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Convergence and divergence of bitterness biosynthesis and regulation in Cucurbitaceae

Nature Plants volume 2, Article number: 16183 (2016) Cite this article

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Abstract

Differentiation of secondary metabolite profiles in closely related plant species provides clues for unravelling biosynthetic pathways and regulatory circuits, an area that is still underinvestigated. Cucurbitacins, a group of bitter and highly oxygenated tetracyclic triterpenes, are mainly produced by the plant family Cucurbitaceae. These compounds have similar structures, but differ in their antitumour activities and ecophysiological roles. By comparative analyses of the genomes of cucumber, melon and watermelon, we uncovered conserved syntenic loci encoding metabolic genes for distinct cucurbitacins. Characterization of the cytochrome P450s (CYPs) identified from these loci enabled us to unveil a novel multi-oxidation CYP for the tailoring of the cucurbitacin core skeleton as well as two other CYPs responsible for the key structural variations among cucurbitacins C, B and E. We also discovered a syntenic gene cluster of transcription factors that regulates the tissue-specific biosynthesis of cucurbitacins and may confer the loss of bitterness phenotypes associated with convergent domestication of wild cucurbits. This study illustrates the potential to exploit comparative genomics to identify enzymes and transcription factors that control the biosynthesis of structurally related yet unique natural products.

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Figure 1: Comparative analysis of cucurbitacin biosynthetic and regulatory genes in cucumber, melon and watermelon.
Figure 2: Elucidation of the catalytic steps involved in CuB and CuE biosynthesis.
Figure 3: Functional elucidations of a multifunctional and a divergent CYP.
Figure 4: Characterization of the tissue-specific bitterness regulators from melon and watermelon.

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Acknowledgements

We thank J. Ren (Institute of Microbiology, Chinese Academy of Sciences) for providing the NMR assay platform and L. Han (Institute of Biotechnology, Chinese Academy of Agricultural Sciences) for experimental assistance. The CYPs were named according to the alignment made by D. Nelson (http://drnelson.uthsc.edu/cytochromeP450.html). This work was supported by founding from the National Key R & D Program for Crop Breeding (2016YFD0100307), National Science Fund for Distinguished Young Scholars (31225025 to S.H.), the National Program on Key Basic Research Projects in China (the 973 Program; 2012CB113900), the leading talents of Guangdong province Program (00201515), National Natural Science Foundation of China (31322047, 31401886, 31101550 and 31672171), The Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-ASTIP-IVFCAAS), the Chinese Ministry of Finance (1251610601001), China Postdoctoral Science Foundation (2014M550902), the Discovery Grant from National Science and Engineering Research Council of Canada (NSERC) and Canada Research Chair program to D.-K.R., and the UK Biotechnological and Biological Sciences Research Council Institute Strategic Programme Grant ‘Understanding and Exploiting Plant and Microbial Metabolism’ (BB/J004561/1), the John Innes Foundation, and the Genomes to Natural Products National Institutes of Health Programme grant U01GM110699 awards to A.O. This work was also supported by the Shenzhen Municipal and Dapeng District Governments. Institute of Flowers and Vegetables has two pending patent applications relating to the genes reported in this study.

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Author notes

  1. Yuan Zhou, Yongshuo Ma, Jianguo Zeng and Lixin Duan: These authors contributed equally to this work.

Authors and Affiliations

  1. Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, 100081, China

    Yuan Zhou, Yongshuo Ma, Huaisong Wang, Tao Lin, Yang Zhong, Shu Zhang, Min Liu, Huimin Zhang, Xinyan Liu, Zhonghua Zhang, Yi Shang & Sanwen Huang

  2. Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Science, Shenzhen, 518124, China

    Yuan Zhou, Tao Lin, Yi Shang & Sanwen Huang

  3. Horticulture and Landscape College, Hunan Agricultural University, National Chinese Medicinal Herbs (Hunan) Technology Centre, Changsha, 410000, China

    Yuan Zhou, Jianguo Zeng, Peng Huang & Xiubin Liu

  4. Institute of Botany, Chinese Academy of Science, Beijing, 100093, China

    Lixin Duan

  5. Institute of Apiculture Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, China

    Xiaofeng Xue

  6. School of Life Science, Shanxi University, Taiyuan, 030006, China

    Zhiqiang Liu

  7. School of Pharmaceutical Sciences, Peking University Health Science Centre, Beijing, 100191, China

    Kewu Zeng & Pengfei Tu

  8. College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China

    Qun Hu & Hanhui Kuang

  9. John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK

    James Reed, Tessa Moses & Anne Osbourn

  10. School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China

    Zhixing Qing

  11. Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada

    Dae-Kyun Ro

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  1. Yuan Zhou
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Contributions

S.H. and Y.S. conceived and organized the research. Y.M., Y.S., J.Z., H.W., Z.L., K.Z., Y.Zhou., M.L., H.Z. and P.H. performed the biology experiments. Y.Zhou., L.D., X.X., Xin.L., Z.Q. and Xiu.L. performed metabolic detection. Y.Zhong, Y.M., Y.S., D.-K.R., J.Z., L.D., X.X., T.L., S.Z., Q.H., J.R., Xin.L., P.H., Z.Q., Xiu.L., Z.Z., H.K. and A.O. performed data analysis. Y.S., D.-K.R., Y.Zhou. and S.H. wrote the manuscript. J.Z., L.D., J.R., P.T., Z.Z., H.K. and A.O. revised the manuscript.

Corresponding authors

Correspondence to Yi Shang or Sanwen Huang.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Methods, Supplementary References, Supplementary Figures 1-22, Supplementary Tables 3 and 4. (PDF 4349 kb)

Supplementary Table 1

Numeric pi values of the SNPs within the domestication sweep region. (XLSX 63 kb)

Supplementary Table 2

Primers used in this study. (XLSX 42 kb)

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Zhou, Y., Ma, Y., Zeng, J. et al. Convergence and divergence of bitterness biosynthesis and regulation in Cucurbitaceae. Nature Plants 2, 16183 (2016). https://doi.org/10.1038/nplants.2016.183

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