Tracing regulatory routes in metabolism using generalised supply-demand analysis

BMC Systems Biology

Volumn 9, Issue 1, 2015, Pages

  Christensen, Carl D ^a   Hofmeyr, Jan Hendrik S ^a   Rohwer, Johann M ^a  

^a STELLENBOSCH UNIVERSITY   (South Africa)

Author keywords

Arabidopsis thaliana; Generalised supply demand analysis; Lactococcus lactis; Metabolic control analysis; Metabolic modelling

Indexed keywords

AMINO ACID; PYRUVIC ACID;

ARABIDOPSIS; BIOLOGICAL MODEL; BIOSYNTHESIS; LACTOCOCCUS LACTIS; METABOLISM; PHYSIOLOGY; PROCEDURES; SYSTEMS BIOLOGY;

AMINO ACIDS; ARABIDOPSIS; LACTOCOCCUS LACTIS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; PYRUVIC ACID; SYSTEMS BIOLOGY;

EID: 84949309347     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/s12918-015-0236-1     Document Type: Article

References (41)

1. Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, et al. A comprehensive genome-scale reconstruction of Escherichia coli metabolism. Mol Syst Biol. 2011;7(1). doi:10.1038/msb.2011.65.
2. Thiele I, Jamshidi N, Fleming RMT, Palsson BØ. Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: A knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput Biol. 2009;5(3):1000312. doi:10.1371/journal.pcbi.1000312.
3. Lloyd CM, Lawson JR, Hunter PJ, Nielsen PF. The CellMLmodel repository. Bioinformatics. 2008;24(18):2122-123. doi:10.1093/bioinformatics/btn390.
4. Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, et al. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 2006;34(Database issue):689-91.
5. Olivier BG, Snoep JL. Web-based kinetic modelling using JWS online. Bioinforma. 2004;20(13):2143-44. doi:10.1093/bioinformatics/bth200.
6. Snoep JL, WesterhoffHV. From isolation to integration, a systems biology approach for building the silicon cell In: Alberghina Ls, WesterhoffHV, editors. Systems Biology. Topics in Current Genetics. Berlin, Heidelberg: Springer; 2005. p. 13-30.
7. Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival Jr B, et al. A whole-cell computational model predicts phenotype from genotype. Cell. 2012;150(2):389-401. doi:10.1016/j.cell.2012.05.044.
8. Rohwer JM, Hofmeyr J-HS. Identifying and characterising regulatory metabolites with generalised supply-demand analysis. J Theor Biol. 2008;252(3):546-54.
9. Kacser H, Burns JA, Fell DA. The control of flux: 21 years on. Biochem Soc Trans. 1995;23(2):341-66.
10. Heinrich R, Rapoport TA. A linear steady-state treatment of enzymatic chains: General properties, control and effector strength. Eur J Biochem. 1974;42(1):89-95. doi:10.1111/j.1432-1033.1974.tb03318.x.
11. Hoefnagel MHN, Starrenburg MJC, Martens DE, Hugenholtz J, Kleerebezem M, Swam IIV, et al. Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis. Microbiology. 2002;148(4):1003-13.
12. Curien G, Bastien O, Robert-Genthon M, Cornish-Bowden A, Cárdenas ML, Dumas R. Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters. Mol Syst Biol. 2009;5:271. doi:10.1038/msb.2009.29.
13. Hofmeyr J-HS, Cornish-Bowden A. Regulating the cellular economy of supply and demand. FEBS Lett. 2000;476(1-2):47-51.
14. Hofmeyr J-HS. Metabolic regulation: a control analytic perspective. J Bioenerg Biomembr. 1995;27(5):479-90.
15. Hofmeyr J-HS, Rohwer JM. Supply-demand analysis: A framework for exploring the regulatory design of metabolism. In: Methods in Enzymology. San Diego, California: Academic Press; 2011. p. 533-54.
16. Olivier BG, Rohwer JM, Hofmeyr J-HS. Modelling cellular systems with PySCeS. Bioinforma. 2004;21(4):560-1. doi:10.1093/bioinformatics/bti046.
17. Olivier B, Rohwer J, Hofmeyr J. PySCeS User Guide. 2015. http://pysces. sourceforge.net/docs/userguide.html Accessed 2015-06-22.
18. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinforma. 2003;19(4): 524-31.
19. Curien G, Dumas R, Cornish-Bowden A, Cardenas ML. Different contributions of the various isoenzymes to the flux in the aspartate-derived amino acid pathway in Arabidopsis thaliana In: Hicks MG, Kettner C, editors. Experimental Standard Conditions of Enzyme Characterizations. Proceedings of the 4th International Beilstein Workshop. Frankfurt: Beilstein-Institut zur Förderung der Chemischen Wissenschaften; 2010. p. 107-21.
20. Kowalczyk M, Bardowski J. Regulation of sugar catabolism in Lactococcus lactis. Crit Rev Microbiol. 2007;33(1):1-13. doi:10.1080/10408410601172164.
21. Hoefnagel MHN, Burgt AVD, Martens DE, Hugenholtz J, Snoep JL. Time dependent responses of glycolytic intermediates in a detailed glycolytic model of Lactococcus lactis during glucose run-out experiments. Mol Biol Rep. 2002;29(1-2):157-61. doi:10.1023/A:1020313409954.
22. Levering J, Musters MWJM, Bekker M, Bellomo D, Fiedler T, de Vos WM, et al. Role of phosphate in the central metabolism of two lactic acid bacteria-a comparative systems biology approach. FEBS J. 2012;279(7): 1274-1290. doi:10.1111/j.1742-4658.2012.08523.x.
23. Oh E, Lu M, Park C, Park C, Oh HB, Lee SY, et al. Dynamic modeling of lactic acid fermentation metabolism with Lactococcus lactis. J Microbiol Biotechnol. 2011;21(2):162-9.
24. Costa RS, Hartmann A, Gaspar P, Neves AR, Vinga S. An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2, 3-butanediol production. Mol BioSyst. 2014;10(3):628-39. doi:10.1039/C3MB70265K.
25. Palmfeldt J, Paese M, Hahn-Hägerdal B, Niel EWJV. The pool of ADP and ATP regulates anaerobic product formation in resting cells of Lactococcus lactis. Appl Environ Microbiol. 2004;70(9):5477-84. doi:10.1128/AEM.70.9.5477-5484.2004.
26. Cao R, Zeidan AA, Rådström P, van Niel EWJ. Inhibition kinetics of catabolic dehydrogenases by elevated moieties of ATP and ADP-implication for a new regulation mechanism in Lactococcus lactis. FEBS J. 2010;277(8):1843-52. doi:10.1111/j.1742-4658.2010.07601.x.
27. Garrigues C, Loubiere P, Lindley ND, Cocaign-Bousquet M. Control of the shift from homolactic acid to mixed-acid fermentation in Lactococcus lactis: predominant role of the NADH/NAD+ ratio. J Bacteriol. 1997;179(17):5282-7.
28. van Hoek MJA, Merks RMH. Redox balance is key to explaining full vs. partial switching to low-yield metabolism. BMC Syst Biol. 2012;6(1):22. doi:10.1186/1752-0509-6-22.
29. Lopez de Felipe F, Starrenburg MJ, Hugenholtz J. The role of NADH-oxidation in acetoin and diacetyl production from glucose in Lactococcus lactis subsp. lactis MG1363. FEMS Microbiol Lett. 1997;156(1): 15-19. doi:10.1111/j.1574-6968.1997.tb12699.x.
30. Hols P, Ramos A, Hugenholtz J, Delcour J, Vos WMD, Santos H, et al. Acetate utilization in Lactococcus lactis deficient in lactate dehydrogenase: a rescue pathway for maintaining redox balance. J Bacteriol. 1999;181(17):5521-6.
31. Heux S, Cachon R, Dequin S. Cofactor engineering in Saccharomyces cerevisiae: Expression of a H2O-forming NADH oxidase and impact on redox metabolism. Metab Eng. 2006;8(4):303-14. doi:10.1016/j.ymben.2005.12.003.
32. Bennett GN, San KY, Berrios-Rivera SJ. The effect of increasing NADH availability on the redistribution of metabolic fluxes in Escherichia coli chemostat cultures. Metab Eng. 2002;4(3):230-7. doi:10.1006/mben.2002.0228.
33. Sánchez AM, Bennett GN, San KY. Effect of different levels of NADH availability on metabolic fluxes of Escherichia coli chemostat cultures in defined medium. J Biotechnol. 2005;117(4):395-405. doi:10.1016/j.jbiotec.2005.02.006.
34. Ying W. NAD +/NADH and NADP +/NADPH in cellular functions and cell death: Regulation and biological consequences. Antioxid Redox Signaling. 2008;10(2):179-206. doi:10.1089/ars.2007.1672.
35. Stadtman ER, Cohen GN, LeBras G. Feedback inhibition and repression of aspartokinase activity in Echerichia coli. Ann NY Acad Sci. 1961;94(3): 952-9. doi:10.1111/j.1749-6632.1961.tb35587.x.
36. Stifel FB, Herman RH. Role of isozymes in metabolic control. Am J Clin Nutr. 1972;25(6):606-11.
37. Hofmeyr J-HS. Control-pattern analysis of metabolic pathways. Eur J Biochem. 1989;186(1-2):343-54. doi:10.1111/j.1432-1033.1989.tb15215.x.
38. Rohwer JM, Hofmeyr J-HS. Kinetic and thermodynamic aspects of enzyme control and regulation. J Phys Chem B. 2010;114(49):16280-9. doi:10.1021/jp108412s.
39. Galili G, Amir R, Hoefgen R, Hesse H. Improving the levels of essential amino acids and sulfur metabolites in plants. Biol Chem. 2005;386(9): 817-31.
40. Galili G, Höfgen R. Metabolic engineering of amino acids and storage proteins in plants. Metab Eng. 2002;4(1):3-11. doi:10.1006/mben.2001.0203.
41. Rohwer JM, Akhurst TJ, Hofmeyr J-HS. Symbolic control analysis of cellular systems In: Hicks MG, Kettner C, editors. Experimental Standard Conditions of Enzyme Characterizations. Proceedings of the 3rd International Beilstein Workshop. Frankfurt: Beilstein-Institut zur Förderung der Chemischen Wissenschaften; 2008. p. 137-48.