Metabolomic analysis of a synthetic metabolic switch in Streptomyces coelicolor A3(2)

Proteomics

Volumn 11, Issue 24, 2011, Pages 4622-4631

  Jankevics, Andris ^a,b   Merlo, M Elena ^a   de Vries, Marcel ^c   Vonk, Roel J ^c   Takano, Eriko ^a   Breitling, Rainer ^a,b  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

^c UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

Author keywords

Glutamine synthetase I; Metabolomics; Microbiology; Non coding RNA; Orbitrap; Streptomyces coelicolor

Indexed keywords

ANALYTIC METHOD; ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BIOTECHNOLOGY; CHROMATOGRAPHY; CONTROLLED STUDY; IONIZATION; METABOLOMICS; NITROGEN FIXATION; NONHUMAN; PRIORITY JOURNAL; REPRODUCIBILITY; RNA ANALYSIS; RNA INTERFERENCE; STREPTOMYCES COELICOLOR;

GENE EXPRESSION REGULATION, BACTERIAL; GLUTAMATE-AMMONIA LIGASE; METABOLOME; METABOLOMICS; RNA INTERFERENCE; RNA, SMALL UNTRANSLATED; STREPTOMYCES COELICOLOR;

EID: 82955187025     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201100254     Document Type: Article

References (43)

1. Clardy, J., Fischbach, M. A., Walsh, C. T., New antibiotics from bacterial natural products. Nat. Biotechnol. 2006, 24, 1541-1550.
2. Fiehn, O., Metabolomics - the link between genotypes and phenotypes. Plant Mol. Biol. 2002, 48, 155-171.
3. Bentley, S. D., Chater, K. F., Cerdeño-Tárraga, A. M., Challis, G. L. et al., Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 2002, 417, 141-147.
4. Challis, G. L., Hopwood, D. A., Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species. Proc. Natl. Acad. Sci. USA 2003, 100, 14555-14561.
5. Nieselt, K., Battke, F., Herbig, A., Bruheim, P. et al., The dynamic architecture of the metabolic switch in Streptomyces coelicolor. BMC Genomics 2010, 11, 10.
6. Ruiz, B., Chávez, A., Forero, A., García-Huante, Y. et al., Production of microbial secondary metabolites: regulation by the carbon source. Crit. Rev. Microbiol. 2010, 36, 146-167.
7. Horinouchi, S., Mining and polishing of the treasure trove in the nacterial genus Streptomyces. Biosci. Biotechnol. Biochem. 2007, 71, 283-299.
8. Alam, M. T., Merlo, M. E., Hodgson, D. A., Wellington, E. M. H. et al., Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor. BMC Genomics 2010, 11, 202.
9. Hebert, C. G., Valdes, J. J., Bentley, W. E., Beyond silencing-engineering applications of RNA interference and antisense technology for altering cellular phenotype. Curr. Opin. Biotechnol. 2008, 19, 500-505.
10. Thomason, M. K., Storz, G., Bacterial antisense RNAs: how many are there, and what are they doing? Annu. Rev. Genetics 2010, 44, 167-188.
11. Waters, L. S., Storz, G., Regulatory RNAs in bacteria. Cell 2009, 136, 615-628.
12. Lioliou, E., Romilly, C., Romby, P., Fechter, P., RNA-mediated regulation in bacteria: from natural to artificial systems. Nat. Biotechnol. 2010, 27, 222-235.
13. D'Alia, D., Nieselt, K., Steigele, S., Müller, J. et al., Noncoding RNA of glutamine synthetase I modulates antibiotic production in Streptomyces coelicolor A3(2). J. Bacteriol. 2010, 192, 1160-1164.
14. Amon, J., Titgemeyer, F., Burkovski, A., Common patterns - unique features: nitrogen metabolism and regulation in Gram-positive bacteria. FEMS Microbiol. Rev. 2010, 34, 588-605.
15. Reuther, J., Wohlleben, W., Nitrogen metabolism in Streptomyces coelicolor: transcriptional and post-translational regulation. J. Mol. Microbiol. Biotechnol. 2007, 12, 139-146.
16. Murakami, T., Holt, T. G., Thompson, C. J., Thiostrepton-induced gene expression in Streptomyces lividans. J. Bacteriol. 1989, 171, 1459-1466.
17. Ali, N., Herron, P. R., Evans, M. C., Dyson, P. J., Osmotic regulation of the Streptomyces lividans thiostrepton-inducible promoter, ptipA. Microbiol. 2002, 148, 381-390.
18. Tautenhahn, R., Böttcher, C., Neumann, S., Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformatics 2008, 9, 504.
19. Smith, C. A., Want, E. J., O'Maille, G., Abagyan, R., Siuzdak, G., XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem. 2006, 78, 779-787.
20. Scheltema, R. A., Jankevics, A., Jansen, R. C., Swertz, M. A., Breitling, R., PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis. Anal. Chem. 2011, 83, 2786-2793.
21. Windig, W., The use of the Durbin-Watson criterion for noise and background reduction of complex liquid chromatography/mass spectrometry data and a new algorithm to determine sample differences. Chemom. Int. Lab. Syst. 2004, 77, 206-214.
22. Scheltema, R., Decuypere, S., Dujardin, J., Watson, D. et al., Simple data-reduction method for high-resolution LC-MS data in metabolomics. Bioanalysis 2009, 1, 1551-1557.
23. Caspi, R., Foerster, H., Fulcher, C. A., Kaipa, P. et al., The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 2008, 36, D623-D631.
24. Kanehisa, M., Goto, S., Kawashima, S., Nakaya, A., The KEGG databases at GenomeNet. Nucleic Acids Res. 2002, 30, 42-46.
25. Fahy, E., Sud, M., Cotter, D., Subramaniam, S., LIPID MAPS online tools for lipid research. Nucleic Acids Res. 2007, 35, W606-W612.
26. Wishart, D. S., Tzur, D., Knox, C., Eisner, R. et al., HMDB: The Human Metabolome Database. Nucleic Acids Res. 2007, 35, D521-D526.
27. Keller, B. O., Sui, J., Young, A. B., Whittal, R. M., Interferences and contaminants encountered in modern mass spectrometry. Anal. Chim. Acta 2008, 627, 71-81.
28. Kendall, M. G., Smith, B. S., The problem of m rankings. Ann. Math. Stat. 1939, 10, 275-287.
29. Legendre, P., Species associations: the Kendall coefficient of concordance revisited. J. Agricult. Biol. Environ. Stat. 2005, 10, 226-245.
30. Benjamini, Y., Hochberg, Y., Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. B 1995, 57, 289-300.
31. Letunic, I., Yamada, T., Kanehisa, M., Bork, P., iPath: Interactive exploration of biochemical pathways and networks. Trends Biochem. Sci. 2008, 33, 101-103.
32. Betts, J. I., Baganz, F., Miniature bioreactors: current practices and future opportunities. Microb. Cell Fact. 2006, 5, 21.
33. Büchs, J., Introduction to advantages and problems of shaken cultures. Biochem. Eng. J. 2001, 7, 91-98.
34. Fink, D., Falke, D., Wohlleben, W., Engels, A., Nitrogen metabolism in Streptomyces coelicolor A3(2): modification of glutamine synthetase I by an adenylyltransferase. Microbiology 1999, 145, 2313-2322.
35. Kol, S., Merlo, M. E., Scheltema, R. A., de Vries, M. et al., Metabolomic characterization of the salt stress response in Streptomyces coelicolor. Appl. Environ. Microbiol. 2010, 76, 2574-2581.
36. Jebbar, M., Sohn-Bösser, L., Bremer, E., Bernard, T., Blanco, C., Ectoine-induced proteins in Sinorhizobium meliloti include an ectoine ABC-type transporter involved in osmoprotection and ectoine catabolism. J. Bacteriol. 2005, 187, 1293-1304.
37. Lewis, R., Shahi, S., Laing, E., Bucca, G. et al., Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2). BMC Res. Notes 2011, 4, 78.
38. Tiffert, Y., Supra, P., Wurm, R., Wohlleben, W. et al., The Streptomyces coelicolor GlnR regulon: identification of new GlnR targets and evidence for a central role of GlnR in nitrogen metabolism in actinomycetes. Mol. Microbiol. 2008, 67, 861-880.
39. Hopwood, D. A., Streptomyces in Nature and Medicine: The Antibiotic Makers, Oxford University Press, New York 2007.
40. Weber, T., Welzel, K., Pelzer, S., Vente, A., Wohlleben, W., Exploiting the genetic potential of polyketide producing streptomycetes. J. Biotechnol. 2003, 106, 221-232.
41. Bode, H. B., Bethe, B., Höfs, R., Zeeck, A., Big effects from small changes: possible ways to explore nature's chemical diversity. J. Chem. Biol. 2002, 3, 619-627.
42. Scherlach, K., Hertweck, C., Triggering cryptic natural product biosynthesis in microorganisms. Org. Biomol. Chem. 2009, 7, 1753-1760.
43. Medema, M. H., Breitling, R., Bovenberg, R., Takano, E., Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms. Nat. Rev. Microbiol. 2010, 9, 131-137.