Developmental tissue differentiation of tRNA modification dynamics in European dewberry (Rubus caesius L.) callus formation and growth

European dewberry (Rubus caesius L.) is one of the five Rubus-species growing on the Finnish mainland. Calli are defined as a mass of actively dividing plant cells formed by hormone-mediated induction, wounding, or reacquisition of embryonic or meristemic route. In hormone-mediated induction, the balance of auxin and cytokinin determines the activation of transcriptional factors leading to change in translation. Post-transcriptional transfer RNA (tRNA) modifications (PTMs) modulate translation by altering tRNA isoacceptor recognition and codon-anticodon base-pairing interactions, affecting the processivity and fidelity of translation. As PTMs are influenced by environmental changes and play a role in regulation of tissue differentiation in plants, I hypothesize that PTMs are an important player in the transitioning to callus, its subsequent growth and morphology. It’s shown that PTMs and their modifying enzymes are differently expressed in leaf and callus.
I set out to assess which PTMs are present in leaf and three morphologically varied callus lines, and how their levels change over time as the callus lines stabilize. First, I performed whole-genome sequencing to obtain the first complete genome of R. caesius. I generated three callus lines and collected tissue samples from five different time points spanning ten months during which one of the lines remained green and hard as two turned yellow and soft. To elucidate how nucleoside modifications and their modifiers modulate tissue morphology changes over time, I utilized quantitative mass spectrometry and RNA-seq to characterize changes in PTM dynamics and differential gene expression. My preliminary results indicate certain PTMs undergo marked changes in their abundance upon differentiation, although the impact on gene expression remains to be elucidated. This project will provide the first detailed insights into RNA-based regulation of plant tissue differentiation and development in R. caesius, as well as advance our understanding of universal mechanisms that are conserved across multiple phyla.