Characterizing the heat response of Arabidopsis thaliana from the perspective of codon usage bias and translational regulation.

mRNA translation is carefully regulated at both the initiation and the elongation step. Under heat stress, it is known that particular genes change their expression and translation levels to respond to the environment. Attention has been paid to the detailed mechanisms of how a few proteins work, and little is done to analyze whether the global evolutionary patterns affect the translational changes. Determinants like codon usage bias and its related evolutionary features are less studied in heat stress experiments, especially for plants. Utilizing the RNA-seq and Ribo-seq data of normal and heat-stressed Arabidopsis thaliana generated from a previous study, we conducted gene-level (global) and codon-resolution (local) translation analyses. We studied how codon usage bias and other evolutionary features could impact the translation patterns in the heat response of the plant. We found that the evolutionary features including codon usage bias, tAI, nitrogen cost, and conservation (identity) could affect the global and local translation efficiency. Under heat stress, the optimal and conserved codons are more likely to alter their local translation elongation speed to modulate the global translation of host genes. Meanwhile, we also verified the widely accepted notions that the secondary structures and proline codons could largely slow down the translation rate. Our results revealed the effect of codon usage bias and other evolutionary patterns on the translation regulation under heat stress. Unveiling the effect of these features on translational regulation of plants might be helpful in understanding the relationship and interaction between plants and the environment.