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The NAT1–bHLH110–CER1/CER1L module regulates heat stress tolerance in rice

Nature Genetics volume 57, pages 427–440 (2025)Cite this article

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An Author Correction to this article was published on 31 January 2025

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Abstract

Rice production is facing substantial threats from global warming associated with extreme temperatures. Here we report that modifying a heat stress-induced negative regulator, a negative regulator of thermotolerance 1 (NAT1), increases wax deposition and enhances thermotolerance in rice. We demonstrated that the C2H2 family transcription factor NAT1 directly inhibits bHLH110 expression, and bHLH110 directly promotes the expression of wax biosynthetic genes CER1/CER1L under heat stress conditions. In situ hybridization revealed that both NAT1 and bHLH110 are predominantly expressed in epidermal layers. By using gene-editing technology, we successfully mutated NAT1 to eliminate its inhibitory effects on wax biosynthesis and improved thermotolerance without yield penalty under normal temperature conditions. Field trials further confirmed the potential of NAT1-edited rice to increase seed-setting rate and grain yield. Therefore, our findings shed light on the regulatory mechanisms governing wax biosynthesis under heat stress conditions in rice and provide a strategy to enhance heat resilience through the modification of NAT1.

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Fig. 1: NAT1 negatively regulates thermotolerance.
Fig. 2: NAT1 represses downstream genes involved in wax biosynthesis under heat stress conditions.
Fig. 3: NAT1 inhibits the expression of bHLH110 and bHLH110 promotes the expression of wax biosynthesis genes CER1/CER1L.
Fig. 4: bHLH110 positively regulates thermotolerance and cuticle wax content.
Fig. 5: CER1-/CER1L-mediated wax deposition is crucial for thermotolerance.
Fig. 6: nat1-conferred thermotolerance requires bHLH110 and CER1/CER1L.
Fig. 7: NAT1 and bHLH110 have nonsynonymous natural variations.
Fig. 8: Improving thermotolerance in rice by editing NAT1 without yield penalty.

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Data availability

The RNA-seq data are deposited in the NCBI-SRA database (PRJNA1171028) and the Genome Sequence Archive database (CRA013469). All data supporting the findings of this study are available within the paper and its Supplementary Information. Source data are provided with this paper.

Code availability

All software used in the study are publicly available from the Internet as described in the Methods and Reporting Summary.

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References

  1. Tilman, D., Balzer, C., Hill, J. & Befort, B. L. Global food demand and the sustainable intensification of agriculture. Proc. Natl Acad. Sci. USA 108, 20260–20264 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Lobell, D. B., Schlenker, W. & Costa-Roberts, J. Climate trends and global crop production since 1980. Science 333, 616–620 (2011).

    Article  CAS  PubMed  Google Scholar 

  3. Lesk, C., Rowhani, P. & Ramankutty, N. Influence of extreme weather disasters on global crop production. Nature 529, 84–87 (2016).

    Article  CAS  PubMed  Google Scholar 

  4. Li, J. Y., Yang, C., Xu, J., Lu, H. P. & Liu, J. X. The hot science in rice research: how rice plants cope with heat stress. Plant Cell Environ. 46, 1087–1103 (2023).

    Article  CAS  PubMed  Google Scholar 

  5. Sun, J. L., Li, J. Y., Wang, M. J., Song, Z. T. & Liu, J. X. Protein quality control in plant organelles: current progress and future perspectives. Mol. Plant 14, 95–114 (2021).

    Article  CAS  PubMed  Google Scholar 

  6. Zhang, J. Y., Li, X. M., Lin, H. X. & Chong, K. Crop improvement through temperature resilience. Annu. Rev. Plant Biol. 70, 753–780 (2019).

    Article  CAS  PubMed  Google Scholar 

  7. Kan, Y., Mu, X. R., Gao, J., Lin, H. X. & Lin, Y. The molecular basis of heat stress responses in plants. Mol. Plant 16, 1612–1634 (2023).

    Article  CAS  PubMed  Google Scholar 

  8. Zhang, H. et al. A genetic module at one locus in rice protects chloroplasts to enhance thermotolerance. Science 376, 1293–1300 (2022).

    Article  CAS  PubMed  Google Scholar 

  9. Li, J. & Liu, J. TT3.1: a journey to protect chloroplasts upon heat stress. Stress Biol. 2, 27 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Liu, X. H. et al. A membrane-associated NAC transcription factor OsNTL3 is involved in thermotolerance in rice. Plant Biotechnol. J. 18, 1317–1329 (2020).

    Article  CAS  PubMed  Google Scholar 

  11. Kan, Y. et al. TT2 controls rice thermotolerance through SCT1-dependent alteration of wax biosynthesis. Nat. Plants 8, 53–67 (2022).

    Article  CAS  PubMed  Google Scholar 

  12. Li, X. M. et al. Natural alleles of a proteasome α2 subunit gene contribute to thermotolerance and adaptation of African rice. Nat. Genet. 47, 827–833 (2015).

    Article  CAS  PubMed  Google Scholar 

  13. Islam, M. A., Du, H., Ning, J., Ye, H. & Xiong, L. Characterization of Glossy1-homologous genes in rice involved in leaf wax accumulation and drought resistance. Plant Mol. Biol. 70, 443–456 (2009).

    Article  CAS  PubMed  Google Scholar 

  14. Sugio, A., Dreos, R., Aparicio, F. & Maule, A. J. The cytosolic protein response as a subcomponent of the wider heat shock response in Arabidopsis. Plant Cell 21, 642–654 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Guo, M. et al. The plant heat stress transcription factors (HSFs): structure, regulation, and function in response to abiotic stresses. Front. Plant Sci. 7, 114 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Zhang, S. S. et al. Tissue-specific transcriptomics reveals an important role of the unfolded protein response in maintaining fertility upon heat stress in Arabidopsis. Plant Cell 29, 1007–1023 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. He, Y. B. et al. Programmed self-elimination of the CRISPR/Cas9 construct greatly accelerates the isolation of edited and transgene-free rice plants. Mol. Plant 11, 1210–1213 (2018).

    Article  CAS  PubMed  Google Scholar 

  18. Arshad, M. S. et al. Thermal stress impacts reproductive development and grain yield in rice. Plant Physiol. Biochem. 115, 57–72 (2017).

    Article  CAS  PubMed  Google Scholar 

  19. Kagale, S. & Rozwadowski, K. EAR motif-mediated transcriptional repression in plants: an underlying mechanism for epigenetic regulation of gene expression. Epigenetics 6, 141–146 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Aarts, M. G. M., Keijzer, C. J., Stiekema, W. J. & Pereira, A. Molecular characterization of the CER1 gene of Arabidopsis involved in epicuticular wax biosynthesis and pollen fertility. Plant Cell 7, 2115–2127 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Ni, E. et al. OsCER1 plays a pivotal role in very-long-chain alkane biosynthesis and affects plastid development and programmed cell death of tapetum in rice (Oryza sativa L.). Front. Plant Sci. 9, 1217 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  22. Persikov, A. V. & Singh, M. De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. Nucleic Acids Res. 42, 97–108 (2014).

    Article  CAS  PubMed  Google Scholar 

  23. Kovach, M. J., Sweeney, M. T. & McCouch, S. R. New insights into the history of rice domestication. Trends Genet. 23, 578–587 (2007).

    Article  CAS  PubMed  Google Scholar 

  24. Huang, X. et al. A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497–501 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Yeats, T. H. & Rose, J. K. C. The formation and function of plant cuticles. Plant Physiol. 163, 5–20 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Lewandowska, M., Keyl, A. & Feussner, I. Wax biosynthesis in response to danger: its regulation upon abiotic and biotic stress. New Phytol. 227, 698–713 (2020).

    Article  CAS  PubMed  Google Scholar 

  27. Lee, S. B. & Suh, M. C. Regulatory mechanisms underlying cuticular wax biosynthesis. J. Exp. Bot. 73, 2799–2816 (2022).

    Article  CAS  PubMed  Google Scholar 

  28. Ni, E. et al. OsCER1 regulates humidity-sensitive genic male sterility through very-long-chain (VLC) alkane metabolism of tryphine in rice. Funct. Plant Biol. 48, 461–468 (2021).

    Article  CAS  PubMed  Google Scholar 

  29. Wang, Z. et al. The E3 ligase drought hypersensitive negatively regulates cuticular wax biosynthesis by promoting the degradation of transcription factor ROC4 in rice. Plant Cell 30, 228–244 (2018).

    Article  CAS  PubMed  Google Scholar 

  30. Jian, L., Kang, K., Choi, Y., Suh, M. C. & Paek, N. C. Mutation of OsMYB60 reduces rice resilience to drought stress by attenuating cuticular wax biosynthesis. Plant J. 112, 339–351 (2022).

    Article  CAS  PubMed  Google Scholar 

  31. Sadok, W., Lopez, J. R. & Smith, K. P. Transpiration increases under high-temperature stress: potential mechanisms, trade-offs and prospects for crop resilience in a warming world. Plant Cell Environ. 44, 2102–2116 (2021).

    Article  CAS  PubMed  Google Scholar 

  32. Masle, J., Gilmore, S. R. & Farquhar, G. D. The ERECTA gene regulates plant transpiration efficiency in Arabidopsis. Nature 436, 866–870 (2005).

    Article  CAS  PubMed  Google Scholar 

  33. Shen, H. et al. Overexpression of receptor-like kinase ERECTA improves thermotolerance in rice and tomato. Nat. Biotechnol. 33, 996–1003 (2015).

    Article  CAS  PubMed  Google Scholar 

  34. Huang, X. Y. et al. A previously unknown zinc finger protein, DST, regulates drought and salt tolerance in rice via stomatal aperture control. Genes Dev. 23, 1805–1817 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Ding, Y. F. et al. Rice DST transcription factor negatively regulates heat tolerance through ROS-mediated stomatal movement and heat-responsive gene expression. Front. Plant Sci. 14, 1068296 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  36. Liu, J. et al. The RING finger ubiquitin E3 ligase OsHTAS enhances heat tolerance by promoting H2O2-induced stomatal closure in rice. Plant Physiol. 170, 429–443 (2016).

    Article  CAS  PubMed  Google Scholar 

  37. Prasad, P. V. V., Bheemanahalli, R. & Jagadish, S. V. K. Field crops and the fear of heat stress—opportunities, challenges and future directions. Field Crops Res. 200, 114–121 (2017).

    Article  Google Scholar 

  38. Yang, C., Luo, A., Lu, H. P., Davis, S. J. & Liu, J. X. Diurnal regulation of alternative splicing associated with thermotolerance in rice by two glycine-rich RNA-binding proteins. Sci. Bull. 69, 59–71 (2024).

    Article  CAS  Google Scholar 

  39. Yang, J. et al. Brassinosteroids modulate meristem fate and differentiation of unique inflorescence morphology in Setaria viridis. Plant Cell 30, 48–66 (2018).

    Article  CAS  PubMed  Google Scholar 

  40. Xie, L. et al. Population genomic analysis unravels the evolutionary roadmap of pericarp color in rice. Plant Commun. 5, 100778 (2024).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This project was financially supported by grants from the State Key Project of Research and Development Plan (2022YFF1001603 to J.-X.L.) and the Zhejiang Provincial Natural Science Foundation of China (LD21C020001 to J.-X.L.). We would like to thank S.-J. Lu for initiating the project, Z. Ma for technical assistance, X. Huang and L. Fan for advice on domestication analysis, and L.-M. Cao and J.-L. Huang for providing the SZX and YZX recipient seeds, respectively.

Author information

Author notes

  1. These authors contributed equally: Hai-Ping Lu, Xue-Huan Liu.

Authors and Affiliations

  1. State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, China

    Hai-Ping Lu, Xue-Huan Liu, Mei-Jing Wang, Qiao-Yun Zhu, Yu-Shu Lyu, Jian-Hang Xu & Jian-Xiang Liu

  2. School of Life Sciences, Fudan University, Shanghai, China

    Xue-Huan Liu

  3. Yuelushan Laboratory of Hunan Province, Changsha, China

    Jian-Xiang Liu

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Contributions

J.-X.L., H.-P.L., X.-H.L. and M.-J.W. designed the experiments. H.P.L., X.-H.L., M.-J.W., Q.-Y.Z., Y.-S.L. and J.-H.X. performed the experiments. J.-X.L. and H.-P.L. analyzed the data. J.-X.L. and H.-P.L. wrote the paper.

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Correspondence to Jian-Xiang Liu.

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Nature Genetics thanks Weiqiang Qian and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Table 1, Supplementary Figs. 1–32 and Supporting data for Supplementary Figs. 2c and 9c (uncropped blots).

Reporting Summary

Supplementary Data

Supplementary Data 1: NAT1-regulated downstream genes. Supplementary Data 2: Natural variations in the promoter and UTR regions of NAT1 and bHLH110.

Source data

Source Data Fig. 3

Uncropped blot for Fig. 3e,i.

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Lu, HP., Liu, XH., Wang, MJ. et al. The NAT1–bHLH110–CER1/CER1L module regulates heat stress tolerance in rice. Nat Genet 57, 427–440 (2025). https://doi.org/10.1038/s41588-024-02065-2

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