Nonlinear Mathematical Simulation and Analysis of Dha Regulon for Glycerol Metabolism in Klebsiella pneumoniae*

Chinese Journal of Chemical Engineering ›› 2012, Vol. 20 ›› Issue (5): 958-970.

Nonlinear Mathematical Simulation and Analysis of Dha Regulon for Glycerol Metabolism in Klebsiella pneumoniae^*

孙亚琴¹, 叶剑雄², 牟晓佳¹, 滕虎¹, 冯恩民², 曾安平³, 修志龙¹

1. Department of Bioscience & Biotechnology, Dalian University of Technology, Dalian 116024, China;
2. Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, China;
3. Institute of Bioprocess and Biochemical Engineering, Technical University of Hamburg-Harburg, D-21073 Hamburg, Germany

收稿日期:2011-03-30 修回日期:2011-07-01 出版日期:2012-10-28 发布日期:2012-11-06
通讯作者: XIU Zhilong,E-mail:zhlxiu@dlut.edu.cn
基金资助:
Supported by the National High Technology Research and Development Program of China (2007AA02Z208);the State Key Development Program for Basic Research of China (2007CB714304)

Nonlinear Mathematical Simulation and Analysis of Dha Regulon for Glycerol Metabolism in Klebsiella pneumoniae^*

SUN Yaqin¹, YE Jianxiong², MU Xiaojia¹, TENG Hu¹, FENG Enmin², ZENG Anping³, XIU Zhilong¹

1. Department of Bioscience & Biotechnology, Dalian University of Technology, Dalian 116024, China;
2. Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, China;
3. Institute of Bioprocess and Biochemical Engineering, Technical University of Hamburg-Harburg, D-21073 Hamburg, Germany

Received:2011-03-30 Revised:2011-07-01 Online:2012-10-28 Published:2012-11-06
Supported by:
Supported by the National High Technology Research and Development Program of China (2007AA02Z208);the State Key Development Program for Basic Research of China (2007CB714304)

摘要/Abstract

摘要： Glycerol may be converted to 1,3-propanediol (1,3-PD) by Klebsiella pneumoniae under anaerobic conditions and glycerol dismutation involves two parallel pathways controlled by the dha regulon. In this study, a fourteen-dimensional nonlinear dynamic system is presented to describe the continuous culture and multiplicity analysis, in which two regulated negative-feedback mechanisms of repression and enzyme inhibition are investigated. The model describing the expression of gene-mRNA-enzyme-product was established according to the repression of the dha regulon by 3-hydroxypropionaldehy (3-HPA). Comparisons between simulated and experimental results indicate that the model can be used to describe the production of 1,3-PD under continuous fermentation. The new model is translated into the corresponding S-system version. The robustness of this model is discussed by using the S-system model and the sensitivity analysis shows that the model is sufficiently robust. The influences of initial glycerol concentration and dilution rate on the biosynthesis of 1,3-PD and the stability of the dha regulon model are investigated. The intracellular concentrations of glycerol, 1,3-PD, 3-HPA, repressor mRNA, repressor, mRNA and protein levels of glycerol dehydratase (GDHt) and 1,3-PD oxydoreductase (PDOR) can be predicted for continuous cultivation. The results of simulation and analysis indicate that 3-HPA accumulation will repress the expression of the dha regulon at the transcriptional level. This model gives new insights into the regulation of glycerol metabolism in K. pneumoniae and explain some of the experimental observations.

关键词: dha regulon, robustness, nonlinear dynamics, genetic regulation, 3-hydroxypropionaldehy

Abstract: Glycerol may be converted to 1,3-propanediol (1,3-PD) by Klebsiella pneumoniae under anaerobic conditions and glycerol dismutation involves two parallel pathways controlled by the dha regulon. In this study, a fourteen-dimensional nonlinear dynamic system is presented to describe the continuous culture and multiplicity analysis, in which two regulated negative-feedback mechanisms of repression and enzyme inhibition are investigated. The model describing the expression of gene-mRNA-enzyme-product was established according to the repression of the dha regulon by 3-hydroxypropionaldehy (3-HPA). Comparisons between simulated and experimental results indicate that the model can be used to describe the production of 1,3-PD under continuous fermentation. The new model is translated into the corresponding S-system version. The robustness of this model is discussed by using the S-system model and the sensitivity analysis shows that the model is sufficiently robust. The influences of initial glycerol concentration and dilution rate on the biosynthesis of 1,3-PD and the stability of the dha regulon model are investigated. The intracellular concentrations of glycerol, 1,3-PD, 3-HPA, repressor mRNA, repressor, mRNA and protein levels of glycerol dehydratase (GDHt) and 1,3-PD oxydoreductase (PDOR) can be predicted for continuous cultivation. The results of simulation and analysis indicate that 3-HPA accumulation will repress the expression of the dha regulon at the transcriptional level. This model gives new insights into the regulation of glycerol metabolism in K. pneumoniae and explain some of the experimental observations.

Key words: dha regulon, robustness, nonlinear dynamics, genetic regulation, 3-hydroxypropionaldehy

孙亚琴, 叶剑雄, 牟晓佳, 滕虎, 冯恩民, 曾安平, 修志龙. Nonlinear Mathematical Simulation and Analysis of Dha Regulon for Glycerol Metabolism in Klebsiella pneumoniae^*[J]. Chinese Journal of Chemical Engineering, 2012, 20(5): 958-970.

SUN Yaqin, YE Jianxiong, MU Xiaojia, TENG Hu, FENG Enmin, ZENG Anping, XIU Zhilong. Nonlinear Mathematical Simulation and Analysis of Dha Regulon for Glycerol Metabolism in Klebsiella pneumoniae^*[J]. Chin.J.Chem.Eng., 2012, 20(5): 958-970.

参考文献

1 Santillan,M.,Zeron,E.S.,"Analytical study of the multiplicity of regulatory mechanisms in the tryptophan operon",Bull Math Biol,68 (2),343-359 (2006).
2 Xiu,Z.L.,Song,B.H.,Sun,L.H.,Feng,E.M.,Zeng,A.P.,"Theoretical analysis of effects of metabolic overflow and time delay on the performance and dynamic behavior of a two-stage fermentation process",Biochem Eng J,11,101-109 (2002).
3 Mccoy,M.,"Chemical makers try biotech paths",Chem.Eng.News,76,13-19 (1998).
4 Mu,Y.,Teng,H.,Zhang,D.J.,Wang,Y.H.,Xiu,Z.L.,"Microbial production of 1,3-propanediol by Klebsiella pneumoniae using crude glycerol from biodiesel preparations",Biotechnol Lett,28 (21),1755-1759 (2006).
5 Papanikolaou,S.,Fick,M.,Aggelis,G.,"The effect of raw glycerol concentration on the production of 1,3-propanediol by Clostridium butyricum ",J Chem Tech Biotechnol,79,1189-1196 (2004).
6 Deckwer,W.D,"Microbial conversion of glycerol into 1,3-propanediol",FEMS Microbiol.Reviews,16,143-149 (1995).
7 Gonzalez-Pajuelo,M.,Andrade,J.C.,Vasconcelos,I.,"Production of 1,3-propanediol by Clostridium butyricum VPI 3266 in continuous cultures with high yield and productivity",J Ind Microbiol Biotechnol,32 (9),391-396 (2005).
8 Sun,J.B.,van den Heuvel,J.,Soucaille,P.,Qu,Y.,Zeng,A.P.,"Comparative genomic analysis of dha regulon and related genes for anaerobic glycerol metabolism in bacteria",Biotechnol Prog,19 (2),263-272 (2003).
9 Biebl,H.,Menzel,K.,Zeng,A.P.,Deckwer,W.D.,"Microbial production of 1,3-propanediol",Appl Microbiol Biotechnol,52 (3),289-297 (1999).
10 Wang,W.,Sun J.B.,Hartlep,M.,Deckwer,W.D.,Zeng,A.P.,"Combined use of proteomic analysis and enzyme activity assays for metabolic pathway analysis of glycerol fermentation by Klebsiella pneumoniae",Biotechnol Bioeng,83 (5),525-536 (2003).
11 Zeng,A.P.,Biebl,H.,"Bulk chemicals from biotechnology: The case of 1,3-propanediol production and the new trends",Adv Biochem Eng Biotechnol,74,239-259 (2002).
12 Forage,R.G.,Lin,E.C.,"DHA system mediating aerobic and anaerobic dissimilation of glycerol in Klebsiella pneumoniae NCIB 418",J Bacteriol,151 (2),591-599 (1982).
13 Tong,I.T.,Liao,H.H.,Cameron,D.C.,"1,3-Propanediol production by Escherichia coli expressing genes from the Klebsiella pneumoniae dha regulon",Appl Environ Microbiol,57 (12),3541-3546 (1991).
14 Sprenger,G.A.,Hammer,B.A.,Johnson,E.A.,Lin,E.C.,"Anaerobic growth of Escherichia coli on glycerol by importing genes of the dha regulon from Klebsiella pneumoniae",J Gen Microbiol,135 (5),1255-1262 (1989).
15 Tong,I.T.,Cameron,D.C.,"Enhancement of 1,3-propanediol production by cofermentation in Escherichia coli expressing Klebsiella pneumoniae dha regulon genes",Appl Biochem Biotechnol,34,149-159 (1992).
16 Toraya,T.,"Radical catalysis of B12 enzymes: Structure,mechanism,inactivation,and reactivation of diol and glycerol dehydratases",Cell Mol Life Sci,57 (1),106-127 (2000).
17 Tran-Dinh,K.,Hill,F.F.,"A method for the preparation of 1,3-propanedid",German Pat.,No.DE 3734764 A1 (1987).
18 Zeng,A.P.,"A kinetic model for product formation of microbial and mammalian cells",Biotechnol.Bioeng.,46,314-324 (1995).
19 Zeng,A.P.,Byun,T.G.,Posten,C.,Deckwer,W.D.,"Use of respiratory quotient as a control parameter for optimum oxygen supply and scale-up of 2,3-butanediol production under microaerobic conditions",Biotechnol.Bioeng.,44 (9),1107-1114 (1994).
20 Zeng,A.P.,Deckwer,W.D.,"A kinetic model for substrate and energy consumption of microbial growth under substrate-sufficient conditions",Biotechnol Prog,11 (1),71-79 (1995).
21 Xiu,Z.L.,Zeng,A.P.,An,L.J.,"Mathematical modeling of kinetics and research on multiplicity of glycerol bioconversion to 1,3-propanediol",J.Dalian Univ.Technol.,40,428-433 (2000).
22 Sun,Y.Q.,Qi,W.T.,Teng,H.,Xiu,Z.L.,Zeng,A.P.,"Mathematical modeling of glycerol fermentation by Klebsiella pneumoniae: Concerning enzyme-catalytic reductive pathway and transport of glycerol and 1,3-propanediol across cell membrane",Biochem.Eng.J.,38,22-32 (2008).
23 Zeng,A.P.,"Quantitative cell physiology,metabolic engineering and modeling of the glycerol fermentation to 1,3-propanediol,habilitation",Ph.D.Thesis,Technical University of Braunschweig,Germany (2000).
24 Barbirato,F.,Grivet,J.P.,Soucaille,P.,Bories,A.,"3-Hydroxypropionaldehyde,an inhibitory metabolite of glycerol fermentation to 1,3-propanediol by enterobacterial species",Appl Environ Microbiol,62 (4),1448-1451 (1996).
25 Barbirato,F.,Soucaille,P.,Bories,A.,"Physiologic mechanisms involved in accumulation of 3-hydroxypropionaldehyde during fermentation of glycerol by Enterobacter agglomerans",Appl Environ Microbiol,62 (12),4405-4409 (1996).
26 Rasch,M.,"The influence of temperature,salt and pH on the inhibitory effect of reuterin on Escherichia coli",Int J Food Microbiol,72 (3),225-231 (2002).
27 Zheng,P.,Wereath,K.,Sun,J.B.,Heuvel,J.,Zeng,A.P,"Overexpression of genes of the dha regulon and its effects on cell growth,glycerol fermentation to 1,3-propanediol and plasmid stability in Klebsiella pneumoniae",Process Biochemistry,41,2160-2169 (2006).
28 Sinha,S.,"Theoretical study of tryptophan operon: Application in microbial technology",Biotechnol.Bioeng.,31 (2),117-124 (1988).
29 Bachler,C.,Schneider,P.,Bahler,P.,Lustig,A.,Erni,B.,"Escherichia coli dihydroxyacetone kinase controls gene expression by binding to transcription factor DhaR",Embo J,24 (2),283-293 (2005).
30 Daniel,R.,Boenigk,R.,Gottschalk,G.,"Purification of 1,3-propanediol dehydrogenase from Citrobacter freundii and cloning,sequencing,and overexpression of the corresponding gene in Escherichia coli",J.Bacteriol.,177,2151-2156 (1995).
31 Zeng,A.P.,Rose,A.,Biebl,H.,Tag,C.,Guenzel,B.,Deckwer,W.D.,"Multiple product inhibition and growth modeling of Clostridium butyricum and Klebsiella pneumoniae in glycerol fermentation",Biotechnol.Bioeng.,44,902-911 (1994).
32 Menzel,K.,Zeng,A.P.,Deckwer,W.D.,"High concentration and productivity of 1,3-propanediol from continuous fermentation of glycerol by Klebsiella pneumoniae",Enzyme Microbiol.Technol.,20,82-86 (1997).
33 Torres,V.N.,Voit,E.,Pathway Analysis and Optimization in Metabolic Engineering,Cambridge University Press,Cambridge (2002).
34 Marin-Sanguino,A.,Torres,N.V.,"Optimization of tryptophan production in bacteria.Design of a strategy for genetic manipulation of the tryptophan operon for tryptophan flux maximization",Biotechnol.Prog.,16 (2),133-145 (2000).
35 Menzel,K.,Zeng,A.P.,Biebl,H.,Deckwer,W.D.,"Kinetic,dynamic,and pathway studies of glycerol metabolism by Klebsiella pneumoniae in anaerobic continuous culture: I.The phenomena and characterization of oscillation and hysteresis",Biotechnol.Bioeng.,52 (5),549-560 (1996).
36 Xiu,Z.L.,Zeng,A.P.,Deckwer,W.D.,"Multiplicity and stability analysis of microorganisms in continuous culture: Effects of metabolic overflow and growth inhibition",Biotechnol.Bioeng.,57 (3),251-261 (1998).
37 Zeng,A.P.,Menzel,K.,Deckwer,W.D.,"Kinetic,dynamic,and pathway studies of glycerol metabolism by Klebsiella pneumoniae in anaerobic continuous culture: II.Analysis of metabolic rates and pathways under oscillation and steady-state conditions",Biotechnol.Bioeng.,52 (5),561-571 (1996).
38 Xiu,Z.L.,Song,B.H.,Wang,Z.T.,Sun,L.H.,Feng,E.M.,Zeng,A.P.,"Optimization of biodissimilation of glycerol to 1,3-propanediol by Klebsiella pneumoniae in oneand two-stage continuous anaerobic cultures",Biochem.Eng.J.,19,189-197 (2004).
39 Ma,Y.F.,Sun,L.H.,Xiu,Z.L.,"Microbial theoretical analysis of oscillatory behavior in process of microbial continuous culture",Chin J Eng Math,20,1-6 (2003).
40 Ye,J.X.,Feng,E.N.,Lian,H.S.,Xiu,Z.L.,"Existence of equilibrium points and stability of the nonlinear dynamical system in microbial continuous culutures",Applied Mathematics and Computation,207,307-318 (2008).
41 Biebl,H.,Marten,S.,Hippe,H.,Deckwer,W.D.,"Glycerol conversion to 1,3-propanediol by newly isolated Clostrida",Appl.Microbiol.Biotechnol.,36,592-597 (1992).
42 Homann,T.,Tag,C.,H B,Deckwer,W.D.,Schink,B.,"Fermentation of glycerol to 1,3-propanediol by Klebsiella and Citrobacter strains ",Appl Microbiol Biotechnol,33,121-126 (1990).
43 Chen,X.,Xiu,Z.L.,Wang,J.F.,Zhang,D.J.,Xu,P.,"Stoichiometric analysis and experimental investigation of glycerol bioconversion to 1,3-propanediol by Klebsiella pneumoniae under microaerobic conditions",Enzyme Microbiol.Technol.,33,386-394 (2003).
44 Papanikolaou,S.,Ruiz-Sanchez,P.,Pariset,B.,Blanchard,F.,Fick,M.,"High production of 1,3-propanediol from industrial glycerol by a newly isolated Clostridium butyricum strain",J.Biotechnol.,77 (2-3),191-208 (2000).
45 Gonz醠ez-Pajuelo,M.,Andrade,J.,Vasconcelos,I.,"Production of 1,3-propanediol by Clostridium butyricum VPI 3266 using a synthetic medium and raw glycerol",J Ind Microbiol Biotechnol,31,442-446 (2004).
46 Gonzalez-Pajuelo,M.,Meynial-Salles,I.,Mendes,F.,Andrade,J.C.,Vasconcelos,I.,Soucaille,P.,"Metabolic engineering of Clostridium acetobutylicum for the industrial production of 1,3-propanediol from glycerol",Metab Eng,7 (5-6),329-336 (2005).
47 Barbirato,F.,Soucaille,P.,Camarasa,C.,Bories,A.,"Uncoupled glycerol distribution as the origin of the accumulation of 3-hydroxypropionaldehyde during the fermentation of glycerol by enterobacter agglomerans CNCM 1210",Biotechnol.Bioeng.,58 (2-3),303-305 (1998).
48 Ahrens,K.,Menzel,K.,Zeng,A.P.,Deckwer,W.D.,"Kinetic,dynamic,and pathway studies of glycerol metabolism by Klebsiella pneumoniae in anaerobic continuous culture: III.Enzymes and fluxes of glycerol dissimilation and 1,3-propanediol formation",Biotechnol.Bioeng.,59,544-552 (1998).
49 Abbad-Andaloussi,S.,Guedon,E.,Spiesser,E.,Petttdemange,H.,"Glycerol dehydratase activity: the limiting step for 1,3-propanediol production by Clostridium butyricum DSM5431",Lett.Appl.Microbiol.,22,311-314 (1996).
50 Wang,W.,Sun,J.B.,Nimtz,M.,Deckwer,W.D.,Zeng,A.P.,"Protein identification from two-dimensional gel electrophoresis analysis of Klebsiella pneumoniae by combined use of mass spectrometry data and raw genome sequences",Proteome Sci,1 (1),525-536 (2003).
51 Skraly,F.A.,Lytle,B.L.,Cameron,D.C.,"Construction and characterization of a 1,3-propanediol operon",Appl Environ Microbiol,64 (1),98-105 (1998).

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Nonlinear Mathematical Simulation and Analysis of Dha Regulon for Glycerol Metabolism in Klebsiella pneumoniae^*

Nonlinear Mathematical Simulation and Analysis of Dha Regulon for Glycerol Metabolism in Klebsiella pneumoniae^*

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