Monitoring novel metabolic pathways using metabolomics and machine learning: Induction of the phosphoketolase pathway in Aspergillus nidulans cultivations

Metabolomics

Volumn 3, Issue 4, 2007, Pages 503-516

  Panagiotou, G ^a   Kouskoumvekaki, I ^a   Jonsdottir S O ^a   Olsson, L ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Aspergillus nidulans; Metabolite profile; Phosphoketolase; Self Organizing Maps (SOM)

Indexed keywords

EMERICELLA NIDULANS;

EID: 36049016078     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-007-0061-7     Document Type: Article

References (39)

1. Alhoniemi E., Hollmén J., Simula O., Vesanto J. (1999). Process monitoring and modeling using the Self-Organizing Map. Int. Comput. Aided Eng. 6(1): 3-14
2. Alhoniemi E., Himberg J., Parhankangas J., Vesanto J. (2000). SOM Toolbox 2.0, a Software Library for Matlab. SOM Toolbox Team, Laboratory of Computer and Information Sciences, Finland
3. Amor C., Dominguez A.I., De Lucas J.R., Laborda F. (2000). The catabolite inactivation of Aspergillus nidulans isocitrate lyase occurs by specific autophagy of peroxisomes. Arch. Microbiol. 174: 59-66
4. Balakin K.V., Eksin S., Bugrim A., Ivanevkov Y.A., Korolev D., Nikolsky T.V., Skorenko A.V., Ivashchenko A.A., Savchuk N.P., Nikolskaya T. (2004). Kohonen Maps for the prediction of binding to human cytochrome P450 3A4. Drug Metabol. Disposit. 32: 1183-1189
5. Bradford M.M. (1976). A rapid and sensitive method for the quantification of microgram quantities of protein utilising the principle of protein-dye binding. Anal. Biochem. 72: 248-254
6. Buchholz A., Hurlebaus J., Wandrey C., Takors R. (2002). Metabolomics: quantification of intracellular metabolite dynamics. Biomol. Eng. 19: 5-15
7. Burkard, U. (2003). Methods for data analysis in Gasteiger, J. and Engel, T. (Eds.), Chemoinformatics. Wiley-VCH, Weinheim International Conference, Kidlington, UK, pp. 239-246. Elsevier Sci
8. Carlsen M., Nielsen J. (2001). Influence of carbon source on alpha-amylase production by Aspergillus oryzae. Appl. Microbiol. Biotechnol. 57: 346-349
9. De Lucas J.R., Dominguez A.I., Valenciano S., Turner G., Laborda F. (1999). The acuH gene of Aspergillus nidulans, required for growth on acetate and long-chain fatty acids, encodes a putative homologue of the mammalian carnitine/acylcarnitine carrier. Arch. Microbiol. 171: 386-396
10. Ebbighausen H., Weil B., Kramer R. (1991). Carrier-mediated acetate uptake in Corynebacterium glutamicum. Arch. Microbiol. 155: 505-510
11. Eikens, B. and Karim, M.N. (1998). Identification of a fermentation with SOM in Computer applications in biotechnology 1998. (CAB7) Horizon of bioprocess systems engineering in 21st century. Proceedings volume from the 7th IFAC
12. Evans C.T., Ratledge C. (1984). Induction of xylulose-5-phosphoketolase in a variety of yeasts grown on d -xylose: The key to efficient xylose metabolism. Arch. Microbiol. 139: 48-52
13. Hans M.A., Heinzle E., Wittmann C. (2001). Quantification of intracellular amino acids in batch cultures of Saccharomyces cerevisiae. Appl Microbiol. Biotechnol. 56: 776-779
14. Hondmann D., Visser J. (1994). Carbon metabolism. In: Martinelli S.D., Kinghorn J.R. (eds) Aspergillus: 50 years on. Elsevier, Amsterdam, pp. 61-139
15. Ingram-Smith C., Martin S.R., Smith K.S. (2006). Acetate kinase: Not just a bacterial enzyme. Trends Biotechnol. 14: 249-253
16. Kell D. (2004). Metabolomics and systems biology; making sense of the soup. Curr. Opin. Microbiol. 7: 296-307
17. Kohonen T. (1989). Self-Organization and Associative Memory. Springer Series in Information Sciences, 3rd edn. Springer-Verlag, Berlin
18. Kohonen T., Oja E., Simula O., Visa A., Kangas J. (1996). Engineering Applications of the Self-Organising Map. IEEE. 84: 1358-1384
19. Kubicek C., Rohr M. (1986). Citric acid fermentation. Crit. Rev. Biotechnol. 3: 331-373
20. Manzoni M., Rollini M. (2002). Biosynthesis and biotechnological production of statins by filamentous fungi and application of these cholesterol-lowering drugs. Appl. Microbiol. Biotechnol. 58: 555-564
21. Martinez-Force E., Benitez T. (1992). Changes in yeast amino acid pool with respiratory versus fermentative metabolism. Biotechnol. Bioengin. 40: 643-649
22. Marwoto B., Nakashimada Y., Kakizono T., Nishio N. (2004). Metabolic analysis of acetate accumulation during xylose consumption by Paenibacillus polymyxa. Appl. Microbiol. BIotechnol. 64: 112-1199
23. Marzulf G.A. (1997) Molecular genetics of sulphur assimilation in filamentous fungi and yeast. Annu. Rev. Microbiol. 51: 73-96
24. Mitjs, B.N. and Schmidt-Dannert, C. (2003). Engineering of secondary metabolite pathways. Curr. Opin. Biotechnol. 14, 597-602
25. Nielsen J. (2003). It is all about metabolic fluxes. J. Bacteriol. 185: 7031-7035
26. Nuesch J., Heim J., Treichler H.J. (1987) The biosynthesis of sulphur-containing b-lactam antibiotics. Annu. Rev. Microbiol. 41: 51-75
27. Oja M., Kaski S., Kohonen T. (2002). Bibliography of Self Organizing Map (SOM) papers: 1998-2001 Addendum. Neural Comput. Surveys 3: 1-156
28. Panagiotou G., Villas-Boas S.G., Christakopoulos P., Nielsen J., Olsson L. (2005a). Intracellular metabolite profiling of Fusarium oxysporum converting glucose to ethanol. J. Biotechnol. 115: 425-434
29. Panagiotou G., Christakopoulos P., Olsson L. (2005b). The influence of different cultivation conditions on the metabolome of F. oxysporum. J. Biotechnol. 108: 304-315
30. Panagiotou G., Christakopoulos P., Grotkjær T., Olsson L. (2006). Engineering of the redox imbalance of F. oxysporum enables anaerobic growth on xylose. Met. Eng. 8: 474-482
31. Park S.J., Lee S.Y., Cho J., Kim T.Y., Lee J.W., Park J.H., Han M.J. (2005). Global physiological understanding and metabolic engineering of microorganisms based on omics studies. Appl. Microbiol. Biotechnol. 68: 567-579
32. Rohr L.M., Teuber M., Meile L. (2002). Phosphoketolase, a neglected enzyme of microbial carbohydrate metabolism. Food Technol. 56: 270-273
33. Schellenberger A. (1998). Sixty years of thiamine diposphate biochemistry. Biochim. Biophys. Acta. 1385: 177
34. Senac T., Hahn-Hagerdal B. (1990). Intermediary metabolite concentrations in xylulose- and glucose-fermenting Saccharomyces cerevisiae cells. Appl. Environ. Microbiol. 56: 120-126
35. Sheu C.W., Konings W.N., Freese E. (1972). Effects of acetate and other short-chain amino acids on sugar and amino acid uptake of Bacillus subtilis. J. Bacteriol. 111: 525-530
36. Smedsgaard J., Nielsen J. (2005). Metabolite profiling of fungi and yeast: From phenotype to metabolome by MS and informatics. J. Exp. Bot. 56: 273-286
37. Villas-Boas S.G., Moxley J.F., Ákesson M., Stephanopoulos G., Nielsen J. (2005). High-throughput metabolic state analysis: The missing link in integrated functional genomics of yeasts. Biochem. J. 388: 669-677
38. Wolfe A.J. (2005). The acetate switch. Microbiol. Mol. Biol. Rev. 69: 12-50
39. Zupan, J. (2003). In Gasteiger, J. (Ed.), Handbook of Chemoinformatics, From Data to Knowledge, Vol. 3. Wiley-VCH, Weinheim, p. 1176