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Phenolic acid-induced phase separation and translation inhibition mediate plant interspecific competition

Abstract

Phenolic acids (PAs) secreted by donor plants suppress the growth of their susceptible plant neighbours. However, how structurally diverse ensembles of PAs are perceived by plants to mediate interspecific competition remains a mystery. Here we show that a plant stress granule (SG) marker, RNA-BINDING PROTEIN 47B (RBP47B), is a sensor of PAs in Arabidopsis. PAs, including salicylic acid, 4-hydroxybenzoic acid, protocatechuic acid and so on, directly bind RBP47B, promote its phase separation and trigger SG formation accompanied by global translation inhibition. Salicylic acid-induced global translation inhibition depends on RBP47 family members. RBP47s regulate the proteome rather than the absolute quantity of SG. The rbp47 quadruple mutant shows a reduced sensitivity to the inhibitory effect of the PA mixture as well as to that of PA-rich rice when tested in a co-culturing ecosystem. In this Article, we identified the long sought-after PA sensor as RBP47B and illustrated that PA-induced SG-mediated translational inhibition was one of the PA perception mechanisms.

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Fig. 1: PAs trigger SG formation in Arabidopsis.
Fig. 2: Phase separation of RBP47B in vitro and in vivo.
Fig. 3: SA binds RBP47B and regulates its foci formation.
Fig. 4: RBP47B binds various PAs and SA derivatives.
Fig. 5: RBP47 family members regulate SA-induced SG proteome.
Fig. 6: RBP47 family members mediate SA-induced global translation inhibition.
Fig. 7: RBP47 family members mediate perception of PAs in Arabidopsis.

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Data availability

The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE72 partner repository with the dataset identifier PXD043123. All data supporting the findings of this study are available in the main text, the supplementary figures and tables, and from the corresponding authors upon reasonable request. Source data are provided with this paper.

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Acknowledgements

We thank Y. Tada of Nagoya University for helping with the pGWB661 vector, Y. Li of Peking University for providing the Monolith NT.115 instrument, L. Lai of Peking University for advice on the initial exploration of the MST assay, P. Li of Tsinghua University for advice on the experiments related to phase separation and X. Dong of Duke University for discussion on this work. We thank the Core Facilities of the School of Life Sciences and the National Center for Protein Sciences at Peking University in Beijing, China, for assistance with large-scale protein purification, live-cell imaging and data analysis, particularly S. Qin and H. Lv for technical help with confocal imaging and 3D image analysis. This work was supported by funds from the National Natural Science Foundation of China (31970641); the State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Center for Life Sciences; the USDA National Institute of Food and Agriculture, Hatch project 3808 to W.W.; the National Natural Science Foundation of China (31970283); Beijing Nova Program of Science and Technology (Z191100001119027); Capital Normal University and State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, to M.Z.; the European Commission Marie Curie-IEF reSGulating-702473 to E.G.B.; Natural Science Foundation of Fujian Province (2020J01546) to J.L.; Knut and Alice Wallenberg Foundation and Swedish Research Council VR to P.V.B.; International Postdoctoral Exchange Fellowship Program and Postdoctoral Fellowship of Center for Life Sciences, and National Natural Science Foundation of China (3220050423) to Z.X.; and the Postdoctoral Fellowship of Center for Life Sciences to S.Z., Y.L. and C.C.

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Authors and Affiliations

Authors

Contributions

M.Z. and W.W. conceived the study. M.Z., W.W. and C.C. performed the initial exploratory experiments of the study. Z.X. performed the liquid–liquid phase separation and FRAP assays. Z.X., Y.D. and P.S. produced the constructs and purified the recombinant proteins. Z.X., Y.D., and Yue L. performed the experiments related to the in vitro binding between RBP47B and SA. Y.D. performed the experiments related to the in vitro binding between RBP47B and PAs. S.Z. and Y.D. performed the immunofluorescence imaging. S.Z., X.C., Y.D. and H.L. performed the in vivo foci formation assays and growth inhibition assays. S.Z. and X.C. performed the PA mixture-related growth inhibition assays. Yue L. measured hypocotyl length. Y.S. performed the riceArabidopsis co-culture assays and obtained aqueous extracts from decomposed rice straws. Z.X. performed the AP–MS and IP–MS experiments. Z.X., E.L. and Y.T. validated the AP–MS and IP–MS data. Ying L. developed and performed the BONCATE, FUNCAT and polysome profiling assays. Ying L. and X.W. performed 3D time-lapse live imaging in Arabidopsis. Z.X., H.L., J.T. and W.Q. generated the CRISPR–Cas9 line of rbp47abcc′. X.W. performed the phylogenetic analysis. J.L. grew, collected and provided the allelopathic and non-allelopathic rice seeds. E.G.-B. and P.V.B. generated GFP–RBP47B and RFP–UBP1B constructs and 35S:GFP–RBP47B transgenic plants. M.Z. and W.W. wrote the manuscript with inputs from all co-authors.

Corresponding authors

Correspondence to Mian Zhou or Wei Wang.

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The authors declare no competing financial interests. Reprints and permissions information is available at www.nature.com/reprints. Correspondence and requests for materials should be addressed to W.W. (oneway1985@pku.edu.cn) or M.Z. (mianzhou@cnu.edu.cn).

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Extended data

Extended Data Fig. 1 Overlap between GFP-RBP47B-positive granules and poly(A)+ RNA granules after treatment with various PAs.

Related to Fig. 1. a, Diagram of root and the region for imaging and quantification of SGs. b-g, Representative images of GFP-RBP47B and poly(A)+ RNA in the roots of 35S:GFP-RBP47B Arabidopsis transgenic seedlings after control (DMSO) (b), 1 mM phthalic acid (c), 1 mM syringic acid (d), 1 mM gentisic acid (e), 1 mM p-coumaric acid (f) or 1 mM ferulic acid (g) treatment for 2 h. Scale bars, 10 µm. Data are representative of three independent experiments.

Extended Data Fig. 2 SA induces foci formation of Arabidopsis SG marker proteins.

Related to Fig. 1. a, Representative images of Arabidopsis protoplasts expressing RFP-UBP1B after dH2O (control) or 1 mM SA treatment for 3 h. Scale bars, 10 µm. Data are representative of three independent experiments. b, Roots of seven-day-old WT, rbp47b, and 35S:GFP-RBP47B plants were collected for protein extraction. Proteins were detected by RBP47B native antibody. Black arrows, target bands. *, nonspecific bands. Data are representative of three independent experiments. c. Representative immunofluorescence images of 35S:GFP-RBP47B roots (c), and WT, 35S:GFP-RBP47B, and rbp47abcc’ roots (d) using RBP47B antibody after 1 mM SA treatment for 2 h. Scale bars, 10 µm. Data are representative of three independent experiments. e, Representative images of poly(A)+ RNA in the roots of WT, acd6, cpr5, and snc1 seedlings. Scale bars, 10 μm. Data are representative of three independent experiments. f, Representative images of poly(A)+ RNA in the roots of WT treated with 1 mM SA for 5, 10, 12.5, 15, 20, 30, 60, or 120 min. Scale bars, 10 μm. Data are representative of three independent experiments. g, Representative images of poly(A)+ RNA in the roots of WT treated with 0.1, 0.2, 0.5, or 1 mM SA for 2 h. Scale bars, 10 μm. Data are representative of three independent experiments. h, Representative images of poly(A)+ RNA in the roots of WT grown on 1/2 MS plate with no SA (control) or 0.03 mM SA for 4 days. Scale bars, 10 μm. Data are representative of three independent experiments. i, Representative images of poly(A)+ RNA in the roots of WT pre-treated with 1 mM SA for 2 h followed by removal from SA for 0, 5, 10, 15, 20, or 30 min. Scale bars, 10 μm. Data are representative of three independent experiments. j, Representative images of poly(A)+ RNA in the roots of NahG seedlings with control (DMSO), 1 mM 4-HBA, protocatechuic acid, or caffeic acid treatment. Scale bars, 10 μm. Data are representative of three independent experiments.

Extended Data Fig. 3 Phase separation of RBP47B.

Related to Fig. 2. a, b, Coomassie staining of protein before and after TEV cleavage (a), and after further purification to remove the MBP tag (b). Arrowheads show the desired proteins. Data are representative of three independent experiments. c-d, Images of in vitro recombinant full-length RBP47B and ΔnPrLD. Images of 8 µM 6×His-TEV-RBP47B (c) and 20 µM 6×His-TEV-ΔnPrLD (d) in 50 mM Tris-HCl buffer (pH 7.4) with 1 M NaCl (in a test tube), 0.15 M NaCl (in a test tube and under DIC microscope; scale bars, 5 µm) and back to 1 M NaCl (in a test tube) were taken. Data are representative of three independent experiments. e, Salt effect on the turbidity of 6×His-TEV-RBP47B and 6×His-TEV-ΔnPrLD. 8 µM 6×His-TEV-RBP47B and 20 µM 6×His-TEV-ΔnPrLD were dialyzed in 50 mM Tris-HCl buffer (pH 7.4) with different concentrations of NaCl. The absorbance at 395 nm was recorded. Data represent the mean ± s. d. (n = 6 independent experiments). f, Representative snapshots of fusion event of RBP47B. 20 µM MBP-8×His-TEV-GFP-RBP47B protein was treated with TEV protease for 2 h. Scale bars, 2 µm. Data are representative of three independent experiments. g, Representative snapshots of fission event of YFP-RBP47B puncta in N. benthamiana after 1 mM SA treatment for 2 h. Scale bars, 10 µm. Data are representative of three independent experiments. h, Representative images (left) and quantification (right) of RNA effect on RBP47B droplet formation. 2.5 µM proteins were incubated with Arabidopsis total RNA ranging from 0.4 to 100 µg/mL. The area of the individual droplet was quantified using ImageJ. Data represent the mean ± s. e. m. (n = 535 for MBP-8×His-TEV-GFP-RBP47B; n = 1925 for GFP-ΔnPrLD); Individual droplets from three independent experiments). Different letters represent statistically different levels: p < 0.05 (Kruskal-Wallis test followed by Dunn’s multiple comparisons test). Scale bars, 10 µm. i, Turbidity of 6×His-TEV-RBP47B protein with ZnCl2 treatment. The absorbance at 395 nm of 1 µM 6×His-TEV-RBP47B protein in the presence of dH2O (control, pH adjusted) or 5 µM ZnCl2 was recorded. Data represent the mean ± s. e. m. (n = 5 individual experiments).

Extended Data Fig. 4 Reduction of spontaneous and SA-induced phase separation of recombinant RBP47B and its truncations in the MST buffer.

Related to Fig. 3. Turbidity of in vitro MBP-8×His-TEV (a), MBP-8×His-TEV-RBP47B (b), MBP-8×His-TEV-nPrLD (c), MBP-8×His-TEV-ΔnPrLD (d), MBP-8×His-TEV-cPrLD (e), MBP-8×His-TEV-ΔcPrLD (f), MBP-8×His-TEV-RRM (g), MBP-8×His-TEV-RRM1 (h), MBP-8×His-TEV-RRM2 (i) and MBP-8×His-TEV-RRM3 (j) with or without 1 mM SA treatment. Data represent the mean ± s. e. m. (n = 5 individual experiments).

Extended Data Fig. 5 RBP47B binds SA directly.

Related to Fig. 3. a, Competition binding assay of RBP47B. 0.5 µM MBP-8×His-TEV-RBP47B and MBP-8×His-TEV were incubated with [3H]-SA in the absence (Hot SA) or presence of unlabelled SA (Hot SA + Cold SA). CPM, count per minute. (n = 3 independent experiments) *, p < 0.05; ns, not significant (two-sided Holm- Sidak’s multiple comparisons test). b, MST binding curves of MBP-8×His-TEV and MBP-8×His-TEV-RBP47B to catechol based on fluorescence quenching induced by catechol (right y-axis). Data represent the mean ± s. e. m. (n = 5 independent titrations). Kd was estimated through nonlinear regression, and the best-fit values are shown. The 95% confidence interval of Kd of MBP-8×His-TEV: 1.531 ~ 2.412 mM; MBP-8×His-TEV-RBP47B: 210.5 ~ 287.1 µM. a.u., arbitrary unit. The MST binding curve of RED-NHS-labelled MBP-8×His-TEV-RBP47B to SA is re-plotted from the same curve in Fig. 3c for comparison purposes (left y-axis). c, MST binding curves of MBP-8×His-TEV and MBP-8×His-TEV-RBP47B to acetic acid. Data represent the mean ± s. e. m. (n = 5 independent titrations). d-e, Representative images of N. benthamiana (top) and Arabidopsis (bottom) expressing YFP-RBP47B (d) or YFP-RBP47B 3×RRM1 (e) after dH2O (control) or 1 mM SA treatment for 2 h. Scale bars, 15 µm. Data are representative of three independent experiments. f-i, Representative fluorescence microscopy images of rbp47abcc’ Arabidopsis protoplasts expressing YFP-IDReIF4GII-RBP47BΔnPrLD (f), YFP-IDReIF4GII-RBP47B3×RRM1 (g), YFP-IDRhnRNPA1-RBP47BΔnPrLD (h) or YFP-IDRhnRNPA1-RBP47B3×RRM1 (i) after dH2O (control) or 1 mM SA treatment for 2 h. Scale bars, 10 µm. Data are representative of three independent experiments. j, MST binding curves of MBP-8×His-TEV-RBP47B3×RRM1 and MBP-8×His-TEV-IDReIF4GII-RBP47BΔnPrLD to SA. Data represent the mean ± s. e. m. (n = 5 independent titrations). Kd was estimated through nonlinear regression, and the best-fit values are shown. The 95% confidence interval of Kd of MBP-8×His-TEV-RBP47B3×RRM1: 393.2 ~ 3182 nM; MBP-8×His-TEV-IDReIF4GII-RBP47BΔnPrLD: 7.153 ~ 17.29 µM. k, Phylogenetic analysis (k) and multiple alignment of protein sequences (l) of RBP47A, RBP47B, RBP47C, RBP47C’, RBP45A, RBP45B, RBP45C and AT5G19350 protein sequences from Arabidopsis and the TIA1 protein sequence from human. Scale bar, 0.5 amino acid substitutions per site. Alignment used ClustalX.

Extended Data Fig. 6 Binding between PAs and RBP47B.

Related to Fig. 4. MST binding curves (a-g) or fluorescence quenching curves (h) of MBP-8×His-TEV and MBP-8×His-TEV-RBP47B to 4-HBA (a), protocatechuic acid (b), phthalic acid (c), syringic acid (d), gentisic acid (e), p-coumaric acid (f), ferulic acid (g) and caffeic acid (h). The shaded region is defined by the cutoffs of significant signals. The results within the shaded region are considered insignificant responses. Data represent the mean ± s. e. m. (n = 5 independent titrations). Kd was estimated through nonlinear regression, and the best-fit values are shown. Outliers detected by the ROUT method during the nonlinear regression analysis were excluded. The 95% confidence interval of the Kd of MBP-8×His-TEV-RBP47B for 4-HBA: 5.036 ~ 20.80 μM; protocatechuic acid: 3.609 ~ 10.19 μM; phthalic acid: 3.769 ~ 13.16 μM; syringic acid: 4.709 ~ 13.69 μM; gentisic acid: 3.010 ~ 15.00 μM; p-coumaric acid: 2.868 ~ 10.43 μM; ferulic acid: 6.720 ~ 20.76 μM; caffeic acid: 976.9 ~ 4790 nM; and MBP-8×His-TEV for caffeic acid: 0.4001 ~ 1.060 mM. 4-HBA, 4-hydroxybenzoic acid.

Extended Data Fig. 7 SA-induced SG formation in RBP47-related mutants.

Related to Fig. 5. a, Diagram and detailed sequences of the target sites of rbp47a, rbp47b, rbp47c, and rbp47c’ generated by CRISPR/Cas9. b-e, The relative gene expression of RBP47A (b), RBP47B (c), RBP47C (d), and RBP47C’ (e) in wild-type (WT) and various rbp47 mutant seedlings analysed by qPCR using the constitutively expressed ACTIN2 as a control. Data represent the mean ± s. e. m. (n = 9, from three independent experiments). *, p < 0.05; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001; ns, not significant (one-way ANOVA followed by Dunnett’s multiple comparisons test). f-m, Representative fluorescence microscopy images of poly(A)+ RNA in the roots of wild-type (WT) (f), rbp47a (g), rbp47b (h), rbp47ab (i), rbp47acc’ (j), rbp47abcc’ (k) and npr1 (l) Arabidopsis seedlings treated with 1 mM SA for 2 h. Scale bars, 10 μm. Data are representative of three independent experiments. m, Quantification of SGs in wild-type (WT), rbp47a, rbp47b, rbp47ab, rbp47acc’, rbp47abcc’ and npr1 Arabidopsis seedlings after 1 mM SA treatment for 2 h. Data represent the mean ± s. e. m. (n = 15 seedlings from three independent experiments). **, p < 0.01; ns, not significant (one-way ANOVA followed by Dunnett’s multiple comparisons test). n, Representative immunofluorescence microscopy images of RBP47B in wild-type (WT) and npr1 Arabidopsis roots using an RBP47B native antibody after 1/2 MS liquid medium (control) or 1 mM SA (both dissolved in 1/2 MS liquid medium) treatment for 2 h. Scale bars, 10 µm. Data are representative of three independent experiments.

Extended Data Fig. 8 Affinity purification-mass spectrometry analysis of SG proteome.

Related to Fig. 5. a, Illustration of the procedures for the separation of SG and supernatant fractions. b, Venn diagram showing the overlap between wild-type (WT) SG enriched components and components that showed significantly different SG/supernatant partition patterns comparing WT and rbp47abcc’ (Differentially enriched WT vs rbp47abcc’). c, Venn diagram showing the overlap between the 245 proteins derived from (b) and rbp47abcc’ SG enriched or depleted components. d-f, Heatmaps of log2 fold changes of the indicated sets of proteins based on the Venn diagram from (c). FC, fold change. g-j, Representative fluorescence microscopy images, the related intensity profiles and Pearson correlation coefficient (PCC) of Arabidopsis protoplasts co-expressing YFP-RBP47B and mCherry tagged RPL5A, RPL23aA, RPS20B, or RPS21B after W5 solution (control) or 1 mM SA treatment for 2 h. Scale bars, 20 µm. Data are representative of three independent experiments. The white arrows indicate the area of related intensity profiles. n = 8 for PCC quantification (mean ± s. e. m was shown).

Extended Data Fig. 9 FRAP of RPL27C and RPS10C.

Related to Fig. 5. a–c, Representative images of FRAP for Arabidopsis protoplasts co-expressing YFP-RBP47B and mCherry-RPL27C (a), or mCherry-RPS10C (b), and expressing YFP-RBP47B alone (c) after 1 mM SA treatment for 2 h. Scale bars, 10 µm. d, e, Representative fluorescence microscopy images (d), and the related intensity profiles and Pearson correlation coefficient (PCC) (e) of Arabidopsis transgenic lines expressing GFP-RBP47B and mCherry tagged RPS10C after 1 mM SA treatment for 2 h. Scale bars, 10 µm. Data are representative of three independent experiments. The white arrows indicate the area of related intensity profiles. n = 8 for PCC quantification (mean ± s. e. m was shown). f-g, Representative images of FRAP (f) and quantification of FRAP data (g) for Arabidopsis transgenic lines co-expressing GFP-RBP47B and mCherry-RPS10C after 1 mM SA treatment for 2 h. Scale bars, 10 µm. Data represent the mean ± s. e. m, n = 9. Time 0 indicates the time of the photobleaching pulse.

Extended Data Fig. 10 SA inhibits global translation in an RBP47-dependent manner.

Related to Fig. 6. a, BONCATE label efficiency. Six-day-old WT seedlings were treated with 1 mM AHA for 10 min, and allowed labelling at indicated durations. Data represent the mean ± s. e. m. (n = 3 biological replicates). b, Representative Western blot image of BONCATE samples treated with increasing doses of CHX. Streptavidin-HRP and anti-Actin were used. Data are representative of three independent experiments. c, BONCATE to detect relative translation efficiency of WT seedlings treated with SA (post-treatment scheme). Data represent the mean ± s. e. m. (n = 3 biological replicates). ns, not significant; **, p < 0.01; ****, p < 0.0001 (two-way ANOVA followed by Sidak’s multiple comparisons test). d, BONCATE to detect relative translation efficiency of WT seedlings treated with SA (co-treatment scheme). Data represent the mean ± s. e. m. (n = 4 biological replicates). ns, not significant; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001 (two-way ANOVA followed by Sidak’s multiple comparisons test). e, Controls for FUNCAT assays. FUNCAT signals in WT roots treated with 1/2 liquid MS medium with or without AHA, Alexa Fluor 488 Alkyne, or CHX for 2 h, as indicated by “+” or “-” above the images. Scale bars, 50 µm. Data are representative of three independent experiments. f, BONCATE to detect relative translation efficiency of rbp47abcc’ seedlings treated with SA at indicated durations (post-treatment scheme). Data represent the mean ± s. e. m. (n = 3 biological replicates). ns, not significant (two-way ANOVA followed by Sidak’s multiple comparisons test). g, BONCATE to detect relative translation efficiency in WT, rbp47abcc’ and npr1-3 (npr1) treated with SA treatment (pre-treatment scheme). Data represent the mean ± s. e. m. (n = 5 biological replicates). ns, not significant; *, p < 0.05; ***, p < 0.001 (two-way ANOVA followed by Sidak’s multiple comparisons test). h, BONCATE to detect relative translation efficiency of rbp47abcc’ seedlings treated with 35 μM CHX (pre-treatment scheme). Data represent the mean ± s. e. m. (n = 3 biological replicates). ***, p < 0.001 (one-way ANOVA followed by Dunnett’s multiple comparisons test).

Source data

Supplementary information

Supplementary Information

Supplementary Figs. 1–5 and text.

Reporting Summary

Supplementary Tables 1 and 2

Supplementary Table 1. List and GO analysis of SG proteome. Supplementary Table 2. List of synthesized primers.

Supplementary Video 1

FRAP of in vitro freshly prepared RBP47B protein droplet.

Supplementary Video 2

FRAP of in vitro overnight-prepared RBP47B droplet.

Supplementary Video 3

Fusion event of in vitro RBP47B protein droplets.

Supplementary Video 4

FRAP of in vivo GFP–RBP47B foci.

Supplementary Video 5

Fusion event of YFP–RBP47B puncta in N. benthamiana.

Supplementary Video 6

Fusion and fission events of YFP–RBP47B foci in protoplast.

Supplementary Video 7

Fusion event of GFP–RBP47B foci in Arabidopsis.

Source data

Source Data Extended Data Fig. 10b

Unprocessed western blot for lower panel.

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Xie, Z., Zhao, S., Li, Y. et al. Phenolic acid-induced phase separation and translation inhibition mediate plant interspecific competition. Nat. Plants 9, 1481–1499 (2023). https://doi.org/10.1038/s41477-023-01499-6

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