IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-33423-5.html
   My bibliography  Save this article

Phosphorylation of Jhd2 by the Ras-cAMP-PKA(Tpk2) pathway regulates histone modifications and autophagy

Author

Listed:
  • Qi Yu

    (School of Life Sciences, Hubei University)

  • Xuanyunjing Gong

    (School of Life Sciences, Hubei University)

  • Yue Tong

    (School of Life Sciences, Hubei University)

  • Min Wang

    (Chinese Academy of Sciences)

  • Kai Duan

    (School of Life Sciences, Hubei University)

  • Xinyu Zhang

    (School of Life Sciences, Hubei University)

  • Feng Ge

    (Chinese Academy of Sciences)

  • Xilan Yu

    (School of Life Sciences, Hubei University)

  • Shanshan Li

    (School of Life Sciences, Hubei University)

Abstract

Cells need to coordinate gene expression with their metabolic states to maintain cell homeostasis and growth. How cells transduce nutrient availability to appropriate gene expression remains poorly understood. Here we show that glycolysis regulates histone modifications and gene expression by activating protein kinase A (PKA) via the Ras-cyclic AMP pathway. The catalytic subunit of PKA, Tpk2 antagonizes Jhd2-catalyzed H3K4 demethylation by phosphorylating Jhd2 at Ser321 and Ser340 in response to glucose availability. Tpk2-catalyzed Jhd2 phosphorylation impairs its nuclear localization, reduces its binding to chromatin, and promotes its polyubiquitination and degradation by the proteasome. Tpk2-catalyzed Jhd2 phosphorylation also maintains H3K14 acetylation by preventing the binding of histone deacetylase Rpd3 to chromatin. By phosphorylating Jhd2, Tpk2 regulates gene expression, maintains normal chronological life span and promotes autophagy. These results provide a direct connection between metabolism and histone modifications and shed lights on how cells rewire their biological responses to nutrient signals.

Suggested Citation

  • Qi Yu & Xuanyunjing Gong & Yue Tong & Min Wang & Kai Duan & Xinyu Zhang & Feng Ge & Xilan Yu & Shanshan Li, 2022. "Phosphorylation of Jhd2 by the Ras-cAMP-PKA(Tpk2) pathway regulates histone modifications and autophagy," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33423-5
    DOI: 10.1038/s41467-022-33423-5
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-33423-5
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-022-33423-5?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Helena Santos-Rosa & Robert Schneider & Andrew J. Bannister & Julia Sherriff & Bradley E. Bernstein & N. C. Tolga Emre & Stuart L. Schreiber & Jane Mellor & Tony Kouzarides, 2002. "Active genes are tri-methylated at K4 of histone H3," Nature, Nature, vol. 419(6905), pages 407-411, September.
    2. Shihao Zhang & Xilan Yu & Yuan Zhang & Xiangyan Xue & Qi Yu & Zitong Zha & Madelaine Gogol & Jerry L. Workman & Shanshan Li, 2021. "Metabolic regulation of telomere silencing by SESAME complex-catalyzed H3T11 phosphorylation," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    3. Jason Ptacek & Geeta Devgan & Gregory Michaud & Heng Zhu & Xiaowei Zhu & Joseph Fasolo & Hong Guo & Ghil Jona & Ashton Breitkreutz & Richelle Sopko & Rhonda R. McCartney & Martin C. Schmidt & Najma Ra, 2005. "Global analysis of protein phosphorylation in yeast," Nature, Nature, vol. 438(7068), pages 679-684, December.
    4. Antonis Kirmizis & Helena Santos-Rosa & Christopher J. Penkett & Michael A. Singer & Michiel Vermeulen & Matthias Mann & Jürg Bähler & Roland D. Green & Tony Kouzarides, 2007. "Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation," Nature, Nature, vol. 449(7164), pages 928-932, October.
    5. Xiaobing Shi & Tao Hong & Kay L. Walter & Mark Ewalt & Eriko Michishita & Tiffany Hung & Dylan Carney & Pedro Peña & Fei Lan & Mohan R. Kaadige & Nicolas Lacoste & Christelle Cayrou & Foteini Davrazou, 2006. "ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression," Nature, Nature, vol. 442(7098), pages 96-99, July.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Dimitrios Spiliotopoulos & Andrea Spitaleri & Giovanna Musco, 2012. "Exploring PHD Fingers and H3K4me0 Interactions with Molecular Dynamics Simulations and Binding Free Energy Calculations: AIRE-PHD1, a Comparative Study," PLOS ONE, Public Library of Science, vol. 7(10), pages 1-13, October.
    2. Shinsuke Ohnuki & Yoshikazu Ohya, 2018. "High-dimensional single-cell phenotyping reveals extensive haploinsufficiency," PLOS Biology, Public Library of Science, vol. 16(5), pages 1-23, May.
    3. Thomas C Whisenant & David T Ho & Ryan W Benz & Jeffrey S Rogers & Robyn M Kaake & Elizabeth A Gordon & Lan Huang & Pierre Baldi & Lee Bardwell, 2010. "Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors," PLOS Computational Biology, Public Library of Science, vol. 6(8), pages 1-21, August.
    4. Victor Lopez Soriano & Alfredo Dueñas Rey & Rajarshi Mukherjee & Frauke Coppieters & Miriam Bauwens & Andy Willaert & Elfride De Baere, 2024. "Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    5. Pengyi Yang & Xiaofeng Zheng & Vivek Jayaswal & Guang Hu & Jean Yee Hwa Yang & Raja Jothi, 2015. "Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data," PLOS Computational Biology, Public Library of Science, vol. 11(8), pages 1-18, August.
    6. Benjamin M. Spector & Mrutyunjaya Parida & Ming Li & Christopher B. Ball & Jeffery L. Meier & Donal S. Luse & David H. Price, 2022. "Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    7. Shijia Zhu & Guohua Wang & Bo Liu & Yadong Wang, 2013. "Modeling Exon Expression Using Histone Modifications," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-15, June.
    8. Steffen Mueller & Gail Dennison & Shujun Liu, 2021. "An Assessment on Ethanol-Blended Gasoline/Diesel Fuels on Cancer Risk and Mortality," IJERPH, MDPI, vol. 18(13), pages 1-23, June.
    9. Sourav Bandyopadhyay & Ryan Kelley & Nevan J Krogan & Trey Ideker, 2008. "Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data," PLOS Computational Biology, Public Library of Science, vol. 4(4), pages 1-8, April.
    10. Fei He & Qi Yu & Min Wang & Rongsha Wang & Xuanyunjing Gong & Feng Ge & Xilan Yu & Shanshan Li, 2022. "SESAME-catalyzed H3T11 phosphorylation inhibits Dot1-catalyzed H3K79me3 to regulate autophagy and telomere silencing," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    11. Dongmei Wang & Haimin Li & Navdeep S. Chandel & Yali Dou & Rui Yi, 2023. "MOF-mediated histone H4 Lysine 16 acetylation governs mitochondrial and ciliary functions by controlling gene promoters," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    12. Iksoo Huh & Isabel Mendizabal & Taesung Park & Soojin V Yi, 2018. "Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals," PLOS Computational Biology, Public Library of Science, vol. 14(10), pages 1-21, October.
    13. Xiaozhen Zhao & Yiming Wang & Bingqin Yuan & Hanxi Zhao & Yujie Wang & Zheng Tan & Zhiyuan Wang & Huijun Wu & Gang Li & Wei Song & Ravi Gupta & Kenichi Tsuda & Zhonghua Ma & Xuewen Gao & Qin Gu, 2024. "Temporally-coordinated bivalent histone modifications of BCG1 enable fungal invasion and immune evasion," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    14. Jacob D Feala & Jorge Cortes & Phillip M Duxbury & Andrew D McCulloch & Carlo Piermarocchi & Giovanni Paternostro, 2012. "Statistical Properties and Robustness of Biological Controller-Target Networks," PLOS ONE, Public Library of Science, vol. 7(1), pages 1-11, January.
    15. Mar González-Ramírez & Cecilia Ballaré & Francesca Mugianesi & Malte Beringer & Alexandra Santanach & Enrique Blanco & Luciano Di Croce, 2021. "Differential contribution to gene expression prediction of histone modifications at enhancers or promoters," PLOS Computational Biology, Public Library of Science, vol. 17(9), pages 1-29, September.
    16. Amy L. Hughes & Aleksander T. Szczurek & Jessica R. Kelley & Anna Lastuvkova & Anne H. Turberfield & Emilia Dimitrova & Neil P. Blackledge & Robert J. Klose, 2023. "A CpG island-encoded mechanism protects genes from premature transcription termination," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    17. Saket Navlakha & Anthony Gitter & Ziv Bar-Joseph, 2012. "A Network-based Approach for Predicting Missing Pathway Interactions," PLOS Computational Biology, Public Library of Science, vol. 8(8), pages 1-13, August.
    18. Kana Shimomura & Naoko Hattori & Naoko Iida & Yukari Muranaka & Kotomi Sato & Yuichi Shiraishi & Yasuhito Arai & Natsuko Hama & Tatsuhiro Shibata & Daichi Narushima & Mamoru Kato & Hiroyuki Takamaru &, 2023. "Sleeping Beauty transposon mutagenesis identified genes and pathways involved in inflammation-associated colon tumor development," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    19. Mengwen Hu & Yu-Han Yeh & Yasuhisa Munakata & Hironori Abe & Akihiko Sakashita & So Maezawa & Miguel Vidal & Haruhiko Koseki & Neil Hunter & Richard M. Schultz & Satoshi H. Namekawa, 2022. "PRC1-mediated epigenetic programming is required to generate the ovarian reserve," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    20. Silvia Martini & Khalil Davis & Rupert Faraway & Lisa Elze & Nicola Lockwood & Andrew Jones & Xiao Xie & Neil Q. McDonald & David J. Mann & Alan Armstrong & Jernej Ule & Peter J. Parker, 2021. "A genetically-encoded crosslinker screen identifies SERBP1 as a PKCε substrate influencing translation and cell division," Nature Communications, Nature, vol. 12(1), pages 1-16, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33423-5. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.