Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Nitrate–NRT1.1B–SPX4 cascade integrates nitrogen and phosphorus signalling networks in plants

Nature Plants volume 5, pages 401–413 (2019)Cite this article

Subjects

An Author Correction to this article was published on 24 April 2019

This article has been updated

Abstract

To ensure high crop yields in a sustainable manner, a comprehensive understanding of the control of nutrient acquisition is required. In particular, the signalling networks controlling the coordinated utilization of the two most highly demanded mineral nutrients, nitrogen and phosphorus, are of utmost importance. Here, we reveal a mechanism by which nitrate activates both phosphate and nitrate utilization in rice (Oryza sativa L.). We show that the nitrate sensor NRT1.1B interacts with a phosphate signalling repressor SPX4. Nitrate perception strengthens the NRT1.1B–SPX4 interaction and promotes the ubiquitination and degradation of SPX4 by recruiting NRT1.1B interacting protein 1 (NBIP1), an E3 ubiquitin ligase. This in turn allows the key transcription factor of phosphate signalling, PHR2, to translocate to the nucleus and initiate the transcription of phosphorus utilization genes. Interestingly, the central transcription factor of nitrate signalling, NLP3, is also under the control of SPX4. Thus, nitrate-triggered degradation of SPX4 activates both phosphate- and nitrate-responsive genes, implementing the coordinated utilization of nitrogen and phosphorus.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Nitrate activates phosphate utilization in rice.
Fig. 2: NRT1.1B is involved in nitrate-induced phosphate signalling.
Fig. 3: The SPX4PHR2 module is regulated by nitrate treatment.
Fig. 4: NRT1.1B–SPX4 interactions underlie nitrate-induced phosphate signalling.
Fig. 5: SPX4 modulates NLP3 cytoplasmic–nuclear shuttling.
Fig. 6: NRT1.1B recruits NBIP1 to mediate SPX4 ubiquitination and degradation.
Fig. 7: Proposed model of N–P coordinated responses.

Similar content being viewed by others

Data availability

The data that support the findings of this study are available from the corresponding authors upon request.

Change history

  • 24 April 2019

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

  • 15 May 2019

    Owing to a technical fault, in the corrected version of the left panel of Fig. 4g, an extraneous vertical line appeared; this has now been removed.

References

  1. Young, V. R. Nutritional balance studies: indicators of human requirements or of adaptive mechanisms? J. Nutr. 116, 700–703 (1986).

    Article  CAS  Google Scholar 

  2. Hill, J. O. et al. Nutrient balance in humans: effects of diet composition. Am. J. Clin. Nutr. 54, 10–17 (1991).

    Article  CAS  Google Scholar 

  3. Carreiro, A. L. et al. The macronutrients, appetite, and energy intake. Annu. Rev. Nutr. 36, 73–103 (2016).

    Article  CAS  Google Scholar 

  4. Güsewell, S. N:P ratios in terrestrial plants: variation and functional significance. New Phytol. 164, 243–266 (2004).

    Article  Google Scholar 

  5. Khan, F. et al. Effect of different levels of nitrogen and phosphorus on the phenology and yield of maize varieties. Am. J. Plant Sci. 5, 2582–2590 (2014).

    Article  CAS  Google Scholar 

  6. Luo, X. et al. Nitrogen: phosphorous supply ratio and allometry in five alpine plant species. Ecol. Evol. 6, 8881–8892 (2016).

    Article  Google Scholar 

  7. Güsewell, S. Responses of wetland graminoids to the relative supply of nitrogen and phosphorus. Plant Ecol. 176, 35–55 (2005).

    Article  Google Scholar 

  8. Liu, K. H. & Tsay, Y. F. Switching between the two action modes of the dual-affinity nitrate transporter CHL1 by phosphorylation. EMBO J. 22, 1005–1013 (2003).

    Article  CAS  Google Scholar 

  9. Ho, C. H., Lin, S. H., Hu, H. C. & Tsay, Y. F. CHL1 functions as a nitrate sensor in plants. Cell 138, 1184–1194 (2009).

    Article  CAS  Google Scholar 

  10. Hu, B. et al. Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies. Nat. Genet. 47, 834–838 (2015).

    Article  CAS  Google Scholar 

  11. Marchive, C. et al. Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants. Nat. Commun. 4, 1713 (2013).

    Article  Google Scholar 

  12. Liu, K. H. et al. Discovery of nitrate–CPK–NLP signalling in central nutrient–growth networks. Nature 545, 311–316 (2017).

    Article  CAS  Google Scholar 

  13. Rubio, V. A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae. Genes Dev. 15, 2122–2133 (2001).

    Article  CAS  Google Scholar 

  14. Lv, Q. et al. SPX4 negatively regulates phosphate signaling and homeostasis through its interaction with PHR2 in rice. Plant Cell 26, 1586–1597 (2014).

    Article  CAS  Google Scholar 

  15. Wild, R. et al. Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains. Science 352, 986–990 (2016).

    Article  CAS  Google Scholar 

  16. Puga, M. I. et al. SPX1 is a phosphate-dependent inhibitor of phosphate starvation response 1 in arabidopsis. Proc. Natl Acad. Sci. USA 111, 14947–14952 (2014).

    Article  CAS  Google Scholar 

  17. Wang, Z. et al. Rice SPX1 and SPX2 inhibit phosphate starvation responses through interacting with PHR2 in a phosphate-dependent manner. Proc. Natl Acad. Sci. USA 111, 14953–14958 (2014).

    Article  CAS  Google Scholar 

  18. Kant, S., Peng, M. & Rothstein, S. J. Genetic regulation by NLA and microRNA827 for maintaining nitrate-dependent phosphate homeostasis in Arabidopsis. PLoS Genet. 7, e1002021 (2011).

    Article  CAS  Google Scholar 

  19. Medici, A. et al. Atnigt1/hrs1 integrates nitrate and phosphate signals at the Arabidopsis root tip. Nat. Commun. 6, 6274 (2015).

    Article  CAS  Google Scholar 

  20. Kiba, T. et al. Repression of nitrogen-starvation responses by members of the Arabidopsis GARP-type transcription factor NIGT1/HRS1 subfamily. Plant Cell 30, 925–945 (2018).

    Article  CAS  Google Scholar 

  21. Maeda, Y. et al. A NIGT1-centred transcriptional cascade regulates nitrate signalling and incorporates phosphorus starvation signals in Arabidopsis. Nat. Commun. 9, 1376 (2018).

    Article  Google Scholar 

  22. Sun, J. et al. Crystal structure of the plant dual-affinity nitrate transporter NRT1.1. Nature 507, 73–77 (2014).

    Article  CAS  Google Scholar 

  23. Parker, J. L. & Newstead, S. Molecular basis of nitrate uptake by the plant nitrate transporter NRT1.1. Nature 507, 68–72 (2014).

    Article  CAS  Google Scholar 

  24. Chardin, C., Girin, T., Roudier, F., Meyer, C. & Krapp, A. The plant RWP-RK transcription factors: key regulators of nitrogen responses and of gametophyte development. J. Exp. Bot. 65, 5577–5587 (2014).

    Article  CAS  Google Scholar 

  25. Lopez-Arredondo, D. L., Leyva-Gonzalez, M. A., Alatorre-Cobos, F. & Herrera-Estrella, L. Biotechnology of nutrient uptake and assimilation in plants. Int. J. Dev. Biol. 57, 595–610 (2013).

    Article  CAS  Google Scholar 

  26. Wang, R. et al. Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol. 136, 2512–2522 (2004).

    Article  CAS  Google Scholar 

  27. Lin, S. I. et al. Complex regulation of two target genes encoding SPX-MFS proteins by rice miR827 in response to phosphate starvation. Plant Cell Physiol. 51, 2119–2131 (2010).

    Article  CAS  Google Scholar 

  28. Yue, W. et al. OsNLA1, a RING-type ubiquitin ligase, maintains phosphate homeostasis in Oryza sativa via degradation of phosphate transporters. Plant J. 90, 1040–1051 (2017).

    Article  CAS  Google Scholar 

  29. Lopez-Bucio, J., Cruz-Ramirez, A. & Herrera-Estrella, L. The role of nutrient availability in regulating root architecture. Curr. Opin. Plant Biol. 6, 280–287 (2003).

    Article  CAS  Google Scholar 

  30. Sánchez-Calderón, L., Chacón-López, A., Alatorre-Cobos, F., Leyva-González, M. A. & Herrera-Estrella, L. in Transporters and Pumps in Plant Signaling (eds Markus Geisler & Kees Venema) 191–224 (Springer, 2011).

  31. Poitout, A. et al. Responses to systemic nitrogen signaling in Arabidopsis roots involve trans-Zeatin in shoots. Plant Cell 30, 1243–1257 (2018).

    Article  CAS  Google Scholar 

  32. Takei, K. et al. AtIPT3 is a key determinant of nitrate-dependent cytokinin biosynthesis in Arabidopsis. Plant Cell Physiol. 45, 1053–1062 (2004).

    Article  CAS  Google Scholar 

  33. Martin, A. C. et al. Influence of cytokinins on the expression of phosphate starvation responsive genes in Arabidopsis. Plant J. 24, 559–567 (2000).

    Article  CAS  Google Scholar 

  34. Wang, X. M. et al. Cytokinin represses phosphate-starvation response through increasing of intracellular phosphate level. Plant Cell Environ. 29, 1924–1935 (2006).

    Article  CAS  Google Scholar 

  35. Lu, Y. et al. Genome-wide targeted mutagenesis in rice using the CRISPR/Cas9 system. Mol. Plant 10, 1242–1245 (2017).

    Article  CAS  Google Scholar 

  36. Hellens, R. P. et al. Transient expression vectors for functional genomics, quantification of promoter activity and RNA silencing in plants. Plant Methods 1, 13 (2005).

    Article  Google Scholar 

  37. Chen, H. et al. Firefly luciferase complementation imaging assay for protein–protein interactions in plants. Plant Physiol. 146, 368–376 (2008).

    Article  CAS  Google Scholar 

  38. Luo, A. et al. EUI1, encoding a putative cytochrome P450 monooxygenase, regulates internode elongation by modulating gibberellin responses in rice. Plant Cell Physiol. 47, 181–191 (2006).

    Article  CAS  Google Scholar 

  39. Hiei, Y., Ohta, S., Komari, T. & Kumashiro, T. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence-analysis of the boundaries of the T-DNA. Plant J. 6, 271–282 (1994).

    Article  CAS  Google Scholar 

  40. Wang, C. et al. Involvement of OsSPX1 in phosphate homeostasis in rice. Plant J. 57, 895–904 (2009).

    Article  CAS  Google Scholar 

  41. Hu, B. et al. Leaf tip necrosis1 plays a pivotal role in the regulation of multiple phosphate starvation responses in rice. Plant Physiol. 156, 1101–1115 (2011).

    Article  CAS  Google Scholar 

  42. Yoo, S. D., Cho, Y. H. & Sheen, J. Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat. Protoc. 2, 1565–1672 (2007).

    Article  CAS  Google Scholar 

  43. Zhang, Y. et al. A highly efficient rice green tissue protoplast system for transient gene expression and studying light/chloroplast-related processes. Plant Methods 7, 30 (2011).

    Article  CAS  Google Scholar 

  44. Hecker, A. et al. Binary 2in1 vectors improve in planta (co)localization and dynamic protein interaction studies. Plant Physiol. 168, 776–787 (2015).

    Article  Google Scholar 

  45. Zhao, Q., Liu, L. & Xie, Q. In vitro protein ubiquitination assay. Methods Mol. Biol. 876, 163–172 (2012).

    Article  CAS  Google Scholar 

  46. Zhao, Q. et al. A plant‐specific in vitro ubiquitination analysis system. Plant J. 74, 524–533 (2013).

    Article  CAS  Google Scholar 

  47. Wang, Z. et al. SCFSAP controls organ size by targeting PPD proteins for degradation in Arabidopsis thaliana. Nat. Commun. 7, 11192 (2016).

    Article  CAS  Google Scholar 

  48. van Dongen, W., Van Heerde, L., Boeren, S. & De Vries, S. C. Identification of brassinosteroid signaling complexes by coimmunoprecipitation and mass spectrometry. Methods Mol. Biol. 1564, 145–154 (2017).

    Article  Google Scholar 

Download references

Acknowledgements

pCAMBIA1300–nLUC/cLUC vectors were kindly provided by J.-M. Zhou, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences. The SPX4pro–gSPX4–GUS transgenic rice was kindly provided by C. Mao, College of Life Sciences, Zhejiang University. The authors thank T. O. Jobe (University of Cologne) for proofreading the manuscript. This work was supported by grants from the Chinese Academy of Sciences (XDA08010400), the National Natural Sciences Foundation of China (31500975 and 31771348) and the China Postdoctoral Science Foundation (2017M610126). Research in the laboratory of S. Kopriva was supported by Deutsche Forschungsgemeinschaft (EXC 1028).

Author information

Author notes

  1. These authors contributed equally: Bin Hu, Zhimin Jiang, Wei Wang, Yahong Qiu.

Authors and Affiliations

  1. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

    Bin Hu, Zhimin Jiang, Wei Wang, Yahong Qiu, Zhihua Zhang, Yongqiang Liu, Aifu Li, Xiaokai Gao, Linchuan Liu, Feifei Yu, Sai Kang, Yiqin Wang, Junpeng Xie, Shouyun Cao, Qi Xie & Chengcai Chu

  2. College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China

    Yahong Qiu, Zhihua Zhang, Yongqiang Liu, Aifu Li, Junpeng Xie & Chengcai Chu

  3. Biogle Genome Editing Center, Changzhou, China

    Yangwen Qian

  4. State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

    Xiahe Huang & Yingchun Wang

  5. School of Agriculture, Henan University of Science and Technology, Luoyang, China

    Lianhe Zhang

  6. Botanical Institute, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany

    Stanislav Kopriva

Authors
  1. Bin Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhimin Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wei Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yahong Qiu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zhihua Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yongqiang Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Aifu Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Xiaokai Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Linchuan Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Yangwen Qian
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Xiahe Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Feifei Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Sai Kang
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Yiqin Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Junpeng Xie
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Shouyun Cao
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Lianhe Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Yingchun Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Qi Xie
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Stanislav Kopriva
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. Chengcai Chu
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

B.H., Z.J. and W.W. designed research, performed experiments, analysed the data and wrote the manuscript. Y. Qiu, Z.Z., Y.L., A.L., X.G., L.L., Y. Qian, X.H., F.Y., S. Kang, Yiq. W., J.X., S.C., L.Z., Ying. W., Q.X. and S. Kopriva conducted some of the experiments. C.C. designed research, wrote the manuscript and supervised the project.

Corresponding authors

Correspondence to Bin Hu or Chengcai Chu.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Journal peer review information: Nature Plants thanks Dong Liu, Nicholaus von Wiren, Ying Liu, Ricardo Giehl and other anonymous reviewers for their contribution to the peer review of this work.

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figures 1–14 and Supplementary Table 1.

Reporting Summary

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hu, B., Jiang, Z., Wang, W. et al. Nitrate–NRT1.1B–SPX4 cascade integrates nitrogen and phosphorus signalling networks in plants. Nat. Plants 5, 401–413 (2019). https://doi.org/10.1038/s41477-019-0384-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41477-019-0384-1

This article is cited by

Search

Advanced search

Quick links

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