Tang HS , Gates CR , Schultz MC .

	Fig 1. GAPDH protein in the oocyte nucleus and cytoplasm. (A) Oocyte isolation. Oocytes are freed from ovary fragments (top left photo) by collagenase digestion. Mechanical treatment yields isolated oocytes without adhering somatic cells (bottom photo). Cells are dissected under oil to obtain nuclei and cytoplasms, which are then homogenized in a physiological buffer (right panel). (B) GAPDH structure. Superimposition of the structure of the human GAPDH monomer (gold) and a model of X. laevis GAPDH generated by RoseTTAFold (cyan). The pullout shows the catalytic cysteine (C152 and 150 in human and frog respectively). (C) GAPDH protein in oocyte nucleus and cytoplasm. Western blotting analysis of GAPDH in ensemble preparations of nuclear and cytoplasmic homogenate from isolated oocytes. vit, full length and processing products of vitellogenin, a storage protein that accumulates exclusively in cytoplasmic yolk granules. (D) Nuclear GAPDH expression: Effect of oocyte isolation and culture. Western blotting analysis of GAPDH in nuclei dissected directly from oocytes in ovary fragments (left three lanes) and in fractions obtained from isolated oocytes (right six lanes). (E) Self-association state of GAPDH in the nucleus and cytoplasm. Analysis of GAPDH by native PAGE (left-most and right-most panels), and native PAGE followed by conventional SDS-PAGE (middle panel). Recombinant human GAPDH and oocyte GAPDH were detected by Western blotting. The three fastest migrating species of human GAPDH resolved by native PAGE are provisionally identified as the enzyme’s monomeric, dimeric and tetrameric forms. GAPDH in the oocyte cytoplasm comigrates with human tetrameric GAPDH (left panel) and oocyte nuclear GAPDH (right panel). (F)–(H) Validation of whole compartment LC-MS analysis and LC-MS profiling of GAPDH.s and GAPDH.l by compartment. (F) Relative abundance of marker proteins in the oocyte nucleus and yolk-free cytoplasm. Box and whisker plots of protein expression in six individual stage VI nuclei (blue bars) and the 7,500 x g supernatant obtained from six individual stage VI cytoplasms (cyto S7500, orange bars). % of total Σ# peptide spectral matches (PSMs) is an estimate of relative protein abundance. X is the mean. Abundance rankings (% rank in each sample) are shown in the right hand plots. The histone chaperone NPM2 was present in all nuclei, but not detectable in the cytoplasms. The cytoplasmic marker ATP6V1B2 (a subunit of the vacuolar H+-ATPase) was only detected in cytoplasm. This validation result applies to the analysis in Figs 1G, 1H and 3A. (G) Raw number of PSMs assigned to GAPDH.s and GAPDH.l (bars with dotted and solid outlines respectively) in the six nuclear homogenates and six cytoplasmic S7500s analyzed. (H) For each sample, ratio of Σ# PSMs assigned to GAPDH.s versus GAPDH.l. The last two bars summarize the data (errors are SD, P = 0.796773).
	Fig 2. A working model of metabolic flux through glycolytic enzymes located in the nucleus and cytoplasm of full-grown Xenopus laevis oocytes. Glycolytic enzymes support opposite directions of flux in the cytoplasm and nucleus. In the cytoplasm, GAPDH activity supports anabolic pathways. The opposite is true in the nucleus, where flux through GAPDH supports ATP synthesis. Grey-filled arrows indicate flux direction and relative intensity (darker shading means higher flux). White-filled arrows represent enzyme abundance; the darker the outline of the arrow, the higher is the enzyme abundance. The white arrows also show flux direction. The dotted line is a multi-enzyme pathway that generates cytosolic PEP and ATP. F1,6BP, fructose 1,6-bisphosphate; G3P, glyceraldehyde 3-phosphate; PEP, phosphoenolpyruvate. See section “GAPDH in oocyte metabolism: A working model of compartmentalized activity” and S1 Fig for details.
	Fig 3. Single cell analysis of enzyme relative abundance in the oocyte nucleus and cytoplasm. (A) Relative abundance of glycolytic enzymes and lactate dehydrogenase in the oocyte nucleus and yolk-free cytoplasm. % of total Σ# PSMs and % rank in each sample as described in Fig 1F. Except for phosphofructokinase PFKM, glycolytic enzymes and LDHB were detected in all nuclei and cytoplasms. (B) Western blotting analysis of GAPDH in five individual nuclei from late stage V cells. (C) Western blotting analysis of GAPDH in S7500s obtained from five individual stage V cytoplasms (same oocyte isolation experiment as panel B).
	Fig 4. Near-native HR buffer is suitable for the assay of GAPDH activity. (A) Initial rate of recombinant human GAPDH in a standard pH 8.5 buffer (grey-filled circles) and HR buffer, which is adjusted to pH 7.4 (open circles). HR buffer supports high activity of this enzyme preparation. (B) Double reciprocal plot of v0 versus NAD+ concentration for rabbit muscle GAPDH in near-native HR buffer. Positive values for kinetic parameters are obtained when purified rabbit GAPDH is assayed in HR buffer. (C) Plot showing the dependence of v0 on G3Pconcentration in reactions catalyzed by rabbit GAPDH. Substrate inhibition by G3P, a long-known property of GAPDH, is readily apparent when purified rabbit GAPDH is assayed in HR buffer. (D) Double reciprocal plot of v0 versus G3P concentration for rabbit muscle GAPDH in near-native HR buffer. Positive values for kinetic parameters are obtained in this buffer. In (B)-(D), the results of three independent assays are shown (each data point is the average of a technical triplicate). The linear trendlines were obtained using Excel. In (B) and (D) the units of Km and Vmax are mM and ΔA340/min respectively.
	Fig 5. The oocyte system for analysis of GAPDH compartmentalization: Validation of enzyme activity assay and estimation of protein expression by Western blotting. (A) Freeze-thawing does not differentially affect GAPDH activity in whole compartment homogenates. Product accumulation due to GAPDH activity in fresh and frozen-thawed homogenates (solid and dotted lines respectively) of nuclei and cytoplasms (blue and orange respectively). (B) High sampling reproducibility of the GAPDH activity assay. GAPDH activity as product accumulation in replicate samples (n = 6) of a single nuclear and a single cytoplasmic homogenate (blue and orange respectively). The flat line traces are for reactions without substrates. (C) GAPDH is predominantly in the soluble phase of the cytoplasm and nucleus. Top two panels. Western blotting analysis of GAPDH protein in whole homogenates (hom) and matched supernatants (supt) depleted of macromolecular cell features by centrifugation at 15,000 x g. Nuc, nucleus; Cyto, cytoplasm. Bottom panel. Western blotting analysis of GAPDH protein in the supernatant and pellet obtained by centrifugation of nuclear homogenate at 15,000 x g. The experiment was performed in duplicate. (D) GAPDH enzyme activity in whole compartment homogenates is not reduced by removal of macromolecular cell features. GAPDH progress curves for reactions containing nuclear and cytoplasmic fractions as labeled. The fractions are whole homogenate (hom, solid line) and homogenate clarified by centrifugation at 15,000 x g (supt, dashed line). (E) Relative expression of GAPDH in whole homogenates of oocyte nuclei and cytoplasms. GAPDH was detected by chemiluminescent Western blotting. Images captured using the LI-COR system were visualized in Image Studio Lite. The signal intensity data were fitted to hyperbolic curves using the logarithmic trendline and Solver functions in Excel. The top panel compares these fits for a sample of cytoplasmic homogenate. The middle panel is the image of a side-by-side analysis of GAPDH in nuclear and cytoplasmic homogenate. Quantitation of the signal intensity data for this blot is shown in the bottom graph.
	Fig 6. GAPDH activity in representative cytoplasmic and nuclear homogenates. (A) and (B) Progress curves obtained at increasing concentrations of NAD+ in cytoplasmic and nuclear homogenate respectively. Identical NAD+ concentrations were used for both experiments (key in panel A). (C) and (D) Progress curves obtained at increasing concentrations of G3P in cytoplasmic and nuclear homogenate respectively. The dotted line in the G3P concentration key indicates the titration point beyond which higher G3P concentrations do not cause the reaction rate to increase (red traces). GAPDH activity is fully inhibited at 3 and 4 mM G3P in both nuclear and cytoplasmic homogenate.
	Fig 7. The activity behavior of GAPDH differs between homogenates of whole cytoplasm and whole nucleus. (A) and (B) Michaelis Menten-like behaviour of cytoplasmic and nuclear GAPDH in assays of v0 versus NAD+ concentration. (A) Plot for cytoplasmic homogenate of the dependence of GAPDH v0 on NAD+ concentration (left panel) and Lineweaver-Burke plot of this data (right panel). (B) Plot for nuclear homogenate of the dependence of GAPDH v0 on NAD+ concentration (left panel) and Lineweaver-Burke plot of this data (right panel). (C)—(F) Departure of nuclear GAPDH from Michaelis Menten-like behaviour in assays of v0 versus G3P concentration. (C) Plots for cytoplasmic homogenate of the dependence of GAPDH v0 on G3P concentration at 6 concentrations of NAD+ (large graph at left). The pullout shows the data at 4 and 6 mM of NAD+ over the 0.25–1.5 mM range of G3P concentrations. The latter plots have a hyperbolic (Michaelis-Menten-like) character. (D) Plots for nuclear homogenate of the dependence of GAPDH v0 on G3P concentration at 6 concentrations of NAD+ (large graph at left). The pullout shows the data at 4 and 6 mM of NAD+ over the 0.25–1.5 mM range of G3P concentrations. The latter plots have an unexpected sigmoidal character. (E) Direct comparison of the G3P v0 data for nuclear and cytoplasmic GAPDH at 5 mM NAD+. At the peak for both (2.5 mM G3P), v0 is 2.5-fold higher in nuclear than cytoplasmic homogenate. (F) Color-coded diagram scoring the fit of the v0 versus [G3P] data to the Michaelis-Menten equation. The fitting methods were Lineweaver-Burke (L), Hanes-Woolf (H) and Eadie-Hofstee (E). Yellow fill indicates that a positive estimate was obtained for the indicated parameter (Km or Vmax). Black fill indicates an invalid estimate. The results are from assays of two independent starting homogenates from four animals. (G) Heatmap highlighting the fold-difference between estimates of kinetic parameters obtained by the Lineweaver-Burke (L), Hanes-Woolf (H) and Eadie-Hofstee (E) methods.
	S1 Fig. A working model of metabolic flux through enzymes of glycolysis located in the nucleus and cytoplasm of oocytes. Flux through glycolytic enzymes (circled steps 2–11) occurs in opposite directions in the cytoplasm and nucleus (orange and blue arrows respectively). GAPDH acts at step 6. Relative flux intensity is indicated by line width. Dotted lines are pathways for which some steps have been omitted. Lines with black arrows identify reactions that are expected to operate similarly in the cytoplasm and nucleus. The orange and blue numbers are enzyme concentrations in nM (Kirli et al., 2015). In the cytoplasm, glycogen and nucleoside synthesis (orange boxes, dark outline) predominate over pyruvate synthesis. In the nucleus, flux through GAPDH supports operation of the payoff phase of glycolysis culminating in ATP and pyruvate synthesis (blue box, dark outline). Flux in the opposite direction is limited by low nuclear expression of critical enzymes of glycogen and nucleoside synthesis. The enzymes of glycogen synthesis shown are glycogen synthase 1 (GSY1) and UDP-glucose pyrophosphorylase (UGP2). The enzymes of nucleoside monophosphate (NMP) synthesis shown are: Carbamoyl-phosphate synthetase 2, Aspartate transcarbamylase, Dihydroorotase (CAD); Phosphoribosyl pyrophosphate synthetases 1 and 2 (PRPS1, PRPS2); Uridine monophosphate synthetase (UMPS); Phosphoribosylglycinamide formyltransferase and synthetase, Phosphoribosyl-aminoimidazole synthetase (GART). Glucose input to G6P is not shown. Most ATP production in the oocyte is fueled by mitochondrial metabolism of amino acids derived from vitellogenin. Kırlı K, Karaca S, Dehne HJ, et al. A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning. eLife. 2015;4:e11466.
	S2 Fig. Estimation of amount of cytoplasm associated with oil isolated nuclei. A challenge in biochemical studies of nuclear enzymes is that isolated nuclei can be associated with cytoplasmic material. This material can be in the form of cytoplasm adhering to the nuclear exterior and cytoplasm present in invaginations of the nuclear envelope (which form a “nucleoplasmic reticulum”; Drozdz and Vaux, 2017). To our knowledge the amount of such cytoplasmic material associated with nuclei isolated from tissue culture cells has not been estimated. Such an estimate can however be made for the oil-isolated X. laevis oocyte (in the diagram the nucleoplasmic reticulum has been enlarged for clarity). This estimate is based on the known volumes of the nucleus and cytosol of stage VI oocytes (Gurdon and Wickens, 1983), and images in two studies of the X. laevis oocyte. The first reveals the nucleoplasmic reticulum in an equatorial section of a stage VI oocyte (plate 1 in Hausen and Riebesell, 1991; link available at https://www.xenbase.org/entry/doNewsRead.do?id=613). The section was stained with a classical dye that colors the cytosol blue. Penetrations of cytoplasm into the nucleus are evident. Using a high-resolution download of this image, we employed the “point hit” method (Elias and Hyde, 1983) to estimate the volume of the nuclear interior that is cytoplasm. That volume is 1.22 nL. The second image is a transmission electron micrograph showing the rim of cytoplasmic material of an oil-isolated nucleus (Paine et al., 1992). From this image we can estimate the maximum depth of the cytoplasmic rim (0.5 mm) and the corresponding volume of the cytoplasmic rim (0.28 nL). The volume of cytoplasm contributed to oil isolated nuclei by the nucleoplasmic reticulum and cytoplasmic rim is therefore approximately 1.5 nL. Based on this estimate and the concentration of GAPDH reported for oocyte cytoplasm (Kirli et al. (2015), the nuclear concentration of GAPDH would be 4.8135 nM if the only source of the GAPDH was nucleus-associated cytoplasm. The actual nuclear concentration of GAPDH (4851 nM) is however 1000-fold higher than this estimate. Therefore, only approximately 0.01% of GAPDH associated with the oil-isolated nucleus will be contributed as associated cytoplasm. Drozdz MM, Vaux DJ. Shared mechanisms in physiological and pathological nucleoplasmic reticulum formation. Nucleus. 2017;8:34–45. Gurdon JB, Wickens MP. The use of Xenopus oocytes for the expression of cloned genes. Methods Enzymol. 1983;101:370–386. Hausen P, Riebesell M. 1991. The Early Development of Xenopus laevis: An Atlas of the Histology. Springer Verlag;1991. Elias H, Hyde DM. A Guide to Practical Stereology. Karger Publishers;1983. Paine PL, Johnson ME, Lau YT, Tluczek LJ, Miller DS. The oocyte nucleus isolated in oil retains in vivo structure and functions. Biotechniques. 1992;13:238–246. Kırlı K, Karaca S, Dehne HJ, et al. A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning. eLife. 2015;4:e11466.
	S3 Fig. Malate dehydrogenase 1 (MDH1) in nuclear and cytoplasmic homogenates of X. laevis oocytes. Human UniProt link in Kirli et al., 2015: P40925 · MDHC_HUMAN. Malate dehydrogenase activity in homogenates of whole cytoplasms and whole nuclei (whole cell activity was previously characterized by Gill and Schultz (2022), who also reported on the expression of full-length MDH1 in these compartments). In the present study enzyme activity was analyzed as described for whole oocyte homogenates by Gill and Schultz (2022). Gill GS, Schultz MC. Multienzyme activity profiling for evaluation of cell-to-cell variability of metabolic state. FASEB BioAdv. 2022;4:709–723.
	S4 Fig. Isocitrate dehydrogenase 1 (IDH1) in nuclear and cytoplasmic homogenates of X. laevis oocytes. Human UniProt link in Kirli et al., 2015: O75874 · IDHC_HUMAN. (A) Expression. Full-length IDH1 protein is present in the oocyte nucleus and cytoplasm. Proteins were resolved by SDS-PAGE and IDH1 was detected by Western blotting using rabbit polyclonal antibody # ARP54787_P050 (Aviva Systems Biology). Migration of the 50 kDa molecular weight marker is indicated at the left. Antibody dilutions: primary 1:2000 and secondary 1:4000. (B) Activity. Isocitrate dehydrogenase activity is detectable in homogenate of whole cytoplasms and nuclei. Assay performed according to standard method for GAPDH. Final substrate concentrations: 2 mM isocitric acid, 1 mM NADP+. The product detected is NADPH. (C) Activity: dependence on NADP+ concentration. Dependence of the velocity of the isocitrate dehydrogenase reaction in nuclear homogenate on the concentration of added NADP+. Each reaction contained the amount of homogenate equivalent to one nucleus. v was estimated from the 5–18 min data points of progress curves.
	S5 Fig. Glucose-6-phosphate dehydrogenase (G6PD) in nuclear and cytoplasmic homogenates of X. laevis oocytes. Human UniProt link in Kirli et al., 2015: P11413 · G6PD_HUMAN. (A) Expression. Full-length G6PD protein is present in the oocyte nucleus and cytoplasm. Proteins were resolved by SDS-PAGE and G6PD was detected by Western blotting using mouse monoclonal antibody # sc-373886 (Santa Cruz Biotechnology). Migration of the 50 kDa molecular weight marker is indicated at the left. Antibody dilutions: primary 1:2000 and secondary 1:8000. (B) Activity. Glucose-6-phosphate dehydrogenase activity is detectable in homogenate of whole cytoplasms and nuclei. Final substrate concentrations: 1 mM glucose 6-phosphate, NADP+ as shown. The product detected is NADPH.
	S6 Fig. 6-Phosphogluconate dehydrogenase (PGD) in nuclear and cytoplasmic homogenates of X. laevis oocytes. Human UniProt link in Kirli et al., 2015: P52209 · 6PGD_HUMAN. (A) Expression. Full-length PGD protein is present in the oocyte nucleus and cytoplasm. Proteins were resolved by SDS-PAGE and PGD was detected by Western blotting using mouse monoclonal antibody # sc-398977 (Santa Cruz Biotechnology). Migration of the 50 kDa molecular weight marker is indicated at the left. Antibody dilutions: primary 1:2000 and secondary 1:8000. (B) Activity. Phosphogluconate dehydrogenase activity is detectable in homogenate of whole cytoplasms and nuclei. Final substrate concentrations: 0.5 mM 6-phosphogluconic acid, trisodium salt; 1 mM NADP+. The product detected is NADPH. (C) Activity–dependence of the phosphogluconate dehydrogenase reaction in nuclear homogenate on the concentration of added NADP+.
	S7 Fig. Individual nuclei contain the active forms of three enzymes that interconvert NADP+ and NADPH. (A) Summary of method. (B) Activity. Each of three individual nuclei supports the activity of IDH1, G6PD and PGD. The nuclei were from oocytes of the same ovary. Assays as in S4–S6 Figs.
	S8 Fig. Enolase α (ENO1) in nuclear and cytoplasmic homogenates of X. laevis oocytes. Human UniProt link in Kirli et al., 2015: P06733 · ENOA_HUMAN. (A) Expression. Full-length ENO1 protein is present in the oocyte nucleus and cytoplasm. Proteins were resolved by SDS-PAGE and ENO1 was detected by Western blotting using mouse monoclonal antibody # sc-271384 (Santa Cruz Biotechnology). Migration of the 50 kDa molecular weight marker is indicated at the left. Antibody dilutions: primary 1:200 and secondary 1:8000. (B) Activity. Enolase activity in homogenate of whole cytoplasms and the low-speed supernatant of nuclear homogenate. Activity in samples from oil-dissected oocytes was assessed using a colorimetric assay kit (Sigma # MAK178). In this detection system, phosphoenolpyruvate synthesis is enzymatically coupled to the production of resofurin, which has an absorbance peak of 570 nm. The reactions were performed without dithiothreitol because this reagent prevents resofurin production. Nuclear supernatant was prepared as described for Fig 5C.
	S9 Fig. Pyruvate kinase M2 (PKM2) in nuclear and cytoplasmic homogenates of X. laevis oocytes. Human UniProt link in Kirli et al., 2015: P14618 · KPYM_HUMAN. (A) Expression. Full-length PKM2 protein is present in the oocyte nucleus and cytoplasm. Proteins were resolved by SDS-PAGE and PKM2 was detected by Western blotting using rabbit polyclonal antibody # ab137791 (Abcam). Monomeric PKM2 has an expected molecular weight of 57309 Da. Migration of the 75 kDa molecular weight marker is indicated on the right. Antibody dilutions: primary 1:2000 and secondary 1:8000. (B) Oligomerization state. PKM2 in the oocyte nucleus exists mainly as a homotetramer. PKM2 protein in nuclear homogenate was resolved by native PAGE, then detected as in A. Migration of Precision Plus molecular weight markers (Bio-Rad) is on the right. PKM2 forms a homotetramer with high pyruvate kinase activity and a dimer without this activity (Gao et al., 2013). In X. laevis the predicted molecular weights of the dimer and tetramer are 114618 and 229239 Da respectively. The band pattern revealed here is consistent with high nuclear expression of tetrameric, metabolically active PKM2. This interpretation is supported by the results in (C). Native PAGE was performed as in Sen et al. (2016). The 2x loading buffer contained 200 mM KCl. Antibody dilutions: primary 1:2000, secondary 1:5000. (C) Activity. Pyruvate kinase activity in homogenates of whole cytoplasms and nuclei (Dworkin et al. (1987) previously characterized whole cell activity). In this enzyme-coupled assay pyruvate synthesized by PKM2 is used by lactate dehydrogenase in a reaction that consumes added NADH (NADH + pyruvate → lactate + NAD+). The coupled reaction driven by PKM2 in the presence of added phosphoenolpyruvate and ADP is supported by LDHA/B resident in the oocyte cytoplasm and nucleus (dashed traces) and is stimulated by addition of exogenous purified LDH (solid traces). Final substrate concentrations: 1.5 mM phosphoenolpyruvate, 2 mM ADP, 0.2 mM NADH. Exogenous LDH is Type III from bovine heart (Sigma # L2625). It was used at 0.4 U/40 μL reaction. Gao X, Wang H, Yang JJ, Chen J, Jie J, Li L, Zhang Y, Liu ZR. Reciprocal regulation of protein kinase and pyruvate kinase activities of pyruvate kinase M2 by growth signals. J Biol Chem. 2013;288:15971–15979. Sen S, Deshmane SL, Kaminski R, Amini S, Datta PK. Non-Metabolic Role of PKM2 in Regulation of the HIV-1 LTR. J Cell Physiol. 2017;232:517–525. Dworkin MB, Segil N, Dworkin-Rastl E. Pyruvate kinase isozymes in oocytes and embryos from the frog Xenopus laevis. Comp Biochem Physiol B. 1987;88:743–749.
	S10 Fig. Lactate dehydrogenase A and B chain (LDHA, LDHB) in nuclear and cytoplasmic homogenates of X. laevis oocytes. LDHA and LDHB are expressed in both the nucleus and cytoplasm, with LDHB predominating (Kirli et al., 2015). Human UniProt links in Kirli et al., 2015: P00338 · LDHA_HUMAN, P07195 · LDHB_HUMAN. (A) Activity–pH dependence. Whole oocyte LDH has been characterized previously (Claycomb and Villee, 1971). Enzyme activity is optimal at pH 10 (Nielands, 1955; Vanderlinde, 1985). In the present study whole cytoplasmic and nuclear homogenate was assayed in standard HR buffer at pH 7.4 (10 mM potassium phosphate) and HR buffer at pH 10 (75.2 mM glycine-NaOH). Activity was observed in samples of both compartments at pH 7.4 and 10, and is clearly higher at pH 10 in both compartments. Final substrate concentrations: 50 mM L-lactate (lithium salt), 5 mM NAD+. (B) Activity–dependence on homogenate amount at pH 10. Claycomb WC, Villee CA. Lactate dehydrogenase isozymes of Xenopus laevis: factors affecting their appearance during early development. Dev Biol. 1971;24:413–427. Neilands JB. Lactic dehydrogenase of heart muscle. Meth Enzymol. 1955;1:449–454. Vanderlinde RE. Measurement of total lactate dehydrogenase activity. Annals Clin Lab Sci. 1985;15:13–31.
	S11 Fig. Raw images.

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