13C metabolic flux analysis.

Metabolic flux analysis using 13C-labeled substrates has become an important tool in metabolic engineering. It allows the detailed quantification of all intracellular fluxes in the central metabolism of a microorganism. The method has strongly evolved in recent years by the introduction of new experimental procedures, measurement techniques, and mathematical data evaluation methods. Many of these improvements require advanced skills in the application of nuclear magnetic resonance and mass spectrometry techniques on the one hand and computational and statistical experience on the other hand. This minireview summarizes these recent developments and sketches the major practical problems. An outlook to possible future developments concludes the text.     

13C NMR investigations on Npi-[13C1]carboxymethyl-histidine-119 ribonuclease.

The ribonuclease A derivative Npi-[13C1]carboxymethyl-histine-119 ribonuclease prepared by using [13C1]bromoacetate as alkylating reagent has been investigated with high resolution 13C NMR spectroscopy. In the 13C NMR spectra two carbon resonances of relatively high intensity appear which can be assigned to carboxyl groups attached to His-119 and Met-30, their intensity ratio being 10 : 1. The pH dependence of the carbon resonance of the carboxy-methyl group bound to the Npi of His-119 differs in the absence and presence of Cyd-2'-P, thus indicating that the catalytically inactive derivative does bind nucleotides. A mechanism of the alkylation reaction at pH 5.6 is proposed in which the epsilon-amino group of Lys-41 acts as the binding site for the carboxyl group of bromoacetate pushing the bromomethylene group towards the Npi of His-119 or the Ntau of His-12.     

THE BIOSYNTHESIS OF C13 COMPOUNDS : I. THE BIOSYNTHESIS OF C13-LABELED STARCH

1. Starch, containing 7.05 atom per cent C¹³ excess has been produced in the mesophyll cells of bean leaves, starting with C¹³O₂ containing 7.26 atom per cent C¹³ excess. Approximately 67 per cent of the C¹³ taken up by the leaves was determined in the starch fraction. 2. The soluble carbohydrate, containing 6.72 atom per cent C¹³ excess, accounts for approximately 23 per cent of the C¹³ taken up by the leaves. The remainder was principally in the coarse tissue fragments fraction (9.73 per cent of the C¹³ utilized). 3. The apparatus and procedures used in this experiment are described.     

Biosynthetic uniform 13C,15N-labelling of zervamicin IIB. Complete 13C and 15N NMR assignment.

Zervamicin IIB is a member of the alpha-aminoisobutyric acid containing peptaibol antibiotics. A new procedure for the biosynthetic preparation of the uniformly 13C- and 15N-enriched peptaibol is described This compound was isolated from the biomass of the fungus-producer Emericellopsis salmosynnemata strain 336 IMI 58330 obtained upon cultivation in the totally 13C, 15N-labelled complete medium. To prepare such a medium the autolysed biomass and the exopolysaccharides of the obligate methylotrophic bacterium Methylobacillus flagellatus KT were used. This microorganism was grown in totally 13C, 15N-labelled minimal medium containing 13C-methanol and 15N-ammonium chloride as the only carbon and nitrogen sources. Preliminary NMR spectroscopic analysis indicated a high extent of isotope incorporation (> 90%) and led to the complete 13C- and 15N-NMR assignment including the stereospecific assignment of Aib residues methyl groups. The observed pattern of the structurally important secondary chemical shifts of 1H(alpha), 13C=O and 13C(alpha) agrees well with the previously determined structure of zervamicin IIB in methanol solution.     

13C NMR studies of bacterial fermentations.

We describe the experimental methods used and the constraints that apply in studies of anaerobic cell metabolism by 13C NMR. We review some of the results of our recent work in this area. Clostridium neopropionicum was shown to ferment ethanol into propionate by the acrylate, non-randomizing pathway. The same metabolic route accounts for 50% of the propionate formed in the complex ecosystem that inhabits the pig's large intestine. The rest is formed via the randomizing succinate pathway. Reductive, hydrogenotrophic acetogenesis was studied in several ecosystems. Although it is usually overshadowed by methanogenesis in the competition for hydrogen, it may become an efficient electron sink when methane biosynthesis is blocked by a specific inhibitor.     

pH-dependence of 13C chemical shifts and 13C,H coupling constants in imidazole and L-histidine.

The pH-dependence of selected 13C chemical shifts reflects the state of ionization of the imidazole ring in both imidazole and L-histidine. Titration of the amino and carboxyl groups of histidine also perturbs the shifts. The coupling constants 1J (13C(2),H) and 1J (13C(5),H) for both compounds also vary with pH, but in L-histidine these constants are relatively insensitive to the titration of groups outside the imidazole ring.     

Solid-state 13C NMR spectroscopy of a 13C carbonyl-labeled polypeptide

High resolution structural elucidation of macromolecular structure by solid-state nuclear magnetic resonance requires the preparation of uniformly aligned samples that are isotopically labeled. In addition, to use the chemical shift interaction as a high resolution constraint requires an in situ tensor characterization for each site of interest. For ¹³C in the peptide backbone, this characterization is complicated by the presence of dipolar coupled ¹⁴N from the peptide bond. Here the ¹³C₁-Gly₂ site in gramicidin A is studied both as a dry powder and in a fully hydrated lipid bilayer environment. Linewidths reported for the oriented samples are a factor of five narrower than those reported elsewhere, and previous misinterpretations of the linewidths are corrected. The observed frequency from oriented samples is shown to be consistent with the recently determined structure for this site in the gramicidin backbone. It is also shown that, whereas a dipolar coupling between ¹³C and ¹⁴N is apparent in dry preparations of the polypeptide, in a hydrated bilayer the dipolar coupling is absent, presumably due to a `self-decoupling' mechanism.     

Intra-erythrocyte microviscosity and diffusion of specifically labelled [glycyl-alpha-13C]glutathione by using 13C n.m.r.

[alpha-13C]Glycine was incubated with suspensions of human erythrocytes under special buffer conditions to enrich specifically intracellular glutathione with 13C. The metabolically active cells were then subjected to 13C n.m.r. spectroscopy in which the longitudinal relaxation time(s) (T1) and nuclear Overhauser enhancement(s) of the free glycine and glutathione were measured. With the appropriate analysis, assuming the molecules to be isotropic rotors, intracellular rotational correlation times were calculated. Using these data together with the Stokes-Einstein equation, viscosity and translational diffusion coefficients were calculated. The results were compared with those from cell lysates and extracts. The cytosolic microviscosity probed by glutathione was only 1.9 +/- 0.3 times that of saline, suggesting, therefore, that most enzyme reactions involving this solute are not likely to be diffusion-controlled inside the erythrocyte.     

13C-n.m.r. study of C hordein.

Insoluble xylan was prepared from ground birch (Betula pubescens) pulp by alkali extraction and precipitation with ethanol. The only sugar detected after acid hydrolysis of the preparation was xylose. The insoluble xylan was used as substrate in a nephelometric assay to determine the xylanase (EC 3.2.1.8, 1,4-beta-D-xylan xylanohydrolase and EC 3.2.1.37, 1,4-beta-D-xylan xylohydrolase) activities of Aspergillus and Trichoderma enzymes. The nephelometric method is reliable in evaluating xylanase hydrolysis of insoluble xylan.     

13C n.m.r. study of L-alanine peptides

The di-, tri-, and tetrapeptides of L-alanine have been studied in aqueous solution by 13C n.m.r. spectroscopy at 25 and 50 MHz. By using selectively 13C enriched analogs containing either 90% 13C methyl or carbonyl carbons and measurements as a function of pH, assignment of the chemical shifts of the peptides has been made. T1 and NOE measurements of the peptides in their cationic, anionic, and zwitterionic states have been recorded as a function of concentration. The results show considerable segmental motion along the backbone carbons of the peptides, with only small changes occurring in the dynamic motions of the peptides as their charge states are altered. The lack of concentration dependence of the chemical shift and T1 values, as well as the similarity of T1 values for individual peptides in the three charge states, indicate that the peptides do not self-associate in aqueous solution.     

A C13-norisoprenoid gentiobioside from quince fruit.

The beta-D-gentiobioside [beta-D-glucopyranosyl(1----6)-beta-D-glucopyranoside] of 3-hydroxy-beta-ionol has been isolated and characterized in quince (Cydonia oblonga) fruit through spectral and chemical studies. Model experiments carried out with this new natural compound revealed its important role as precursor of a number of C13-norisoprenoid flavour compounds of quince essential oil.     

Kinetic studies of C. pyrenoidosa using 94% 13C CO2

The alga Chlorella pyrenoidosa has been grown in mass quantities on 94 at. % ¹³CO₂. The algal cells have been labeled to the 90 at. % ¹³C level. Neither inhibition nor a requirement for adaptation was encountered; changes in morphology were not evident. A statistically significant increase in mass of cells produced in the presence of ¹³CO₂ was observed.     

High-resolution solid state 13C NMR of bacteriorhodopsin: characterization of [4-13C]Asp resonances.

Solid state 13C nuclear magnetic resonance measurements of bacteriorhodopsin labeled with [4-13C]Asp show that resonances of single amino acids can be resolved. In order to assign and characterize the resonances of specific Asp residues, three different approaches were used. (1) Determination of the chemical shift anisotropy from side-band intensities provides information about the protonation state of Asp residues. (2) Relaxation studies and T1 filtering allow one to discriminate between resonances with different mobility. (3) A comparison of the spectra of light- and dark-adapted bacteriorhodopsin provides evidence for resonances from aspartic acid residues in close neighborhood of the chromophore. In agreement with other investigations, four resonances are assigned to internal residues. Two of them are protonated in the ground state up to pH 10 (Asp96 and Asp115). All other detected resonances, including Asp85 and Asp212, are due to deprotonated aspartic acid. Two lines due to the two internal deprotonated groups change upon dark and light adaptation, whereas the protonated Asp residues are unaffected.     

Synthesis of methyl 4'-O-methyl-beta-D-cellobioside-13C12 from D-glucose-13C6. Part 2: solid-state NMR studies

Double Quantum (DQ) NMR, which utilizes the magnetic dipole interaction between the (13)C atoms, was used for the complete assignment of the (13)C NMR resonances to the corresponding carbon ring positions for the monoclinic and triclinic allomorphs of methyl 4'-O-methyl-beta-D-cellobioside-(13)C(12)(1-(13)C(12)), a cellodextrin model compound of cellulose (13)C-perlabeled at the cellobiose core. The through-space interactions were used to identify the direct chemical bonds between adjacent carbon atoms in the rings. More importantly, the (13)C NMR signals of the carbon sites C1' and C4 involved in the glycosidic bond were identified. This allowed for the complete (13)C chemical shift assignment, that when combined with the X-ray crystallography data provides a complete characterization.     

Quantitation of model digestive mixtures by 13C NMR.

13C nuclear magnetic resonance (NMR) spectra were obtained at 50.3 and 100.5 MHz for methanolic and aqueous mixtures of sodium taurocholate, 1-monocapryloyl-rac-glycerol, and caprylic acid. Distortionless Enhancement by Polarization Transfer (DEPT) was used to improve spectral sensitivity and resolution, and to generate calibration curves for quantitative determinations of each lipid in methanol. Alternatively, the heights for nonoverlapping peaks in a 13C NMR spectrum acquired with inverse-gated decoupling provide reliable quantitative estimates for each component of the mixture, particularly when the data are obtained in methanol. These experiments also demonstrate the feasibility of detailed NMR structural investigations in model systems for glyceride digestion.     

13C NMR analysis of methionine sulfoxide in protein.

The 13C epsilon NMR signal of methionine sulfoxide is 22.6 ppm downfield from that of methionine. This affords a method by which the extent of methionine oxidation can be determined in intact protein. We demonstrate the utility of this approach with beta-galactosidase enriched with 13C in its methionine methyls.     

A universal framework for 13C metabolic flux analysis.

A general methodology is presented for the modeling, simulation, design, evaluation, and statistical analysis of (13)C-labeling experiments for metabolic flux analysis. The universal software framework 13C-FLUX was implemented to support all steps of this process. Guided by the example of anaplerotic flux determination in Corynebacterium glutamicum, the technical details of the model setup, experimental design, and data evaluation are discussed. It is shown how the network structure, the input substrate composition, the assumptions about fluxes, and the measurement configuration are specified within 13C-FLUX. Based on the network model, different experimental designs are computed depending on the goal of the investigations. Finally, a specific experiment is evaluated and the various statistical methods used to analyze the results are briefly explained. The appendix gives some details about the software implementation and availability.