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Complete reconstitution of the diverse pathways of gentamicin B biosynthesis

Nature Chemical Biology volume 15, pages 295–303 (2019)Cite this article

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A Publisher Correction to this article was published on 02 June 2020

An Author Correction to this article was published on 06 February 2019

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Abstract

Gentamicin B (GB), a valuable starting material for the preparation of the semisynthetic aminoglycoside antibiotic isepamicin, is produced in trace amounts by the wild-type Micromonospora echinospora. Though the biosynthetic pathway to GB has remained obscure for decades, we have now identified three hidden pathways to GB production via seven hitherto unknown intermediates in M. echinospora. The narrow substrate specificity of a key glycosyltransferase and the C6′-amination enzymes, in combination with the weak and unsynchronized gene expression of the 2′-deamination enzymes, limits GB production in M. echinospora. The crystal structure of the aminotransferase involved in C6′-amination explains its substrate specificity. Some of the new intermediates displayed similar premature termination codon readthrough activity but with reduced toxicity compared to the natural aminoglycoside G418. This work not only led to the discovery of unknown biosynthetic routes to GB, but also demonstrated the potential to mine new aminoglycosides from nature for drug discovery.

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Fig. 1: Structures of DOS-containing aminoglycoside antibiotics.
Fig. 2: Two glycosylation steps to GA2 and its new analogs.
Fig. 3: The diverse pathways to the analogs of GA and GX2.
Fig. 4: The interconnecting C6′-amination and C2′-deamination pathways to GB.
Fig. 5: Analysis of C2′-deamination reactions catalyzed by GenJ-GenK2.
Fig. 6: Crystal structure of GenB1.

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Data availability

The sequences of genJ and genK2 genes have been deposited in the GenBank under accession numbers MG879478 (genJ); MG879479 (genK2). Atomic coordinates and structure factors of the reported crystal structures have been deposited in the Protein Data Bank under the accession codes 5Z83 (GenB1/PLP); 5Z8A (GenB1/PLP/JI-20A); 5Z8K (GenB1/PLP/NM).

Change history

  • 02 June 2020

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

  • 06 February 2019

    In the version of this article originally published, reference to another structure of GenB1 was omitted (Dow, G. T., Thoden, J. B., & Holden, H. M. The three-dimensional structure of NeoB: an aminotransferase involved in the biosynthesis of neomycin. Protein Sci. 27, 945–956 (2018)). This paper is now cited as reference 32, and “Another structure of GenB1 was also reported independently during the revision of this article32” was added to the text in the Discussion section. This error has been corrected in the PDF and HTML versions of the article.

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Acknowledgements

This work was supported by the National Research Foundation of Korea grant (2016R1A2A1A05005078; (Y.J.Y.) funded by the Ministry of Science and ICT, Cooperative Research Program for Agriculture Science & Technology Development (PJ01316001; M.C.S.) and (PJ013179; J.W.P.) was funded by Rural Development Administration, under the project titled “Development of biomedical materials based on marine proteins” funded by the Ministry of Oceans and Fisheries (S.-S.C.), Republic of Korea, and the National Institutes of Health (GM035906) and the Welch Foundation (F-1511), USA (H.-w.L.)

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  1. These authors contributed equally: Yeon Hee Ban, Myoung Chong Song, Jae-yeon Hwang, Hea-lyung Shin, Hak Joong Kim, Seung Kon Hong.

Authors and Affiliations

  1. Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, Republic of Korea

    Yeon Hee Ban, Myoung Chong Song, Jae-yeon Hwang, Hea-lyung Shin, Seung Kon Hong, Sun-Shin Cha & Yeo Joon Yoon

  2. Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, USA

    Hak Joong Kim & Hung-wen Liu

  3. Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, Republic of Korea

    Na Joon Lee

  4. School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea

    Je Won Park

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Contributions

Y.J.Y., H.-w.L, S.-S.C., and J.W.P. designed the research and wrote the paper. M.C.S. analyzed chemical structures. Y.H.B., J.-y.H., and H.-l.S. performed genetic and enzymatic experiments. H.J.K. performed chemical experiments. S.K.H. performed structural biological experiments. N.J.L. analyzed toxicity and biological activity.

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Correspondence to Sun-Shin Cha, Hung-wen Liu or Yeo Joon Yoon.

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Synthetic procedures and structural characterization

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Ban, Y.H., Song, M.C., Hwang, Jy. et al. Complete reconstitution of the diverse pathways of gentamicin B biosynthesis. Nat Chem Biol 15, 295–303 (2019). https://doi.org/10.1038/s41589-018-0203-4

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