Biosynthesis of the ansamycin antibiotic rifamycin: Deductions from the molecular analysis of the rif biosynthetic gene cluster of Amycolatopsis mediterranei S699

Chemistry and Biology

Volumn 5, Issue 2, 1998, Pages 69-79

  August, Paul R ^a,c   Tang, Li ^b   Yoon, Yeo J ^b   Ning, Sandra ^a   Müller, Rolf ^a,d   Yu, Tin Wein ^a   Taylor, Matthew ^a   Hoffmann, Dietmar ^a,d   Kim, Chun Gyu ^a,e   Zhang, Xiaohong ^a   Hutchinson, C Richard ^b   Floss, Heinz G ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c MDS Inc   (Canada)

^d UNIVERSITY OF BONN   (Germany)

^e Inje University   (South Korea)

Author keywords

3 amino 5 hydroxy benzoic acid; Combinatorial biosynthesis; Gene disruption; Modular type I polyketide synthase; Shikimate pathway

Indexed keywords

3 AMINO 5 HYDROXYBENZOIC ACID; ACETIC ACID; ANTIBIOTIC SYNTHESIS; BIOSYNTHESIS; GENE CLUSTER; PROPIONIC ACID; REGULATORY SEQUENCE; RIFAMYCIN;

ACTINOBACTERIA (CLASS); AMYCOLATOPSIS MEDITERRANEI;

EID: 13144258781     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(98)90141-7     Document Type: Article

References (68)

1. Rinehart, K.L. Jr. & Shields, L.S. (1976). Chemistry of the ansamycin antibiotics. Fortschr. Chem. Org. Naturst. 33, 231-273.
2. Brufani, M., Fedeli, W., Giacomello, G. & Vaciago, A. (1964). X-ray analysis of the structure of rifamycin B. Experientia 20, 339-342.
3. Oppolzer, W. & Prelog, V. (1973). Über die konstitution und die konfiguration der rifamycine B, O, S und SV. Helv. Chim. Acta 56, 2287-2314.
4. Sepkowitz, K. A., Rafalli, J., Riley, L., Kiehn, T.E. & Armstrong, D. (1995). Tuberculosis in the AIDS era. Clinical Microbiol. Revs. 8, 180-199.
5. Chiao, J.S., Xia, T.H., Mei, B.C., Jin, Z.K. & Gu, W.L. (1995). Rifamycin SV and related ansamycins. In: Genetics and Biochemistry of Antibiotic Production, L. C. Vining, C. Stuttard, Eds., Butterworth-Heinemann, Boston, pp. 477-498.
6. Lancini, G. & Cavalleri, B. (1997). Rifamycins. In Biotechnology of Antibiotics, 2nd Ed., W. R. Strohl, Ed., Dekker, New York, pp. 521-549.
7. Katz, L. & S. Donadio. (1993). Polyketide synthesis: prospects for hybrid antibiotics. Annu. Rev. Microbiol. 47, 875-912.
8. Ghisalba, O. & Nüesch, J. (1981). A genetic approach to the biosynthesis of the rifamuycin chromophore in Nocardia mediterranei. III. Isolation and identification of 3-amino-5-hydroxybenzoic acid as a direct precursor of the seven carbon amino starter-unit. J. Antibiot. 34:64-71.
9. 7N units in ansamycin antibiotics. J. Amer. Chem. Soc. 18, 7486-7491.
10. 7N units in rifamycin and related antibiotics. J. Biol. Chem., in press.
11. Hopwood, D.A. (1988). Towards an understanding of gene switching in Streptomyces, the basis of sporulation and antibiotic production. Proc. Roy. Soc. London B 235, 121-138.
12. Dewick, P.M. (1990). The biosynthesis of shikimate metabolites. Nat. Prod. Repts 7, 165-189.
13. Sosio, M., Lorenzetti, R., Robbiati, F. & Denaro, M. (1991). Nucleotide sequence to a teicoplanin resistance gene from Actinoplanes teichomyceticus. Biochim. Biophys. Acta, Gene Struct. Expr. 1089, 401-403.
14. Millar, G., & Coggins, J.R. (1986). the complete amino acid sequence of 3-dehydroquinate synthase of Escherichia coli K12. FEBS Letters, 200, 11-17.
15. Charles, I.G., Keyte, J.W., Brammar, W.J. & Hawkins, A.R. (1985). Nucleotide sequence encoding the biosynthetic dehydroquinase function of the penta-functional arom locus of Aspergillus nidulans. Nucleic Acids Res. 13, 8119-8128.
16. Tercero, J.A. , Espinosa, J.C.R., Lacalle, R.A. & Jiménez, A. (1995). The biosynthetic pathway for the aminoglycoside antibiotic puromycin, as deduced from the molecular analysis of the pur cluster of Streptomyces alboniger. J. Biol. Chem. 271, 1579-1590.
17. Loos, H., Sahm, H. & Sprenger, G.A. (1993). Glucose-fructose oxidoreductase, a periplasmic enzyme of Zymomonas mobilis, is active in its precursor form. FEMS Microbiol. Lett. 107, 293-298.
18. Schaferjohann, J., Yoo, J.G., Kusian, B., & Bowien, B. (1993). The cbb Operons of the facultative chemoautotroph Alcaligenes eutrophus encode phosphoglycolate phosphatase. J. Bacteriol. 175, 7329-7340.
19. Lyngstadaas, A., Lebner-Olesen, A. & Boye, E. (1995). Characterization of three genes in the dam-containing operon of Escherichia coli. Mol. Gen. Genet. 247, 546-554.
20. Angell, S., Schwartz, E. & Bibb, M.J. (1992). The glucose kinase gene of Streptomyces coelicolor a3(2): its nucleotide sequence, transcriptional analysis and role in glucose repression. Mol. Microbiol. 6, 2833-2844.
21. Ning, S. (1996). Studies on the biosynthesis of rifamycin by Amycolatopsis mediterranei. Ph.D. thesis, University of Washington.
22. Donadio, S., Staver, M.J., McAlpine, J.B., Swanson, S.J. & Katz, L. (1991). Modular organization of genes required for complex polyketide biosynthesis. Science 252, 675-679.
23. Schwecke, T., et al., & Leadlay, P. (1995). The biosynthetic gene cluster for the polyketide immunosuppressant rapamycin. Proc. Natl Acad. Sci. USA 92, 7839-7843.
24. Haydock, S.F., et al., & Leadlay, P.F. (1995). Divergent sequence motifs correlated with the substrate specificity of (methyl) malonyl-CoA:acyl carrier protein transacylase domains in modular polyketide syntheses. FEBS Lett. 374, 246-248.
25. MacNeil, D.J., Occi, J.L., Gewain, K.M. & MacNeil, T. (1994). Correlation of the avermectin polyketide synthase genes to the avermectin structure: implications for designing novel avermectins. Annu. NY Acad. Sci. 721, 123-132.
26. Ruan, X., Stassi, D., Lax, S. & Katz, L. (1997). A second type-I PKS gene cluster isolated from Streptomyces hygroscopicus ATCC 29253, a rapamycin-producing strain. Gene 203, 1-9.
27. Ghisalba, O., Fuhrer, H., Richter, W.J. & Moss, S. (1981). A genetic approach to the biosynthesis of the rifamycin-chromophore in Nocardia mediterranei. III. Isolation and identification of an early aromatic ansamycin-precursor containing the seven-carbon amino start-unit and three initial acetate/propionate-units of the ansa chain. J. Antibiot. 34, 58-63.
28. Anderson, M.G., Monypenny, D., Rickards, R.W. & Rothschild, J.M. (1989). Biosynthetic origins of the oxygen atoms in the ansamycin antibiotics rifamycin B, O & S. J. C. S. Chem. Commun. 1989, 311-313.
29. Ghisalba, O., Auden, J.A.L., Schupp, T. & Nüesch, J. (1984). The rifamycins: Properties, biosynthesis and fermentation. In Biotechnology of Industrial Antibiotics (E. Vandamme, ed), pp. 281-327, Marcel Dekker, Basel.
30. Ohsako, S., Ohtomi, M., Sakamoto, Y., Uyemura, K. & Deguchi, T. (1988). Arylamine N-acetyltransferase from chicken liver II. Cloning of cDNA and expression in Chinese hamster ovary cells. J. Biol. Chem. 263, 7534-7538.
31. Blanc, V., Salah-Bey, K., Folcher, M. & Thompson, C.J. (1995). Molecular characterization and transcriptional analysis of a multidrug resistance gene cloned from the pristinamycin-producing organism, Streptomyces pristinaespiralis. Mol. Microbiol. 17, 989-999.
32. Fernández-Moreno, M.A., Caballero, J.L., Hopwood, D.A. & Malpartida, F. (1991). The act cluster contains regulatory and antibiotic export genes, direct targets for translational control by the bldA tRNA gene of Streptomyces. Cell 66, 769-780.
33. Caballero, J.L., Malpartida, F. & Hopwood, D.A. (1991). Transcriptional organization and regulation of an antibiotic export complex in the producing Streptomyces culture. Mol. Gen. Genet. 228, 372-380
34. Peschke, U., Schmidt, H., Zhang, H., & Piepersberg, W. (1995). Molecular characterization of the lincomycin-production gene cluster of Streptomyces lincolnensis 78-11. Mol. Microbiol. 16, 1137-1156.
35. Kawaguchi, T., Asahi, T., Satoh, T., Uozumi, T. & Beppu, T. (1984). B-factor, an essential regulatory substance inducing the production of rifamycin in a Nocardia sp. J. Antibiot. 37, 1587-1595.
36. Kawaguchi, T., Azuma, M., Horinuchi, S. & Beppu, T. (1988). Effect of B-factor and its analogues on rifamycin biosynthesis in Nocardia sp. J. Antibiot. 41, 360-365.
37. 3H: Functional analysis and comparative genomics. J. Bacteriol. 179, 7135-7155.
38. Kishi, T., Yamana, H., Muroi, M., Harada, S., Asai, M., Hasegawa, T. & Mizuno, K. (1972). Tolypomycin, a new antibiotic, iii. Isolation and characterization of tolypomycin Y. J. Antibiot. 25, 11-15.
39. Haydock, S.F., Dowson, J.A., Dhillon, N., Roberts, G.A., Cortes, J. & Leadlay, P.F. (1991). Cloning and sequence analysis of genes involved in erythromycin biosynthesis in Saccharopolyspora erythrea: sequence similarities between EryG and a family of S-adenosylmethionine-dependent methyltransferases. Mol. Gen. Genet. 230, 120-128.
40. Van den Bergh, E.R.E., et al., & Meijer, W.G. (1996). Primary structure and phylogeny of the Calvin cycle enzymes transketolase and fructose bisphosphate aldolase of Xanthobacter flavus. J. Bacteriol. 178, 888-893.
41. Kaneko, T., et al., & Tabata, S. (1996). Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3, 109-136.
42. Frost, J.W. & Draths, K.M. (1995). Biocatalytic syntheses of aromatic compounds from D-glucose: renewable microbial sources of aromatic compounds. Annu. Rev. Microbiol. 49, 557-579.
43. Merson-Davies, L.A. & Cundliffe, E. (1994). Analysis of five tylosin biosynthetic genes from the tyllBA region of the Streptomyces fradiae genome. Mol. Microbiol. 13, 349-355.
44. Floss, H.G. & Beale, J.M. (1989). Studies on the biosynthesis of antibiotics. Angew. Chem. Int. Ed. Engl. 28, 146-177.
45. Konig, A., et al., & Leadlay, P.F. (1997). The pipecolate-incorporating enzyme for the biosyntheiss of the immunosuppressent rapamycin. Eur. J. Biochem. 247, 526-534.
46. Margalith, P. & Pagani, H. (1961). Rifomycin. XIII. Fermentation and production of rifomycin complex. Appl. Microbiol. 9, 320-324.
47. Margalith, P. & Pagani, H. (1961). Rifomycin. XIV. Production of rifomycin B. Appl. Microbiol. 9, 325-334.
48. Kirst, H.A. & Sides, G.D. (1989). New directions for macrolide antibiotics: pharmacokinetics and clinical efficacy. Antimicrob. Agents Chemother. 33, 1419-1422.
49. Hardy, D.J., Swanson, R.N., Shipkowitz, N.L, Freiberg, L.A., Lortey, P.A & Clement, J.J. (1991). In vitro activity and in vivo efficacy of a new series of 9-deoxo-12-deoxy-9,12-epoxyerythromycin A derivatives. Antimicrobial Agents Chemother. 35, 922-928.
50. Hutchinson, C.R. (1997). Antibiotics from genetically engineered microorganisms. In: Biotechnology of Antibiotics, 2nd Ed., W.R. Strahl, Ed., Dekker, New York, pp. 659-682.
51. Sambrook, J., Fritsch, E.F. & Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual. 2nd edn., Cold Spring Harbor Laboratory Press, NY.
52. Hopwood, D.A., et al., & Schrempf, H. (1985). Genetic manipulation of Streptomyces, a laboratory manual. The John Innes Foundation, Norwich, UK.
53. Devereux, J., Haeberli, P & Smithies, O. (1984). A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12, 387-395.
54. Bierman, M., Logan, R., O'Brien, K., Seno, E.T., Rao, R.N. & Schoner, B.E. (1992). plasmid cloning vectors for the conjugal transfer of DNA from E. coli to Streptomyces spp. Gene, 116, 43-49.
55. Horii, M., Ishizaki,T., Paik, S.-Y., Manome,T. & Murooka,Y. (1990). An operon containing the gene for cholesterol oxidase and a cytochrome P450-like protein from Streptomyces sp. J. Bacteriol. 172, 3644-3653.
56. Gorlach, J., et al., & Amrhein, N. (1993). Differential expression of tomato (Lycopersicon esculentum L.) genes encoding shikimate pathway isoenzymes. I. 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase. Plant Mol. Biol. 23, 697-706.
57. Valentin, H.E., Zwingmann, G., Schonebaum, A. & Steinbuchel, A. (1995). Metabolic pathway for biosynthesis of poly (3-hydroxybutyrate-co-4-hydroxybutyrate) from 4-hydroxybutyrate by Alcaligenes eutrophus. Eur. J. Biochem. 227, 43-60.
58. Trower, M.K., Lenstra, R., Omer, C., Buchholz, S.E. & Sariaslani, F.S. (1992). Cloning, nucleotide sequence determination and expression of the genes encoding cytochrome P-450soy (soyC) and ferredoxinsoy (soyB) from Streptomyces griseus. Mol. Microbiol. 6, 2125-2134.
59. Arisawa, A., Tsunekawa, H., Okamura, K. & Okamoto, R. (1995). Nucleotide sequence analysis of the carbomycin biosynthetic genes including the 3-O-acyltransferase gene from Streptomyces thermotolerans. Biosci. Biotechnol. Biochem. 59, 582-588.
60. Jiang, X.M., Neal, B., Santiago, F., Lee, S. J., Romana, L.K. & Reeves, P.R. (1991). Structure and sequence of the rfb (O antigen) gene cluster of Salmonella serovar typhimurium (strain LT2). Mol. Microbiol. 5, 695-713.
61. Bechthold, A., Sohng, J.K., Smith, T.M., Chu, X. & Floss, H.G. (1995). Identification of Streptomyces violaceoruber Tü22 genes involved in the biosynthesis of granaticin. Mol. Gen. Genet. 248, 610-620.
62. Pissowotzki, K., Mansouri, K. & Piepersberg, W. (1991). Genetics of streptomycin production in Streptomyces griseus: molecular structure and putative function of genes strELMB2N. Mol. Gen. Genet. 231, 113-123.
63. Niemi, J., Ylihonko, K., Hakala, J., Parssinen, R., Kopio, A. & Mantsala, P. (1994). Hybrid anthracycline antibiotics: production of new anthracyclines by cloned genes from Streptomyces purpurascens in Streptomyces galilaeus. Microbiol. 140, 1351-1358.
64. 10-methylenetetrahydromethanopterin reductase (Mer) from Methanobacterium thermoautotrophicum strain Marburg. Cloning, sequencing, transcriptional analysis, and functional expression in Escherichia coli of the mer gene. Eur. J. Biochem. 231, 773-778.
65. Weber, J.M., Leung, J.O., Swanson, S.J., Idler, K.B. & McAlpine, J.B. (1991). An erythromycin derivative produced by targeted gene disruption in Saccharopolyspora erythraea. Science 252, 114-117.
66. Crespi, M., Vereecke, D., Temmerman, W., Van Montagu, M. & Desomer, J. (1994). The fas operon of Rhodococcus fascians encodes new genes required for efficient fasciation of host plants. J. Bacteriol. 176, 2492-2501.
67. Omer, C.A., et al., & O'Keefe, D.P. (1990). Genes for two herbicide-inducible cytochromes P-450 from Streptomyces griseolus. J. Bacteriol. 172, 3335-3345.
68. Lalonde, G., O'Hanley, P.D., Stocker, B.A. & Denich, K.T. (1994). Characterization of a 3-dehydroquinase gene from Actinobacillus pleuropneumoniae with homology to the eukaryotic genes qa-2 and QUTE. Mol. Microbiol. 11, 273-280.