Exploring Transfer RNA Modifications during Rhizome Development in Oryza longistaminata

Research using non-plant models reveals that the dynamic deposition of tRNA modifications is an efficient regulatory mechanism during multiple developmental processes and disease progressions, positioning tRNA modification as a frontier in biomedical research. By contrast, plant tRNA modification research is still in its infancy. In particular, the connection between tRNA modification and plant organ development has not been established. As a case study, we investigated tRNA modifications during rhizome development in Oryza longistaminata. A nascent rhizome generally first elongates horizontally and then enters a developmental transition stage to produce an aerial shoot. Notably, both these stages display exceptional developmental plasticity; thus, the complex interconnections between rhizome development and the environment are presumably underpinned by tRNA modification-based regulation. Using liquid chromatography-mass spectrometry, we conducted systematic profiling of modified nucleosides in rhizomes. The abundances of m²G, m² ₂G, m¹G, m⁶t⁶A and ψ were detected to correlate with rhizome elongation, and m¹A, m⁶A, m¹I, m⁵U and mnm⁵s²U were differentially abundant when rhizomes were treated with different transition-related environmental factors. Through profiling rhizomes treated with hormones with known regulatory roles, we pinpointed several tRNA modifications that are likely associated with the hormonal signalling pathways relevant to the two rhizome developmental stages-m²G, m¹G and m² ₂G for elongation, and m¹I and m⁵U for transition. In addition, genome-wide analysis of tRNA-modifying genes was performed to set the stage for functional characterisation. These results and analyses deepen our understanding of rhizome development and underscore the potential regulatory significance of tRNA modification in plant organ development.