7e40

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Mechanism of Phosphate Sensing and Signaling Revealed by Rice SPX1-PHR2 Complex StructureMechanism of Phosphate Sensing and Signaling Revealed by Rice SPX1-PHR2 Complex Structure

Structural highlights

7e40 is a 4 chain structure with sequence from Escherichia virus T4 and Oryza sativa Japonica Group. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PHR2_ORYSJ Transcription factor involved in phosphate starvation signaling (PubMed:18263782, PubMed:26082401). Binds to P1BS, an imperfect palindromic sequence 5'-GNATATNC-3', to promote the expression of inorganic phosphate (Pi) starvation-responsive genes (PubMed:25657119, PubMed:26082401). Functionally redundant with PHR1 and PHR3 in regulating Pi starvation response and Pi homeostasis (PubMed:26082401). Involved in both systematic and local Pi-signaling pathways (PubMed:19704822). Regulates several Pi transporters (PubMed:18263782). Regulates the expression of PT2 (PubMed:20149131). Directly up-regulates SPX1 and SPX2 expression, but PHR2 binding to DNA is repressed redundantly by SPX1 and SPX2 in a PI-dependent manner (PubMed:25271318). The DNA-binding activity is also repressed by SPX4 (PubMed:24692424). Involved in root growth under Pi deprivation (PubMed:18263782). Involved in the modulation of Pi response and homeostasis together with RLI1; promotes RLI1 expression in response to nitrate availability, thus triggering the nitrate-induced phosphate response (NIPR) (PubMed:33316467, PubMed:35640569).[1] [2] [3] [4] [5] [6] [7] [8] [9]

Publication Abstract from PubMed

Phosphate, a key plant nutrient, is perceived through inositol polyphosphates (InsPs) by SPX domain-containing proteins. SPX1 an inhibit the PHR2 transcription factor to maintain Pi homeostasis. How SPX1 recognizes an InsP molecule and represses transcription activation by PHR2 remains unclear. Here we show that, upon binding InsP(6), SPX1 can disrupt PHR2 dimers and form a 1:1 SPX1-PHR2 complex. The complex structure reveals that SPX1 helix alpha1 can impose a steric hindrance when interacting with the PHR2 dimer. By stabilizing helix alpha1, InsP(6) allosterically decouples the PHR2 dimer and stabilizes the SPX1-PHR2 interaction. In doing so, InsP(6) further allows SPX1 to engage with the PHR2 MYB domain and sterically block its interaction with DNA. Taken together, our results suggest that, upon sensing the surrogate signals of phosphate, SPX1 inhibits PHR2 via a dual mechanism that attenuates dimerization and DNA binding activities of PHR2.

Mechanism of phosphate sensing and signaling revealed by rice SPX1-PHR2 complex structure.,Zhou J, Hu Q, Xiao X, Yao D, Ge S, Ye J, Li H, Cai R, Liu R, Meng F, Wang C, Zhu JK, Lei M, Xing W Nat Commun. 2021 Dec 2;12(1):7040. doi: 10.1038/s41467-021-27391-5. PMID:34857773[10]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Zhou J, Jiao F, Wu Z, Li Y, Wang X, He X, Zhong W, Wu P. OsPHR2 is involved in phosphate-starvation signaling and excessive phosphate accumulation in shoots of plants. Plant Physiol. 2008 Apr;146(4):1673-86. PMID:18263782 doi:10.1104/pp.107.111443
  2. ↑ Wu P, Wang X. Role of OsPHR2 on phosphorus homeostasis and root hairs development in rice (Oryza sativa L.). Plant Signal Behav. 2008 Sep;3(9):674-5. PMID:19704822 doi:10.4161/psb.3.9.5781
  3. ↑ Liu F, Wang Z, Ren H, Shen C, Li Y, Ling HQ, Wu C, Lian X, Wu P. OsSPX1 suppresses the function of OsPHR2 in the regulation of expression of OsPT2 and phosphate homeostasis in shoots of rice. Plant J. 2010 May;62(3):508-17. PMID:20149131 doi:10.1111/j.1365-313X.2010.04170.x
  4. ↑ Lv Q, Zhong Y, Wang Y, Wang Z, Zhang L, Shi J, Wu Z, Liu Y, Mao C, Yi K, Wu P. SPX4 Negatively Regulates Phosphate Signaling and Homeostasis through Its Interaction with PHR2 in Rice. Plant Cell. 2014 Apr;26(4):1586-1597. PMID:24692424 doi:10.1105/tpc.114.123208
  5. ↑ Wang Z, Ruan W, Shi J, Zhang L, Xiang D, Yang C, Li C, Wu Z, Liu Y, Yu Y, Shou H, Mo X, Mao C, Wu P. Rice SPX1 and SPX2 inhibit phosphate starvation responses through interacting with PHR2 in a phosphate-dependent manner. Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):14953-8. PMID:25271318 doi:10.1073/pnas.1404680111
  6. ↑ Ruan W, Guo M, Cai L, Hu H, Li C, Liu Y, Wu Z, Mao C, Yi K, Wu P, Mo X. Genetic manipulation of a high-affinity PHR1 target cis-element to improve phosphorous uptake in Oryza sativa L. Plant Mol Biol. 2015 Mar;87(4-5):429-40. PMID:25657119 doi:10.1007/s11103-015-0289-y
  7. ↑ Guo M, Ruan W, Li C, Huang F, Zeng M, Liu Y, Yu Y, Ding X, Wu Y, Wu Z, Mao C, Yi K, Wu P, Mo X. Integrative Comparison of the Role of the PHOSPHATE RESPONSE1 Subfamily in Phosphate Signaling and Homeostasis in Rice. Plant Physiol. 2015 Aug;168(4):1762-76. PMID:26082401 doi:10.1104/pp.15.00736
  8. ↑ Zhang Z, Li Z, Wang W, Jiang Z, Guo L, Wang X, Qian Y, Huang X, Liu Y, Liu X, Qiu Y, Li A, Yan Y, Xie J, Cao S, Kopriva S, Li L, Kong F, Liu B, Wang Y, Hu B, Chu C. Modulation of nitrate-induced phosphate response by the MYB transcription factor RLI1/HINGE1 in the nucleus. Mol Plant. 2021 Mar 1;14(3):517-529. PMID:33316467 doi:10.1016/j.molp.2020.12.005
  9. ↑ Guo M, Zhang Y, Jia X, Wang X, Zhang Y, Liu J, Yang Q, Ruan W, Yi K. Alternative splicing of REGULATOR OF LEAF INCLINATION 1 modulates phosphate starvation signaling and growth in plants. Plant Cell. 2022 Aug 25;34(9):3319-3338. PMID:35640569 doi:10.1093/plcell/koac161
  10. ↑ Zhou J, Hu Q, Xiao X, Yao D, Ge S, Ye J, Li H, Cai R, Liu R, Meng F, Wang C, Zhu JK, Lei M, Xing W. Mechanism of phosphate sensing and signaling revealed by rice SPX1-PHR2 complex structure. Nat Commun. 2021 Dec 2;12(1):7040. PMID:34857773 doi:10.1038/s41467-021-27391-5

7e40, resolution 2.60Å

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