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Journal of Bacteriology, July 2008, p. 5057-5062, Vol. 190, No. 14
0021-9193/08/$08.00+0 doi:10.1128/JB.00228-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

George Kosály,2 and
Mary E. Lidstrom1,3*
Department of Chemical Engineering,1 Department of Mechanical Engineering,2 Department of Microbiology, University of Washington, Seattle, Washington 981953
Received 14 February 2008/ Accepted 14 May 2008
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FIG. 1. Traditional scheme of methylotrophic metabolism in serine cycle methylotrophs (12, 19). CH2
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mtdA mutant (26), this strain was grown in chemostat cultures to a steady-state OD600 of approximately 0.6 with 3.7 mM succinate plus 12.5 mM methanol. The
ftfL strain (25) was grown in a batch culture on 15 mM succinate and then pelleted, washed, and exposed to 120 mM methanol for 3 to 4 h to promote induction of C1 enzymes. The following antibiotic concentrations were used: kanamycin, 25 to 50 µg/ml, and rifamycin, 25 to 50 µg/ml. 14C-labeling experiments. The rate of assimilation of labeled carbon from [14C]methanol was determined by incubating cell samples (OD600 between 0.2 and 1.0; high-flux samples diluted to an OD600 of 0.2 to 0.3 to avoid oxygen limitation) with 1 mM labeled methanol (1.4 µCi/µmol final specific activity) in 2-ml autosampling vials (Kimble) for 12 min at 28°C and then pipetting samples onto 0.2-µm polyvinylidene difluoride filters (Millipore), submerging the filters in scintillation fluid, and quantifying the radioactivity with one of two scintillation counters (Beckman LS3801 and Perkin-Elmer 2800TR). Experiments to determine the relative contributions of labeled methylene H4F and labeled CO2 to labeled biomass were performed by modifying a previous method (18). Prior to incubation, cells were diluted with medium bubbled with an N2-O2 gas mixture containing either 0% CO2 or 5% CO2 and then injected into vials containing the same gases.
2H-labeling experiments. Incorporation of deuterium (2H) into serine was quantified as previously described (27). Briefly, concentrated cell suspensions were incubated with 1 mM fully deuterated methanol (CD3OD) for 20 s (unless otherwise noted) and then lysed via the addition of 3 volumes of boiling ethanol and derivatized with ethyl chloroformate and trifluoroacetic anhydride (ECF/TFAA). Fragments of ECF/TFAA-derivatized serine containing either 0, 1, or 2 deuterium atoms were quantified according to their differences in mass by gas chromatography-mass spectrometry. Data were corrected for the natural abundance of heavy isotopes in the derivatized serine fragments.
Flux calculations.
Methanol input rate for methanol-limited chemostat cultures is 41.0 nmol/(ml·min). The methanol concentration in the effluent was below the detection limit (
50 µM) of our assay (23), indicating essentially complete consumption of the methanol. For a steady-state OD600 of 0.99 (the average of nine cultures), the consumption rate therefore is 41.5 nmol/(ml·OD600·min). This methanol consumption generates a biomass flux of 18.3 nmol/(ml·OD600·min), assuming 47.33% of biomass is carbon (8), using measured dry-weight values (0.278 mg biomass per ml of culture at an OD600 of 1.0 [X. Guo and M. Lidstrom, unpublished data]) and the chemostat growth rate of 0.1 h–1. Biomass fluxes were corrected for CO2 fixation using a value of 47% of biomass carbon from CO2 (see Results).
Conversion of flux rates per culture volume to flux rates per intracellular volume. Calculations were made assuming 4 x 108 cells per ml of culture at an OD600 of 1.0 (9) and that an M. extorquens AM1 cell may be approximated as a cylinder with a radius of 0.4 µm and length of 3 µm such that the volume of a cell is approximately 1.5 x 10–15 liter (T. Strovas, personal communication).
Measurement of the rate constant for the spontaneous reaction of formaldehyde with H4F.
The reaction of formaldehyde with H4F was monitored at pHs of 6.0, 6.5, 6.7, 7.0, and 8.0 at temperatures of 26 to 28°C. H4F powder (Sigma) was dissolved in 100 mM potassium phosphate buffer (degassed with N2) and used immediately. The final concentration of H4F was determined by measuring the A297, applying an extinction coefficient of 27 mM–1 cm–1 (41). Solutions of formaldehyde (5 to 20 mM) were also made fresh shortly before use by heating paraformaldehyde suspended in 100 mM potassium phosphate buffer (22). The assay was started by adding 100 µl of 5 to 20 mM formaldehyde to 900 µl of 10 to 20 µM H4F in a 1-ml cuvette. An increase in A295 was taken to reflect formation of methylene H4F, and the slope of this increase (
A295/min) and the corresponding extinction coefficient of 3.0 mM–1 cm–1 were used to calculate the rate of methylene H4F production (40).
Kinetic model of C1 metabolism. The previous kinetic model for growth on methanol (27) was modified in several ways. Changes A through E described below represent the new "default" version of the model. In change A, concentrations of energy and redox cofactors (ADP, ATP, NAD+, NADH, NADP+, and NADPH) as measured in Escherichia coli were replaced with newly published values (9) for chemostat cultures of M. extorquens AM1. In change B, kinetic rate constants (Vmaxs) were recalculated from enzyme activities reported in previous publications (5, 6, 10, 25, 31, 32, 39, 40) using a conversion factor of 1 µmol/(min·mg protein) = 3.86 mM/s, with mM referring to intracellular volume in this case. This conversion factor is based on (i) the assumption that 50% of biomass is protein and (ii) the numbers listed above under "Conversion of flux rates per culture volume to flux rates per intracellular volume." In change C, the spontaneous reaction rate constant for the condensation of formaldehyde with H4F was changed to the maximum measured rate of 0.08 mM–1 s–1. The spontaneous condensation of formaldehyde with tetrahydromethanopterin (H4MPT) was ignored because of its modest contribution of methylene H4MPT relative to the enzyme-catalyzed reaction (40). In change D, formylhydrolase, part of the formyltransferase/hydrolase complex (Fhc), was removed from the model because its activity is not limiting to the flux through Fhc (30) and because no experimental data on Vmax or Km are available for this reaction. In change E, new modeling was used to represent formyltetrahydrofolate ligase (FtfL). This enzyme forms a bond between formate and H4F, hydrolyzing ATP to make the reaction energetically favorable. In this respect, the enzyme is analogous to pyruvic carboxylase, which catalyzes the formation of oxaloacetate from HCO3– and pyruvate at the expense of ATP. Based on this analogy, we used equation IX-337 in Segel's enzyme kinetics text (34) to represent the flux through FtfL. The Keq value used in the modeling was taken from previous measurements (13).
One model feature retained from the previous version was the use of a formate dehydrogenase (FDH) activity that is double the published value. The published value is only for the NAD-linked FDH activity, but M. extorquens AM1 also has two other functional FDHs whose activities are not measurable, since their electron acceptors are unknown (4, 5).
To explore conditions that would predict fluxes similar to those measured, additional changes were then made in an iterative manner to generate a version that predicted measured fluxes. Changes were made solely to parameters for which some uncertainty existed for the published values. The changes made were as follows. The first change was made because total H4F and H4MPT published concentrations (39) are minimum values because (i) the method used did not capture formyl H4F or formyl H4MPT and (ii) capture of the other molecular species was likely incomplete due to the thermodynamics of the reactions involved (J. Vorholt, personal communication). Therefore, the values for total [H4F] and [H4MPT] were increased from 0.15 mM to 0.2 mM and from 0.4 mM to 0.5 mM, respectively. In the second change, involving formaldehyde-activating enzyme (Fae), the Km for H4MPT was reduced to 15% of the published value. The published value is dependent on H4MPT from another species, which is chemically different (6). In the third change, involving Ftr hydrolase complex (Fhc), the activity was increased fivefold from the published value. The enzyme is unstable, and the cofactor used is from a different species. The cofactor in M. extorquens is expected to be different (6, 30). In the fourth change, involving methenyl-H4F cyclohydrolase (Fch), the value of the Keq is pH dependent because H+ participates in the reaction (17). Since the intracellular pH of M. extorquens may be close to 6.5 (see Results), a value determined at this pH (21) was used in the model.
Statistics. Values reported are means ± standard deviations unless otherwise indicated.
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FIG. 2. The assay for methylene-tetrahydrofolate synthesis routes in whole cells using deuterated methanol (CD3OD). (A) Spontaneous condensation consists of joining formaldehyde (in this case, DCDO) and H4F to form doubly deuterated methylene-tetrahydrofolate (CD2
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Biomass assimilation flux in mutants.
To directly test the capacity for flux through the direct condensation reaction, we examined serine production and biomass flux in the
ftfL mutant strain of M. extorquens AM1, which is defective in formyl H4F ligase. In this mutant, the alternate pathway for synthesis of methylene H4F is interrupted and the only route for methylene H4F synthesis is direct condensation. This strain is unable to grow on methanol, but it was grown on succinate and then exposed to methanol, conditions known to induce methylotrophic enzymes in this mutant (15).
If the direct condensation reaction is quantitatively important in vivo, production of +2 serine and positive biomass fluxes should be observed in the
ftfL mutant. However, biomass flux was not significantly different from zero (0.0005 ± 0.0032 mM/s; n = 6). In addition, +2 serine was very low when CD3OD was provided to these strains, constituting only 2.6% ± 1.6% (n = 4) of the total (+0, +1, and + 2) serine detected as compared to percentages of
70% for wild-type cells grown on methanol. This is not inconsistent with previous results demonstrating a drop in +2 serine in this mutant compared to the wild type (27). That experiment involved cells grown on succinate, and the much lower fluxes make direct comparisons difficult. Similar results were obtained with another mutant defective in this pathway, the
mtdA strain, for which biomass flux was 0.0013 ± 0.0037 mM/s (n = 8) and +2 serine was 1.1% ± 0.5% (n = 3). These data are consistent with the results presented above suggesting that little methylene H4F is produced via the direct condensation route under these conditions.
Flux measurements in chemostat-grown cultures. If the direct condensation reaction plays a minor role during methylotrophic growth, then the alternate route, involving the H4MPT and H4F pathways (Fig. 1), must be able to accommodate nearly all of the formaldehyde flux. In order to test this prediction, we carried out new flux measurements using methanol-limited chemostat-grown cells. The use of chemostat cultures allows a direct calculation of fluxes to biomass occurring in the growing cells using the substrate input rate, the dilution rate, and the amount of cells in the culture (see Materials and Methods). For methanol utilization, these calculations must be corrected for incorporation of CO2 via the serine cycle and other carboxylation reactions in the cell. To determine the proportion of biomass carbon from CO2, radioactive labeling of biomass was measured in the presence of 5% unlabeled CO2 as compared to a CO2-free environment. In the absence of external CO2, all or nearly all of the CO2 incorporated into biomass should be derived from labeled methanol and therefore should be labeled, while in high unlabeled CO2, all or nearly all of the CO2 incorporated should be unlabeled. Therefore, the difference between the two conditions should reflect the proportion of biomass derived from CO2. The average values for five replicate 14C-labeling experiments indicated that at least 47% of the biomass carbon comes from CO2, with the remainder coming from methylene H4F. These results are in keeping with previous labeling studies of flask-grown cells, suggesting approximately half of the biomass carbon comes from CO2 (18).
It has previously been shown that methanol-limited cells grown at a dilution rate equivalent to 80% of the batch culture growth rate are generally similar to batch culture cells in terms of enzyme activities and nucleotide concentrations, suggesting that these conditions are roughly comparable (9).
By assuming that all methanol not converted to methylene H4F is converted to CO2, a complete flux distribution for the C1 network can be calculated for cells in a methanol-limited chemostat (Fig. 3). In order to evaluate whether the H4MPT and H4F pathways could accommodate such fluxes, a kinetic model was utilized.
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FIG. 3. Distribution of fluxes (in mM/s) in wild-type M. extorquens AM1 chemostat cells grown on methanol, assuming that no methylene H4F is produced via spontaneous condensation.
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0.026 mM–1s–1 can be estimated at 20°C and pH 7.2. Therefore, the maximum rate constant measured (0.08 mM–1s–1) was used in the model, to provide a high-flux scenario. In keeping with the other results presented in this study, this model predicted that even with the use of a relatively high rate constant for spontaneous formaldehyde condensation with H4F, this rate constant does not allow significant flux through this route unless formaldehyde rises to levels known to inhibit growth (concentrations greater than 1 mM). A number of simulations were run to identify conditions that would accommodate the measured fluxes to CO2 and biomass. Parameters for one such simulation are shown in Tables 1 and 2. In this case, published values for kinetic parameters and concentrations were used aside from the exceptions noted in Materials and Methods. Each of these changes results in values that are within expected tolerances, given the uncertainties of in vitro enzyme measurements with regard to in vivo conditions (see Materials and Methods). Using these parameters, the model predicted fluxes similar to the measured fluxes (Table 2).
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TABLE 1. Concentrations of the compounds used
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TABLE 2. Parameters used in the final model and predicted fluxes
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ftfL mutant defective in the alternate route involving the H4F pathway. The results from these analyses demonstrate that under these conditions, the flux through the direct condensation route is minor. However, the
ftfL mutant does not grow on methanol and must be tested in cells that have been grown on succinate, washed, and incubated with methanol. These conditions are known to induce methylotrophic enzymes in this mutant (16), but the flux capacity through the assimilatory pathways is unknown. Removal of methylene H4F by the serine cycle is likely to be important to sustain flux through this route (27). In addition, if an enzyme exists that converts formaldehyde plus H4F to methylene H4F, it may not be fully induced under these conditions. Therefore, these results do not rule out a higher flux through this route in the wild type during growth on methanol. However, even if the contribution of this route to the synthesis of methylene H4F increases an order of magnitude during growth on methanol, the alternate route, including the enzymes Fae, MtdA/MtdB, Mch, Fhc, FtfL, Fch, and MtdA (Fig. 4), should dominate the total biomass production. This suggestion is supported by the kinetic model generated in this study, which predicts that this alternate route can support the measured fluxes during methylotrophic growth using kinetic and cofactor concentration parameters that are within known or predicted ranges. In addition, these results explain the finding that FtfL, Fch, and MtdA mutants are all unable to grow on methanol.
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FIG. 4. Proposed scheme of methylotrophic metabolism in M. extorquens AM1 showing formate (HCOO–) as the branch point between assimilatory and dissimilatory metabolism.
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These results suggesting that, under laboratory growth conditions, methylene H4F is mainly formed by the route involving the H4MPT and H4F pathways lead to the suggestion that formate represents the primary metabolic branch point between assimilation of C1 units into biomass (via methylene H4F and the serine cycle) and dissimilation to CO2 for energy generation in this bacterium (Fig. 4). The linear conversion of formaldehyde to formate by the high-capacity enzymes of the H4MPT pathway is a straightforward but effective method to maintain high fluxes of formaldehyde without allowing its accumulation. The disadvantage is that it requires an extra ATP for every formaldehyde assimilated, compared to a direct condensation route. Since growth on methanol is predicted to be limited by reducing power rather than ATP (36), it is possible that the tradeoffs are positive for metabolism as a whole.
Optimal partitioning of formate between these two branches may require extensive control of the relevant branch point enzymes, namely, FtfL, Fch, and MtdA for the H4F pathway, and FDH. The importance of FDH is suggested by the presence of four isoforms in M. extorquens AM1, which vary greatly in terms of their expression patterns, dependence on cofactors (NAD+) and metal ions (molybdenum and tungsten), and mutant phenotypes (4, 5). These results now direct attention to these enzymes as the likely main control points for balancing of metabolism during methylotrophic growth in M. extorquens AM1.
This work was supported by grants from the National Institutes of Health (GM070297 to G.J.C. and GM58933 to M.E.L.).
Published ahead of print on 23 May 2008. ![]()
Present address: Department of Medicine, University of Washington, Box 357185, Seattle, WA 98195-7185. ![]()
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