Applied Microbiology and Biotechnology

, Volume 98, Issue 1, pp 351–360 | Cite as

Allantoin catabolism influences the production of antibiotics in Streptomyces coelicolor

  • Laura Navone
  • Paula Casati
  • Cuauhtémoc Licona-Cassani
  • Esteban Marcellin
  • Lars K. Nielsen
  • Eduardo Rodriguez
  • Hugo Gramajo
Genomics, transcriptomics, proteomics


Purines are a primary source of carbon and nitrogen in soil; however, their metabolism is poorly understood in Streptomyces. Using a combination of proteomics, metabolomics, and metabolic engineering, we characterized the allantoin pathway in Streptomyces coelicolor. When cells grew in glucose minimal medium with allantoin as the sole nitrogen source, quantitative proteomics identified 38 enzymes upregulated and 28 downregulated. This allowed identifying six new functional enzymes involved in allantoin metabolism in S. coelicolor. From those, using a combination of biochemical and genetic engineering tools, it was found that allantoinase (EC and allantoicase (EC are essential for allantoin metabolism in S. coelicolor. Metabolomics showed that under these growth conditions, there is a significant intracellular accumulation of urea and amino acids, which eventually results in urea and ammonium release into the culture medium. Antibiotic production of a urease mutant strain showed that the catabolism of allantoin, and the subsequent release of ammonium, inhibits antibiotic production. These observations link the antibiotic production impairment with an imbalance in nitrogen metabolism and provide the first evidence of an interaction between purine metabolism and antibiotic biosynthesis.


Streptomyces Allantoin Ammonium Antibiotic regulation 



This work was supported by ANPCyT grants PICT 2007–00711 to PC and PICT2008-644 to HG, Fundación Perez-Guerrero grant to ER and PIP 100764 from CONICET to ER. ER, PC, and HG are members of the Research Career and LN is a doctoral fellow of CONICET. CLC is a doctoral fellow of CONACYT. We kindly thank Dr. Alun Jones and Dr. Amanda Nouwens for LC-MS assistance and David Hopwood for helpful comments. All proteomics work was performed at the proteomics facility at IMB and/or SCMB. We thank Paul Dyson (Swansea University) for kindly providing the derivative cosmids carrying transposon insertions and Monica Hourcade (Universidad Nacional de Rosario) for technical assistance in the metabolomic analysis.

Conflict of interest

The authors declare no competing financial interests.

Supplementary material

253_2013_5372_MOESM1_ESM.pdf (348 kb)
ESM 1 (PDF 347 kb)


  1. Ashiuchi M, Misono H (1999) Biochemical evidence that Escherichia coli hyi (orf b0508, gip) gene encodes hydroxypyruvate isomerase. Biochim Biophys Acta 1435(1–2):153–159Google Scholar
  2. 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(6885):141–147PubMedCrossRefGoogle Scholar
  3. Brana AF, Wolfe S, Demain AL (1985) Ammonium repression of cephalosporin production by Streptomyces clavuligerus. Can J Microbiol 31(8):736–743PubMedCrossRefGoogle Scholar
  4. Brana AF, Wolfe S, Demain AL (1986) Relationship between nitrogen assimilation and cephalosporin synthesis in Streptomyces clavuligerus. Arch Microbiol 146(1):46–51PubMedCrossRefGoogle Scholar
  5. Bystrykh LV, Fernandez-Moreno MA, Herrema JK, Malpartida F, Hopwood DA, Dijkhuizen L (1996) Production of actinorhodin-related “blue pigments” by Streptomyces coelicolor A3(2). J Bacteriol 178(8):2238–2244PubMedCentralPubMedGoogle Scholar
  6. Doull JL, Vining LC (1990) Nutritional control of actinorhodin production by Streptomyces coelicolor A3(2): suppressive effects of nitrogen and phosphate. Appl Microbiol Biotechnol 32(4):449–454PubMedCrossRefGoogle Scholar
  7. Gupta NK, Vennesland B (1964) Glyoxylate carboligase of Escherichia coli: a flavoprotein. J Biol Chem 239:3787–3789PubMedGoogle Scholar
  8. Herron PR, Hughes G, Chandra G, Fielding S, Dyson PJ (2004) Transposon Express, a software application to report the identity of insertions obtained by comprehensive transposon mutagenesis of sequenced genomes: analysis of the preference for in vitro Tn5 transposition into GC-rich DNA. Nucleic Acids Res 32(14):e113PubMedCentralPubMedCrossRefGoogle Scholar
  9. Hobbs G, Frazer CM, Gardner DCJ, Flett F, Oliver SG (1990) Pigmented antibiotic production by Streptomyces coelicolor A3(2): kinetics and the influence of nutrients. Microbiology 136:2291–2296Google Scholar
  10. Hodgson DA (2000) Primary metabolism and its control in streptomycetes: a most unusual group of bacteria. Adv Microb Physiol 42:47–238PubMedCrossRefGoogle Scholar
  11. Kieser T, Bibb MJ, Buttner MJ, Chater KF, Hopwood DA (2000) Practical Streptomyces genetics, 2000th edn. Norwich, UKGoogle Scholar
  12. Loewen PC, Switala J (1986) Purification and characterization of catalase HPII from Escherichia coli K12. Biochem Cell Biol 64(7):638–646PubMedCrossRefGoogle Scholar
  13. Loke P, Sim TS (2000) Molecular cloning, heterologous expression, and functional characterisation of a malate synthase gene from Streptomyces coelicolor A3(2). Can J Microbiol 46(8):764–769PubMedGoogle Scholar
  14. Manteca A, Mader U, Connolly BA, Sanchez J (2006) A proteomic analysis of Streptomyces coelicolor programmed cell death. Proteomics 6(22):6008–6022PubMedCrossRefGoogle Scholar
  15. McIninch JK, McIninch JD, May SW (2003) Catalysis, stereochemistry, and inhibition of ureidoglycolate lyase. J Biol Chem 278(50):50091–50100PubMedCrossRefGoogle Scholar
  16. Molina I, Pellicer MT, Badia J, Aguilar J, Baldoma L (1994) Molecular characterization of Escherichia coli malate synthase G. Differentiation with the malate synthase A isoenzyme. FEBS J 224(2):541–548Google Scholar
  17. Mulrooney SB, Hausinger RP (2003) Metal ion dependence of recombinant Escherichia coli allantoinase. J Bacteriol 185(1):126–134PubMedCentralPubMedCrossRefGoogle Scholar
  18. Njau RK, Herndon CA, Hawes JW (2000) Novel beta -hydroxyacid dehydrogenases in Escherichia coli and Haemophilus influenzae. J Biol Chem 275(49):38780–38786PubMedCrossRefGoogle Scholar
  19. Nygaard P (1983) Utilization of preformed purine bases and nucleosides. In: Munch-Petersen A (ed) Metabolism of nucleotides, nucleosides and nucleobases in microorganisms. Academic, London, UK, pp 27–93Google Scholar
  20. Ohe T, Watanabe Y (1979) Purification and properties of xanthine dehydrogenase from Streptomyces cyanogenus. J Biochem 86(1):45–53PubMedGoogle Scholar
  21. Ohe T, Watanabe Y (1980) Purification and properties of hypoxanthine phosphoribosyltransferase from Streptomyces cyanogenus. Agric Biol Chem 44(9):1999–2006CrossRefGoogle Scholar
  22. Ohe T, Watanabe Y (1981) Purification and properties of urate oxidase from Streptomyces cyanogenus. J Biochem 89(6):1769–1776PubMedGoogle Scholar
  23. Omura S, Oiwa R (1984) Studies on bioactive compounds from microorganisms. Kitasato Arch Exp Med 57(2):75–204PubMedGoogle Scholar
  24. Omura S, Tanaka Y, Mamada H, Masuma R (1983) Ammonium ion suppresses the biosynthesis of tylosin aglycone by interference with valine catabolism in Streptomyces fradiae. J Antibiot (Tokyo) 36(12):1792–1794CrossRefGoogle Scholar
  25. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29(9):e45PubMedCentralPubMedCrossRefGoogle Scholar
  26. Piedras P, Munoz A, Aguilar M, Pineda M (2000) Allantoate amidinohydrolase (Allantoicase) from Chlamydomonas reinhardtii: its purification and catalytic and molecular characterization. Arch Biochem Biophys 378(2):340–348PubMedCrossRefGoogle Scholar
  27. Ramazzina I, Cendron L, Folli C, Berni R, Monteverdi D, Zanotti G, Percudani R (2008) Logical identification of an allantoinase analog (puuE) recruited from polysaccharide deacetylases. J Biol Chem 283(34):23295–23304Google Scholar
  28. Rodriguez E, Hu Z, Ou S, Volchegursky Y, Hutchinson CR, McDaniel R (2003) Rapid engineering of polyketide overproduction by gene transfer to industrially optimized strains. J Ind Microbiol Biotechnol 30(8):480–488PubMedCrossRefGoogle Scholar
  29. Rodriguez E, Navone L, Casati P, Gramajo H (2012) Impact of malic enzymes on antibiotic and triacylglycerol production in Streptomyces coelicolor. Appl Environ Microbiol 78(13):4571–4579PubMedCentralPubMedCrossRefGoogle Scholar
  30. Schultz AC, Nygaard P, Saxild HH (2001) Functional analysis of 14 genes that constitute the purine catabolic pathway in Bacillus subtilis and evidence for a novel regulon controlled by the PucR transcription activator. J Bacteriol 183(11):3293–3302PubMedCentralPubMedCrossRefGoogle Scholar
  31. Shen YQ, Heim J, Solomon NA, Wolfe S, Demain AL (1984) Repression of beta-lactam production in Cephalosporium acremonium by nitrogen sources. J Antibiot (Tokyo) 37(5):503–511CrossRefGoogle Scholar
  32. Shilov IV, Seymour SL, Patel AA, Loboda A, Tang WH, Keating SP, Hunter CL, Nuwaysir LM, Schaeffer DA (2007) The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol Cell Proteomics 6(9):1638–1655PubMedCrossRefGoogle Scholar
  33. Takada Y, Noguchi T (1983) The degradation of urate in liver peroxisomes. Association of allantoinase with allantoicase in amphibian liver but not in fish and invertebrate liver. J Biol Chem 258(8):4762–4764PubMedGoogle Scholar
  34. Trijbels F, Vogels GD (1966) Allantoicase and ureidoglycolase in Pseudomonas and Penicillium species. Biochim Biophys Acta 118(2):387–395PubMedCrossRefGoogle Scholar
  35. Tsao SW, Rudd BA, He XG, Chang CJ, Floss HG (1985) Identification of a red pigment from Streptomyces coelicolor A3(2) as a mixture of prodigiosin derivatives. J Antibiot (Tokyo) 38(1):128–131CrossRefGoogle Scholar
  36. Vogels GD, Van der Drift C (1976) Degradation of purines and pyrimidines by microorganisms. Bacteriol Rev 40(2):403–468PubMedCentralPubMedGoogle Scholar
  37. Wang P, Kong CH, Hu F, Xu XH (2007) Allantoin involved in species interactions with rice and other organisms in paddy soil. Plant Soil 296(1–2):43–51CrossRefGoogle Scholar
  38. Wang P, Kong C, Sun B, Xu X (2010) Allantoin-induced changes of microbial diversity and community in rice soil. Plant Soil 332(1–2):357–368CrossRefGoogle Scholar
  39. Watanabe Y (1971) Studies on the formation of uricase by Streptomyces. Part III. The Effect of incubation with or without purines. Agric Biol Chem 35(13):2008–2014CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Laura Navone
    • 1
  • Paula Casati
    • 2
  • Cuauhtémoc Licona-Cassani
    • 3
  • Esteban Marcellin
    • 3
  • Lars K. Nielsen
    • 3
  • Eduardo Rodriguez
    • 1
  • Hugo Gramajo
    • 1
  1. 1.Instituto de Biología Molecular y Celular de Rosario (IBR)Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de RosarioRosarioArgentina
  2. 2.Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-Consejo Nacional de Investigaciones Científicas y Técnicas), Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de RosarioRosarioArgentina
  3. 3.Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandBrisbaneAustralia

Personalised recommendations