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Regulated Expression of an Environmental DNA-Derived Type II Polyketide Gene Cluster in Streptomyces Hosts Identified a New Tetracenomycin Derivative TCM Y

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Abstract

As bacterial natural products have been proved to be the most important source of many therapeutic medicines, the need to discover novel natural products becomes extremely urgent. Despite the fact that the majority of bacterial species are yet to be cultured in a laboratory setting, and that most of the bacterial natural product biosynthetic genes are silent, “metagenomics technology” offers a solution to help clone natural product biosynthetic genes from environmental samples, and genetic engineering enables the silent biosynthetic genes to be activated. In this work, a type II polyketide biosynthetic gene cluster was identified from a soil metagenomic library and was activated by over-expression of a SARP regulator gene in the gene cluster in Streptomyces hosts. A new tetracenomycin type compound tetracenomycin Y was identified from the fermentation broth. This study shows that metagenomics and genetic engineering could be combined to provide access to new natural metabolites.

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References

  1. Jung WS, Kim ES, Kang HY, Choi CY, Sherman DH, Yoon YJ (2003) Site-directed mutagenesis on putative macrolactone ringsize determinant in the hybrid pikromycin–tylosin polyketidesynthase. J Microbiol Biotechnol 13:823–827

    CAS  Google Scholar 

  2. Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5(10):R245-249. https://doi.org/10.1016/s1074-5521(98)90108-9

    Article  PubMed  CAS  Google Scholar 

  3. Katz M, Hover BM, Brady SF (2016) Culture-independent discovery of natural products from soil metagenomes. J Ind Microbiol Biotechnol 43(2–3):129–141. https://doi.org/10.1007/s10295-015-1706-6

    Article  PubMed  CAS  Google Scholar 

  4. Owen JG, Charlop-Powers Z, Smith AG, Ternei MA, Calle PY, Reddy BV, Montiel D, Brady SF (2015) Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors. Proc Natl Acad Sci USA 112(14):4221–4226. https://doi.org/10.1073/pnas.1501124112

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  5. Wang Z, Forelli N, Hernandez Y, Ternei M, Brady SF (2022) Lapcin, a potent dual topoisomerase I/II inhibitor discovered by soil metagenome guided total chemical synthesis. Nat Commun 13(1):842. https://doi.org/10.1038/s41467-022-28292-x

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Li L, MacIntyre LW, Ali T, Russo R, Koirala B, Hernandez Y, Brady SF (2021) Biosynthetic interrogation of soil metagenomes reveals metamarin, an uncommon cyclomarin congener with activity against Mycobacterium tuberculosis. J Nat Prod 84(4):1056–1066. https://doi.org/10.1021/acs.jnatprod.0c01104

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  7. Weissman KJ (2009) Chapter 1 introduction to polyketide biosynthesis. Complex enzymes in microbial natural product biosynthesis, part B: polyketides, aminocoumarins and carbohydrates. Academic Press, Cambridge, pp 3–16

    Book  Google Scholar 

  8. Zhang Z, Pan HX, Tang GL (2017) New insights into bacterial type II polyketide biosynthesis. F1000Research 6:172. https://doi.org/10.12688/f1000research.10466.1

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  9. Gillespie DE, Brady SF, Bettermann AD, Cianciotto NP, Liles MR, Rondon MR, Clardy J, Goodman RM, Handelsman J (2002) Isolation of antibiotics turbomycin a and B from a metagenomic library of soil microbial DNA. Appl Environ Microbiol 68(9):4301–4306. https://doi.org/10.1128/AEM.68.9.4301-4306.2002

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  10. Feng Z, Kallifidas D, Brady SF (2011) Functional analysis of environmental DNA-derived type II polyketide synthases reveals structurally diverse secondary metabolites. Proc Natl Acad Sci USA 108(31):12629–12634. https://doi.org/10.1073/pnas.1103921108

    Article  PubMed  PubMed Central  Google Scholar 

  11. Kallifidas D, Kang HS, Brady SF (2012) Tetarimycin A, an MRSA-active antibiotic identified through induced expression of environmental DNA gene clusters. J Am Chem Soc 134(48):19552–19555. https://doi.org/10.1021/ja3093828

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  12. Stevenson LJ, Bracegirdle J, Liu L, Sharrock AV, Ackerley DF, Keyzers RA, Owen JG (2021) Metathramycin, a new bioactive aureolic acid discovered by heterologous expression of a metagenome derived biosynthetic pathway. RSC Chem Biol 2(2):556–567. https://doi.org/10.1039/d0cb00228c

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  13. Brady SF, Simmons L, Kim JH, Schmidt EW (2009) Metagenomic approaches to natural products from free-living and symbiotic organisms. Nat Prod Rep 26(11):1488–1503. https://doi.org/10.1039/b817078a

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  14. Lewis K, Epstein S, D’Onofrio A, Ling LL (2010) Uncultured microorganisms as a source of secondary metabolites. J Antibiot (Tokyo) 63(8):468–476. https://doi.org/10.1038/ja.2010.87

    Article  CAS  Google Scholar 

  15. Liu Z, Zhao Y, Huang C, Luo Y (2021) Recent advances in silent gene cluster activation in Streptomyces. Front Bioeng Biotechnol 9:632230. https://doi.org/10.3389/fbioe.2021.632230

    Article  PubMed  PubMed Central  Google Scholar 

  16. Baltz RH (2010) Streptomyces and Saccharopolyspora hosts for heterologous expression of secondary metabolite gene clusters. J Ind Microbiol Biotechnol 37(8):759–772. https://doi.org/10.1007/s10295-010-0730-9

    Article  PubMed  CAS  Google Scholar 

  17. Liu G, Chater KF, Chandra G, Niu G, Tan H (2013) Molecular regulation of antibiotic biosynthesis in Streptomyces. Microbiol Mol Biol Rev 77(1):112–143. https://doi.org/10.1128/MMBR.00054-12

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  18. Bibb MJ (2005) Regulation of secondary metabolism in Streptomycetes. Curr Opin Microbiol 8(2):208–215. https://doi.org/10.1016/j.mib.2005.02.016

    Article  PubMed  CAS  Google Scholar 

  19. Chen Y, Wendt-Pienkowski E, Shen B (2008) Identification and utility of FdmR1 as a Streptomyces antibiotic regulatory protein activator for fredericamycin production in Streptomyces griseus ATCC 49344 and heterologous hosts. J Bacteriol 190(16):5587–5596. https://doi.org/10.1128/JB.00592-08

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Beck C, Gren T, Ortiz-Lopez FJ, Jorgensen TS, Carretero-Molina D, Martin Serrano J, Tormo JR, Oves-Costales D, Kontou EE, Mohite OS, Mingyar E, Stegmann E, Genilloud O, Weber T (2021) Activation and identification of a Griseusin cluster in Streptomyces sp. CA-256286 by employing transcriptional regulators and multi-omics methods. Molecules. https://doi.org/10.3390/molecules26216580

    Article  PubMed  PubMed Central  Google Scholar 

  21. Wang S, Gao X, Gao Y, Li Y, Cao M, Xi Z, Zhao L, Feng Z (2017) Tetracycline resistance genes identified from distinct soil environments in China by functional metagenomics. Front Microbiol 8:1406. https://doi.org/10.3389/fmicb.2017.01406

    Article  PubMed  PubMed Central  Google Scholar 

  22. Brady SF (2007) Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules. Nat Protoc 2(5):1297–1305. https://doi.org/10.1038/nprot.2007.195

    Article  PubMed  CAS  Google Scholar 

  23. Wawrik B, Kerkhof L, Zylstra GJ, Kukor JJ (2005) Identification of unique type II polyketide synthase genes in soil. Appl Environ Microbiol 71(5):2232–2238. https://doi.org/10.1128/AEM.71.5.2232-2238.2005

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  24. Hutchinson CR (1997) Biosynthetic studies of daunorubicin and tetracenomycin C. Chem Rev 97:2525–2535

    Article  PubMed  CAS  Google Scholar 

  25. Qiao X, Gan M, Wang C, Liu B, Shang Y, Li Y, Chen S (2019) Tetracenomycin X exerts antitumour activity in lung cancer cells through the downregulation of cyclin D1. Mar Drugs. https://doi.org/10.3390/md17010063

    Article  PubMed  PubMed Central  Google Scholar 

  26. Osterman IA, Wieland M, Maviza TP, Lashkevich KA, Lukianov DA, Komarova ES, Zakalyukina YV, Buschauer R, Shiriaev DI, Leyn SA, Zlamal JE, Biryukov MV, Skvortsov DA, Tashlitsky VN, Polshakov VI, Cheng J, Polikanov YS, Bogdanov AA, Osterman AL, Dmitriev SE, Beckmann R, Dontsova OA, Wilson DN, Sergiev PV (2020) Tetracenomycin X inhibits translation by binding within the ribosomal exit tunnel. Nat Chem Biol 16(10):1071–1077. https://doi.org/10.1038/s41589-020-0578-x

    Article  PubMed  CAS  Google Scholar 

  27. Walsh CT, Fischbach MA (2010) Natural products version 2.0: connecting genes to molecules. J Am Chem Soc 132(8):2469–2493. https://doi.org/10.1021/ja909118a

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Rutledge PJ, Challis GL (2015) Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat Rev Microbiol 13(8):509–523. https://doi.org/10.1038/nrmicro3496

    Article  PubMed  CAS  Google Scholar 

  29. Mao D, Okada BK, Wu Y, Xu F, Seyedsayamdost MR (2018) Recent advances in activating silent biosynthetic gene clusters in bacteria. Curr Opin Microbiol 45:156–163. https://doi.org/10.1016/j.mib.2018.05.001

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  30. Jiang ZB, Ren WC, Shi YY, Li XX, Lei X, Fan JH, Zhang C, Gu RJ, Wang LF, Xie YY, Hong B (2018) Structure-based manual screening and automatic networking for systematically exploring sansanmycin analogues using high performance liquid chromatography tandem mass spectroscopy. J Pharm Biomed Anal 158:94–105. https://doi.org/10.1016/j.jpba.2018.05.024

    Article  PubMed  CAS  Google Scholar 

  31. Nguyen JT, Riebschleger KK, Brown KV, Gorgijevska NM, Nybo SE (2021) A BioBricks toolbox for metabolic engineering of the tetracenomycin pathway. Biotechnol J. https://doi.org/10.1002/biot.202100371

    Article  PubMed  Google Scholar 

  32. Yoon YJ, Beck BJ, Kim BS, Kang HY, Reynolds KA, Sherman DH (2002) Generation of multiple bioactive macrolides by hybrid modular polyketide synthases in Streptomyces venezuelae. Chem Biol 9(2):203–214. https://doi.org/10.1016/s1074-5521(02)00095-9

    Article  PubMed  CAS  Google Scholar 

  33. Hong JS, Park SH, Choi CY, Sohng JK, Yoon YJ (2004) New olivosyl derivatives of methymycin/pikromycin from an engineered strain of Streptomyces venezuelae. FEMS Microbiol Lett 238(2):391–399. https://doi.org/10.1016/j.femsle.2004.08.002

    Article  PubMed  CAS  Google Scholar 

  34. Xue Y, Sherman DH (2001) Biosynthesis and combinatorial biosynthesis of pikromycin-related macrolides in Streptomyces venezuelae. Metab Eng 3(1):15–26. https://doi.org/10.1006/mben.2000.0167

    Article  PubMed  CAS  Google Scholar 

  35. Jung WS, Lee SK, Hong JS, Park SR, Jeong SJ, Han AR, Sohng JK, Kim BG, Choi CY, Sherman DH, Yoon YJ (2006) Heterologous expression of tylosin polyketide synthase and production of a hybrid bioactive macrolide in Streptomyces venezuelae. Appl Microbiol Biotechnol 72(4):763–769. https://doi.org/10.1007/s00253-006-0318-5

    Article  PubMed  CAS  Google Scholar 

  36. Martin JF, Liras P (2010) Engineering of regulatory cascades and networks controlling antibiotic biosynthesis in Streptomyces. Curr Opin Microbiol 13(3):263–273. https://doi.org/10.1016/j.mib.2010.02.008

    Article  PubMed  CAS  Google Scholar 

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Funding

This study was supported by the National Natural Science Foundation of China under Grant Number 31770049.

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Authors and Affiliations

  1. College of Food Science and Technology, Nanjing Agricultural University, Weigang, Nanjing, 210095, China

    Lishuang Nie, Mingming Cao, Qingqing Ji, Yuejiao Gao, Shaochen Wang, Yunbin Lyu & Zhiyang Feng

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  1. Lishuang Nie
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Contributions

ZF designed the experiments; LN, YG and QJ carried out the experiments; MC performed NMR measurements; SW, YL, and ZF analyzed the experimental results; ZF and LN wrote the manuscript. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Zhiyang Feng.

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Nie, L., Cao, M., Ji, Q. et al. Regulated Expression of an Environmental DNA-Derived Type II Polyketide Gene Cluster in Streptomyces Hosts Identified a New Tetracenomycin Derivative TCM Y. Curr Microbiol 79, 336 (2022). https://doi.org/10.1007/s00284-022-03039-5

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