Selective inhibition reveals the regulatory function of DYRK2 in protein synthesis and calcium entry

  1. Tiantian Wei
  2. Jue Wang
  3. Ruqi Liang
  4. Wendong Chen
  5. Yilan Chen
  6. Mingzhe Ma
  7. An He
  8. Yifei Du
  9. Wenjing Zhou
  10. Zhiying Zhang
  11. Xin Zeng
  12. Chu Wang
  13. Jin Lu
  14. Xing Guo
  15. Xiao-Wei Chen
  16. Youjun Wang
  17. Dr. Ruijun Tian
  18. Junyu Xiao  Is a corresponding author
  19. Xiaoguang Lei  Is a corresponding author
  1. Peking University, China
  2. Southern University of Science and Technology, China
  3. Beijing Normal University, China
  4. Zhejiang University, China

Abstract

The dual-specificity tyrosine phosphorylation-regulated kinase DYRK2 has emerged as a critical regulator of cellular processes. We took a chemical biology approach to gain further insights into its function. We developed C17, a potent small-molecule DYRK2 inhibitor, through multiple rounds of structure-based optimization guided by several cocrystallized structures. C17 displayed an effect on DYRK2 at a single-digit nanomolar IC50 and showed outstanding selectivity for the human kinome containing 467 other human kinases. Using C17 as a chemical probe, we further performed quantitative phosphoproteomic assays and identified several novel DYRK2 targets, including eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1) and stromal interaction molecule 1 (STIM1). DYRK2 phosphorylated 4E-BP1 at multiple sites, and the combined treatment of C17 with AKT and MEK inhibitors showed synergistic 4E-BP1 phosphorylation suppression. The phosphorylation of STIM1 by DYRK2 substantially increased the interaction of STIM1 with the ORAI1 channel, and C17 impeded the store-operated calcium entry process. These studies collectively further expand our understanding of DYRK2 and provide a valuable tool to pinpoint its biological function.

Data availability

The structural coordinates of DYRK2 in complex with compounds 5, 6, 7, 8, 10, 13, 14, 17, 18, 19, and 20 have been deposited in the Protein Data Bank with accession codes 7DH3, 7DG4, 7DH9, 7DHV, 7DHC, 7DHK, 7DHO, 7DJO, 7DL6, 7DHH, and 7DHN, respectively.All the raw mass spectrometry data as well as the identified and significantly regulated phosphosites tables have been deposited in the public proteomics repository MassIVE and are accessible at ftp://massive.ucsd.edu/MSV000087106/.

Article and author information

Author details

  1. Tiantian Wei

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  2. Jue Wang

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  3. Ruqi Liang

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  4. Wendong Chen

    SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
    Competing interests
    The authors declare that no competing interests exist.
  5. Yilan Chen

    Beijing Normal University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  6. Mingzhe Ma

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  7. An He

    SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
    Competing interests
    The authors declare that no competing interests exist.
  8. Yifei Du

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  9. Wenjing Zhou

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  10. Zhiying Zhang

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  11. Xin Zeng

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  12. Chu Wang

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  13. Jin Lu

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  14. Xing Guo

    Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  15. Xiao-Wei Chen

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4564-5120
  16. Youjun Wang

    Beijing Normal University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0961-1716
  17. Dr. Ruijun Tian

    SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
    Competing interests
    The authors declare that no competing interests exist.
  18. Junyu Xiao

    Peking University, Beijing, China
    For correspondence
    junyuxiao@pku.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1822-1701
  19. Xiaoguang Lei

    Peking University, Beijing, China
    For correspondence
    xglei@pku.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0380-8035

Funding

National Key Research and Development Plan (2017YFA0505200)

  • Tiantian Wei
  • Jue Wang
  • Ruqi Liang
  • Wendong Chen
  • Yilan Chen
  • Mingzhe Ma
  • An He
  • Yifei Du
  • Wenjing Zhou
  • Zhiying Zhang
  • Xin Zeng
  • Chu Wang
  • Jin Lu
  • Xing Guo
  • Xiao-Wei Chen
  • Youjun Wang
  • Junyu Xiao
  • Xiaoguang Lei

National Natural Science Foundation of China (91853202,21625201,21961142010,21661140001,and 21521003)

  • Tiantian Wei
  • Jue Wang
  • Ruqi Liang
  • Wendong Chen
  • Yilan Chen
  • Mingzhe Ma
  • An He
  • Yifei Du
  • Wenjing Zhou
  • Zhiying Zhang
  • Xin Zeng
  • Chu Wang
  • Jin Lu
  • Xing Guo
  • Xiao-Wei Chen
  • Youjun Wang
  • Junyu Xiao
  • Xiaoguang Lei

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2022, Wei et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 1,704
    views
  • 429
    downloads
  • 9
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Tiantian Wei
  2. Jue Wang
  3. Ruqi Liang
  4. Wendong Chen
  5. Yilan Chen
  6. Mingzhe Ma
  7. An He
  8. Yifei Du
  9. Wenjing Zhou
  10. Zhiying Zhang
  11. Xin Zeng
  12. Chu Wang
  13. Jin Lu
  14. Xing Guo
  15. Xiao-Wei Chen
  16. Youjun Wang
  17. Dr. Ruijun Tian
  18. Junyu Xiao
  19. Xiaoguang Lei
(2022)
Selective inhibition reveals the regulatory function of DYRK2 in protein synthesis and calcium entry
eLife 11:e77696.
https://doi.org/10.7554/eLife.77696

Share this article

https://doi.org/10.7554/eLife.77696

Further reading

    1. Biochemistry and Chemical Biology
    Meina He, Yongxin Tao ... Wenli Chen
    Research Article

    Copper is an essential enzyme cofactor in bacteria, but excess copper is highly toxic. Bacteria can cope with copper stress by increasing copper resistance and initiating chemorepellent response. However, it remains unclear how bacteria coordinate chemotaxis and resistance to copper. By screening proteins that interacted with the chemotaxis kinase CheA, we identified a copper-binding repressor CsoR that interacted with CheA in Pseudomonas putida. CsoR interacted with the HPT (P1), Dimer (P3), and HATPase_c (P4) domains of CheA and inhibited CheA autophosphorylation, resulting in decreased chemotaxis. The copper-binding of CsoR weakened its interaction with CheA, which relieved the inhibition of chemotaxis by CsoR. In addition, CsoR bound to the promoter of copper-resistance genes to inhibit gene expression, and copper-binding released CsoR from the promoter, leading to increased gene expression and copper resistance. P. putida cells exhibited a chemorepellent response to copper in a CheA-dependent manner, and CsoR inhibited the chemorepellent response to copper. Besides, the CheA-CsoR interaction also existed in proteins from several other bacterial species. Our results revealed a mechanism by which bacteria coordinately regulated chemotaxis and resistance to copper by CsoR.

    1. Biochemistry and Chemical Biology
    2. Immunology and Inflammation
    Pavla Nedbalová, Nikola Kaislerova ... Tomáš Doležal
    Research Article

    During parasitoid wasp infection, activated immune cells of Drosophila melanogaster larvae release adenosine to conserve nutrients for immune response. S-adenosylmethionine (SAM) is a methyl group donor for most methylations in the cell and is synthesized from methionine and ATP. After methylation, SAM is converted to S-adenosylhomocysteine, which is further metabolized to adenosine and homocysteine. Here, we show that the SAM transmethylation pathway is up-regulated during immune cell activation and that the adenosine produced by this pathway in immune cells acts as a systemic signal to delay Drosophila larval development and ensure sufficient nutrient supply to the immune system. We further show that the up-regulation of the SAM transmethylation pathway and the efficiency of the immune response also depend on the recycling of adenosine back to ATP by adenosine kinase and adenylate kinase. We therefore hypothesize that adenosine may act as a sensitive sensor of the balance between cell activity, represented by the sum of methylation events in the cell, and nutrient supply. If the supply of nutrients is insufficient for a given activity, adenosine may not be effectively recycled back into ATP and may be pushed out of the cell to serve as a signal to demand more nutrients.