Advertisement

A3 foresight network on natural products

  • Linquan Bai
  • Yasuo Ohnishi
  • Eung-Soo KimEmail author
Natural Products - Original Paper

Abstract

Discovery and development of natural products (NPs) have played important roles in the fields of human medicine and other biotechnology fields for the past several decades. Recent genome-mining approaches for the isolation of novel and cryptic NP biosynthetic gene clusters (BGCs) have led to the growing interest in NP research communities including Asian NP researchers from China, Japan, and Korea. Recently, a three-nation government-sponsored program named ‘A3 Foresight Network on Chemical and Synthetic Biology of NPs’ has been launched with a goal of establishing an Asian hub for NP research-&-personnel exchange program. This brief commentary describes introduction, main researchers, and future perspective of A3 NP network program.

Keywords

A3 Natural product Genome mining Streptomyces Synthetic biology 

Notes

Acknowledgements

This work was supported by the ‘A3 Foresight Network Program’ funded by the NSFC (National Natural Science Foundation of China, No. 21661140002), JSPS (Japan Society for the Promotion of Science), and NRF (National Research Foundation of Korea, NRF-2016K2A9A2A10005545).

References

  1. 1.
    Arakawa K, Tsuda N, Taniguchi A, Kinashi H (2012) The butenolide signaling molecules SRB1 and SRB2 induce lankacidin and lankamycin production in Streptomyces rochei. ChemBioChem 13(10):1447–1457CrossRefGoogle Scholar
  2. 2.
    Arakawa K (2018) Manipulation of metabolic pathways controlled by signaling molecules, inducers of antibiotic production, for genome mining in Streptomyces spp. Antonie Van Leeuwenhoek 111(5):743–751CrossRefGoogle Scholar
  3. 3.
    Bachmann BO, Van Lanen SG, Baltz RH (2014) Microbial genome mining for accelerated natural products discovery: is a renaissance in the making? J Ind Microbiol Biotechnol 41:175–184CrossRefGoogle Scholar
  4. 4.
    Baltz RH (2016) Genetic manipulation of secondary metabolite biosynthesis for improved production in Streptomyces and other actinomycetes. J Ind Microbiol Biotechnol 43:343–370CrossRefGoogle Scholar
  5. 5.
    Choi SS, Katsuyama Y, Bai L, Deng Z, Ohnishi Y, Kim ES (2018) Genome engineering for microbial natural product discovery. Curr Opin Microbiol 45:55–60CrossRefGoogle Scholar
  6. 6.
    Chung GY, Shim KH, Kim HJ, Min SK, Shin HS (2018) Chitosan-coated C-phycocyanin liposome for extending the neuroprotective time window against ischemic brain stroke. Curr Pharm Des.  https://doi.org/10.2174/1381612824666180515123543 CrossRefPubMedGoogle Scholar
  7. 7.
    Du D, Katsuyama Y, Shin-Ya K, Ohnishi Y (2018) Reconstitution of a type II polyketide synthase that catalyzes polyene formation. Angew Chem Int Ed Engl 57(7):1954–1957CrossRefGoogle Scholar
  8. 8.
    Jeong Y, Kim JN, Kim MW, Bucca G, Cho S, Yoon YJ, Kim BK, Roe JH, Kim SC, Smith CP, Cho BK (2016) The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2). Nat Commun 7:11605CrossRefGoogle Scholar
  9. 9.
    Jiang C, Qi Z, Kang Q, Liu J, Jiang M, Bai L (2015) Formation of the Δ(18,19) double bond and bis(spiroacetal) in salinomycin is atypically catalyzed by SlnM, a methyltransferase-like enzyme. Angew Chem Int Ed Engl 54(31):9097–9100CrossRefGoogle Scholar
  10. 10.
    Jin WB, Wu S, Jian XH, Yuan H, Tang GL (2018) A radical S-adenosyl-l-methionine enzyme and a methyltransferase catalyze cyclopropane formation in natural product biosynthesis. Nat Commun 9(1):2771CrossRefGoogle Scholar
  11. 11.
    Katz L, Baltz RH (2016) Natural product discovery: past, present, and future. J Ind Microbiol Biotechnol 43:155–176CrossRefGoogle Scholar
  12. 12.
    Kim E, Moore BS, Yoon YJ (2015) Reinvigorating natural product combinatorial biosynthesis with synthetic biology. Nat Chem Biol 11:649–659CrossRefGoogle Scholar
  13. 13.
    Kim HA, Kim HJ, Lee MJ, Park J, Choi AR, Jeong H, Jung K-H, Kim P, Lee SJ (2018) Genome variations of evolved Escherichia coli ET8 with rhodopsin-based phototrophic metabolism. Biotechnol J 13:e1700497CrossRefGoogle Scholar
  14. 14.
    Kong D, Zou Y, Zhang Z, Xu F, Brock NL, Zhang L, Deng Z, Lin S (2016) Identification of (2S,3S)-β-methyltryptophan as the real biosynthetic intermediate of antitumor agent streptonigrin. Sci Rep 6:20273CrossRefGoogle Scholar
  15. 15.
    Kudo K, Ozaki T, Shin-Ya K, Nishiyama M, Kuzuyama T (2017) Biosynthetic origin of the hydroxamic acid moiety of trichostatin A: identification of unprecedented enzymatic machinery involved in hydroxylamine transfer. J Am Chem Soc 139(20):6799–6802CrossRefGoogle Scholar
  16. 16.
    Lee DS, Kim P, Kim ES, Kim Y, Lee HS (2018) Corynebacterium glutamicum WhcD interacts with WhiA to exert a regulatory effect on cell division genes. Antonie Van Leeuwenhoek 111:641–648CrossRefGoogle Scholar
  17. 17.
    Li S, Guo J, Reva A, Huang F, Xiong B, Liu Y, Deng Z, Leadlay PF, Sun Y (2018) Methyltransferases of gentamicin biosynthesis. Proc Natl Acad Sci USA 115(6):1340–1345CrossRefGoogle Scholar
  18. 18.
    Lu C, Zhang X, Jiang M, Bai L (2016) Enhanced salinomycin production by adjusting the supply of polyketide extender units in Streptomyces albus. Metab Eng 35:129–137CrossRefGoogle Scholar
  19. 19.
    Ma F, Chung MT, Yao Y, Nidetz R, Lee LM, Liu AP, Feng Y, Kurabayashi K, Yang GY (2018) Efficient molecular evolution to generate enantioselective enzymes using a dual-channel microfluidic droplet screening platform. Nat Commun 9(1):1030CrossRefGoogle Scholar
  20. 20.
    Maruyama C, Niikura H, Izumikawa M, Hashimoto J, Shin-Ya K, Komatsu M, Ikeda H, Kuroda M, Sekizuka T, Ishikawa J, Hamano Y (2016) tRNA-dependent aminoacylation of an amino sugar intermediate in the biosynthesis of a streptothricin-related antibiotic. Appl Environ Microbiol 82(12):3640–3648CrossRefGoogle Scholar
  21. 21.
    Maruyama C, Toyoda J, Kato Y, Izumikawa M, Takagi M, Shin-ya K, Katano H, Utagawa T, Hamano Y (2012) A stand-alone adenylation domain forms amide bonds in streptothricin biosynthesis. Nat Chem Biol 8(9):791–797CrossRefGoogle Scholar
  22. 22.
    Miyanaga A, Ouchi R, Ishikawa F, Goto E, Tanabe G, Kudo F, Eguchi T (2018) Structural basis of protein–protein interactions between a trans-acting acyltransferase and acyl carrier protein in polyketide disorazole biosynthesis. J Am Chem Soc 140(25):7970–7978CrossRefGoogle Scholar
  23. 23.
    Muliandi A, Katsuyama Y, Sone K, Izumikawa M, Moriya T, Hashimoto J, Kozone I, Takagi M, Shin-ya K, Ohnishi Y (2014) Biosynthesis of the 4-methyloxazoline-containing nonribosomal peptides, JBIR-34 and -35, in Streptomyces sp. Sp080513GE-23. Chem Biol 21(8):923–934CrossRefGoogle Scholar
  24. 24.
    Nah HJ, Pyeon HR, Kang SH, Choi SS, Kim ES (2017) Cloning and heterologous expression of a large-sized natural product biosynthetic gene cluster in Streptomyces species. Front Microbiol 8:394CrossRefGoogle Scholar
  25. 25.
    Newman DJ, Cragg GM (2016) Natural products as sources of new drugs from 1981 to 2014. J Nat Prod 79:629–661CrossRefGoogle Scholar
  26. 26.
    Onaka H (2017) Novel antibiotic screening methods to awaken silent or cryptic secondary metabolic pathways in actinomycetes. J Antibiot 70(8):865–870CrossRefGoogle Scholar
  27. 27.
    Ozaki T, Yamashita K, Goto Y, Shimomura M, Hayashi S, Asamizu S, Sugai Y, Ikeda H, Suga H, Onaka H (2017) Dissection of goadsporin biosynthesis by in vitro reconstitution leading to designer analogues expressed in vivo. Nat Commun 8:14207CrossRefGoogle Scholar
  28. 28.
    Park J, Lim MC, Ryu H, Shim J, Kim YR, Jeon TJ (2018) Nanopore based detection of Bacillus thuringiensis HD-73 spores using aptamers and versatile DNA hairpins. Nanoscale 10:11955CrossRefGoogle Scholar
  29. 29.
    Sato S, Kudo F, Kim S-Y, Kuzuyama T, Eguchi T (2017) Methylcobalamin-dependent radical SAM C-methyltransferase Fom3 recognizes cytidylyl-2-hydroxyethylphosphonate and catalyzes the nonstereoselective C-methylation in fosfomycin biosynthesis. Biochemistry 56(28):3519–3522CrossRefGoogle Scholar
  30. 30.
    Shi G, Shi N, Li Y, Chen W, Deng J, Liu C, Zhu J, Wang H, Shen Y (2016) d-Alanylation in the assembly of ansatrienin side chain is catalyzed by a modular NRPS. ACS Chem Biol 11(4):876–881CrossRefGoogle Scholar
  31. 31.
    Shi T, Liu LX, Tao WT, Luo SG, Fan SB, Wang XL, Bai LQ, Zhao YL (2018) Theoretical studies on the catalytic mechanism and substrate diversity for macrocyclization of pikromycin thioesterase. ACS Catal 8(5):4323–4332CrossRefGoogle Scholar
  32. 32.
    Shin WS, Lee D, Lee SJ, Chun GT, Choi SS, Kim ES, Kim S (2018) Characterization of a non-phosphotransferase system for cis, cis-muconic acid production in Corynebacterium glutamicum. Biochem Biophys Res Commun 499(2):279–284CrossRefGoogle Scholar
  33. 33.
    Sugai Y, Katsuyama Y, Ohnishi Y (2016) A nitrous acid biosynthetic pathway for diazo group formation in bacteria. Nat Chem Biol 12(2):73–75CrossRefGoogle Scholar
  34. 34.
    Thuan NH, Dhakal D, Pokhrel AR, Chu LL, Van Pham TT, Shrestha A, Sohng JK (2018) Genome-guided exploration of metabolic features of Streptomyces peucetius ATCC 27952: past, current, and prospect. Appl Microbiol Biotechnol 102:4355–4370CrossRefGoogle Scholar
  35. 35.
    Tomita H, Katsuyama Y, Minami H, Ohnishi Y (2017) Identification and characterization of a bacterial cytochrome P450 monooxygenase catalyzing the 3-nitration of tyrosine in rufomycin biosynthesis. J Biol Chem 292(38):15859–15869CrossRefGoogle Scholar
  36. 36.
    Tomita T, Kobayashi M, Karita Y, Yasuno Y, Shinada T, Nishiyama M, Kuzuyama T (2017) Structure and mechanism of the monoterpene cyclolavandulyl diphosphate synthase that catalyzes consecutive condensation and cyclization. Angew Chem Int Ed Engl 56(47):14913–14917CrossRefGoogle Scholar
  37. 37.
    Tsutsumi H, Katsuyama Y, Izumikawa M, Takagi M, Fujie M, Satoh N, Shin-Ya K, Ohnishi Y (2018) Unprecedented cyclization catalyzed by a cytochrome P450 in benzastatin biosynthesis. J Am Chem Soc 140(21):6631–6639CrossRefGoogle Scholar
  38. 38.
    Vilian ATE, Dinesh B, Rethinasabapathy M, Hwang SK, Jin CS, Huh YS, Han YK (2018) Hexagonal Co3O4 anchored reduced graphene oxide sheets for high-performance supercapacitors and non-enzymatic glucose sensing. J Mater Chem A 6:14367–14379CrossRefGoogle Scholar
  39. 39.
    Xu M, Wang Y, Zhao Z, Gao G, Huang SX, Kang Q, He X, Lin S, Pang X, Deng Z, Tao M (2016) Functional genome mining for metabolites encoded by large gene clusters through heterologous expression of a whole-genome bacterial artificial chromosome library in Streptomyces spp. Appl Environ Microbiol 82(19):5795–5805CrossRefGoogle Scholar
  40. 40.
    Yu P, Bu QT, Tang YL, Mao XM, Li YQ (2018) Bidirectional regulation of AdpA(ch) in controlling the expression of scnRI and scnRII in the natamycin biosynthesis of Streptomyces chattanoogensis L10. Front Microbiol 9:316CrossRefGoogle Scholar
  41. 41.
    Zhang L, Ji J, Yuan M, Feng Y, Wang L, Deng Z, Bai L, Zheng J (2018) Stereospecificity of enoylreductase domains from modular polyketide synthases. ACS Chem Biol 13(4):871–87539CrossRefGoogle Scholar
  42. 42.
    Zhang Y, Zou Y, Brock NL, Huang T, Lan Y, Wang X, Deng Z, Tang Y, Lin S (2017) Characterization of 2-oxindole forming heme enzyme MarE, expanding the functional diversity of the tryptophan dioxygenase superfamily. J Am Chem Soc 139(34):11887–11894CrossRefGoogle Scholar
  43. 43.
    Zheng X, Cheng Q, Yao F, Wang X, Kong L, Cao B, Xu M, Lin S, Deng Z, Chooi YH, You D (2017) Biosynthesis of the pyrrolidine protein synthesis inhibitor anisomycin involves novel gene ensemble and cryptic biosynthetic steps. Proc Natl Acad Sci USA 114(16):4135–4140CrossRefGoogle Scholar

Copyright information

© Society for Industrial Microbiology and Biotechnology 2018

Authors and Affiliations

  1. 1.State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
  2. 2.Department of Biotechnology, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
  3. 3.Collaborative Research Institute for Innovative MicrobiologyThe University of TokyoTokyoJapan
  4. 4.Department of Biological EngineeringInha UniversityIncheonSouth Korea

Personalised recommendations