Genome-based cryptic gene discovery and functional identification of NRPS siderophore peptide in Streptomyces peucetius

Applied Microbiology and Biotechnology

Volumn 97, Issue 3, 2013, Pages 1213-1222

  Park, Hae Min ^a   Kim, Byung Gee ^a   Chang, Dongsook ^a   Malla, Sailesh ^a   Joo, Hwang Soo ^a   Kim, Eun Jung ^a   Park, Sei Jin ^a   Sohng, Jae Kyung ^b   Kim, Pyoung Il ^a,c  

^a Seoul National University   (South Korea)

^b SunMoon University   (South Korea)

^c Chosun University   (South Korea)

Author keywords

Genome mining; Mass spectrometry; Nonribosomal peptide synthetase; Siderophore peptide; Streptomyces peucetius

Indexed keywords

AMINO ACID COMPOSITIONS; BIOINFORMATIC ANALYSIS; BIOSYNTHETIC GENE CLUSTER; CYCLIC STRUCTURES; DNA SEQUENCE ANALYSIS; DOMAIN STRUCTURE; FUNCTIONAL IDENTIFICATION; GENE CLUSTERS; GENE DISCOVERY; GENOME MINING; GENOMIC SEQUENCE; HYBRID ANTIBIOTIC; NONRIBOSOMAL PEPTIDE; NONRIBOSOMAL PEPTIDE SYNTHETASES; SECONDARY METABOLITES; SECRETOME; SIDEROPHORES; STREPTOMYCES PEUCETIUS; TANDEM MASS SPECTROMETRY;

AMINO ACIDS; BACTERIA; BIOINFORMATICS; MASS SPECTROMETRY; METABOLITES; PEPTIDES;

GENES;

NONRIBOSOMAL PEPTIDE SYNTHETASE; SIDEROPHORE;

AMINO ACID; BIOINFORMATICS; CRYPSIS; DNA; GENE; GENOME; MASS SPECTROMETRY; METABOLITE; MICROBIAL ACTIVITY; MOLECULAR ANALYSIS; PEPTIDE;

ADENYLATION; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARTICLE; BIOSYNTHESIS; COLLISIONALLY ACTIVATED DISSOCIATION; DNA SEQUENCE; GENE CLUSTER; GENE IDENTIFICATION; GENE SEQUENCE; ION PAIR CHROMATOGRAPHY; METABOLITE; MOLECULAR WEIGHT; NONHUMAN; STREPTOMYCES; STREPTOMYCES PEUCETIUS; STRUCTURAL GENOMICS; TANDEM MASS SPECTROMETRY; WILD TYPE;

COMPUTATIONAL BIOLOGY; DNA, BACTERIAL; GENETIC ASSOCIATION STUDIES; GENOME, BACTERIAL; GENOMICS; MASS SPECTROMETRY; MOLECULAR WEIGHT; MULTIGENE FAMILY; PEPTIDE SYNTHASES; PEPTIDES, CYCLIC; SEQUENCE ANALYSIS, DNA; SIDEROPHORES; STREPTOMYCES;

STREPTOMYCES PEUCETIUS; STREPTOMYCES PEUCETIUS ATCC 27952;

EID: 84874118808     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-012-4268-9     Document Type: Article

References (28)

1. Ansari MZ, Yadav G, Gokhale RS, Mohanty D (2004) NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases. Nucleic Acids Res 32(Web Server issue):W405-W413
2. 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(2):111-114
3. Challis GL, Ravel J, Townsend CA (2000) Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains. Chem Biol 7(3):211-224
4. Essen SA, Bylund D, Holmstrom SJ, Moberg M, Lundstrom US (2006) Quantification of hydroxamate siderophores in soil solutions of podzolic soil profiles in Sweden. Biometals 19(3):269-282
5. Felnagle EA, Barkei JJ, Park H, Podevels AM, McMahon MD, Drott DW, Thomas MG (2010) MbtH-like proteins as integral components of bacterial nonribosomal peptide synthetases. Biochemistry 49(41):8815-8817
6. Fuchs R, Budzikiewicz H (2001) Rearrangement reactions in the electrospray ionization mass spectra of pyoverdins. Int J Mass Spectrom 210(1-3):603-612
7. Gillam AH, Lewis AG, Andersen RJ (1981) Quantitative-determination of hydroxamic acids. Anal Chem 53(6):841-844
8. Gross H, Stockwell VO, Henkels MD, Nowak-Thompson B, Loper JE, Gerwick WH (2007) The genomisotopic approach: a systematic method to isolate products of orphan biosynthetic gene clusters. Chem Biol 14(1):53-63
9. Hayen H, Volmer DA (2005) Rapid identification of siderophores by combined thin-layer chromatography/matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 19(5):711-720
10. Lautru S, Challis GL (2004) Substrate recognition by nonribosomal peptide synthetase multi-enzymes. Microbiology 150(Pt 6):1629-1636
11. 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(5):265-269
12. Malla S, Niraula NP, Liou K, Sohng JK (2009) Enhancement of doxorubicin production by expression of structural sugar biosynthesis and glycosyltransferase genes in Streptomyces peucetius. J Biosci Bioeng 108(2):92-98
13. McClerren AL, Cooper LE, Quan C, Thomas PM, Kelleher NL, van der Donk WA (2006) Discovery and in vitro biosynthesis of haloduracin, a two-component lantibiotic. Proc Natl Acad Sci USA 103(46):17243-17248
14. Muller G, Raymond KN (1984) Specificity and mechanism of ferrioxamine-mediated iron transport in Streptomyces pilosus. J Bacteriol 160(1):304-312
15. Qi W, Jia CX, He ZM, Qiao B (2007) Multistep tandem mass spectrometry for sequencing cyclic peptides axinastatin 1 and deducing fragmentation pathways. Acta Chimica Sin 65(3):233-238
16. 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(3):663-676
17. Schwyn B, Neilands JB (1987) Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160(1):47-56
18. Sharman GJ, Williams DH, Ewing DF, Ratledge C (1995a) Determination of the structure of exochelin MN, the extracellular siderophore from Mycobacterium neoaurum. Chem Biol 2(8):553-561
19. Sharman GJ, Williams DH, Ewing DF, Ratledge C (1995b) Isolation, purification and structure of exochelin MS, the extracellular siderophore from Mycobacterium smegmatis. Biochem J 305(Pt 1):187-196
20. Silakowski B, Kunze B, Muller R (2001) Multiple hybrid polyketide synthase/non-ribosomal peptide synthetase gene clusters in the myxobacterium Stigmatella aurantiaca. Gene 275(2):233-240
21. Simionato AV, de Souza GD, Rodrigues-Filho E, Glick J, Vouros P, Carrilho E (2006) Tandem mass spectrometry of coprogen and deferoxamine hydroxamic siderophores. Rapid Commun Mass Spectrom 20(2):193-199
22. Stegmann E, Rausch C, Stockert S, Burkert D, Wohlleben W (2006) The small MbtH-like protein encoded by an internal gene of the balhimycin biosynthetic gene cluster is not required for glycopeptide production. FEMS Microbiol Lett 262(1):85-92
23. Sudek S, Haygood MG, Youssef DT, Schmidt EW (2006) Structure of trichamide, a cyclic peptide from the bloom-forming cyanobacterium Trichodesmium erythraeum, predicted from the genome sequence. Appl Environ Microbiol 72(6):4382-4387
24. Wenzel SC, Muller R (2005) Formation of novel secondary metabolites by bacterial multimodular assembly lines: deviations from textbook biosynthetic logic. Curr Opin Chem Biol 9(5):447-458
25. Wenzel SC, Kunze B, Hofle G, Silakowski B, Scharfe M, Blocker H, Muller R (2005) Structure and biosynthesis of myxochromides S1-3 in Stigmatella aurantiaca: evidence for an iterative bacterial type I polyketide synthase and for module skipping in nonribosomal peptide biosynthesis. Chembiochem 6(2):375-385
26. Wong GB, Kappel MJ, Raymond KN, Matzanke B, Winkelmann G (1983) Coordination chemistry of microbial iron transport compounds. 24. Characterization of coprogen and ferricrocin, 2 ferric hydroxamate siderophores. J Am Chem Soc 105(4):810-815
27. Wong DK, Gobin J, Horwitz MA, Gibson BW (1996) Characterization of exochelins of Mycobacterium avium: evidence for saturated and unsaturated and for acid and ester forms. J Bacteriol 178(21):6394-6398
28. Zhang W, Heemstra JR Jr, Walsh CT, Imker HJ (2010) Activation of the pacidamycin PacL adenylation domain by MbtH-like proteins. Biochemistry 49(46):9946-9947