Analysis of a 108-kb Region of the Saccharopolyspora spinosa Genome Covering the Obscurin Polyketide Synthase Locus

References

• Aparicio, J.F., Molna´r, I., Schwecke, T., Ko¨ nig, A., Haydock, S.F., Khaw, L.E., Staunton, J. and Leadlay, P.F. (1996) “Organization of the biosynthetic gene cluster for rapamycin in Streptomyces hygroscopicus: analysis of the enzymatic domains in the modular polyketide synthase”, Gene 169, 9 – 16.
   PubMed Web of Science ®Google Scholar
• August, P.R., Tang, L., Yoon, Y.J., Ning, S., Mu¨ ller, R., Yu, T.-W., Taylor, M., Hoffmann, D., Kim, C.-G., Zhang, X., Hutchinson, C.R. and Floss, H.G. (1998) “Biosynthesis of the ansamycin antibiotic rifamycin: deductions from the mole- cular analysis of the rif biosynthetic gene cluster of Amycolatopsis mediterranei S699”, Chemistry and Biology 5, 69 – 79.
   PubMedGoogle Scholar
• Bentley, S.D., Chater, K.F., Cerdeno-Tarraga, A.M., Challis, G.L., Thomson, N.R., James, K.D., Harris, D.E., Quail, M.A., Kieser, H., Harper, D., Bateman, A., Brown, S., Chandra, G., Chen, C.W., Collins, M., Cronin, A., Fraser, A., Goble, A., Hidalgo, J., Hornsby, T., Howarth, S., Huang, C.H., Kieser, T., Larke, L., Murphy, L., Oliver, K., O’Neil, S., Rabbinowitsch, E., Rajandream, M.A., Rutherford, K., Rutter, S., Seeger, K., Saunders, D., Sharp, S., Squares, R., Squares, S., Taylor, K., Warren, T., Wietzorrek, A., Woodward, J., Barrell, B.G., Parkhill, J. and Hopwood, D.A. (2002) “Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)”, Nature 417, 141– 147.
   PubMed Web of Science ®Google Scholar
• Berdy, J. (1995) “Are actinomycetes exhausted as a source of secondary metabolites?”, Biotekhnologiya 7– 8, 13 – 34.
   Google Scholar
• Bevitt, D.J., Corte´s, J., Haydock, S.F. and Leadlay, P.F. (1992) “6-Deoxyerythronolide B synthase 2 from Saccharopolyspora erythraea. Cloning of the structural gene, sequence analysis and inferred domain structure of the multifunctional enzyme”, European Journal of Biochemistry 204, 39– 49.
   PubMedGoogle Scholar
• Beyer, S., Kunze, B., Silakowski, B. and Mu¨ ller, R. (1999) “Metabolic diversity in myxobacteria: identification of the myxalamid and the stigmatellin biosynthetic gene cluster of Stigmatella aurantiaca Sg a15 and a combined polyketide- (poly)peptide gene cluster from the epothilone producing strain Sorangium cellulosum So ce90”, Biochimica et Biophysica Acta 1445, 185 – 195.
   Google Scholar
• Bierman, M., Logan, R., O’Brien, K., Seno, E.T., Rao, R.N. and Schoner, B.E. (1992) “Plasmid cloning vectors for the conjugal transfer of DNA from Escherichia coli to Streptomyces spp.”, Gene 116, 43– 49.
   PubMed Web of Science ®Google Scholar
• Bisang, C., Long, P.F., Corte´s, J., Westcott, J., Crosby, J., Matharu, A.-L., Cox, R.J., Simpson, T.J., Staunton, J. and Leadlay, P.F. (1999) “A chain initiation factor common to both modular and aromatic polyketide synthases”, Nature 401, 502– 505.
   PubMed Web of Science ®Google Scholar
• Cane, D.E. and Walsh, C.T. (1999) “The parallel and convergent universes of polyketide synthases and nonribosomal peptide synthetases”, Chemistry and Biology 6, 319– 325.
   PubMed Web of Science ®Google Scholar
• Challis, G.L. and Hopwood, D.A. (2003) “Synergy and con- tingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species”, Proceedings of the National Academy of Sciences USA 100, 14555– 14561.
   PubMed Web of Science ®Google Scholar
• Challis, G.L. and Ravel, J. (2000) “Coelichelin, a new peptide siderophore encoded by the Streptomyces coelicolor genome: structure prediction from the sequence of its non-ribosomal peptide synthetase”, FEMS Microbiology Letters 187, 111– 114.
   PubMed Web of Science ®Google Scholar
• Demain, A.L. (2002) “Prescription for an ailing pharmaceutical industry”, Nature Biotechnology 20, 331.
   PubMed Web of Science ®Google Scholar
• Devereux, J., Haeberli, P. and Smithies, O. (1984) “A comprehen- sive set of sequence-analysis programs for the VAX”, Nucleic Acids Research 12, 387– 395.
   PubMed Web of Science ®Google Scholar
• Donadio, S. and Katz, L. (1992) “Organization of the enzymatic domains in the multifunctional polyketide synthase involved in erythromycin formation in Saccharopolyspora erythraea”, Gene 111, 51– 60.
   Google Scholar
• Ewing, B. and Green, P. (1998) “Base-calling of automated sequencer traces using Phred. II. Error probabilities”, Genome Research 8, 186– 194.
   PubMed Web of Science ®Google Scholar
• Ewing, B., Hillier, L.D., Wendl, M.C. and Green, P. (1998) “Base- calling automated sequencer traces using Phred. I. Accuracy assessment”, Genome Research 8, 175– 183.
   PubMed Web of Science ®Google Scholar
• Gordon, D., Abajian, C. and Green, P. (1998) “Consed: a graphical tool for sequence finishing”, Genome Research 8, 195– 202.
   PubMed Web of Science ®Google Scholar
• Haydock, S., Aparicio, J.F., Molna´r, I., Schwecke, T., Ko¨ nig, A., Marsden, A.F.A., Galloway, I.S., Staunton, J. and Leadlay, P.F. (1995) “Divergent structural motifs correlated with the substrate specificity of (methyl)malonyl-CoA: acyl carrier protein transacylase domains in modular polyketide synthase”, FEBS Letters 374, 246 – 248.
   PubMed Web of Science ®Google Scholar
• Hopwood, D.A. (2003) “The Streptomyces genome-be prepared!”, Nature Biotechnology 21, 505 – 506.
   Google Scholar
• Hutchinson, C.R. and McDaniel, R. (2001) “Combinatorial biosynthesis in microorganisms as a route to new anti- microbial, antitumor and neuroregenerative drugs”, Current Opinion in Investigational Drugs 2, 1681– 1690.
   PubMedGoogle Scholar
• Ikeda, H., Ishikawa, J., Hanamoto, A., Shinose, M., Kikuchi, H., Shiba, T., Sakaki, Y., Hattori, M. and Omura, S. (2003) “Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis”, Nature Biotechnology 21, 526– 531.
   PubMed Web of Science ®Google Scholar
• Katz, L. (1997) “Manipulation of modular polyketide synthases”, Chemical Reviews 97, 2557– 2575.
   PubMed Web of Science ®Google Scholar
• Kieser, T., Bibb, M.J., Buttner, M.J., Chater, K.F. and Hopwood, D.A. (2000) Practical Streptomyces Genetics (The John Innes Foundation, Norwich, UK).
   Google Scholar
• Kirst, H.A., Michel, K.H., Martin, J.W., Creemer, L.C., Chio, E.H., Yao, R.C., Nakatsukasa, W.M., Boeck, L.D., Occolowitz, J.L., et al. (1991) “A83543A-D, unique fermentation-derived tetra- cyclic macrolides”, Tetrahedron Letters 32, 4839– 4842.
   Google Scholar
• Lamb, D.C., Skaug, T., Song, H.-L., Jackson, C.J., Podust, L.M., Waterman, M.R., Kell, D.B., Kelly, D.E. and Kelly, S.L. (2002) “The cytochrome P450 complement (CYPome) of Streptomyces coelicolor A3(2)”, Journal of Biological Chemistry 277, 24000– 24005.
   PubMed Web of Science ®Google Scholar
• Leadlay, P.F. (1997) “Combinatorial approaches to polyketide biosynthesis”, Chemistry and Biology 1, 162– 168.
   Google Scholar
• Ligon, J., Hill, S., Beck, J., Zirkle, R., Molna´r, I., Zawodny, J., Money, S. and Schupp, T. (2002) “Characterization of the biosynthetic gene cluster for the antifungal polyketide soraphen A from Sorangium cellulosum So ce26”, Gene 285, 257– 267.
   PubMedGoogle Scholar
• MacNeil, D.J., Gewain, K.M., Ruby, C.L., Dezeny, G., Gibbons, P.H. and MacNeil, T. (1992) “Analysis of Streptomyces avermitilis genes required for avermectin biosynthesis utilizing a novel integration vector”, Gene 111, 61– 68.
   PubMed Web of Science ®Google Scholar
• Manly, S.P., Padmanabha, R. and Lowe, S.E. (2002) “Natural products or not? How to screen for natural products in the emerging HTS paradigm”, In: Janzen, W., ed, Methods in Molecular Biology (Humana Press Inc., Totowa) Vol. 190, pp 153– 168.
   Google Scholar
• Matsushima, P., Broughton, M.C., Turner, J.R. and Baltz, R.H. (1994) “Conjugal transfer of cosmid DNA from Escherichia coli to Saccharopolyspora spinosa: effects of chromosomal insertions on macrolide A83543 production”, Gene 146, 39– 45.
   PubMed Web of Science ®Google Scholar
• Mendez, C., Kuenzel, E., Lipata, F., Lombo, F., Cotham, W., Walla, M., Bearden, D.W., Brana, A.F., Salas, J.A. and Rohr, J. (2002) “Oviedomycin, an unusual angucyclinone encoded by genes of the oleandomycin-producer Streptomyces antibioticus ATCC 11891”, Journal of Natural Products 65, 779– 782.
   Google Scholar
• Moore, B.S. (1999) “Biosynthesis of marine natural products: microorganisms and macroalgae”, Natural Product Reports 16, 653– 674.
   PubMed Web of Science ®Google Scholar
• Nelson, D.R., Kamataki, T., Waxman, D.J., Guengerich, F.P., Estabrook, R.W., Feyereisen, R., Gonzalez, F.J., Coon, M.J., Gunsalus, I.C., Gotoh, O., et al. (1993) “The P450 superfamily: update on new sequences, gene mapping, accession numbers, early trivial names of enzymes, and nomenclature”, DNA and Cell Biology 12, 1– 51.
   PubMed Web of Science ®Google Scholar
• Newman, D.J., Cragg, G.M. and Snader, K.M. (2003) “Natural products as sources of new drugs over the period 1981 – 2002”, Journal of Natural Products 66, 1022– 1037.
   PubMed Web of Science ®Google Scholar
• Paget, M.S.B., Chamberlin, L., Atrih, A., Foster, S.J. and Buttner, M.J. (1999) “Evidence that the extracytoplasmic function sigma factor sE is required for normal cell wall structure in Streptomyces coelicolor A3(2)”, Journal of Bacteriology 181, 204– 211.
   Google Scholar
• Piel, J. (2002) “A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles”, Proceedings of the National Academy of Sciences USA 99, 14002– 14007.
   PubMed Web of Science ®Google Scholar
• Reichenbach, H. and Ho¨fle, G. (1999) “Myxobacteria as producers of secondary metabolites”, In: Grabley, S. and Thiericke, R., eds, Drug Discovery from Nature (Springer-Verlag, Berlin Heidelberg), pp 149 – 179.
   Google Scholar
• Ruan, X., Stassi, D., Lax, S.A. and Katz, L. (1997) “A second type-I PKS gene cluster isolated from Streptomyces hygroscopicus ATCC 29253, a rapamycin-producing strain”, Gene 203, 1–9.
   Google Scholar
• Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd Ed. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY).
   Google Scholar
• Schupp, T., Toupet, C., Engel, N. and Goff, S. (1998) “Cloning and sequence analysis of the putative rifamycin polyketide synthase gene cluster from Amycolatopsis mediterranei”, FEMS Microbiology Letters 159, 201– 207.
   PubMedGoogle Scholar
• Schwecke, T., Aparicio, J.F., Molna´r, I., Ko¨ nig, A., Khaw, L.E., Haydock, S.F., Oliynyk, M., Caffrey, P., Corte´ s, J., Lester, J.B., Bo¨ hm, G.A., Staunton, J. and Leadlay, P.F. (1995) “The biosynthetic gene cluster for the polyketide immuno- suppressant rapamycin”, Proceedings of the National Academy of Sciences USA 92, 7839 – 7843.
   PubMed Web of Science ®Google Scholar
• Scrutton, N.S., Berry, A. and Perham, R.N. (1990) “Redesign of the coenzyme specificity of a dehydrogenase by protein engin- eering”, Nature 343, 38– 43.
   PubMed Web of Science ®Google Scholar
• Seow, K.-T., Meurer, G., Gerlitz, M., Wendt-Pienkowski, E., Hutchinson, C.R. and Davies, J. (1997) “A study of iterative type II polyketide synthases, using bacterial genes cloned from soil DNA: a means to access and use genes from uncultured microorganisms”, Journal of Bacteriology 179, 7360– 7368.
   PubMed Web of Science ®Google Scholar
• Sosio, M., Bossi, E., Bianchi, A. and Donadio, S. (2000) “Multiple peptide synthetase gene clusters in Actinomycetes”, Molecular and General Genetics 264, 213– 221.
   PubMedGoogle Scholar
• Waldron, C., Matsushima, P., Rosteck, P.R. Jr., Broughton, M.C., Turner, J., Madduri, K., Crawford, K.P., Merlo, D.J. and Baltz, R.H. (2001) “Cloning and analysis of the spinosad bio- synthetic gene cluster of Saccharopolyspora spinosa”, Chemistry and Biology 8, 487– 499.
   PubMedGoogle Scholar
• Watve, M.G., Tickoo, R., Jog, M.M. and Bhole, B.D. (2001) “How many antibiotics are produced by the genus Streptomyces?”, Archives of Microbiology 176, 386– 390.
   PubMed Web of Science ®Google Scholar
• Witkowski, A., Naggert, J., Wessa, B. and Smith, S. (1991) “A catalytic role for histidine 237 in rat mammary gland thioesterase II”, Journal of Biological Chemistry 266, 18514– 18519.
   Google Scholar
• Wu, K., Chung, L., Revill, W.P., Katz, L. and Reeves, C.D. (2000) “The FK520 gene cluster of Streptomyces hygroscopicus var. ascomyceticus (ATCC 14891) contains genes for biosynthesis of unusual polyketide extender units”, Gene 251, 81– 90.
   Google Scholar
• Yu, T.-W., Shen, Y., Doi-Katayama, Y., Tang, L., Park, C., Moore, B.S., Hutchinson, C.R. and Floss, H.G. (1999) “Direct evidence that the rifamycin polyketide synthase assembles polyketide chains processively“, Proceedings of the National Academy of Sciences USA, 96, pp. 9051– 9056.
   PubMed Web of Science ®Google Scholar
• Zazopoulos, E., Huang, K., Staffa, A., Liu, W., Bachmann, B.O., Nonaka, K., Ahlert, J., Thorson, J.S., Shen, B. and Farnet, C.M. (2003) “A genomics-guided approach for discovering and expressing cryptic metabolic pathways”, Nature Biotechnology 21, 187– 190.
   PubMed Web of Science ®Google Scholar
• Zengler, K., Toledo, G., Rappe, M., Elkins, J., Mathur, E.J., Short, J.M. and Keller, M. (2002) “Cultivating the uncultured”, Proceedings of the National Academy of Sciences USA 99, 15681– 15686.
   PubMed Web of Science ®Google Scholar