Supplementary Information 1. Deuterium Enrichment of Sodium [U- 2 H 3,2-13

Transcription

1 Supplementary Information for Following Metabolism in Living Microorganisms by Hyperpolarized H NMR Piotr Dzien, Anne Fages, Ghil Jona, Kevin M. Brindle, Markus Schwaiger and Lucio Frydman* These authors contributed equally to this work. * lucio.frydman@weizmann.ac.il Supplementary Information. Deuterium Enrichment of Sodium [U- 2 H 3,2-3 C]Pyruvate and [U- 2 H 3,2-3 C]pyruvic Acid. Sodium [U- H 3,2-3 C]pyruvate (Isotec, Sigma-Aldrich) was deuterated as described previously. The reaction mixture was applied to PD-0 desalting columns (GE Healthcare, Amersham, UK) pre- equilibrated with D 2O. Pyruvate-containing samples were pooled and freeze-dried. To measure [2-3 C]pyruvate content in dry solid, 3 C NMR spectra (64 transients, TR = 50 s) were acquired at 50 MHz from a sample which contained 7 mg of solid dissolved in 600 µl PBS (ph 7.4) and containing 5 mm 3 C urea, and 5 mm TMSP. Sodium [2-3 C]pyruvate content was calculated by dividing the integrated intensity of 3 C carbonyl carbon signal by that of 3 C urea, and multiplying by the molarity urea present in the sample. To measure [U- H 3]pyruvate content in the solid, H NMR spectra were acquired at 600 MHz (28 transients, TR = 5 s) from the sample described above. [U- H 3]pyruvate content was calculated by dividing the integrated signal from the methyl proton of pyruvate by that of TMSP, and multiplying by the molarity of methyl group in TMSP present in the sample (5 mm). The results were compared with spectra acquired as described above from a sample which otherwise had the same composition except that it contained a known concentration of [U- H 3,2-3 C] sodium pyruvate. Deuteration was approximately 87 % and dry solid contained approximately 84 % sodium pyruvate. For preparing [U- 2 H 3,2-3 C]pyruvic acid, 500 mg of sodium [U- H 3,2-3 C]pyruvate (Isotec, Sigma-Aldrich) were dissolved in 50 ml of D 2O, and the ph of the solution was adjusted to pd = with 0 M NaOD. This mixture was stirred at 00 rpm at room temperature for 24 hours 2. The mixture was then acidified to ph.2 by the addition of 00 µl DCl and 250 µl D 2SO 4. This was then lyophilised and pyruvic acid was extracted with diethyl ether. The solvent was removed by evaporation. The extracted liquid was not further purified and contained approximately 70% [U- 2 H 3,2-3 C]pyruvic acid as measured by 3 C NMR. These analytical 3 C NMR spectra were acquired at 25 MHz (90 flip angle, 64 transients, TR = 80 s) from a sample containing 3 mg of 3 C - enriched pyruvic acid and 5 mm 3 C urea dissolved in 600 ul of 9: distilled water : D 2O mixture, and neutralised with NaOH. Molarity of pyruvic acid was calculated as outlined above. S

2 . Simpson, R.; Brindle, K.M.; Brown, F.F.; Campbell, I.D.; Foxall, D.L. A p.m.r. isotope-exchange method for studying the kinetic properties of dehydrogenases in intact cells. Biochem J 982, 202, Supplementary Information 2. Analytical solutions to the Bloch McConnell differential equations describing the three step process HP 3 C(substrate) k cat 3 C(product) k x rel H(product). The evolution of M z C,substrate, M z C,product, M z H,product magnetizations over time can be obtained by solving the system of differential equations given in Eqs. [-3]. Assuming that the initial magnetizations of the observed species are M z C,substrate (t=0)=polarization substrate. [Sub] 0=sub, M z C,product (t=0)=0 and M z H,product (t=0)=0 as initial conditions, these solutions become M z c,substrate (t) = sub. e R cs.t M z C,product (t) = k cat.sub.e R cp.t R cp R cs + k cat.sub.e Rcs.t R cp R cs [S] [S2] M H,product z (t) = ( (k R cp R x rel ( k cat.sub.e cs k cat.sub.r cs.e R cp.t+r hp.t (R cp R cs ).(R hp R cp ) with R cs = ( cos θ) TR )) + Rcs.t+R hp.t R hp R cs k cat.sub.k x rel R cp.r cs R cp.r hp R cs.r hp +R hp T c,substrate + k cat, R cp = k cat k Rcp.t+R cat.sub.r cp.e hp.t + (R cp R cs ).(R hp R cp ) 2 )e R hp.t [S3] T c,product k x rel and R hp = k x rel H,product T. Other variables in these equations are as defined for Eqs [-3]. As revealed by the M z H,product (t) function in Eq. [S3], k cat always comes multiplying M z C,substrate (t=0) (referred as sub in the equation), given by the product of the initial substrate concentration times the 3 C hyperpolarization. Equation [S3] was used to fit the [- H]acetaldehyde signal evolution over time in order to extract k pdc. For this fitting the initial substrate concentration [Sub] 0 was assessed through the collection of the thermally polarized product ([- H]acetaldehyde) H NMR signal recorded 30 minutes after the injection of HP substrate ([2-3 C]pyruvate), which was assumed proportional to [Sub] 0. For estimating k cat a 3 C signal enhancement Polarization substrate 8000 was also assumed. Supplementary Information 3. MRS experiments using HEK293T cells constitutively expressing zmpdc. Generation of Clonal HEK293T Cells Stably Transfected with zmpdc. A DNA sequence encoding a monomer of pyruvate decarboxylase from Zymomonas mobilis (zmpdc) fused to a green fluorescent protein (GFP) was cloned into the pef6-v5/his vector (Life Technologies S2

3 Ltd,Paisley, UK), to generate a plasmid carrying zmpdc-gfp-v5/his fusion protein expressed from the constitutive mammalian EF-α promoter. HEK293T cells were grown at 37 C in Dulbecco s Modified Eagle s Medium (DMEM) (GIBCO Invitrogen, Carlsbad California, USA) with 0% fetal bovine serum (PAA Laboratories Ltd, Yeovil Somerset, UK), 4 mm glutamine (GIBCO Invitrogen) and 5% CO 2. Plasmid DNA transfections were performed with Lipofectamine (Life Technologies Ltd) essentially as recommended by the manufacturer. Stably transfected clones were selected in media containing 5 μg/ml blasticidin, picked and expanded. NMR Measurements using HP [2-3 C]pyruvate. Clonal cells expressing zmpdc were harvested by trypsinization, centrifuged at room temperature at 000 G for 5 min and resuspended in pyruvate-, and FBS-free DMEM and maintained at 30 K inside of the MR spectrometer. For experiments using 5 mm NMR probes (for further details regarding probes and pulse sequences see the main Materials and Methods section), 5 x 0 7 cells re-suspended in 0.3 ml DMEM, ph = 7.4, were used. Approximately 3 s after dissolution, 500 μl of dissolved sample containing HP [2-3 C]pyruvate, ph = 7.0, were injected automatically and spectral acquisitions were started 9 s later. The experiments used either regular H detection with a 90 shaped pulse and TR = 3 s (n =), H detection using the reversed INEPT sequence (n = ), or 3 C detection using a single transient pulse with 2 flip angle and TR = 3 s (n = ). Final concentration of [2-3 C]pyruvate was approximately 6 mm. In some experiments (n = 2), 2 x 0 8 cells re-suspended in ml DMEM and placed in a 0 mm test tube located inside of a 0 mm probe tuned to 3 C were used. Approximately 3 s after dissolution, 3 ml of the dissolved sample of HP [2-3 C]pyruvate were injected manually into the cell suspension, and spectral acquisitions were started immediately. Final concentration of [2-3 C]pyruvate was approximately 6 mm. While neither single-pulse H or 3 C NMR on this HP substrate using a standard low flip angle excitation allowed the detection of the activity of the transgenic zmpdc expressed by HEK293T cells, the figure below shows the single-scan H-detected INEPT NMR spectrum revealing the production of HP acetaldehyde. Figure S: H MRS measurement of acetaldehyde production by zmpdc - expressing HEK293T cells. H spectrum was acquired using reversed INEPT pulse sequence from a sample of 5 x0 7 cells resuspended in DMEM, ph = 7.0 and maintained at 30 K, 9 s after the addition of HP [2-3 C]pyruvate to a final concentration of approximately 6 mm. S3

4 Supplementary Information 4. Figures describing the effects of kinetic parameters on the observed NMR signals in the process: HP 3 C(substrate) k cat H(product). 3 C(product) k x rel Figure S2. Influence of various kinetic parameters in the expected H magnetization of a 3 C hyperpolarized product. The simulated time course signals were obtained from equation Eq [S3] varying: (a) k cat rate constant of the 3 C(substrate) k cat 3 C(product) enzymatic reaction; (b) the k x-rel cross-relaxation rate constant of the magnetization transfer 3 C(product) k x rel H(product); (c) the longitudinal relaxation time of 3 C-product (T C,product ); (d) the longitudinal relaxation time of H-product (T H,product ); (e) the longitudinal relaxation time of 3 C-substrate (T C,substrate ) by the specified values. When not indicated different, the values S4

5 for the parameters used in the simulation were: k x-rel = 0. Hz, k cat = s -, T c,substrate = 30 s, T c,product = 2 s, T H,product = 4 s, θ =30, TR = 4 s and Polarization substratex[sub] 0 =. The dotted lines show the maximum H-product signal intensity for the lowest and the highest values of each parameter considered. Notice that lowering the k x-rel cross-relaxation rate constant decreases the intensity of signal amplitude and increases the build up time, while decreasing k cat enzymatic rate constant decreases the signal amplitude due to a slower product formation and slightly decreases the build up time for this range of k cat values considered. Increasing T H,product, T C,product T C,substrate increase the signal intensity and the build up time. Figure S3. Superimposed time courses expected for 3 C(substrate), 3 C(product) and H(product). Simulation of the 3 C substrate magnetization (blue curve) and the 3 C and H product magnetizations (red curve and orange curve respectively) were obtained from solutions to the modified Bloch McConnell differential equations Eqs [S-S3] using the following parameters : T c,substrate = 30 s, T c,product = 2 s, T H,product = 4 s, k x-rel = 0. Hz, k cat = 2x0-4 s -, θ = 30, TR = 4 s and using M z C,substrate (t=0)=polarization substratex[sub] 0 =. For these parameters, the signal intensities of 3 C(product) and H(product) were multiplied by 000. The maximum peak intensities of 3 C(product) and H(product), marked by dotted lines, are separated by 5 s. This time shift in maximum signal intensities between 3 C and H magnetizations can be explained by the T s of the different species. S5