Genome-wide ribosome profiling reveals dynamic translational landscape in Arabidopsis seedling roots under simulated microgravity

Abstract Plants can adapt to environmental change through a variety of transcriptional and translational mechanisms. Although extensive knowledge exists about plant stress responses at the transcriptional level, understanding of these responses at the translational level is limited. This study aimed to evaluate the translational dynamics of plants in a simulated microgravity environment through the utilization of a ribosome profiling assay. A comparative analysis of ribosome profiling data and RNA-seq on a global scale demonstrated a modest correlation in the alteration of gene expression between transcriptional and translational levels. However, under one third of responsive genes exhibited concurrent transcriptional and translational activities. We found that simulated microgravity simulation elicited separate transcriptional and translational responses in plants. The findings indicated a significant alteration in the translational efficiency (TE) of 1081 genes under simulated microgravity conditions. Subsequent analysis identified specific sequence characteristics, including GC content and coding sequence length, as influential factors on gene TE. The abundance of upstream open reading frames (uORFs) within gene promoters indicates a possible influence on the translation efficiency of primary open reading frames located downstream. These results suggested that in response to simulated microgravity, plants had a responsive translational mechanism that interacted with transcription in a coordinated manner.