Abstract
Increase in atmospheric carbon dioxide (CO2) has a significant effect on plant growth and development. To explore the elevated-CO2 response, we generated transcriptional profiles over a time course (2 h–14 days) of exposure to elevated CO2 in Arabidopsis thaliana. Genes related to photosynthesis were down-regulated and circadian rhythm-related genes were abnormally regulated in the early to middle phase of elevated CO2 exposure. To understand the novel mechanism of elevated CO2 signaling, we focused on 42 unknown small coding genes that showed differential expression patterns under elevated CO2 conditions. Four transgenic plants overexpressing the small coding gene exhibited a growth-defective phenotype under elevated CO2 but not under current CO2. Transcriptome analysis showed that circadian rhythm-related genes were commonly regulated in four transgenic plants. These circadian rhythm-related genes were transcribed in the dark when CO2 concentrations in the leaf was high. Taken together, our identified four small coding genes are likely to participate in elevated CO2 signaling to the circadian rhythm.
Key Message
Transcriptome analysis was performed under elevated CO2 condition in Arabidopsis thaliana. We identified small coding genes associated with signal molecules from elevated CO2 to circadian rhythm genes.
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The raw unfiltered microarray results are available in the Gene Expression Omnibus (GEO) database under the subseries entry GSE49960.
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Abbreviations
- ABA:
-
Abscisic acid
- ANOVA:
-
One-way analysis of variance
- FACE:
-
Free-air CO2 enrichment
- FDR:
-
False discovery rate
- GEO:
-
Gene expression omnibus
- GO:
-
Gene ontology
- GUS:
-
β-Glucuronidase
- LIMMA:
-
Linear models for microarray data
- sORFs:
-
Small open reading frames
- X-gluc:
-
5-Bromo-4-chloro-3-indolyl-β-d-glucuronic acid
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Acknowledgements
We thank Dr H. Sakakibara, Dr T. Kiba and Dr K. Kusumi for use of the CO2 chambers. This work was supported by the Program for Promotion of Basic and Applied Research for Innovations in Bio-oriented Industry (BRAIN, to M.H. and K.H.), Grants-in-Aid for Scientific Research 19H05348, 19K22313, 18H02420, 18KK0176, 17H03727 (to K.H.), 16K00593 (to M. H.) and the Core Research for Evolutional Science and Technology (CREST) Program “Creation of essential technologies to utilize carbon dioxide as a resource through the enhancement of plant productivity and the exploitation of plant products” of the Japan Science and Technology Agency (JST, JPMJCR11B3 to K.H.).
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M. H.-T. and K. H. conceived the study and obtained funding. M. H.-T., T. K., M. S. and Y. K. performed experiments. K. H. conducted informatics analyses. M. H.-T., T. K. and K. H. wrote the paper. K.S. participated in the experimental design and coordination, and helped to draft the manuscript. All authors read and approved the final manuscript.
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Higuchi-Takeuchi, M., Kondo, T., Shimizu, M. et al. Effect of small coding genes on the circadian rhythms under elevated CO2 conditions in plants. Plant Mol Biol 104, 55–65 (2020). https://doi.org/10.1007/s11103-020-01023-w
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DOI: https://doi.org/10.1007/s11103-020-01023-w