, Volume 28, Issue 2, pp 381–389 | Cite as

Isolation and structure determination of new siderophore albachelin from Amycolatopsis alba

  • Shinya Kodani
  • Hisayuki Komaki
  • Masahiro Suzuki
  • Hikaru Hemmi
  • Mayumi Ohnishi-Kameyama


A new siderophore named albachelin was isolated from iron deficient culture of Amycolatopsis alba. The planar structure of albachelin was elucidated by the combination of ESI–MS/MS experiment and NMR spectroscopic analyses of the gallium (III) complex. The structure of albachelin was determined to be a linear peptide consisting of 6 mol of amino acids including 3 mol of serine, one mol each of N-α-acethyl-N-δ-hydroxy-N-δ-formylornithine, N-α-methyl-N-δ-hydroxyornithine, and cyclic N-hydroxyornithine. The stereochemistries of amino acids constituting albachelin were analyzed by applying modified Marfey method to the hydrolysate of albachelin. Based on bioinformatics, we deduced and discussed the possible biosynthetic gene cluster involved in albachelin biosynthesis from the genome sequence of A. alba. By prediction of substrates for adenylation domains, a non-ribosomal peptide biosynthetase gene (AMYAL_RS0130210) was proposed to be the main biosynthetic gene for albachelin biosynthesis. The related genes including transporter for siderophore were found near the NRPS gene as a gene cluster.


Siderophore Amycolatopsis alba Peptide Biosynthesis 



This study was supported by the Japan Society for the Promotion of Science by Grants-in-aids (Grant Number 25350964).

Conflict of interest

The authors had no conflict of interest in undertaking this project.

Supplementary material

10534_2015_9842_MOESM1_ESM.doc (642 kb)
(DOC 643 kb)


  1. Ahmed E, Holmstrom SJ (2014) Siderophores in environmental research: roles and applications. Microb Biotechnol 7:196–208. doi: 10.1111/1751-7915.12117 CrossRefPubMedCentralPubMedGoogle Scholar
  2. Bachmann BO, Ravel J (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. Methods Enzymol 458:181–217. doi: 10.1016/S0076-6879(09)04808-3 CrossRefPubMedGoogle Scholar
  3. Barona-Gomez F, Wong U, Giannakopulos AE, Derrick PJ, Challis GL (2004) Identification of a cluster of genes that directs desferrioxamine biosynthesis in Streptomyces coelicolor M145. J Am Chem Soc 126:16282–16283. doi: 10.1021/ja045774k CrossRefPubMedGoogle Scholar
  4. Challis GL (2005) A widely distributed bacterial pathway for siderophore biosynthesis independent of nonribosomal peptide synthetases. Chembiochem Eur J Chem Biol 6:601–611. doi: 10.1002/cbic.200400283 CrossRefGoogle Scholar
  5. Challis GL, Ravel J (2000) Coelichelin, a new peptide siderophore encoded by the Streptomyces coelicolor genome: structure prediction from the sequence of its non-ribosomal peptide synthetase. FEMS Microbiol Lett 187:111–114CrossRefPubMedGoogle Scholar
  6. Challis GL, Ravel J, Townsend CA (2000) Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains. Chem Biol 7:211–224CrossRefPubMedGoogle Scholar
  7. Clardy J (2006) Stopping trouble before it starts. ACS Chem Biol 1:17–19. doi: 10.1021/cb0600029 CrossRefPubMedGoogle Scholar
  8. Crosa JH, Walsh CT (2002) Genetics and assembly line enzymology of siderophore biosynthesis in bacteria. Microbiol Mol Biol Rev 66:223–249CrossRefPubMedCentralPubMedGoogle Scholar
  9. Harada KI, Fujii K, Hayashi K, Suzuki M, Ikai Y, Oka H (1996) Application of D, L-FDLA derivatization to determination of absolute configuration of constituent amino acids in peptide by advanced Marfey’s method. Tetrahedron Lett 37:3001–3004CrossRefGoogle Scholar
  10. Kodani S et al (2013a) Structure and biosynthesis of scabichelin, a novel tris-hydroxamate siderophore produced by the plant pathogen Streptomyces scabies 87.22. Org Biomol Chem 11:4686–4694. doi: 10.1039/c3ob40536b CrossRefPubMedGoogle Scholar
  11. Kodani S, Kobayakawa F, Hidaki M (2013b) Isolation and structure determination of new siderophore tsukubachelin B from Streptomyces sp. TM-74. Nat Prod Res 27:775–781. doi: 10.1080/14786419.2012.698412 CrossRefPubMedGoogle Scholar
  12. Komaki H, Ichikawa N, Oguchi A, Hanamaki T, Fujita N (2012) Genome-wide survey of polyketide synthase and nonribosomal peptide synthetase gene clusters in Streptomyces turgidiscabies NBRC 16081. J Gen Appl Microbiol 58:363–372CrossRefPubMedGoogle Scholar
  13. Komaki H et al (2014) Genome based analysis of type-I polyketide synthase and nonribosomal peptide synthetase gene clusters in seven strains of five representative Nocardia species. BMC Genomics 15:323. doi: 10.1186/1471-2164-15-323 CrossRefPubMedCentralPubMedGoogle Scholar
  14. Lautru S, Deeth RJ, Bailey LM, Challis GL (2005) Discovery of a new peptide natural product by Streptomyces coelicolor genome mining. Nat Chem Biol 1:265–269. doi: 10.1038/nchembio731 CrossRefPubMedGoogle Scholar
  15. Lazos O, Tosin M, Slusarczyk AL, Boakes S, Cortes J, Sidebottom PJ, Leadlay PF (2010) Biosynthesis of the putative siderophore erythrochelin requires unprecedented crosstalk between separate nonribosomal peptide gene clusters. Chem Biol 17:160–173. doi: 10.1016/j.chembiol.2010.01.011 CrossRefPubMedGoogle Scholar
  16. Mercier A, Labbe S (2010) Iron-dependent remodeling of fungal metabolic pathways associated with ferrichrome biosynthesis. Appl Environ Microbiol 76:3806–3817. doi: 10.1128/AEM.00659-10 CrossRefPubMedCentralPubMedGoogle Scholar
  17. Ochi K, Hosaka T (2013) New strategies for drug discovery: activation of silent or weakly expressed microbial gene clusters. Appl Microbiol Biotechnol 97:87–98. doi: 10.1007/s00253-012-4551-9 CrossRefPubMedCentralPubMedGoogle Scholar
  18. Park HM et al (2013) Genome-based cryptic gene discovery and functional identification of NRPS siderophore peptide in Streptomyces peucetius. Appl Microbiol Biotechnol 97:1213–1222. doi: 10.1007/s00253-012-4268-9 CrossRefPubMedGoogle Scholar
  19. Robbel L, Knappe TA, Linne U, Xie X, Marahiel MA (2010) Erythrochelin -a hydroxamate-type siderophore predicted from the genome of Saccharopolyspora erythraea. FEBS J 277:663–676. doi: 10.1111/j.1742-4658.2009.07512.x CrossRefPubMedGoogle Scholar
  20. Rottig M, Medema MH, Blin K, Weber T, Rausch C, Kohlbacher O (2011) NRPSpredictor2 -a web server for predicting NRPS adenylation domain specificity. Nucleic Acids Res 39:W362–W367. doi: 10.1093/nar/gkr323 CrossRefPubMedCentralPubMedGoogle Scholar
  21. Seyedsayamdost MR, Traxler MF, Zheng SL, Kolter R, Clardy J (2011) Structure and biosynthesis of amychelin, an unusual mixed-ligand siderophore from Amycolatopsis sp. AA4. J Am Chem Soc 133:11434–11437. doi: 10.1021/ja203577e CrossRefPubMedCentralPubMedGoogle Scholar
  22. Sieber SA, Marahiel MA (2005) Molecular mechanisms underlying nonribosomal peptide synthesis: approaches to new antibiotics. Chem Rev 105:715–738. doi: 10.1021/cr0301191 CrossRefPubMedGoogle Scholar
  23. Zerikly M, Challis GL (2009) Strategies for the discovery of new natural products by genome mining. Chembiochem Eur J Chem Biol 10:625–633. doi: 10.1002/cbic.200800389 CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Shinya Kodani
    • 1
  • Hisayuki Komaki
    • 2
  • Masahiro Suzuki
    • 1
  • Hikaru Hemmi
    • 3
  • Mayumi Ohnishi-Kameyama
    • 3
  1. 1.Graduate School of AgricultureShizuoka UniversityShizuokaJapan
  2. 2.Biological Resource CenterNational Institute of Technology and Evaluation (NBRC)KisarazuJapan
  3. 3.National Food Research InstituteNational Agriculture and Food Research Organization (NARO)TsukubaJapan

Personalised recommendations