Journal of Industrial Microbiology & Biotechnology

, Volume 41, Issue 2, pp 285–299

Merging chemical ecology with bacterial genome mining for secondary metabolite discovery



The integration of chemical ecology and bacterial genome mining can enhance the discovery of structurally diverse natural products in functional contexts. By examining bacterial secondary metabolism in the framework of its ecological niche, insights into the upregulation of orphan biosynthetic pathways and the enhancement of the enzyme substrate supply can be obtained, leading to the discovery of new secondary metabolic pathways that would otherwise be silent or undetected under typical laboratory cultivation conditions. Access to these new natural products (i.e., the chemotypes) facilitates experimental genotype-to-phenotype linkages. Here, we describe certain functional natural products produced by Xenorhabdus and Photorhabdus bacteria with experimentally linked biosynthetic gene clusters as illustrative examples of the synergy between chemical ecology and bacterial genome mining in connecting genotypes to phenotypes through chemotype characterization. These Gammaproteobacteria share a mutualistic relationship with nematodes and a pathogenic relationship with insects and, in select cases, humans. The natural products encoded by these bacteria distinguish their interactions with their animal hosts and other microorganisms in their multipartite symbiotic lifestyles. Though both genera have similar lifestyles, their genetic, chemical, and physiological attributes are distinct. Both undergo phenotypic variation and produce a profuse number of bioactive secondary metabolites. We provide further detail in the context of regulation, production, processing, and function for these genetically encoded small molecules with respect to their roles in mutualism and pathogenicity. These collective insights more widely promote the discovery of atypical orphan biosynthetic pathways encoding novel small molecules in symbiotic systems, which could open up new avenues for investigating and exploiting microbial chemical signaling in host–bacteria interactions.


Chemical signaling Natural products Secondary metabolism Biosynthesis Structure elucidation Symbiosis 


  1. 1.
    Akhurst RJ (1980) Morphological and functional dimorphism in Xenorhabdus spp., bacteria symbiotically associated with the insect pathogenic nematodes Neoaplectana and Heterorhabditis. J Gen Microbiol 121:303–309Google Scholar
  2. 2.
    Bian X, Fu J, Plaza A, Herrmann J, Pistorius D, Stewart AF, Zhang Y, Muller R (2013) In vivo evidence for a prodrug activation mechanism during colibactin maturation. Chem Biochem 14(10):1194–1197Google Scholar
  3. 3.
    Bian X, Plaza A, Zhang Y, Muller R (2012) Luminmycins A-C, cryptic natural products from Photorhabdus luminescens identified by heterologous expression in Escherichia coli. J Nat Prod 75(9):1652–1655PubMedGoogle Scholar
  4. 4.
    Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T (2013) AntiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res 41:W204–W212PubMedPubMedCentralGoogle Scholar
  5. 5.
    Bode HB (2009) Entomopathogenic bacteria as a source of secondary metabolites. Curr Opin Chem Biol 13(2):224–230PubMedGoogle Scholar
  6. 6.
    Bode HB, Bethe B, Hofs R, Zeeck A (2002) Big effects from small changes: possible ways to explore nature’s chemical diversity. Chem Biochem 3(7):619–627Google Scholar
  7. 7.
    Brachmann AO, Bode HB (2013) Identification and bioanalysis of natural products from insect symbionts and pathogens. Adv Biochem Eng Biot. doi:10.1007/10_2013_192 Google Scholar
  8. 8.
    Brachmann AO, Joyce SA, Jenke-Kodama H, Schwar G, Clarke DJ, Bode HB (2007) A type II polyketide synthase is responsible for anthraquinone biosynthesis in Photorhabdus luminescens. Chem Biochem 8(14):1721–1728Google Scholar
  9. 9.
    Brachmann AO, Reimer D, Lorenzen W, Augusto Alonso E, Kopp Y, Piel J, Bode HB (2012) Reciprocal cross talk between fatty acid and antibiotic biosynthesis in a nematode symbiont. Angew Chem Int Ed 51(48):12086–12089Google Scholar
  10. 10.
    Brady SF, Bauer JD, Clarke-Pearson MF, Daniels R (2007) Natural products from isnA-containing biosynthetic gene clusters recovered from the genomes of cultured and uncultured bacteria. J Am Chem Soc 129(40):12102–12103PubMedGoogle Scholar
  11. 11.
    Brady SF, Simmons L, Kim JH, Schmidt EW (2009) Metagenomic approaches to natural products from free-living and symbiotic organisms. Nat Prod Rep 26(11):1488–1503PubMedPubMedCentralGoogle Scholar
  12. 12.
    Brotherton CA, Balskus EP (2013) A prodrug resistance mechanism is involved in colibactin biosynthesis and cytotoxicity. J Am Chem Soc 135(9):3359–3362PubMedGoogle Scholar
  13. 13.
    Chan YA, Boyne MT 2nd, Podevels AM, Klimowicz AK, Handelsman J, Kelleher NL, Thomas MG (2006) Hydroxymalonyl-acyl carrier protein (ACP) and aminomalonyl-ACP are two additional type I polyketide synthase extender units. Proc Natl Acad Sci USA 103(39):14349–14354PubMedGoogle Scholar
  14. 14.
    Chaston JM, Suen G, Tucker SL, Andersen AW, Bhasin A, Bode E, Bode HB et al (2011) The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes. PLoS One 6(11):e27909PubMedPubMedCentralGoogle Scholar
  15. 15.
    Choulet F, Aigle B, Gallois A, Mangenot S, Gerbaud C, Truong C, Francou FX, Fourrier C, Guerineau M, Decaris B, Barbe V, Pernodet JL, Leblond P (2006) Evolution of the terminal regions of the Streptomyces linear chromosome. Mol Biol Evol 23(12):2361–2369PubMedGoogle Scholar
  16. 16.
    Ciche TA, Blackburn M, Carney JR, Ensign JC (2003) Photobactin: a catechol siderophore produced by Photorhabdus luminescens, an entomopathogen mutually associated with Heterorhabditis bacteriophora NC1 nematodes. Appl Environ Microbiol 69(8):4706–4713PubMedPubMedCentralGoogle Scholar
  17. 17.
    Clarke DJ (2008) Photorhabdus: a model for the analysis of pathogenicity and mutualism. Cell Microbiol 10(11):2159–2167PubMedGoogle Scholar
  18. 18.
    Cocito C (1979) Antibiotics of the virginiamycin family, inhibitors which contain synergistic components. Microbiol Rev 43(2):145–192PubMedPubMedCentralGoogle Scholar
  19. 19.
    Copping LG, Duke SO (2007) Natural products that have been used commercially as crop protection agents. Pest Manag Sci 63(6):524–554PubMedGoogle Scholar
  20. 20.
    Costa SC, Girard PA, Brehelin M, Zumbihl R (2009) The emerging human pathogen Photorhabdus asymbiotica is a facultative intracellular bacterium and induces apoptosis of macrophage-like cells. Infect Immun 77(3):1022–1030PubMedPubMedCentralGoogle Scholar
  21. 21.
    Cowles KN, Cowles CE, Richards GR, Martens EC, Goodrich-Blair H (2007) The global regulator Lrp contributes to mutualism, pathogenesis and phenotypic variation in the bacterium Xenorhabdus nematophila. Cell Microbiol 9(5):1311–1323PubMedGoogle Scholar
  22. 22.
    Craig JW, Brady SF (2011) Discovery of a metagenome-derived enzyme that produces branched-chain acyl-(acyl-carrier-protein)s from branched-chain alpha-keto acids. Chem Biochem 12(12):1849–1853Google Scholar
  23. 23.
    Crawford JM, Clardy J (2011) Bacterial symbionts and natural products. Chem Commun 47(27):7559–7566Google Scholar
  24. 24.
    Crawford JM, Kontnik R, Clardy J (2010) Regulating alternative lifestyles in entomopathogenic bacteria. Curr Biol 20(1):69–74PubMedPubMedCentralGoogle Scholar
  25. 25.
    Crawford JM, Mahlstedt SA, Malcolmson SJ, Clardy J, Walsh CT (2011) Dihydrophenylalanine: a prephenate-derived Photorhabdus luminescens antibiotic and intermediate in dihydrostilbene biosynthesis. Chem Biol 18(9):1102–1112PubMedPubMedCentralGoogle Scholar
  26. 26.
    Crawford JM, Portmann C, Kontnik R, Walsh CT, Clardy J (2011) NRPS substrate promiscuity diversifies the xenematides. Org Lett 13(19):5144–5147PubMedPubMedCentralGoogle Scholar
  27. 27.
    Crawford JM, Portmann C, Zhang X, Roeffaers MB, Clardy J (2012) Small molecule perimeter defense in entomopathogenic bacteria. Proc Natl Acad Sci USA 109(27):10821–10826PubMedGoogle Scholar
  28. 28.
    Crosa JH, Walsh CT (2002) Genetics and assembly line enzymology of siderophore biosynthesis in bacteria. Microbiol Mol Biol Rev 66(2):223–249PubMedPubMedCentralGoogle Scholar
  29. 29.
    D’Onofrio A, Crawford JM, Stewart EJ, Witt K, Gavrish E, Epstein S, Clardy J, Lewis K (2010) Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chem Biol 17(3):254–264PubMedPubMedCentralGoogle Scholar
  30. 30.
    Daniela R, Klaas MP, Marco T, Peter G, Helge BB (2011) A natural prodrug activation mechanism in nonribosomal peptide synthesis. Nat Chem Biol 7(12):888–890Google Scholar
  31. 31.
    Demain AL (2013) Importance of microbial natural products and the need to revitalize their discovery. J Ind Microbiol BiotGoogle Scholar
  32. 32.
    Dobrindt U, Hochhut B, Hentschel U, Hacker J (2004) Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2(5):414–424PubMedGoogle Scholar
  33. 33.
    Dongjin P (2009) Genetic analysis of xenocoumacin antibiotic production in the mutualistic bacterium Xenorhabdus nematophila. Mol Microbiol 73(5):938–949Google Scholar
  34. 34.
    Duchaud E, Rusniok C, Frangeul L, Buchrieser C, Givaudan A, Taourit S, Bocs S, Boursaux-Eude C, Chandler M, Charles JF, Dassa E, Derose R, Derzelle S, Freyssinet G, Gaudriault S, Medigue C, Lanois A, Powell K, Siguier P, Vincent R, Wingate V, Zouine M, Glaser P, Boemare N, Danchin A, Kunst F (2003) The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens. Nat Biotechnol 21(11):1307–1313PubMedGoogle Scholar
  35. 35.
    Eleftherianos I, Boundy S, Joyce SA, Aslam S, Marshall JW, Cox RJ, Simpson TJ, Clarke DJ, Ffrench-Constant RH, Reynolds SE (2007) An antibiotic produced by an insect-pathogenic bacterium suppresses host defenses through phenoloxidase inhibition. Proc Natl Acad Sci USA 104(7):2419–2424PubMedGoogle Scholar
  36. 36.
    Eleftherianos I, Ffrench-Constant RH, Clarke DJ, Dowling AJ, Reynolds SE (2010) Dissecting the immune response to the entomopathogen Photorhabdus. Trends Microbiol 18(12):552–560PubMedGoogle Scholar
  37. 37.
    Fedorova ND, Moktali V, Medema MH (2012) Bioinformatics approaches and software for detection of secondary metabolic gene clusters. Method Mol Biol 944:23–45Google Scholar
  38. 38.
    Fischbach MA, Walsh CT, Clardy J (2008) The evolution of gene collectives: how natural selection drives chemical innovation. Proc Natl Acad Sci USA 105(12):4601–4608PubMedGoogle Scholar
  39. 39.
    Fraenkel GS (1959) The raison d’ĕtre of secondary plant substances: these odd chemicals arose as a means of protecting plants from insects and now guide insects to food. Science 129(3361):1466–1470Google Scholar
  40. 40.
    Franke S, Ibarra F, Schulz CM, Twele R, Poldy J, Barrow RA, Peakall R, Schiestl FP, Francke W (2009) The discovery of 2,5-dialkylcyclohexan-1,3-diones as a new class of natural products. Proc Natl Acad Sci USA 106(22):8877–8882PubMedGoogle Scholar
  41. 41.
    Fu J, Bian X, Hu S, Wang H, Huang F, Seibert PM, Plaza A, Xia L, Muller R, Stewart AF, Zhang Y (2012) Full-length RecE enhances linear–linear homologous recombination and facilitates direct cloning for bioprospecting. Nat Biotechnol 30(5):440–446PubMedGoogle Scholar
  42. 42.
    Fuchs SW, Bozhuyuk KA, Kresovic D, Grundmann F, Dill V, Brachmann AO, Waterfield NR, Bode HB (2013) Formation of 1,3-cyclohexanediones and resorcinols catalyzed by a widely occuring ketosynthase. Angew Chemie 52(15):4108–4112Google Scholar
  43. 43.
    Fuchs SW, Proschak A, Jaskolla TW, Karas M, Bode HB (2011) Structure elucidation and biosynthesis of lysine-rich cyclic peptides in Xenorhabdus nematophila. Org Biomol Chem 9(9):3130–3132PubMedGoogle Scholar
  44. 44.
    Gaudriault S, Duchaud E, Lanois A, Canoy AS, Bourot S, Derose R, Kunst F, Boemare N, Givaudan A (2006) Whole-genome comparison between Photorhabdus strains to identify genomic regions involved in the specificity of nematode interaction. J Bacteriol 188(2):809–814PubMedPubMedCentralGoogle Scholar
  45. 45.
    Gerrard J, Waterfield N, Vohra R, Ffrench-Constant R (2004) Human infection with Photorhabdus asymbiotica: an emerging bacterial pathogen. Microbes Infect 6(2):229–237PubMedGoogle Scholar
  46. 46.
    Gerrard JG, Joyce SA, Clarke DJ, Ffrench-Constant RH, Nimmo GR, Looke DF, Feil EJ, Pearce L, Waterfield NR (2006) Nematode symbiont for Photorhabdus asymbiotica. Emerg Infect Dis 12(10):1562–1564PubMedGoogle Scholar
  47. 47.
    Gerrard JG, Waterfield NR, Sanchez-Contreeras M (2011) Photorhabdus asymbiotica: shedding light on a human pathogenic bioluminescent bacterium. Clin Microbiol Newslett 33(14):103–110Google Scholar
  48. 48.
    Goodrich-Blair H (2007) They’ve got a ticket to ride: Xenorhabdus nematophila–Steinernema carpocapsae symbiosis. Curr Opin Microbiol 10(3):225–230PubMedGoogle Scholar
  49. 49.
    Goodrich-Blair H, Clarke DJ (2007) Mutualism and pathogenesis in Xenorhabdus and Photorhabdus: two roads to the same destination. Mol Microbiol 64(2):260–268PubMedGoogle Scholar
  50. 50.
    Griffiths GL, Sigel SP, Payne SM, Neilands JB (1984) Vibriobactin, a siderophore from Vibrio cholerae. J Biol Chem 259(1):383–385PubMedGoogle Scholar
  51. 51.
    Gross H, Loper JE (2009) Genomics of secondary metabolite production by Pseudomonas spp. Nat Prod Rep 26(11):1408–1446PubMedGoogle Scholar
  52. 52.
    Gualtieri M, Aumelas A, Thaler JO (2009) Identification of a new antimicrobial lysine-rich cyclolipopeptide family from Xenorhabdus nematophila. J Antibiot 62(6):295–302PubMedGoogle Scholar
  53. 53.
    Hacker J, Kaper JB (2000) Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol 54:641–679PubMedGoogle Scholar
  54. 54.
    Hartmann T (2004) Plant-derived secondary metabolites as defensive chemicals in herbivorous insects: a case study in chemical ecology. Planta 219(1):1–4PubMedGoogle Scholar
  55. 55.
    Hartmann T (2008) The lost origin of chemical ecology in the late 19th century. Proc Natl Acad Sci USA 105(12):4541–4546PubMedGoogle Scholar
  56. 56.
    Heermann R, Fuchs TM (2008) Comparative analysis of the Photorhabdus luminescens and the Yersinia enterocolitica genomes: uncovering candidate genes involved in insect pathogenicity. BMC Genomics 9:40PubMedPubMedCentralGoogle Scholar
  57. 57.
    Henderson DP, Payne SM (1994) Vibrio cholerae iron transport systems: roles of heme and siderophore iron transport in virulence and identification of a gene associated with multiple iron transport systems. Infect Immun 62(11):5120–5125PubMedPubMedCentralGoogle Scholar
  58. 58.
    Hentschel U, Piel J, Degnan SM, Taylor MW (2012) Genomic insights into the marine sponge microbiome. Nat Rev 10(9):641–654Google Scholar
  59. 59.
    Herbert EE, Goodrich-Blair H (2007) Friend and foe: the two faces of Xenorhabdus nematophila. Nat Rev 5(8):634–646Google Scholar
  60. 60.
    Hu K, Li J, Webster JM (1997) Quantitative analysis of a bacteria-derived antibiotic in nematode-infected insects using HPLC-UV and TLC-UV methods. J Chromatogr 703(1–2):177–183Google Scholar
  61. 61.
    Hu K, Webster JM (2000) Antibiotic production in relation to bacterial growth and nematode development in PhotorhabdusHeterorhabditis infected Galleria mellonella larvae. FEMS Microb Lett 189(2):219–223Google Scholar
  62. 62.
    Hung KY, Harris PW, Heapy AM, Brimble MA (2011) Synthesis and assignment of stereochemistry of the antibacterial cyclic peptide xenematide. Org Biomol Chem 9(1):236–242PubMedGoogle Scholar
  63. 63.
    Jenke-Kodama H, Muller R, Dittmann E (2008) Evolutionary mechanisms underlying secondary metabolite diversity. Prog Drug Res 65(119):121–140Google Scholar
  64. 64.
    Jensen PR (2010) Linking species concepts to natural product discovery in the post-genomic era. J Ind Microbiol 37(3):219–224Google Scholar
  65. 65.
    Joyce SA, Brachmann AO, Glazer I, Lango L, Schwar G, Clarke DJ, Bode HB (2008) Bacterial biosynthesis of a multipotent stilbene. Angew Chem Int Ed 47(10):1942–1945Google Scholar
  66. 66.
    Joyce SA, Clarke DJ (2003) A hexA homologue from Photorhabdus regulates pathogenicity, symbiosis and phenotypic variation. Mol Microbiol 47(5):1445–1457PubMedGoogle Scholar
  67. 67.
    Kalaitzis JA, Lauro FM, Neilan BA (2009) Mining cyanobacterial genomes for genes encoding complex biosynthetic pathways. Nat Prod Rep 26(11):1447–1465PubMedGoogle Scholar
  68. 68.
    Kelley LA, Sternberg MJ (2009) Protein structure prediction on the web: a case study using the Phyre server. Nat Protoc 4(3):363–371PubMedGoogle Scholar
  69. 69.
    Kevany BM, Rasko DA, Thomas MG (2009) Characterization of the complete zwittermicin A biosynthesis gene cluster from Bacillus cereus. Appl Environ Microbiol 75(4):1144–1155PubMedPubMedCentralGoogle Scholar
  70. 70.
    Khush RS, Lemaitre B (2000) Genes that fight infection: what the Drosophila genome says about animal immunity. Trends Genet 16(10):442–449PubMedGoogle Scholar
  71. 71.
    Kontnik R, Crawford JM, Clardy J (2010) Exploiting a global regulator for small molecule discovery in Photorhabdus luminescens. ACS Chem Biol 5(7):659–665PubMedPubMedCentralGoogle Scholar
  72. 72.
    Kroken S, Glass NL, Taylor JW, Yoder OC, Turgeon BG (2003) Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes. Proc Natl Acad Sci USA 100(26):15670–15675PubMedGoogle Scholar
  73. 73.
    Kwan JC, Donia MS, Han AW, Hirose E, Haygood MG, Schmidt EW (2012) Genome streamlining and chemical defense in a coral reef symbiosis. Proc Natl Acad Sci USA 109(50):20655–20660PubMedGoogle Scholar
  74. 74.
    Lang G, Kalvelage T, Peters A, Wiese J, Imhoff JF (2008) Linear and cyclic peptides from the entomopathogenic bacterium Xenorhabdus nematophilus. J Nat Prod 71(6):1074–1077PubMedGoogle Scholar
  75. 75.
    Lanois A, Ogier JC, Gouzy J, Laroui C, Rouy Z, Givaudan A, Gaudriault S (2013) Draft genome sequence and annotation of the entomopathogenic bacterium Xenorhabdus nematophila strain F1. Genome Announc 1(3):e00342-13. doi:10.1128/genomeA.00342-13
  76. 76.
    Lewis K, Epstein S, D’Onofrio A, Ling LL (2010) Uncultured microorganisms as a source of secondary metabolites. J Antibiot 63(8):468–476Google Scholar
  77. 77.
    Li J, Chen G, Wu H, Webster JM (1995) Identification of two pigments and a hydroxystilbene antibiotic from Photorhabdus luminescens. Appl Environ Microbiol 61(12):4329–4333PubMedPubMedCentralGoogle Scholar
  78. 78.
    Lin H-Y, Rao YK, Wu W-S, Tzeng Y-M (2007) Ferrous ion enhanced lipopeptide antibiotic Iturin A production from Bacillus amyloliquefaciens B128. Int J Appl Sci Eng 5(2):123–132Google Scholar
  79. 79.
    Luo Y, Ruan LF, Zhao CM, Wang CX, Peng DH, Sun M (2011) Validation of the intact zwittermicin A biosynthetic gene cluster and discovery of a complementary resistance mechanism in Bacillus thuringiensis. Antimicrob Agents Chemother 55(9):4161–4169PubMedPubMedCentralGoogle Scholar
  80. 80.
    Mahlstedt S, Fielding EN, Moore BS, Walsh CT (2010) Prephenate decarboxylases: a new prephenate-utilizing enzyme family that performs nonaromatizing decarboxylation en route to diverse secondary metabolites. Biochemistry 49(42):9021–9023PubMedPubMedCentralGoogle Scholar
  81. 81.
    Mahlstedt SA, Walsh CT (2010) Investigation of anticapsin biosynthesis reveals a four-enzyme pathway to tetrahydrotyrosine in Bacillus subtilis. Biochemistry 49(5):912–923PubMedPubMedCentralGoogle Scholar
  82. 82.
    Martinez-Molina E, Del Rio LA, Olivares J (1976) Copper and iron as determinant factors of antibiotic production by Pseudomonas reptilivora. J Appl Bacteriol 41(1):69–74PubMedGoogle Scholar
  83. 83.
    Mast Y, Weber T, Golz M, Ort-Winklbauer R, Gondran A, Wohlleben W, Schinko E (2011) Characterization of the ‘pristinamycin supercluster’ of Streptomyces pristinaespiralis. Microb Biotechnol 4(2):192–206PubMedGoogle Scholar
  84. 84.
    Maxwell PW, Chen G, Webster JM, Dunphy GB (1994) Stability and activities of antibiotics produced during infection of the insect Galleria mellonella by two isolates of Xenorhabdus nematophilus. Appl Environ Microbiol 60(2):715–721PubMedPubMedCentralGoogle Scholar
  85. 85.
    McInerney BV, Gregson RP, Lacey MJ, Akhurst RJ, Lyons GR, Rhodes SH, Smith DR, Engelhardt LM, White AH (1991) Biologically active metabolites from Xenorhabdus spp., part 1. Dithiolopyrrolone derivatives with antibiotic activity. J Nat Prod 54(3):774–784PubMedGoogle Scholar
  86. 86.
    Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R (2011) AntiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39:W339–W346PubMedPubMedCentralGoogle Scholar
  87. 87.
    Medema MH, Breitling R, Bovenberg R, Takano E (2011) Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms. Nat Rev Microbiol 9(2):131–137PubMedGoogle Scholar
  88. 88.
    Medema MH, Trefzer A, Kovalchuk A, van den Berg M, Muller U, Heijne W, Wu L, Alam MT, Ronning CM, Nierman WC, Bovenberg RA, Breitling R, Takano E (2010) The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways. Genome Biol Evol 2:212–224PubMedPubMedCentralGoogle Scholar
  89. 89.
    Miethke M, Marahiel MA (2007) Siderophore-based iron acquisition and pathogen control. Microbiol Mol Biol Rev 71(3):413–451PubMedPubMedCentralGoogle Scholar
  90. 90.
    Mitchell W (2011) Natural products from synthetic biology. Curr Opin Chem Biol 15(4):505–515PubMedGoogle Scholar
  91. 91.
    Molnar K, Farkas E (2010) Current results on biological activities of lichen secondary metabolites: a review. Z Naturforsch 65(3–4):157–173Google Scholar
  92. 92.
    Müller-Schwarze D (2006) Chemical ecology of vertebrates. Cambridge University Press, CambridgeGoogle Scholar
  93. 93.
    Murfin KE, Dillman AR, Foster JM, Bulgheresi S, Slatko BE, Sternberg PW, Goodrich-Blair H (2012) Nematode-bacterium symbioses—cooperation and conflict revealed in the “omics” age. Biol Bull 223(1):85–102PubMedPubMedCentralGoogle Scholar
  94. 94.
    Neilands JB (1995) Siderophores: structure and function of microbial iron transport compounds. J Biol Chem 270(45):26723–26726PubMedGoogle Scholar
  95. 95.
    Nett M, Ikeda H, Moore BS (2009) Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 26(11):1362–1384PubMedPubMedCentralGoogle Scholar
  96. 96.
    Newman DJ, Cragg GM (2012) Natural products as sources of new drugs over the 30 years from 1981 to 2010. J Nat Prod 75(3):311–335PubMedPubMedCentralGoogle Scholar
  97. 97.
    Nougayrede JP, Homburg S, Taieb F, Boury M, Brzuszkiewicz E, Gottschalk G, Buchrieser C, Hacker J, Dobrindt U, Oswald E (2006) Escherichia coli induces DNA double-strand breaks in eukaryotic cells. Science 313(5788):848–851PubMedGoogle Scholar
  98. 98.
    Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405(6784):299–304PubMedGoogle Scholar
  99. 99.
    Ogier JC, Calteau A, Forst S, Goodrich-Blair H, Roche D, Rouy Z, Suen G, Zumbihl R, Givaudan A, Tailliez P, Medigue C, Gaudriault S (2010) Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus. BMC Genomics 11:568PubMedPubMedCentralGoogle Scholar
  100. 100.
    Oku H, Kaneda T (1988) Biosynthesis of branched-chain fatty acids in Bacillus subtilis. A decarboxylase is essential for branched-chain fatty acid synthetase. J Biol Chem 263(34):18386–18396PubMedGoogle Scholar
  101. 101.
    Ong SA, Peterson T, Neilands JB (1979) Agrobactin, a siderophore from Agrobacterium tumefaciens. J Biol Chem 254(6):1860–1865PubMedGoogle Scholar
  102. 102.
    Oves-Costales D, Kadi N, Challis GL (2009) The long-overlooked enzymology of a nonribosomal peptide synthetase-independent pathway for virulence-conferring siderophore biosynthesis. Chem Commun 43:6530–6541Google Scholar
  103. 103.
    Pawlik JR (2011) The chemical ecology of sponges on Caribbean reefs: natural products shape natural systems. Bioscience 61(11):888–898Google Scholar
  104. 104.
    Penn K, Jenkins C, Nett M, Udwary DW, Gontang EA, McGlinchey RP, Foster B, Lapidus A, Podell S, Allen EE, Moore BS, Jensen PR (2009) Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J 3(10):1193–1203PubMedPubMedCentralGoogle Scholar
  105. 105.
    Perham RN (1991) Domains, motifs, and linkers in 2-oxo acid dehydrogenase multienzyme complexes: a paradigm in the design of a multifunctional protein. Biochemistry 30(35):8501–8512PubMedGoogle Scholar
  106. 106.
    Phelan VV, Liu WT, Pogliano K, Dorrestein PC (2012) Microbial metabolic exchange—the chemotype-to-phenotype link. Nat Chem Biol 8(1):26–35Google Scholar
  107. 107.
    Pinchuk IV, Bressollier P, Sorokulova IB, Verneuil B, Urdaci MC (2002) Amicoumacin antibiotic production and genetic diversity of Bacillus subtilis strains isolated from different habitats. Res Microbiol 153(5):269–276PubMedGoogle Scholar
  108. 108.
    Proctor RA, von Eiff C, Kahl BC, Becker K, McNamara P, Herrmann M, Peters G (2006) Small colony variants: a pathogenic form of bacteria that facilitates persistent and recurrent infections. Nat Rev 4(4):295–305Google Scholar
  109. 109.
    Purdy AE, Watnick PI (2011) Spatially selective colonization of the arthropod intestine through activation of Vibrio cholerae biofilm formation. Proc Natl Acad Sci USA 108(49):19737–19742PubMedGoogle Scholar
  110. 110.
    Rath CM, Dorrestein PC (2012) The bacterial chemical repertoire mediates metabolic exchange within gut microbiomes. Curr Opin Microbiol 15(2):147–154PubMedGoogle Scholar
  111. 111.
    Reimer D (2009) A new type of pyrrolidine biosynthesis is involved in the late steps of xenocoumacin production in Xenorhabdus nematophila. Chem Biochem 10(12):1997–2001Google Scholar
  112. 112.
    Richards GR, Goodrich-Blair H (2009) Masters of conquest and pillage: Xenorhabdus nematophila global regulators control transitions from virulence to nutrient acquisition. Cell Microbiol 11:1025–1033PubMedPubMedCentralGoogle Scholar
  113. 113.
    Richardson WH, Schmidt TM, Nealson KH (1988) Identification of an anthraquinone pigment and a hydroxystilbene antibiotic from Xenorhabdus luminescens. Appl Environ Microbiol 54(6):1602–1605PubMedPubMedCentralGoogle Scholar
  114. 114.
    Rollins MJ, Jensen SE, Westlake DWS (1989) Regulation of antibiotic production by iron and oxygen during defined medium fermentations of Streptomyces clavuligerus. Appl Environ Microbiol 31:390–396Google Scholar
  115. 115.
    Sanchez JF, Somoza AD, Keller NP, Wang CC (2012) Advances in Aspergillus secondary metabolite research in the post-genomic era. Nat Prod Rep 29(3):351–371PubMedGoogle Scholar
  116. 116.
    Scherlach K, Graupner K, Hertweck C (2013) Molecular bacterial–fungal interactions with impact on the environment, food and medicine. Annu Rev Microbiol. doi:10.1146/annurev-micro-092412-155702
  117. 117.
    Schmidt EW, Donia MS, McIntosh JA, Fricke WF, Ravel J (2012) Origin and variation of tunicate secondary metabolites. J Nat Prod 75(2):295–304PubMedPubMedCentralGoogle Scholar
  118. 118.
    Somvanshi VS, Kaufmann-Daszczuk B, Kim KS, Mallon S, Ciche TA (2010) Photorhabdus phase variants express a novel fimbrial locus, mad, essential for symbiosis. Mol Microbiol 77:1021–1038Google Scholar
  119. 119.
    Somvanshi VS, Sloup RE, Crawford JM, Martin AR, Heidt AJ, Kim KS, Clardy J, Ciche TA (2012) A single promoter inversion switches Photorhabdus between pathogenic and mutualistic states. Science 337(6090):88–93PubMedGoogle Scholar
  120. 120.
    Stein ML, Beck P, Kaiser M, Dudler R, Becker CF, Groll M (2012) One-shot NMR analysis of microbial secretions identifies highly potent proteasome inhibitor. Proc Natl Acad Sci USA 109(45):18367–18371PubMedGoogle Scholar
  121. 121.
    Stocker-Worgotter E (2008) Metabolic diversity of lichen-forming ascomycetous fungi: culturing, polyketide and shikimate metabolite production, and PKS genes. Nat Prod Rep 25(1):188–200PubMedGoogle Scholar
  122. 122.
    Sugar DR, Murfin KE, Chaston JM, Andersen AW, Richards GR, deLeon L, Baum JA, Clinton WP, Forst S, Goldman BS, Krasomil-Osterfeld KC, Slater S, Stock SP, Goodrich-Blair H (2012) Phenotypic variation and host interactions of Xenorhabdus bovienii SS-2004, the entomopathogenic symbiont of Steinernema jollieti nematodes. Environ Microbiol 14(4):924–939PubMedPubMedCentralGoogle Scholar
  123. 123.
    Theodore CM, King JB, You J, Cichewicz RH (2012) Production of cytotoxic glidobactins/luminmycins by Photorhabdus asymbiotica in liquid media and live crickets. J Nat Prod 75(11):2007–2011Google Scholar
  124. 124.
    Tounsi S, Blight M, Jaoua S, de Lima Pimenta A (2006) From insects to human hosts: identification of major genomic differences between entomopathogenic strains of Photorhabdus and the emerging human pathogen Photorhabdus asymbiotica. IJMM 296(8):521–530PubMedGoogle Scholar
  125. 125.
    Uvell H, Engstrom Y (2007) A multilayered defense against infection: combinatorial control of insect immune genes. Trends Genet 23(7):342–349PubMedGoogle Scholar
  126. 126.
    Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, Rouy Z, Roche D, Salvignol G, Scarpelli C, Medigue C (2009) MicroScope: a platform for microbial genome annotation and comparative genomics. Database (Oxford) 2009:bap021Google Scholar
  127. 127.
    Walsh CT, O’Brien RV, Khosla C (2013) Nonproteinogenic amino acid building blocks for nonribosomal peptide and hybrid polyketide scaffolds. Angew Chem Int Ed 52(28):7098–7124Google Scholar
  128. 128.
    Wandersman C, Delepelaire P (2004) Bacterial iron sources: from siderophores to hemophores. Annu Rev Microbiol 58:611–647PubMedGoogle Scholar
  129. 129.
    Wang G, Jia S, Wang T, Chen L, Song Q, Li W (2011) Effect of ferrous ion on epsilon-poly-l-lysine biosynthesis by Streptomyces diastatochromogenes CGMCC3145. Curr Microbiol 62(3):1062–1067PubMedGoogle Scholar
  130. 130.
    Waterfield NR, Ciche T, Clarke D (2009) Photorhabdus and a host of hosts. Annu Rev Microbiol 63:557–574PubMedGoogle Scholar
  131. 131.
    Waterfield NR, Sanchez-Contreras M, Eleftherianos I, Dowling A, Wilkinson P, Parkhill J, Thomson N, Reynolds SE, Bode HB, Dorus S, Ffrench-Constant RH (2008) Rapid virulence annotation (RVA): identification of virulence factors using a bacterial genome library and multiple invertebrate hosts. Proc Natl Acad Sci USA 105(41):15967–15972PubMedGoogle Scholar
  132. 132.
    Waterfield NR, Wren BW, Ffrench-Constant RH (2004) Invertebrates as a source of emerging human pathogens. Nat Rev Microbiol 2(10):833–841PubMedGoogle Scholar
  133. 133.
    Watson RJ, Millichap P, Joyce SA, Reynolds S, Clarke DJ (2010) The role of iron uptake in pathogenicity and symbiosis in Photorhabdus luminescens TT01. BMC Microbiol 10:177PubMedPubMedCentralGoogle Scholar
  134. 134.
    Weissfeld AS, Halliday RJ, Simmons DE, Trevino EA, Vance PH, O’Hara CM, Sowers EG, Kern R, Koy RD, Hodde K, Bing M, Lo C, Gerrard J, Vohra R, Harper J (2005) Photorhabdus asymbiotica, a pathogen emerging on two continents that proves that there is no substitute for a well-trained clinical microbiologist. J Clin Microbiol 43(8):4152–4155PubMedPubMedCentralGoogle Scholar
  135. 135.
    Wenzel SC, Muller R (2009) The impact of genomics on the exploitation of the myxobacterial secondary metabolome. Nat Prod Rep 26(11):1385–1407PubMedGoogle Scholar
  136. 136.
    Wilkinson P, Waterfield NR, Crossman L, Corton C, Sanchez-Contreras M, Vlisidou I, Barron A, Bignell A, Clark L, Ormond D, Mayho M, Bason N, Smith F, Simmonds M, Churcher C, Harris D, Thompson NR, Quail M, Parkhill J, Ffrench-Constant RH (2009) Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens. BMC Genomics 10:302PubMedPubMedCentralGoogle Scholar
  137. 137.
    Wink M (2003) Evolution of secondary metabolites from an ecological and molecular phylogenetic perspective. Phytochemistry 64(1):3–19PubMedGoogle Scholar
  138. 138.
    Winter JM, Behnken S, Hertweck C (2011) Genomics-inspired discovery of natural products. Curr Opin Chem Biol 15(1):22–31PubMedGoogle Scholar
  139. 139.
    Wyckoff EE, Mey AR, Payne SM (2007) Iron acquisition in Vibrio cholerae. Biometals 20(3–4):405–416PubMedGoogle Scholar
  140. 140.
    Zhou T (2011) Global transcriptional responses of Bacillus subtilis to xenocoumacin 1. J Appl Microbiol 111(3):652–662PubMedGoogle Scholar
  141. 141.
    Zotchev SB, Sekurova ON, Katz L (2012) Genome-based bioprospecting of microbes for new therapeutics. Curr Opin Biotechnol 23(6):941–947PubMedGoogle Scholar

Copyright information

© Society for Industrial Microbiology and Biotechnology 2013

Authors and Affiliations

  • Maria I. Vizcaino
    • 1
    • 3
  • Xun Guo
    • 1
    • 3
  • Jason M. Crawford
    • 1
    • 2
    • 3
  1. 1.Department of ChemistryYale UniversityNew HavenUSA
  2. 2.Department of Microbial PathogenesisYale School of MedicineNew HavenUSA
  3. 3.Chemical Biology InstituteYale UniversityWest HavenUSA

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