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A dual-function chemical probe for detecting erasers of lysine lipoylation

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Abstract

Lysine lipoylation plays vital roles in cell metabolism and redox processes. For example, removal of lipoylation will decrease pyruvate dehydrogenase activity and affect the citric acid cycle. Despite the important functions of lysine lipoylation, the mechanisms for the addition and removal of this modification remain largely unexplored. Very few useful chemical tools are available to study the interactions of lysine lipoylation with its regulatory delipoylation proteins. For example, immunoaffinity purification-mass spectrometry is one of such tools, which highly relies on antibody efficiency and purification techniques. Single-step activity based fluorogenic probes developed by our groups and others is also an efficient method to study the deacylation activity. Affinitybased labeling probe using photo-cross-linker is a powerful platform to study the transient and dynamic interactions of peptide ligands with the interacting proteins. Herein, we have designed and synthesized a dual-function probe KTLlip for studying enzymatic delipoylation (eraser) activity and interaction of lysine lipoylation with the eraser at the same time. We show that KTLlip can be used as a useful tool to detect delipoylation as demonstrated by its ability to fluorescently label the eraser activity of recombinant Sirt2. We envision that the probe will help delineate the roles of delipoylation enzyme in biology.

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References

  1. Spalding M D, Prigge S T. Lipoic acid metabolism in microbial pathogens. Microbiology and Molecular Biology Reviews: MMBR, 2010; 74(2): 200–228

    Article  CAS  Google Scholar 

  2. Mathias R A, Greco T M, Oberstein A, Budayeva H G, Chakrabarti R, Rowland E A, Kang Y, Shenk T, Cristea I M. Sirtuin 4 is a lipoamidase regulating pyruvate dehydrogenase complex activity. Cell, 2014; 159(7): 1615–1625

    Article  CAS  Google Scholar 

  3. Perham R N. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annual Review of Biochemistry, 2000; 69(1): 961–1004

    Article  CAS  Google Scholar 

  4. Rowland E A, Snowden C K, Cristea I M. Protein lipoylation: an evolutionarily conserved metabolic regulator of health and disease. Current Opinion in Chemical Biology, 2018, 42: 76–85

    Article  CAS  Google Scholar 

  5. Naiyanetr P, Butler J D, Meng L, Pfeiff J, Kenny T P, Guggenheim K G, Reiger R, Lam K, Kurth M J, Ansari A A, Coppel R L, López-Hoyos M, Gershwin M E, Leung P S C. Electrophile-modified lipoic derivatives of PDC-E2 elicits anti-mitochondrial antibody reactivity. Journal of Autoimmunity, 2011; 37(3): 209–216

    Article  CAS  Google Scholar 

  6. Thekkumkara T J, Ho L, Wexler I D, Pons G, Te-Chung L, Patel M S. Nucleotide sequence of a cDNA for the dihydrolipoamide acetyltransferase component of human pyruvate dehydrogenase complex. FEBS Letters, 1988; 240(1–2): 45–48

    Article  CAS  Google Scholar 

  7. Packer L, Witt E H, Tritschler H J. Alpha-lipoic acid as a biological antioxidant. Free Radical Biology & Medicine, 1995; 19(2): 227–250

    Article  CAS  Google Scholar 

  8. Moini H, Packer L, Saris N E L. Antioxidant and prooxidant activities of α-lipoic acid and dihydrolipoic acid. Toxicology and Applied Pharmacology, 2002; 182(1): 84–90

    Article  CAS  Google Scholar 

  9. Holbert M A, Marmorstein R. Structure and activity of enzymes that remove histone modifications. Current Opinion in Structural Biology, 2005; 15(6): 673–680

    Article  CAS  Google Scholar 

  10. Houtkooper R H, Pirinen E, Auwerx J. Sirtuins as regulators of metabolism and healthspan. Nature Reviews. Molecular Cell Biology, 2012; 13(4): 225–238

    Article  CAS  Google Scholar 

  11. Watroba M, Szukiewicz D. The role of sirtuins in aging and age-related diseases. Advances in Medical Sciences, 2016; 61(1): 52–62

    Article  Google Scholar 

  12. Müller M M, Muir T W. Histones: at the crossroads of peptide and protein chemistry. Chemical Reviews, 2015; 115(6): 2296–2349

    Article  Google Scholar 

  13. Komatsu T, Urano Y. Evaluation of enzymatic activities in living systems with small-molecular fluorescent substrate probes. Analytical Sciences, 2015; 31(4): 257–265

    Article  CAS  Google Scholar 

  14. Chalkiadaki A, Guarente L. The multifaceted functions of sirtuins in cancer. Nature Reviews. Cancer, 2015; 15(10): 608–624

    Article  CAS  Google Scholar 

  15. Bheda P, Jing H, Wolberger C, Lin H. The substrate specificity of sirtuins. Annual Review of Biochemistry, 2016; 85(1): 405–429

    Article  CAS  Google Scholar 

  16. Du J, Zhou Y, Su X, Yu J J, Khan S, Jiang H, Kim J, Woo J, Kim J H, Choi B H, He B, Chen W, Zhang S, Cerione R A, Auwerx J, Hao Q, Lin H. Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase. Science, 2011; 334(6057): 806–809

    Article  CAS  Google Scholar 

  17. Jiang H, Khan S, Wang Y, Charron G, He B, Sebastian C, Du J, Kim R, Ge E, Mostoslavsky R, Hang H C, Hao Q, Lin H. SIRT6 regulates TNF-α secretion through hydrolysis of long-chain fatty acyl lysine. Nature, 2013; 496(7443): 110–113

    Article  CAS  Google Scholar 

  18. Liu Z, Yang T, Li X, Peng T, Hang H C, Li X D. Integrative chemical biology approaches to examine ‘erasers’ for protein lysine fatty-acylation. Angewandte Chemie International Edition, 2015; 54(4): 1149–1152

    Article  CAS  Google Scholar 

  19. Xie Y, Chen L, Wang R, Wang J, Li J, Xu W, Li Y, Yao S Q, Zhang L, Hao Q, Sun H. Chemical probes reveal sirt2′s new function as a robust “eraser” of lysine lipoylation. Journal of the American Chemical Society, 2019; 141(46): 18428–18436

    Article  CAS  Google Scholar 

  20. Baba R, Hori Y, Mizukami S, Kikuchi K. Development of a fluorogenic probe with a transesterification switch for detection of histone deacetylase activity. Journal of the American Chemical Society, 2012; 134(35): 14310–14313

    Article  CAS  Google Scholar 

  21. Rooker D R, Buccella D. Real-time detection of histone deacetylase activity with a small molecule fluorescent and spectrophotometric probe. Chemical Science (Cambridge), 2015; 6(11): 6456–6461

    Article  CAS  Google Scholar 

  22. Gober I N, Waters M L. Supramolecular affinity labeling of histone peptides containing trimethyllysine and its application to histone deacetylase assays. Journal of the American Chemical Society, 2016; 138(30): 9452–9459

    Article  CAS  Google Scholar 

  23. Xie Y, Ge J, Lei H, Peng B, Zhang H, Wang D, Pan S, Chen G, Chen L, Wang Y, Hao Q, Yao S Q, Sun H. Fluorescent probes for singlestep detection and proteomic profiling of histone deacetylases. Journal of the American Chemical Society, 2016; 138(48): 15596–15604

    Article  CAS  Google Scholar 

  24. Li Z, Hao P, Li L, Tan C Y, Cheng X, Chen G Y, Sze S K, Shen H M, Yao S Q. Design and synthesis of minimalist terminal alkyne-containing diazirine photo-crosslinkers and their incorporation into kinase inhibitors for cell- and tissue-based proteome profiling. Angewandte Chemie International Edition, 2013; 52(33): 8551–8556

    Article  CAS  Google Scholar 

  25. Cravatt B F, Wright A T, Kozarich J W. Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annual Review of Biochemistry, 2008; 77(1): 383–414

    Article  CAS  Google Scholar 

  26. Nomura D K, Dix M M, Cravatt B F. Activity-based protein profiling for biochemical pathway discovery in cancer. Nature Reviews. Cancer, 2010; 10(9): 630–638

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the Science Technology and Innovation Committee of Shenzhen Municipality (Grant Nos. JCYJ20180507181654823 and JCYJ20170413141047772) and the National Natural Science Foundation of China (Grant No. 21778044).

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Authors and Affiliations

  1. Department of Chemistry, City University of Hong Kong, Hong Kong, China

    Yusheng Xie, Jie Zhang, Liu Yang, Qingxin Chen & Hongyan Sun

  2. Key Laboratory of Biochip Technology, Biotech and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China

    Yusheng Xie, Jie Zhang, Liu Yang, Qingxin Chen, Liang Zhang & Hongyan Sun

  3. School of Biomedical Sciences, University of Hong Kong, Hong Kong, China

    Quan Hao

  4. Department of Biomedical Science, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China

    Liang Zhang

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  1. Yusheng Xie
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  2. Jie Zhang
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  3. Liu Yang
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  4. Qingxin Chen
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  5. Quan Hao
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  6. Liang Zhang
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  7. Hongyan Sun
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Correspondence to Hongyan Sun.

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Xie, Y., Zhang, J., Yang, L. et al. A dual-function chemical probe for detecting erasers of lysine lipoylation. Front. Chem. Sci. Eng. 16, 121–127 (2022). https://doi.org/10.1007/s11705-021-2051-0

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  • DOI: https://doi.org/10.1007/s11705-021-2051-0

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