Biodiversity of genes encoding anti-microbial traits within plant associated microbes

Frontiers in Plant Science

Volumn 6, Issue APR, 2015, Pages

  Mousa, Walaa K ^a,b   Raizada, Manish N ^a  

^a UNIVERSITY OF GUELPH   (Canada)

^b MANSOURA UNIVERSITY   (Egypt)

Author keywords

Antimicrobial secondary metabolites; Biodiversity; Endophyte; Evolution; Genes; Plant associated microbes; Rhizosphere

Indexed keywords

FUNGI;

EID: 84928162784     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2015.00231     Document Type: Article

References (221)

1. Anjaiah, V., Koedam, N., Nowak-Thompson, B., Loper, J. E., Hofte, M., Tam- bong, J. T., et al. (1998). Involvement of phenazines and anthranilate in the antagonism of Pseudomonas aeruginosa PNA1 and Tn5 derivatives toward Fusarium spp. and Pythium spp. Mol. Plant Microbelnteract. 11, 847-854. doi: 10.1094/MPMI.1998.11.9.847
2. Arima, K., Imanaka, H., Kousaka, M., Fukuta, A., and Tamura, G. (1964). Pyrrolni- trin, a new antibiotic substance, produced by Pseudomonas. Agric. Biol. Chem. 28, 575-576. doi: 10.1271/bbb1961.28.575
3. Arvas, M., Kivioja, T., Mitchell, A., Saloheimo, M., Ussery, D., Penttila, M., et al. (2007). Comparison of protein coding gene contents of the fungal phyla Pez- izomycotina and Saccharomycotina. BMC Genomics 8:325. doi: 10.1186/14712164-8-325
4. Audenaert, K., Pattery, T., Cornelis, P., and Hofte, M. (2002). Induction of systemic resistance to Botrytis cinerea in tomato by Pseudomonas aeruginosa 7NSK2: role of salicylic acid, pyochelin, and pyocyanin. Mol. Plant Microbe Interact. 15, 1147-1156. doi: 10.1094/MPMI.2002.15.11.1147
5. Bangera, M. G., and Thomashow, L. S. (1999). Identification and characterization of a gene cluster for synthesis of the polyketide antibiotic 2,4- diacetylphloroglucinol from Pseudomonas fluorescens Q2-87. J. Bacteriol. 181, 3155-3163.
6. Barbe, V., Cruveiller, S., Kunst, F., Lenoble, P., Meurice, G., Sekowska, A., et al. (2009). From a consortium sequence to a unified sequence: the Bacillus sub- tilis 168 reference genome a decade later. Microbiology 155, 1758-1775. doi: 10.1099/mic.0.027839-0
7. Barea, J. M., Pozo, M. J., Azcon, R., and Azcon-Aguilar, C. (2005). Microbial co- operationintherhizosphere. J.Exp. Bot. 56,1761-1778. doi: 10.1093/jxb/eri197
8. Beatty, P. H., and Jensen, S. E. (2002). Paenibacilluspolymyxa produces fusaricidin- type antifungal antibiotics active against Leptosphaeria maculans, the causative agent of blackleg disease of canola. Can. J. Microbiol. 48, 159-169. doi: 10.1139/w02-002
9. Beimforde, C., Feldberg, K., Nylinder, S., Rikkinen, J., Tuovila, H., Dorfelt, H., et al. (2014). Estimating the phanerozoic history of the Ascomycota lineages: combining fossil and molecular data. Mol. Phylogenet. Evol. 78, 386-398. doi: 10.1016/j.ympev.2014.04.024
10. Belda, E., Sekowska, A., Le Fevre, F., Morgat, A., Mornico, D., Ouzounis, C., et al. (2013). An updated metabolic view of the Bacillus subtilis 168 genome. Microbiology 159,757-770. doi: 10.1099/mic.0.064691-0
11. Bhattacharya, D., Nagpure, A., and Gupta, R. K. (2007). Bacterial chiti- nases: properties and potential. Crit. Rev. Biotechnol. 27, 21-28. doi: 10.1080/07388550601168223
12. Blackwell, M. (2011). The fungi: 1, 2, 3… 5.1 million species? Am. J. Bot. 98, 426-438. doi: 10.3732/ajb.1000298
13. Blankenship, J. D., Spiering, M. J., Wilkinson, H. H., Fannin, F. F., Bush, L. P., and Schardl, C. L. (2001). Production of loline alkaloids by the grass endophyte, Neotyphodium uncinatum, in defined media. Phytochemistry 58, 395-401. doi: 10.1016/S0031-9422(01)00272-2
14. Blom, D., Fabbri, C., Eberl, L., and Weisskopf, L. (2011). Volatile-mediated killing of Arabidopsis thaliana by bacteria is mainly due to hydrogen cyanide. Appl. Environ. Microbiol. 77, 1000-1008. doi: 10.1128/AEM.01968-10
15. Blom, J., Rueckert, C., Niu, B., Wang, Q., and Borriss, R. (2012). The complete genome of Bacillus amyloliquefaciens subsp. plantarum CAU B946 contains a gene clusterfornonribosomal synthesis ofiturinA. J. Bacteriol. 194,1845-1846. doi: 10.1128/JB.06762-11
16. Blumer, C., and Haas, D. (2000). Mechanism, regulation, and ecological role of bacterial cyanide biosynthesis. Arch. Microbiol. 173, 170-177. doi: 10.1007/s002039900127
17. Brandl, H., Lehmann, S., Faramarzi, M. A., and Martinelli, D. (2008). Biomobilization of silver, gold, and platinum from solid waste materials by HCN-forming microorganisms. Hydrometallurgy 94, 14-17. doi: 10.1016/j.hydromet.2008.05.016
18. Broderick, N. A., Goodman, R. M., Raffa, K. F., and Handelsman, J. (2000). Synergy between zwittermicin A and Bacillus thuringiensis subsp. kurstaki against gypsy moth (Lepidoptera: Lymantriidae). Environ. Entomol. 29, 101-107. doi: 10.1603/0046-225X-29.1.101
19. Bulgarelli, D., Rott, M., Schlaeppi, K., van Themaat, E., Ahmadinejad, N., Assenza, F. et al. (2012). Revealing structure and assembly cues for Arabidopsis root- inhabiting bacterial microbiota. Nature 488, 91-95. doi: 10.1038/nature11336
20. Cane, D. E. (1997). A special thematic issue on polyketide and nonribosomal polypeptide biosynthesis. Chem. Rev. 97, 2463-2706. doi: 10.1021/cr970097g
21. Cardoza, R. E., Malmierca, M. G., Hermosa, M. R., Alexander, N. J., McCormick, S. P., Proctor, R. H., et al. (2011). Identification ofloci and functional characterization of trichothecene biosynthesis genes in filamentous fungi of the genus Trichoderma. Appl. Environ. Microbiol. 77, 4867-4877. doi: 10.1128/AEM.00595-11
22. Carter, C. J., Cannon, M., and Smith, K. E. (1976). Inhibition of protein synthesis in Reticulocyte lysates by trichodermin. Biochem. J. 154, 171-178.
23. Castric, P. (1994). Influence of oxygen on the Pseudomonas aeruginosa hydrogen cyanide synthase. Curr. Microbiol. 29, 19-21. doi: 10.1007/BF01570186
24. Castric, P. A. (1977). Glycine metabolism by Pseudomonas aeruginosa: hydrogen cyanide biosynthesis. J. Bacteriol. 130, 826-831.
25. Chen I., and Dubnau D. (2004). DNA uptake during bacterial transformation. Nat. Rev. Microbiol. 2, 241-249. doi: 10.1038/nrmicro844
26. Chen, L., Chen, J., Zheng, X., Zhang, J., and Yu, X. (2007). Identification and antifungal activity of the metabolite of endophytic fungi isolated from Llex cornuta. Chin. J. Pestic. Sci. 9, 143-150.
27. Chen, X.-H., Scholz, R., Borriss, M., Junge, H., Mogel, G., Kunz, S., et al. (2009). Difficidin and bacilysin produced by plant-associated Bacillus amyloliquefa- ciens are efficient in controlling fire blight disease. J. Biotechnol. 140, 38-44. doi: 10.1016/j.jbiotec.2008.10.015
28. Chen, X.-H., Vater, J., Piel, J., Franke, P., Scholz, R., Schneider, K., et al. (2006). Structural and functional characterization of three polyketide synthase gene clusters in Bacillus amyloliquefaciens FZB 42. J. Bacteriol. 188, 4024-4036. doi: 10.1128/JB.00052-06
29. Chernin, L., Brandis, A., Ismailov, Z., and Chet, I. (1996). Pyrrolnitrin production by an Enterobacter agglomerans strain with a broad spectrum of antagonistic activity towards fungal and bacterial phytopathogens. Curr. Microbiol. 32, 208-212. doi: 10.1007/s002849900037
30. Chin-A-Woeng, T. F., Bloemberg, G. V., van der Bij, A. J., van der Drift, K. M. M., Schripsema, J., Kroon, B., et al. (1998). Biocontrol by phenazine-1- carboxamide-producing Pseudomonas chlororaphis PCL1391 of tomato root rot caused by Fusarium oxysporum f. sp. Radicis-lycopersici. Mol. Plant Microbe Interact. 11, 1069-1077. doi: 10.1094/MPMI.1998.11.11.1069
31. Choi, S.-K., Park, S.-Y., Kim, R., Lee, C.-H., Kim, J. F., and Park, S. H. (2008). Identification and functional analysis of the fusaricidin biosynthetic gene of Paenibacilluspolymyxa E681. Biochem. Biophys. Res. Commun. 365, 89-95. doi: 10.1016/j.bbrc.2007.10.147
32. Choi, S.-K., Park, S.-Y., Kim, R., Kim, S.-B., Lee, C.-H., and Kim, J. F. (2009). Identification of a polymyxin synthetase gene cluster of Paenibacilluspolymyxa and heterologous expression of the gene in Bacillus subtilis. J. Bacteriol. 191, 3350-3358. doi: 10.1128/JB.01728-08
33. Chopra, S., Palencia, A., Virus, C., Tripathy, A., Temple, B. R., Velazquez-Campoy, A., et al. (2013). Plant tumour biocontrol agent employs a tRNA-dependent mechanism to inhibit leucyl-tRNA synthetase. Nat. Commun. 4, 1417. doi: 10.1038/ncomms2421
34. Compant, S., Duffy, B., Nowak, J., Clement, C., and Barka, E. A. (2005). Use ofplant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl. Environ. Microbiol. 71, 4951-4959. doi: 10.1128/AEM.71.9.4951-4959.2005
35. Constantinescu, F. (2001). Extraction and identification of antifungal metabolites produced by some B. subtilis strains. Analele Institutului de Cercetari 31, 17-23.
36. Costa, R., van Aarle, I. M., Mendes, R., and Elsas, J. D. (2009). Genomics of pyrrolnitrin biosynthetic loci: evidence for conservation and whole-operon mobility within Gram-negative bacteria. Environ. Microbiol. 11, 159-175. doi: 10.1111/j.1462-2920.2008.01750.x
37. Das, P. K., Basu, M., and Chatterjee, G. C. (1978). Studies on the mode of action of agrocin84. J. Antibiot. 31,490-492. doi: 10.7164/antibiotics.31.490
38. Deane, C. D., and Mitchell, D. A. (2014). Lessons learned from the transformation of natural product discovery to a genome-driven endeavor. J. Ind. Microbiol. Biotechnol. 41, 315-331. doi: 10.1007/s10295-013-1361-8
39. de Groot, A. N., van Dongen, P. W., Vree, T. B., Hekster, Y. A., and van Roos- malen, J. (1998). Ergot Alkaloids. Drugs 56, 523-535. doi: 10.2165/00003495199856040-00002
40. Delaney, S. M., Mavrodi, D. V., Bonsall, R. F., and Thomashow, L. S. (2001). phzO, a gene for biosynthesis of 2- hydroxylate phenazine compounds in Pseu- domonas auerofacines. J. Bacteriol. 183, 5376-5384. doi: 10.1128/JB.183.1.318-3272001
41. Delany, I., Sheehan, M. M., Fenton, A., Bardin, S., Aarons, S., and OGara, F. (2000). Regulation of production of the antifungal metabolite 2, 4- diacetylphloroglucinol in Pseudomonas fluorescens F113: genetic analysis of phlF as a transcriptional repressor. Microbiology 146, 537-546.
42. Dini-Andreote, F., and van Elsas, J. D. (2013). Back to the basics: the need for eco- physiological insights to enhance our understanding of microbial behaviour in the rhizosphere. Plant Soil 373, 1-15. doi: 10.1007/s11104-013-1687-z
43. Dotz, W. (1980). St. Anthony's fire. Am. J. Dermatopathol. 2, 249-254. doi: 10.1097/00000372-198000230-00013
44. Doull, J. L., Singh, A. K., Hoare, M., and Ayer, S. W. (1994). Conditions for the production of jadomycin B by Streptomyces venezuelae ISP5230: effects of heat shock, ethanol treatment and phage infection. J. Ind. Microbiol. 13, 120-125. doi: 10.1007/BF01584109
45. Dunlap, C. A., Bowman, M. J., and Schisler, D. A. (2013). Genomic analysis and secondary metabolite production in Bacillus amyloliquefaciens AS 43.3: a biocontrol antagonist of Fusarium head blight. Biol. Control 64, 166-175. doi: 10.1016/j.biocontrol.2012.11.002
46. Eilenberg, J. (2006). “Concepts and visions of biological control," in An Ecological and Societal Approach to Biological Control, eds J. Eilenberg and H. M. T. Hokkanen (Dordrecht: Springer), 1-11.
47. El-Banna, N., and Winkelmann, G. (1998). Pyrrolnitrin from Burkholderia cepacia: antibiotic activity against fungi and novel activities against streptomycetes. J. Appl. Microbiol. 85, 69-78. doi: 10.1046/j.1365-2672.1998.00473.x
48. Ellis, J., and Murphy, P. (1981). Four new opines from crown gall tumours - their detection and properties. Mol. Gen. Genet. 181, 36-43. doi: 10.1007/BF00339002
49. El-Sayed, A. K., Hothersall, J., Cooper, S. M., Stephens, E., Simpson, T. J., and Thomas, C. M. (2003). Characterization of the mupirocin biosynthesis gene cluster from Pseudomonas fluorescens NCIMB 10586. Chem. Biol. 10,419-430. doi: 10.1016/S1074-5521(03)00091-7
50. El-Sayed, A. K., Hothersall, J., and Thomas, C. M. (2001). Quorum-sensing- dependent regulation of biosynthesis of the polyketide antibiotic mupirocin in Pseudomonas fluorescens NCIMB 10586. Microbiology 147, 2127-2139.
51. El-Tarabily, K. A. (2003). An endophytic chitinase-producing isolate with potential for biological control of root rot of lupin caused by Plectosporium tabacinum. Aust. J. Bot. 51, 257-266. doi: 10.1071/BT02107
52. Eltringham, I. (1997). Mupirocin resistance and methicillin-resistant Staphylococcus aureus (MRSA). J. Hosp. Inf. 35, 1-8. doi: 10.1016/S0195-6701(97)90162-6
53. Emmert, E. A., Klimowicz, A. K., Thomas, M. G., and Handelsman, J. (2004). Genetics of zwittermicin A production by Bacillus cereus. Appl. Environ. Microbiol. 70, 104-113. doi: 10.1128/AEM.70.1.104-113.2004
54. Espinosa-Urgel, M. (2004). Plant-associated Pseudomonas populations: molecular biology, DNA dynamics, and gene transfer. Plasmid 52, 139-150. doi: 10.1016/j.plasmid.2004.06.004
55. Farrand, S. K., Slota, J. E., Shim, J. S., and Kerr, A. (1985). Tn5 insertions in the agrocin 84 plasmid: the conjugal nature of pAgK84 and the locations of determinants for transfer and agrocin 84 production. Plasmid 13, 106-117. doi: 10.1016/0147-619X(85)90063-0
56. Fleetwood, D. J., Scott, B., Lane, G. A., Tanaka, A., and Johnson, R. D. (2007). A complex ergovaline gene cluster in Epichloe endophytes of grasses. Appl. Environmen. Microbiol. 73,2571-2579. doi: 10.1128/AEM.00257-07
57. Flieger, M., Wurst, M., and Shelby, R. (1997). Ergot alkaloids-sources, structures and analytical methods. Folia Microbiol. 42, 3-30. doi: 10.1007/BF02898641
58. Frapolli, M., Pothier, J. F., Defago, G., and Moenne, Y. (2012). Evolutionary history of synthesis pathway genes for phloroglucinol and cyanide antimicrobials in plant-associated fluorescent pseudomonads. Mol. Phylogen. Evol. 63, 877-890. doi: 10.1016/j.ympev.2012.02.030
59. Freitas-Junior, L. H., Bottius, E., Pirrit, L. A., Deitsch, K. W., Scheidig, C., Guinet, F., et al. (2000). Frequent ectopic recombination of virulence factor genes in telomeric chromosome clusters of P. falciparum. Nature 407, 1018-1022. doi: 10.1038/35039531
60. Fuller, A., Mellows, G., Woolford, M., Banks, G., Barrow, K., and Chain, E. (1971). Pseudomonic acid: an antibiotic produced by Pseudomonas fluorescens. Nature 234, 416-417. doi: 10.1038/234416a0
61. Gales, A., Jones, R., and Sader, H. (2006). Global assessment of the antimicrobial activity of polymyxin B against 54 731 clinical isolates of Gram negative bacilli: report from the SENTRY antimicrobial surveillance programme (2001-2004). Clin. Microbiol. Infect. 12, 315-321. doi: 10.1111/j.1469-0691.2005.01351.x
62. Garbeva, P., and de Boer, W. (2009). Inter-specific interactions between carbon- limited soil bacteria affect behavior and gene expression. Microb. Ecol. 58, 36-46. doi: 10.1007/s00248-009-9502-3
63. Ge, Y.-H., Pei, D.-L., Zhao, Y.-H., Li, W.-W., Wang, S.-F., and Xu, Y.-Q. (2007). Correlation between antifungal agent phenazine-1-carboxylic acid and pyolu- teorin biosynthesis in Pseudomonas sp. m18. Curr. Microbiol. 54, 277-281. doi: 10.1007/s00284-006-0317-x
64. Giddens, S. R., Feng, Y., and Mahanty, H. K. (2002). Characterization of a novel phenazine antibiotic gene cluster in Erwinia herbicola Eh1087. Mol. Microbiol. 45, 769-783. doi: 10.1046/j.1365-2958.2002.03048.x
65. Groger, D., and Floss, H. G. (1998). “Biochemistry of ergot alkaloids - achievements and challenges," in TheAlkaloids: Chemistry and Biology, ed G. A. Cordell (New York, NY: Academic Press), 171-218.
66. Gueldner, R. C., Reilly, C. C., Pusey, P. L., Costello, C. E., Arrendale, R. F., Cox, R. H., et al. (1988). Isolation and identification of iturins as antifungal peptides in biological control of peach brown rot with Bacillus subtilis. J. Agric. Food Chem. 36, 366-370. doi: 10.1021/jf00080a031
67. Gurney, R., and Thomas, C. M. (2011). Mupirocin: biosynthesis, special features and applications of an antibiotic from a Gram-negative bacterium. Appl. Microbiol. Biotechnol. 90, 11-21. doi: 10.1007/s00253-011-3128-3
68. Gurusiddaiah, S., Weller, D., Sarkar, A., and Cook, R. (1986). Characterization of an antibiotic produced by a strain of Pseudomonas fluorescens inhibitory to Gaeumannomyces graminis var. tritici and Pythium spp. Antimicrob. Agent Chemother. 29,488-495. doi: 10.1128/AAC.29.3.488
69. Haarmann, T., Lorenz, N., and Tudzynski, P. (2008). Use of a nonhomolo- gous end joining deficient strain (Deltaku70) of the ergot fungus Clavi- ceps purpurea for identification of a nonribosomal peptide synthetase gene involved in ergotamine biosynthesis. Fungal Genet. Biol. 45, 35-44. doi: 10.1016/j.fgb.2007.04.008
70. Haarmann, T., Machado, C., Lubbe, Y., Correia, T., Schardl, C. L., Panaccione, D., et al. (2005). The ergot alkaloid gene cluster in Claviceps purpurea: extension of the cluster sequence and intra species evolution. Phytochemistry 66, 1312-1320. doi: 10.1016/j.phytochem.2005.04.011
71. Hamdache, A., Azarken, R., Lamarti, A., Aleu, J., and Collado, I. (2013). Comparative genome analysis of Bacillus spp. and its relationship with bioactive nonribosomal peptide production. Phytochem. Rev. 12, 685-716. doi: 10.1007/s11101-013-9278-4
72. Hammer, P. E., Burd, W., Hill, D. S., Ligon, J. M., and van Pee, K.-H. (1999). Conservation of the pyrrolnitrin biosynthetic gene cluster among six pyrrolnitrin- producing strains. FEMS Microbiol. Lett. 180, 39-44. doi: 10.1111/j.1574-6968.1999.tb08775.x
73. Hammer, P. E., Hill, D. S., Lam, S. T., van Pee, K. H., and Ligon, J. M. (1997). Four genes from Pseudomonas fluorescens that encode the biosynthesis of pyrrolnitrin. Appl. Environ. Microbiol. 63, 2147-2154.
74. Hammer, P., Evensen, K., and Janisiewicz, W. (1993). Postharvest control of Botrytis cinerea on cut rose flowers with pyrrolnitrin. Plant Dis. 77, 283-286. doi: 10.1094/PD-77-0283
75. Han, J. W., Kim, E. Y., Lee, J. M., Kim, Y. S., Bang, E., and Kim, B. S. (2012). Site-directed modification of the adenylation domain of the fusaricidin non- ribosomal peptide synthetase for enhanced production of fusaricidin analogs. Biotechnol. Lett. 34, 1327-1334. doi: 10.1007/s10529-012-0913-8
76. Han, L., Yang, K., Ramalingam, E., Mosher, R. H., and Vining, L. C. (1994). Cloning and characterization of polyketide synthase genes for jadomycin B biosynthesis in Streptomyces venezuelae ISP5230. Microbiology 140, 3379-3389. doi: 10.1099/13500872-140-12-3379
77. Hassan, H. M., and Fridovich, I. (1980). Mechanism of the antibiotic action pyocyanine. J. Bacteriol. 141, 156-163.
78. Hassett, D. J., Schweizer, H. P., and Ohman, D. E. (1995). Pseudomonas aeruginosa sodA and sodB mutants defective in manganese-and iron-cofactored superoxide dismutase activity demonstrate the importance of the iron-cofactored form in aerobic metabolism. J. Bacteriol. 177, 6330-6337.
79. Hayman, G., and Farrand, S. (1988). Characterization and mapping of the agrocinopine-agrocin 84 locus on the nopaline Ti plasmid pTiC58. J. Bacteriol. 170, 1759-1767.
80. Heinig, U., Scholz, S., and Jennewein, S. (2013). Getting to the bottom of taxol biosynthesis by fungi. Fungal Divers. 60, 161-170. doi: 10.1007/s13225-013-0228-7
81. Heinstein, P. F., Lee, S. I., and Floss, H. G. (1971). Isolation of dimethylal- lylpyrophosphate: tryptophan dimethylallyl transferase from the ergot fungus (Claviceps spec.). Biochem. Biophys. Res. Commun. 44, 1244-1251. doi: 10.1016/S0006-291X(71)80219-X
82. Hezari, M., Lewis, N. G., and Croteau, R. (1995). Purification and characterization of taxa-4(5),11(12)-diene synthase from pacific yew (Taxus brevifolia) that catalyzes the first committed step of taxol biosynthesis. Arch. Biochem. Biophys. 322, 437-444. doi: 10.1006/abbi.1995.1486
83. Hilton, M. D., Alaeddinoglu, N. G., and Demain, A. L. (1988). Synthesis of bacilysin by Bacillus subtilis branches from prephenate of the aromatic amino acid pathway. J. Bacteriol. 170, 482-484.
84. Hjort, K., Bergstrom, M., Adesina, M. F., Jansson, J. K., Smalla, K., and Sjoling, S. (2010). Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen suppressive soil. FEMSMicrobiol. Ecol. 71, 197-207. doi: 10.1111/j.1574-6941.2009.00801.x
85. Hohn, T. M., and Beremand, P. D. (1989). Isolation and nucleotide sequence of a sesquiterpene cyclase gene from the trichothecene-producing fungus Fusarium sporotrichioides. Gene 79, 131-138. doi: 10.1016/0378-1119(89)90098-X
86. Hong, S. Y., and Linz, J. E. (2008). Functional expression and subcellular localization of the aflatoxin pathway enzyme Ver-1 fused to enhanced green fluorescent protein. Appl. Environ. Microbiol. 74, 6385-6396. doi: 10.1128/AEM.01185-08
87. Horwitz, S. B. (1994). Taxol (paclitaxel): mechanisms of action. Ann. Oncol. 5(Suppl. 6), S3-S6.
88. Howard, M. B., Ekborg, N. A., Taylor, L. E., Weiner, R. M., and Hutcheson, S. W. Chitinase B of “microbulbifer degradans" 2-40 contains two catalytic domains with different chitinolytic activities. J. Bacteriol. 186, 1297-1303. doi: 10.1128/JB.186.5.1297-1303.2004
89. Howell, C. R., and Stipanovic, R. D. (1980). Suppression of Pythium ultimum- induced damping-off of cotton seedlings by Pseudomonas fluorescens and its antibiotic, pyoluteorin. Phytopathology70, 712-715. doi: 10.1094/Phyto-70-712
90. Hughes, J., and Mellows, G. (1980). Interaction of pseudomonic acid A with Escherichia coli B isoleucyl-tRNA synthetase. Biochem. J. 191, 209-219.
91. Humair, B., Wackwitz, B., and Haas, D. (2010). GacA-controlled activation of promoters for small RNA genes in Pseudomonas fluorescens. Appl. Environ. Microbiol. 76, 1497-1506. doi: 10.1128/AEM.02014-09
92. Ibba, M., and Soll, D. (2000). Aminoacyl-tRNA synthesis. Ann. Rev. Biochem. 69, 617-650. doi: 10.1146/annurev.biochem.69.1.617
93. Inaoka, T., Takahashi, K., Ohnishi-Kameyama, M., Yoshida, M., and Ochi, K. (2003). Guanine nucleotides guanosine 5x-diphosphate 3x-diphosphate and GTP co-operatively regulate the production of an antibiotic bacilysin in Bacillus subtilis. J. Biol. Chem. 278,2169-2176. doi: 10.1074/jbc.M208722200
94. Inaoka, T., Wang, G., and Ochi, K. (2009). ScoC regulates bacilysin production at the transcription level in Bacillus subtilis. J. Bacteriol. 191, 7367-7371. doi: 10.1128/JB.01081-09
95. Jakeman, D. L., Bandi, S., Graham, C. L., Reid, T. R., Wentzell, J. R., and Douglas, S. E. (2009). Antimicrobial activities of jadomycin B and structurally related analogues. Antimicrob. Agent Chemother. 53, 1245-1247. doi: 10.1128/AAC.00801-08
96. Janczarek, M., Rachwal, K., Marzec, A., Grza, J., and Palusmska-Szysz, M. (2015). Signal molecules and cell-surface components involved in early stages of the legume-rhizobium interactions. Appl. Soil Ecol. 85, 94-113. doi: 10.1016/j.apsoil.2014.08.010
97. Johnston-Monje, D., and Raizada, M. N. (2011). Conservation and diversity of seed associated endophytes in across boundaries of evolution, ethnography and ecology. PLoS ONE. 6:e20396. doi: 10.1371/journal.pone.0020396
98. Kajimura, Y., and Kaneda, M. (1996). Fusaricidin A, a new depsipeptide antibiotic produced by Bacillus polymyxa KT-8. Taxonomy, fermentation, isolation, structure elucidation and biological activity. J. Antibiot. 49, 129-135. doi: 10.7164/antibiotics.49.129
99. Kajimura, Y., and Kaneda, M. (1997). Fusaricidins B, C and D, new depsipeptide antibiotics produced by Bacillus polymyxa KT-8: isolation, structure elucidation and biological activity. J. Antibiot. 50, 220-228. doi: 10.7164/antibiotics.50.220
100. Karlsson, M., and Stenlid, J. (2008). Evolution of family 18 glycoside hydrolases: diversity, domain structures and phylogenetic relationships. J. Mol. Microbiol. Biotechnol. 16, 208-223. doi: 10.1159/000151220
101. Keller, L., and Surette, M. G. (2006). Communication in bacteria: an ecological and evolutionary perspective. Nat. Rev. Microbiol. 4, 249-258. doi: 10.1038/nrmicro1383
102. Keller, N. P., Turner, G., and Bennett, J. W. (2005). Fungal secondary metabolism- from biochemistry to genomics. Nat. Rev. Microbiol. 3, 937-947. doi: 10.1038/nrmicro1286
103. Kenig, M., and Abraham, E. (1976). Antimicrobial activities and antagonists of bacilysin and anticapsin. J. Gen. Microbiol. 94, 37-45. doi: 10.1099/0022128794-1-37
104. Kenig, M., vandamme, E. T., and Abraham, E. (1976). The mode of action of bacilysin and anticapsin and biochemical properties of bacilysin-resistant mutants. J. Gen. Microbiol. 94, 46-54. doi: 10.1099/00221287-94-1-46
105. Kevany, B. M., Rasko, D. A., and Thomas, M. G. (2009). Characterization of the complete zwittermicin A biosynthesis gene cluster from Bacillus cereus. Appl. Environ. Microbiol. 75, 1144-1155. doi: 10.1128/AEM.02518-08
106. Kidane, D., Carrasco, B., Manfredi, C., Rothmaier, K., Ayora, S., Tadesse, S., et al. (2009). Evidence for different pathways during horizontal gene transfer in competent Bacillus subtilis cells. PLoS Genet. 5:e1000630. doi: 10.1371/journal.pgen.1000630
107. Kim, B.-Y., Lee, S.-Y., Ahn, J.-H., Song, J., Kim, W.-G., and Weon, H.-Y. (2015). Complete genome sequence of Bacillus amyloliquefaciens subsp. plantarum CC178, a phyllosphere bacterium antagonistic to plant pathogenic fungi. Genome Announc. 3, e01368-e01314. doi: 10.1128/genomeA.01368-14
108. Kim, H., and Farrand, S. K. (1997). Characterization of the acc operon from the nopaline-type Ti plasmid pTiC58, which encodes utilization of agrocinopines A and B and susceptibility to agrocin 84. J. Bacteriol. 179, 7559-7572.
109. Kim, J.-G., Park, B. K., Kim, S.-U., Choi, D., Nahm, B. H., Moon, J. S., et al. (2006). Bases of biocontrol: sequence predicts synthesis and mode of action of agrocin 84, the trojan horse antibiotic that controls crown gall. Proc. Natl. Acad. Sci. U.S.A. 103,8846-8851. doi: 10.1073/pnas.0602965103
110. Kirner, S., Hammer, P. E., Hill, D. S., Altmann, A., Fischer, I., Weislo, L. J., et al. (1998). Functions encoded by pyrrolnitrin biosynthetic genes from Pseu- domonas fluorescens. J. Bacteriol. 180, 1939-1943.
111. Kistler, H., and Broz, K. (2015). Cellular compartmentalization of secondary metabolism. Front. Microbiol. 6:68. doi: 10.3389/fmicb.2015.00068
112. Kobayashi, D. Y., Reedy, R. M., Bick, J., and Oudemans, P. V. (2002). Characterization of a chitinase gene from Stenotrophomonas maltophilia strain 34S1 and its involvement in biological control. Appl. Environ. Microbiol. 68, 1047-1054. doi: 10.1128/AEM.68.3.1047-1054.2002
113. Koroglu, T. E., Ogulur, I., Mutlu, S., Yazgan-Karatas, A., and Ozcengiz, G. (2011). Global regulatory systems operating in bacilysin biosynthesis in Bacillus sub- tilis. J. Mol. Microbiol. Biotechnol. 20, 144-155. doi: 10.1159/000328639
114. Kraus, J., and Loper, J. E. (1995). Characterization of a genomic region required for production of the antibiotic pyoluteorin by the biological control agent Pseudomonas fluorescens Pf-5. Appl. Environ. Microbiol. 61, 849-854.
115. Kusari, S., Hertweck, C., and Spiteller, M. (2012). Chemical ecology of endophytic fungi: origins of secondary metabolites. Chem. Biol. 19, 792-798. doi: 10.1016/j.chembiol.2012.06.004
116. Laville, J., Blumer, C., Von Schroetter, C., Gaia, V., Defago, G., Keel, C., et al. (1998). Characterization of the hcnABC gene cluster encoding hydrogen cyanide synthase and anaerobic regulation by ANR in the strictly aerobic biocontrol agent Pseudomonas fluorescens CHA0. J. Bacteriol. 180, 3187-3196.
117. Leclere, V., Bechet, M., Adam, A., Guez, J., Wathelet, B., Ongena, M., et al. Mycosubtilin overproduction by Bacillus subtilis BBG100 enhances the organism's antagonistic and biocontrol activities. Appl. Environ. Microbiol. 71, 4577-4584. doi: 10.1128/AEM.71.8.4577-4584.2005
118. Lee, C. A., Auchtung, J. M., Monson, R. E., and Grossman, A. D. (2007). Identification and characterization of int (integrase), xis (excisionase) and chromosomal attachment sites of the integrative and conjugative element ICEBs1 of Bacillus subtilis. Mol. Microbiol. 66, 1356-1369. doi: 10.1111/j.1365-2958.2007.06000.x
119. Leoffler, W., Tschen, J., Venittanakom, N., Kugler, M., Knorpp, E., Hsieh, T. F., et al. (1986). Antifungal effects of bacilysin and fengycin from Bacillus subtilis F-29-3: a comparison with activaties of other Bacillus antibiotics. J. Phytopathol. 115,204-213. doi: 10.1111/j.1439-0434.1986.tb00878.x
120. Letunic, I., and Bork, P. (2011). Interactive Tree of Life v2: online annotation and display of phylogenetic trees made easy. Nucl. Acids Res. 39, W475-W478. doi: 10.1093/nar/gkr201
121. Ligon, J. M., Hill, D. S., Hammer, P. E., Torkewitz, N. R., Hofmann, D., Kempf, H. J., et al. (2000). Natural products with antifungal activity from Pseu- domonas biocontrol bacteria. Pest Manag. Sci. 56, 688-695. doi: 10.1002/1526-4998(200008)56:8
122. Li, J., and Jensen, S. E. (2008). Nonribosomal biosynthesis of fusaricidins by Paenibacilluspolymyxa pkb1 involves direct activation of a d-amino acid. Chem. Biol. 15, 118-127. doi: 10.1016/j.chembiol.2007.12.014
123. Li, J., Nation, R. L., Turnidge, J. D., Milne, R. W., Coulthard, K., Rayner, C. R., et al. (2006). Colistin: the re-emerging antibiotic for multidrug-resistant Gram- negative bacterial infections. Lancet Infect. Dis. 6, 589-601. doi: 10.1016/S1473-3099(06)70580-1
124. Li, S., Zhang, R., Wang, Y., Zhang, N., Shao, J., Qiu, M., et al. (2013). Promoter analysis and transcription regulation of fus gene cluster responsible for fusaricidin synthesis of Paenibacillus polymyxa SQR-21. Appl. Microbiol. Biotechnol. 97, 9479-9489. doi: 10.1007/s00253-013-5157-6
125. Lim, F. Y., and Keller, N. P. (2014). Spatial and temporal control of fungal natural product synthesis. Nat. Prod. Rep. 31, 1277-1286. doi: 10.1039/C4NP00083H
126. Lodeiro, S., Xiong, Q., Wilson, W. K., Ivanova, Y., Smith, M. L., May, G. S., et al. (2009). Protostadienol biosynthesis and metabolism in the pathogenic fungus Aspergillus fumigatus. Org. Lett. 11, 1241-1244. doi: 10.1021/ol802696a
127. Lu, J., Huang, X., Li, K., Li, S., Zhang, M., Wang, Y., et al. (2009). LysR family transcriptional regulator PqsR as repressor of pyoluteorin biosynthesis and activator of phenazine-1-carboxylic acid biosynthesis in Pseudomonas sp. M18. J. Biotechnol. 143, 1-9. doi: 10.1016/j.jbiotec.2009.06.008
128. Luo, Y., Ruan, L.-F., Zhao, C.-M., Wang, C.-X., Peng, D.-H., and Sun, M. (2011). Validation of the intact zwittermicin A biosynthetic gene cluster and discovery of a complementary resistance mechanism in Bacillus thuringiensis. Antimi- crob. Agent Chemother. 55, 4161-4169. doi: 10.1128/AAC.00111-11
129. Marcet-Houben, M., and Gabaldon, T. (2010). Acquisition of prokaryotic genes by fungal genomes. Trends Genet. 26, 5-8. doi: 10.1016/j.tig.2009.11.007
130. Martinez-Garcia, P. M., Ruano-Rosa, D., Schiliro, E., Prieto, P., Ramos, C., Rodriguez-Palenzuela, P., et al. (2015). Complete genome sequence of Pseu- domonas fluorescens strain PICF7, an indigenous root endophyte from olive (Olea europaea L.) and effective biocontrol agent against Verticillium dahliae. Stand. GenomicSci. 10:10. doi: 10.1186/1944-3277-10-10
131. Mavrodi, D. V., Blankenfeldt, W., and Thomashow, L. S. (2006). Phenazine compounds in fluorescent Pseudomonas spp. biosynthesis and regulation. Annu. Rev. Phytopathol. 44, 417-445. doi: 10.1146/annurev.phyto.44.013106.145710
132. Mavrodi, D. V., Parejko, J. A., Mavrodi, O. V., Kwak, Y., Weller, D. M., Blanken- feldt, W., et al. (2013). Recent insights into the diversity, frequency and ecological roles of phenazines in fluorescent Pseudomonas spp. Environ. Microbiol. 15, 675-686. doi: 10.1111/j.1462-2920.2012.02846.x
133. Mavrodi, D. V., Peever, T. L., Mavrodi, O. V., Parejko, J. A., Raaijmak- ers, J. M., Lemanceau, P., et al. (2010). Diversity and evolution of the phenazine biosynthesis pathway. Appl. Environ. Microbiol. 76, 866-879. doi: 10.1128/AEM.02009-09
134. Mavrodi, O. V., McSpadden, G. B. B., Mavrodi, D. V., Bonsall, R. F., Weller, D. M., and Thomashow, L. S. (2001). Genetic diversity of phlD from 2,4- diacetylphloroglucinol-producing fluorescent Pseudomonas spp. Phytopathology 91, 35-43. doi: 10.1094/PHYTO.2001.91.1.35
135. Mazzola, M., Cook, R. J., Thomashow, L. S., Weller, D., and Pierson, L. (1992). Contribution of phenazine antibiotic biosynthesis to the ecological competence of fluorescent pseudomonads in soil habitats. Appl. Environ. Microbiol. 58, 2616-2624.
136. McDonald, M., Mavrodi, D. V., Thomashow, L. S., and Floss, H. G. (2001). Phenazine biosynthesis in Pseudomonas fluorescens: branchpoint from the primary shikimate biosynthetic pathway and role of phenazine-1,6-dicarboxylic acid. J.Am. Chem. Soc. 123, 9459-9460. doi: 10.1021/ja011243+
137. McSpadden Gardener, B. B., Schroeder, K. L., Kalloger, S. E., Raaijmakers, J. M., Thomashow, L. S., and Weller, D. M. (2000). Genotypic and phenotypic diversity of phlD containing Pseudomonas strains isolated from the rhizosphere of wheat. Appl. Environ. Microbiol. 66, 1939-1946. doi: 10.1128/AEM.66.5.1939-1946.2000
138. Moule, Y., Jemmali, M., and Rousseau, N. (1976). Mechanism of the inhibition of transcription by pr toxin, a mycotoxin from Penicillium roqueforti. Chem. Biol. Interact. 14,207-216. doi: 10.1016/0009-2797(76)90101-0
139. Mousa, W. K., and Raizada, M. N. (2013). The diversity of anti-microbial secondary metabolites produced by fungal endophytes: an interdisciplinary perspective. Front. Microbiol. 4:65. doi: 10.3389/fmicb.2013.00065
140. Nodwell, J. R. (2014). Are you talking to me? a possible role for y butyrolactones in interspecies signalling. Mol. Microbiol. 94, 483-485. doi: 10.1111/mmi.12787
141. Nowak-Thompson, B., Chaney, N., Wing, J. S., Gould, S. J., and Loper, J. E. (1999). Characterization of the pyoluteorin biosynthetic gene cluster of Pseudomonas fluorescens Pf-5. J. Bacteriol. 181, 2166-2174.
142. Parker, J. B., and Walsh, C. T. (2012). Olefin isomerization regiochemistries during tandem action of bacA and bacB on prephenate in bacilysin biosynthesis. Biochemistry 51, 3241-3251. doi: 10.1021/bi300254u
143. Pessi, G., and Haas, D. (2000). Transcriptional control of the hydrogen cyanide biosynthetic genes hcnABC by the anaerobic regulator ANR and the quorum-sensing regulators LasR and RhlR in Pseudomonas aeruginosa. J. Bacteriol. 182, 6940-6949. doi: 10.1128/JB.182.24.6940-6949.2000
144. Pham, V. H., and Kim, J. (2012). Cultivation of unculturable soil bacteria. Trends Biotechnol. 30,475-484. doi: 10.1016/j.tibtech.2012.05.007
145. Phister, T. G., O'Sullivan, D. J., and McKay, L. L. (2004). Identification of bacilysin, chlorotetaine, and iturin a produced by Bacillus sp. strain cs93 isolated from pozol, a Mexican fermented maize dough. Appl. Environ. Microbiol. 70, 631-634. doi: 10.1128/AEM.70.1.631-634.2004
146. Picard, C., Di Cello, F., Ventura, M., Fani, R., and Guckert, A. (2000). Frequency and biodiversity of 2, 4-diacetylphloroglucinol-producing bacteria isolated from the maize rhizosphere at different stages of plant growth. Appl. Environ. Microbiol. 66, 948-955. doi: 10.1128/AEM.66.3.948-955.2000
147. Pierson, I. L. S., and Pierson, E. A. (2010). Metabolism and function of phenazines in bacteria: impacts on the behavior of bacteria in the environment and biotechnological processes. Appl. Microbiol. Biotechnol. 86, 1659-1670. doi: 10.1007/s00253-010-2509-3
148. Pierson, I. L., Wood, D., Pierson, E., and Chancey, S. (1998). N-acyl-homoserine lactone-mediated gene regulation in biological control by fluorescent pseudomonads: current knowledge and future work. Eur. J. Plant Pathol. 104, 1-9. doi: 10.1023/A:1008674417007
149. Prakash, N. U., Jayanthi, M., Sabarinathan, R., Kangueane, P., Mathew, L., and Sekar, K. (2010). Evolution, homology conservation, and identification of unique sequence signatures in GH19 family chitinases. J. Mol. Evol. 70, 466-478. doi: 10.1007/s00239-010-9345-z
150. Prieto, M., and Wedin, M. (2013). Dating the diversification of the major lineages of Ascomycota (Fungi). PLoS ONE 8:e65576. doi: 10.1371/journal.pone.0065576
151. Proctor, R. H., and Hohn, T. M. (1993). Aristolochene synthase. isolation, characterization, and bacterial expression of a sesquiterpenoid biosynthetic gene (Ari1) from Penicillium roqueforti. J. Biol. Chem. 268, 4543-4548.
152. Proctor, R. H., McCormick, S. P., Alexander, N. J., and Desjardins, A. E. (2009). Evidence that a secondary metabolic biosynthetic gene cluster has grown by gene relocation during evolution of the filamentous fungus Fusarium. Mol. Microbiol. 74, 1128-1142. doi: 10.1111/j.1365-2958.2009.06927.x
153. Quecine, M. C., Araujo, W. L., Marcon, J., Gai, C. S., Azevedo, J. L., and Pizzirani- Kleiner, A. A. (2008). Chitinolytic activity of endophytic Streptomyces and potential for biocontrol. Lett. Appl. Microbiol. 47,486-491. doi: 10.1111/j.1472-765X.2008.02428.x
154. Raffel, S. J., Stabb, E. V., Milner, J. L., and Handelsman, J. (1996). Genotypic and phenotypic analysis of zwittermicin A-producing strains of Bacillus cereus. Microbiology 142, 3425-3436. doi: 10.1099/13500872-142-12-3425
155. Rajavel, M., Mitra, A., and Gopal, B. (2009). Role of Bacillus subtilis BacB in the synthesis of bacilysin. J. Biol. Chem. 284, 31882-31892. doi: 10.1074/jbc.M109.014522
156. Reader, J. S., Ordoukhanian, P. T., Kim, J.-G., de Crecy-Lagard, V., Hwang, I., Far- rand, S., et al. (2005). Major biocontrol of plant tumors targets tRNA synthetase. Science 309, 1533-1533. doi: 10.1126/science.1116841
157. Rehmeyer, C., Li, W., Kusaba, M., Kim, Y.-S., Brown, D., Staben, C., et al. (2006). Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae. Nucl. Acids Res. 34, 4685-4701. doi: 10.1093/nar/gkl588
158. Roberts, W., and Tate, M. (1977). Agrocin 84 is a 6-N-phosphoramidate of an adenine nucleotide analogue. Nature 265, 379-381. doi: 10.1038/265379a0
159. Roze, L. V., Chanda, A., and Linz, J. E. (2011). Compartmentalization and molecular traffic in secondary metabolism: a new understanding of established cellular processes. Fungal Genet. Biol. 48, 35-48. doi: 10.1016/j.fgb.2010.05.006
160. Santoyo, G., Orozco-Mosqueda, M. D. C., and Govindappa, M. (2012). Mechanisms of biocontrol and plant growth-promoting activity in soil bacterial species of Bacillus and Pseudomonas: a review. Bio. Sci. Technol. 22, 855-872. doi: 10.1080/09583157.2012.694413
161. Schaberle, T. F., Vollmer, W., Frasch, H.-J., Huttel, S., Kulik, A., Rottgen, M., et al. (2011). Self-resistance and cell wall composition in the glycopeptide producer Amycolatopsis balhimycina. Antimicrob. Agent. Chemother. 55, 4283-4289. doi: 10.1128/AAC.01372-10
162. Schardl, C. L. (2010). The epichloae, symbionts of the grass subfamily pooideae1. Ann. Mo. Bot. Gard. 97, 646-665. doi: 10.3417/2009144
163. Scheffler, R., Colmer, S., Tynan, H., Demain, A., and Gullo, V. (2013). Antimicrobials, drug discovery, and genome mining. Appl. Microbiol. Biotechnol. 97, 969-978. doi: 10.1007/s00253-012-4609-8
164. Schneider, K., Chen, X.-H., Vater, J., Franke, P., Nicholson, G., Borriss, R., et al. (2007). Macrolactin is the polyketide biosynthesis product of the pks2 cluster of Bacillus amyloliquefaciens FZB42. J. Nat. Prod. 70, 1417-1423. doi: 10.1021/np070070k
165. Schwarzer, D., Finking, R., and Marahiel, M. A. (2003). Nonribosomal peptides: from genes to products. Nat. Prod. Rep. 20, 275-287. doi: 10.1039/b111145k
166. Shaheen, M., Li, J., Ross, A. C., Vederas, J. C., and Jensen, S. E. (2011). Paenibacillus polymyxa PKB1 produces variants of polymyxin B-type antibiotics. Chem. Biol. 18, 1640-1648. doi: 10.1016/j.chembiol.2011.09.017
167. Shanahan, P., Borro, A., O'Gara, F., and Glennon, J. D. (1992). Isolation, trace enrichment and liquid chromatographic analysis of diacetylphloroglucinol in culture and soil samples using UV and amperometric detection. J. Chromatogr. 606, 171-177. doi: 10.1016/0021-9673(92)87022-Z
168. Silby, M. W., Winstanley, C., Godfrey, S. A., Levy, S. B., and Jackson, R. W. Pseudomonas genomes: diverse and adaptable. FEMS Microbiol. Rev. 35, 652-680. doi: 10.1111/j.1574-6976.2011.00269.x
169. Silo-Suh, L. A., Stabb, E. V., Raffel, S. J., and Handelsman, J. (1998). Target range of zwittermicin A, an aminopolyol antibiotic from Bacillus cereus. Curr. Microbiol. 37, 6-11. doi: 10.1007/s002849900328
170. Silva, G. H., de Oliveira, C. M., Teles, H. L., Pauletti, P. M., Castro-Gamboa, I., Silva, D. H. S., et al. (2010). Sesquiterpenes from Xylaria sp., an endophytic fungus associated with Piper aduncum (Piperaceae). Phytochem. Lett. 3, 164-167. doi: 10.1016/j.phytol.2010.07.001
171. Soliman, S., and Raizada, M. N. (2013). Interactions between co-habitating fungi elicit synthesis of Taxol from an endophytic fungus in host Taxus plants. Front. Microbiol. 4:3. doi: 10.3389/fmicb.2013.00003
172. Soliman, S., Trobacher, C., Tsao, R., Greenwood, J., and Raizada, M. N. (2013). A fungal endophyte induces transcription of genes encoding a redundant fungicide pathway in its host plant. BMC Plant Biol. 13:93. doi: 10.1186/14712229-13-93
173. Souza, J. T., and Raaijmakers, J. M. (2003). Polymorphisms within the prnD and pltC genes from pyrrolnitrin and pyoluteorin-producing Pseudomonas and Burkholderia spp. FEMS Microbiol. Ecol. 43, 21-34. doi: 10.1111/j.1574-6941.2003.tb01042.x
174. Spatafora, J. W., Sung, G.-H., Johnson, D., Hesse, C., O'Rourke, B., Serdani, M., et al. (2006). A five-gene phylogeny of Pezizomycotina. Mycologia 98, 1018-1028. doi: 10.3852/mycologia.98.6.1018
175. Spiering, M. J., Moon, C. D., Wilkinson, H. H., and Schardl, C. L. (2005). Gene clusters for insecticidal loline alkaloids in the grass-endophytic fungus Neotyphodium uncinatum. Genetics 169, 1403-1414. doi: 10.1534/genetics.104.035972
176. Stegmann, E., Frasch, H.-J., Kilian, R., and Pozzi, R. (2015). Self-resistance mechanisms of actinomycetes producing lipid II-targeting antibiotics. Int. J. Med. Microbiol. 305, 190-195. doi: 10.1016/j.ijmm.2014.12.015
177. Stein, T. (2005). Bacillus subtilis antibiotics: structures, synthesis and specific functions. Mol. Microbiol. 56, 845-857. doi: 10.1111/j.1365-2958.2005.04587.x
178. Steinborn, G., Hajirezaei, M.-R., and Hofemeister, J. (2005). bac genes for recombinant bacilysin and anticapsin production in Bacillus host strains. Arch. Microbiol. 183, 71-79. doi: 10.1007/s00203-004-0743-8
179. Stewart, E. J. (2012). Growing unculturable bacteria. J. Bacteriol. 194, 4151-4160. doi: 10.1128/JB.00345-12
180. Storm, D. R., Rosenthal, K. S., and Swanson, P. E. (1977). Polymyxin and related peptide antibiotics. Ann. Rev. Biochem. 46, 723-763. doi: 10.1146/annurev.bi.46.070177.003451
181. Sutherland, R., Boon, R., Griffin, K., Masters, P., Slocombe, B., and White, A. (1985). Antibacterial activity of mupirocin (pseudomonic acid), a new antibiotic for topical use. Antimicrob. Agents Chemother. 27, 495-498. doi: 10.1128/AAC.27.4.495
182. Svercel, M., Duffy, B., and Defago, G. (2007). PCR amplification of hydrogen cyanide biosynthetic locus hcnaB in Pseudomonas spp. J. Microbiol. Methods 70,209-213. doi: 10.1016/j.mimet.2007.03.018
183. Takeno, A., Okamoto, A., Tori, K., Oshima, K., Hirakawa, H., Toh, H., et al. Complete genome sequence of Bacillus cereus NC7401, which produces high levels of the emetic toxin cereulide. J. Bacteriol. 194, 4767-4768. doi: 10.1128/JB.01015-12
184. Tazawa, J., Watanabe, K., Yoshida, H., Sato, M., and Homma, Y. (2000). Simple method of detection of the strains of fluorescent Pseudomonas spp. producing antibiotics, pyrrolnitrin and phloroglucinol. SoilMicroorg. 54, 61-67.
185. Thimon, L., Peypoux, F., Wallach, J., and Michel, G. (1995). Effect of the lipopeptide antibiotic, iturin A, on morphology and membrane ultrastructure of yeast cells. FEMS Microbiol. Lett. 128, 101-106. doi: 10.1111/j.1574-6968.1995.tb07507.x
186. Tijerino, A., Elena, C. R., Moraga, J., Malmierca, M. G., Vicente, F., Aleu, J., et al. (2011). Overexpression of the trichodiene synthase gene tri5 increases tricho- dermin production and antimicrobial activity in Trichoderma brevicompactum. Fungal Gene. Biol. 48,285-296. doi: 10.1016/j.fgb.2010.11.012
187. Tobes, R., and Pareja, E. (2005). Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation. Res. Microbiol. 156, 424-433. doi: 10.1016/j.resmic.2004.10.014
188. Tobes, R., and Pareja, E. (2006). Bacterial repetitive extragenic palindromic sequences are DNA targets for insertion sequence elements. BMC Genomics 7:62. doi: 10.1186/1471-2164-7-62
189. Tsuge, K., Akiyama, T., and Shoda, M. (2001). Cloning, sequencing, and characterization of the iturin A operon. J. Bacteriol. 183, 6265-6273. doi: 10.1128/JB.183.21.6265-6273.2001
190. van Rij, E. T., Girard, G., Lugtenberg, B. J., and Bloemberg, G. V. (2005). Influence of fusaric acid on phenazine-1-carboxamide synthesis and gene expression of Pseudomonas chlororaphis strain PCL1391. Microbiology 151, 2805-2814. doi: 10.1099/mic.0.28063-0
191. Vetsigian, K., Jajoo, R., and Kishony, R. (2011). Structure and evolution of Strep- tomyces interaction networks in soil and in silico. PLoS Biol. 9:e1001184. doi: 10.1371/journal.pbio.1001184
192. Vining, L. C. (1992). Secondary metabolism, inventive evolution and biochemical diversity - a review. Gene 115, 135-140. doi: 10.1016/0378-1119(92)90551-Y
193. Viswanathan, R., and Samiyappan, R. (2001). Antifungal activity of chitinases produced by some fluorescent pseudomonads against Colletotrichum falcatum Went causing red rot disease in sugarcane. Microbiol. Res. 155, 309-314. doi: 10.1016/S0944-5013(01)80009-4
194. Vizcaino, M. I., Guo, X., and Crawford, J. M. (2014). Merging chemical ecology with bacterial genome mining for secondary metabolite discovery. J. Ind. Microbiol. Biotechnol. 41,285-299. doi: 10.1007/s10295-013-1356-5
195. Voisard, C., Bull, C. T., Keel, C., Laville, J., Maurhofer, M., Schnider, U., et al. (1994). “Biocontrol of root diseases by Pseudomonas fluorescens CHA0: current concepts and experimental approaches" in Molecular Ecology of Rhizosphere Microorganisms, eds F. O'Gara, D. Dowling, and B. Boesten (Weinheim: VCH Publishers), 67-89.
196. Voisard, C., Keel, C., Haas, D., and Defago, G. (1989). Cyanide production byPseu- domonas fluorescens helps suppress black root rot of tobacco under gnotobiotic conditions. EMBO J. 8, 351-358.
197. Walker, J., and Abraham, E. (1970). The structure of bacilysin and other products of Bacillus subtilis. Biochem. J. 118, 563-570.
198. Wallwey, C., and Li, S. (2011). Ergot alkaloids: structure diversity, biosynthetic gene clusters and functional proof of biosynthetic genes. Nat. Prod. Rep. 28, 496-510. doi: 10.1039/C0NP00060D
199. Wang, C.-L., Farrand, S. K., and Hwang, I. (1994). Organization and expression of the genes on pAgK84 that encode production of agrocin 84. Mol. Plant Microbe Interact. 7, 472-481. doi: 10.1094/MPMI-7-0472
200. Wani, M. C., Taylor, H. L., Wall, M. E., Coggon, P., and McPhail, A. T. (1971). Plant antitumor agents. VI. isolation and structure of Taxol, a novel antileukemic and antitumor agent from Taxus brevifolia. J. Am. Chem. Soc. 93, 2325-2327. doi: 10.1021/ja00738a045
201. Wei, C., Hansen, B. S., Vaughan, M. H., and McLaughlin, C. S. (1974). Mechanism of action of the mycotoxin trichodermin, a 12,13-epoxytrichothecene. Proc. Natl. Acad. Sci. U.S.A. 71,713-717. doi: 10.1073/pnas.71.3.713
202. Westman, E. L., Yan, M., Waglechner, N., Koteva, K., and Wright, G. D. (2013). Self resistance to the atypical cationic antimicrobial peptide edeine of Brevibacil- lus brevis Vm4 by the N-acetyltransferase EdeQ. Chem. Biol. 20, 983-990. doi: 10.1016/j.chembiol.2013.06.010
203. Whatling, C. A., Hodgson, J. E., Burnham, M. K. R., Clarke, N. J., Franklin, F. C. H., and Thomas, C. M. (1995). Identification of a 60 kb region of the chromosome of Pseudomonas fluorescens NCIB 10586 required for the biosynthesis of pseudomonic acid. Microbiology 141, 973-982. doi: 10.1099/13500872141-4-973
204. Whitehead, N. A., Barnard, A. M., Slater, H., Simpson, N. J., and Salmond, G. P. (2001). Quorum-sensing in Gram-negative bacteria. FEMS Microbiol. Rev. 25, 365-404. doi: 10.1111/j.1574-6976.2001.tb00583.x
205. Wissing, F. (1974). Cyanide formation from oxidation of glycine by a Pseudomonas species. J. Bacteriol. 117, 1289-1294.
206. Xie, N.-Z., Li, J.-X., Song, L.-F., Hou, J.-F., Guo, L., Du, Q.-S., et al. (2014). Genome sequence of type strain Paenibacilluspolymyxa DSM 365, a highly efficient producer of optically active (R, R)-2, 3-butanediol. J. Biotechnol. 195, 72-73. doi: 10.1016/j.jbiotec.2014.07.441
207. Xiong, Z.-Q., Yang, Y.-Y., Zhao, N., and Wang, Y. (2013). Diversity of endophytic fungi and screening of fungal paclitaxel producer from Anglo- jap yew, Taxus x media. BMC Microbiol. 13:71. doi: 10.1186/1471-2180-13-71
208. Yanagisawa, T., Lee, J. T., Wu, H. C., and Kawakami, M. (1994). Relationship of protein-structure of isoleucyl-transfer-RNA synthetase with pseudomonic acid resistance of Escherichia coli - proposed mode of action of pseudomonic acid as an inhibitorof isoleucyl-transfer-RNA synthetase. J. Biol. Chem. 269, 24304-24309.
209. Yang, F., and Cao, Y. (2012). Biosynthesis of phloroglucinol compounds in microorganisms - review. Appl. Microbiol. Biotechnol. 93, 487-495. doi: 10.1007/s00253-011-3712-6
210. Yang, K., Han, L., and Vining, L. C. (1995). Regulation ofjadomycin B production in Streptomyces venezuelae ISP5230: involvement of a repressor gene, jadR2. J. Bacteriol. 177,6111-6117.
211. Yang, Y., Zhao, H., Barrero, R. A., Zhang, B., Sun, G., Wilson, I. W., et al. (2014). Genome sequencing and analysis of the paclitaxel-producing endophytic fungus Penicillium aurantiogriseum NRRL 62431. BMC Genomics 15:69. doi: 10.1186/1471-2164-15-69
212. Yazgan, A., Ozcengiz, G., and Marahiel, M. A. (2001). Tn10 insertional mutations of Bacillus subtilis that block the biosynthesis of bacilysin. Biochim. Biophys. Acta 1518, 87-94. doi: 10.1016/S0167-4781(01)00182-8
213. Zeigler, D. R. (2011). The genome sequence of Bacillus subtilis subsp. spizizenii W23: insights into speciation within the B. subtilis complex and into the history of B. subtilis genetics. Microbiology 157, 2033-2041. doi: 10.1099/mic.0.048520-0
214. Zhang, D.-X., Nagabhyru, P., Blankenship, J. D., and Schardl, C. L. (2010). Are loline alkaloid levels regulated in grass endophytes by gene expression or substrate availability? Plant Signal. Behav. 5, 1419-1422. doi: 10.4161/psb.5.11.13395
215. Zhang, L., Li, X., Zhang, F., and Wang, G. (2014). Genomic analysis of Agrobacterium radiobacter DSM 30147T and emended description of A. radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980) emend. Sawada et al. 1993. Stand. Genomic Sci. 9, 574. doi: 10.4056/sigs.4688352
216. Zhao, J., Mou, Y., Shan, T., Li, Y., Zhou, L., Wang, M., et al. (2010). Antimicrobial metabolites from the endophytic fungus Pichia guilliermondii isolated from Paris polyphylla var. yunnanensis. Molecules 15, 7961-7970. doi: 10.3390/molecules15117961
217. Zhou, R., Rasooly, R., and Linz, J. E. (2000). Isolation and analysis of fluP, a gene associated with hyphal growth and sporulation in Aspergillus parasiticus. Mol. Gen. Genet. 264, 514-520. doi: 10.1007/s004380000335
218. Zhou, X., Zhu, H., Liu, L., Lin, J., and Tang, K. (2010). A review: recent advances and future prospects of Taxol-producing endophytic fungi. Appl. Microbiol. Biotechnol. 86, 1707-1717. doi: 10.1007/s00253-010-2546-y
219. Zimmerman, S. B., Schwartz, C. D., Monaghan, R. L., Pelak, B. A., Weiss- berger, B., Gilfillan, E. C., et al. (1987). Difficidin and oxydifficidin: novel broad spectrum antibacterial antibiotics produced by Bacillus subtilis. I. production, taxonomy and antibacterial activity. J. Antibiot. 40, 1677-1681. doi: 10.7164/antibiotics.40.1677
220. Zotchev, S. B., Sekurova, O. N., and Katz, L. (2012). Genome-based bioprospecting of microbes for new therapeutics. Curr. Opin. Biotechnol. 23, 941-947. doi: 10.1016/j.copbio.2012.04.002
221. Zou, Z., Du, D., Zhang, Y., Zhang, J., Niu, G., and Tan, H. (2014). A y—butyrolactone-sensing activator/repressor, JadR3, controls a regulatory mini—network for jadomycin biosynthesis. Mol. Microbiol. 94, 490-505. doi: 10.1111/mmi.12752