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Bisphosphoglycerate mutase controls serine pathway flux via 3-phosphoglycerate

Nature Chemical Biology volume 13, pages 1081–1087 (2017)Cite this article

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Abstract

Lower glycolysis involves a series of reversible reactions, which interconvert intermediates that also feed anabolic pathways. 3-phosphoglycerate (3-PG) is an abundant lower glycolytic intermediate that feeds serine biosynthesis via the enzyme phosphoglycerate dehydrogenase, which is genomically amplified in several cancers. Phosphoglycerate mutase 1 (PGAM1) catalyzes the isomerization of 3-PG into the downstream glycolytic intermediate 2-phosphoglycerate (2-PG). PGAM1 needs to be histidine phosphorylated to become catalytically active. We show that the primary PGAM1 histidine phosphate donor is 2,3-bisphosphoglycerate (2,3-BPG), which is made from the glycolytic intermediate 1,3-bisphosphoglycerate (1,3-BPG) by bisphosphoglycerate mutase (BPGM). When BPGM is knocked out, 1,3-BPG can directly phosphorylate PGAM1. In this case, PGAM1 phosphorylation and activity are decreased, but nevertheless sufficient to maintain normal glycolytic flux and cellular growth rate. 3-PG, however, accumulates, leading to increased serine synthesis. Thus, one biological function of BPGM is controlling glycolytic intermediate levels and thereby serine biosynthetic flux.

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Figure 1: BPGM deletion diminishes cellular 2,3-BPG and PGAM1 phosphorylation.
Figure 2: BPGM deletion does not affect cell growth or glycolytic flux.
Figure 3: 1,3-BPG is an alternative source of PGAM1 phosphorylation.
Figure 4: BPGM deletion results in higher serine de novo synthesis flux.
Figure 5: Effect of BPGM disruption on lower glycolysis.

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References

  1. Vander Heiden, M.G., Cantley, L.C. & Thompson, C.B. Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science 324, 1029–1033 (2009).

    Article  CAS  Google Scholar 

  2. Hitosugi, T. et al. Phosphoglycerate mutase 1 coordinates glycolysis and biosynthesis to promote tumor growth. Cancer Cell 22, 585–600 (2012).

    Article  CAS  Google Scholar 

  3. Possemato, R. et al. Functional genomics reveal that the serine synthesis pathway is essential in breast cancer. Nature 476, 346–350 (2011).

    Article  CAS  Google Scholar 

  4. Labuschagne, C.F., van den Broek, N.J., Mackay, G.M., Vousden, K.H. & Maddocks, O.D. Serine, but not glycine, supports one-carbon metabolism and proliferation of cancer cells. Cell Rep. 7, 1248–1258 (2014).

    Article  CAS  Google Scholar 

  5. Mattaini, K.R. et al. An epitope tag alters phosphoglycerate dehydrogenase structure and impairs ability to support cell proliferation. Cancer Metab. 3, 5 (2015).

    Article  Google Scholar 

  6. Samanta, D. et al. PHGDH expression is required for mitochondrial redox homeostasis, breast cancer stem cell maintenance, and lung metastasis. Cancer Res. 76, 4430–4442 (2016).

    Article  CAS  Google Scholar 

  7. Fothergill-Gilmore, L.A. & Watson, H.C. The phosphoglycerate mutases. Adv. Enzymol. 62, 227–313 (1989).

    CAS  PubMed  Google Scholar 

  8. Rose, Z.B. The enzymology of 2,3-bisphosphoglycerate. Adv. Enzymol. 51, 211–253 (1980).

    CAS  PubMed  Google Scholar 

  9. Nelson, D.L., Lehninger, A.L. & Cox, M.M. Lehninger Principles of Biochemistry (W.H. Freeman, New York, 2008).

  10. Sutherland, E.W., Posternak, T.Z. & Cori, C.F. The mechanism of action of phosphoglucomutase and phosphoglyceric acid mutase. J. Biol. Chem. 179, 501 (1949).

    CAS  PubMed  Google Scholar 

  11. Rose, Z.B. The purification and properties of diphosphoglycerate mutase from human erythrocytes. J. Biol. Chem. 243, 4810–4820 (1968).

    CAS  PubMed  Google Scholar 

  12. Narita, H., Yanagawa, S., Sasaki, R. & Chiba, H. Induction of 2,3-bisphosphoglycerate synthase in Friend leukemia cells. Biochem. Biophys. Res. Commun. 103, 90–96 (1981).

    Article  CAS  Google Scholar 

  13. Joulin, V. et al. Isolation and characterization of the human 2,3-bisphosphoglycerate mutase gene. J. Biol. Chem. 263, 15785–15790 (1988).

    CAS  PubMed  Google Scholar 

  14. Chiba, H. & Sasaki, R. Functions, of 2,3-bisphosphoglycerate and its metabolism. Curr. Top. Cell. Regul. 14, 75–116 (1978).

    Article  CAS  Google Scholar 

  15. Sasaki, R., Ikura, K., Narita, H., Yanagawa, S.-i. & Chiba, H. 2,3-bisphosphoglycerate in erythroid cells. Trends Biochem. Sci. 7, 140–142 (1982).

    Article  CAS  Google Scholar 

  16. Rigden, D.J., Walter, R.A., Phillips, S.E. & Fothergill-Gilmore, L.A. Sulphate ions observed in the 2.12 A structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism. J. Mol. Biol. 286, 1507–1517 (1999).

    Article  CAS  Google Scholar 

  17. White, M.F. & Fothergill-Gilmore, L.A. Mutase versus synthase: the phosphoglycerate mutase family studied by protein engineering. Biochem. Soc. Trans. 18, 257 (1990).

    Article  CAS  Google Scholar 

  18. Hitosugi, T. et al. Tyr26 phosphorylation of PGAM1 provides a metabolic advantage to tumours by stabilizing the active conformation. Nat. Commun. 4, 1790 (2013).

    Article  Google Scholar 

  19. Kee, J.M., Villani, B., Carpenter, L.R. & Muir, T.W. Development of stable phosphohistidine analogues. J. Am. Chem. Soc. 132, 14327–14329 (2010).

    Article  CAS  Google Scholar 

  20. Kee, J.M., Oslund, R.C., Perlman, D.H. & Muir, T.W. A pan-specific antibody for direct detection of protein histidine phosphorylation. Nat. Chem. Biol. 9, 416–421 (2013).

    Article  CAS  Google Scholar 

  21. Oslund, R.C. et al. A phosphohistidine proteomics strategy based on elucidation of a unique gas-phase phosphopeptide fragmentation mechanism. J. Am. Chem. Soc. 136, 12899–12911 (2014).

    Article  CAS  Google Scholar 

  22. Kee, J.M., Oslund, R.C., Couvillon, A.D. & Muir, T.W. A second-generation phosphohistidine analog for production of phosphohistidine antibodies. Org. Lett. 17, 187–189 (2015).

    Article  CAS  Google Scholar 

  23. Pritlove, D.C., Gu, M., Boyd, C.A., Randeva, H.S. & Vatish, M. Novel placental expression of 2,3-bisphosphoglycerate mutase. Placenta 27, 924–927 (2006).

    Article  CAS  Google Scholar 

  24. Ran, F.A. et al. Genome engineering using the CRISPR-Cas9 system. Nat. Protoc. 8, 2281–2308 (2013).

    Article  CAS  Google Scholar 

  25. Johnson, C.M. & Price, N.C. Denaturation and renaturation of the monomeric phosphoglycerate mutase from Schizosaccharomyces pombe. Biochem. J. 245, 525–530 (1987).

    Article  CAS  Google Scholar 

  26. Vander Heiden, M.G. et al. Evidence for an alternative glycolytic pathway in rapidly proliferating cells. Science 329, 1492–1499 (2010).

    Article  CAS  Google Scholar 

  27. Moellering, R.E. & Cravatt, B.F. Functional lysine modification by an intrinsically reactive primary glycolytic metabolite. Science 341, 549–553 (2013).

    Article  CAS  Google Scholar 

  28. Negelein, E. Synthesis, determination, analysis, and properties of 1,3-diphosphoglyceric acid. in Methods in Enzymology 3, 216–220 (1957).

    Article  CAS  Google Scholar 

  29. Han, C.H. & Rose, Z.B. Active site phosphohistidine peptides from red cell bisphosphoglycerate synthase and yeast phosphoglycerate mutase. J. Biol. Chem. 254, 8836–8840 (1979).

    CAS  PubMed  Google Scholar 

  30. Wang, Y. et al. Seeing the process of histidine phosphorylation in human bisphosphoglycerate mutase. J. Biol. Chem. 281, 39642–39648 (2006).

    Article  CAS  Google Scholar 

  31. Fuhs, S.R. et al. Monoclonal 1- and 3-phosphohistidine antibodies: new tools to study histidine phosphorylation. Cell 162, 198–210 (2015).

    Article  CAS  Google Scholar 

  32. Lu, W., Kimball, E. & Rabinowitz, J.D. A high-performance liquid chromatography-tandem mass spectrometry method for quantitation of nitrogen-containing intracellular metabolites. J. Am. Soc. Mass Spectrom. 17, 37–50 (2006).

    Article  CAS  Google Scholar 

  33. Rose, Z.B. & Dube, S. Rates of phosphorylation and dephosphorylation of phosphoglycerate mutase and bisphosphoglycerate synthase. J. Biol. Chem. 251, 4817–4822 (1976).

    CAS  PubMed  Google Scholar 

  34. Rose, Z.B. & Dube, S. Phosphoglycerate mutase. Kinetics and effects of salts on the mutase and bisphosphoglycerate phosphatase activities of the enzyme from chicken breast muscle. J. Biol. Chem. 253, 8583–8592 (1978).

    CAS  PubMed  Google Scholar 

  35. Samanta, D. & Semenza, G.L. Serine synthesis helps hypoxic cancer stem cells regulate redox. Cancer Res. 76, 6458–6462 (2016).

    Article  CAS  Google Scholar 

  36. Melamud, E., Vastag, L. & Rabinowitz, J.D. Metabolomic analysis and visualization engine for LC–MS data. Anal. Chem. 82, 9818–9826 (2010).

    Article  CAS  Google Scholar 

  37. Clasquin, M.F., Melamud, E. & Rabinowitz, J.D. LC–MS data processing with MAVEN: a metabolomic analysis and visualization engine. Curr. Protoc. Bioinformatics 37, 14.11 (2011).

    Google Scholar 

  38. Shevchenko, A., Tomas, H., Havlis, J., Olsen, J.V. & Mann, M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 1, 2856–2860 (2006).

    Article  CAS  Google Scholar 

  39. Rappsilber, J., Ishihama, Y. & Mann, M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 75, 663–670 (2003).

    Article  CAS  Google Scholar 

  40. David, Y., Vila-Perelló, M., Verma, S. & Muir, T.W. Chemical tagging and customizing of cellular chromatin states using ultrafast trans-splicing inteins. Nat. Chem. 7, 394–402 (2015).

    Article  CAS  Google Scholar 

  41. Brinkman, E.K., Chen, T., Amendola, M. & van Steensel, B. Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res. 42, e168 (2014).

    Article  Google Scholar 

  42. Sanjana, N.E., Shalem, O. & Zhang, F. Improved vectors and genome-wide libraries for CRISPR screening. Nat. Methods 11, 783–784 (2014).

    Article  CAS  Google Scholar 

  43. Park, J.O. et al. Metabolite concentrations, fluxes and free energies imply efficient enzyme usage. Nat. Chem. Biol. 12, 482–489 (2016).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank current and former members of the Muir and Rabinowitz laboratories for helpful discussions during the preparation of this manuscript and V. Suri of Raze Therapeutics for technical help. This work was funded by the US National Institutes of Health for T.W.M. (5R01GM095880) and J.D.R. (R01 CA163591 and P30DK019525), the US Department of Energy for J.D.R. (DE-SC0012461), Stand Up to Cancer for J.D.R. (SU2C-AACR-DT0509), and the Brewster Foundation and Breast Cancer Research Foundation for Y.K. R.C.O. and J.-M.K. were supported by postdoctoral fellowships from the National Institutes of Health Research Service Award (1F32CA167901) and Damon Runyon Cancer Research Foundation (DRG-2005-09), respectively.

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Author notes

  1. Rob C Oslund

    Present address: Cambridge Exploratory Science Center, Merck Research Laboratories, Cambridge, Massachusetts, USA

  2. Xiaoyang Su

    Present address: Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey, USA

  3. Jung-Min Kee

    Present address: Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea

  4. Yael David

    Present address: Zuckerman Research Center, Memorial Sloan-Kettering Cancer Center, New York, New York, USA

  5. Boyuan Wang

    Present address: Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

  6. Rob C Oslund, Xiaoyang Su and Michael Haugbro: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Chemistry, Princeton University, Princeton, New Jersey, USA

    Rob C Oslund, Michael Haugbro, Jung-Min Kee, Yael David, Boyuan Wang, Eva Ge, David H Perlman, Tom W Muir & Joshua D Rabinowitz

  2. Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA

    Xiaoyang Su & Joshua D Rabinowitz

  3. Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA

    Mark Esposito & Yibin Kang

  4. Graduate Program, The Rockefeller University, New York, New York, USA

    Boyuan Wang

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Contributions

R.C.O. designed experiments, prepared materials, analyzed data, interpreted results, generated HEK 293T and HCT116 knockout cell lines, and conducted experiments for metabolomic data analysis, western blotting, cell growth measurements, and in vitro phosphorylation analysis. X.S. designed experiments, prepared materials, analyzed data, interpreted results, designed primers and performed all DNA sequencing analysis for BPGM knockout experiments, conducted all metabolomic experiments and data analysis, prepared 1,3-BPG, and derived and conducted all serine flux calculations. M.H. designed experiments, analyzed data, interpreted results, performed cell assays for metabolomic data analysis, performed western blots for BPGM rescue and PGAM1 knockdown experiments, and performed cell growth measurements of knockout cells with serine/glycine or oxygen depletion. J.-M.K. designed experiments, analyzed data, interpreted results, and performed western blot analysis of BPGM protein levels. M.E. generated MDA-MB-231 knockout cells, prepared PGAM1 knockdown cells, and designed, performed, and analyzed mouse xenograft experiments. Y.D. designed and conducted RNA-seq analysis of wild-type and knockout HEK 293T cells. B.W. designed and conducted 32P-labeling experiments, analyzed data, and interpreted results of metabolomic experiments. E.G. performed phosphorylated PGAM1 western blot analysis from multiple cell lines. D.H.P. performed LC–MS-based proteomic analysis of phosphorylated PGAM1, analyzed data, and interpreted results. T.W.M. designed experiments, analyzed data, and interpreted results. J.D.R. designed experiments, analyzed data, and interpreted results. R.C.O., X.S., M.H., T.W.M., and J.D.R. wrote the manuscript with contributions from all authors.

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Correspondence to Tom W Muir or Joshua D Rabinowitz.

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Oslund, R., Su, X., Haugbro, M. et al. Bisphosphoglycerate mutase controls serine pathway flux via 3-phosphoglycerate. Nat Chem Biol 13, 1081–1087 (2017). https://doi.org/10.1038/nchembio.2453

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