Microbial technologies for the discovery of novel bioactive metabolites

Journal of Biotechnology

Volumn 99, Issue 3, 2002, Pages 187-198

  Donadio, Stefano ^a   Monciardini, Paolo ^a   Alduina, Rosa ^b   Mazza, Paola ^a   Chiocchini, Claudia ^a   Cavaletti, Linda ^a   Sosio, Margherita ^a   Puglia, Anna Maria ^b  

^a Biosearch Italia   (Italy)

^b UNIVERSITY OF PALERMO   (Italy)

Author keywords

Actinomycete; Secondary metabolites; Soil microbes

Indexed keywords

DNA; ESCHERICHIA COLI; FUNGI; GENES; METABOLITES; MICROORGANISMS;

BIOACTIVE MOLECULES;

BIOTECHNOLOGY;

BACTERIAL DNA;

ACTINOBACTERIA; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM ISOLATE; BIOTECHNOLOGY; CONTROLLED STUDY; ESCHERICHIA COLI; MEDICAL RESEARCH; METABOLITE; MOLECULAR BIOLOGY; MOLECULAR CLONING; MOLECULAR GENETICS; NONHUMAN; PHYSIOLOGY; PRIORITY JOURNAL; STREPTOMYCES; CLASSIFICATION; DIRECTED MOLECULAR EVOLUTION; GENE EXPRESSION REGULATION; GENE VECTOR; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; MICROBIOLOGY; POLYMERASE CHAIN REACTION; REVIEW; SPECIES DIFFERENCE;

ACTINOBACTERIA (CLASS); ESCHERICHIA COLI; FUNGI; STREPTOMYCES; UNCULTURED ACTINOMYCETE;

ACTINOBACTERIA; DIRECTED MOLECULAR EVOLUTION; GENE EXPRESSION REGULATION, BACTERIAL; GENETIC VECTORS; POLYMERASE CHAIN REACTION; SOIL MICROBIOLOGY; SPECIES SPECIFICITY;

EID: 0037073188     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-1656(02)00209-2     Document Type: Article

References (46)

1. Amann R.I., Ludwig W., Schleifer K.-H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:1995;143-169.
2. August P.R., Tang L., Yoon Y.J., Ning S., Muller R., Yu T.W., Taylor M., Hoffmann D., Kim C.G., Zhang Z.H., Hutchinson C.R., Floss H. Biosynthesis of the ansamycin antibiotic rifamycin: deductions from the molecular analysis of the rif biosynthetic gene cluster of Amycolatopsis mediterranei S699. Chem. Biol. 5:1998;69-79.
3. Beja O., Aravind L., Koonin E.V., Suzuki M.T., Hadd A., Nguyen L.P., Jovanovich S.B., Gates C.M., Feldman R.A., Spudich J.L., Spudich E.N., DeLong E.F. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science. 289:2000a;1902-1906.
4. Beja O., Suzuki M.T., Koonin E.V., Aravind L., Hadd A., Nguyen L.P., Villacorta R., Amjadi M., Garrigues C., Jovanovich S.B., Feldman R.A., DeLong E.F. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2:2000b;516-529.
5. 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., Woodwardm J., Barrell B.G., Parkhill J., Hopwood D.A. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature. 417:2002;141-147.
6. Birren B., Lai E. Pulsed Field Gel Electrophoresis: a Practical Guide. 1993;Academic Press, New York.
7. Brawner M.E. Advances in heterologous gene expression by Streptomyces. Curr. Opin. Biotechnol. 5:1994;475-481.
8. Brosch R., Gordon S.V., Billault A., Garnier T., Eiglemeier K., Soravito C., Barrell B.G., Cole S.T. Infect. Immun. 66:1998;2221-2229.
9. Carrano L., Donadio S. Key ingredients for efficient high throughput screening. Miertus S., Fassina G., Combinatorial Chemistry and Technology: Principles, Methods and Applications. 1999;233-250 Marcel Dekker, New York.
10. Doignon-Bourcier F., Willems A., Coopman R., Laguerre G., Gills M., De Lajudie P. Genotypic characterization of Bradyrhizobium strains nodulating small senegalese legumes by 16S-23S rDNA intergenic gene spacers and amplified fragment length polymorphism fingerprint analyses. Appl. Environ. Microbiol. 66:2000;3987-3997.
11. Donadio, S., Carrano, L., Brandi, L., Serina, S., Soffientini, A., Raimondi, E., Montanini, N., Sosio, M., Gualerzi, C.O. 2002. Targets and assays for discovering novel antibacterial agents. J. Biotechnol. 99, 175-185.
12. Du L., Sanchez C., Chen M., Edwards D.J., Shen B. The biosynthetic gene cluster for the antitumor drug bleomycin from Streptomyces verticillus ATCC15003 supporting functional interactions between nonribosomal peptide synthetases and a polyketide synthase. Chem. Biol. 7:2000;623-642.
13. Goodacre R., Kell D.B. Pyrolysis mass spectrometry and its applications in biotechnology. Curr. Opin. Biotechnol. 7:1996;20-28.
14. Gordon S.V., Brosch R., Billault A., Garnier T., Eiglmeier K., Cole S.T. Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays. Mol. Microbiol. 32:1999;643-655.
15. Gürtler V., Stanisich V.A. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology. 142:1996;3-16.
16. Hamilton C.M., Aldea M., Washburn B.K., Babitzke P., Kushner S.R. New method for generating deletions and gene replacements in Escherichia coli. J. Bacteriol. 171:1989;4617-4622.
17. Handelsman J., Rondon M.R., Brady S.F., Clardy J., Goodman R.M. Molecular biological access to the chemistry of unknown microbes: a new frontier for natural products. Chem. Biol. 5:1998;R245-R249.
18. Helm D., Labischinski H., Schallehn G., Naumann D. Classification and identification of bacteria by Fourier transform infrared spectroscopy. J. Gen. Microbiol. 137:1991;69-79.
19. Ioannou P.A., Amemiya C.T., Garnes J., Kroisel P.M., Shizuya H., Chen C., Batzer M.A., de Jong P.J. A new bacteriophage P1-derived vector for the propagation of large human DNA fragments. Nature Genet. 6:1994;84-89.
20. Kieser T., Bibb M.J., Buttner M.J., Chater K.F., Hopwood D.A. Practical Streptomyces Genetics. 2000;The John Innes Foundation, Norwich, UK.
21. Knight I.T. Molecular genetic methods for detection and identification of viable but nonculturable microorganisms. Colwell R.R., Grimes D.J., Nonculturable Microorganisms in the Environment. 2000;77-85 ASM Press, Washington, DC.
22. Kwon H.J., Smith W.C., Xiang L., Shen B. Cloning and heterologous expression of the macrotetrolide biosynthetic gene cluster revealed a novel polyketide synthase that lacks an acyl carrier protein. J. Am. Chem. Soc. 123:2001;3385-3386.
23. Lazzarini A., Cavaletti L., Toppo G., Marinelli F. Rare genera of actinomycetes as potential producers of new antibiotics. Antonie Van Leeuwenhoek. 78:2000;399-405.
24. Mehling A., Wehmeier U.F., Piepersberg W. Nucleotide sequence of streptomycete 16S ribosomal DNA: towards a specific identification system for streptomycetes using PCR. Microbiology. 141:1995;2139-2147.
25. Monciardini, P., Sosio, M., Cavaletti, L., Chiocchini, C., Donadio, S., 2002. New PCR primers for the selective amplification of 16S rDNA from different groups of actinomycetes. FEMS Microbiol. Ecol., in press.
26. Moròn R., Gonzàlez I., Genilloud O. New genus-specific primers for the PCR identification of members of the genera Pseudonocardia and Saccharopolyspora. Int. J. Syst. Bacteriol. 49:1999;149-162.
27. Muyrers J.P., Zhang Y., Testa G., Stewart A.F. Rapid modification of bacterial artificial chromosomes by ET-recombination. Nucleic Acids Res. 27:1999;1555-1557.
28. Narayanan K., Williamson R., Zhang Y., Stewart A.F., Ioannou P.A. Efficient and precise engineering of a 200 kb beta-globin human/bacterial artificial chromosome in E. coli DH10B using an inducible homologous recombination system. Gene Ther. 6:1999;442-447.
29. Naumann D., Helm D., Labischinski H. Microbiological characterizations by FT-IR Spectroscopy. Nature. 351:1991;81-82.
30. Omura S., Ikeda H., Ishikawa J., Hanamoto A., Takahashi C., Shinose M., Takahashi Y., Horikawa H., Nakazawa H., Osonoe T., Kikuchi H., Shiba T., Sakaki Y., Hattori M. Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc. Natl Acad. Sci. USA. 98:2001;12215-12220.
31. Osoegawa K., Woon P.Y., Zhao B., Frenge E., Tateno M., Catanese J.J., de Jong P.J. An improved approach for the construction of bacterial artificial chromosome libraries. Genomics. 52:1998;1-8.
32. Piel J., Hoang K., Moore B.S. Metabolic diversity encoded by the enterocin biosynthesis gene cluster. J. Am. Chem. Soc. 122:2000;5415-5416.
33. Ray T., Mills A., Dyson P. Tris-dependent oxidative DNA strand scission during electrophoresis. Electrophoresis. 16:1995;888-894.
34. Rondon M.R., Raffel S.J., Goodman R.M., Handelsman J. Towards functional genomics in bacteria: Analysis of expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus. Proc. Natl Acad. Sci. USA. 96:1999;6451-6455.
35. Rondon M.R., August P.R., Bettermann P.D., Brady S.J., Grossman T.H., Liles M.R., Loiacono K.A., Lynch B.A., MacNeil I.A., Minor C., Clardy J., Handelsman J., Goodman R.M. Cloning of the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:2000;2541-2547.
36. Sheng Y., Mancino V., Birren B. Transformation of Escherichia coli with large DNA molecules by electroporation. Nucleic Acids Res. 23:1995;1990-1996.
37. Sosio M., Bossi E., Bianchi A., Donadio S. Multiple peptide synthetase gene clusters in actinomycetes. Mol. Gen. Genet. 264:2000a;213-221.
38. Sosio M., Giusino F., Cappellano C., Bossi E., Puglia A.M., Donadio S. Artificial chromosomes for antibiotic producing actinomycetes. Nature Biotechnol. 18:2000b;343-345.
39. Sosio M., Bossi E., Donadio S. Assembly of large genomic segments in artificial chromosomes by homologous recombination in Escherichia coli. Nucleic Acids Res. 37:2001;e37.
40. Stackebrandt E., Rainey F.A., Ward-Rainey N.L. Proposal for a new hierarchic classification system, actinobacteria classis nov. Int. J. Syst. Bacteriol. 47:1997;479-491.
41. Steffan R.J., Goskøyr J., Bej A.K., Atlas R.M. Recovery of DNA from soils and sediments. Appl. Environ. Microbiol. 54:1988;2908-2915.
42. Tang L., Shah S., Chung L., Carney J., Katz L., Khosla C., Julien B. Cloning and heterologous expression of the epothilone gene cluster. Science. 287:2000;640-642.
43. Weinbauer M.G., Beckmann C., Höfle M.G. Utility of green fluorescent nucleic acid dyes and aluminum oxide membrane filters for rapid epifluorescence enumeration of soil and sediment bacteria. Appl. Environ. Micorbiol. 64:1998;5000-5003.
44. Woese C.R. Bacterial evolution. Microbiol. Rev. 51:1987;221-271.
45. Yang X.W., Model P., Heintz N. Homologous recombination based modification in Escherichia coli and germline transmission in transgenic mice of a bacterial artificial chromosome. Nature Biotechnol. 15:1997;859-865.
46. Yu D., Ellis H.M., Lee E.C., Jenkins N.A., Copeland N.G., Court D.L. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl Acad. Sci. USA. 97:2000;5978-5983.