Two bifunctional inositol pyrophosphate kinases/phosphatases control plant phosphate homeostasis

  1. Jinsheng Zhu
  2. Kelvin Lau
  3. Robert Puschmann
  4. Robert K Harmel
  5. Youjun Zhang
  6. Verena Pries
  7. Philipp Gaugler
  8. Larissa Broger
  9. Amit K Dutta
  10. Henning J Jessen
  11. Gabriel Schaaf
  12. Alisdair R Fernie
  13. Ludwig A Hothorn
  14. Dorothea Fiedler
  15. Michael Hothorn  Is a corresponding author
  1. University of Geneva, Switzerland
  2. Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Germany
  3. Max-Planck Institute of Molecular Plant Physiology, Germany
  4. University of Bonn, Germany
  5. Albert-Ludwigs-Universität Freiburg, Germany
  6. Max-Planck Institute for Molecular Plant Physiology, Germany
  7. Leibniz University, Germany

Abstract

Many eukaryotic proteins regulating phosphate (Pi) homeostasis contain SPX domains that are receptors for inositol pyrophosphates (PP-InsP), suggesting that PP-InsPs may regulate Pi homeostasis. Here we report that deletion of two diphosphoinositol pentakisphosphate kinases VIH1/2 impairs plant growth and leads to constitutive Pi starvation responses. Deletion of phosphate starvation response transcription factors partially rescues vih1 vih2 mutant phenotypes, placing diphosphoinositol pentakisphosphate kinases in plant Pi signal transduction cascades. VIH1/2 are bifunctional enzymes able to generate and break-down PP-InsPs. Mutations in the kinase active site lead to increased Pi levels and constitutive Pi starvation responses. ATP levels change significantly in different Pi growth conditions. ATP-Mg2+ concentrations shift the relative kinase and phosphatase activities of diphosphoinositol pentakisphosphate kinases in vitro. Pi inhibits the phosphatase activity of the enzyme. Thus, VIH1 and VIH2 relay changes in cellular ATP and Pi concentrations to changes in PP-InsP levels, allowing plants to maintain sufficient Pi levels.

Data availability

Pi measurements: raw data included in actual figurePhenotypes: representative lines shown in main figures, at least three independent lines shown in figure supplementsWestern blots: full western blots shown in figure supplementsProtein gels: Full gels shown in figure 5 supplement 1 and figure 6 supplement 1DNA sequences of the truncated VIH2 transcript is in figure 2 supplement 1NMR data: full 1D and 2D spectra shown in figure 5 and figure 5 supplement 2, figure 6 supplement 2

Article and author information

Author details

  1. Jinsheng Zhu

    Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneve, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8131-1876
  2. Kelvin Lau

    Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneve, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  3. Robert Puschmann

    Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6443-2326
  4. Robert K Harmel

    Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Youjun Zhang

    Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Verena Pries

    Department of Plant Nutrition, University of Bonn, Bonn, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Philipp Gaugler

    Department of Plant Nutrition, University of Bonn, Bonn, Germany
    Competing interests
    The authors declare that no competing interests exist.
  8. Larissa Broger

    Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneve, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  9. Amit K Dutta

    Institute of Organic Chemistry, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  10. Henning J Jessen

    Institute of Organic Chemistry, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  11. Gabriel Schaaf

    Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Bonn, Germany
    Competing interests
    The authors declare that no competing interests exist.
  12. Alisdair R Fernie

    Max-Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
    Competing interests
    The authors declare that no competing interests exist.
  13. Ludwig A Hothorn

    Institute of Biostatistics, Leibniz University, Hannover, Germany
    Competing interests
    The authors declare that no competing interests exist.
  14. Dorothea Fiedler

    Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  15. Michael Hothorn

    Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneve, Switzerland
    For correspondence
    michael.hothorn@unige.ch
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3597-5698

Funding

H2020 European Research Council (310856)

  • Michael Hothorn

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (CRSII5_170925)

  • Dorothea Fiedler
  • Michael Hothorn

Howard Hughes Medical Institute (55008733)

  • Michael Hothorn

European Molecular Biology Organization (ALTF 493-2015)

  • Kelvin Lau

Leibniz-Gemeinschaft (SAW-2017-FMP-1)

  • Dorothea Fiedler

Deutsche Forschungsgemeinschaft (SCHA 1274/4-1)

  • Gabriel Schaaf

Max-Planck-Gesellschaft

  • Youjun Zhang
  • Alisdair R Fernie

Horizon 2020 Framework Programme (PlantaSYST)

  • Youjun Zhang
  • Alisdair R Fernie

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

Reviewing Editor

  1. Jürgen Kleine-Vehn, University of Natural Resources and Life Sciences, Austria

Publication history

  1. Received: November 12, 2018
  2. Accepted: August 21, 2019
  3. Accepted Manuscript published: August 22, 2019 (version 1)
  4. Version of Record published: September 6, 2019 (version 2)

Copyright

© 2019, Zhu 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

  • 4,501
    Page views
  • 774
    Downloads
  • 63
    Citations

Article citation count generated by polling the highest count across the following sources: Scopus, Crossref, PubMed Central.

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. Jinsheng Zhu
  2. Kelvin Lau
  3. Robert Puschmann
  4. Robert K Harmel
  5. Youjun Zhang
  6. Verena Pries
  7. Philipp Gaugler
  8. Larissa Broger
  9. Amit K Dutta
  10. Henning J Jessen
  11. Gabriel Schaaf
  12. Alisdair R Fernie
  13. Ludwig A Hothorn
  14. Dorothea Fiedler
  15. Michael Hothorn
(2019)
Two bifunctional inositol pyrophosphate kinases/phosphatases control plant phosphate homeostasis
eLife 8:e43582.
https://doi.org/10.7554/eLife.43582
  1. Further reading

Further reading

    1. Biochemistry and Chemical Biology
    2. Neuroscience
    Jinli Geng, Yingjun Tang ... Xiaodong Liu
    Research Article Updated

    Dynamic Ca2+ signals reflect acute changes in membrane excitability, and also mediate signaling cascades in chronic processes. In both cases, chronic Ca2+ imaging is often desired, but challenged by the cytotoxicity intrinsic to calmodulin (CaM)-based GCaMP, a series of genetically-encoded Ca2+ indicators that have been widely applied. Here, we demonstrate the performance of GCaMP-X in chronic Ca2+ imaging of cortical neurons, where GCaMP-X by design is to eliminate the unwanted interactions between the conventional GCaMP and endogenous (apo)CaM-binding proteins. By expressing in adult mice at high levels over an extended time frame, GCaMP-X showed less damage and improved performance in two-photon imaging of sensory (whisker-deflection) responses or spontaneous Ca2+ fluctuations, in comparison with GCaMP. Chronic Ca2+ imaging of one month or longer was conducted for cultured cortical neurons expressing GCaMP-X, unveiling that spontaneous/local Ca2+ transients progressively developed into autonomous/global Ca2+ oscillations. Along with the morphological indices of neurite length and soma size, the major metrics of oscillatory Ca2+, including rate, amplitude and synchrony were also examined. Dysregulations of both neuritogenesis and Ca2+ oscillations became discernible around 2–3 weeks after virus injection or drug induction to express GCaMP in newborn or mature neurons, which were exacerbated by stronger or prolonged expression of GCaMP. In contrast, neurons expressing GCaMP-X were significantly less damaged or perturbed, altogether highlighting the unique importance of oscillatory Ca2+ to neural development and neuronal health. In summary, GCaMP-X provides a viable solution for Ca2+ imaging applications involving long-time and/or high-level expression of Ca2+ probes.

    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression
    Radhika A Varier, Theodora Sideri ... Folkert Jacobus van Werven
    Research Article

    N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3’end of meiotic mRNAs in both an m6A-dependent and independent manner. Within cells, Pho92 transitions from the nucleus to the cytoplasm, and associates with translating ribosomes. In the nucleus Pho92 associates with target loci through its interaction with transcriptional elongator Paf1C. Functionally, we show that Pho92 promotes and links protein synthesis to mRNA decay. As such, the Pho92-mediated m6A-mRNA decay is contingent on active translation and the CCR4-NOT complex. We propose that the m6A reader Pho92 is loaded co-transcriptionally to facilitate protein synthesis and subsequent decay of m6A modified transcripts, and thereby promotes meiosis.