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DWARF 53 acts as a repressor of strigolactone signalling in rice

Nature volume 504, pages 401–405 (2013)Cite this article

A Corrigendum to this article was published on 29 January 2014

Abstract

Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching. SL signalling requires the hormone-dependent interaction of DWARF 14 (D14), a probable candidate SL receptor, with DWARF 3 (D3), an F-box component of the Skp–Cullin–F-box (SCF) E3 ubiquitin ligase complex. Here we report the characterization of a dominant SL-insensitive rice (Oryza sativa) mutant dwarf 53 (d53) and the cloning of D53, which encodes a substrate of the SCFD3 ubiquitination complex and functions as a repressor of SL signalling. Treatments with GR24, a synthetic SL analogue, cause D53 degradation via the proteasome in a manner that requires D14 and the SCFD3 ubiquitin ligase, whereas the dominant form of D53 is resistant to SL-mediated degradation. Moreover, D53 can interact with transcriptional co-repressors known as TOPLESS-RELATED PROTEINS. Our results suggest a model of SL signalling that involves SL-dependent degradation of the D53 repressor mediated by the D14–D3 complex.

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Figure 1: D53 acts as a negative regulator in SL signalling.
Figure 2: SL-induced D53 degradation by the ubiquitin proteasome system.
Figure 3: Interactions among D3, D14 and D53.
Figure 4: Interaction of D53 with TPR proteins.
Figure 5: A proposed model of D53 action.

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Accession codes

Accessions

GenBank/EMBL/DDBJ

Data deposits

The sequence of DWARF53 coding region has been deposited in the GenBank database under accession number KF623088.

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Acknowledgements

We thank K. Yoneyama for assistance in SL analysis and C. Yan for SL measurement. This work was supported by grants from Ministry of Science and Technology of the People’s Republic of China (2012AA10A301) and National Natural Science Foundation of China (31025004, 90817108 and 91217311).

Author information

Author notes

  1. Liang Jiang, Xue Liu, Guosheng Xiong and Huihui Liu: These authors contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China

    Liang Jiang, Xue Liu, Guosheng Xiong, Huihui Liu, Fulu Chen, Lei Wang, Xiangbing Meng, Guifu Liu, Hong Yu, Yundong Yuan, Yonghong Wang & Jiayang Li

  2. VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China

    Wei Yi, Lihua Zhao, Honglei Ma & H. Eric Xu

  3. Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Avenue Northeast, Grand Rapids, Michigan 49503, USA ,

    Yuanzheng He, Zhongshan Wu, Karsten Melcher & H. Eric Xu

  4. State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China

    Qian Qian

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Contributions

L.J., X.L., G.X. and H.L. designed research, performed experiments, analysed data and wrote the paper; F.C., L.W., X.M., H.Y., Y.Y., G.L., W.Y., L.Z., H.M., Y.H., Z.W. and K.M. performed some of the experiments. Q.Q. provided and planted the rice materials. J.L., Y.W. and H.E.X. designed research, analysed data and wrote the paper. J.L. conceived and supervised the project.

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Correspondence to H. Eric Xu, Yonghong Wang or Jiayang Li.

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Extended data figures and tables

Extended Data Figure 1 Characterization of the e9 mutant.

a, Tiller number and plant height of wild-type, homozygous and heterozygous e9 plants at the heading stage. Values are means ± s.d. (n = 8). The double asterisks represent significant difference determined by the Student’s t-test at P < 0.01. b, Kinetic comparison of tiller numbers between wild-type and e9 plants at different developmental stages. Values are means ± s.d. (n = 8). DAG, days after germination. Rice plants (a and b) were cultivated in the field in Beijing in the natural growing season. c, Four-week-old seedlings of wild-type, e9, d3 and d27 upon 1 μM GR24 treatment. Scale bars, 10 cm. Ten individual plants for each material were treated with GR24. d, The expression levels of the D10 gene revealed by qPCR in wild-type, e9, d3 and d27 mutant seedlings. Values are means ± s.d. (n = 3). The double asterisks represent significant difference determined by the Student’s t-test at P < 0.01. e, The representative LC/MS–MS chromatograms for epi-5DS in root exudates of wild type and e9 before calibration against an internal standard.

Extended Data Figure 2 Cloning and confirmation of E9/D53.

a, E9 was mapped in the interval between molecular markers Ds3 and K81114 on chromosome 11 using 142 recessive individual plants showing normal tillering phenotype from an F2 population. Numbers under the markers indicate recombinants. b, E9/D53 mutation sites in e9/d53 in the coding region and its amino acid changes. c, Schematic diagram of D53:d53 constructs. d, Phenotypes of wild-type and D53:d53 transgenic plants at the mature stage. Scale bar, 20 cm. Nine independent transgenic lines showed the similar tillering and dwarf phenotypes. e, Comparison of tiller numbers between wild-type and D53:d53 transgenic plants at the mature stage. Values are means ± s.d. (n = 15). The double asterisks represent significant difference determined by the Student’s t-test at P < 0.01. The plants were grown in the field in Beijing in the natural growing season.

Extended Data Figure 3 Phylogenetic tree of D53-like family proteins in rice and Arabidopsis.

BlastP was done using the D53 protein sequence against all rice and Arabidopsis proteins at the MSU Rice Genome Annotation Project. In the BlastP result, rice proteins were filtered using cut-off E value < 0.1 plus top query coverage > 10% and Arabidopsis proteins were filtered using cut-off E value < 0.0005. Multiple sequence alignment of the protein sequences was done using Clustalw2. Maximum-likelihood phylogenetic tree was drawn by MEGA 5.05 using default parameters with 100 times bootstrapping. Numbers above the branches represent bootstrap support based on 100 bootstrap replicates. Branch length represents substitutions per site.

Extended Data Figure 4 Alignment of D53 and D53-like proteins in rice and Arabidopsis.

The graphic view of alignment was generated by BioEdit using Clustalw for multiple sequence alignment of protein sequences. Blue underline refers to the Double Clp-N domain, light green to atypical walker A motifs, dark green box to walker B motifs and red boxes to putative EAR motifs. D53, Os11g01330; D53-like, Os12g01360; AtD53-like 1, At1g07200; AtD53-like 2, At2g29970; AtD53-like 3, At2g40130; AtHSP101, At1g74310; OsHSP101, Os05g44340.

Extended Data Figure 5 D53 expression levels in d mutants and the mutation sites in other d mutants used in this study.

a, Expression levels of D53 revealed by qPCR in wild-type, d3, d10, d14, d17 and d27 seedlings. Values are means with s.d. of three independent experiments. The double asterisks represent significant difference determined by the Student’s t-test at P < 0.01. b, The mutation sites in other d mutants identified in this study.

Extended Data Figure 6 D3 and D14 protein levels are unaffected by GR24 treatment.

a, Phenotypes of mature transgenic plants of D3-GFP and D14-GFP in the d3 or d14 background, respectively, showing that D3–GFP and D14–GFP can rescue the corresponding phenotypes of d3 and d14. Scale bar, 10 cm. Five independent transgenic lines were shown to have similar phenotypes. b, Comparison of the tiller number of transgenic plants of D3-GFP/d3 and D14-GFP/d14. Values are means ± s.d. (n = 5). The double asterisks represent significant difference determined by the Student’s t-test at P < 0.01. c, D3–GFP abundance in d3 treated with 10 μM GR24 for 60 min. Protein level was analysed by immunoblotting using GFP antibody. d, The D14–GFP protein level in the d14 background as analysed by immunoblotting using GFP antibody. Transgenic plants of D14-GFP in the d14 background were treated with 10 μM GR24 for 60 min. Rice plants (T2 generation) were grown in the field in Hainan province.

Extended Data Figure 7 Effects of GR24 and SL mimics on rice tillering.

a, Chemical structures of GR24 and SL mimics. A, 4-[(2,5-dihydro-4-methyl-5-oxo-2-furanyl)oxy]benzonitrile; B, 5-(4-bromophenoxy)-3-methyl-2(5H)-furanone; C, 5-(4-iodophenoxy)-3-methyl-2(5H)-furanone. D, 3,3a,4,8b-tetrahydro-3-(hydroxymethylene)-2H-Indeno[1,2-b]furan-2-one (ABC rings of GR24); E, 5-hydroxy-3-methyl-2(5H)-furanone (D ring of GR24). b, Effects of 1 μM GR24 and SL mimics on tillering of 4-week-old seedlings. Values are means ± s.d. (n = 5).

Extended Data Figure 8 Phenotypes of transgenic plants of constitutively expressed D53–GFP in d3 and d14.

a, Phenotypes of wild-type, d3 and Act:D53-GFP/d3 transgenic plants at the mature stage. Scale bar, 10 cm. Six independent transgenic lines showed similar phenotypes. b, Phenotypes of wild-type, d14 and Act:D53-GFP/d14 transgenic plants at the mature stage. Scale bar, 10 cm. Six independent transgenic plants showed similar phenotypes. c, Tiller numbers of Act: D53-GFP/d14 and Act:D53-GFP/d3 transgenic plants at the mature stage. Values are means ± s.d. (n = 8). d, The D53–GFP abundance in d3 or d14 plants treated with 10 μM GR24 for 60 min. Protein levels were analysed by immunoblotting using GFP antibody. Rice plants (T1 generation) were grown in the field in Hainan province.

Extended Data Figure 9 Phenotypes and confirmation of transgenic plants of D53-RNAi in d3 and d14.

a, Phenotypes of wild-type, d3 and D53-RNAi/d3 transgenic plants. Scale bar, 10 cm. Four independent transgenic plants showed similar phenotypes. b, Phenotypes of wild-type, d14 and D53-RNAi/d14 transgenic plants at the mature stage. Scale bar, 10 cm. Five independent transgenic plants showed similar phenotypes. c, Tiller numbers of transgenic plants of D53-RNAi in d3 and d14 backgrounds at the mature stage. Values are means ± s.d. (n = 5). The double asterisks represent significant difference determined by the Student’s t-test at P < 0.01. d, The D53 abundance of D53-RNAi in d3 or d14 transgenic plants. Protein levels were analysed by immunoblotting using D53 polyclonal antibodies. Rice plants (T1 generation) were cultivated in the field in Hainan province. e, Sequence information of D53-RNAi constructs. Two complementary inverted D53 fragments are shown in black and the intron sequence between inverted DNA fragments is in red.

Extended Data Figure 10 Determination of D53 antibody specificity.

Determination of D53 antibody specificity by D53–GFP transgenic calli. Left, anti-GFP (Roche), 1:10,000 dilution; right, anti-D53 (1:10,000). Horseradish-peroxidase-conjugated anti-rabbit IgG and anti-mouse IgG antibodies were used as secondary antibodies to detect anti-D53 and anti-GFP.

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Jiang, L., Liu, X., Xiong, G. et al. DWARF 53 acts as a repressor of strigolactone signalling in rice. Nature 504, 401–405 (2013). https://doi.org/10.1038/nature12870

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