Advertisement

Applied Microbiology and Biotechnology

, Volume 98, Issue 18, pp 7935–7948 | Cite as

GlnR-mediated regulation of nitrogen metabolism in the actinomycete Saccharopolyspora erythraea

  • Li-Li Yao
  • Cheng-Heng Liao
  • Gang Huang
  • Ying Zhou
  • Sebastien Rigali
  • Buchang Zhang
  • Bang-Ce YeEmail author
Applied microbial and cell physiology

Abstract

Nitrogen source sensing, uptake, and assimilation are central for growth and development of microorganisms which requires the participation of a global control of nitrogen metabolism-associated genes at the transcriptional level. In soil-dwelling antibiotic-producing actinomycetes, this role is played by GlnR, an OmpR family regulator. In this work, we demonstrate that SACE_7101 is the ortholog of actinomycetes’ GlnR global regulators in the erythromycin producer Saccharopolyspora erythraea. Indeed, the chromosomal deletion of SACE_7101 severely affects the viability of S. erythraea when inoculated in minimal media supplemented with NaNO3, NaNO2, NH4Cl, glutamine, or glutamate as sole nitrogen source. Combination of in silico prediction of cis-acting elements, subsequent in vitro (through gel shift assays) and in vivo (real-time reverse transcription polymerase chain reaction) validations of the predicted target genes revealed a very large GlnR regulon aimed at adapting the nitrogen metabolism of S. erythraea. Indeed, enzymes/proteins involved in (i) uptake and assimilation of ammonium, (ii) transport and utilization of urea, (iii) nitrite/nitrate, (iv) glutamate/glutamine, (v) arginine metabolism, (vi) nitric oxide biosynthesis, and (vii) signal transduction associated with the nitrogen source supplied have at least one paralog gene which expression is controlled by GlnR. Our work highlights a GlnR-binding site consensus sequence (t/gna/cAC-n6-GaAAc) which is similar although not identical to the consensus sequences proposed for other actinomycetes. Finally, we discuss the distinct and common features of the GlnR-mediated transcriptional control of nitrogen metabolism between S. erythraea and the model organism Streptomyces coelicolor.

Keywords

Actinomycetes Nitrogen metabolism GlnR regulator Erythromycin Nitrogen utilization 

Notes

Acknowledgments

This study was supported by the China NSF 21276079, SRFDP 20120074110009 of the Chinese Ministry of Education, the National Key Technologies R&D Programs (2007AA02Z331 and 2014AA021502), and the Fundamental Research Funds for the Central Universities. SR is a Research Associate of the FRS-FNRS (Belgium).

Supplementary material

253_2014_5878_MOESM1_ESM.pdf (304 kb)
ESM 1 (PDF 304 kb)

References

  1. Amin R, Reuther J, Bera A, Wohlleben W, Mast Y (2012) Novel GlnR-target gene, nnaR, is involved in nitrate/nitrite assimilation in Streptomyces coelicolor. Microbiology 158:1172–1182PubMedCrossRefGoogle Scholar
  2. Amon J, Brau T, Grimrath A, Hanler E, Hasselt K, Höller M, Jessberger N, Ott L, Szököl J, Titgemeyer F, Burkovski A (2008) Nitrogen control in Mycobacterium smegmatis: nitrogen-dependent expression of ammonium transport and assimilation proteins depends on the OmpR-type regulator GlnR. J Bacteriol 190:7108–7116PubMedCentralPubMedCrossRefGoogle Scholar
  3. Amon J, Titgemeyer F, Burkovski A (2010) Common patterns-unique features: nitrogen metabolism and regulation in Gram-positive bacteria. FEMS Microbiol Rev 34:588–605PubMedGoogle Scholar
  4. Elisabetta C, Clelia P, Salvatore MT, Francesco F, Adelfia T, Giorgio C, Silvio B, Gianluca DB, Pietro A (2009) Phenotypes and gene expression profiles of Saccharopolyspora erythraea rifampicin-resistant (rif) mutants affected in erythromycin production. Microb Cell Factories 8:18CrossRefGoogle Scholar
  5. Fink D, Weisschuh N, Reuther J, Wohlleben W, Engels A (2002) Two transcriptional regulators GlnR and GlnRII are involved in regulation of nitrogen metabolism in Streptomyces coelicolor A3(2). Mol Microbiol 46:331–347PubMedCrossRefGoogle Scholar
  6. Hiard S, Marée R, Colson S, Hoskisson PA, Titgemeyer F, van Wezel GP, Joris B, Wehenkel L, Rigali S (2007) PREDetector: a new tool to identify regulatory elements in bacterial genomes. Biochem Biophys Res Commun 357:861–864PubMedCrossRefGoogle Scholar
  7. Kloosterman TG, Hendriksen WT, Bijlsma JJ, Bootsma HJ, van Hijum SA, Kok J, Hermans PW, Kuipers OP (2006) Regulation of glutamine and glutamate metabolism by GlnR and GlnA in Streptococcus pneumoniae. J Biol Chem 281:25097–25109PubMedCrossRefGoogle Scholar
  8. Li YY, Chang X, Yu WB, Li H, Ye ZQ, Yu H, Liu BH, Zhang Y, Zhang SL, Ye BC, Li YX (2013) Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains. BMC Genomics 14:523PubMedCentralPubMedCrossRefGoogle Scholar
  9. Liu H, Huang XD, Liu DQ, Zhao W, Fan W, Han S, Zhang BC (2009) Rapid chromosomic gene inactivating technology of Saccharopolyspora erythraea. Bull Acad Mil Med Sci 33:365–369Google Scholar
  10. Martín JF, Sola-Landa A, Santos-Beneit F, Fernández-Martínez LT, Prieto C, Rodríguez-García A (2011) Cross-talk of global nutritional regulators in the control of primary and secondary metabolism in Streptomyces. Microbiol Biotechnol 4:165–174CrossRefGoogle Scholar
  11. Oliynyk M, Samborskyy M, Lester JB, Mironenko T, Scott N, Dickens S, Haydock SF, Leadlay PF (2007) Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338. Nat Biotechnol 25:447–453PubMedCrossRefGoogle Scholar
  12. Potvin J, Peringer P (1994) Ammonium regulation in Saccharopolyspora erythraea. Biotechnol Lett 16:63–68CrossRefGoogle Scholar
  13. Pullan ST, Chandra G, Bibb MJ, Merrick M (2011) Genome-wide analysis of the role of GlnR in Streptomyces venezuelae provides new insights into global nitrogen regulation in actinomycetes. BMC Genomics 12:175PubMedCentralPubMedCrossRefGoogle Scholar
  14. Reeve M, Baumberg S (1998) Physiological controls of erythromycin production by Saccharopolyspora erythraea are exerted at least in part at the level of transcription. Biotechnol Lett 20:585–589CrossRefGoogle Scholar
  15. Reuther J, Wohlleben W (2007) Nitrogen metabolism in Streptomyces coelicolor: transcriptional and post-translational regulation. J Mol Microbiol Biotechnol 12:139–146PubMedCrossRefGoogle Scholar
  16. Rigali S, Titgemeyer F, Barends S, Mulder S, Thomae AW, Hopwood DA, van Wezela GP (2008) Feast or famine: the global regulator DasR links nutrient stress to antibiotic production by Streptomyces. EMBO Rep 9:670–675PubMedCentralPubMedCrossRefGoogle Scholar
  17. 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 67:861–880PubMedCrossRefGoogle Scholar
  18. 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 89:1149–1159PubMedCrossRefGoogle Scholar
  19. van Wezela GP, McDowall KJ (2011) The regulation of the secondary metabolism of Streptomyces: new links and experimental advances. Nat Prod Rep 28:1311–1333CrossRefGoogle Scholar
  20. Wang J, Zhao GP (2009) GlnR positively regulates nasA transcription in Streptomyces coelicolor. Biochem Biophys Res Commun 386:77–81PubMedCrossRefGoogle Scholar
  21. Weiss V, Kramer G, Dunnebier T, Flotho A (2002) Mechanism of regulation of the bifunctional histidine kinase NtrB in Escherichia coli. J Mol Microbiol Biotechnol 4:229–233PubMedGoogle Scholar
  22. Yoshida K, Yamaguchi H, Kinehara M, Ohki YH, Nakaura Y, Fujita Y (2003) Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box. Mol Microbiol 49:157–165PubMedCrossRefGoogle Scholar
  23. Yu H, Yao Y, Liu Y, Jiao R, Jiang W, Zhao GP (2007) A complex role of Amycolatopsis mediterranei GlnR in nitrogen metabolism and related antibiotics production. Arch Microbiol 188:89–96PubMedCrossRefGoogle Scholar
  24. Zou X, Hang H, Chu J, Zhuang Y, Zhang S (2009) Enhancement of erythromycin A production with feeding available nitrogen sources in erythromycin biosynthesis phase. Bioresour Technol 100:3358–3365PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Li-Li Yao
    • 1
  • Cheng-Heng Liao
    • 1
  • Gang Huang
    • 1
  • Ying Zhou
    • 1
  • Sebastien Rigali
    • 2
  • Buchang Zhang
    • 3
  • Bang-Ce Ye
    • 1
    Email author
  1. 1.Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghaiChina
  2. 2.Centre for Protein Engineering, Institut de Chimie B6aUniversity of LiègeLiègeBelgium
  3. 3.Institute of Health Sciences, School of Life SciencesAnhui UniversityHefeiChina

Personalised recommendations