Impact of translational regulation on diel expression revealed by time‐series ribosome profiling in Arabidopsis

• Published in: The Plant journal : for cell and molecular biology Vol. 118; no. 6; pp. 1889 - 1906
• Main Authors: Aoyama, Haruka, Arae, Toshihiro, Yamashita, Yui, Toyoda, Atsushi, Naito, Satoshi, Sotta, Naoyuki, Chiba, Yukako
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.06.2024
• Subjects: Arabidopsis; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; circadian clocks; Circadian Clocks - genetics; Circadian Rhythm - genetics; Circadian rhythms; clock genes; diel expression; Environmental changes; Environmental stress; flowering; Gene expression; Gene Expression Regulation, Plant; Gene regulation; Genes; Glycosylation; Oscillations; Photoperiod; Photosynthesis; Protein Biosynthesis; Ribosome Profiling; ribosomes; Ribosomes - genetics; Ribosomes - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; sequence analysis; Stress response; temperature; time series analysis; transcription (genetics); Translation; translation control; upstream open reading frame; clock genes; translation control; upstream open reading frame; Arabidopsis; diel expression
• ISSN: 0960-7412; 1365-313X; 1365-313X
• DOI: 10.1111/tpj.16716

SUMMARY Plants have developed the ability to adjust to the day/night cycle through the expression of diel genes, which allow them to effectively respond to environmental changes and optimise their growth and development. Diel oscillations also have substantial implications in many physiological processes, including photosynthesis, floral development, and environmental stress responses. The expression of diel genes is regulated by a combination of the circadian clock and responses to environmental cues, such as light and temperature. A great deal of information is available on the transcriptional regulation of diel gene expression. However, the extent to which translational regulation is involved in controlling diel changes in expression is not yet clear. To investigate the impact of translational regulation on diel expression, we conducted Ribo‐seq and RNA‐seq analyses on a time‐series sample of Arabidopsis shoots cultivated under a 12 h light/dark cycle. Our results showed that translational regulation is involved in about 71% of the genes exhibiting diel changes in mRNA abundance or translational activity, including clock genes, many of which are subject to both translational and transcriptional control. They also revealed that the diel expression of glycosylation and ion‐transporter‐related genes is mainly established through translational regulation. The expression of several diel genes likely subject to translational regulation through upstream open‐reading frames was also determined. Significance Statement For plants, adaptation to diel oscillations in the environment is important for many biological processes; however, the impact of translational regulation on diel gene expression is not fully understood. In this study, time‐series ribosome profiling (Ribo‐seq) revealed that many diel genes, including clock genes, are translationally regulated; moreover, genes exhibiting diel oscillation solely in terms of translational activity tend to be more highly expressed at night.