A phytochrome-B-mediated regulatory mechanism of phosphorus acquisition


Phosphorus (P) is a key macronutrient whose availability has a profound effect on plant growth and productivity. The understanding of the mechanism underlying P availability-responsive P acquisition has expanded largely in the past decade; however, effects of other environmental factors on P acquisition and utilization remain elusive. Here, by imaging natural variation in phosphate uptake in 200 natural accessions of Arabidopsis, we identify two accessions with low phosphate uptake activity, Lm-2 and CSHL-5. In these accessions, natural variants of phytochrome B were found to cause both decreased light sensitivity and lower phosphate uptake. Furthermore, we also found that expression levels of phosphate starvation-responsive genes are directly modulated by phytochrome interacting factors (PIF) PIF4/PIF5 and HY5 transcription factors whose activity is under the control of phytochromes. These findings disclose a new molecular mechanism underlying red-light-induced activation of phosphate uptake, which is responsible for different activity for P acquisition in some natural accessions of Arabidopsis.

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Fig. 1: Natural variation in phyB affects Pi uptake activity.
Fig. 2: Effect of red light on Pi uptake and accumulation.
Fig. 3: PIF4 and PIF5 are involved in the regulation of Pi uptake.
Fig. 4: Modifications in expression of Pi uptake-related and Pi starvation-responsive genes in the pif4 pif5 mutant.
Fig. 5: PIF4 and PIF5 directly repress transcription of PHT1;1 and PHL1.
Fig. 6: HY5 directly activates PHT1;1 transcription.

Data availability

The datasets generated and/or analysed in this study are available from the corresponding author upon any reasonable request.


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We thank the Arabidopsis Biological Resource Center for seeds from the transfer-DNA lines, J. Paz-Ares (Centro Nacional de Biotecnología, Spain) for seeds of the phr1 phl1 mutant and M. Tsumura in our laboratory for assistance in plant cultivation. This work was supported in part by JST CREST grant number JPMJCR 15O5 to S.Y. and K.I., JSPS KAKENHI grant number 26221103 to K.I. and S.Y., and grant numbers 25252014 to S.Y., 17H05024 to Y.S. and 16H07045 to K.M.

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Y.S. and S.Y. designed the research. Y.S. performed experiments. S.K., A.M., K.M. and K.I. provided the new analytical tools and plant materials used in this study. Y.S. and S.Y. analysed the data and wrote the article.

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Correspondence to Shuichi Yanagisawa.

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Supplementary Figures 1–21

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Supplementary Tables 1–6

Supplementary Table 1: List of Arabidopsis accessions used in this study and their Pi uptake activities. Supplementary Table 2: Genes upregulated or downregulated in pif4 pif5 seedlings grown under the standard Pi condition. Supplementary Table 3: Genes upregulated or downregulated in pif4 pif5 seedlings grown under the Pi-deficient condition. Supplementary Table 4: List of Arabidopsis mutants used in this study. Supplementary Table 5: List of primer sequences used in this study. Supplementary Table 6: List of Arabidopsis accessions used for GWAS.

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Sakuraba, Y., Kanno, S., Mabuchi, A. et al. A phytochrome-B-mediated regulatory mechanism of phosphorus acquisition. Nature Plants 4, 1089–1101 (2018). https://doi.org/10.1038/s41477-018-0294-7

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