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Granaticins and their biosynthetic gene cluster from Streptomyces vietnamensis: evidence of horizontal gene transfer

Antonie van Leeuwenhoek volume 100, pages 607–617 (2011)Cite this article

Abstract

Streptomyces vietnamensis, a recently designated species isolated from tropical forest soil, was found to be a new granaticin producer. The granaticin biosynthetic gene cluster (gra) and flanking genes from S. vietnamensis were cloned and sequenced by a sequential cloning strategy. All biosynthetic genes were found as expected. The high overall homology of the gra cluster from S. vietnamensis to that of Streptomyces violaceoruber Tü22 indicated a recent common ancestor of the two clusters. However, a flanking gene orf35 was missing from the gra cluster of S. vietnamensis, and high frequency of insertions and deletions of short fragment (shorter than 63 bp) were observed throughout the sequenced region compared to that of S. violaceoruber Tü22. These revealed a rapid evolution of the gra cluster and suggested that small insertions and deletions might be one of the basic evolution mechanisms for streptomycete genomes. The phylogenetic incongruence between 16S rDNA and the gra cluster and the scattered distribution of the granaticin producers within Streptomyces implicated horizontal gene transfer (HGT) being involved in the gra cluster dispersion. The remnants of orf35 found in S. vietnamensis present a scenario on how the antibiotic gene clusters evolved after HGT. The contemporary gra cluster residing in S. vietnamensis could be interpreted as a combination of HGT and highly variable vertical transmission.

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Acknowledgements

This work was supported by the International Science and Technology Cooperation Programs of China (2008DFA31560), the Chinese Academy of Sciences for Key Topics in Innovation Engineering (KSCX2-YW-G-075-11) and the Foundation for Young Scientists of Guangdong Academy of Sciences (qnjj20092). The authors are grateful to Dr. Zi-Xin Deng for critical suggestion and helpful discussion.

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Affiliations

  1. State Key Laboratory of Applied Microbiology (Ministry—Guangdong Province Jointly Breeding Base), South China, Guangdong Institute of Microbiology, Guangzhou, 510070, People’s Republic of China

    Ming-Rong Deng, Jun Guo, Chun-Hua Zhu & Hong-Hui Zhu

  2. Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, 510070, People’s Republic of China

    Ming-Rong Deng, Jun Guo, Chun-Hua Zhu & Hong-Hui Zhu

  3. Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, People’s Republic of China

    Ming-Rong Deng, Jun Guo, Chun-Hua Zhu & Hong-Hui Zhu

  4. Key Laboratory of Marine Bio-resources Sustainable Utilization (LMB-CAS), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People’s Republic of China

    Xiang Li

  5. Guangdong Key Laboratory of Marine Materia Medica (LMMM-GD), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People’s Republic of China

    Xiang Li

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  1. Ming-Rong Deng
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  2. Jun Guo
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  3. Xiang Li
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  5. Hong-Hui Zhu
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Correspondence to Hong-Hui Zhu.

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Deng, MR., Guo, J., Li, X. et al. Granaticins and their biosynthetic gene cluster from Streptomyces vietnamensis: evidence of horizontal gene transfer. Antonie van Leeuwenhoek 100, 607–617 (2011). https://doi.org/10.1007/s10482-011-9615-9

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Keywords

  • Granaticin
  • Biosynthetic gene cluster
  • Evolution
  • Horizontal gene transfer
  • Streptomyces