The m6A reader MhYTP2 regulates the stability of its target mRNAs contributing to low nitrogen tolerance in apple (Malus domestica)

Abstract

Studies have shown that the m⁶A reader primarily affects genes expression by participating in the regulation of mRNA localization, splicing, degradation, translation, and other metabolic processes. Previously, we discovered that the apple (Malus domestica) m⁶A reader MhYTP2 bound with and destabilized m⁶A-modified MdMLO19 mRNA. In addition, it enhanced the translation efficiency of m⁶A-modified mRNA of MdGDH1L, encoding a glutamate dehydrogenase, which confers resistance to powdery mildew. In this study, we report the function of MhYTP2 in the regulation of resistance to low nitrogen (N). The overexpression of MhYTP2 enhances the resistance of apple to low N. We show that MhYTP2 binds with and stabilizes the mRNAs of MdALN, which participates in the allantoin catabolic process and cellular response to N starvation in apple; MdPIDL, which participates in root hair elongation; MdTTG1, which is involved in the differentiation process of trichomes; and MdATG8A, which is a core participant in the regulation of autophagy. In addition, MhYTP2 accelerates the degradation of MdRHD3 mRNA, which regulates root development. RNA immunoprecipitation-seq and electrophoretic mobility shift assays show that the mRNAs of MdALN, MdATG8A, MdPIDL, MdTTG1, and MdRHD3 are the direct targets of MhYTP2. Overexpressing or knocking down the above genes in MhYTP2 overexpressing plants dismisses the function of MhYTP2 under low N, suggesting the role of MhYTP2 is dependent on those genes. Together, these results demonstrate that MhYTP2 enhances the resistance of apple to N deficiency by affecting the stability of the bound mRNAs.

Acknowledgements

This work was financially supported grants from the National Natural Science Foundation of China (31972391, 32172529), the China Agriculture Research System of MOF and MARA (CARS-27), the Special Funds for Major Scientific and Technological Innovation from Shaanxi Province (2020zdzx03-01-01).

Author contributions

T.G.: experiment design and implementation, manuscript composition; Z.Y., R.B., X.F., and N.W.: experiment implementation and assistance; C.L. and F.M.: experiment design and implementation, composition and review of manuscript, financial support for experiments and laboratory apparatus.

Data availability

All relevant data can be found within the paper and its supporting materials.

Conflict of interest statement

The authors declare no conflict of interest.

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