title: Dynamic metabolic flux analysis demonstrated on cultures where the limiting substrate is changed from carbon to nitrogen and vice versa.
abstract: The main requirement for metabolic flux analysis (MFA) is that the cells are in a pseudo-steady state, that there is no accumulation or depletion of intracellular metabolites. In the past, the applications of MFA were limited to the analysis of continuous cultures. This contribution introduces the concept of dynamic MFA and extends MFA so that it is applicable to transient cultures. Time series of concentration measurements are transformed into flux values. This transformation involves differentiation, which typically increases the noisiness of the data. Therefore, a noise-reducing step is needed. In this work, polynomial smoothing was used. As a test case, dynamic MFA is applied on Escherichia coli cultivations shifting from carbon limitation to nitrogen limitation and vice versa. After switching the limiting substrate from N to C, a lag phase was observed accompanied with an increase in maintenance energy requirement. This lag phase did not occur in the C- to N-limitation case.
authors.affiliation: Department of Applied Mathematics, Biometrics and Process Control, Ghent University, Coupure Links 653, 9000 Gent, Belgium. gaspard.lequeux@biomath.ugent.be
authors.forename: Gaspard
authors.initials: G
authors.lastname: Lequeux
authors.forename: Joeri
authors.initials: J
authors.lastname: Beauprez
authors.forename: Jo
authors.initials: J
authors.lastname: Maertens
authors.forename: Ellen
authors.initials: E
authors.lastname: Van Horen
authors.forename: Wim
authors.initials: W
authors.lastname: Soetaert
authors.forename: Erick
authors.initials: E
authors.lastname: Vandamme
authors.forename: Peter A
authors.initials: PA
authors.lastname: Vanrolleghem
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D018533:Biomass; D002244:Carbon / Q000378:metabolism / Q000494:pharmacology*; D002245:Carbon Dioxide / Q000378:metabolism; D018929:Cell Culture Techniques / Q000379:methods*; D004926:Escherichia coli / Q000166:cytology / Q000187:drug effects* / Q000254:growth & development / Q000378:metabolism*; D006868:Hydrolysis / Q000187:drug effects; D053858:Metabolic Networks and Pathways / Q000187:drug effects; D009584:Nitrogen / Q000494:pharmacology*; D010101:Oxygen Consumption / Q000187:drug effects; D013379:Substrate Specificity / Q000187:drug effects; D013997:Time Factors
chemical_list: D002245:Carbon Dioxide; D002244:Carbon; D000255:Adenosine Triphosphate; D009584:Nitrogen
references.citation: Biotechnol Bioeng. 1983 Sep;25(9):2177-208
references.pmid: 18574815
references.citation: J Bacteriol. 2003 Sep;185(18):5611-26
references.pmid: 12949114
references.citation: Biotechnol Bioeng. 1997 Sep 5;55(5):747-57
references.pmid: 18636585
references.citation: Biotechnol Bioeng. 1994 Jan 5;43(1):11-20
references.pmid: 18613306
references.citation: Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):15112-7
references.pmid: 12415116
references.citation: Biotechnol Bioeng. 2002 Jul 5;79(1):53-73
references.pmid: 17590932
references.citation: Genome Biol. 2007;8(7):R136
references.pmid: 17617894
references.citation: J Bacteriol. 2003 Dec;185(24):7053-67
references.pmid: 14645264
references.citation: Microbiol Rev. 1995 Mar;59(1):48-62
references.pmid: 7708012
references.citation: Mol Syst Biol. 2006;2:2006.0031
references.pmid: 16760902
references.citation: Antonie Van Leeuwenhoek. 1991 Oct-Nov;60(3-4):225-34
references.pmid: 1687236
references.citation: Biotechnol Prog. 2006 Jul-Aug;22(4):1056-70
references.pmid: 16889381
references.citation: Biotechnol Bioeng. 2008 Apr 1;99(5):1170-85
references.pmid: 17972325
references.citation: Trends Biochem Sci. 2003 May;28(5):250-8
references.pmid: 12765837
references.citation: Science. 1950 Dec 15;112(2920):715-6
references.pmid: 14787503
references.citation: J Theor Biol. 2000 Apr 7;203(3):229-48
references.pmid: 10716907
references.citation: Biophys J. 2002 Sep;83(3):1331-40
references.pmid: 12202358
references.citation: PLoS Comput Biol. 2008 May 23;4(5):e1000086
references.pmid: 18483615
references.citation: J Bacteriol. 2002 Oct;184(19):5358-63
references.pmid: 12218022
references.citation: J Biotechnol. 2004 Sep 30;113(1-3):263-79
references.pmid: 15380660
references.citation: Metab Eng. 2001 Jul;3(3):265-83
references.pmid: 11461148
references.citation: BMC Syst Biol. 2008 Aug 07;2:71
references.pmid: 18687109
references.citation: Biotechnol Prog. 2007 Sep-Oct;23(5):1053-63
references.pmid: 17715942
references.citation: Biotechnol Bioeng. 1994 Jan 5;43(1):3-10
references.pmid: 18613305
references.citation: J Bacteriol. 1994 Aug;176(16):5101-7
references.pmid: 8051023
references.citation: Mol Gen Genet. 1984;197(2):309-17
references.pmid: 6151621
references.citation: Curr Microbiol. 2006 May;52(5):400-6
references.pmid: 16604417
references.citation: J Theor Biol. 2006 Oct 7;242(3):547-63
references.pmid: 16750836
references.citation: Appl Environ Microbiol. 1994 Oct;60(10):3724-31
references.pmid: 7986045
references.citation: J Bacteriol. 1977 Aug;131(2):446-52
references.pmid: 18438
references.citation: Biomol Eng. 2002 Jun;19(1):5-15
references.pmid: 12103361
references.citation: Mol Microbiol. 1998 Jul;29(2):431-47
references.pmid: 9720863
references.citation: J Theor Biol. 1993 Dec 21;165(4):477-502
references.pmid: 21322280
references.citation: Proc Natl Acad Sci U S A. 2001 Mar 27;98(7):4255-8
references.pmid: 11274450
references.citation: Biotechnol Prog. 2010 Mar-Apr;26(2):313-31
references.pmid: 20052739