Identifying producers of antibacterial compounds by screening for antibiotic resistance

Nature Biotechnology

Volumn 31, Issue 10, 2013, Pages 922-927

  Thaker, Maulik N ^a   Wang, Wenliang ^a   Spanogiannopoulos, Peter ^a   Waglechner, Nicholas ^a   King, Andrew M ^a   Medina, Ricardo ^b   Wright, Gerard D ^a  

^a MCMASTER UNIVERSITY   (Canada)

^b CENTRAL UNIVERSITY OF LAS VILLAS   (Cuba)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBACTERIAL COMPOUNDS; ANTIBIOTIC RESISTANCE; BIOSYNTHETIC ENZYMES; BIOSYNTHETIC GENE; CHEMICAL DIVERSITY; EFFICIENT STRATEGY; ORDERS OF MAGNITUDE; PEPTIDE SCAFFOLDS;

BIOLOGY; BIOSYNTHESIS; PEPTIDES; SCAFFOLDS;

ANTIBIOTICS;

ANSAMYCIN DERIVATIVE; ANTIINFECTIVE AGENT; GELDANAMYCIN; GLYCOPEPTIDE; NATURAL PRODUCT; PEKISKOMYCIN; TEICOPLANIN; UNCLASSIFIED DRUG; VANCOMYCIN;

ACTINOBACTERIA; ANTIBACTERIAL ACTIVITY; ANTIBIOTIC RESISTANCE; ARTICLE; BIOSYNTHESIS; CHEMICAL MODIFICATION; FILTER; GENE SEQUENCE; GENOTYPE; METAGENOMICS; NONHUMAN; OPERON; PHYLOGENETIC TREE; PRIORITY JOURNAL;

ACTINOBACTERIA; ANTI-BACTERIAL AGENTS; BIOSYNTHETIC PATHWAYS; DRUG EVALUATION, PRECLINICAL; DRUG RESISTANCE, MICROBIAL; GLYCOPEPTIDES; PHYLOGENY; REPRODUCIBILITY OF RESULTS; RIFAMPIN; VANCOMYCIN;

EID: 84885660159     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.2685     Document Type: Article

References (36)

1. Wright, G. D. Antibiotics: a new hope. Chem. Biol. 19, 3-10 (2012).
2. Anonymous. A call to arms. Nat. Rev. Drug Discov. 6, 8-12 (2007).
3. Cooper, M. A. & Shlaes, D. Fix the antibiotics pipeline. Nature 472, 32 (2011).
4. Reddy, B. V. B. et al. Natural product biosynthetic gene diversity in geographically distinct soil microbiomes. Appl. Environ. Microbiol. 78, 3744-3752 (2012).
5. Nett, M., Ikeda, H. & Moore, B. S. Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat. Prod. Rep. 26, 1362-1384 (2009).
6. Lamb, S. S. & Wright, G. D. Accessorizing natural products: adding to nature's toolbox. Proc. Natl. Acad. Sci. USA 102, 519-520 (2005).
7. Baltz, R. H. Marcel Faber Roundtable: is our antibiotic pipeline unproductive because of starvation, constipation or lack of inspiration? J. Ind. Microbiol. Biotechnol. 33, 507-513 (2006).
8. Thaker, M. N. & Wright, G. D. Opportunities for synthetic biology in antibiotics: expanding glycopeptide chemical diversity. ACS Synth. Biol. doi:10. 1021/sb300092n (17 December 2012).
9. Cundliffe, E. & Demain, A. L. Avoidance of suicide in antibiotic-producing microbes. J. Ind. Microbiol. Biotechnol. 37, 643-672 (2010).
10. Wright, G. D. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat. Rev. Microbiol. 5, 175-186 (2007).
11. Courvalin, P. Vancomycin resistance in Gram-positive cocci. Clin. Infect. Dis. 42, S25-S34 (2006).
12. Chiu, H. T. et al. Molecular cloning and sequence analysis of the complestatin biosynthetic gene cluster. Proc. Natl. Acad. Sci. USA 98, 8548-8553 (2001).
13. Lanoot, B. et al. BOX-PCR fingerprinting as a powerful tool to reveal synonymous names in the genus Streptomyces. Emended descriptions are proposed for the species Streptomyces cinereorectus, S. fradiae, S. tricolor, S. colombiensis, S. filamentosus, S. vinaceus and S. phaeopurpureus. Syst. Appl. Microbiol. 27, 84-92 (2004).
14. Thaker, M. N. et al. Biosynthetic gene cluster and antimicrobial activity of the elfamycin antibiotic factumycin. Med. Chem. Commun. 3, 1020-1026 (2012).
15. Nagarajan, R. et al. M43 antibiotics: methylated vancomycins and unrearranged CDP-I analogs. J. Am. Chem. Soc. 110, 7896-7897 (1988).
16. Yim, G., Wang, H. H. & Davies, J. Antibiotics as signalling molecules. Phil. Trans. R. Soc. Lond. B 362, 1195-1200 (2007).
17. Pootoolal, J. et al. Assembling the glycopeptide antibiotic scaffold: The biosynthesis of A47934 from Streptomyces toyocaensis NRRL15009. Proc. Natl. Acad. Sci. USA 99, 8962-8967 (2002).
18. Skelton, N. J., Williams, D. H., Monday, R. A. & Ruddock, J. C. Structure elucidation of the novel glycopeptide antibiotic UK-68,597. J. Org. Chem. 55, 3718-3723 (1990).
19. Banik, J. J. & Brady, S. F. Cloning and characterization of new glycopeptide gene clusters found in an environmental DNA megalibrary. Proc. Natl. Acad. Sci. USA 105, 17273-17277 (2008).
20. Banik, J. J., Craig, J. W., Calle, P. Y. & Brady, S. F. Tailoring enzyme-rich environmental DNA clones: a source of enzymes for generating libraries of unnatural natural products. J. Am. Chem. Soc. 132, 15661-15670 (2010).
21. Bibikova, M. V., Ivanitskaia, L. P. & Singal, E. M. Antibiotiki Directed screening of aminoglycoside antibiotic producers on selective media with gentamycin. (Original in Russian. ) 26, 488-492 (1981).
22. Ivanitskaia, L. P., Bibikova, M. V., Gromova, M. N., Zhdanovich Iu, V. & Istratov, E. N. Antibiotiki Use of selective media with lincomycin for the directed screening of antibiotic producers. (Original in Russian. ) 26, 83-86 (1981).
23. Hong, H. J., Hutchings, M. I. & Buttner, M. J. Vancomycin resistance VanS/VanR two-component systems. Adv. Exp. Med. Biol. 631, 200-213 (2008).
24. Koteva, K. et al. A vancomycin photoprobe identifies the histidine kinase VanSsc as a vancomycin receptor. Nat. Chem. Biol. 6, 327-329 (2010).
25. Berdy, J. Bioactive microbial metabolites. J. Antibiot. (Tokyo) 58, 1-26 (2005).
26. Hosaka, T. et al. Antibacterial discovery in actinomycetes strains with mutations in RNA polymerase or ribosomal protein S12. Nat. Biotechnol. 27, 462-464 (2009).
27. Martín, J.-F. & Liras, P. Engineering of regulatory cascades and networks controlling antibiotic biosynthesis in Streptomyces. Curr. Opin. Microbiol. 13, 263-273 (2010).
28. D'Costa, V. M., McGrann, K. M., Hughes, D. W. & Wright, G. D. Sampling the antibiotic resistome. Science 311, 374-377 (2006).
29. Hayakawa, M. & Nonomura, H. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J. Ferment. Technol. 65, 501-509 (1987).
30. He, W., Wu, L., Gao, Q., Du, Y. & Wang, Y. Identification of AHBA biosynthetic genes related to geldanamycin biosynthesis in Streptomyces hygroscopicus 17997. Curr. Microbiol. 52, 197-203 (2006).
31. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004).
32. Folena-Wasserman, G., Sitrin, R. D., Chapin, F. & Snader, K. M. Affinity chromatography of glycopeptide antibiotics. J. Chromatogr. A 392, 225-238 (1987).
33. Li, H. Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics 28, 1838-1844 (2012).
34. Chevreux, B., Wetter, T. & Suhai, S. in Computer Science and Biology: Proceedings of the German Conference on Bioinformatics, Hannover, Germany, 4-6 October, pp. 45-56 (GCB, 1999).
35. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
36. Medema, M. H. et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 39, W339-W346 (2011).