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4 Weber, T., Blin, K., Duddela, S., Krug, D., Kim, H.U., Bruccoleri, R., Lee, S.Y., Fischbach, M.A., Müller, R., Wohlleben, W., antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43 (2015), 237–243.
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5
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5•• Rutledge, P.J., Challis, G.L., Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat Rev Microbiol 13 (2015), 509–523 This is a comprehensive review on various approaches for activating silent BGCs.
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Rutledge, P.J.1
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Prospecting for new bacterial metabolites: a glossary of approaches for inducing, activating and upregulating the biosynthesis of bacterial cryptic or silent natural products
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7 Zarins-Tutt, J.S., Barberi, T.T., Gao, H., Mearns-Spragg, A., Zhang, L., Newman, D.J., Goss, R.J.M., Prospecting for new bacterial metabolites: a glossary of approaches for inducing, activating and upregulating the biosynthesis of bacterial cryptic or silent natural products. J Nat Prod 33 (2016), 54–72.
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8 Weber, T., Kim, H.U., The secondary metabolite bioinformatics portal: computational tools to facilitate synthetic biology of secondary metabolite production. Synth Syst Biotechnol 1 (2016), 69–79.
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Weber, T.1
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Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters
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9 Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Brown, L.C.W., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 158 (2014), 412–421.
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10
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Phylogenomic analysis of natural products biosynthetic gene clusters allows discovery of arseno-organic metabolites in model streptomycetes
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10 Cruz-Morales, P., Kopp, J.F., Martínez-Guerrero, C., Yáñez-Guerra, L.A., Selem-Mojica, N., Ramos-Aboites, H., Feldmann, J., Barona-Gómez, F., Phylogenomic analysis of natural products biosynthetic gene clusters allows discovery of arseno-organic metabolites in model streptomycetes. Genome Biol Evol 8 (2016), 1906–1916.
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Cruz-Morales, P.1
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11 Liu, G., Chater, K.F., Chandra, G., Niu, G., Tan, H., Molecular regulation of antibiotic biosynthesis in Streptomyces. Microbiol Mol Biol Rev 77 (2013), 112–143.
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Discovery of unusual biaryl polyketides by activation of a silent Streptomyces venezuelae biosynthetic gene cluster
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12 Thanapipatsiri, A., Gomez-Escribano, J.P., Song, L., Bibb, M., Al-Bassam, M., Chandra, G., Thamchaipenet, A., Challis, G., Bibb, M., Discovery of unusual biaryl polyketides by activation of a silent Streptomyces venezuelae biosynthetic gene cluster. ChemBioChem 17 (2016), 2189–2198.
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13
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Identification of AstG1, a LAL family regulator that positively controls ansatrienins production in Streptomyces sp. XZQH13
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13 Xie, C., Deng, J.J., Wang, H.X., Identification of AstG1, a LAL family regulator that positively controls ansatrienins production in Streptomyces sp. XZQH13. Curr Microbiol 70 (2015), 859–864.
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Xie, C.1
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14
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Genome mining-directed activation of a silent angucycline biosynthetic gene cluster in Streptomyces chattanoogensis
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14 Zhou, Z.X., Xu, Q.Q., Bu, Q.T., Guo, Y.Y., Liu, S.P., Liu, Y., Du, Y.L., Li, Y.Q., Genome mining-directed activation of a silent angucycline biosynthetic gene cluster in Streptomyces chattanoogensis. ChemBioChem 16 (2015), 496–502.
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Zhou, Z.X.1
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15
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84938875734
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Activating a cryptic ansamycin biosynthetic gene cluster to produce three new naphthalenic octaketide ansamycins with n-pentyl and n-butyl side chains
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15 Li, S.R., Li, Y.Y., Lu, C.H., Zhang, J.L., Zhu, J., Wang, H.X., Shen, Y.M., Activating a cryptic ansamycin biosynthetic gene cluster to produce three new naphthalenic octaketide ansamycins with n-pentyl and n-butyl side chains. Org Lett 17 (2015), 3706–3709.
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Li, S.R.1
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16
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84921496414
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Targeted activation of silent natural product biosynthesis pathways by reporter-guided mutant selection
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This work alied the reporter method for activation of silent gene clusters and used a double-reporter system, xylE-neo, to lower the false postive rate dramatically. In principle, the target cluster activated mutants can be directly selelcted after the double-reporter screening.
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16• Guo, F., Xiang, S.H., Li, L.Y., Wang, B., Rajasarkka, J., Grondahl-Yli-Hannuksela, K., Ai, G.M., Metsa-Ketela, M., Yang, K.G., Targeted activation of silent natural product biosynthesis pathways by reporter-guided mutant selection. Metab Eng 28 (2015), 134–142 This work alied the reporter method for activation of silent gene clusters and used a double-reporter system, xylE-neo, to lower the false postive rate dramatically. In principle, the target cluster activated mutants can be directly selelcted after the double-reporter screening.
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Guo, F.1
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17
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Identification of novel mureidomycin analogues via rational activation of a cryptic gene cluster in Streptomyces roseosporus NRRL 15998
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17 Jiang, L.J., Wang, L., Zhang, J.H., Liu, H., Hong, B., Tan, H.R., Niu, G.Q., Identification of novel mureidomycin analogues via rational activation of a cryptic gene cluster in Streptomyces roseosporus NRRL 15998. Sci Rep, 5, 2015, 14111, 10.11038/srep14111.
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18 Ahuja, M., Chiang, Y.-M., Chang, S.-L., Praseuth, M.B., Entwistle, R., Sanchez, J.F., Lo, H.-C., Yeh, H.-H., Oakley, B.R., Wang, C.C.C., Illuminating the diversity of aromatic polyketide synthases in Aspergillus nidulans. J Am Chem Soc 134 (2012), 8212–8221.
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19 Bok, J.W., Soukup, A.A., Chadwick, E., Chiang, Y.M., Wang, C.C.C., Keller, N.P., VeA and MvlA repression of the cryptic orsellinic acid gene cluster in Aspergillus nidulans involves histone 3 acetylation. Mol Microbiol 89 (2013), 963–974.
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20
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20 Cobb, R.E., Wang, Y.J., Zhao, H.M., High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS Synth Biol 4 (2015), 723–728.
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Cobb, R.E.1
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21
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This work applied the CRISPR-Cas9 system based promoter knockin strategy to activate multiple silent BGCs in five different Streptomyces species, demonstrating a great potential for high throughput discovery of natural products in the native hosts.
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21•• Zhang, M., Wong, F., Wang, Y., Luo, S., Lim, Y., Heng, E., Yeo, W., Cobb, R., Enghiad, B., Ang, E., et al. An efficient CRISPR-Cas9 mediated knock-in strategy for activation of silent Streptomyces biosynthetic gene clusters for natural product discovery. Nat Chem Biol, 2017, 10.1038/nchembio.2341 This work applied the CRISPR-Cas9 system based promoter knockin strategy to activate multiple silent BGCs in five different Streptomyces species, demonstrating a great potential for high throughput discovery of natural products in the native hosts.
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Zhang, M.1
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22
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22 Tong, Y., Charusanti, P., Zhang, L., Weber, T., Lee, S.Y., CRISPR-Cas9 based engineering of actinomycetal genomes. ACS Synth Biol 4 (2015), 1020–1029.
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Tong, Y.1
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23
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23 Liu, Y., Tao, W., Wen, S., Li, Z., Yang, A., Deng, Z., Sun, Y., In vitro CRISPR/Cas9 system for efficient targeted DNA editing. mBio 6 (2015), e01714–e01715.
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24
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This work combined CRISPR/Cas9 and TAR to enable efficient large gene cluster assembly and multiplexed promoter engineering in a single round. It also provides a mCRISTAR python package and Webapp for transcriptional activation of complex natural product BGCs.
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24• Kang, H.S., Charlop-Powers, Z., Brady, S.F., Multiplexed CRISPR/Cas9- and TAR-mediated promoter engineering of natural product biosynthetic gene clusters in yeast. ACS Synth Biol 5 (2016), 1002–1010 This work combined CRISPR/Cas9 and TAR to enable efficient large gene cluster assembly and multiplexed promoter engineering in a single round. It also provides a mCRISTAR python package and Webapp for transcriptional activation of complex natural product BGCs.
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Kang, H.S.1
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25
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Functional reconstitution of a fungal natural product gene custer by advanced genome editing
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25 Weber, J., Valiante, V., Nødvig, C.S., Mattern, D.J., Slotkowski, R.A., Mortensen, U.H., Brakhage, A.A., Functional reconstitution of a fungal natural product gene custer by advanced genome editing. ACS Synth Biol 6 (2017), 62–68.
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26
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26 Billingsley, J.M., DeNicola, A.B., Tang, Y., Technology development for natural product biosynthesis in Saccharomyces cerevisiae. Curr Opin Biotechnol 42 (2016), 74–83.
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27 Bode, H.B., Bethe, B., Höfs, R., Zeeck, A., Big effects from small changes: possible ways to explore nature's chemical diversity. ChemBioChem 3 (2002), 619–627.
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28
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28 Netzker, T., Fischer, J., Weber, J., Mattern, D.J., Konig, C.C., Valiante, V., Schroeckh, V., Brakhage, A.A., Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters. Front Microbiol, 6, 2015, 299.
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29 Ochi, K., Tanaka, Y., Tojo, S., Activating the expression of bacterial cryptic genes by rpoB mutations in RNA polymerase or by rare earth elements. J Ind Microbiol Biotechnol 41 (2014), 403–414.
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30 Okada, B.K., Seyedsayamdost, M.R., Antibiotic dialogues: induction of silent biosynthetic gene clusters by exogenous small molecules. FEMS Microbiol Rev 41 (2017), 19–33.
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31 Seyedsayamdost, M.R., High-throughput platform for the discovery of elicitors of silent bacterial gene clusters. Proc Natl Acad Sci U S A 111 (2014), 7266–7271.
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32 Larionov, V., Kouprina, N., Graves, J., Chen, X.N., Korenberg, J.R., Resnick, M.A., Specific cloning of human DNA as yeast artificial chromosomes by transformation-associated recombination. Proc Natl Acad Sci U S A 93 (1996), 491–496.
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33 Kouprina, N., Larionov, V., Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae. Nat Protoc 3 (2008), 371–377.
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34•• Yamanaka, K., Reynolds, K.A., Kersten, R.D., Ryan, K.S., Gonzalez, D.J., Nizet, V., Dorrestein, P.C., Moore, B.S., Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A. Proc Natl Acad Sci U S A 111 (2014), 1957–1962 This is the first application of TAR in natural product discovery.
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35
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Directed natural product biosynthesis gene cluster capture and expression in the model bacterium Bacillus subtilis
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35 Li, Y.X., Li, Z.R., Yamanaka, K., Xu, Y., Zhang, W.P., Vlamakis, H., Kolter, R., Moore, B.S., Qian, P.Y., Directed natural product biosynthesis gene cluster capture and expression in the model bacterium Bacillus subtilis. Sci Rep, 5, 2015, 9383.
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36
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Targeted capture and heterologous expression of the Pseudoalteromonas alterochromide gene cluster in Escherichia coli represents a promising natural product exploratory platform
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36 Ross, A.C., Gulland, L.E.S., Dorrestein, P.C., Moore, B.S., Targeted capture and heterologous expression of the Pseudoalteromonas alterochromide gene cluster in Escherichia coli represents a promising natural product exploratory platform. ACS Synth Biol 4 (2015), 414–420.
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37 Tang, X., Li, J., Millán-Aguiñaga, N., Zhang, J.J., O'Neill, E.C., Ugalde, J.A., Jensen, P.R., Mantovani, S.M., Moore, B.S., Identification of thiotetronic acid antibiotic bosynthetic pathways by target-directed genome mining. ACS Chem Biol 10 (2015), 2841–2849.
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