The same pocket in menin binds both MLL and JUND but has opposite effects on transcription

Abstract

Menin is a tumour suppressor protein whose loss or inactivation causes multiple endocrine neoplasia 1 (MEN1), a hereditary autosomal dominant tumour syndrome that is characterized by tumorigenesis in multiple endocrine organs1. Menin interacts with many proteins and is involved in a variety of cellular processes2,3,4,5,6,7,8. Menin binds the JUN family transcription factor JUND and inhibits its transcriptional activity2,9. Several MEN1 missense mutations disrupt the menin–JUND interaction, suggesting a correlation between the tumour-suppressor function of menin and its suppression of JUND-activated transcription2,10. Menin also interacts with mixed lineage leukaemia protein 1 (MLL1), a histone H3 lysine 4 methyltransferase, and functions as an oncogenic cofactor to upregulate gene transcription and promote MLL1-fusion-protein-induced leukaemogenesis5,7,11,12. A recent report on the tethering of MLL1 to chromatin binding factor lens epithelium-derived growth factor (LEDGF) by menin indicates that menin is a molecular adaptor coordinating the functions of multiple proteins13. Despite its importance, how menin interacts with many distinct partners and regulates their functions remains poorly understood. Here we present the crystal structures of human menin in its free form and in complexes with MLL1 or with JUND, or with an MLL1–LEDGF heterodimer. These structures show that menin contains a deep pocket that binds short peptides of MLL1 or JUND in the same manner, but that it can have opposite effects on transcription. The menin–JUND interaction blocks JUN N-terminal kinase (JNK)-mediated JUND phosphorylation and suppresses JUND-induced transcription. In contrast, menin promotes gene transcription by binding the transcription activator MLL1 through the peptide pocket while still interacting with the chromatin-anchoring protein LEDGF at a distinct surface formed by both menin and MLL1.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Overview of the human menin–MLL1 MBM complex structure.
Figure 2: Structural and mutational analyses of the menin–MLL1 MBM interaction.
Figure 3: Structure of the menin–MLL1 MBM-LBM –LEDGF IBD ternary complex.
Figure 4: Structural and functional studies of the menin–JUND interaction.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The atomic coordinates and structure factors of menin, menin– MLL1MBM, menin–JUNDMBM, and menin–MLL1MBM-LBM–LEDGFIBD have been deposited in the RCSB Protein Data Bank under accession codes 3U84, 3U85, 3U86 and 3U88, respectively.

References

  1. 1

    Chandrasekharappa, S. C. et al. Positional cloning of the gene for multiple endocrine neoplasia-type 1. Science 276, 404–407 (1997)

    CAS  Article  Google Scholar 

  2. 2

    Agarwal, S. K. et al. Menin interacts with the AP1 transcription factor JunD and represses JunD-activated transcription. Cell 96, 143–152 (1999)

    CAS  Article  Google Scholar 

  3. 3

    Busygina, V., Kottemann, M. C., Scott, K. L., Plon, S. E. & Bale, A. E. Multiple endocrine neoplasia type 1 interacts with forkhead transcription factor CHES1 in DNA damage response. Cancer Res. 66, 8397–8403 (2006)

    CAS  Article  Google Scholar 

  4. 4

    Chen, G. et al. Menin promotes the Wnt signaling pathway in pancreatic endocrine cells. Mol. Cancer Res. 6, 1894–1907 (2008)

    CAS  PubMed  Google Scholar 

  5. 5

    Hughes, C. M. et al. Menin associates with a trithorax family histone methyltransferase complex and with the Hoxc8 locus. Mol. Cell 13, 587–597 (2004)

    CAS  Article  Google Scholar 

  6. 6

    Jin, S. et al. Menin associates with FANCD2, a protein involved in repair of DNA damage. Cancer Res. 63, 4204–4210 (2003)

    CAS  PubMed  Google Scholar 

  7. 7

    Yokoyama, A. et al. Leukemia proto-oncoprotein MLL forms a SET1-like histone methyltransferase complex with menin to regulate Hox gene expression. Mol. Cell. Biol. 24, 5639–5649 (2004)

    CAS  Article  Google Scholar 

  8. 8

    Yang, Y. & Hua, X. In search of tumor suppressing functions of menin. Mol. Cell. Endocrinol. 265–266, 34–41 (2007)

    Article  Google Scholar 

  9. 9

    Knapp, J. I. et al. Identification and characterization of JunD missense mutants that lack menin binding. Oncogene 19, 4706–4712 (2000)

    CAS  Article  Google Scholar 

  10. 10

    Groussin, L. & Bertherat, J. Mechanisms of multiple endocrine neoplasia type 1: evidence for regulation of the AP-1 family of transcription factors by menin. Eur. J. Endocrinol. 141, 15–16 (1999)

    CAS  Article  Google Scholar 

  11. 11

    Krivtsov, A. V. & Armstrong, S. A. MLL translocations, histone modifications and leukaemia stem-cell development. Nature Rev. Cancer 7, 823–833 (2007)

    CAS  Article  Google Scholar 

  12. 12

    Yokoyama, A. et al. The menin tumor suppressor protein is an essential oncogenic cofactor for MLL-associated leukemogenesis. Cell 123, 207–218 (2005)

    CAS  Article  Google Scholar 

  13. 13

    Yokoyama, A. & Cleary, M. L. Menin critically links MLL proteins with LEDGF on cancer-associated target genes. Cancer Cell 14, 36–46 (2008)

    CAS  Article  Google Scholar 

  14. 14

    Caslini, C. et al. Interaction of MLL amino terminal sequences with menin is required for transformation. Cancer Res. 67, 7275–7283 (2007)

    CAS  Article  Google Scholar 

  15. 15

    Grembecka, J., Belcher, A. M., Hartley, T. & Cierpicki, T. Molecular basis of the mixed lineage leukemia-menin interaction: implications for targeting mixed lineage leukemias. J. Biol. Chem. 285, 40690–40698 (2010)

    CAS  Article  Google Scholar 

  16. 16

    Murai, M. J., Chruszcz, M., Reddy, G., Grembecka, J. & Cierpicki, T. Crystal structure of menin reveals binding site for mixed lineage leukemia (MLL) protein. J. Biol. Chem. 286, 31742–31748 (2011)

    CAS  Article  Google Scholar 

  17. 17

    Lamb, J. R., Tugendreich, S. & Hieter, P. Tetratrico peptide repeat interactions: to TPR or not to TPR? Trends Biochem. Sci. 20, 257–259 (1995)

    CAS  Article  Google Scholar 

  18. 18

    Llano, M., Morrison, J. & Poeschla, E. M. Virological and cellular roles of the transcriptional coactivator LEDGF/p75. Curr. Top. Microbiol. Immunol. 339, 125–146 (2009)

    CAS  PubMed  PubMed Central  Google Scholar 

  19. 19

    Gallo, A. et al. Menin uncouples Elk-1, JunD and c-Jun phosphorylation from MAP kinase activation. Oncogene 21, 6434–6445 (2002)

    CAS  Article  Google Scholar 

  20. 20

    Yang, S. H., Whitmarsh, A. J., Davis, R. J. & Sharrocks, A. D. Differential targeting of MAP kinases to the ETS-domain transcription factor Elk-1. EMBO J. 17, 1740–1749 (1998)

    CAS  Article  Google Scholar 

  21. 21

    Yazgan, O. & Pfarr, C. M. Regulation of two JunD isoforms by Jun N-terminal kinases. J. Biol. Chem. 277, 29710–29718 (2002)

    CAS  Article  Google Scholar 

  22. 22

    Mensah-Osman, E. J., Veniaminova, N. A. & Merchant, J. L. Menin and JunD regulate gastrin gene expression through proximal DNA elements. Am. J. Physiol. Gastrointest. Liver Physiol. 301, G783–G790 (2011)

    CAS  Article  Google Scholar 

  23. 23

    Otwinowski, Z. & Minor, W. in Methods in Enzymology Vol. 26 (eds Carter, C. W. Jr & Sweet, R. M.) 307–326 (Academic Press, 1997)

    Google Scholar 

  24. 24

    de La Fortelle, E. & Bricogne, G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472–494 (1997)

    CAS  Article  Google Scholar 

  25. 25

    Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991)

    Article  Google Scholar 

  26. 26

    Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)

    CAS  Article  Google Scholar 

  27. 27

    McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007)

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank G. Wilding for the human JUND complementary DNA and P. Cherepanov for the human LEDGF cDNA. We thank Y. Chen and W. Deng for help at various stages of the project. M.L. is a Howard Hughes Medical Institute Early Career Scientist. Work was supported by National Institutes of Health grants (GM 083015-01 to M.L., R01-DK085121 to X.H. and R37-DK45729 to J.L.M.), an American Cancer Society Research Scholar grant (to M.L.) and an American Association for Cancer Research Caring for Carcinoid Foundation Grant (to X.H.). The General Medicine and Cancer Institutes Collaborative Access Team has been funded in whole or in part with federal funds from the National Cancer Institute (grant Y1-CO-1020) and the National Institute of General Medical Science (grant Y1-GM-1104). Use of the Advanced Photon Source was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under contract number DE-AC02-06CH11357.

Author information

Affiliations

Authors

Contributions

J.H. is responsible for the bulk of the experiments, B.G. for the qRT-PCR and ChIP assays; B.W. for the co-immunoprecipitation and in vivo phosphorylation analyses, S.M. for the luciferase assay, N.A.V. and J.L.M. for the analysis of gastrin expression, and K.W. for some of the protein purification. M.L. and X.H. supervised the project and wrote the paper.

Corresponding authors

Correspondence to Xianxin Hua or Ming Lei.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-19 with legends, Supplementary Tables 1-6, Supplementary Text, a Supplementary Discussions and additional references. (PDF 2464 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Huang, J., Gurung, B., Wan, B. et al. The same pocket in menin binds both MLL and JUND but has opposite effects on transcription. Nature 482, 542–546 (2012). https://doi.org/10.1038/nature10806

Download citation

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing