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Dirigent gene editing of gossypol enantiomers for toxicity-depleted cotton seeds

Nature Plants volume 9, pages 605–615 (2023)Cite this article

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Abstract

Axial chirality of biaryls can generate varied bioactivities. Gossypol is a binaphthyl compound made by cotton plants. Of its two axially chiral isomers, (−)-gossypol is the bioactive form in mammals and has antispermatogenic activity, and its accumulation in cotton seeds poses health concerns. Here we identified two extracellular dirigent proteins (DIRs) from Gossypium hirsutum, GhDIR5 and GhDIR6, which impart the hemigossypol oxidative coupling into (−)- and (+)-gossypol, respectively. To reduce cotton seed toxicity, we disrupted GhDIR5 by genome editing, which eliminated (−)-gossypol but had no effects on other phytoalexins, including (+)-gossypol, that provide pest resistance. Reciprocal mutagenesis identified three residues responsible for enantioselectivity. The (−)-gossypol-forming DIRs emerged later than their enantiocomplementary counterparts, from tandem gene duplications that occurred shortly after the cotton genus diverged. Our study offers insight into how plants control enantiomeric ratios and how to selectively modify the chemical spectra of cotton plants and thereby improve crop quality.

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Fig. 1: GhDIR5 guides (−)-gossypol formation in cotton.
Fig. 2: Blocking (−)-gossypol formation in cotton by GhDIR5 editing.
Fig. 3: Toxicity-depleted cotton seeds and retention of pest resistance in CR-Ghdir5 plants.
Fig. 4: Evolutionary landscape of GhDIR5 and (−)-gossypol.

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Data availability

All relevant data supporting the findings of this study are available within the paper and its Supplementary Information. Public RNA-seq data can be obtained from the Sequence Read Archive repository (https://www.ncbi.nlm.nih.gov/sra) under accession nos. PRJNA248163, PRJNA265955 and PRJNA493958. Sequence data and gene IDs can be found in the Cottongen database (https://www.cottongen.org/). The template of DIR used for molecular modelling was downloaded from the PDB (https://www.rcsb.org/) with PDB ID 6OOD. Moreover, the datasets generated and/or analysed during the current study are available from the corresponding authors upon reasonable request. Source data are provided with this paper.

Code availability

All code used in this study is available from the corresponding authors upon reasonable request.

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Acknowledgements

We thank W. Hu, X. Xu, S. Wang and X. Liao for help with the HPLC–MS analyses and S. Zhan, X. Wang, Y. Li, C. Li, B. Yang, P. Chen and L. Chen for their kind and generous help. The research was supported by grants from the National Key R&D Program of China (no. 2022YFF1001400) to J.-Q.H., the Chinese Academy of Sciences (no. XDB27020207) to X.-Y.C., the National Natural Science Foundation of China (nos. 31788103 and 31690092) to X.-Y.C., the Foundation of Youth Innovation Promotion Association of the Chinese Academy of Sciences to J.-Q.H., the Young Elite Scientists Sponsorship Program by CAST (no. 2019QNRC001) to J.-Q.H., the Hainan Yazhou Bay Seed Laboratory (no. B21HJ0223) to X.-Y.C. and the Yunnan Revitalization Talent Support Program ‘Top Team’ Project to X.-Y.C. We also acknowledge the support of the SANOFI Scholarship Program (to J.-Q.H.). Leaves of diploid or allotetraploid Gossypium species and Gossypioides kirkii were acquired from the Sanya National Research Station of Wild Cotton Germplasm, China.

Author information

Authors and Affiliations

  1. National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China

    Jia-Ling Lin, Jian-Xu Li, Wen-Kai Wu, Xiao-Xiang Guo, Jia-Fa Huang, Fang-Yan Chen, Ling-Jian Wang, Xiao-Ya Chen & Jin-Quan Huang

  2. School of Life Science and Technology, ShanghaiTech University, Shanghai, China

    Jia-Ling Lin & Xiao-Ya Chen

  3. State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China

    Xin Fang

  4. Hainan Yazhou Bay Seed Laboratory, Sanya, China

    Zhi-Wen Chen

  5. School of Life Sciences, East China Normal University, Shanghai, China

    Ning-Jing Liu

  6. Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, China

    Baofu Xu

  7. State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China

    Baofu Xu

  8. John Innes Centre, Norwich, UK

    Cathie Martin

  9. Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China

    Xiao-Ya Chen

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  1. Jia-Ling Lin
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Contributions

J.-Q.H., J.-L.L. and X.-Y.C. conceived the idea and designed the study. C.M., X.F., B.X., N.-J.L. and L.-J.W. discussed the results and provided advice. J.-L.L. and J.-Q.H. isolated the DIRs and characterized their function. J.-Q.H., J.-L.L. and L.-J.W. generated the transgenic plants. J.-L.L., W.-K.W. and F.-Y.C. completed the LC–MS analysis. J.-Q.H., J.-L.L., X.-X.G. and J.-F.H. evaluated the resistance and toxicity of the transgenic plants. J.-L.L., J.-Q.H. and Z.-W.C. carried out the bioinformatic analysis. J.-X.L. performed the protein modelling. J.-Q.H., X.-Y.C., J.-L.L. and C.M. wrote, reviewed and edited the paper.

Corresponding authors

Correspondence to Xiao-Ya Chen or Jin-Quan Huang.

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Nature Plants thanks Reuben Peters, Xiaoquan QI and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Transcriptome analysis to identify the (−)-gossypol biosynthetic gene in upland cotton.

a, Scatter plot, constructed from 35 RNA-seq samples, illustrates the correlation values of the downregulated genes in glandless cotton (edgeR, log2[FC] < = −8, log2[FC]: log2-transformed fold change) with CYP71BE79. Differential RNA expression of genes was analyzed in R software using edgeR68. Point sizes indicate the FDR-adjusted P-value of differential expression. FDR-adjusted P values were calculated using Benjamini-Hochberg correction of the obtained P values. Different colors distinguish between protein families. Correlation analysis was measured by Pearson’s correlation coefficient with ‘Cor’ function from R software. b, Sequence alignment of Gh_A04G0066 (GhDIR5) and Gh_A05G2499 (GhDIR6) conducted by BioEdit software 7.2.5. c, Global heatmap showing the abundance of gossypol in different organs or in ovules at different stages. d, Global heatmap showing the expressions of CYP71BE79, Gh_A04G0066 (GhDIR5) and Gh_A05G2499 (GhDIR6) in different organs or in ovules at different stages. For c and d: DPA, days post anthesis. ROT: root; STE, stem; LEA, leaf; PET, petal; PIS, pistil; CAL, calycle. e, Relative expressions of Gh_A04G0066 (GhDIR5) and Gh_A05G2499 (GhDIR6) in leaf and ovule (35 DPA) of the wild-type (gland, G) and gossypol-deficient (glandless, GL) cultivars, in cotyledons two days post-elicitor treatment, and in GoPGF-silencing leaves. GoPGF is the regulator of pigment gland formation. FPKM (fragments per kilobase million) values obtained from the gland cotton leaves or ovules and the elicitor-treated cotyledons were set to 1 and used to estimate relative values of the paired samples. Data shown are means ± s. d. (n = 3 biological replicates).

Source data

Extended Data Fig. 2 Phylogenetic analysis of the DIR family proteins from upland cotton (n = 121), rice (n = 49), and Arabidopsis thaliana (n = 26).

Proteins whose function has been described in the literature are indicated. [AtDIR6 and AtDIR5, (−)-pinoresinol-forming DIRs from A. thaliana69, in the DIR-a subfamily; AtDP1/AtDIR12, a neolignan biosynthesis DIR from A. thaliana52, in the DIR-a subfamily; AtDIR10 (ESB1), a Casparian band lignin-forming DIR from A. thaliana53, in the DIR-e subfamily; GhDIR1, a DIR involved in cotton lignification which could limit the spread of fungal pathogen Verticillium dahlia70, in the DIR-b/d subfamily]. GhDIR5, GhDIR6 and the previously reported GhDIR412 and GhDIR371 (another Gossypium hirsutum DIR for (+)-2 formation) are classified to the DIR-b/d subfamily, in which GhDIR6 belongs to a branch separated earlier.

Extended Data Fig. 3 GhDIR5 and GhDIR6 were computationally predicted to contain N-terminal signal peptide.

a,b, Signal peptides were predicted using the SignalP-6.0 (https://services.healthtech.dtu.dk/service.php?SignalP)72.

Extended Data Fig. 4 Subcellular localization of GhDIR5 and GhDIR6.

a, Confocal microscopy (Leica TSC SP8 STED 3X) of pGhDIR5::GhDIR5-EGFP and pGhDIR6::GhDIR6-EGFP transgenic cotton leaves. Scale bars, 30 μm. b, GUS staining of pGhDIR5::GUS and pGhDIR6::GUS transgenic cotton leaves. Scale bars, 50 μm. c, Immunoelectron microscopy with monoclonal antibodies against GhDIR5 and gold-labelled secondary antibodies, showing the localization of GhDIR5 in pigmented glands. The magnification of the box is shown in the panel below. Arrows indicate the immunogold particles in cotton pigmented glands. Scale bars of original and amplified panels are 10 μm and 500 nm, respectively. For controls the primary antibodies were replaced with the non-immune serum. All experiments were repeated independently at least two times with similar results, representative images are shown.

Extended Data Fig. 5 Sequence similarity network analysis of DIRs.

Protein sequence similarity network (SSN) of DIRs from eight Gossypium species and from Gossypioides kirkii. Each node within the resulting SSN contains sequences with >93% amino acid identity, rendering different DIRs into different clusters. Each color denotes a plant species. Protein sequences were downloaded from CottonGen (https://www.cottongen.org/). The SSN was constructed by EFI-EST webtool (http.//efi.igb.illinois.edu/efi-est/) and visualized with Cytoscape 3.9.1.

Extended Data Fig. 6 GhDIR5 and GhDIR6 expression and activity assays.

a, Western blot of purified GhDIR5 and GhDIR6 proteins extracted from agroinfiltrated leaves of N. benthamiana and affinity purified with Ni sepharose column. Mouse anti-His antibody (TA-02, ORIGENE) was used at a dilution of 1:5000 using goat-anti-mouse IgG horseradish peroxidase conjugate (1:10000, ZB2305, ORIGENE) as secondary antibody. Molecular weight of selected bands was indicated in kDa. The experiments were repeated independently three times with similar results. b, Enantiomeric ratio of (±)-2 resulted from oxidative coupling of 1, the reaction was incubated with commercialized RvLac and GhDIR5 or GhDIR6, as indicated. Reaction without DIR was used as control. (Data are means ± s. d., n = 3 independent experiments). c, Production of total 2 increased with the amounts of GhDIR5 (0.5–5 μg in 100 μL), RvLac was used as the oxidative enzyme. 2 formed in the absence of GhDIR5 was set to 1 (means ± s. d., n = 2 or 3 independent experiments).

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Extended Data Fig. 7 VIGS analysis of GhDIR5.

a–e, Relative contents of hemigossypolone and heliocides in the virus-mediated GhDIR5-silencing leaves of G. hirsutum. Value of the empty tobacco rattle virus (TRV) vector control (TRV:00) was set to 1 (means ± s. d., n = 5 independent experiments), hereinafter inclusive. f, g, Relative expression levels of GhDIR5 (f) and GhDIR4 (g) in the TRV:GhDIR5 leaves, compared to the EV control (means ± s. d., n = 3 independent experiments).

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Extended Data Fig. 8 Identification of CRISPR/Cas9–edited GhDIR5 knockout lines.

a, Western blot detection of leaf proteins after SDS-PAGE. GhDIR5 antibody (Abmart) was used at a dilution of 1:1000, using goat-anti-mouse IgG horseradish peroxidase conjugate (1:10000, ZB2305, ORIGENE) as secondary antibody. The experiments were repeated independently three times with similar results. b-c, CRISPR/Cas9-introduced GhDIR5 mutation didn’t led to off-target mutations at the GhDIR4 (b) and GhDIR6 (c) loci, as determined by Sanger sequencing after PCR amplification.

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Extended Data Fig. 9 Content of phytoalexins in CR-Ghdir5 lines.

a-d, Relative contents of (±)-2 in WT and CR-Ghdir5 cotton plant organs. e-n, Relative contents of hemigossypolone and heliocides in WT and CR-Ghdir5 cotton leaf (e-i) and sepal (j-n). Content value of the WT cotton was set to 1 (means ± s. d., n = 3 independent experiments).

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Extended Data Fig. 10 Representative HE-stained semi-thin sections of testes of the control and the cottonseed extracts-treated mice.

The seed extracts contained 1 mM racemic 2 (WT) or (+)-2 (CR-Ghdir5) from the WT and CR-Ghdir5 seeds, respectively. The mock group was treated with DMSO. Scale bars are indicated in the right. The experiments were repeated independently three times with similar results.

Supplementary information

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Supplementary Figs. 1–6, Tables 1 and 2, and source data for Supplementary Fig. 5.

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Lin, JL., Fang, X., Li, JX. et al. Dirigent gene editing of gossypol enantiomers for toxicity-depleted cotton seeds. Nat. Plants 9, 605–615 (2023). https://doi.org/10.1038/s41477-023-01376-2

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