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Condensation of SEUSS promotes hyperosmotic stress tolerance in Arabidopsis

Nature Chemical Biology volume 18, pages 1361–1369 (2022)Cite this article

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Abstract

Osmotic stress imposed by drought and high salinity inhibits plant growth and crop yield. However, our current knowledge on the mechanism by which plants sense osmotic stress is still limited. Here, we identify the transcriptional regulator SEUSS (SEU) as a key player in hyperosmotic stress response in Arabidopsis. SEU rapidly coalesces into liquid-like nuclear condensates when extracellular osmolarity increases. The intrinsically disordered region 1 (IDR1) of SEU is responsible for its condensation. IDR1 undergoes conformational changes to adopt more compact states after an increase in molecular crowding both in vitro and in cells, and two predicted α-helical peptides are required. SEU condensation is indispensable for osmotic stress tolerance, and loss of SEU dramatically compromises the expression of stress tolerance genes. Our work uncovers a critical role of biomolecular condensates in cellular stress perception and response and expands our understanding of the osmotic stress pathway.

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Fig. 1: SEU undergoes reversible and dynamic condensation in response to hyperosmotic stress.
Fig. 2: IDR1 of SEU is responsible for its condensation.
Fig. 3: SEU condensation primarily depends on an increase in molecular crowding.
Fig. 4: IDR1 of SEU is a bona fide molecular crowding sensor.
Fig. 5: SEU condensation is indispensable for osmotic stress tolerance.
Fig. 6: SEU is required for the expression of osmotic stress-responsive genes.

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Data availability

RNA-sequencing datasets generated in this study can be found in the NCBI Gene Expression Omnibus under accession number GSE213934. The Arabidopsis genome information for mapping of RNA-sequencing reads is available from TAIR10 (www.arabidopsis.org). Source data are provided with this paper. All other data supporting the findings of this work are available within the paper and its Supplementary Information or from the corresponding authors on reasonable request.

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Acknowledgements

We thank X. Zhang for the synthesis of the b-isox compound. We thank L. Du for sharing the plasmids and yeast cells used in the heterologous expression system and Golz (The University of Melbourne) for sharing the seeds. This work was supported by grants from the National Natural Science Foundation of China to X.F. (32161133001), J.H. (31800235) and R.L. (32030009), Beijing Natural Science Foundation to X.F. (JQ21020) and the Strategic Priority Research Program of the Chinese Academy of Sciences to R.L. (XDB27030205).

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  1. These authors contributed equally: Boyu Wang, Honghong Zhang, and Junling Huai.

Authors and Affiliations

  1. Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China

    Boyu Wang, Honghong Zhang, Fangyu Peng, Jie Wu & Xiaofeng Fang

  2. Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China

    Junling Huai & Rongcheng Lin

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Contributions

B.W., H.Z., J.H., R.L. and X.F. conceived the study. B.W. and J.W. performed the imaging of tobacco and Arabidopsis, RNA and genetic analyses. H.Z. performed b-isox precipitation imaging of yeast cells and all in vitro experiments. J.H. performed the phenotypic analyses. F.P. did all bioinformatic analyses. R.L. and X.F. wrote the manuscript. All authors contributed ideas and reviewed the manuscript.

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Correspondence to Rongcheng Lin or Xiaofeng Fang.

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Extended data

Extended Data Fig. 1 SEU undergoes condensation in response to hyperosmotic stress.

a, Illustration of the screen for osmotic stress-responsive biomolecular condensates. b, Representative confocal microscopic images of SEU-GFP expressed in yeast cells that were treated as indicated. Scale bars, 2 μm. c, Representative confocal microscopic images of tobacco epidermal cells expressing SEU-mVenus. The cells were treated as indicated. Scale bars, 5 μm. d, The protein levels of SEU and SEU-GFP in the indicated plants as determined by western blot. e, Expression of SEU relative to ACTIN in the indicated plants. Data are presented as the mean ± SD (n = 3 biologically independent experiments). Asterisk indicates a significant difference (two-tailed t test). f-i, Representative confocal microscopic images of Arabidopsis root tip cells expressing SEU-GFP. The roots were treated as indicated. Scale bars, 5 μm. j, Immunostaining of Arabidopsis root tip nuclei from plants treated with or without 300 mM NaCl. Scale bars, 5 μm. k, Representative confocal microscopic images of yeast cells expressing SEU. The cells were treated as indicated. Scale bars, 2 μm. l, Representative confocal microscopic images of tobacco epidermal cells expressing SEU. The cells were treated as indicated. Scale bars, 5 μm.

Source data

Extended Data Fig. 2 Analyses of SEU-Like proteins (SLKs).

a, Multiple sequence alignment of SEU and SLK protein sequences by Clustal W. b, The phylogenetic tree of SEU and SLK proteins inferred using the Neighbor-Joining method. c, The protein domain structures of SLKs. Disordered regions were predicted by IUpred algorithm. d, Representative confocal microscopic images of SLK2-GFP expressed in yeast cells that were treated by sorbitol for 30 min. Scale bars, 2 μm. e, The protein domain structure of a chimeric protein swapping the IDR1 of SLK2 with that of SEU. f, Representative confocal microscopic images of tobacco epidermal cells expressing the chimeric protein shown in (e). The cells were treated with or without NaCl for 5 min. Scale bars, 5 μm unless indicated.

Extended Data Fig. 3 SUMOylation of SEU is not required for its condensation in response to hyperosmotic stress.

a, The protein domain structure of SEU with four SUMOylation sites indicated. b, Representative confocal microscopic images of tobacco epidermal cells expressing SEU3KR-mVenus. The cells were treated with or without NaCl for 5 min. Scale bars, 5 μm. c-e, Confocal microscopy of Arabidopsis root tip cells of indicated genotypes. The roots were treated as indicated. Scale bars, 5 μm.

Extended Data Fig. 4 SEU condensation is sensitive to crowding.

a, Representative confocal microscopic images of yeast cells expressing IDR1-GFP. The cells were treated with or without NaCl and KCl for 5 min. Scale bars, 2 μm. b, Representative confocal microscopic images of yeast cells expressing SEU-IDR13KR-GFP. The cells were treated with or without sorbitol for 5 min. Scale bars, 2 μm. c, Representative confocal microscopic images of tobacco epidermal cells expressing SEU-mVenus under the ethanol inducible promoter. The cells were treated with 1% ethanol for indicated time. Scale bars, 5 μm. d, Coomassie staining of indicated protein samples before and after TEV cleavage to remove the MBP tag. e, In vitro phase separation assay of IDR1-mScarlet in the presence of indicated concentrations of PEG, NaCl or KCl. Scale bars, 5 μm.

Source data

Extended Data Fig. 5 IDR1 of SEU senses molecular crowding.

a, Illustration of IDR1 truncations. b, Representative confocal microscopic images of yeast cells expressing IDR1 truncations shown in (a) in the presence of 1.2 M sorbitol. Scale bars, 2 μm. c, In vitro phase separation assay of 0.2 μM IDR1-GFP protein in the presence of indicated concentrations of PEG8000. Scale bars, 5 μm. d, FRET with 0.2 μM IDR1 in the presence of indicated concentrations of PEG8000. e, Quantification of the donor fluorescence lifetime in yeast cells expressing indicated proteins. The cells were treated with 1.2 M sorbitol for 1 min. Asterisks indicate significant differences (****P ≤ 0.0001, two-tailed t test). 18 independent yeast cells were analyzed.

Source data

Extended Data Fig. 6 Phenotypic analysis of seu mutant.

a, The phenotypes of indicated genotypes grown horizontally on 1/2 MS media plates containing mannitol or NaCl. b, Photographs of indicated genotypes after 7 days of germination on 1/2 MS medium containing 0.5 μM ABA. c, Confocal microscopy of pSEU::SEU-GFP/seu transgenic root tip cells that were treated with 50 μM ABA for 20 min. Scale bars, 5 μm. d, Representative photographs of the indicated genotypes grown vertically on 1/2 MS media plates with or without 250 mM sorbitol under red light condition. e, The hypocotyl length of the indicated genotypes under sorbitol treatment relative to control. Data are presented as the mean ± SD (n ≥ 9 independent seedlings). Asterisks indicate significant differences (****P ≤ 0.0001, two-tailed t test).

Source data

Extended Data Fig. 7 SEU is required for the expression of osmotic stress-tolerance genes.

a,b, Volcano plot of differentially expressed genes (DEGs) in seu-6 compared with Col-0 under control (a) or NaCl (b) treatment conditions determined by RNA‐sequencing. 10‐day‐old seedlings were transferred into liquid 1/2 MS medium or medium containing 300 mM NaCl and collected for RNA extraction after 15 min of treatment. Genes with at least 2-fold changes and P‐adjust less than 0.01 were considered as up- or down-regulated genes. c, Venn diagram showing the overlap of DEGs shown in (a) and (b). d, Heatmaps showing the relative expression changes (z‐normalized) of osmotic stress tolerance‐related genes under indicated conditions.

Extended Data Fig. 8 Condensation of SEU is evolutionarily conserved.

a, The phylogenetic tree of SEU homologs inferred using the Neighbor-Joining method. Evolutionary analysis was performed in MEGA X. b, Multiple sequence alignment of SEU homologs. The regions corresponding to IDR1, LDB and IDR2 were indicated. c, Zoom-in of the region marked by a rectangle in (b) showing the conservation of the two predicted α-helical peptides between SEU homologs. d, The structures of SEU homologs as predicted by AlphaFold. e, Representative confocal microscopic images of tobacco epidermal cells expressing SEU homologs. The cells were treated with or without NaCl for 5 min. Scale bars, 5 μm. f, The phylogenetic tree of AtSEU and its counterparts in yeast inferred using the Neighbor-Joining method. g, Top, protein domain structure of fission yeast Ssn6. Bottom, prediction of the disordered regions by IUpred algorithm. h, Representative confocal microscopic images of yeast cells expressing Ssn6. The cells were treated with or without sorbitol for 5 min. Scale bars, 2 μm.

Extended Data Fig. 9 A working model for SEU during osmotic response.

Under normal growth condition, SEU is diffused in the nucleus. When cells encounter hyperosmotic stress, shrinkage of cell volume leads to an increase of macromolecular crowding inside cells. Due to the hypersensitivity to crowding, IDR1 adopts more compact conformation, leading to the increase of local concentration and subsequent phase separation of SEU. Phase-separated SEU promotes the expression of stress-tolerance genes, thereby support cell survival.

Supplementary information

Supplementary Information

Supplementary Table 1.

Reporting Summary

Supplementary Data 1

List of DEGs in seu-6 mutants compared to wild-type Col-0.

Supplementary Video 1

Time-lapse imaging showing the recovery after half-bleaching of SEU nuclear condensates in tobacco epidermal cells. The red arrowhead indicates the area of bleaching. The photobleaching pulse was performed at time 3 s; scale bar, 2 μm.

Supplementary Video 2

Time-lapse imaging showing the condensation of IDR1SEU–GFP in yeast cells in the presence of 1.2 M sorbitol. Time 0 s indicates the addition of sorbitol; scale bars, 2 µm.

Supplementary Video 3

Time-lapse imaging showing the fusion of two IDR1–GFP droplets formed in vitro in the presence of 8% PEG8000; scale bar, 2 μm.

Supplementary Video 4

Time-lapse imaging showing the wetting of the slide surface by an IDR1–GFP droplet after contacting the slide; scale bar, 2 µm.

Source data

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Source Data Extended Data Fig. 1

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Unprocessed western blots.

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Unprocessed western gels.

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Wang, B., Zhang, H., Huai, J. et al. Condensation of SEUSS promotes hyperosmotic stress tolerance in Arabidopsis. Nat Chem Biol 18, 1361–1369 (2022). https://doi.org/10.1038/s41589-022-01196-z

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