Institute of Organic Chemistry, Technical University Graz, Stremayrgasse 16, A-8010 Graz, Austria1
Institute of Biotechnology, Technical University Graz, Petersgasse 12, A-8010 Graz, Austria2
Author for correspondence: Douglas W. Ribbons. Tel: +43 316 873 8241. Fax: +43 316 873 8740. e-mail: sekretariat{at}orgc.tu- graz.ac.at
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ABSTRACT |
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Keywords: proton-NMR, in situ analysis, deuterium-labelled products, Escherichia coli fermentations
Abbreviations: FT, Fourier-transform
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INTRODUCTION |
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Another NMR-active nucleus is the proton (1H). It possesses two very useful properties: (i) it has a high natural abundance (99·98%) and the highest gyromagnetic ratio of all stable nuclei, leading to a high NMR sensitivity; (ii) the proton nucleus is present in almost all carbon-containing biological molecules, substrates and products. On the other hand, there are the disadvantages of a relatively small spectral range and an overwhelming 1H2O signal in the spectra which saturates the analogue digital converter of Fourier-transform (FT) spectrometers (Brown et al., 1977 ). So proton-NMR measurements have been rarely used in the past to provide information about in vivo metabolic processes (Alam & Clark, 1989
; Brown et al., 1977
; Gaines et al., 1996
; Morawski et al., 1997
, Ogino et al., 1978a
, b
, 1980
; L. Brecker, P. Urdl, W. Schmidt, H. Griengl & D. W. Ribbons, unpublished results). To avoid the large water signal in these cases, D 2O was used instead of 1H2O (Gaines et al., 1996
) or the water signal was suppressed with suitable pulse sequences (Guéron et al., 1991
; Hore, 1989
; Ogg et al., 1994
, Smallcombe et al., 1995
).
We have recently monitored 1H-NMR signal changes during enzymic reactions and anaerobic bacterial biotransformations in situ (Brecker et al., 1999 ; Hickel et al. , 1996
; Pokorny et al., 1997
, 1999
). These measurements were made in 1H2 O and the water signal was suppressed by a presaturation pulse sequence (Guéron et al., 1991
; Hore, 1989
). Here, we describe the kinetics and stoicheiometries of the mixed acid fermentation by an Escherichia coli K-12 strain, HB101, growing in the magnet, in normal 1 H2O and in D2O media.
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METHODS |
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NMR measurements.
A 200 MHz narrow-bore magnet (Varian Gemini 200 system) and a 5 mm broad-band probe head were used. The NMR tube was rotated at 20 revolutions s-1. A D2O vortex capillary was added to the cultures to avoid 1H/D exchange reactions and kinetic isotope effects (Brecker et al., 1999 ; Kalinowski et al., 1984
). For measurements with D2 O in the solvent, the deuterium signal was also used as an internal lock signal. The overwhelming water signal was suppressed with a presaturation method (Guéron et al. , 1991
; Hore, 1989
), in contrast to the experiments of Ogino et al. (1978a
, b
, 1980
). The following parameters were adjusted for a 1 H-frequency of 200 MHz: presaturation duration of 1·0 s, 1H-pulse angle of 90°, an acquisition time of 2·0 s and a relaxation delay of 1·5 s. One hundred and twenty-eight scans were accumulated and one spectrum was provided in about 13 min. After a zero filling to 32k datapoints, the free induction decay was Fourier-transformed to spectra with a resolution of 0·11 Hz. The water signal (4·70 p.p.m.) was used as a reference. Between the spectral accumulations for the kinetic measurements, a delay time of 47 min was used. The control experiments external to the magnet were analysed only at the inoculation and end-point of the reactions.
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RESULTS |
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The stoicheiometric non-equivalence of acetate and ethanol production and the utilization of citrate by E. coli HB101 suggested that growth on citrate as a single carbon source could occur. This would have been counter to expectations, as a nutritional differentiation amongst the Enterobacteriaceae is made on the basis that citrate alone does not support the growth of E. coli species (Koser, 1924 ; Dagley, 1954
). To check the nutritional phenotype of strain HB101, citrate and glucose were supplied as single carbon sources to compare the growth characteristics. Glucose, but not citrate, as sole carbon source supported the growth of this organism. The amount of yeast extract (0·05%, w/v) in the media did not support significant growth. Control fermentations were not followed in detail by NMR measurements and they are not illustrated here.
Ogino et al. (1978a , b
, 1980
) reported that the pH-dependent chemical shifts of the proton signals in E. coli cultures allow a measure of the pH change. The pH value of the solution can therefore be estimated from the spectra. This behaviour is very pronounced for the methyl group of acetate. However, there is no absolute relationship between the shift and the pH value because the shift depends on several other conditions (e.g. temperature and the concentrations of salts and other compounds in the solution, including D 2O). Nevertheless, if the starting and end points of the pH changes and the chemical shift are measured and calibrated, the pH value can be deduced from the chemical shift of the acetate signal in every spectrum obtained. For the monitored reaction, the pH value was calculated from the chemical shift of the acetate signal by comparison with standard solutions of known pH values (Ogino et al., 1978a
, b
, 1980
). A pKa value of 4·5 was obtained from the 1H-NMR spectra. The results from fermentations showed that the pH value first rises from 6·8 to 7·3 after 3 h, and later decreases during growth to pH 5·1 (14 h). These changes are probably the consequence of the use of citrate at the beginning, and then of the production of several acids as products from glucose.
All these results were verified with parallel fermentations in static flasks of the same divided cultures. These were sampled and analysed by 1H-NMR, and a very similar progress of the fermentations was observed. The influence of the magnetic field or of the rotation of the NMR tube can therefore be excluded, or is minimal.
Effect of D2O as solvent
Additional information is given about fermentations with different amounts of D2O in the solvent, because it is also used as a reactant in metabolism. Deuterium in the solution is consequently built into the intermediates and products of metabolism. So the kinetic effect of the deuterium can be detected as well as proton/deuterium exchange reactions. Furthermore, the position of the deuterium in these substances and the relative ratios of protons to deuterium give helpful and detailed information for investigations of physiology and metabolism. This information can be interpreted from the 1H- NMR spectra because the deuterium nucleus is not directly detected by the 1H-NMR measurements, but it influences the shape and number of the 1H signals in a defined way. The relative amount of deuterium in a group of a molecule reduces the relative integral over the assigned characteristic 1H-signal proportionally. This is related to standard signals of known concentration and pH in solutions with and without D2O. More details about the structure are revealed by the shapes of the signals. A deuterium nucleus has a nuclear spin of I=1 and shows a coupling to all 1H nuclei in geminal and vicinal positions. Each of these proton signals is then divided into three equidistant lines with the same integral. This signal is designated as a triplet in this article. For a detailed explanation of D-couplings, see Sanders & Hunter (1987) . Additionally, the shift of the proton signal of the deuterated compound changes slightly in comparison to that of the fully protonated compound.
We used this technique for an investigation of the E. coli HB101 fermentation described above (Figs 1, 2b
and 3
). The cultures were repeated with 0, 25, 50, 75 and 98% D2O in the media. In 98% D2O media, the proton concentration is still very large (~3000 meq. l -1) whereas carbon substrate proton concentrations of interest are ~0·5200 meq. l-1. These media were prepared by freeze-drying the original medium and redissolving the residue in 1H2O enriched with D 2O. For these fermentations, 1H-NMR spectra were only taken initially and after 42 h incubation, while the progress of growth was followed by the measurement of cell density (Fig. 4
). The results showed that there is a kinetic hindrance due to the use of deuterium in metabolism. The cultures with the higher amounts of D2O show a much slower progress of growth, product formation and use of the substrates than the reactions with less deuterium in the solution (Fig. 4
and Table 1
). In all five fermentations there was a switch in the metabolic progress after about 8 h that was not further investigated. The apparent stoicheiometries of the products formed were influenced by the amount of deuterium supplied (Table 1
). We did not attempt to assess the virtual reactions (Abeles et al., 1992
; Sprinson & Rittenberg, 1951
) of isotope exchange from these experiments, and the quantitative distribution of the two major pathways for glucose metabolism [glycolysis (~80%) and the pentose phosphate cycle (~20%)] (Neidhardt et al., 1987
) was not calculated. Only the glycolytic metabolism of E. coli is considered in our discussion. The relative ratios of the products were different from the fermentations with and without D2O but were not related to the D2O content (Table 1
). On the other hand, calculations from the integrals showed that the amounts of deuterium in the products were related to the D2O content in the solvent. There was an isotopic discrimination of the species of succinate formed with D2O in all cases and also, to a lesser extent, exchange into acetate. The most interesting fact is that lactate was produced as the major product in D2O although there was still citrate in the solution. So the time course of the formation of fermentation products was also influenced by the amount of deuterium in the water.
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DISCUSSION |
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The 1H-NMR measurement technique
A non-invasive analytical technique to obtain information about metabolism is desirable. 1H-NMR spectroscopy is, in spite of its low sensitivity, such a method. Spectra can be taken directly in situ at any stage of the fermentation without sampling the culture. This can be done simultaneously for several compounds, automatically and without attention overnight (Figs 2b and 3
). The increase in cell mass only slightly influences the quality of the spectra, so that measurements in vivo and during growth are possible. Additionally, the large number of protons in 1H2O is not a significant problem, although they are also detected by our method, because the signal can be suppressed by special measurement techniques (Guéron et al., 1991
; Hore, 1989
; Ogg et al., 1994
; Smallcombe et al., 1995
). The suppression of the 1H2 O signal also partially suppresses signals from solutes in the 3·75·7 p.p.m. range, but the extent of this can be easily assessed by reference to standard solutions (Fig. 2a
).
These three advantages (in situ, in vivo and in aqua) as well as simultaneous analysis of several substrates and products and of pH changes distinguish the method from other analytical techniques. If there are no samples taken from a culture there is no possibility of influencing the fermentation process or perturbing the experimental conditions. This makes the method superior to all invasive techniques and analyses. Additionally, the data are collected directly from the growing cultures. There is no loss of time, and expensive labour is reduced. Further, the structures and the concentrations of the detected substances are not influenced by losses due to self-decomposition during concentration, chemical or physical treatments, or extraction, separation, chromatography or derivatization. The separation of each compound is automatically achieved via the characteristic signals in the spectra obtained.
The 1H-NMR method described has more advantages than disadvantages compared with the use of other NMR-active nuclei. One reason is its much higher sensitivity because of a natural abundance of 99·98% and the largest gyromagnetic ratio of all nuclei (Braun et al., 1996 ). It is not necessary to use isotopically labelled compounds except for specific purposes. A second reason is the presence of protons in all organic molecules so that most accumulated metabolites in concentrations of
12 meq. 1H l -1 can be detected. Other advantages are the distinguishing shifts of each signal and the 1H-couplings that lead to characteristic signal forms for identification of isotopically formed species (Figs 5
and 6
).
There are also some disadvantages of the 1H-NMR method. The spectral range for the protons is low (~12 p.p.m.) so that signals may overlap. This can lead to difficulties in the interpretation of some more complex spectra, for example carbohydrates and other signals close to the suppressed 1H2O signal. Other problems are a relatively low sensitivity in comparison to other analytical methods and an inherent error of about ±5% in the integrations of signals. Many of these reasons are of less consequence when magnets with higher fields are used, for example 600 MHz.
Further possible problems are the presence of a deuterated compound (D2O) in the sample that is used routinely for a lock. If it is in the solvent, it can lead to several influences on the fermentation. There can be kinetic isotope effects, 1H/D exchanges or inhibition of the fermentations as we show (Fig. 4 and Table 1
). This can be circumvented by the use of a D2O capillary added to the NMR tube (Brecker et al., 1999
; Kalinowski et al., 1984
) external to the reaction mixture. On the other hand, D 2O in the solvent can be a helpful probe to analyse kinetic isotope effects and isotope distributions. Additional information can be obtained about the preferential use of the isotope when D2 O is part of the solvent used in metabolism. The incorporation of deuterium into the intermediates and products gives further insights into metabolism.
E. coli HB101 fermentation in 1H2 O and D2O
Monitoring the time course of the E. coli HB101 fermentations by 1H-NMR revealed a large number of details concerning metabolic events as the cultures progressed (e.g. Fig. 2b and Fig. 3
). First, citrate (5 mM) supplied as a metal ion chelator in the media was used preferentially to glucose during growth. Citrate alone does not support growth (Dagley, 1954
; Lütgens & Gottschalk, 1980
), and this characteristic is routinely used to differentiate E. coli strains from other members of the Enterobactericeae (Koser, 1924
). L ütgens & Gottschalk (1980)
convincingly showed that citrate (20 mM) was metabolized by E. coli B when a co-substrate, such as glucose, L-lactate or peptone, was also provided. From chemical and enzymic assays they concluded that the co-substrates were required to provide reducing equivalents to reduce oxaloacetate formed by citrate lyase (Fig. 1
).
In the absence of a co-substrate, oxaloacetate is formed from citrate (Dagley, 1954 ; Lü tgens & Gottschalk, 1980
). Enzymes for metabolism of oxaloacetate to C3 compounds (pyruvate or phosphoenol pyruvate), for example oxaloacetate decarboxylase and malic enzyme, are absent or of very low activity, respectively (L ütgens & Gottschalk, 1980
). Oxaloacetate is thus an electron sink for the formation of succinate, whilst inability to form C3 intermediates from citrate can account for the lack of growth on citrate alone. This conclusion is supported by the high acetate to succinate ratio in glucose plus citrate fermentations (Figs 2b
and 3
), compared with the almost equimolar formation of acetate and ethanol with glucose alone (Wood, 1961
).
The use of deuterium in the solvent for the fermentation provides evidence that water is used as co-substrate. Growth rates progressively decreased with increased D2O in the media (Fig. 4 ). The number and positions of the deuterium atoms bonded to carbon atoms in the metabolites show which hydrogen atoms come from the substrate (glucose or citrate) and which from the D2O in the solvent. This is discussed for acetate. Acetate is formed from the C-1 and C-2 and from the C-5 and C-6 carbon atoms of glucose in equal amounts by glycolysis (Neidhardt et al., 1987
; Wood, 1961
). In acetate, one or two hydrogen atoms come from the substrate and are retained at the same carbon atom. The other hydrogen atoms are derived from the water and should have the same ratio of 1H/D in the metabolite as in the solvent. This is exactly the situation observed in all fermentations with different amounts of D2O which we describe here (Figs 5
and 6
). The E. coli HB101 strain therefore does not prefer one hydrogen isotope to the other, except kinetically.
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ACKNOWLEDGEMENTS |
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REFERENCES |
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Received 2 July 1999;
revised 16 August 1999;
accepted 19 August 1999.