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Enhancement of antibiotic productions by engineered nitrate utilization in actinomycetes

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Abstract

Nitrate is necessary for primary and secondary metabolism of actinomycetes and stimulates the production of a few antibiotics, such as lincomycin and rifamycin. However, the mechanism of this nitrate-stimulating effect was not fully understood. Two putative ABC-type nitrate transporters were identified in Streptomyces lincolnensis NRRL2936 and verified to be involved in lincomycin biosynthesis. With nitrate supplementation, the transcription of nitrogen assimilation genes, nitrate-specific ABC1 transporter genes, and lincomycin exporter gene lmrA was found to be enhanced and positively regulated by the global regulator GlnR, whose expression was also improved. Moreover, heterologous expression of ABC2 transporter genes in Streptomyces coelicolor M145 resulted in an increased actinorhodin production. Further incorporation of a nitrite-specific transporter gene nirC, as in nirC-ABC2 cassette, led to an even higher actinorhodin production. Similarly, the titers of salinomycin, ansamitocin, lincomycin, and geldanamycin were increased with the integration of this cassette to Streptomyces albus BK3-25, Actinosynnema pretiosum ATCC31280, S. lincolnensis LC-G, and Streptomyces hygroscopicus XM201, respectively. Our work expanded the nitrate-stimulating effect to many antibiotic producers by utilizing the nirC-ABC2 cassette for enhanced nitrate utilization, which could become a general tool for titer increase of antibiotics in actinomycetes.

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References

  • Amin R, Reuther J, Bera A, Wohlleben W, Mast Y (2012) A novel GlnR target gene, nnaR, is involved in nitrate/nitrite assimilation in Streptomyces coelicolor. Microbiology 158(Pt 5):1172–1182

  • Bentley SD, Chater KF, Cerdeñotárraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417(6885):141–147

    Article  PubMed  Google Scholar 

  • Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117(19):5179–5197

    Article  CAS  Google Scholar 

  • Fukuda M, Takeda H, Kato HE, Doki S, Ito K, Maturana AD, Ishitani R, Nureki O (2015) Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK. Nat Commun 6:7097

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Harder W, Dijkhuizen L (1983) Physiological responses to nutrient limitation. Annu Rev Microbiol 37(1):1–23

    Article  CAS  PubMed  Google Scholar 

  • Ivanova N, Sikorski J, Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Del Rio TG, Nolan M (2009) Complete genome sequence of Sanguibacter keddieii type strain (ST-74T). Stand Genomic Sci 1(2):110–118

    Article  PubMed  PubMed Central  Google Scholar 

  • Janata J, Kadlcik S, Koberska M, Ulanova D, Kamenik Z, Novak P, Kopecky J, Novotna J, Radojevic B, Plhackova K, Gazak R, Najmanova L (2015) Lincosamide synthetase-a unique condensation system combining elements of nonribosomal peptide synthetase and mycothiol metabolism. PLoS One 10(3):e0118850

    Article  PubMed  PubMed Central  Google Scholar 

  • Jenkins VA, Barton GR, Robertson BD, Williams KJ (2013) Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis. BMC Genomics 14(1):301

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jiang C, Wang H, Kang Q, Liu J, Bai L (2012) Cloning and characterization of the polyether salinomycin biosynthesis gene cluster of Streptomyces albus XM211. Appl Environ Microb 78(4):994–1003

    Article  CAS  Google Scholar 

  • Jin Z, Jiao R (1996) Stimulative effects of nitrate and magnesium salts on biosynthesis of lincomycin by Streptomyces lincolnensis. Chinese Biochem J 13(6):709–715

    Google Scholar 

  • Kang Q, Shen Y, Bai L (2012) Biosynthesis of 3,5-AHBA-derived natural products. Nat Prod Rep 29(2):243–263

    Article  CAS  PubMed  Google Scholar 

  • Kieser T, Bibb MJ, Buttner MJ, Charter KF, Hopwood DA (2000) Practical Streptomyces Genetics

  • Kitani S, Miyamoto KT, Takamatsu S, Herawati E, Iguchi H, Nishitomi K, Uchida M, Nagamitsu T, Omura S, Ikeda H, Nihira T (2011) Avenolide, a Streptomyces hormone controlling antibiotic production in Streptomyces avermitilis. Proc Natl Acad Sci U S A 108(39):16410–16415

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li X, Chu J, Zhang SL, Hang HF, Zhuang YP, Ge YQ (2008) Effects of biotin and amino acids on biosynthesis of lincomycin. Chinese J Antibiot 33(1):6–10

  • Liao C-H, Yao L, Xu Y, Liu W-B, Zhou Y, Ye B-C (2015) Nitrogen regulator GlnR controls uptake and utilization of non-phosphotransferase-system carbon sources in actinomycetes. Proc Natl Acad Sci U S A 112(51):15630–15635

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lillo C (1984) Diurnal variations of nitrite reductase, glutamine synthetase, glutamate synthase, alanine aminotransferase and aspartate aminotransferase in barley leaves. Physiol Plantarum 61(2):214–218

    Article  CAS  Google Scholar 

  • Lin C-I, Sasaki E, Zhong A, Liu H-W (2014) In vitro characterization of LmbK and LmbO: identification of GDP-D-erythro-α-D-gluco-octose as a key intermediate in lincomycin A biosynthesis. J Am Chem Soc 136(3):906–909

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu J, Chen Y, Wang W, Ren M, Wu P, Wang Y, Li C, Zhang LX, Wu H, Weaver DT, Zhang BC (2017) Engineering of an Lrp family regulator SACE_Lrp improves erythromycin production in Saccharopolyspora erythraea. Metab Eng 39:29–37

    Article  PubMed  Google Scholar 

  • Lü W, Schwarzer NJ, Du J, Gerbig-Smentek E, Andrade SL, Einsle O (2012) Structural and functional characterization of the nitrite channel NirC from Salmonella typhimurium. Proc Natl Acad Sci U S A 109(45):18395–18400

    Article  PubMed  PubMed Central  Google Scholar 

  • Peschke U, Schmidt H, Zhang HZ, Piepersberg W (1995) Molecular characterization of the lincomycin-production gene cluster of Streptomyces lincolnensis 78-11. Mol Microbiol 16(6):1137–1156

    Article  CAS  PubMed  Google Scholar 

  • Qiu J, Zhuo Y, Zhu D, Zhou X, Zhang L, Bai L, Deng Z (2011) Overexpression of the ABC transporter AvtAB increases avermectin production in Streptomyces avermitilis. Appl Microbiol Biotechnol 92(2):337–345

    Article  CAS  PubMed  Google Scholar 

  • Reuther J, Wohlleben W (2007) Nitrogen metabolism in Streptomyces coelicolor: transcriptional and post-translational regulation. J Mol Microb Biotech 12(1–2):139–146

    CAS  Google Scholar 

  • Rowe JJ, Ubbink-Kok T, Molenaar D, Konings WN, Driessen A (1994) Nark is a nitrite-extrusion system involved in anaerobic nitrate respiration by Escherichia coli. Mol Microbiol, 12: 579–586

  • Sanz-Luque E, Chamizo-Ampudia A, Llamas A, Galvan A, Fernandez E (2015) Understanding nitrate assimilation and its regulation in microalgae. Front Plant Sci 6:899

    Article  PubMed  PubMed Central  Google Scholar 

  • Sasaki E, Lin CI, Lin KY, Liu HW (2012) Construction of the octose 8-phosphate intermediate in lincomycin A biosynthesis: characterization of the reactions catalyzed by LmbR and LmbN. J Am Chem Soc 134(42):17432–17435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sekurova ON, Brautaset T, Sletta H, Borgos SEF, Jakobsen ØM, Ellingsen TE, Strøm AR, Valla S, Zotchev SB (2004) In vivo analysis of the regulatory genes in the nystatin biosynthetic gene cluster of Streptomyces noursei ATCC 11455 reveals their differential control over antibiotic biosynthesis. J Bacteriol 186(5):1345–1354

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shao Z, Gao J, Ding X, Wang J, Chiao J, Zhao G (2011) Identification and functional analysis of a nitrate assimilation operon nasACKBDEF from Amycolatopsis mediterranei U32. Arch Microbiol 193(7):463–477

    Article  CAS  PubMed  Google Scholar 

  • Shao ZH, Ren SX, Liu XQ, Xu J, Yan H, Zhao GP, Wang J (2015) A preliminary study of the mechanism of nitrate-stimulated remarkable increase of rifamycin production in Amycolatopsis mediterranei U32 by RNA-seq. Microb Cell Factories 14(1):75

    Article  Google Scholar 

  • Sola-Landa A, Rodríguez-García A, Amin R, Wohlleben W, Martín JF (2012) Competition between the GlnR and PhoP regulators for the glnA and amtB promoters in Streptomyces coelicolor. Nucleic Acids Res 41(3):1767–1782

    Article  PubMed  PubMed Central  Google Scholar 

  • Tiffert Y, Supra P, Wurm R, Wohlleben W, Wagner R, Reuther J (2008) The Streptomyces coelicolor GlnR regulon: identification of new GlnR targets and evidence for a central role of GlnR in nitrogen metabolism in actinomycetes. Mol Microbiol 67(4):861–880

    Article  CAS  PubMed  Google Scholar 

  • Tiffert Y, Franz-Wachtel M, Fladerer C, Nordheim A, Reuther J, Wohlleben W, Mast Y (2011) Proteomic analysis of the GlnR-mediated response to nitrogen limitation in Streptomyces coelicolor M145. Appl Microbiol Biotechnol 89(4):1149–1159

    Article  CAS  PubMed  Google Scholar 

  • Van Keulen G, Alderson J, White J, Sawers R (2005) Nitrate respiration in the actinomycete Streptomyces coelicolor. Biochem Soc Trans 33(1):210–212

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Zhao G-P (2009) GlnR positively regulates nasA transcription in Streptomyces coelicolor. Biochem Biophys Res Commun 386(1):77–81

    Article  CAS  PubMed  Google Scholar 

  • Wang R, Mast Y, Wang J, Zhang W, Zhao G, Wohlleben W, Lu Y, Jiang W (2013a) Identification of two-component system AfsQ1/Q2 regulon and its cross-regulation with GlnR in Streptomyces coelicolor. Mol Microbiol 87(1):30–48

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Wang J-Z, Shao Z-H, Yuan H, Lu Y-H, Jiang W-H, Zhao G-P, Wang J (2013b) Three of four GlnR binding sites are essential for GlnR-mediated activation of transcription of the Amycolatopsis mediterranei nas operon. J Bacteriol 195(11):2595–2602

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Li C, Duan N, Li B, Ding XM, Yao YF, Hu J, Zhao GP, Wang J (2014) GlnR negatively regulates the transcription of the alanine dehydrogenase encoding gene ald in Amycolatopsis mediterranei U32 under nitrogen limited conditions via specific binding to its major transcription initiation site. PLoS One 9(8):e104811

    Article  PubMed  PubMed Central  Google Scholar 

  • Wray LV, Fisher SH (1993) The Streptomyces coelicolor glnR gene encodes a protein similar to other bacterial response regulators. Gene 130(1):145–150

    Article  CAS  PubMed  Google Scholar 

  • Yan H, Huang W, Yan C, Gong X, Jiang S, Zhao Y, Wang J, Shi Y (2013) Structure and mechanism of a nitrate transporter. Cell Rep 301(3):716–723

    Article  Google Scholar 

  • Yao LL, Ye BC (2015) Reciprocal regulation of GlnR and PhoP in response to nitrogen and phosphate limitations in Saccharopolyspora erythraea. Appl Environ Microbiol 82(1):409–420

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang YQ, Chen J, Liu HY, Zhang YQ, Li WJ, Yu LY (2011) Geodermatophilus ruber sp. nov., isolated from rhizosphere soil of a medicinal plant. Int J Syst Evol Microbiol 61(1):190–193

    Article  CAS  PubMed  Google Scholar 

  • Zhao W, Zhong Y, Yuan H, Wang J, Zheng H, Wang Y, Cen X, Xu F, Bai J, Han X, Lu G, Zhu Y, Shao Z, Yan H, Li C, Peng N, Zhang Z, Zhang Y, Lin W, Fan Y, Qin Z, Hu Y, Zhu B, Wang S, Ding X, Zhao GP (2010) Complete genome sequence of the rifamycin SV-producing Amycolatopsis mediterranei U32 revealed its genetic characteristics in phylogeny and metabolism. Cell Res 20(10):1096–1108

    Article  CAS  PubMed  Google Scholar 

  • Zhao Q, Wang M, Xu D, Zhang Q, Liu W (2015) Metabolic coupling of two small-molecule thiols programs the biosynthesis of lincomycin A. Nature 518(7537):115–119

    Article  CAS  PubMed  Google Scholar 

  • Zheng H, Wisedchaisri G, Gonen T (2013) Crystal structure of a nitrate/nitrite exchanger. Nature 497(7451):647–651

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (No. 31401056, 31300081, 21661140002, 31470157, 31400030), the Ministry of Science and Technology of China (No. 2012CB721005), and the Open Funding Project of State Key Laboratory of Microbial Metabolism.

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Correspondence to Linquan Bai.

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Meng, S., Wu, H., Wang, L. et al. Enhancement of antibiotic productions by engineered nitrate utilization in actinomycetes. Appl Microbiol Biotechnol 101, 5341–5352 (2017). https://doi.org/10.1007/s00253-017-8292-7

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