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Metabolic Flux Analysis and Principal Nodes Identification for Daptomycin Production Improvement by Streptomyces roseosporus

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Abstract

In the present work, a comprehensive metabolic network of Streptomyces roseosporus LC-54-20 was proposed for daptomycin production. The analysis of extracellular metabolites throughout the batch fermentation was evaluated in addition to daptomycin and biomass production. Metabolic flux distributions were based on stoichiometrical reaction as well as the extracellular metabolites fluxes. Experimental and calculated values for both the specific growth rate and daptomycin production rate indicated that the in silico model proved a powerful tool to analyze the metabolic behaviors based on the analysis under different initial glucose concentrations throughout the fermentation. Through manipulating different pH values, the production rates of various extracellular metabolites were also presented in this paper. Flux distribution variations revealed that the daptomycin production could be significantly influenced by the branch points of glucose 6-phosphate, 3-phosphoglycerate, phosphoenolpyruvate, pyruvate, and oxaloacetate. The five principal metabolites were certified as the flexible nodes and could form potential bottlenecks for a further enhancement of daptomycin production. Furthermore, various concentrations of the five precursors were added into the batch fermentation and led to the enhancement of daptomycin concentration and production rate.

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References

  1. Eliopoulos, G. M. (2009). Microbiology of drugs for treating multiply drug-resistant Gram-positive bacteria. Journal of Infection, 59, s17–s24.

    Article  Google Scholar 

  2. Nailor, M. D., & Sobel, J. D. (2009). Antibiotics for gram-positive bacterial infections: Vancomycin, teicoplanin, quinupristin/dalfopristin, oxazolidinones, daptomycin, dalbavancin, and telavancin. Infectious Disease Clinics of North America, 23, 965–982.

    Article  Google Scholar 

  3. Hojati, Z., Milne, C., Harvey, B., Gordon, L., Borg, M., Flett, F., et al. (2002). Structure, biosynthetic origin, and engineered biosynthesis of calcium-dependent antibiotics from Streptomyces coelicolor. Chemistry & Biology, 9, 1175–1187.

    Article  CAS  Google Scholar 

  4. Vertesy, L., Ehlers, E., Kogler, H., Kurz, M., Meiwes, J., Seibert, G., et al. (2000). Friulimicins: novel lipopeptide antibiotics with peptidoglycan synthesis inhibiting activity from Actinoplanes friuliensis sp. nov. II. Isolation and structural characterization. The Journal of Antibiotics, 53, 816–827.

    CAS  Google Scholar 

  5. Miao, V., Brost, R., Chapple, J., She, K., Gal, M. F., & Baltz, R. H. (2006). The lipopeptide antibiotic A54145 biosynthetic gene cluster from Streptomyces fradiae. Journal of Industrial Microbiology and Biotechnology, 33, 129–140.

    Article  CAS  Google Scholar 

  6. Borders, D. B., Leese, R. A., Jarolmen, H., Francis, N. D., Fantini, A. A., Falla, T., et al. (2007). Laspartomycin, an acidic lipopeptide antibiotic with a unique peptide core. Journal of Natural Products, 70, 443–446.

    Article  CAS  Google Scholar 

  7. Baltz, R. H. (2008). Biosynthesis and genetic engineering of lipopeptide antibiotics related to daptomycin. Current Topics in Medicinal Chemistry, 8, 618–638.

    Article  CAS  Google Scholar 

  8. Alper, H., Jin, Y. S., Moxley, J. F., & Stephanopoulos, G. (2005). Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metabolic Engineering, 7, 155–164.

    Article  CAS  Google Scholar 

  9. David, H., Ozçelik, I. S., Hofmann, G., & Nielsen, J. (2008). Analysis of Aspergillus nidulans metabolism at the genome-scale. BMC Genomics, 9, 163.

    Article  Google Scholar 

  10. Boyle, N. R., & Morgan, J. A. (2009). Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii. BMC Systems Biology, 3, 4.

    Google Scholar 

  11. Lee, S. J., Lee, D. Y., Kim, T. Y., Kim, B. H., Lee, J., & Lee, S. Y. (2005). Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation. Applied and Environmental Microbiology, 71, 7880–7887.

    Article  CAS  Google Scholar 

  12. Mukhopadhyay, A., Redding, A. M., Rutherford, B. J., & Keasling, J. D. (2008). Importance of systems biology in engineering microbes for biofuel production. Current Opinion in Biotechnology, 19, 228–234.

    Article  CAS  Google Scholar 

  13. Gunnarsson, N., Eliasson, A., & Nielsen, J. (2004). Control of fluxes towards antibiotics and the role of primary metabolism in production of antibiotics. Advances in Biochemical Engineering/Biotechnology, 88, 137–178.

    CAS  Google Scholar 

  14. Borodina, I., Siebring, J., Zhang, J., Smith, C. P., van Keulen, G., Dijkhuizen, L., et al. (2008). Antibiotic overproduction in Streptomyces coelicolor A3(2) mediated by phosphofructokinase deletion. The Journal of Biological Chemistry, 283, 25186–25199.

    Article  CAS  Google Scholar 

  15. Huber, F. M., Pieper, R. L., & Tietz, A. J. (1988). The formation of daptomycin by supplying decanoic acid to Streptomyces roseosporus cultures producing the antibiotic complex A21978C. Journal of Biotechnology, 7, 283–292.

    Article  CAS  Google Scholar 

  16. Vallino, J. J., & Stephanopoulos, G. (1993). Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproduction. Biotechnology and Bioengineering, 41, 633–646.

    Article  CAS  Google Scholar 

  17. Vallino, J. J., & Stephanopoulos, G. (1994). Carbon flux distributions at the pyruvate branch point in Corynebacterium glutamicum during lysine overproduction. Biotechnology Progress, 10, 320–326.

    Article  CAS  Google Scholar 

  18. Kim, H. B., Smith, C. P., Micklefield, J., & Mavituna, F. (2004). Metabolic flux analysis for calcium dependent antibiotic (CDA) production in Streptomyces coelicolor. Metabolic Engineering, 6, 313–325.

    Article  CAS  Google Scholar 

  19. Blank, L. M., & Kuepfer, L. (2010). Metabolic flux distributions: Genetic information, computational predictions, and experimental validation. Applied Microbiology and Biotechnology, 86, 1243–1255.

    Article  CAS  Google Scholar 

  20. Melzer, G., Dalpiaz, A., Grote, A., Kucklick, M., Göcke, Y., Jonas, R., et al. (2007). Metabolic flux analysis using stoichiometric models for Aspergillus niger: Comparison under glucoamylase-producing and non-producing conditions. Journal of Biotechnology, 132, 405–417.

    Article  CAS  Google Scholar 

  21. Xu, H., Dou, W. F., Xu, H. Y., Zhang, X. M., Rao, Z. M., Shi, Z. P., et al. (2009). A two-stage oxygen supply strategy for enhanced l-arginine production by Corynebacterium crenatum based on metabolic fluxes analysis. Biochemical Engineering Journal, 43, 41–51.

    Article  CAS  Google Scholar 

  22. Celik, E., Calik, P., & Oliver, S. G. (2010). Metabolic flux analysis for recombinant protein production by Pichia pastoris using dual carbon sources: Effects of methanol feeding rate. Biotechnology and Bioengineering, 105, 317–329.

    Article  CAS  Google Scholar 

  23. Sauer, U., & Eikmanns, B. J. (2005). The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria. FEMS Microbiology Reviews, 29, 765–794.

    Article  CAS  Google Scholar 

  24. Gao, H. J., Du, G. C., & Chen, J. (2006). Analysis of metabolic fluxes for hyaluronic acid (HA) production by Streptococcus zooepidemicus. World Journal of Microbiology and Biotechnology, 22, 399–408.

    Article  CAS  Google Scholar 

  25. Nie, Z. K., Ji, X. J., Huang, H., Du, J., Li, Z. Y., Qu, L., et al. (2011). An effective and simplified fed-batch strategy for improved 2,3-butanediol production by Klebsiella oxytoca. Applied Biochemistry and Biotechnology, 163, 946–953.

    Article  CAS  Google Scholar 

  26. Ji, X. J., Huang, H., Li, S., Du, J., & Lian, M. (2008). Enhanced 2,3-butanediol production by altering the mixed acid fermentation pathway in Klebsiella oxytoca. Biotechnology Letters, 30, 731–734.

    Article  CAS  Google Scholar 

  27. Miao, V., Coëffet-Legal, M. F., Brian, P., Brost, R., Penn, J., Whiting, A., et al. (2005). Daptomycin biosynthesis in Streptomyces roseosporus: Cloning and analysis of the gene cluster and revision of peptide stereochemistry. Microbiology, 151, 1507–1523.

    Article  CAS  Google Scholar 

  28. Yu, G., Jia, X., Wen, J., Lu, W., Wang, G., Caiyin, Q., et al. (2011). Strain improvement of Streptomyces roseosporus for daptomycin production by rational screening of He-Ne laser and NTG induced mutants and kinetic modeling. Applied Biochemistry and Biotechnology, 163, 729–743.

    Article  CAS  Google Scholar 

  29. Varma, A., & Palsson, B. O. (1994). Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Applied and Environmental Microbiology, 60, 3724–3731.

    CAS  Google Scholar 

  30. Gheshlaghi, R., Scharer, J. M., Moo-Young, M., & Douglas, P. L. (2007). Metabolic flux analysis for optimizing the specific growth rate of recombinant Aspergillus niger. Bioprocess and Biosystems Engineering, 30, 397–418.

    Article  CAS  Google Scholar 

  31. Madden, T., Ward, J. M., & Ison, A. P. (1996). Organic acid excretion by Streptomyces lividans TK24 during growth on defined carbon and nitrogen sources. Microbiology, 142, 3181–3185.

    Article  CAS  Google Scholar 

  32. Naeimpoor, F., & Mavituna, F. (2000). Metabolic flux analysis in Streptomyces coelicolor under various nutrient limitations. Metabolic Engineering, 2, 140–148.

    Article  CAS  Google Scholar 

  33. Pons, A., Dussap, C. G., Péquignot, C., & Gros, J. B. (1996). Metabolic flux distribution in Corynebacterium melassecola ATCC 17965 for various carbon sources. Biotechnology and Bioengineering, 51, 177–189.

    Article  Google Scholar 

  34. Fürch, T., Wittmann, C., Wang, W., Franco-Lara, E., Jahn, D., & Deckwer, W. D. (2007). Effect of different carbon sources on central metabolic fluxes and the recombinant production of a hydrolase from Thermobifida fusca in Bacillus megaterium. Journal of Biotechnology, 132, 385–394.

    Article  Google Scholar 

  35. Rokem, J. S., Lantz, A. E., & Nielsen, J. (2007). Systems biology of antibiotic production by microorganisms. Natural Product Reports, 24, 1262–1287.

    Article  CAS  Google Scholar 

  36. van Gulik, W. M., de Laat, W. T., Vinke, J. L., & Heijnen, J. J. (2000). Application of metabolic flux analysis for the identification of metabolic bottlenecks in the biosynthesis of penicillin-G. Biotechnology and Bioengineering, 68, 602–618.

    Article  Google Scholar 

Download references

Acknowledgments

The authors wish to acknowledge the financial support provided by the National 973 Project of China (No. 2011CB710800), the Key Program of National Natural Science Foundation of China (Grant No. 20936002), National Natural Science Foundation of China (No. 21076022).

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Authors and Affiliations

  1. Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People’s Republic of China

    Di Huang, Xiaoqiang Jia, Jianping Wen, Guoying Wang, Guanghai Yu & Qinggele Caiyin

  2. Key Laboratory of Systems Bioengineering (Tianjin University), Ministry of Education, Tianjin, 300072, People’s Republic of China

    Xiaoqiang Jia, Jianping Wen & Qinggele Caiyin

  3. School of Science, Beijing Jiaotong University, Beijing, 100044, People’s Republic of China

    Yunlin Chen

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  1. Di Huang
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  2. Xiaoqiang Jia
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Correspondence to Jianping Wen.

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Huang, D., Jia, X., Wen, J. et al. Metabolic Flux Analysis and Principal Nodes Identification for Daptomycin Production Improvement by Streptomyces roseosporus . Appl Biochem Biotechnol 165, 1725–1739 (2011). https://doi.org/10.1007/s12010-011-9390-0

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