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.
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Source data for main Figs. 2a, b, 2d, 3a, 5a, 6a–c, and 7a–e, and Supplementary Fig. 5a, b and 6a–c, are available in Supplementary Data 4. The RNA-seq (GSA: CRA028515) and Ribo-seq (GSA: CRA028542) data reported in this paper have been deposited in the Genome Sequence Archive (GSA)65 in the National Genomics Data Center66, China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences, and are publicly accessible at https://ngdc.cncb.ac.cn/gsa.
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Acknowledgements
We thank Professor WR Hu for organizing the Strategic Priority Research Program of CAS, CSU of CAS for organizing the China’s Manned Space Program. This work was supported by the National Natural Science Foundation of China (Grant Nos. 32171232, 31570859, 31500236, 31070237, 90917009, and 31971172), Natural Science Foundation of Shanghai (Grant No. 22ZR1469500), CAS (No. XDA04020202-15), and China’s Manned Space Program.
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P.X., H.Z., and W.C. conceived and designed the research project. T.Z., L.Z., and Y.Y. performed the experiments, and J.H. provided technical recommendations. T.Z. and P.X. analyzed the data. T.Z. and P.X. wrote and revised the manuscript. All authors have read and approved the final version of the manuscript for submission.
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Communications Biology thanks Isabel Cristina Vélez-Bermúdez, Imara Perera and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editor: David Favero.
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Zhang, T., Zhang, L., Yang, Y. et al. Genome-wide ribosome profiling reveals a dynamic translational landscape in Arabidopsis seedling roots under simulated microgravity. Commun Biol (2026). https://doi.org/10.1038/s42003-026-09991-3
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DOI: https://doi.org/10.1038/s42003-026-09991-3
