Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis

BACKGROUND: Modification of nucleosides on transfer RNA (tRNA) is important either for correct mRNA decoding process or for tRNA structural stabilization. Nucleoside methylations catalyzed by MTase (methyltransferase) are the most common type among all tRNA nucleoside modifications. Although tRNA modified nucleosides and modification enzymes have been extensively studied in prokaryotic systems, similar research remains preliminary in higher plants, especially in crop species, such as rice (Oryza sativa). Rice is a monocot model plant as well as an important cereal crop, and stress tolerance and yield are of great importance for rice breeding. RESULTS: In this study, we investigated how the composition and abundance of tRNA modified nucleosides could change in response to drought, salt and cold stress, as well as in different tissues during the whole growth season in two model plants–O. sativa and Arabidopsis thaliana. Twenty two and 20 MTase candidate genes were identified in rice and Arabidopsis, respectively, by protein sequence homology and conserved domain analysis. Four methylated nucleosides, Am, Cm, m(1)A and m(7)G, were found to be very important in stress response both in rice and Arabidopsis. Additionally, three nucleosides,Gm, m(5)U and m(5)C, were involved in plant development. Hierarchical clustering analysis revealed consistency on Am, Cm, m(1)A and m(7)G MTase candidate genes, and the abundance of the corresponding nucleoside under stress conditions. The same is true for Gm, m(5)U and m(5)C modifications and corresponding methylation genes in different tissues during different developmental stages. CONCLUSIONS: We identified candidate genes for various tRNA modified nucleosides in rice and Arabidopsis, especially on MTases for methylated nucleosides. Based on bioinformatics analysis, nucleoside abundance assessments and gene expression profiling, we propose four methylated nucleosides (Am, Cm, m(1)A and m(7)G) that are critical for stress response in rice and Arabidopsis, and three methylated nucleosides (Gm, m(5)U and m(5)C) that might be important during development. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-017-1206-0) contains supplementary material, which is available to authorized users.