In Here we show that an open reading frame at 9 min on the chromosomal map of E. coli encodes an enzyme (deoxyxylulose-5-phosphate synthase, DXP synthase) that catalyzes a thiamin diphosphate-dependent acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield DXP. We have cloned and overexpressed the gene (dxs), and the enzyme was purified 17-fold to a specific activity of 0.85 unit͞mg of protein. The reaction catalyzed by DXP synthase yielded exclusively DXP, which was characterized by 1 H and 31 P NMR spectroscopy. Although DXP synthase of E. coli shows sequence similarity to both transketolases and the E1 subunit of pyruvate dehydrogenase, it is a member of a distinct protein family, and putative DXP synthase sequences appear to be widespread in bacteria and plant chloroplasts.

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To determine the in vivo fluxes of the central metabolism we have developed a comprehensive approach exclusively based on the fundamental enzyme reactions known to be present, the fate of the carbon atoms of individual reactions, and the metabolite balance of the culture. No information on the energy balance is required, nor information on enzyme activities, or the directionalities of reactions. Our approach combines the power of 'H-detected 13C nuclear magnetic resonance spectroscopy t o follow individual carbons with the simplicity of establishing carbon balances of bacterial cultures. We grew a lysine-producing strain of Corynebacterium glutamicum to the metabolic and isotopic steady state with [l-'3Clglucose and determined the fractional enrichments in 27 carbon atoms of 11 amino acids isolated from the cell. Since precursor metabolites of the central metabolism are incorporated in an exactly defined manner in the carbon skeleton of amino acids, the fractional enrichments i n carbons of precursor metabolites (oxaloacetate, glyceraldehyde 3-phosphate, erythrose 4-phosphate, etc.) became directly accessible. A concise and generally applicable mathematical model was established using matrix calculus to express all metabolite mass and carbon labeling balances. An appropriate all-purpose software for the iterative solution of the equations is supplied. Applying this comprehensive methodology t o C. glutamicum, all major fluxes within the central metabolism were determined. The result is that the flux through the pentose phosphate pathway is 66.4% (relative to the glucose input flux of 1.49 mmol/g dry weight h), that of entry into the tricarboxylic acid cycle 62.2%, and the contribution of the succinylase pathway of lysine synthesis 73.7%. Due t o the large amount and high quality of measured data in vivo exchange reactions could also be quantitated with particularly high exchange rates within the pentose phosphate pathway for the ribose 5-phosphate transketolase reaction. Moreover, the total net flux of the anaplerotic reactions was quantitated as 38.0%. Most importantly, we found that in vivo one component within these anaplerotic reactions is a back flux from the carbon 4 units of the tricarboxylic acid cycle to the carbon 3 units of glycolysis of

Growth of Corynebacterium glutamicum on mixtures of the carbon sources glucose and acetate is shown to be distinct from growth on either substrate alone. The organism showed nondiauxic growth on media containing acetate-glucose mixtures and simultaneously metabolized these substrates. Compared to those for growth on acetate or glucose alone, the consumption rates of the individual substrates were reduced during acetateglucose cometabolism, resulting in similar total carbon consumption rates for the three conditions. By 13 Clabeling experiments with subsequent nuclear magnetic resonance analyses in combination with metabolite balancing, the in vivo activities for pathways or single enzymes in the central metabolism of C. glutamicum were quantified for growth on acetate, on glucose, and on both carbon sources. ) on glucose plus acetate also. Consistent with the predictions deduced from the metabolic flux analyses, a glyoxylate cycle-deficient mutant of C. glutamicum, constructed by targeted deletion of the isocitrate lyase and malate synthase genes, exhibited impaired growth on acetate-glucose mixtures.In their natural environments microorganisms often encounter situations when not a single carbon source but mixtures of carbon and energy sources are present. Under such conditions, bacteria often utilize one carbon source preferentially, with the further carbon source(s) being consumed only, when the preferred one is exhausted. As already shown by Monod (29), the preferred carbon source in general supports the best growth rate and/or growth yield, and the successive utilization of the substrates is often represented by a biphasic growth behavior (29). The classical example of this phenomenon is the diauxic growth of Escherichia coli on glucose plus lactose, and the study of the underlying principles initiated the era of research on gene regulation. On the other hand, by analysis of growth and carbon source consumption, it was shown that, e.g., Leuconostoc oenos cometabolizes glucose with citrate or fructose (38). Also, E. coli cometabolizes hexoses under carbon limitation conditions (reviewed in reference 20). Several other bacteria use two carbon sources in parallel (reviewed in reference 16); among these is Corynebacterium glutamicum, a gram-positive bacterium known for its ability to excrete amino acids. C. glutamicum grows aerobically on a variety of carbohydrates and organic acids as carbon sources (23). The organism cometabolizes glucose and fructose, glucose and lactate, and glucose and pyruvate (6, 7), whereas it shows diauxic growth on glucose-glutamate mixtures (21). The carbon sources glucose and acetate have been shown to serve as substrates for amino acid production by C. glutamicum (17). There is considerable knowledge about the enzymes and genes involved in acetate and glucose metabolism as well as their regulation (35,36,52,53), whereas neither growth on acetate-glucose mixtures nor metabolite fluxes during growth on acetate have been studied in detail.The utilization of acetate involves its uptake ...

Escherichia coli grew in a minimal medium on propionate as the sole carbon and energy source. Initially a lag phase of 4-7 days was observed. Cells adapted to propionate still required 1-2 days before growth commenced. Incorporation of (2-13C), (3-13C) or (2H3)propionate into alanine revealed by NMR that propionate was oxidized to pyruvate without randomisation of the carbon skeleton and excluded pathways in which the methyl group was transiently converted to a methylene group. Extracts of propionate-grown cells contained a specific enzyme that catalyses the condensation of propionyl-CoA with oxaloacetate, most probably to methylcitrate. The enzyme was purified and identified as the already-known citrate synthase II. By 2-D gel electrophoresis, the formation of a second propionate-specific enzyme with sequence similarities to isocitrate lyases was detected. The genes of both enzymes were located in a putative operon with high identities (at least 76% on the protein level) with the very recently discovered prp operon from Salmonella typhimurium. The results indicate that E. coli oxidises propionate to pyruvate via the methylcitrate cycle known from yeast. The 13C patterns of aspartate and glutamate are consistent with the further oxidation of pyruvate to acetyl-CoA. Oxaloacetate is predominantly generated via the glyoxylate cycle rather than by carboxylation of phosphoenolpyruvate.

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The C 3 -C 4 metabolite interconversion at the anaplerotic node in many microorganisms involves a complex set of reactions. C 3 carboxylation to oxaloacetate can originate from phosphoenolpyruvate and pyruvate, and at the same time multiple C 4 -decarboxylating enzymes may be present. The functions of such parallel reactions are not yet fully understood. Using a 13 C NMR-based strategy, we here quantify the individual fluxes at the anaplerotic node of Corynebacterium glutamicum, which is an example of a bacterium possessing multiple carboxylation and decarboxylation reactions. C. glutamicum was grown with a 13 C-labeled glucose isotopomer mixture as the main carbon source and 13 C-labeled lactate as a cosubstrate. 58 isotopomers as well as 15 positional labels of biomass compounds were quantified. Applying a generally applicable mathematical model to include metabolite mass and carbon labeling balances, it is shown that pyruvate carboxylase contributed 91 ؎ 7% to C 3 carboxylation. The total in vivo carboxylation rate of 1.28 ؎ 0.14 mmol/g dry weight/h exceeds the demand of carboxylated metabolites for biosyntheses 3-fold. Excess oxaloacetate was recycled to phosphoenolpyruvate by phosphoenolpyruvate carboxykinase. This shows that the reactions at the anaplerotic node might serve additional purposes other than only providing C 4 metabolites for biosynthesis.The interconversions between the C 3 metabolism and the C 4 metabolites of the tricarboxylic acid cycle function either as a replenishment of tricarboxylic acid cycle intermediates (anaplerosis) or as the initial steps of gluconeogenesis. These carboxylation and decarboxylation reactions are catalyzed by a number of enzymes (1, 2). Synthesis of oxaloacetate via carboxylation of C 3 metabolites may be catalyzed by phosphoenolpyruvate (PEP) 1 carboxylase, PEP carboxytransphosphorylase, or pyruvate carboxylase. The reverse reaction, decarboxylation of oxaloacetate, may analogously lead to PEP or pyruvate, catalyzed by PEP carboxykinase or oxaloacetate decarboxylase, respectively. NAD ϩ -or NADP ϩ -dependent malic enzyme catalyzes the reaction from malate to pyruvate. In some organisms, this enzyme is also thought to act in a pyruvate-carboxylating sense (3).To date, a full understanding of these enzymatic reactions and their functions has been hindered by a lack of knowledge about their activities in vivo. The occurrence of parallel reactions and the involvement of a set of metabolites in activity control of the enzymes prevents reliable estimations on the actual enzyme use. Moreover, it is not possible to derive quantitative data on in vivo flux rates by enzyme characterizations alone. Instead, carbon-13 labeling techniques, which employed NMR spectroscopy (for an overview, see e.g. Refs. 4 and 5) or mass spectrometry, as well as carbon-14 radiolabeling methods have been used to quantify in vivo intracellular fluxes in central metabolism including conversions between PEP, pyruvate, and oxaloacetate/malate. However, although these studies quantified the total C ...

This article generalizes the statistical tools for the evaluation of carbon‐labeling experiments that have been developed for the case of positional enrichment systems in part II of this series to the general case of isotopomer systems. For this purpose, a new generalized measurement equation is introduced that can describe all kinds of measured data, like positional enrichments, relative 13C nuclear magnetic resonance (13C NMR) multiplet intensities, or mass isotopomer fractions produced with mass spectroscopy (MS) instruments. Then, to facilitate the specification of the various measurement procedures available, a new flexible textual notation is introduced from which the complicated generalized measurement equations are generated automatically. Based on these measurement equations, a statistically optimal flux estimator is established and parameter covariance matrices for the flux estimation are computed. Having implemented these tools, different kinds of labeling experiments can be compared by using statistical quality measures. A general framework for the optimal design of carbon‐labeling experiments is established on the basis of this method. As an example it is applied to the Corynebacterium network from part II extended by various NMR and MS measurements. In particular, the positional enrichment, multiplet, or mass isotopomer measurements with the greatest information content for flux estimation are computed (measurement design) and various differently labeled input substrates are compared with respect to flux estimation (input design). It is examined in detail how the measurement procedure influences the estimation quality of specific fluxes like the pentose phosphate pathway influx. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 66: 86–103, 1999.