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Impaired 2′,3′-cyclic phosphate tRNA repair causes thermo-sensitive genic male sterility in rice

Cell Research volume 34, pages 763–775 (2024)Cite this article

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Abstract

Hybrid rice, widely planted in Asia, is pathogen resistant and has superior yields, making it a major contributor to global food security. The two-line hybrid rice system, which utilizes mutants exhibiting photo-/thermo-sensitive genic male sterility (P/TGMS), is the leading hybrid rice breeding technology. Mutations in THERMO-SENSITIVE GENIC MALE STERILE 5 (TMS5) accounts for over 95% of current TGMS lines. We previously found that tms5 carries a mutation in ribonuclease ZS1. Despite its importance for breeding robust rice lines, the mechanism underlying tms5-mediated TGMS remains elusive. Here, we demonstrate that TMS5 is a tRNA 2′,3′-cyclic phosphatase. The tms5 mutation leads to accumulation of 2′,3′-cyclic phosphate (cP)-ΔCCA-tRNAs (tRNAs without 3′ CCA ended with cP), which is exacerbated by high temperatures, and reduction in the abundance of mature tRNAs, particularly alanine tRNAs (tRNA-Alas). Overexpression of tRNA-Alas in the tms5 mutant restores male fertility to 70%. Remarkably, male fertility of tms5 mutant is completely restored at high temperatures by knocking out OsVms1 which encodes the enzyme for cP-ΔCCA-tRNA generation. Our study reveals the mechanism underlying tms5-mediated TGMS in rice and provides mechanistic insight into the further improvement of TGMS in hybrid crop development.

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Fig. 1: TMS5 is a 2′,3′-cyclic phosphatase for cP-ΔCCA-tRNA repair.
Fig. 2: High temperature exacerbates the aberrant accumulation of cP-ΔCCA-tRNAs in Zhu1S.
Fig. 3: Lack of mature tRNAs is the major cause of the TGMS phenotype in Zhu1S.
Fig. 4: The effect of overexpressing tRNA-Alas in Zhu1S on male fertility.
Fig. 5: Preventing the generation of cP-ΔCCA-tRNAs fully restores the male fertility of Zhu1S.
Fig. 6: A model elucidating impaired 2′,3′-cyclic phosphate tRNA repair underlying tms5-mediated TGMS in rice.

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Data availability

The RcP-RNA-seq and FINE-tRNA-seq data have been deposited in the Genome Sequence Archive in National Genomics Data Center, China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences (https://ngdc.cncb.ac.cn/gsa/) with the accession number: CRA014058. Crystal structure information of rice TMS5 has been deposited in the PDB (https://www.rcsb.org/) with ID 7XGT. All other data are available in the manuscript or the supplementary information.

References

  1. Tester, M. & Langridge, P. Breeding technologies to increase crop production in a changing world. Science 327, 818–822 (2010).

    Article  CAS  PubMed  Google Scholar 

  2. Qian, Q., Zhang, F. & Xin, Y. Yuan longping and hybrid rice research. Rice 14, 101 (2021).

    Article  PubMed  Google Scholar 

  3. Normile, D. Crossing rice strains to keep Asia’s rice bowls brimming. Science 283, 313–313 (1999).

    Article  CAS  Google Scholar 

  4. Jones, J. W. Hybrid vigor in rice1. Agron. J. 18, 423–428 (1926).

    Article  Google Scholar 

  5. He, Q. et al. Hybrid Rice. Engineering 6, 967–973 (2020).

    Article  Google Scholar 

  6. Fan, Y. & Zhang, Q. Genetic and molecular characterization of photoperiod and thermo-sensitive male sterility in rice. Plant Reprod. 31, 3–14 (2018).

    Article  CAS  PubMed  Google Scholar 

  7. Yu, J. et al. Two rice receptor-like kinases maintain male fertility under changing temperatures. Proc. Natl. Acad. Sci. USA 114, 12327–12332 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Chen, R. et al. Rice UDP-glucose pyrophosphorylase1 is essential for pollen callose deposition and its cosuppression results in a new type of thermosensitive genic male sterility. Plant Cell 19, 847–861 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Wu, L. et al. A natural allele of OsMS1 responds to temperature changes and confers thermosensitive genic male sterility. Nat. Commun. 13, 2055 (2022).

    Article  CAS  PubMed  Google Scholar 

  10. Zhou, H. et al. Photoperiod- and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA. Cell Res. 22, 649–660 (2012).

    Article  CAS  PubMed  Google Scholar 

  11. Ding, J. et al. A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc. Natl. Acad. Sci. USA 109, 2654–2659 (2012).

    Article  CAS  PubMed  Google Scholar 

  12. Teng, C. et al. Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize. Nat. Commun. 11, 2912 (2020).

    Article  CAS  PubMed  Google Scholar 

  13. Zhu, J. et al. Slowing development restores the fertility of thermo-sensitive male-sterile plant lines. Nat. Plants 6, 360–367 (2020).

    Article  CAS  PubMed  Google Scholar 

  14. Shi, Q. S. et al. A cellular mechanism underlying the restoration of thermo/photoperiod-sensitive genic male sterility. Mol. Plant 14, 2104–2114 (2021).

    Article  CAS  PubMed  Google Scholar 

  15. Peng, G. et al. The E3 ubiquitin ligase CSIT1 regulates critical sterility-inducing temperature by ribosome-associated quality control to safeguard two-line hybrid breeding in rice. Mol. Plant 16, 1695–1709 (2023).

    Article  CAS  PubMed  Google Scholar 

  16. Zhou, H. et al. RNase Z(S1) processes UbL40 mRNAs and controls thermosensitive genic male sterility in rice. Nat. Commun. 5, 4884 (2014).

    Article  CAS  PubMed  Google Scholar 

  17. Liu, W. et al. Reproductive tissue-specific translatome of a rice thermo-sensitive genic male sterile line. J. Genet. Genomics 49, 624–635 (2022).

    Article  CAS  PubMed  Google Scholar 

  18. Li, J. et al. Generation of thermosensitive male-sterile maize by targeted knockout of the ZmTMS5 gene. J. Genet. Genomics 44, 465–468 (2017).

    Article  CAS  PubMed  Google Scholar 

  19. Yip, M. C. J., Savickas, S., Gygi, S. P. & Shao, S. ELAC1 repairs tRNAs cleaved during ribosome-associated quality control. Cell Rep. 30, 2106–2114 (2020).

    Article  CAS  PubMed  Google Scholar 

  20. Pinto, P. H. et al. ANGEL2 is a member of the CCR4 family of deadenylases with 2’,3’-cyclic phosphatase activity. Science 369, 524–530 (2020).

    Article  CAS  PubMed  Google Scholar 

  21. Yip, M. C. J. et al. Mechanism for recycling tRNAs on stalled ribosomes. Nat. Struct. Mol. Biol. 26, 343–349 (2019).

    Article  CAS  PubMed  Google Scholar 

  22. Li de la Sierra-Gallay, I., Mathy, N., Pellegrini, O. & Condon, C. Structure of the ubiquitous 3’ processing enzyme RNase Z bound to transfer RNA. Nat. Struct. Mol. Biol. 13, 376–377 (2006).

    Article  PubMed  Google Scholar 

  23. Kostelecky, B., Pohl, E., Vogel, A., Schilling, O. & Meyer-Klaucke, W. The crystal structure of the zinc phosphodiesterase from Escherichia coli provides insight into function and cooperativity of tRNase Z-family proteins. J. Bacteriol. 188, 1607–1614 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Ishii, R. et al. Crystal structure of the tRNA 3’ processing endoribonuclease tRNase Z from Thermotoga maritima. J. Biol. Chem. 280, 14138–14144 (2005).

    Article  CAS  PubMed  Google Scholar 

  25. Li de la Sierra-Gallay, I., Pellegrini, O. & Condon, C. Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z. Nature 433, 657–661 (2005).

    Article  PubMed  Google Scholar 

  26. Gu, H. et al. A 5’ tRNA-Ala-derived small RNA regulates anti-fungal defense in plants. Sci. China Life Sci. 65, 1–15 (2022).

    Article  CAS  PubMed  Google Scholar 

  27. Tanaka, N., Meineke, B. & Shuman, S. RtcB, a novel RNA ligase, can catalyze tRNA splicing and HAC1 mRNA splicing in vivo. J. Biol. Chem. 286, 30253–30257 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Behrens, A., Rodschinka, G. & Nedialkova, D. D. High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq. Mol. Cell 81, 1802–1815 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Sakata, T. & Higashitani, A. Male sterility accompanied with abnormal anther development in plants – genes and environmental stresses with special reference to high temperature injury. Int. J. Plant Dev. Biol. 2, 42–51 (2008).

    Google Scholar 

  30. Dimitrova, L. N., Kuroha, K., Tatematsu, T. & Inada, T. Nascent peptide-dependent translation arrest leads to Not4p-mediated protein degradation by the proteasome. J. Biol. Chem. 284, 10343–10352 (2009).

    Article  PubMed  Google Scholar 

  31. Letzring, D. P., Wolf, A. S., Brule, C. E. & Grayhack, E. J. Translation of CGA codon repeats in yeast involves quality control components and ribosomal protein L1. RNA 19, 1208–1217 (2013).

    Article  CAS  PubMed  Google Scholar 

  32. Gamble, C. E., Brule, C. E., Dean, K. M., Fields, S. & Grayhack, E. J. Adjacent codons act in concert to modulate translation efficiency in yeast. Cell 166, 679–690 (2016).

    Article  CAS  PubMed  Google Scholar 

  33. Simms, C. L., Hudson, B. H., Mosior, J. W., Rangwala, A. S. & Zaher, H. S. An active role for the ribosome in determining the fate of oxidized mRNA. Cell Rep. 9, 1256–1264 (2014).

    Article  CAS  PubMed  Google Scholar 

  34. Doma, M. K. & Parker, R. Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature 440, 561–564 (2006).

    Article  CAS  PubMed  Google Scholar 

  35. Shen, P. S. et al. Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains. Science 347, 75–78 (2015).

    Article  CAS  PubMed  Google Scholar 

  36. Choe, Y. J. et al. Failure of RQC machinery causes protein aggregation and proteotoxic stress. Nature 531, 191–195 (2016).

    Article  CAS  PubMed  Google Scholar 

  37. Yonashiro, R. et al. The Rqc2/Tae2 subunit of the ribosome-associated quality control (RQC) complex marks ribosome-stalled nascent polypeptide chains for aggregation. ELife 5, e11794 (2016).

    Article  PubMed  Google Scholar 

  38. Lei, D., Tang, W., Xie, Z., Liu, H. & Chen, L. Solutions to insecurity problems in seed production of two-line hybrid rice. Agric. Sci. Technol. 15, 1160–1166 (2014).

    Google Scholar 

  39. Ma, X. et al. A Robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol. plant 8, 1274–1284 (2015).

    Article  CAS  PubMed  Google Scholar 

  40. Kabsch, W. XDS. Acta Crystallogr. Sect. D Biol. Crystallogr. 66, 125–132 (2010).

    Article  CAS  Google Scholar 

  41. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. Sect. D Biol. Crystallogr. 66, 213–221 (2010).

    Article  CAS  Google Scholar 

  42. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. Sect. D Biol. Crystallogr. 66, 486–501 (2010).

    Article  CAS  Google Scholar 

  43. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. Sect. D Biol. Crystallogr. 66, 12–21 (2010).

    Article  CAS  Google Scholar 

  44. Li, X. et al. Base-resolution mapping reveals distinct m(1)A methylome in nuclear- and mitochondrial-encoded transcripts. Mol. Cell 68, 993–1005 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Martin, M. CUTADAPT removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).

    Article  Google Scholar 

  46. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank Dr. Bo Cao at Shanghai Jiao Tong University, Dr. Chengqi Yi and Dr. Xiaoyu Li at Peking University for helping in constructing tRNA-seq library, and Dr. Xuan Ma at Tianjin Normal University for his assistance with previous bioinformatics analyses. We particularly thank Dr. Falong Lu at the Institute of Genetics & Developmental Biology, CAS and Dr. Yusheng Liu at the Northeast Forestry University for discussing and revising the manuscript. We also thank Mr. Zhenhua Guo at the Institute of Genetics and Developmental Biology, CAS, and Dr. Guocheng Hu at China National Rice Research Institute for rice cultivation. This work was supported by grants from the Biological Breeding-National Science and Technology Major Project of China (2023ZD04073), the National Key R&D Program of China (2020YFA0509900), the National Natural Science Foundation of China (32330019, 32171284, 32170620 and 32370633), the Strategic Priority Research Program of Chinese Academy of Sciences (XDA24010302).

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Author notes

  1. These authors contributed equally: Bin Yan, Chunyan Liu, Jing Sun, Yang Mao, Can Zhou.

Authors and Affiliations

  1. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

    Bin Yan, Chunyan Liu, Jing Sun, Can Zhou, Ji Li, Wei Liu, Shengdong Li & Xiaofeng Cao

  2. Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China

    Jing Sun

  3. Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

    Yang Mao, Jiawei Nie, Feng Gao & Yuhang Chen

  4. University of the Chinese Academy of Sciences, Beijing, China

    Can Zhou, Ji Li, Shengdong Li, Jiawei Nie, Yuhang Chen & Xiaofeng Cao

  5. Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China

    Wei Yan

  6. Yuan Longping High-tech Agriculture Co., Ltd., Changsha, Hunan, China

    Chenjian Fu, Peng Qin, Xingxue Fu, Xinghui Zhao & Yuanzhu Yang

  7. Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

    Xianwei Song

  8. State Key Laboratory of Hybrid Rice, Changsha, Hunan, China

    Yuanzhu Yang

  9. Key Laboratory of Rice Germplasm Enhancement in Southern China, Ministry of Agriculture and Rural Affairs, Changsha, Hunan, China

    Yuanzhu Yang

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Contributions

X.C., Y.C., Y.Y., C.L., and B.Y. conceived and planned the experiments. B.Y., C.L., Y.M., C.Z., J.L., W.L., S.L., W.Y., C.F., P.Q., X.F., X.Z., X.S., J.N., and F.G. performed and analyzed the experiments. J.S. worked on bioinformatics analysis. B.Y., C.L., J.S., Y.Y., Y.C., and X.C. interpreted the results and wrote the manuscript.

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Correspondence to Chunyan Liu, Yuanzhu Yang, Yuhang Chen or Xiaofeng Cao.

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Yan, B., Liu, C., Sun, J. et al. Impaired 2′,3′-cyclic phosphate tRNA repair causes thermo-sensitive genic male sterility in rice. Cell Res 34, 763–775 (2024). https://doi.org/10.1038/s41422-024-01012-4

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