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Photo-lysine captures proteins that bind lysine post-translational modifications

Nature Chemical Biology volume 12, pages 70–72 (2016)Cite this article

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Abstract

Post-translational modifications (PTMs) have key roles in regulating protein-protein interactions in living cells. However, it remains a challenge to identify these PTM-mediated interactions. Here we develop a new lysine-based photo-reactive amino acid, termed photo-lysine. We demonstrate that photo-lysine, which is readily incorporated into proteins by native mammalian translation machinery, can be used to capture and identify proteins that recognize lysine PTMs, including 'readers' and 'erasers' of histone modifications.

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Figure 1: Design of photo-lysine to mediate photo-cross-linking to capture readers and erasers of histone PTMs in vitro.
Figure 2: Photo-lysine enables identification of histone- and chromatin-binding proteins.

References

  1. Walsh, C.T. Posttranslational Modifications of Proteins: Expanding Nature's Inventory (Roberts and Co. Publishers, Greenwood Village, Colorado, USA, 2006).

  2. Pham, N.D., Parker, R.B. & Kohler, J.J. Curr. Opin. Chem. Biol. 17, 90–101 (2013).

    Article  CAS  Google Scholar 

  3. Suchanek, M., Radzikowska, A. & Thiele, C. Nat. Methods 2, 261–267 (2005).

    Article  CAS  Google Scholar 

  4. Lan, F. et al. Nature 448, 718–722 (2007).

    Article  CAS  Google Scholar 

  5. Musrati, R.A., Kollárová, M., Mernik, N. & Mikulásová, D. Gen. Physiol. Biophys. 17, 193–210 (1998).

    CAS  PubMed  Google Scholar 

  6. Nemoto, T., Ohara-Nemoto, Y., Ota, M., Takagi, T. & Yokoyama, K. Eur. J. Biochem. 233, 1–8 (1995).

    Article  CAS  Google Scholar 

  7. Bukau, B. & Horwich, A.L. Cell 92, 351–366 (1998).

    Article  CAS  Google Scholar 

  8. Walker, J.R., Corpina, R.A. & Goldberg, J. Nature 412, 607–614 (2001).

    Article  CAS  Google Scholar 

  9. Roth, S.Y., Denu, J.M. & Allis, C.D. Annu. Rev. Biochem. 70, 81–120 (2001).

    Article  CAS  Google Scholar 

  10. Wang, H. et al. Mol. Cell 8, 1207–1217 (2001).

    Article  CAS  Google Scholar 

  11. Nishioka, K. et al. Genes Dev. 16, 479–489 (2002).

    Article  CAS  Google Scholar 

  12. Houtkooper, R.H., Pirinen, E. & Auwerx, J. Nat. Rev. Mol. Cell Biol. 13, 225–238 (2012).

    Article  CAS  Google Scholar 

  13. Li, Y. et al. Cell 159, 558–571 (2014).

    Article  CAS  Google Scholar 

  14. Tippmann, E.M., Liu, W., Summerer, D., Mack, A.V. & Schultz, P.G. ChemBioChem 8, 2210–2214 (2007).

    Article  CAS  Google Scholar 

  15. Chou, C.J., Uprety, R., Davis, L., Chin, J.W. & Deiters, A. Chem. Sci. (Camb.) 2, 480–483 (2011).

    Article  CAS  Google Scholar 

  16. Zhang, M. et al. Nat. Chem. Biol. 7, 671–677 (2011).

    Article  CAS  Google Scholar 

  17. Muir, T.W. Annu. Rev. Biochem. 72, 249–289 (2003).

    Article  CAS  Google Scholar 

  18. Chin, J.W. Annu. Rev. Biochem. 83, 379–408 (2014).

    Article  CAS  Google Scholar 

  19. Yang, Y.Y., Grammel, M., Raghavan, A.S., Charron, G. & Hang, H.C. Chem. Biol. 17, 1212–1222 (2010).

    Article  CAS  Google Scholar 

  20. Du, J. et al. Science 334, 806–809 (2011).

    Article  CAS  Google Scholar 

  21. Hubbard, B.P. et al. Science 339, 1216–1219 (2013).

    Article  CAS  Google Scholar 

  22. Bao, X. et al. eLife 3, e02999 (2014).

    Article  Google Scholar 

  23. Yang, T.P., Liu, Z. & Li, X.D. Chem. Sci. (Camb.) 6, 1011–1017 (2015).

    Article  CAS  Google Scholar 

  24. Filippakopoulos, P. et al. Cell 149, 214–231 (2012).

    Article  CAS  Google Scholar 

  25. Couture, J.F., Collazo, E., Hauk, G. & Trievel, R.C. Nat. Struct. Mol. Biol. 13, 140–146 (2006).

    Article  CAS  Google Scholar 

  26. Shechter, D., Dormann, H.L., Allis, C.D. & Hake, S.B. Nat. Protoc. 2, 1445–1457 (2007).

    Article  CAS  Google Scholar 

  27. Goldberg, D. et al. J. Proteome Res. 6, 3995–4005 (2007).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We acknowledge support from the Hong Kong Research Grants Council General Research Fund (GRF 17303114, GRF 17127915), Early Career Scheme (ECS) (HKU 709813P ) and Collaborative Research Fund (CRF C7037-14G). We acknowledge the University of Hong Kong for an e-SRT on Integrative Biology and grants from the Seed Funding Program (201411159101, 201409160027, 201311159007 and 201309176090). We thank X. Li for discussion. We thank E. Verdin (University of California, San Francisco), Q. Hao (The University of Hong Kong), H. Li (Tsinghua University), R.C. Trievel (University of Michigan), K. Guan (Fudan University) and H. Sun (City University of Hong Kong) for providing the plasmids.

Author information

Author notes

  1. Tangpo Yang and Xiao-Meng Li: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong, China

    Tangpo Yang, Xiao-Meng Li, Xiucong Bao, Yi Man Eva Fung & Xiang David Li

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  1. Tangpo Yang
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  2. Xiao-Meng Li
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Contributions

T.Y., X.-M.L. and X.D.L. designed the experiments and wrote the paper. T.Y. synthesized the small-molecule compounds and peptides and performed all of the photo-lysine–based cross-linking experiments in vitro. X.-M.L. performed all of the photo-lysine–based cross-linking experiments in living cells and prepared the MS sample. X.B. performed the ITC experiments. X.B. and Y.M.E.F. conducted the MS-based proteomics experiments. X.-M.L., X.B. and X.D.L. analyzed the MS/MS data.

Corresponding author

Correspondence to Xiang David Li.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Figures 1–14 and Supplementary Notes 1–4. (PDF 12956 kb)

Supplementary Table 1

The estimated incorporation rates of photo-Lys at the identified sites. (XLSX 14 kb)

Supplementary Table 2

The estimated incorporation rates of photo-Lys at the identified histone sites. (XLSX 11 kb)

Supplementary Table 3

Summary of the identified histone- and chromatin-binding proteins. (XLSX 17 kb)

Supplementary Data Set 1

Proteins quantified in HeLa S3 cells with/without photo-Lys labeling. (XLSX 222 kb)

Supplementary Data Set 2

Proteins quantified in SILAC experiment to identify histone-/chromatin-binding proteins (XLSX 193 kb)

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Yang, T., Li, XM., Bao, X. et al. Photo-lysine captures proteins that bind lysine post-translational modifications. Nat Chem Biol 12, 70–72 (2016). https://doi.org/10.1038/nchembio.1990

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  • DOI: https://doi.org/10.1038/nchembio.1990

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