A subcellular map of the human kinome

  1. Haitao Zhang
  2. Xiaolei Cao
  3. Mei Tang
  4. Guoxuan Zhong
  5. Yuan Si
  6. Haidong Li
  7. Feifeng Zhu
  8. Qinghua Liao
  9. Liuju Li
  10. Jianhui Zhao
  11. Jia Feng
  12. Shuaifeng Li
  13. Chenliang Wang
  14. Manuel Kaulich
  15. Fangwei Wang
  16. Liangyi Chen
  17. Li Li
  18. Zongping Xia
  19. Tingbo Liang
  20. Huasong Lu
  21. Xin-Hua Feng
  22. Bin Zhao  Is a corresponding author
  1. Zhejiang University, China
  2. Yulin Normal University, China
  3. Peking University, China
  4. Goethe University Frankfurt, Germany
  5. Hangzhou Normal University, China
  6. First Affiliated Hospital of Zhengzhou University, China

Abstract

The human kinome comprises 538 kinases playing essential functions by catalyzing protein phosphorylation. Annotation of subcellular distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 cellular compartments. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a similar condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other structures. Furthermore, KA demonstrated the role of liquid-liquid phase separation in formation of kinase condensates. Identification of MOK as a mitochondrial kinase revealed its function in cristae dynamics, respiration, and oxidative stress response. Although limited by possible mislocalization due to overexpression or epitope tagging, this subcellular map of the kinome can be used to refine regulatory mechanisms involving protein phosphorylation.

Data availability

All data generated or analyzed during this study are included in the manuscript and supporting files. Images of KA were available at the Cell Image Library database (http://flagella.crbs.ucsd.edu/pages/kinome_atlas?token=dHqMbfi06S).

The following data sets were generated

Article and author information

Author details

  1. Haitao Zhang

    Life Sciences Institute, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  2. Xiaolei Cao

    Life Sciences Institute, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  3. Mei Tang

    Life Sciences Institute, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  4. Guoxuan Zhong

    Life Sciences Institute, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  5. Yuan Si

    Life Sciences Institute, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  6. Haidong Li

    College of Biology and Pharmacy, Yulin Normal University, Yulin, China
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4427-7920
  7. Feifeng Zhu

    Life Sciences Institute, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  8. Qinghua Liao

    Life Sciences Institute, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  9. Liuju Li

    State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  10. Jianhui Zhao

    Department of Hepatobiliary and Pancreatic Surgery, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  11. Jia Feng

    Department of ophthalmology, The Children's Hospital, School of Medicine, and National Clinical Research Center for Child Health, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6742-484X
  12. Shuaifeng Li

    Life Sciences Institute, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  13. Chenliang Wang

    Life Sciences Institute, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  14. Manuel Kaulich

    Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt am Main, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9528-8822
  15. Fangwei Wang

    Life Sciences Institute, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5617-282X
  16. Liangyi Chen

    Institute of Molecular Medicine, 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:" 0000-0003-1270-7321
  17. Li Li

    Institute of Aging Research, Hangzhou Normal University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  18. Zongping Xia

    Translational Medicine Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  19. Tingbo Liang

    Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  20. Huasong Lu

    Life Sciences Institute, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  21. Xin-Hua Feng

    Life Sciences Institute, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  22. Bin Zhao

    Life Sciences Institute, Zhejiang University, Hangzhou, China
    For correspondence
    binzhao@zju.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1690-646X

Funding

National Natural Science Foundation of China (31970726)

  • Bin Zhao

National Natural Science Foundation of China (81730069)

  • Bin Zhao

Ministry of Science and Technology of the People's Republic of China (2017YFA0504502)

  • Bin Zhao

Natural Science Foundation of Zhejiang Province (LZ21C070002)

  • Bin Zhao

Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province

  • Bin Zhao

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

Copyright

© 2021, Zhang 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

  • 15,272
    views
  • 1,817
    downloads
  • 56
    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. Haitao Zhang
  2. Xiaolei Cao
  3. Mei Tang
  4. Guoxuan Zhong
  5. Yuan Si
  6. Haidong Li
  7. Feifeng Zhu
  8. Qinghua Liao
  9. Liuju Li
  10. Jianhui Zhao
  11. Jia Feng
  12. Shuaifeng Li
  13. Chenliang Wang
  14. Manuel Kaulich
  15. Fangwei Wang
  16. Liangyi Chen
  17. Li Li
  18. Zongping Xia
  19. Tingbo Liang
  20. Huasong Lu
  21. Xin-Hua Feng
  22. Bin Zhao
(2021)
A subcellular map of the human kinome
eLife 10:e64943.
https://doi.org/10.7554/eLife.64943

Share this article

https://doi.org/10.7554/eLife.64943

Further reading

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease
    Mai Nguyen, Elda Bauda ... Cecile Morlot
    Research Article

    Teichoic acids (TA) are linear phospho-saccharidic polymers and important constituents of the cell envelope of Gram-positive bacteria, either bound to the peptidoglycan as wall teichoic acids (WTA) or to the membrane as lipoteichoic acids (LTA). The composition of TA varies greatly but the presence of both WTA and LTA is highly conserved, hinting at an underlying fundamental function that is distinct from their specific roles in diverse organisms. We report the observation of a periplasmic space in Streptococcus pneumoniae by cryo-electron microscopy of vitreous sections. The thickness and appearance of this region change upon deletion of genes involved in the attachment of TA, supporting their role in the maintenance of a periplasmic space in Gram-positive bacteria as a possible universal function. Consequences of these mutations were further examined by super-resolved microscopy, following metabolic labeling and fluorophore coupling by click chemistry. This novel labeling method also enabled in-gel analysis of cell fractions. With this approach, we were able to titrate the actual amount of TA per cell and to determine the ratio of WTA to LTA. In addition, we followed the change of TA length during growth phases, and discovered that a mutant devoid of LTA accumulates the membrane-bound polymerized TA precursor.

    1. Biochemistry and Chemical Biology
    2. Computational and Systems Biology
    Shinichi Kawaguchi, Xin Xu ... Toshie Kai
    Research Article

    Protein–protein interactions are fundamental to understanding the molecular functions and regulation of proteins. Despite the availability of extensive databases, many interactions remain uncharacterized due to the labor-intensive nature of experimental validation. In this study, we utilized the AlphaFold2 program to predict interactions among proteins localized in the nuage, a germline-specific non-membrane organelle essential for piRNA biogenesis in Drosophila. We screened 20 nuage proteins for 1:1 interactions and predicted dimer structures. Among these, five represented novel interaction candidates. Three pairs, including Spn-E_Squ, were verified by co-immunoprecipitation. Disruption of the salt bridges at the Spn-E_Squ interface confirmed their functional importance, underscoring the predictive model’s accuracy. We extended our analysis to include interactions between three representative nuage components—Vas, Squ, and Tej—and approximately 430 oogenesis-related proteins. Co-immunoprecipitation verified interactions for three pairs: Mei-W68_Squ, CSN3_Squ, and Pka-C1_Tej. Furthermore, we screened the majority of Drosophila proteins (~12,000) for potential interaction with the Piwi protein, a central player in the piRNA pathway, identifying 164 pairs as potential binding partners. This in silico approach not only efficiently identifies potential interaction partners but also significantly bridges the gap by facilitating the integration of bioinformatics and experimental biology.