Effects of deletions of -like genes on clorobiocin biosynthesis in Free

Abstract

In the biosynthetic gene cluster of the aminocoumarin antibiotic clorobiocin, the small ORF encodes a 71 aa protein which shows significant sequence similarity to from the mycobactin biosynthetic gene cluster of . -like genes are frequently found in the biosynthetic gene clusters of peptide antibiotics and siderophores, but their function has remained enigmatic. In a recent publication it has been suggested that these genes may have no function for secondary metabolite biosynthesis. An in-frame deletion of in the clorobiocin cluster has now been carried out. When the modified cluster was expressed in the heterologous host M512, clorobiocin was still formed. However, when the two further -like genes from elsewhere in the host genome were inactivated as well, clorobiocin formation was reduced dramatically. Complementation with or with any of three other -like genes restored clorobiocin formation. This is the first report proving the requirement of an -like gene for secondary metabolite formation, and the first proof that different -like genes can functionally replace each other. Feeding of an -defective triple mutant strain with an intact 3-amino-4,7-dihydroxy-coumarin moiety restored antibiotic production, showing that is specifically required for the formation of this moiety of the clorobiocin molecule.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2006/002998-0
2007-05-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/micro/153/5/1413.html?itemId=/content/journal/micro/10.1099/mic.0.2006/002998-0&mimeType=html&fmt=ahah

References

  1. Agnoli K., Lowe C. A., Farmer K. L., Husnain S. I., Thomas M. S. 2006; The ornibactin biosynthesis and transport genes of Burkholderia cenocepacia are regulated by an extracytoplasmic function sigma factor which is a part of the Fur regulon. J Bacteriol 188:3631–3644 [CrossRef]
    [Google Scholar]
  2. 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. other authors 2002; Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2. Nature 417:141–147 [CrossRef]
    [Google Scholar]
  3. Blodgett J. A., Zhang J. K., Metcalf W. W. 2005; Molecular cloning, sequence analysis, and heterologous expression of the phosphinothricin tripeptide biosynthetic gene cluster from Streptomyces viridochromogenes DSM 40736. Antimicrob Agents Chemother 49:230–240 [CrossRef]
    [Google Scholar]
  4. Carter R. A., Worsley P. S., Sawers G., Challis G. L., Dilworth M. J., Carson K. C., Lawrence J. A., Wexler M., Johnston A. W., Yeoman K. H. 2002; The vbs genes that direct synthesis of the siderophore vicibactin in Rhizobium leguminosarum : their expression in other genera requires ECF sigma factor RpoI. Mol Microbiol 44:1153–1166 [CrossRef]
    [Google Scholar]
  5. Challis G. L., 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 Microbiol Lett 187:111–114 [CrossRef]
    [Google Scholar]
  6. Chen H., Walsh C. T. 2001; Coumarin formation in novobiocin biosynthesis: β -hydroxylation of the aminoacyl enzyme tyrosyl- S -NovH by a cytochrome P450 NovI. Chem Biol 8:301–312 [CrossRef]
    [Google Scholar]
  7. Chen H., Hubbard B. K., O'Connor S. E., Walsh C. T. 2002; Formation of β -hydroxy histidine in the biosynthesis of nikkomycin antibiotics. Chem Biol 9:103–112 [CrossRef]
    [Google Scholar]
  8. Chiu H.-T., Hubbard B. K., Shah A. N., Eide J., Fredenburg R. A., Walsh C. T., Khosla C. 2001; Molecular cloning and sequence analysis of the complestatin biosynthetic gene cluster. Proc Natl Acad Sci U S A 98:8548–8553 [CrossRef]
    [Google Scholar]
  9. Cole S. T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S. V., Eiglmeier K., Gas S. other authors 1998; Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537–544 [CrossRef]
    [Google Scholar]
  10. Crosa J. H., Walsh C. T. 2002; Genetics and assembly line enzymology of siderophore biosynthesis in bacteria. Microbiol Mol Biol Rev 66:223–249 [CrossRef]
    [Google Scholar]
  11. Datsenko K. A., Wanner B. L. 2000; One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97:6640–6645 [CrossRef]
    [Google Scholar]
  12. Doumith M., Weingarten P., Wehmeier U. F., Salah-Bey K., Benhamou B., Capdevila C., Michel J.-M., Piepersberg W., Raynal M.-C. 2000; Analysis of genes involved in 6-deoxyhexose biosynthesis and transfer in Saccharopolyspora erythraea. Mol Gen Genet 264:477–485 [CrossRef]
    [Google Scholar]
  13. Edwards D. J., Gerwick W. H. 2004; Lyngbyatoxin biosynthesis: sequence of biosynthetic gene cluster and identification of a novel aromatic prenyltransferase. J Am Chem Soc 126:11432–11433 [CrossRef]
    [Google Scholar]
  14. Eustáquio, A. S., Gust B., Luft T., Li S.-M., Chater K. F., Heide L. 2003a; Clorobiocin biosynthesis in Streptomyces . Identification of the halogenase and generation of structural analogs. Chem Biol 10:279–288 [CrossRef]
    [Google Scholar]
  15. Eustáquio, A. S., Luft T., Wang Z.-X., Gust B., Chater K. F., Li S.-M., Heide L. 2003b; Novobiocin biosynthesis: inactivation of the putative regulatory gene novE and heterologous expression of genes involved in aminocoumarin ring formation. Arch Microbiol 180:25–32 [CrossRef]
    [Google Scholar]
  16. Eustáquio, A. S., Gust B., Li S.-M., Pelzer S., Wohlleben W., Chater K. F., Heide L. 2004; Production of 8′-halogenated and 8′-unsubstituted novobiocin derivatives in genetically engineered Streptomyces coelicolor strains. Chem Biol 11:1561–1572 [CrossRef]
    [Google Scholar]
  17. Eustáquio, A. S., Gust B., Galm U., Li S.-M., Chater K. F., Heide L. 2005a; Heterologous expression of novobiocin and clorobiocin biosynthetic gene clusters. Appl Environ Microbiol 71:2452–2459 [CrossRef]
    [Google Scholar]
  18. Eustáquio, A. S., Li S.-M., Heide L. 2005b; NovG, a DNA-binding protein acting as a positive regulator of novobiocin biosynthesis. Microbiology 151:1949–1961 [CrossRef]
    [Google Scholar]
  19. Flatman R. H., Howells A. J., Heide L., Fiedler H. P., Maxwell A. 2005; Simocyclinone D8, an inhibitor of DNA gyrase with a novel mode of action. Antimicrob Agents Chemother 49:1093–1100 [CrossRef]
    [Google Scholar]
  20. Flatman R. H., Eustaquio A., Li S. M., Heide L., Maxwell A. 2006; Structure–activity relationships of aminocoumarin-type gyrase and topoisomerase IV inhibitors obtained by combinatorial biosynthesis. Antimicrob Agents Chemother 50:1136–1142 [CrossRef]
    [Google Scholar]
  21. Freitag A., Galm U., Li S.-M., Heide L. 2004; New aminocoumarin antibiotics from a cloQ -defective mutant of the clorobiocin producer Streptomyces roseochromogenes DS12.976. J Antibiot 57:205–209 [CrossRef]
    [Google Scholar]
  22. Freitag A., Wemakor E., Li S.-M., Heide L. 2005; Acyl transfer in clorobiocin biosynthesis: involvement of several proteins in the transfer of the pyrrole-2-carboxyl moiety to the deoxysugar. Chembiochem 6:2316–2325 [CrossRef]
    [Google Scholar]
  23. Galm U., Schimana J., Fiedler H. P., Schmidt J., Li S.-M., Heide L. 2002; Cloning and analysis of the simocyclinone biosynthetic gene cluster of Streptomyces antibioticus Tü 6040. Arch Microbiol 178:102–114 [CrossRef]
    [Google Scholar]
  24. Garneau S., Dorrestein P. C., Kelleher N. L., Walsh C. T. 2005; Characterization of the formation of the pyrrole moiety during clorobiocin and coumermycin A1 biosynthesis. Biochemistry 44:2770–2780 [CrossRef]
    [Google Scholar]
  25. Gunsior M., Breazeale S. D., Lind A. J., Ravel J., Janc J. W., Townsend C. A. 2004; The biosynthetic gene cluster for a monocyclic beta-lactam antibiotic, nocardicin A. Chem Biol 11:927–938 [CrossRef]
    [Google Scholar]
  26. Gust B., Challis G. L., Fowler K., Kieser T., Chater K. F. 2003; PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin. Proc Natl Acad Sci U S A 100:1541–1546 [CrossRef]
    [Google Scholar]
  27. Gust B., Chandra G., Jakimowicz D., Yuqing T., Bruton C. J., Chater K. F. 2004; λ RED-mediated genetic manipulation of antibiotic-producing Streptomyces. Adv Appl Microbiol 54:107–128
    [Google Scholar]
  28. Hopwood D. A., Wright H. M. 1983; CDA is a new chromosomally-determined antibiotic from Streptomyces coelicolor A3(2. J Gen Microbiol 129:3575–3579
    [Google Scholar]
  29. Kieser T., Bibb M. J., Buttner M. J., Chater K. F., Hopwood D. A. 2000 Practical Streptomyces Genetics Norwich: John Innes Foundation;
    [Google Scholar]
  30. Li S.-M., Heide L. 2004; Functional analysis of biosynthetic genes of aminocoumarins and production of hybrid antibiotics. Curr Med Chem Anti-Infect Agents 3:279–295 [CrossRef]
    [Google Scholar]
  31. Li S.-M., Heide L. 2005; New aminocoumarin antibiotics from genetically engineered Streptomyces strains. Curr Med Chem 12:419–427 [CrossRef]
    [Google Scholar]
  32. Lombo F., Velasco A., Castro A., de la Calle F., Brana A. F., Sanchez-Puelles J. M., Mendez C., Salas J. A. 2006; Deciphering the biosynthesis pathway of the antitumor thiocoraline from a marine actinomycete and its expression in two Streptomyces species. Chembiochem 7:366–376 [CrossRef]
    [Google Scholar]
  33. MacNeil D. J., Gewain K. M., Ruby C. L., Dezeny G., Gibbons P. H., MacNeil T. 1992; Analysis of Streptomyces avermitilis genes required for avermectin biosynthesis utilizing a novel integration vector. Gene 111:61–68 [CrossRef]
    [Google Scholar]
  34. Magarvey N. A., Haltli B., He M., Greenstein M., Hucul J. A. 2006; Biosynthetic pathway for mannopeptimycins, lipoglycopeptide antibiotics active against drug-resistant gram-positive pathogens. Antimicrob Agents Chemother 50:2167–2177 [CrossRef]
    [Google Scholar]
  35. Miao V., Coeffet-Legal M. F., Brian P., Brost R., Penn J., Whiting A., Martin S., Ford R., Parr I. other authors 2005; Daptomycin biosynthesis in Streptomyces roseosporus : cloning and analysis of the gene cluster and revision of peptide stereochemistry. Microbiology 151:1507–1523 [CrossRef]
    [Google Scholar]
  36. Miao V., Brost R., Chapple J., She K., Gal M. F., Baltz R. H. 2006; The lipopeptide antibiotic A54145 biosynthetic gene cluster from Streptomyces fradiae. J Ind Microbiol Biotechnol 33:129–140 [CrossRef]
    [Google Scholar]
  37. Pacholec M., Hillson N. J., Walsh C. T. 2005; NovJ/NovK catalyze benzylic oxidation of a β -hydroxyl tyrosyl- S -pantetheinyl enzyme during aminocoumarin ring formation in novobiocin biosynthesis. Biochemistry 44:12819–12826 [CrossRef]
    [Google Scholar]
  38. Paget M. S., Chamberlin L., Atrih A., Foster S. J., Buttner M. J. 1999; Evidence that the extracytoplasmic function sigma factor sigmaE is required for normal cell wall structure in Streptomyces coelicolor A3(2). J Bacteriol 181:204–211
    [Google Scholar]
  39. Pojer F., Li S.-M., Heide L. 2002; Molecular cloning and sequence analysis of the clorobiocin biosynthetic gene cluster: new insights into the biosynthesis of aminocoumarin antibiotics. Microbiology 148:3901–3911
    [Google Scholar]
  40. Quadri L. E., Sello J., Keating T. A., Weinreb P. H., Walsh C. T. 1998; Identification of a Mycobacterium tuberculosis gene cluster encoding the biosynthetic enzymes for assembly of the virulence-conferring siderophore mycobactin. Chem Biol 5:631–645 [CrossRef]
    [Google Scholar]
  41. Redenbach M., Kieser H. M., Denapaite D., Eichner A., Cullum J., Kinashi H., Hopwood D. A. 1996; A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome. Mol Microbiol 21:77–96 [CrossRef]
    [Google Scholar]
  42. Sambrook J., Russell D. W. 2001 Molecular Cloning: a Laboratory Manual Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  43. Schwartz D., Berger S., Heinzelmann E., Muschko K., Welzel K., Wohlleben W. 2004; Biosynthetic gene cluster of the herbicide phosphinothricin tripeptide from Streptomyces viridochromogenes Tü494. Appl Environ Microbiol 70:7093–7102 [CrossRef]
    [Google Scholar]
  44. Shen B., Du L., Sanchez C., Edwards D. J., Chen M., Murrell J. M. 2002; Cloning and characterization of the bleomycin biosynthetic gene cluster from Streptomyces verticillus ATCC15003(1. J Nat Prod 65:422–431 [CrossRef]
    [Google Scholar]
  45. Sosio M., Bianchi A., Bossi E., Donadio S. 2000; Teicoplanin biosynthesis genes in Actinoplanes teichomyceticus. Antonie Van Leeuwenhoek 78:379–384 [CrossRef]
    [Google Scholar]
  46. Sosio M., Stinchi S., Beltrametti F., Lazzarini A., Donadio S. 2003; The gene cluster for the biosynthesis of the glycopeptide antibiotic A40926 by Nonomuraea species. Chem Biol 10:541–549 [CrossRef]
    [Google Scholar]
  47. Steffensky M., Wang Z.-X., Li S.-M., Heide L., Mühlenweg A. 2000; Identification of the novobiocin biosynthetic gene cluster of Streptomyces spheroides NCIB 11891. Antimicrob Agents Chemother 44:1214–1222 [CrossRef]
    [Google Scholar]
  48. Stegmann E., Rausch C., Stockert S., Burkert D., Wohlleben W. 2006; The small MbtH-like protein encoded by an internal gene of the balhimycin biosynthetic gene cluster is not required for glycopeptide production. FEMS Microbiol Lett 262:85–92 [CrossRef]
    [Google Scholar]
  49. Thomas M. G., Chan Y. A., Ozanick S. G. 2003; Deciphering tuberactinomycin biosynthesis: isolation, sequencing, and annotation of the viomycin biosynthetic gene cluster. Antimicrob Agents Chemother 47:2823–2830 [CrossRef]
    [Google Scholar]
  50. Wang G., Nie L., Tan H. 2003; Cloning and characterization of sanO , a gene involved in nikkomycin biosynthesis in Streptomyces ansochromogenes. Lett Appl Microbiol 37:452–457 [CrossRef]
    [Google Scholar]
  51. Wang Z.-X., Li S.-M., Heide L. 2000; Identification of the coumermycin A1 biosynthetic gene cluster of Streptomyces rishiriensis DSM 40489. Antimicrob Agents Chemother 44:3040–3048 [CrossRef]
    [Google Scholar]
  52. Xu H., Kahlich R., Kammerer B., Heide L., Li S.-M. 2003; CloN2, a novel acyltransferase involved in the attachment of the pyrrole-2-carboxyl moiety to the deoxysugar of clorobiocin. Microbiology 149:2183–2191 [CrossRef]
    [Google Scholar]
  53. Yeats C., Bentley S., Bateman A. 2003; New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor. BMC Microbiol 3:3 [CrossRef]
    [Google Scholar]
  54. Zerbe K., Pylypenko O., Vitali F., Zhang W., Rouset S., Heck M., Vrijbloed J. W., Bischoff D., Bister B. other authors 2002; Crystal structure of OxyB, a cytochrome P450 implicated in an oxidative phenol coupling reaction during vancomycin biosynthesis. J Biol Chem 277:47476–47485 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.2006/002998-0
Loading
/content/journal/micro/10.1099/mic.0.2006/002998-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed