Investigating alginate production and carbon utilization in Pseudomonas fluorescens SBW25 using mass spectrometry-based metabolic profiling

Metabolomics

Volumn 9, Issue 2, 2013, Pages 403-417

  Lien, Stina K ^a   Sletta, Håvard ^b   Ellingsen, Trond E ^b   Valla, Svein ^a   Correa, Elon ^c   Goodacre, Royston ^c   Vernstad, Kai ^b   Borgos, Sven Even Finborud ^a,b   Bruheim, Per ^a  

^a NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

^b SINTEF MATERIALS AND CHEMISTRY   (Norway)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Alginate synthesis; Anti sigma factor MucA; Mass spectrometry; Metabolic profiling; Pseudomonas fluorescens

Indexed keywords

ADENOSINE PHOSPHATE; ALGINIC ACID; CARBON; CYTIDINE TRIPHOSPHATE; FRUCTOSE; GLYCEROL; GUANOSINE DIPHOSPHATE; GUANOSINE PHOSPHATE; NITROGEN;

ARTICLE; BACTERIAL GENE; BACTERIAL METABOLISM; BACTERIAL STRAIN; BIOSYNTHESIS; CARBON SOURCE; CARBON UTILIZATION; CITRIC ACID CYCLE; CONTROLLED STUDY; DRY WEIGHT; ENERGY METABOLISM; GENE INACTIVATION; LIQUID CHROMATOGRAPHY; MASS FRAGMENTOGRAPHY; MASS SPECTROMETRY; METABOLOMICS; MUCA GENE; NONHUMAN; PENTOSE PHOSPHATE CYCLE; PSEUDOMONAS FLUORESCENS; UPREGULATION; WILD TYPE;

BACTERIA (MICROORGANISMS); PSEUDOMONAS FLUORESCENS;

EID: 84875542334     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-012-0454-0     Document Type: Article

References (39)

1. Barrette, W. C., Hannum, D. M., Wheeler, W. D., & Hurst, J. K. (1988). Viability and metabolic capability are maintained by Escherichia coli, Pseudomonas aeruginosa, and Streptococcus lactis at very low adenylate energy-charge. Journal of Bacteriology, 170, 3655-3659.
2. Behrends, V., Ryall, B., Wang, X. Z., Bundy, J. G., & Williams, H. D. (2010). Metabolic profiling of Pseudomonas aeruginosa demonstrates that the anti-sigma factor MucA modulates osmotic stress tolerance. Molecular BioSystems, 6, 562-569. doi: 10. 1039/b918710c.
3. Bolten, C. J., Kiefer, P., Letisse, F., Portais, J. C., & Wittmann, C. (2007). Sampling for metabolome analysis of microorganisms. Analytical Chemistry, 79, 3843-3849. doi: 10. 1021/ac0623888.
4. Borgos, S. E., et al. (2012). Mapping global effects of the transcription factor MucA in Pseudomonas fluorescens through genome-scale metabolic modeling. BMC Genome Biology, (submitted).
5. Canelas, A. B., Ras, C., ten Pierick, A., van Dam, J. C., Heijnen, J. J., & van Gulik, W. M. (2008). Leakage-free rapid quenching technique for yeast metabolomics. Metabolomics, 4, 226-239. doi: 10. 1007/s11306-008-0116-4.
6. Carnicer, M., et al. (2012). Development of quantitative metabolomics for Pichia pastoris. Metabolomics, 8, 284-298. doi: 10. 1007/s11306-011-0308-1.
7. Chapman, A. G., Fall, L., & Atkinson, D. E. (1971). Adenylate charge in Escherichia coli during growth and starvation. Journal of Bacteriology, 108, 1072-1086.
8. Conway, T. (1992). The Entner-Doudoroff pathway-history, physiology and molecular-biology. FEMS Microbiology Reviews, 103, 1-28. doi: 10. 1016/0378-1097(92)90334-k.
9. de Koning, W., & van Dam, K. (1992). A method for the determination of changes of glycolytic metabolites in yeast on a subsecond time scale using extraction at neutral pH. Analytical Biochemistry, 204(1), 118-123.
10. Droste, P., Miebach, S., Niedenfuhr, S., Wiechert, W., & Noh, K. (2011). Visualizing multi-omics data in metabolic networks with the software Omix-a case study. Biosystems, 105, 154-161. doi: 10. 1016/j. biosystems. 2011. 04. 003.
11. Ellis, D. I., & Goodacre, R. (2012). Metabolomics-assisted synthetic biology. Current Opinion in Biotechnology, 23, 22-28.
12. Firoved, A. M., & Deretic, V. (2003). Microarray analysis of global gene expression in mucoid Pseudomonas aeruginosa. Journal of Bacteriology, 185, 1071-1081. doi: 10. 1128/jb. 185. 3. 1071-1081. 2003.
13. Frimmersdorf, E., Horatzek, S., Pelnikevich, A., Wiehlmann, L., & Schomburg, D. (2010). How Pseudomonas aeruginosa adapts to various environments: a metabolomic approach. Environmental Microbiology, 12, 1734-1747. doi: 10. 1111/j. 1462-2920. 2010. 02253. x.
14. Gjersing, E. L., Herberg, J. L., Horn, J., Schaldach, C. M., & Maxwell, R. S. (2007). NMR metabolomics of planktonic and Biofilm modes of growth in Pseudomonas aeruginosa. Analytical Chemistry, 79, 8037-8045. doi: 10. 1021/ac070800t.
15. Hassett, D. J., Sutton, M. D., Schurr, M. J., Herr, A. B., Caldwell, C. C., & Matu, J. O. (2009). Pseudomonas aeruginosa hypoxic or anaerobic biofilm infections within cystic fibrosis airways. Trends in Microbiology, 17, 130-138. doi: 10. 1016/j. tim. 2008. 12. 003.
16. Hay, I. D., Rehman, Z. U., Ghafoor, A., & Rehm, B. H. A. (2010). Bacterial biosynthesis of alginates. Journal of Chemical Technology and Biotechnology, 85, 752-759. doi: 10. 1002/jctb. 2372.
17. Kvitvang, H. F. N., Andreassen, T., Adam, T., Villas-Boâs, S. G., & Bruheim, P. (2011). Highly sensitive GC/MS/MS method for quantitation of amino and nonamino organic acids. Analytical Chemistry, 83, 2705-2711. doi: 10. 1021/ac103245b.
18. Lien, S. K., Kvitvang, H. F., & Bruheim, P. (2012). Utilization of a deuterated derivatization agent to synthesize internal standards for gas chromatography-tandem mass spectrometry quantification of silylated metabolites. Journal of Chromatography A,. doi: 10. 1016/j. chroma. 2012. 05. 053.
19. Lu, W., Bennett, B. D., & Rabinowitz, J. D. (2008). Analytical strategies for LC-MS-based targeted metabolomics. Journal of Chromatography B-Analytical Technologies in the Biomedical and Life Sciences, 871, 236-242. doi: 10. 1016/j. jchromb. 2008. 04. 031.
20. Luo, B., Groenke, K., Takors, R., Wandrey, C., & Oldiges, M. (2007). Simultaneous determination of multiple intracellular metabolites in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle by liquid chromatography-mass spectrometry. Journal of Chromatography A, 1147, 153-164. doi: 10. 1016/j. chroma. 2007. 02. 034.
21. Martin, D. W., Schurr, M. J., Mudd, M. H., Govan, J. R. W., Holloway, B. W., & Deretic, V. (1993). Mechanism of conversion to mucoidy in Pseudomonas aeruginosa infecting cystic-fibrosis patients. Proceedings of the National academy of Sciences of the United States of America, 90, 8377-8381. doi: 10. 1073/pnas. 90. 18. 8377.
22. Mashego, M. R., Rumbold, K., de Mey, M., Vandamme, E., Soetaert, W., & Heijnen, J. J. (2007). Microbial metabolomics: past, present and future methodologies. Biotechnology Letters, 29(1), 1-16.
23. Meyer, H., Liebeke, M., & Lalk, M. (2010). A protocol for the investigation of the intracellular Staphylococcus aureus metabolome. Analytical Biochemistry, 401, 250-259. doi: 10. 1016/j. ab. 2010. 03. 003.
24. Nielsen, J., & Oliver, S. (2005). The next wave in metabolome analysis. Trends in Biotechnology, 23, 544-546. doi: 10. 1016/j. tibtech. 2005. 08. 005.
25. Rehm, B. H. A. (2010). Bacterial polymers: biosynthesis, modifications and applications. Nature Reviews Microbiology, 8, 578-592. doi: 10. 1038/nrmicro2354.
26. Schnider-Keel, U., Lejbolle, K. B., Baehler, E., Haas, D., & Keel, C. (2001). The sigma factor AlgU (AlgT) controls exopolysaccharide production and tolerance towards desiccation and osmotic stress in the biocontrol agent Pseudomonas fluorescens CHA0. Applied and Environmental Microbiology, 67, 5683-5693. doi: 10. 1128/aem. 67. 12. 5683-5693. 2001.
27. Smart, K. F., Aggio, R. B. M., van Houtte, J. R., & Villas-Boâs, S. G. (2010). Analytical platform for metabolome analysis of microbial cells using methyl chloroformate derivatization followed by gas chromatography-mass spectrometry. Nature Protocols, 5, 1709-1729. doi: 10. 1038/nprot. 2010. 108.
28. Sumner, L. W., et al. (2007). Proposed minimum reporting standards for chemical analysis. Metabolomics, 3, 211-221. doi: 10. 1007/s11306-007-0082-2.
29. Taylor, J. R. (1997). 7. 2 The weighted average. An introduction to error analysis (2nd ed., pp. 174-176). Sausalito, USA: University Science Books.
30. Taymaz-Nikerel, H., et al. (2009). Development and application of a differential method for reliable metabolome analysis in Escherichia coli. Analytical Biochemistry, 386, 9-19. doi: 10. 1016/j. ab. 2008. 11. 018.
31. van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., & Hankemeier, T. (2007). Microbial metabolomics: Toward a platform with full metabolome coverage. Analytical Biochemistry, 370, 17-25. doi: 10. 1016/j. ab. 2007. 07. 022.
32. van der Werf, M. J., et al. (2008). Comprehensive analysis of the metabolome of Pseudomonas putida S12 grown on different carbon sources. Molecular BioSystems, 4, 315-327. doi: 10. 1039/b717340g.
33. van Gulik, W. M. (2010). Fast sampling for quantitative microbial metabolomics. Current Opinion in Biotechnology, 21, 27-34. doi: 10. 1016/j. copbio. 2010. 01. 008.
34. Villas-Boâs, S. G., & Bruheim, P. (2007). The potential of metabolomics tools in bioremediation studies. Omics-A Journal of Integrative Biology, 11, 305-313. doi: 10. 1089/omi. 2007. 0005.
35. Villas-Boâs, S. G., & Bruheim, P. (2007). Cold glycerol-saline: The promising quenching solution for accurate intracellular metabolite analysis of microbial cells. Analytical Biochemistry, 370, 87-97. doi: 10. 1016/j. ab. 2007. 06. 028.
36. Villas-Boâs, S. G., Delicado, D. G., Akesson, M., & Nielsen, J. (2003). Simultaneous analysis of amino and nonamino organic acids as methyl chloroformate derivatives using gas chromatography-mass spectrometry. Analytical Biochemistry, 322, 134-138. doi: 10. 1016/j. ab. 2003. 07. 018.
37. Villas-Boâs, S. G., Moxley, J. F., Åkesson, M., Stepanopolous, G., & Nielsen, J. (2005). High-throughput metabolic state analysis: the missing link in integrated functional genomics of yeasts. Biochemical Journal, 388, 669-677.
38. Wentzel, A., Sletta, H., Consortium, S., Ellingsen, T. E., & Bruheim, P. (2012). Intracellular metabolite pool changes in response to nutrient depletion induced metabolic switching in Streptomyces coelicolor. Metabolites, 2, 178-194. doi: 10. 3390/Metabo2010178.
39. Winder, C. L., et al. (2008). Global metabolic profiling of Escherichia coli cultures: An evaluation of methods for quenching and extraction of intracellular metabolites. Analytical Chemistry, 80, 2939-2948. doi: 10. 1021/ac7023409.