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Serine is a natural ligand and allosteric activator of pyruvate kinase M2

A Corrigendum to this article was published on 17 April 2013

This article has been updated

Abstract

Cancer cells exhibit several unique metabolic phenotypes that are critical for cell growth and proliferation1. Specifically, they overexpress the M2 isoform of the tightly regulated enzyme pyruvate kinase (PKM2), which controls glycolytic flux, and are highly dependent on de novo biosynthesis of serine and glycine2. Here we describe a new rheostat-like mechanistic relationship between PKM2 activity and serine biosynthesis. We show that serine can bind to and activate human PKM2, and that PKM2 activity in cells is reduced in response to serine deprivation. This reduction in PKM2 activity shifts cells to a fuel-efficient mode in which more pyruvate is diverted to the mitochondria and more glucose-derived carbon is channelled into serine biosynthesis to support cell proliferation.

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Figure 1: Characterization of PKM-silenced HCT116 cells.
Figure 2: The effect of PKM silencing on glycolytic flux.
Figure 3: Serine and glycine deprivation changes glucose metabolism.
Figure 4: Serine is an allosteric activator of PKM2.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the PKM2 crystal structures have been deposited in the Protein Data Bank (PDB) under accession code 4B2D.

Change history

  • 14 November 2012

    A url at the end of the Methods section was corrected.

  • 17 April 2013

    Nature 491, 458–462 (2012); doi:10.1038/nature11540 In Fig. 1a of this Letter, the western blot originally published in the PKM2 panel was a re-probe of the blot used in the PKM1 panel and the signal picked up was from the first antibody (PKM1) and not from PKM2. We have repeated the experiment on three different membranes with the antibodies used in the original paper for PKM1, PKM2 and total PKM, using actin as the loading control (Fig.

References

  1. 1

    Tennant, D. A., Duran, R. V. & Gottlieb, E. Targeting metabolic transformation for cancer therapy. Nature Rev. Cancer 10, 267–277 (2010)

    CAS  Article  Google Scholar 

  2. 2

    Chaneton, B. & Gottlieb, E. Rocking cell metabolism: revised functions of the key glycolytic regulator PKM2 in cancer. Trends Biochem. Sci. 37, 309–316 (2012)

    CAS  Article  Google Scholar 

  3. 3

    Christofk, H. R. et al. The M2 splice isoform of pyruvate kinase is important for cancer metabolism and tumour growth. Nature 452, 230–233 (2008)

    ADS  CAS  Article  Google Scholar 

  4. 4

    Altenberg, B. & Greulich, K. O. Genes of glycolysis are ubiquitously overexpressed in 24 cancer classes. Genomics 84, 1014–1020 (2004)

    CAS  Article  Google Scholar 

  5. 5

    Mazurek, S., Boschek, C. B., Hugo, F. & Eigenbrodt, E. Pyruvate kinase type M2 and its role in tumor growth and spreading. Semin. Cancer Biol. 15, 300–308 (2005)

    CAS  Article  Google Scholar 

  6. 6

    Yamada, K. & Noguchi, T. Nutrient and hormonal regulation of pyruvate kinase gene expression. Biochem. J. 337, 1–11 (1999)

    CAS  Article  Google Scholar 

  7. 7

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

    ADS  CAS  Article  Google Scholar 

  8. 8

    Locasale, J. W. et al. Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis. Nature Genet. 43, 869–874 (2011)

    CAS  Article  Google Scholar 

  9. 9

    Pollari, S. et al. Enhanced serine production by bone metastatic breast cancer cells stimulates osteoclastogenesis. Breast Cancer Res. Treat. 125, 421–430 (2011)

    CAS  Article  Google Scholar 

  10. 10

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

    ADS  CAS  Article  Google Scholar 

  11. 11

    Dombrauckas, J. D., Santarsiero, B. D. & Mesecar, A. D. Structural basis for tumor pyruvate kinase M2 allosteric regulation and catalysis. Biochemistry 44, 9417–9429 (2005)

    CAS  Article  Google Scholar 

  12. 12

    Hitosugi, T. et al. Tyrosine phosphorylation inhibits PKM2 to promote the Warburg effect and tumor growth. Sci. Signal. 2, ra73 (2009)

    Article  Google Scholar 

  13. 13

    Christofk, H. R., Vander Heiden, M. G., Wu, N., Asara, J. M. & Cantley, L. C. Pyruvate kinase M2 is a phosphotyrosine-binding protein. Nature 452, 181–186 (2008)

    ADS  CAS  Article  Google Scholar 

  14. 14

    Ashizawa, K., Willingham, M. C., Liang, C. M. & Cheng, S. Y. In vivo regulation of monomer-tetramer conversion of pyruvate kinase subtype M2 by glucose is mediated via fructose 1,6-bisphosphate. J. Biol. Chem. 266, 16842–16846 (1991)

    CAS  PubMed  Google Scholar 

  15. 15

    Spellman, C. M. & Fottrell, P. F. Similarities between pyruvate kinase from human placenta and tumours. FEBS Lett. 37, 281–284 (1973)

    CAS  Article  Google Scholar 

  16. 16

    Eigenbrodt, E., Leib, S., Kramer, W., Friis, R. R. & Schoner, W. Structural and kinetic differences between the M2 type pyruvate kinases from lung and various tumors. Biomed. Biochim. Acta 42, S278–S282 (1983)

    CAS  PubMed  Google Scholar 

  17. 17

    Ye, J. et al. Pyruvate kinase M2 promotes de novo serine synthesis to sustain mTORC1 activity and cell proliferation. Proc. Natl Acad. Sci. USA 109, 6904–6909 (2012)

    ADS  CAS  Article  Google Scholar 

  18. 18

    Davies, T. G. & Tickle, I. J. Fragment screening using X-ray crystallography. Top. Curr. Chem. 317, 33–59 (2012)

    CAS  Article  Google Scholar 

  19. 19

    Allali-Hassani, A. et al. A survey of proteins encoded by non-synonymous single nucleotide polymorphisms reveals a significant fraction with altered stability and activity. Biochem. J. 424, 15–26 (2009)

    CAS  Article  Google Scholar 

  20. 20

    Medina, M. A., Marquez, J. & Nunez de Castro, I. Interchange of amino acids between tumor and host. Biochem. Med. Metab. Biol. 48, 1–7 (1992)

    CAS  Article  Google Scholar 

  21. 21

    Márquez, J., Sanchez-Jimenez, F., Medina, M. A., Quesada, A. R. & Nunez de Castro, I. Nitrogen metabolism in tumor bearing mice. Arch. Biochem. Biophys. 268, 667–675 (1989)

    Article  Google Scholar 

  22. 22

    Mattevi, A., Bolognesi, M. & Valentini, G. The allosteric regulation of pyruvate kinase. FEBS Lett. 389, 15–19 (1996)

    CAS  Article  Google Scholar 

  23. 23

    Anastasiou, D. et al. Inhibition of pyruvate kinase M2 by reactive oxygen species contributes to cellular antioxidant responses. Science 334, 1278–1283 (2011)

    ADS  CAS  Article  Google Scholar 

  24. 24

    de Koning, T. J. et al. l-serine in disease and development. Biochem. J. 371, 653–661 (2003)

    CAS  Article  Google Scholar 

  25. 25

    Luo, B., Groenke, K., Takors, R., Wandrey, C. & Oldiges, M. Simultaneous determination of multiple intracellular metabolites in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle by liquid chromatography-mass spectrometry. J. Chromatogr. A 1147, 153–164 (2007)

    CAS  Article  Google Scholar 

  26. 26

    Salituro, F. G. & Saunders, J. O. Therapeutic compositions and related methods of use. PTC patent application WO/2010/118063. (2010)

  27. 27

    Boxer, M. B. et al. Evaluation of substituted N,N′-diarylsulfonamides as activators of the tumor cell specific M2 isoform of pyruvate kinase. J. Med. Chem. 53, 1048–1055 (2010)

    CAS  Article  Google Scholar 

  28. 28

    Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

    Article  Google Scholar 

  29. 29

    Mooij, W. T. et al. Automated protein-ligand crystallography for structure-based drug design. Chem Med Chem 1, 827–838 (2006)

    CAS  Article  Google Scholar 

  30. 30

    Brünger, A. T. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472–475 (1992)

    ADS  Article  Google Scholar 

  31. 31

    Diederichs, K. & Karplus, P. A. Improved R factors for diffraction data analysis in macromolecular crystallography. Nature Struct. Biol. 4, 269–275 (1997)

    CAS  Article  Google Scholar 

  32. 32

    Weiss, M. S. & Hilgenfeld, R. On the use of the merging R factor as a quality indicator for X-ray data. J. Appl. Crystallogr. 30, 203–205 (1997)

    CAS  Article  Google Scholar 

  33. 33

    Weiss, M. S. Global indicators of X-ray data quality. J. Appl. Crystallogr. 34, 130–135 (2001)

    CAS  Article  Google Scholar 

  34. 34

    Pedrioli, P. G. et al. A common open representation of mass spectrometry data and its application to proteomics research. Nature Biotechnol. 22, 1459–1466 (2004)

    CAS  Article  Google Scholar 

  35. 35

    Kessner, D., Chambers, M., Burke, R., Agus, D. & Mallick, P. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24, 2534–2536 (2008)

    CAS  Article  Google Scholar 

  36. 36

    Tautenhahn, R., Bottcher, C. & Neumann, S. Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformatics 9, 504 (2008)

    Article  Google Scholar 

  37. 37

    Smith, C. A., Want, E. J., O’Maille, G., Abagyan, R. & Siuzdak, G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem. 78, 779–787 (2006)

    CAS  Article  Google Scholar 

  38. 38

    Fernandez, C. A., Des Rosiers, C., Previs, S. F., David, F. & Brunengraber, H. Correction of 13C mass isotopomer distributions for natural stable isotope abundance. J. Mass Spectrom. 31, 255–262 (1996)

    ADS  CAS  Article  Google Scholar 

  39. 39

    Scheltema, R. A., Jankevics, A., Jansen, R. C., Swertz, M. A. & Breitling, R. PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis. Anal. Chem. 83, 2786–2793 (2011)

    CAS  Article  Google Scholar 

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Acknowledgements

The work performed at the Beatson Institute for Cancer Research was supported by Cancer Research UK. We thank D. Sumpton for technical support with two-dimensional gel electrophoresis and N. Thompson, N. Wallis and M. Jones for comments provided during manuscript preparation. We would also like to thank D. M. Sabatini for the Scramble shRNA plasmid used as a control (shCntrla) and the Structural Genomics Consortium for providing us with the PKM2 expression plasmid from their collection. We thank A. King for editorial work and S. Tardito for graphical help.

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M.O. and E.G. conceived the project and wrote the manuscript with the help of B.C., P.H. and C.F. L.Z., B.C. and C.F. performed the LC–MS assay and analysed the raw data. A.C. and A.J. analysed the LC–MS data and identified the different isotopomers of each metabolite. A.C.L.M. performed the in vitro enzymatic activity, J.E.C. performed the ITC, M.O. generated the point mutant constructs, purified the proteins and solved the crystal structure. F.P.H. performed the LC–MS validation of the point mutant constructs. O.D.K.M. and K.H.V. performed, analysed and discussed the long-term serine and glycine starvation experiment. B.C. and P.H. generated and characterized the cell lines and performed all other experiments and data analysis. All the authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to Marc O’Reilly or Eyal Gottlieb.

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E.G. is a consultant of Astex Pharmaceuticals.

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Chaneton, B., Hillmann, P., Zheng, L. et al. Serine is a natural ligand and allosteric activator of pyruvate kinase M2. Nature 491, 458–462 (2012). https://doi.org/10.1038/nature11540

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