Advertisement

Streptomycin resistance-aided genome shuffling to improve doramectin productivity of Streptomyces avermitilis NEAU1069

  • Ji Zhang
  • Xiangjing Wang
  • Jinna Diao
  • Hairong He
  • Yuejing Zhang
  • Wensheng Xiang
Fermentation, Cell Culture and Bioengineering

Abstract

Genome shuffling is an efficient approach for the rapid engineering of microbial strains with desirable industrial phenotypes. In this study, a strategy of incorporating streptomycin resistance screening into genome shuffling (GS-SR) was applied for rapid improvement of doramectin production by Streptomyces avermitilis NEAU1069. The starting mutant population was generated through treatment of the spores with N-methyl-N’-nitro-N-nitrosoguanidine and ultraviolet (UV) irradiation, respectively, and five mutants with higher productivity of doramectin were selected as starting strains for GS-SR. Finally, a genetically stable strain F4-137 was obtained and characterized to be able to yield 992 ± 4.4 mg/l doramectin in a shake flask, which was 7.3-fold and 11.2-fold higher than that of the starting strain UV-45 and initial strain NEAU1069, respectively. The doramectin yield by F4-137 in a 50-l fermentor reached 930.3 ± 3.8 mg/l. Furthermore, the factors associated with the improved doramectin yield were investigated and the results suggested that mutations in ribosomal protein S12 and the enhanced production of cyclohexanecarboxylic coenzyme A may contribute to the improved performance of the shuffled strains. The random amplified polymorphic DNA analysis showed a genetic diversity among the shuffled strains, which confirmed the occurrence of genome shuffling. In conclusion, our results demonstrated that GS-SR is a powerful method for enhancing the production of secondary metabolites in Streptomyces.

Keywords

Genome shuffling Streptomycin resistance screening Doramectin Streptomyces avermitilis NEAU1069 

Notes

Acknowledgments

This work was financially supported by the National Natural Science Foundation of China (31071750), the National Key Project for Basic Research (2010CB126102), the China Postdoctoral Science Foundation (20110491023), the Heilongjiang Postdoctoral Fund (LBH-Z11234), and Doctor Start-up Fund of Northeast Agricultural University (2012RCB05), and the Innovative Program for Postgraduates in Heilongjiang Province (YJSCX2011-087HLJ).

References

  1. 1.
    Bajwa PK, Pinel D, Martin VJJ, Trevors JT, Lee H (2010) Strain improvement of the pentose-fermenting yeast Pichia stipitis by genome shuffling. J Microbiol Methods 81:179–186PubMedCrossRefGoogle Scholar
  2. 2.
    Baltz RH (2011) Strain improvement in actinomycetes in the postgenomic era. J Ind Microbiol Biotechnol 38:657–666PubMedCrossRefGoogle Scholar
  3. 3.
    Beltrametti F, Rossi R, Selva E, Marinelli F (2006) Antibiotic production improvement in the rare actinomycete Planobispora rosea by selection of mutants resistant to the aminoglycosides Streptomycin and Gentamycin and to Rifamycin. J Ind Microbiol Biotechnol 33:283–288PubMedCrossRefGoogle Scholar
  4. 4.
    Cao X, Song Q, Wang C, Hou L (2012) Genome shuffling of Hansenula anomala to improve flavour formation of soy sauce. World J Microbiol Biotechnol 28:1857–1862PubMedCrossRefGoogle Scholar
  5. 5.
    Dai MH, Copley SD (2004) Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723. Appl Environ Microbiol 70:2391–2397PubMedCrossRefGoogle Scholar
  6. 6.
    Gendy MMA, EL-Bondkly AMA (2011) Genome shuffling of marine derived bacterium Nocardia sp. ALAA 2000 for improved ayamycin production. Antonie van Leeuwenhoek 99:773–780Google Scholar
  7. 7.
    Gong J, Zheng H, Wu Z, Chen T, Zhao X (2009) Genome shuffling: progress and applications for phenotype improvement. Biotechnol Adv 27:996–1005PubMedCrossRefGoogle Scholar
  8. 8.
    Hafner EW, Holley BW, Holdom KS (1991) Branched-chain fatty acid requirement for avermectin production by a mutant of Streptomyces avermitilis lacking branched-chain 2-oxo acid dehydrogenase activity. J Antibiot 44:349–356PubMedCrossRefGoogle Scholar
  9. 9.
    Hida H, Yamada T, Yamada Y (2007) Genome shuffling of Streptomyces sp. U121 for improved production of hydroxycitric acid. Appl Microbiol Biotechnol 73:1387–1393PubMedCrossRefGoogle Scholar
  10. 10.
    Hopwood DA, Bibb MJ, Chater KF, Kieser T, Bruton CJ, Kieser HM, Lydiate DJ, Smith CP, Ward JM (1985) Genetic manipulation of Streptomyces, a laboratory manual. John Innes Foundation, Norwich, p 356Google Scholar
  11. 11.
    Jin Q, Jin Z, Zhang L, Yao S, Li F (2012) Probing the molecular mechanisms for pristinamycin yield enhancement in Streptomyces pristinaespiralis. Curr Microbiol 65:792–798PubMedCrossRefGoogle Scholar
  12. 12.
    Jingping G, Hongbing S, Gang S, Hongzhi L, Wenxiang P (2012) A genome shuffling-generated Saccharomyces cerevisiae isolate that ferments xylose and glucose to produce high levels of ethanol. J Ind Microbiol Biotechnol 39:777–787PubMedCrossRefGoogle Scholar
  13. 13.
    Kieser T, Bibb MJ, Buttner MJ, Chater KF, Hopwood DA (2000) Preparation and analysis of genomic and plasmid DNA. In: Practical Streptomyces genetics. The John Innes Foundation, Norwich, pp 161–171Google Scholar
  14. 14.
    Lanusse C, Lifschitz A, Virkel G, Alvarez L, Sánchez S, Sutra JF, Galtier P, Alvinerie M (1997) Comparative plasma disposition kinetic of ivermectin, moxidectin and doramectin in cattle. J Vet Pharmacol Ther 20:91–99PubMedCrossRefGoogle Scholar
  15. 15.
    Liu JJ, Ding WT, Zhang GC, Wang JY (2011) Improving ethanol fermentation performance of Saccharomyces cerevisiae in very high-gravity fermentation through chemical mutagensis. Appl Microbiol Biotechnol 91:1239–1246PubMedCrossRefGoogle Scholar
  16. 16.
    Lu Y, Cheng YF, He XP, Guo XN, Zhang BR (2012) Improvement of robustness and ethanol production of ethanologenic Saccharomyces cerevisiae under co-stress of heat and inhibitors. J Ind Microbiol Biotechnol 39:73–80PubMedCrossRefGoogle Scholar
  17. 17.
    Luo JM, Li JS, Liu D, Liu F, Wang YT, Song XR, Wang M (2012) Genome shuffling of Streptomyces gilvosporeus for improving natamycin production. J Agric Food Chem 60:6026–6036CrossRefGoogle Scholar
  18. 18.
    Lv X-A, Jin Y-Y, Li Y-D, Zhang H, Liang X-L (2013) Genome shuffling of Streptomyces viridochromogenes for improved production of avilamycin. Appl Microbiol Biotechnol 97(2):641–648PubMedCrossRefGoogle Scholar
  19. 19.
    Ochi K, Hosaka T (2012) New strategies for drug discovery: activation of silent or weakly expressed microbial gene clusters. Appl Microbiol Biotechnol. doi: 10.1007/s00253-012-4551-9 Google Scholar
  20. 20.
    Olano C, Lombó F, Méndez C, Salas JA (2008) Improving production of bioactive secondary metabolites in actinomycetes by metabolic engineering. Metab Eng 10:281–292PubMedCrossRefGoogle Scholar
  21. 21.
    Patnaik R, Louie S, Gavrilovic V, Perry K, Stemmer WP, Ryan CM, del Cardayré S (2002) Genome shuffling of Lactobacillus for improved acid tolerance. Nat Biotechnol 20:707–712PubMedCrossRefGoogle Scholar
  22. 22.
    Petri R, Schmidt-Dannert C (2004) Dealing with complexity: evolutionary engineering and genome shuffling. Curr Opin Biotechnol 15:298–304PubMedCrossRefGoogle Scholar
  23. 23.
    Pinel D, D’Aoust F, del Cardayre SB, Bajwa PK, Lee H, Martin VJ (2011) Saccharomyces cerevisiae genome shuffling through recursive population mating leads to improved tolerance to spent sulfite liquor. Appl Environ Microbiol 77:4736–4743PubMedCrossRefGoogle Scholar
  24. 24.
    Stephanopoulos G (2002) Metabolic engineering by genome shuffling-two reports on whole-genome shuffling demonstrate the application of combinatorial methods for phenotypic improvement in bacteria. Nat Biotechnol 20:666–668PubMedCrossRefGoogle Scholar
  25. 25.
    Stutzman-Engwall K, Conlon S, Fedechko R, Kaczmarek F, McArthur H, Krebber A, Chen Y, Minshull J, Raillard SA, Gustafsson C (2003) Engineering the aveC gene to enhance the ratio of doramectin to its CHC-B2 analogue produced in Streptomyces avermitilis. Biotechnol Bioeng 82:359–369PubMedCrossRefGoogle Scholar
  26. 26.
    Stutzman-Engwall K, Conlon S, Fedechko R, McArthur H, Pekrun K, Chen Y, Jenne S, La C, Trinh N, Kim S, Zhang YX, Fox R, Gustafsson C, Krebber A (2005) Semi-synthetic DNA shuffling of aveC leads to improved industrial scale production of doramectin by Streptomyces avermitilis. Metab Eng 7:27–37PubMedCrossRefGoogle Scholar
  27. 27.
    Tanaka Y, Komoru M, Okamoto S, Tokuyama S, Kaji A, Ikeda H, Ochi K (2009) Antibiotic overproduction by rpsL and rsmG mutants of various actinomycetes. Appl Environ Microbiol 75:4919–4922PubMedCrossRefGoogle Scholar
  28. 28.
    Tao X, Zheng D, Liu T, Wang P, Zhao W, Zhu M, Jiang X, Zhao Y, Wu X (2012) A novel strategy to construct yeast Saccharomyces cerevisiae strains for very high gravity fermentation. PLoS ONE 7(2):e31235PubMedCrossRefGoogle Scholar
  29. 29.
    Wang G, Inaoka T, Okamoto S, Ochi K (2009) A novel insertion mutation in Streptomyces coelicolor ribosomal S12 protein results in paromomycin resistance and antibiotic overproduction. Antimicrob Agents Chemother 53(3):1019–1026PubMedCrossRefGoogle Scholar
  30. 30.
    Wang H, Zhang J, Wang XJ, Qi W, Dai YJ (2012) Genome shuffling improves production of the low-temperature alkalophilic lipase by Acinetobacter johnsonii. Biotechnol Lett 34:145–151PubMedCrossRefGoogle Scholar
  31. 31.
    Wang J-B, Pan H-X, Tang G-L (2011) Production of doramectin by rational engineering of the avermectin biosynthetic pathway. Bioorg Med Chem Lett 21:3320–3323PubMedCrossRefGoogle Scholar
  32. 32.
    Wang M, Yang X-H, Wang J-D, Wang X-J, Chen Z-J, Xiang W-S (2009) New β-class milbemycin compound from Streptomyces avermitilis NEAU1069: fermentation, isolation and structure elucidation. J Antibiot 62:587–591PubMedCrossRefGoogle Scholar
  33. 33.
    Wang PM, Zheng DQ, Liu TZ, Tao XL, Feng MG, Min H, Jiang XH, Wu XC (2012) The combination of glycerol metabolic engineering and drug resistance marker-aided genome shuffling to improve very-high-gravity fermentation performances of industrial Saccharomyces cerevisiae. Bioresource Technol 108:203–210CrossRefGoogle Scholar
  34. 34.
    Wang X-J, Wang M, Wang J-D, Jiang L, Wang J-J, Xiang W-S (2010) Isolation and identification of novel macrocyclic lactones from Streptomyces avermitilis NEAU1069 with acaricidal and nematocidal activity. J Agric Food Chem 58:2710–2714PubMedCrossRefGoogle Scholar
  35. 35.
    Wang XJ, Wang XC, Xiang WS (2009) Improvement of milbemycin-producing Streptomyces bingchenggensis by rational screening of ultraviolet- and chemically induced mutants. World J Microbiol Biotechnol 25:1051–1056CrossRefGoogle Scholar
  36. 36.
    Wang Y, Li Y, Pei X, Yu L, Feng Y (2007) Genome-shuffling improved acid tolerance and L-lactic acid volumetric productivity in Lactobacillus rhamnosus. J Biotechnol 129:510–515PubMedCrossRefGoogle Scholar
  37. 37.
    Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535PubMedCrossRefGoogle Scholar
  38. 38.
    Xu B, Jin Z, Wang H, Jin Q, Jin X, Cen P (2008) Evolution of Streptomyces pristinaespiralis for resistance and production of pristinamycin by genome shuffling. Appl Microbiol Biotechnol 80:261–267PubMedCrossRefGoogle Scholar
  39. 39.
    Xu D, Pan L, Zhao H, Zhao M, Sun J, Liu D (2011) Breeding and identification of novel koji molds with high activity of acid protease by genome recombination between Aspergillus oryzae and Aspergillus niger. J Ind Microbiol Biotechnol 38:1255–1265PubMedCrossRefGoogle Scholar
  40. 40.
    Xu F, Jin H, Li H, Tao L, Wang J, Lv J, Chen S (2012) Genome shuffling of Trichoderma viride for enhanced cellulase production. Ann Microbiol 62:509–515CrossRefGoogle Scholar
  41. 41.
    Zhang YX, Perry K, Vinci VA, Powell K, Stemmer WP, del Cardayré SB (2002) Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature 415:644–646PubMedCrossRefGoogle Scholar
  42. 42.
    Zhao J, Li Y, Zhang C, Yao Z, Zhang L, Bie X, Lu F, Lu Z (2012) Genome shuffling of Bacillus amyloliquefaciens for improving antimicrobial lipopeptide production and an analysis of relative gene expression using FQ RT-PCR. J Ind Microbiol Biotechnol 39:889–896PubMedCrossRefGoogle Scholar
  43. 43.
    Zheng D-Q, Wu X-C, Wang P-M, Chi X-Q, Tao X-L, Li P, Jiang X-H, Zhao Y-H (2011) Drug resistance marker-aided genome shuffling to improve acetic acid tolerance in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 38:415–422PubMedCrossRefGoogle Scholar
  44. 44.
    Zheng H, Gong J, Chen T, Chen X, Zhao X (2010) Strain improvement of Sporolactobacillus inulinus ATCC 15538 for acid tolerance and production of d-lactic acid by genome shuffling. Appl Microbiol Biotechnol 85:1541–1549PubMedCrossRefGoogle Scholar

Copyright information

© Society for Industrial Microbiology and Biotechnology 2013

Authors and Affiliations

  • Ji Zhang
    • 1
  • Xiangjing Wang
    • 1
  • Jinna Diao
    • 1
  • Hairong He
    • 1
  • Yuejing Zhang
    • 1
  • Wensheng Xiang
    • 1
  1. 1.College of Life ScienceNortheast Agricultural UniversityHarbinPeople’s Republic of China

Personalised recommendations