Heterologous expression-facilitated natural products’ discovery in actinomycetes

  • Min Xu
  • Gerard D. WrightEmail author
Natural Products - Original Paper


Actinomycetes produce many of the drugs essential for human and animal health as well as crop protection. Genome sequencing projects launched over the past two decades reveal dozens of cryptic natural product biosynthetic gene clusters in each actinomycete genome that are not expressed under regular laboratory conditions. This so-called ‘chemical dark matter’ represents a potentially rich untapped resource for drug discovery in the genomic era. Through improved understanding of natural product biosynthetic logic coupled with the development of bioinformatic and genetic tools, we are increasingly able to access this ‘dark matter’ using a wide variety of strategies with downstream potential application in drug development. In this review, we discuss recent research progress in the field of cloning of natural product biosynthetic gene clusters and their heterologous expression in validating the potential of this methodology to drive next-generation drug discovery.


Natural products Streptomyces Heterologous expression Drug discovery 



Attachment site of bacteria/phage


Bacterial artificial chromosome


Biosynthetic gene cluster


Cas9-assisted targeting of chromosome segment


Clustered regularly interspaced short palindromic repeats


Direct pathway cloning


Double strand break


Environmental DNA


Exonuclease in vitro assembly combined with RecET


5-Fluoroorotic acid


Heterologous expression


High molecular weight


Integrase-mediated site-specific recombination


Linear–circular homologous recombination


Linear–linear homologous recombination


Multiplexed CRISPR/Cas9- and TAR-mediated promoter engineering


Non-homologous end joining


Natural product


Nonribosomal peptide


Nonribosomal peptide synthetase


Phage P1 artificial chromosome


Polymerase chain reaction




Polyketide synthetase


Phosphopantetheinyl transferase


Polycyclic tetramate macrolactam


Ribosomally synthesized and post-translationally modified peptides


Streptomyces antibiotics regulatory protein


Transformation-associated recombination


Transcription start site



We thank Dr. Grace Yim and Elizabeth Culp for critical reading and discussion of the manuscript and Christy Groves for assistance in the preparation of Fig. 3. The authors gratefully acknowledge funding from the Canadian Institutes of Health Research (MT-14981), the Bill and Melinda Gates Foundation, and the Ontario Research Fund. G. D. W. is supported by a Canada Research Chair.


  1. 1.
    Alberti F, Leng DJ, Wilkening I, Song L, Tosin M, Corre C (2018) Triggering the expression of a silent gene cluster from genetically intractable bacteria results in scleric acid discovery. bioRxiv. Google Scholar
  2. 2.
    Alduina R, De Grazia S, Dolce L, Salerno P, Sosio M, Donadio S, Puglia AM (2003) Artificial chromosome libraries of Streptomyces coelicolor A3(2) and Planobispora rosea. FEMS Microbiol Lett 218:181–186Google Scholar
  3. 3.
    Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, Camarero JA, Campopiano DJ, Challis GL, Clardy J, Cotter PD, Craik DJ, Dawson M, Dittmann E, Donadio S, Dorrestein PC, Entian KD, Fischbach MA, Garavelli JS, Goransson U, Gruber CW, Haft DH, Hemscheidt TK, Hertweck C, Hill C, Horswill AR, Jaspars M, Kelly WL, Klinman JP, Kuipers OP, Link AJ, Liu W, Marahiel MA, Mitchell DA, Moll GN, Moore BS, Müller R, Nair SK, Nes IF, Norris GE, Olivera BM, Onaka H, Patchett ML, Piel J, Reaney MJ, Rebuffat S, Ross RP, Sahl HG, Schmidt EW, Selsted ME, Severinov K, Shen B, Sivonen K, Smith L, Stein T, Sussmuth RD, Tagg JR, Tang GL, Truman AW, Vederas JC, Walsh CT, Walton JD, Wenzel SC, Willey JM, van der Donk WA (2013) Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 30:108–160. Google Scholar
  4. 4.
    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 41:175–184. Google Scholar
  5. 5.
    Bai C, Zhang Y, Zhao X, Hu Y, Xiang S, Miao J, Lou C, Zhang L (2015) Exploiting a precise design of universal synthetic modular regulatory elements to unlock the microbial natural products in Streptomyces. Proc Natl Acad Sci USA 112:12181–12186. Google Scholar
  6. 6.
    Baltz RH (2012) Streptomyces temperate bacteriophage integration systems for stable genetic engineering of actinomycetes (and other organisms). J Ind Microbiol Biotechnol 39:661–672. Google Scholar
  7. 7.
    Baltz RH (2016) Genetic manipulation of secondary metabolite biosynthesis for improved production in Streptomyces and other actinomycetes. J Ind Microbiol Biotechnol 43:343–370. Google Scholar
  8. 8.
    Baltz RH (2017) Gifted microbes for genome mining and natural product discovery. J Ind Microbiol Biotechnol 44:573–588. Google Scholar
  9. 9.
    Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O’Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141–147. Google Scholar
  10. 10.
    Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA, Suarez Duran HG, de Los Santos ELC, Kim HU, Nave M, Dickschat JS, Mitchell DA, Shelest E, Breitling R, Takano E, Lee SY, Weber T, Medema MH (2017) antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res 45:W36–W41. Google Scholar
  11. 11.
    Bonet B, Teufel R, Crusemann M, Ziemert N, Moore BS (2015) Direct capture and heterologous expression of Salinispora natural product genes for the biosynthesis of enterocin. J Nat Prod 78:539–542. Google Scholar
  12. 12.
    Challis GL (2014) Exploitation of the Streptomyces coelicolor A3(2) genome sequence for discovery of new natural products and biosynthetic pathways. J Ind Microbiol Biotechnol 41:219–232. Google Scholar
  13. 13.
    Chang FY, Brady SF (2013) Discovery of indolotryptoline antiproliferative agents by homology-guided metagenomic screening. Proc Natl Acad Sci USA 110:2478–2483. Google Scholar
  14. 14.
    Chen L, Wang Y, Guo H, Xu M, Deng Z, Tao M (2012) High-throughput screening for Streptomyces antibiotic biosynthesis activators. Appl Environ Microbiol 78:4526–4528. Google Scholar
  15. 15.
    Chen X, Xu M, Lu J, Xu J, Wang Y, Lin S, Deng Z, Tao M (2018) Biosynthesis of tropolones in Streptomyces spp.: interweaving biosynthesis and degradation of phenylacetic acid and hydroxylations on tropone ring. Appl Environ Microbiol. Google Scholar
  16. 16.
    Choi SS, Katsuyama Y, Bai L, Deng Z, Ohnishi Y, Kim ES (2018) Genome engineering for microbial natural product discovery. Curr Opin Microbiol 45:53–60. Google Scholar
  17. 17.
    Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, Pati A, Godfrey PA, Koehrsen M, Clardy J, Birren BW, Takano E, Sali A, Linington RG, Fischbach MA (2014) Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 158:412–421. Google Scholar
  18. 18.
    Cobb RE, Wang Y, Zhao H (2015) High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS Synth Biol 4:723–728. Google Scholar
  19. 19.
    Dai S, Ouyang Y, Wang G, Li X (2011) Streptomyces autolyticus JX-47 large-insert bacterial artificial chromosome library construction and identification of clones covering geldanamycin biosynthesis gene cluster. Curr Microbiol 63:68–74. Google Scholar
  20. 20.
    Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97:6640–6645. Google Scholar
  21. 21.
    Deng Q, Zhou L, Luo M, Deng Z, Zhao C (2017) Heterologous expression of avermectins biosynthetic gene cluster by construction of a bacterial artificial chromosome library of the producers. Synth Syst Biotechnol 2:59–64. Google Scholar
  22. 22.
    Doroghazi JR, Albright JC, Goering AW, Ju KS, Haines RR, Tchalukov KA, Labeda DP, Kelleher NL, Metcalf WW (2014) A roadmap for natural product discovery based on large-scale genomics and metabolomics. Nat Chem Biol 10:963–968. Google Scholar
  23. 23.
    Du D, Wang L, Tian Y, Liu H, Tan H, Niu G (2015) Genome engineering and direct cloning of antibiotic gene clusters via phage ϕphiBT1 integrase-mediated site-specific recombination in Streptomyces. Sci Rep 5:8740. Google Scholar
  24. 24.
    Fayed B, Younger E, Taylor G, Smith MC (2014) A novel Streptomyces spp. integration vector derived from the S. venezuelae phage, SV1. BMC Biotechnol 14:51. Google Scholar
  25. 25.
    Fedoryshyn M, Welle E, Bechthold A, Luzhetskyy A (2008) Functional expression of the Cre recombinase in actinomycetes. Appl Microbiol Biotechnol 78:1065–1070. Google Scholar
  26. 26.
    Finking R, Marahiel MA (2004) Biosynthesis of nonribosomal peptides 1. Annu Rev Microbiol 58:453–488. Google Scholar
  27. 27.
    Fogg PC, Haley JA, Stark WM, Smith MC (2017) Genome integration and excision by a new Streptomyces bacteriophage, ϕJoe. Appl Environ Microbiol. Google Scholar
  28. 28.
    Fu J, Bian X, Hu S, Wang H, Huang F, Seibert PM, Plaza A, Xia L, Müller R, Stewart AF, Zhang Y (2012) Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nat Biotechnol 30:440–446. Google Scholar
  29. 29.
    Furter-Graves EM, Hall BD (1990) DNA sequence elements required for transcription initiation of the Schizosaccharomyces pombe ADH gene in Saccharomyces cerevisiae. Mol Gen Genet 223:407–416Google Scholar
  30. 30.
    Gao G, Liu X, Xu M, Wang Y, Zhang F, Xu L, Lv J, Long Q, Kang Q, Ou HY, Wang Y, Rohr J, Deng Z, Jiang M, Lin S, Tao M (2017) Formation of an angular aromatic polyketide from a linear anthrene precursor via oxidative rearrangement. Cell Chem Biol 24(881–891):e884. Google Scholar
  31. 31.
    Genilloud O (2017) Actinomycetes: still a source of novel antibiotics. Nat Prod Rep 34:1203–1232. Google Scholar
  32. 32.
    Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA 3rd, Smith HO (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6:343–345. Google Scholar
  33. 33.
    Gomez-Escribano JP, Alt S, Bibb MJ (2016) Next generation sequencing of Actinobacteria for the discovery of novel natural products. Mar Drugs. Google Scholar
  34. 34.
    Gomez-Escribano JP, Bibb MJ (2011) Engineering Streptomyces coelicolor for heterologous expression of secondary metabolite gene clusters. Microb Biotechnol 4:207–215. Google Scholar
  35. 35.
    Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17:333–351. Google Scholar
  36. 36.
    Greunke C, Duell ER, D’Agostino PM, Glockle A, Lamm K, Gulder TAM (2018) Direct Pathway Cloning (DiPaC) to unlock natural product biosynthetic potential. Metab Eng 47:334–345. Google Scholar
  37. 37.
    Gust B, Challis GL, Fowler K, Kieser T, Chater KF (2003) PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin. Proc Natl Acad Sci USA 100:1541–1546. Google Scholar
  38. 38.
    Harvey CJB, Tang M, Schlecht U, Horecka J, Fischer CR, Lin HC, Li J, Naughton B, Cherry J, Miranda M, Li YF, Chu AM, Hennessy JR, Vandova GA, Inglis D, Aiyar RS, Steinmetz LM, Davis RW, Medema MH, Sattely E, Khosla C, St Onge RP, Tang Y, Hillenmeyer ME (2018) HEx: a heterologous expression platform for the discovery of fungal natural products. Sci Adv. Google Scholar
  39. 39.
    Hosaka T, Ohnishi-Kameyama M, Muramatsu H, Murakami K, Tsurumi Y, Kodani S, Yoshida M, Fujie A, Ochi K (2009) Antibacterial discovery in actinomycetes strains with mutations in RNA polymerase or ribosomal protein S12. Nat Biotechnol 27:462–464. Google Scholar
  40. 40.
    Hover BM, Kim SH, Katz M, Charlop-Powers Z, Owen JG, Ternei MA, Maniko J, Estrela AB, Molina H, Park S, Perlin DS, Brady SF (2018) Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens. Nat Microbiol 3:415–422. Google Scholar
  41. 41.
    Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, Omura S (2003) Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol 21:526–531. Google Scholar
  42. 42.
    Jiang W, Zhao X, Gabrieli T, Lou C, Ebenstein Y, Zhu TF (2015) Cas9-assisted targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene clusters. Nat Commun 6:8101. Google Scholar
  43. 43.
    Jiang W, Zhu TF (2016) Targeted isolation and cloning of 100-kb microbial genomic sequences by Cas9-assisted targeting of chromosome segments. Nat Protoc 11:960–975. Google Scholar
  44. 44.
    John D, Sidda LS, Poon Vincent, Al-Bassam Mahmoud, Lazos Orestis, Buttner Mark J, Challis Gregory L, Corre Christophe (2014) Discovery of a family of γ-aminobutyrate ureas via rational derepression of a silent bacterial gene cluster. Chem Sci 5:4. Google Scholar
  45. 45.
    Jones AC, Gust B, Kulik A, Heide L, Buttner MJ, Bibb MJ (2013) Phage p1-derived artificial chromosomes facilitate heterologous expression of the FK506 gene cluster. PLoS One 8:e69319. Google Scholar
  46. 46.
    Kallifidas D, Jiang G, Ding Y, Luesch H (2018) Rational engineering of Streptomyces albus J1074 for the overexpression of secondary metabolite gene clusters. Microb Cell Factories 17:25. Google Scholar
  47. 47.
    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 134:19552–19555. Google Scholar
  48. 48.
    Kang HS, Brady SF (2013) Arimetamycin A: improving clinically relevant families of natural products through sequence-guided screening of soil metagenomes. Angew Chem Int Ed Engl 52:11063–11067. Google Scholar
  49. 49.
    Kang HS, Charlop-Powers Z, Brady SF (2016) Multiplexed CRISPR/Cas9- and TAR-mediated promoter engineering of natural product biosynthetic gene clusters in yeast. ACS Synth Biol 5:1002–1010. Google Scholar
  50. 50.
    Katz M, Hover BM, Brady SF (2016) Culture-independent discovery of natural products from soil metagenomes. J Ind Microbiol Biotechnol 43:129–141. Google Scholar
  51. 51.
    Komatsu M, Komatsu K, Koiwai H, Yamada Y, Kozone I, Izumikawa M, Hashimoto J, Takagi M, Omura S, Shin-ya K, Cane DE, Ikeda H (2013) Engineered Streptomyces avermitilis host for heterologous expression of biosynthetic gene cluster for secondary metabolites. ACS Synth Biol 2:384–396. Google Scholar
  52. 52.
    Komatsu M, Uchiyama T, Omura S, Cane DE, Ikeda H (2010) Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. Proc Natl Acad Sci USA 107:2646–2651. Google Scholar
  53. 53.
    Kouprina N, Larionov V (2008) Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae. Nat Protoc 3:371–377. Google Scholar
  54. 54.
    Kouprina N, Larionov V (2016) Transformation-associated recombination (TAR) cloning for genomics studies and synthetic biology. Chromosoma 125:621–632. Google Scholar
  55. 55.
    Kuhstoss S, Rao RN (1991) Analysis of the integration function of the streptomycete bacteriophage phiC31. J Mol Biol 222:897–908Google Scholar
  56. 56.
    Larson CB, Crusemann M, Moore BS (2017) PCR-independent method of transformation-associated recombination reveals the cosmomycin biosynthetic gene cluster in an ocean Streptomycete. J Nat Prod 80:1200–1204. Google Scholar
  57. 57.
    Laureti L, Song L, Huang S, Corre C, Leblond P, Challis GL, Aigle B (2011) Identification of a bioactive 51-membered macrolide complex by activation of a silent polyketide synthase in Streptomyces ambofaciens. Proc Natl Acad Sci USA 108:6258–6263. Google Scholar
  58. 58.
    Lee NC, Larionov V, Kouprina N (2015) Highly efficient CRISPR/Cas9-mediated TAR cloning of genes and chromosomal loci from complex genomes in yeast. Nucleic Acids Res 43:e55. Google Scholar
  59. 59.
    Levy SE, Myers RM (2016) Advancements in next-generation sequencing. Annu Rev Genom Hum Genet 17:95–115. Google Scholar
  60. 60.
    Li J, Qu X, He X, Duan L, Wu G, Bi D, Deng Z, Liu W, Ou HY (2012) ThioFinder: a web-based tool for the identification of thiopeptide gene clusters in DNA sequences. PLoS One 7:e45878. Google Scholar
  61. 61.
    Li L, Jiang W, Lu Y (2017) New strategies and approaches for engineering biosynthetic gene clusters of microbial natural products. Biotechnol Adv 35:936–949. Google Scholar
  62. 62.
    Li L, Jiang W, Lu Y (2018) A modified gibson assembly method for cloning large DNA fragments with high GC contents. Methods Mol Biol 1671:203–209. Google Scholar
  63. 63.
    Li L, Wei K, Zheng G, Liu X, Chen S, Jiang W, Lu Y (2018) CRISPR-Cpf1 assisted multiplex genome editing and transcriptional repression in Streptomyces. Appl Environ Microbiol. Google Scholar
  64. 64.
    Li L, Xu Z, Xu X, Wu J, Zhang Y, He X, Zabriskie TM, Deng Z (2008) The mildiomycin biosynthesis: initial steps for sequential generation of 5-hydroxymethylcytidine 5′-monophosphate and 5-hydroxymethylcytosine in Streptoverticillium rimofaciens ZJU5119. ChemBioChem 9:1286–1294. Google Scholar
  65. 65.
    Li L, Zhao Y, Ruan L, Yang S, Ge M, Jiang W, Lu Y (2015) A stepwise increase in pristinamycin II biosynthesis by Streptomyces pristinaespiralis through combinatorial metabolic engineering. Metab Eng 29:12–25. Google Scholar
  66. 66.
    Li S, Wang J, Li X, Yin S, Wang W, Yang K (2015) Genome-wide identification and evaluation of constitutive promoters in streptomycetes. Microb Cell Factories 14:172. Google Scholar
  67. 67.
    Li Y, Li Z, Yamanaka K, Xu Y, Zhang W, Vlamakis H, Kolter R, Moore BS, Qian PY (2015) Directed natural product biosynthesis gene cluster capture and expression in the model bacterium Bacillus subtilis. Sci Rep 5:9383. Google Scholar
  68. 68.
    Lincke T, Behnken S, Ishida K, Roth M, Hertweck C (2010) Closthioamide: an unprecedented polythioamide antibiotic from the strictly anaerobic bacterium Clostridium cellulolyticum. Angew Chem Int Ed Engl 49:2011–2013. Google Scholar
  69. 69.
    Liu Q, Xiao L, Zhou Y, Deng K, Tan G, Han Y, Liu X, Deng Z, Liu T (2016) Development of Streptomyces sp. FR-008 as an emerging chassis. Synth Syst Biotechnol 1:207–214. Google Scholar
  70. 70.
    Liu R, Deng Z, Liu T (2018) Streptomyces species: ideal chassis for natural product discovery and overproduction. Metab Eng. Google Scholar
  71. 71.
    Luo Y, Cobb RE, Zhao H (2014) Recent advances in natural product discovery. Curr Opin Biotechnol 30:230–237. Google Scholar
  72. 72.
    Luo Y, Enghiad B, Zhao H (2016) New tools for reconstruction and heterologous expression of natural product biosynthetic gene clusters. Nat Prod Rep 33:174–182. Google Scholar
  73. 73.
    Luo Y, Huang H, Liang J, Wang M, Lu L, Shao Z, Cobb RE, Zhao H (2013) Activation and characterization of a cryptic polycyclic tetramate macrolactam biosynthetic gene cluster. Nat Commun 4:2894. Google Scholar
  74. 74.
    Luo Y, Li BZ, Liu D, Zhang L, Chen Y, Jia B, Zeng BX, Zhao H, Yuan YJ (2015) Engineered biosynthesis of natural products in heterologous hosts. Chem Soc Rev 44:5265–5290. Google Scholar
  75. 75.
    Mast Y, Weber T, Golz M, Ort-Winklbauer R, Gondran A, Wohlleben W, Schinko E (2011) Characterization of the ‘pristinamycin supercluster’ of Streptomyces pristinaespiralis. Microb Biotechnol 4:192–206. Google Scholar
  76. 76.
    Miao V, Coeffet-Legal MF, Brian P, Brost R, Penn J, Whiting A, Martin S, Ford R, Parr I, Bouchard M, Silva CJ, Wrigley SK, Baltz RH (2005) Daptomycin biosynthesis in Streptomyces roseosporus: cloning and analysis of the gene cluster and revision of peptide stereochemistry. Microbiology 151:1507–1523. Google Scholar
  77. 77.
    Murakami T, Burian J, Yanai K, Bibb MJ, Thompson CJ (2011) A system for the targeted amplification of bacterial gene clusters multiplies antibiotic yield in Streptomyces coelicolor. Proc Natl Acad Sci USA 108:16020–16025. Google Scholar
  78. 78.
    Murphy KC (1998) Use of bacteriophage lambda recombination functions to promote gene replacement in Escherichia coli. J Bacteriol 180:2063–2071Google Scholar
  79. 79.
    Muyrers JP, Zhang Y, Buchholz F, Stewart AF (2000) RecE/RecT and Redα/Redβ initiate double-stranded break repair by specifically interacting with their respective partners. Genes Dev 14:1971–1982Google Scholar
  80. 80.
    Muyrers JP, Zhang Y, Testa G, Stewart AF (1999) Rapid modification of bacterial artificial chromosomes by ET-recombination. Nucleic Acids Res 27:1555–1557Google Scholar
  81. 81.
    Myronovskyi M, Luzhetskyy A (2016) Native and engineered promoters in natural product discovery. Nat Prod Rep 33:1006–1019. Google Scholar
  82. 82.
    Myronovskyi M, Rosenkranzer B, Nadmid S, Pujic P, Normand P, Luzhetskyy A (2018) Generation of a cluster-free Streptomyces albus chassis strains for improved heterologous expression of secondary metabolite clusters. Metab Eng 49:316–324. Google Scholar
  83. 83.
    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 8:394. Google Scholar
  84. 84.
    Nah HJ, Woo MW, Choi SS, Kim ES (2015) Precise cloning and tandem integration of large polyketide biosynthetic gene cluster using Streptomyces artificial chromosome system. Microb Cell Factories 14:140. Google Scholar
  85. 85.
    Nett M, Ikeda H, Moore BS (2009) Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 26:1362–1384. Google Scholar
  86. 86.
    Newman DJ, Cragg GM (2016) Natural products as sources of new drugs from 1981 to 2014. J Nat Prod 79:629–661. Google Scholar
  87. 87.
    Niu G (2018) Genomics-driven natural product discovery in Actinomycetes. Trends Biotechnol 36:238–241. Google Scholar
  88. 88.
    Noskov VN, Kouprina N, Leem SH, Ouspenski I, Barrett JC, Larionov V (2003) A general cloning system to selectively isolate any eukaryotic or prokaryotic genomic region in yeast. BMC Genom 4:16. Google Scholar
  89. 89.
    Olano C, Garcia I, Gonzalez A, Rodriguez M, Rozas D, Rubio J, Sanchez-Hidalgo M, Brana AF, Mendez C, Salas JA (2014) Activation and identification of five clusters for secondary metabolites in Streptomyces albus J1074. Microb Biotechnol 7:242–256. Google Scholar
  90. 90.
    Osoegawa K, Woon PY, Zhao B, Frengen E, Tateno M, Catanese JJ, de Jong PJ (1998) An improved approach for construction of bacterial artificial chromosome libraries. Genomics 52:1–8. Google Scholar
  91. 91.
    Owen JG, Reddy BV, Ternei MA, Charlop-Powers Z, Calle PY, Kim JH, Brady SF (2013) Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products. Proc Natl Acad Sci USA 110:11797–11802. Google Scholar
  92. 92.
    Pootoolal J, Thomas MG, Marshall CG, Neu JM, Hubbard BK, Walsh CT, Wright GD (2002) Assembling the glycopeptide antibiotic scaffold: the biosynthesis of A47934 from Streptomyces toyocaensis NRRL15009. Proc Natl Acad Sci USA 99:8962–8967. Google Scholar
  93. 93.
    Poteete AR (2001) What makes the bacteriophage lambda Red system useful for genetic engineering: molecular mechanism and biological function. FEMS Microbiol Lett 201:9–14Google Scholar
  94. 94.
    Pyeon HR, Nah HJ, Kang SH, Choi SS, Kim ES (2017) Heterologous expression of pikromycin biosynthetic gene cluster using Streptomyces artificial chromosome system. Microb Cell Factories 16:96. Google Scholar
  95. 95.
    Ross AC, Gulland LE, Dorrestein PC, Moore BS (2015) Targeted capture and heterologous expression of the Pseudoalteromonas alterochromide gene cluster in Escherichia coli represents a promising natural product exploratory platform. ACS Synth Biol 4:414–420. Google Scholar
  96. 96.
    Rutledge PJ, Challis GL (2015) Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat Rev Microbiol 13:509–523. Google Scholar
  97. 97.
    Seyedsayamdost MR (2014) High-throughput platform for the discovery of elicitors of silent bacterial gene clusters. Proc Natl Acad Sci USA 111:7266–7271. Google Scholar
  98. 98.
    Shao Z, Luo Y, Zhao H (2011) Rapid characterization and engineering of natural product biosynthetic pathways via DNA assembler. Mol BioSyst 7:1056–1059. Google Scholar
  99. 99.
    Shao Z, Luo Y, Zhao H (2012) DNA assembler method for construction of zeaxanthin-producing strains of Saccharomyces cerevisiae. Methods Mol Biol 898:251–262. Google Scholar
  100. 100.
    Shao Z, Zhao H (2012) DNA assembler: a synthetic biology tool for characterizing and engineering natural product gene clusters. Methods Enzymol 517:203–224. Google Scholar
  101. 101.
    Shao Z, Zhao H (2013) Construction and engineering of large biochemical pathways via DNA assembler. Methods Mol Biol 1073:85–106. Google Scholar
  102. 102.
    Shao Z, Zhao H (2014) Manipulating natural product biosynthetic pathways via DNA assembler. Curr Protoc Chem Biol 6:65–100. Google Scholar
  103. 103.
    Shao Z, Zhao H, Zhao H (2009) DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res 37:e16. Google Scholar
  104. 104.
    Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 89:8794–8797Google Scholar
  105. 105.
    Skinnider MA, Merwin NJ, Johnston CW, Magarvey NA (2017) PRISM 3: expanded prediction of natural product chemical structures from microbial genomes. Nucleic Acids Res 45:W49–W54. Google Scholar
  106. 106.
    Staunton J, Weissman KJ (2001) Polyketide biosynthesis: a millennium review. Nat Prod Rep 18:380–416Google Scholar
  107. 107.
    Tang X, Li J, Millan-Aguinaga N, Zhang JJ, O’Neill EC, Ugalde JA, Jensen PR, Mantovani SM, Moore BS (2015) Identification of thiotetronic acid antibiotic biosynthetic pathways by target-directed genome mining. ACS Chem Biol 10:2841–2849. Google Scholar
  108. 108.
    Thanapipatsiri A, Gomez-Escribano JP, Song L, Bibb MJ, Al-Bassam M, Chandra G, Thamchaipenet A, Challis GL, Bibb MJ (2016) Discovery of unusual biaryl polyketides by activation of a silent Streptomyces venezuelae biosynthetic gene cluster. ChemBioChem 17:2189–2198. Google Scholar
  109. 109.
    Thierry A, Gaillon L, Galibert F, Dujon B (1995) Construction of a complete genomic library of Saccharomyces cerevisiae and physical mapping of chromosome XI at 3.7 kb resolution. Yeast 11:121–135. Google Scholar
  110. 110.
    Tingli Bai YY, Zhong Xu, Tao Meifeng (2014) Construction of Streptomyces lividans SBT5 as an efficient heterologous expression host. J Huazhong Agric Univ 33:6. Google Scholar
  111. 111.
    Tong Y, Charusanti P, Zhang L, Weber T, Lee SY (2015) CRISPR-Cas9 based engineering of Actinomycetal genomes. ACS Synth Biol 4:1020–1029. Google Scholar
  112. 112.
    van Heel AJ, de Jong A, Song C, Viel JH, Kok J, Kuipers OP (2018) BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Res 46:W278–W281. Google Scholar
  113. 113.
    Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigo R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X (2001) The sequence of the human genome. Science 291:1304–1351. Google Scholar
  114. 114.
    Wang H, Li Z, Jia R, Yin J, Li A, Xia L, Yin Y, Müller R, Fu J, Stewart AF, Zhang Y (2018) ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes. Nucleic Acids Res 46:2697. Google Scholar
  115. 115.
    Wang W, Li X, Wang J, Xiang S, Feng X, Yang K (2013) An engineered strong promoter for Streptomycetes. Appl Environ Microbiol 79:4484–4492. Google Scholar
  116. 116.
    Wang W, Yang T, Li Y, Li S, Yin S, Styles K, Corre C, Yang K (2016) Development of a synthetic oxytetracycline-inducible expression system for Streptomycetes using de novo characterized genetic parts. ACS Synth Biol 5:765–773. Google Scholar
  117. 117.
    Xu F, Nazari B, Moon K, Bushin LB, Seyedsayamdost MR (2017) Discovery of a cryptic antifungal compound from Streptomyces albus J1074 using high-throughput elicitor screens. J Am Chem Soc 139:9203–9212. Google Scholar
  118. 118.
    Xu J, Zhang J, Zhuo J, Li Y, Tian Y, Tan H (2017) Activation and mechanism of a cryptic oviedomycin gene cluster via the disruption of a global regulatory gene, adpA, in Streptomyces ansochromogenes. J Biol Chem 292:19708–19720. Google Scholar
  119. 119.
    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 82:5795–5805. Google Scholar
  120. 120.
    Yamanaka K, Reynolds KA, Kersten RD, Ryan KS, Gonzalez DJ, Nizet V, Dorrestein PC, Moore BS (2014) Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A. Proc Natl Acad Sci USA 111:1957–1962. Google Scholar
  121. 121.
    Yanai K, Murakami T, Bibb M (2006) Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Proc Natl Acad Sci USA 103:9661–9666. Google Scholar
  122. 122.
    Yim G, Wang W, Thaker MN, Tan S, Wright GD (2016) How to make a glycopeptide: a synthetic biology approach to expand antibiotic chemical diversity. ACS Infect Dis 2:642–650. Google Scholar
  123. 123.
    Yin J, Hoffmann M, Bian X, Tu Q, Yan F, Xia L, Ding X, Stewart AF, Müller R, Fu J, Zhang Y (2015) Direct cloning and heterologous expression of the salinomycin biosynthetic gene cluster from Streptomyces albus DSM41398 in Streptomyces coelicolor A3(2). Sci Rep 5:15081. Google Scholar
  124. 124.
    Zhang B, Wang KB, Wang W, Bi SF, Mei YN, Deng XZ, Jiao RH, Tan RX, Ge HM (2018) Discovery, biosynthesis, and heterologous production of streptoseomycin, an anti-microaerophilic bacteria macrodilactone. Org Lett 20:2967–2971. Google Scholar
  125. 125.
    Zhang L, Wang L, Wang J, Ou X, Zhao G, Ding X (2010) DNA cleavage is independent of synapsis during Streptomyces phage phiBT1 integrase-mediated site-specific recombination. J Mol Cell Biol 2:264–275. Google Scholar
  126. 126.
    Zhang MM, Qiao Y, Ang EL, Zhao H (2017) Using natural products for drug discovery: the impact of the genomics era. Expert Opin Drug Discov 12:475–487. Google Scholar
  127. 127.
    Zhang MM, Wang Y, Ang EL, Zhao H (2016) Engineering microbial hosts for production of bacterial natural products. Nat Prod Rep 33:963–987. Google Scholar
  128. 128.
    Zhang MM, Wong FT, Wang Y, Luo S, Lim YH, Heng E, Yeo WL, Cobb RE, Enghiad B, Ang EL, Zhao H (2017) CRISPR-Cas9 strategy for activation of silent Streptomyces biosynthetic gene clusters. Nat Chem Biol. Google Scholar
  129. 129.
    Zhang Y, Buchholz F, Muyrers JP, Stewart AF (1998) A new logic for DNA engineering using recombination in Escherichia coli. Nat Genet 20:123–128. Google Scholar
  130. 130.
    Zhao Z, Shi T, Xu M, Brock NL, Zhao YL, Wang Y, Deng Z, Pang X, Tao M (2016) Hybrubins: bipyrrole tetramic acids obtained by crosstalk between a truncated undecylprodigiosin pathway and heterologous tetramic acid biosynthetic genes. Org Lett 18:572–575. Google Scholar
  131. 131.
    Zhou Y, Murphy AC, Samborskyy M, Prediger P, Dias LC, Leadlay PF (2015) Iterative mechanism of macrodiolide formation in the anticancer compound conglobatin. Chem Biol 22:745–754. Google Scholar
  132. 132.
    Ziemert N, Alanjary M, Weber T (2016) The evolution of genome mining in microbes—a review. Nat Prod Rep 33:988–1005. Google Scholar

Copyright information

© Society for Industrial Microbiology and Biotechnology 2018

Authors and Affiliations

  1. 1.M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical SciencesDeGroote School of Medicine, McMaster UniversityHamiltonCanada

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