Skip to main content
SpringerLink
Log in

Evaluation of the Moonlighting Histone H3 Specific Protease (H3ase) Activity and the Dehydrogenase Activity of Glutamate Dehydrogenase (GDH)

  • Original Paper
  • Published:
Cell Biochemistry and Biophysics Aims and scope Submit manuscript

Abstract

The N-terminus of Histone H3 is proteolytically processed in aged chicken liver. A histone H3 N-terminus specific endopeptidase (named H3ase) has been purified from the nuclear extract of aged chicken liver. By sequencing and a series of biochemical methods including the demonstration of H3ase activity in bacterially expressed GDH, it was established that the H3ase activity was a moonlighting protease activity of glutamate dehydrogenase (GDH). However, the active site for the H3ase in the GDH remains elusive. Here, using cross-linking studies of the homogenously purified H3ase, we show that the GDH and the H3ase remain in the same native state. Further, the H3ase and GDH activities could be uncoupled by partial denaturation of GDH, suggesting strong evidence for the involvement of different active sites for GDH and H3ase activities. Through densitometry of the H3ase clipped H3 products, the H3ase activity was quantified and it was compared with the GDH activity of the chicken liver nuclear GDH. Furthermore, the H3ase mostly remained distributed in the perinuclear area as demonstrated by MNase digestion and immuno-localization of H3ase in chicken liver nuclei, as well as cultured mouse hepatocyte cells, suggesting that H3ase demonstrated regulated access to the chromatin. The present study thus broadly compares the H3ase and GDH activities of the chicken liver GDH.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Data availability

The data of the present work can be made available on request.

References

  1. Kouzarides, T. (2007). Chromatin modifications and their function. Cell, 128(4), 693–705. https://doi.org/10.1016/j.cell.2007.02.005.

    Article  CAS  PubMed  Google Scholar 

  2. Allis, C. D., Bowen, J. K., Abraham, G. N., Glover, C. V., & Gorovsky, M. A. (1980). Proteolytic processing of histone H3 in chromatin: a physiologically regulated event in Tetrahymena micronuclei. Cell, 20(1), 55–64.

    Article  CAS  PubMed  Google Scholar 

  3. Jenuwein, T., & Allis, C. D. (2001). Translating the histone code. Science, 293(5532), 1074–1080. https://doi.org/10.1126/science.1063127.

    Article  CAS  PubMed  Google Scholar 

  4. Santos-Rosa, H., Kirmizis, A., Nelson, C., Bartke, T., Saksouk, N., Cote, J., & Kouzarides, T. (2009). Histone H3 tail clipping regulates gene expression. Nature Structural and Molecular Biology, 16(1), 17–22. https://doi.org/10.1038/nsmb.1534.

    Article  CAS  PubMed  Google Scholar 

  5. Purohit, J. S., & Chaturvedi, M. M. (2016). Chromatin and aging. In P. C. Rath, R. Sharma & S. Prasad eds, Topics in Biomedical Gerontology (pp. 205–241). Singapore: Springer Nature Press.

    Google Scholar 

  6. Allis, C. D., Allen, R. L., Wiggins, J. C., Chicoine, L. G., & Richman, R. (1984). Proteolytic processing of h1-like histones in chromatin: a physiologically and developmentally regulated event in Tetrahymena micronuclei. Journal of Cell Biology, 99(5), 1669–1677. https://doi.org/10.1083/jcb.99.5.1669.

    Article  CAS  PubMed  Google Scholar 

  7. Grigera, P. R., & Tisminetzky, S. G. (1984). Histone H3 modification in BHK cells infected with foot-and-mouth disease virus. Virology, 136(1), 10–19. https://doi.org/10.1016/0042-6822(84)90243-5.

    Article  CAS  PubMed  Google Scholar 

  8. Lin, R., Cook, R. G., & Allis, C. D. (1991). Proteolytic removal of core histone amino termini and dephosphorylation of histone H1 correlate with the formation of condensed chromatin and transcriptional silencing during Tetrahymena macronuclear development. Genes and Development, 5(9), 1601–1610. https://doi.org/10.1101/gad.5.9.1601.

    Article  CAS  PubMed  Google Scholar 

  9. Purohit, J. S., Chaturvedi, M. M. & Panda, P. (2012). Histone proteases: the tale of tail clippers. International journal of integrative sciences, innovation and technology, 1(1), 51–60.

    CAS  Google Scholar 

  10. Azad, G. K., Swagatika, S., Kumawat, M., Kumawat, R., & Tomar, R. S. (2014). Modifying chromatin by histone tail clipping. Journal of Molecular Biology, 430(18 Pt B), 3051–3067. https://doi.org/10.1016/j.jmb.2018.07.013.

    Article  CAS  Google Scholar 

  11. Duncan, E. M., Muratore-Schroeder, T. L., Cook, R. G., Garcia, B. A., Shabanowitz, J., Hunt, D. F., & Allis, C. D. (2008). Cathepsin L proteolytically processes histone H3 during mouse embryonic stem cell differentiation. Cell, 135(2), 284–294. https://doi.org/10.1016/j.cell.2008.09.055.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Iribarren, C., Morin, V., Puchi, M., & Imschenetzky, M. (2008). Sperm nucleosomes disassembly is a requirement for histones proteolysis during male pronucleus formation. Journal of Cellular Biochemistry, 103(2), 447–455. https://doi.org/10.1002/jcb.21410.

    Article  CAS  PubMed  Google Scholar 

  13. Morin, V., Sanchez-Rubio, A., Aze, A., Iribarren, C., Fayet, C., Desdevises, Y., Garcia-Huidobro, J., Imschenetzky, M., Puchi, M., & Geneviere, A. M. (2012). The protease degrading sperm histones post-fertilization in sea urchin eggs is a nuclear cathepsin L that is further required for embryo development. PLoS One, 7(11), e46850. https://doi.org/10.1371/journal.pone.0046850.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  14. Khalkhali-Ellis, Z., Goossens, W., Margaryan, N. V., & Hendrix, M. J. C. (2014). cleavage of histone 3 by Cathepsin D in the involuting mammary gland. PLoS One, 9(7), e103230. https://doi.org/10.1371/journal.pone.0103230.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  15. Panda, P., Chaturvedi, M. M., Panda, A. K., Suar, M., & Purohit, J. S. (2013). Purification and characterization of a novel histone H2A specific protease (H2Asp) from chicken liver nuclear extract. Gene, 512(1), 47–54. https://doi.org/10.1016/j.gene.2012.09.098.

    Article  CAS  PubMed  Google Scholar 

  16. Panda, P., Bohot, M., Chaturvedi, M. M., & Purohit, J. S. (2021). Purification and partial characterization of vinculin from chicken liver nuclear extract. Biologia, 76(4), 1349–1357. https://doi.org/10.1007/s11756-021-00691-3.

    Article  CAS  Google Scholar 

  17. Vossaert, L., Meert, P., Scheerlinck, E., Glibert, P., Roy, N. V., Heindryckx, B., Sutter, P. D., Dhaenens, M., & Deforce, D. (2014). Identification of histone H3 clipping activity in human embryonic stem cells. Stem Cell Research, 13(1), 123–134. https://doi.org/10.1016/j.scr.2014.05.002.

    Article  CAS  PubMed  Google Scholar 

  18. Kim, K., Punj, V., Kim, J. M., Lee, S., Ulmer, T. S., Lu, W., Rice, J. C., & An, W. (2016). MMP-9 facilitates selective proteolysis of the histone H3 tail at genes necessary for proficient osteoclastogenesis. Genes and Development, 30(2), 208–19. https://doi.org/10.1101/gad.268714.115.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Ferrari, K. J., Amato, S., Noberini, R., Toscani, C., Fernández-Pérez, D., Rossi, A., Conforti, P., Zanotti, M., Bonaldi, T., Tamburri, S., & Pasini, D. (2021). Intestinal differentiation involves cleavage of histone H3 N-terminal tails by multiple proteases. Nucleic Acids Research, 49(2), 791–804. https://doi.org/10.1093/nar/gkaa1228.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Singh, N., Purohit, J. S., Shanti, S., Singh, A., Panigrahi, A. K., & Chaturvedi, M. M. (2017). Characterization of the N-terminally clipped histone H3 (∆H3) from old chicken and rat liver. International Journal of Clinical and Experimental Pathology, 10(5), 5334–5342. www.ijcep.com/ISSN:1936-2625/IJCEP0047442..

  21. Chaturvedi, M. M., Purohit, J. S., Tomar, R. S., & Panigrahi, A. K. (2010). An irreversible modification of histone H3‐identification and characterization of histone H3‐specific protease from chicken liver. FASEB, 24(S1), lb64–lb64. https://doi.org/10.1096/fasebj.24.1_supplement.lb64.

    Article  Google Scholar 

  22. Purohit, J. S., Tomar, R. S., Panigrahi, A. K., Pandey, S. M., Singh, D., & Chaturvedi, M. M. (2013). Chicken liver glutamate dehydrogenase (GDH) demonstrates a histone H3 specific protease (H3ase) activity in vitro. Biochimie, 95(11), 1999–2009. https://doi.org/10.1016/j.biochi.2013.07.005.

    Article  CAS  PubMed  Google Scholar 

  23. Mandal, P., Verma, N., Chauhan, S., & Tomar, R. S. (2013). Unexpected histone H3 tail-clipping activity of glutamate dehydrogenase. Journal of Biological Chemistry, 288(26), 18743–18757. https://doi.org/10.1074/jbc.M113.462531.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Mandal, P., Chauhan, S., & Tomar, R. S. (2014). H3 clipping activity of glutamate dehydrogenase is regulated by stefin B and chromatin structure. FEBS Journal, 281(23), 5292–5308. https://doi.org/10.1111/febs.13069.

    Article  CAS  PubMed  Google Scholar 

  25. Edmondson, D. G., Smith, M. M., & Roth, S. Y. (1996). Repression domain of the yeast global repressor Tup1 interacts directly with histones H3 and H4. Genes and Development, 10(10), 1247–1259. https://doi.org/10.1101/gad.10.10.1247.

    Article  CAS  PubMed  Google Scholar 

  26. Gorski, K., Carneiro, M., & Schibler, U. (1986). Tissue-specific in vitro transcription from the mouse albumin promoter. Cell, 47(5), 767–776. https://doi.org/10.1016/0092-8674(86)90519-2.

    Article  CAS  PubMed  Google Scholar 

  27. Bradford, M. M. (1976). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Analytical Biochemistry, 72, 248–254. https://doi.org/10.1006/abio.1976.9999.

    Article  CAS  PubMed  Google Scholar 

  28. Panda, P., Suar, M., Singh, D., Pandey, S. M., Chaturvedi, M. M., & Purohit, J. S. (2011). Characterization of nuclear glutamate dehydrogenase of chicken liver and brain. Protein and Peptide Letters, 18(12), 1194–1203. https://doi.org/10.2174/092986611797642698.

    Article  CAS  PubMed  Google Scholar 

  29. Corman, L., Prescott, L.M., & Kaplan, N.O. (1967). Purification and kinetic characteristics of dogfish liver glutamate dehydrogenase. Journal of Biological Chemistry, 242 (7), 1383–1390.

  30. Panigrahi, A. K., Tomar, R. S., & Chaturvedi, M. M. (2003). Mechanism of nucleosome disruption and octamer transfer by the chicken SWI/SNF-like complex. Biochemical and Biophysical Research Communications, 306(1), 72–78. https://doi.org/10.1016/s0006-291x(03)00906-9.

    Article  CAS  PubMed  Google Scholar 

  31. Bitensky, M. W., Yielding, K. L., & Tomkins, G. M. (1965). The effect of allosteric modifiers on the rate of denaturation of glutamate dehydrogenase. Journal of Biological Chemistry, 240(3), 1077–1082. https://doi.org/10.1016/S0021-9258(18)97540-X.

    Article  CAS  PubMed  Google Scholar 

  32. Li, M., Li, C., Allen, A., Stanley, C. A., & Smith, T. J. (2011). The structure and allosteric regulation of glutamate dehydrogenase. Neurochemistry International, 59(4), 445–455. https://doi.org/10.1016/j.neuint.2010.10.017.

    Article  CAS  PubMed  Google Scholar 

  33. Rooki, H., Khajeh, K., Mostafaie, A., Kashanian, S., & Ghobadi, S. (2007). Partially folded conformations of bovine liver glutamate dehydrogenase induced by mild acidic conditions. Journal of Biochemistry, 142(2), 193–200. https://doi.org/10.1093/jb/mvm112.

    Article  CAS  PubMed  Google Scholar 

  34. Rose, S. M., & Garrard, W. T. (1984). Differentiation-dependent chromatin alterations precede and accompany transcription of immunoglobulin light chain genes. Journal of Biological Chemistry, 259(13), 8534–8544. https://doi.org/10.1016/S0021-9258(17)39763-6.

    Article  CAS  PubMed  Google Scholar 

  35. Jackson, D. A., & Cook, P. R. (1985). Transcription occurs at a nucleoskeleton. The EMBO Journal, 4(4), 919–925. https://doi.org/10.1002/j.1460-2075.1985.tb03719.x.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Jackson, D. A., Hassan, A. B., Errington, R. J., & Cook, P. R. (1993). Visualization of focal sites of transcription within human nuclei. The EMBO Journal, 12(3), 1059–1065. https://doi.org/10.1002/j.1460-2075.1993.tb05747.x.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

Department of Science and Technology, India and the Indian Council of Medical Research are acknowledged for extramural grants to J.S.P. and M.M.C. The University of Delhi is acknowledged for the DU R&D grants to J.S.P. Anil Panigrahi is acknowledged for his valuable suggestions for the work. Raghuvir S Tomar is acknowledged for his localization data for his PhD work at Banaras Hindu University, under the supervision of MMC. Anju Shrivastava, Department of Zoology, University of Delhi is acknowledged for extending the animal house facility and cell culture facility.

Funding

The present study was supported by funding from the Department of Science and Technology (EMR/2016/002571), India and the Indian Council of Medical Research (5/10/FR/51/2020-RBMCH) to J.S.P. and M.M.C. The University of Delhi is acknowledged for the DU R&D grants to J.S.P.

Author information

Authors and Affiliations

  1. Cluster Innovation Centre, University of Delhi, 110007, Delhi, India

    Jogeswar Satchidananda Purohit & Yashankita Raghuvanshi

  2. Department of Zoology, University of Delhi, 110007, Delhi, India

    Jogeswar Satchidananda Purohit, Madhulika Singh, Yashankita Raghuvanshi, Saima Syeda & Madan M. Chaturvedi

  3. SGT University, Gurugram (Delhi-NCR), Haryana, 122505, India

    Madan M. Chaturvedi

Authors
  1. Jogeswar Satchidananda Purohit
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Madhulika Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yashankita Raghuvanshi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Saima Syeda
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Madan M. Chaturvedi
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

J.S.P.: research design, experimental work, manuscript writing and correction; M.S.: dose and time kinetics assays and discussions; Y.S.: G.D.H. assays and manuscript writing; S.S.: Confocal localization; M.M.C.: experimental design, manuscript correction and discussions.

Corresponding authors

Correspondence to Jogeswar Satchidananda Purohit or Madan M. Chaturvedi.

Ethics declarations

Conflict of Interest

The authors declare no competing interests.

Ethical Approval

All the experiments of the present study were approved by the Institutional Ethical Committee.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Purohit, J.S., Singh, M., Raghuvanshi, Y. et al. Evaluation of the Moonlighting Histone H3 Specific Protease (H3ase) Activity and the Dehydrogenase Activity of Glutamate Dehydrogenase (GDH). Cell Biochem Biophys 82, 223–233 (2024). https://doi.org/10.1007/s12013-023-01201-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12013-023-01201-9

Keywords

Search

Navigation