. griseus
13258_2019_878_MOESM4_ESM.xlsx (3.6 mb)
Table S1 Integrated results of functional annotation of S. seoulensis genes using multiple database
13258_2019_878_MOESM5_ESM.xlsx (1.4 mb)
Table S2 List of strain specific genes compared to S. coelicolor A3(2) and S. griseus

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Copyright information

© The Genetics Society of Korea 2019

Authors and Affiliations

  • Jihoon Shin
    • 1
  • Shinae Park
    • 2
  • Jung-Shin Lee
    • 2
  • Eun-Jin Lee
    • 3
  • Hong-Duk Youn
    • 1
    • 4
    Email author
  1. 1.Department of Biomedical Sciences, National Creative Research Center for Epigenome Reprogramming Network, Ischemic/Hypoxic Disease InstituteSeoul National University College of MedicineSeoulRepublic of Korea
  2. 2.Department of Molecular Bioscience, College of Biomedical ScienceKangwon National UniversityChuncheonRepublic of Korea
  3. 3.Department of Life Sciences, College of Life Sciences and BiotechnologyKorea UniversitySeoulRepublic of Korea
  4. 4.Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and TechnologySeoul National UniversitySeoulRepublic of Korea

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