Table 1. ODEs used in the model based on mass balances.

Transcription

1 Table. ODEs used in the model based on mass balances. ODE s _ = _ 6 = + _ 6 = + + = +! 3 = +2!!$ = +!$ %&' ( = _ + %&' ) *+ = + _, - +2 ),$.(/0 = +,!%!-.(023 = + - $!. 56..(023_ = +! ,3 8.3(20 = + 9 = + + _; = + ; _ = _; + ; ( =+,$ (h.30 = +!%.(.( = +!- 2 = +! +2 6= 56.!$ + 2_ = 6= 56.. =! +!- = %&' + ) 3. = +2!% + $ +!$ +,$ /0 = +!-, +!% 0+9.( = +,

2 Table 2. Initial and optimized kinetic model parameters. Enzyme Index Parameter Initial PTS_Glc ATPase 8 0 pi Trsp PGI PFK FBA GAPDH ENO _.. _!! "# $ "$ % &' &' % () ( *+, *+, value Source [3] [4] [3] [4] [5] [5] Estimated value 3.7 mmol/s 0.07 mm.7 mm 0.28 mm mm 0.3 mm.96 mm 3.29 mm/s 4.34 mm 3.60 mmol/s 6 mm 0.9 mm 2 mm 0.75 mm 0.30 mm 2.68 mm/s 3.4 mm 0.20 mm 8.36 mm/s 0.74 mm mm.02 mm mm 56.3 mm/s 0.30 mm 0. mm 30.0 mm/s mm 0.8 mm 0.64 mm mm 6.75 mm 29.3 mm/s 0.4 mm 0.75 mm mm.39 mm

3 PYK LDH PFL AE ACK PDC # -#.&' () ( ". /0 ". % /0 0 * /0 /0 )(0 () ( /# /0 /0 &/ &/ 0( [7] [8] [9] [] [0] 2.22 mm/s mm 3.70 mm 3.08 mm mm 0.33 mm mm mmol/s 0.08 mm mm 94.2 mm 0.4 mm 3.08 mm 0.0 mm 0.2 mm mmol/s mm 7.34 mm mm 5.78 mm 2.2 mmol/s 6.28 mm 7.38 mm mm 2.28 mm 0.43 mm.3 mm 3.84 mmol/s.7 mm 4.6 mm 6 mm 5 mm 0.7 mm 0.35 mm/s mm 0.26 mm

4 BDH 82 $&' $&' 0( (0 () ( mmol/s 5.62 mm.8 mm 3.55 mm.30 mm MPD 88 2& 200 [2] & 3 () ( [2] [2] [2] [2] [2] [2].33 mm/s mm 0.32 mm mm mm 0.37 mm MP ((0 0.2 [3] 3.49 mm/s 3.52 mm 0.24 mm PTS_Mtl ((0_* 4.45 mmol/s 0.36 mm 0.03 mm 2.2 mm 0.34 mm Ace. Trsp (.60 mmol/s.89 mm Mtl. Trsp (_* 2.. ((0_* (( mm.62 mmol/s 0.94 mm mm FBPase "$ mm/s.9 mm 0.4 mm 0.0 mm Parameters with missing reference or not estimated represented by. Here the initial V max values units are given in mm/s and the initial K m values in mm. All the abbreviations for the enzymes are explained in nomenclature. Reference List. Levering J, Musters MWJM, Bekker M, Bellomo D, Fiedler T, de Vos WM et al.: Role of phoshate in the central metabolism of two lactic acid bacteria - a comparative systems biology approach. FEBS J 202, 279:

5 2. Brown AT, Bowles RD: Polyol Metabolism by A Caries-Conducive Streptococcus - Purification and Properties of A Nicotinamide Adenine Dinucleotide-Dependent Mannitol--Phosphate Dehydrogenase. Infection and Immunity 977, 6: Pettersson G: What Metabolite Levels May be Evolutionarily Reached in the Glycolytic Pathway. European Journal of Biochemistry 990, 94: Gao H, Chen Y, Leary JA: Kinetic measurements of phosphoglucose isomerase and phosphomannose isomerase by direct analysis of phosphorylated aldose-ketose isomers using tandem mass spectrometry. International Journal of Mass Spectrometry 2005, 240: Hansen T, Schonheit P: Purification and properties of the first-identified, archaeal, ATP-dependent 6-phosphofructokinase, an extremely thermophilic non-allosteric enzyme, from the hyperthermophile Desulfurococcus amylolyticus. Archives of Microbiology 2000, 73: Hoefnagel MHN, Starrenburg MJC, Martens DE, Hugenholtz J, Kleerebezem M, Van Swam II et al.: Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis. Microbiology 2002, 48: Andersen AZ, Carvalho AL, Neves AR, Santos H, Kummer U, Olsen LF: The metabolic ph response in Lactococcus lactis: An integrative experimental and modelling approach. Computational Biology and Chemistry 2009, 33: Takahashi S, Abbe K, Yamada T: Purification of Pyruvate Formate-Lyase from Streptococcus-Mutans and Its Regulatory Properties. Journal of Bacteriology 982, 49: Asanuma N, Hino T: Effects of ph and energy supply on activity and amount of pyruvate formate-lyase in Streptococcus bovis. Applied and Environmental Microbiology 2000, 66: Tittmann K, Vyazmensky M, Hubner G, Barak Z, Chipman DM: The carboligation reaction of acetohydroxyacid synthase II: Steady-state intermediate distributions in wild type and mutants by NMR. Proceedings of the National Academy of Sciences of the United States of America 2005, 02: Hoefnagel MHN, van der Burgt A, 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. Molecular Biology Reports 2002, 29: Wolff JB, Kaplan NO: D-Mannitol -Phosphate Dehydrogenase from Escherichia-Coli. Journal of Biological Chemistry 956, 28: Schomburg I, Chang A, Schomburg D: BRENDA, enzyme data and metabolic information. Nucleic Acids Research 2002, 30:

6 Table 3. Initial conditions of state variables (metabolites concentrations) for 40mM glucose pulse in the kinetic model. Metabolite Initial concentration Source (mm) glc_ext 40 experimental g6p 0 assumed f6p 0 assumed fbp 5.3 experimental g3p 0 experimental bpg.26 estimated pep 2.48 estimated pyr 0 experimental lactate 0 experimental acetoin 0 experimental acetoin_ext 0 experimental 2,3-butanediol 0 experimental acetcoa 0 experimental CoA ethanol 0 experimental formate 0 experimental acetate 0 experimental mp 0 experimental mannitol 0 experimental mannitol_ext 0 experimental atp 4.89 estimated adp estimated nad 4.67 experimental nadh estimated pi experimental pi_ext 50 experimental All the abbreviations for the metabolites are explained in nomenclature. Reference List. Hoefnagel MHN, van der Burgt A, 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. Molecular Biology Reports 2002, 29: 57-6.

7 Table 4. Kinetic rate expressions used in the model. Phosphotransferase System (PTS_Glc): = [pi] +[pi] +[fbp] _ [glc_ext] ' _() [pep] + + [glc_ext] ' _() +[pep] ++ + [g6p] '. +[pyr] 2 Phosphoglucose isomerase (PGI): Phosphofructokinase (PFK): 4 = 4 4 [g6p] ' [f6p] '. + [g6p] '. +[f6p]. 67 = 67 [f6p]. [atp] ) + [f6p]. +[atp] )+ + [fbp] +[adp] : Fructose-,6-bisphosphate phosphatase (FBPase): 6;<+ = 6;<+ [fbp] + [fbp] + +[f6p]. +[pi] Fructose-,6-bisphosphate aldolase (FBA): 6;= = 6;=[fbp] 6;= 6;= +5 [>3@] A + [fbp] +[g3p] 'B + [g3p] A 'B Glyceraldehyde-3-phosphate dehydrogenase (GAPDH): =CD = =CD[g3p] [nad][pi] 'B F: +5 =CD =CD [bpg] 'B [nadh] F: + [g3p] 'B +[pi] H+[nad] F: I+ +[bpg] ' H+[nadh] F:J I Enolase (ENO): (KL = (KL[bpg][adp] F: 'B (KL (KL +5 [pep][atp] ' : + [bpg] ' +[adp] :+ +[pep] + + [atp] )

8 Pyruvate kinase (PYK): M7 = [fbp] +[fbp] N O P FQRS V O P FQRS +T[pi]U FQRS M7 [adp] : [pep] + + [adp] : +[pep] ++ + [atp] ) + [pyr] 2 L-lactate dehydrogenase (LDH): WCD = [fbp] +[fbp] +[pi] WCD [pyr] 2H [nadh] F:J I + [pyr] 2H+ [nadh] F:J I+H+[lactate] ))+ IH+[nad] F: I Pyruvate dehydrogenase (PFL): 6W = 'B 'B +[g3p] 6W[pyr] [CoA] [\= 6W 6W 2 +5 [acetcoa][formate] 2 [\= + [pyr] 2H+ [CoA] [\= I+H+[acetCoA] ^_`abcd I +[formate] \2)+ Alcohol dehydrogenase (AE): =( = ) ) +[atp] =( H [acetcoa] A +)[\= IH[nadh] F:J I H+ [acetcoa] A +)[\= I +[nadh] F:J +H[nadh] F:J I +H+ [ethanol] A +)JF\ IH+[CoA] [\= I +[nad] F: +H[nad] F: I Acetate kinase (ACK): =[7 = =[7 H [acetcoa] +)[\= I [adp] : H+ [acetcoa] +)[\= I +[adp] : +H+[acetate] +))+I + [atp] )H+ [CoA] [\= I Pyruvate decarboxylase (PDC): C[ = C [pyr] A 2 C [acetoin] C [pyr] 2 + [pyr] A 2 +H+ [acetoin] +)\F I

9 2,3-Butanediol dehydrogenase (BDH): ;C H [acetoin] +)\F IH[nadh] F:J I [2,3 butanediol] [nad] ;C +5 +)\F F:J ;CD = H+ [acetoin] +)\F IH+[nadh] F:J I+H+[2,3 butanediol] h)f+:\ IH+ [nad] F: I ;C Acetoin transport (Ace. Trsp.): = +.2<. = = +.2<. H [acetoin] +)\F I H+ [acetoin] +)\F I+ +[acetoin_ext] +)\F_() Mannitol--Phosphate dehydrogenase (MPD):. jc =. +[f6p] jc[f6p] [nadh] F:J. jc +5 jc [mp]. [nad] F:J + [f6p]. H+[nadh] F:JI+ +[mp] k H+[nad] F: I Mannitol--Phosphatase (MP): j = j [mp] k + [mp] k +H+[mannitol] FF)\ I Phosphotransferase System (PTS_Mtl): _j) = _j) [mannitol_ext] FF)\_() [pep] + + [mannitol_ext] FF)\_() +[pep] ++ + [mp] k +[pyr] 2 Mannitol transport (Mtl. Trsp.): j).2<. = Phosphate transport (pi Trsp.): j).2<. H [mannitol] FF)\ I H+ [mannitol] FF)\ I+ +[mannitol_ext] FF)\_() 2<. = +[pi] 2<. [atp] ) [pi_ext] _() + [atp] ) + [pi_ext] _() + +[adp] : +[pi] + [pi] A

10 ATP phosphatase (ATPase): =<+ = =<+ o n m F [atp] pqqrst ) [atp] ) F pqqrst + w v u

11 Figure. Variance analysis of the parameter set values of the kinetic model. For a better visualization the variance of every parameter are plotted with a logarithmic scale. The parameter indices correspond to the reaction numbers shown in Additional File 2.

12 Figure 2. Simulation results for the initial metabolite concentrations and estimated kinetic parameter values listed in Additional File 3 and 2, respectively.

13 Figure 3. Correlation values of sensitivities between all pairs of fits from wilt-type strain for 2,3-butanediol (plots in lower triangle) and mannitol (plots in upper triangle).

14 Figure 4. Correlation values of sensitivities between all pairs of fits from LDH mutant strain for 2,3-butanediol (plots in lower triangle) and mannitol (plots in upper triangle).

15 Figure 5. Correlation values of sensitivities between all pairs of fits from LDH/PTS Mtl mutant strain for 2,3-butanediol (plots in lower triangle) and mannitol (plots in upper triangle).

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18 Figure 6. Heat maps showing the integrated response coefficients to variation in V max parameters for all ten fits.