Various aspects of the organisms adapt to cyclically changing environmental conditions via transcriptional regulation. However, the role of rhythmicity in altering the global aspects of metabolism is poorly characterized. Here, we subjected four rice (Oryza sativa) varieties to a range of metabolic profiles and RNA-seq to investigate the temporal relationships of rhythm between transcription and metabolism. More than 40% of the rhythmic genes and a quarter of metabolites conservatively oscillated across four rice accessions. Compared with the metabolome, the transcriptome was more strongly regulated by rhythm; however, the rhythm of metabolites had an obvious opposite trend between day and night. Through association analysis, the time delay of rhythmic transmission from the transcript to the metabolite level was ∼4 h under long-day conditions, although the transmission was nearly synchronous for carbohydrate and nucleotide metabolism. The rhythmic accumulation of metabolites maintained highly coordinated temporal relationships in the metabolic network, whereas the correlation of some rhythmic metabolites, such as branched-chain amino acids (BCAAs), was significantly different intervariety. We further demonstrated that the cumulative diversity of BCAAs was due to the differential expression of branched-chain aminotransferase 2 at dawn. Our research reveals the flexible pattern of rice metabolic rhythm existing with conservation and diversity.
This is a preview of subscription content, access via your institution.
Buy single article
Instant access to the full article PDF.
Price excludes VAT (USA)
Tax calculation will be finalised during checkout.
Adams, S., Grundy, J., Veflingstad, S.R., Dyer, N.P., Hannah, M.A., Ott, S., and Carré, I.A. (2018). Circadian control of abscisic acid biosynthesis and signalling pathways revealed by genome-wide analysis of lhy binding targets. New Phytol 220, 893–907.
Annunziata, M.G., Apelt, F., Carillo, P., Krause, U., Feil, R., Koehl, K., Lunn, J.E., and Stitt, M. (2018). Response of Arabidopsis primary metabolism and circadian clock to low night temperature in a natural light environment. J Exp Bot 69, 4881–4895.
Armengaud, P., Sulpice, R., Miller, A.J., Stitt, M., Amtmann, A., and Gibon, Y. (2009). Multilevel analysis of primary metabolism provides new insights into the role of potassium nutrition for glycolysis and nitrogen assimilation in Arabidopsis roots. Plant Physiol 150, 772–785.
Bass, J., and Takahashi, J.S. (2010). Circadian integration of metabolism and energetics. Science 330, 1349–1354.
Bendix, C., Marshall, C.M., and Harmon, F.G. (2015). Circadian clock genes universally control key agricultural traits. Mol Plant 8, 1135–1152.
Binder, S. (2010). Branched-chain amino acid metabolism in Arabidopsis thaliana. Arabidopsis Book 8, e0137.
Caster, S.Z., Castillo, K., Sachs, M.S., and Bell-Pedersen, D. (2016). Circadian clock regulation of mRNA translation through eukaryotic elongation factor eEF-2. Proc Natl Acad Sci USA 113, 9605–9610.
Chen, C., Chen, H., Zhang, Y., Thomas, H.R., Frank, M.H., He, Y., and Xia, R. (2020). Tbtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant 13, 1194–1202.
Chen, R., Deng, Y., Ding, Y., Guo, J., Qiu, J., Wang, B., Wang, C., Xie, Y., Zhang, Z., Chen, J., et al. (2022). Rice functional genomics: decades’ efforts and roads ahead. Sci China Life Sci 65, 33–92.
Chen, Z.J., and Mas, P. (2019). Interactive roles of chromatin regulation and circadian clock function in plants. Genome Biol 20, 62.
Covington, M.F., Maloof, J.N., Straume, M., Kay, S.A., and Harmer, S.L. (2008). Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol 9, R130.
de Montaigu, A., Giakountis, A., Rubin, M., Tóth, R., Cremer, F., Sokolova, V., Porri, A., Reymond, M., Weinig, C., and Coupland, G. (2015). Natural diversity in daily rhythms of gene expression contributes to phenotypic variation. Proc Natl Acad Sci USA 112, 905–910.
Dyar, K.A., Lutter, D., Artati, A., Ceglia, N.J., Liu, Y., Armenta, D., Jastroch, M., Schneider, S., de Mateo, S., Cervantes, M., et al. (2018). Atlas of circadian metabolism reveals system-wide coordination and communication between clocks. Cell 174, 1571–1585.e11.
Eckel-Mahan, K., and Sassone-Corsi, P. (2013). Metabolism and the circadian clock converge. Physiol Rev 93, 107–135.
Edgar, R.S., Green, E.W., Zhao, Y., van Ooijen, G., Olmedo, M., Qin, X., Xu, Y., Pan, M., Valekunja, U.K., Feeney, K.A., et al. (2012). Peroxiredoxins are conserved markers of circadian rhythms. Nature 485, 459–464.
Espinoza, C., Degenkolbe, T., Caldana, C., Zuther, E., Leisse, A., Willmitzer, L., Hincha, D.K., and Hannah, M.A. (2010). Interaction with diurnal and circadian regulation results in dynamic metabolic and transcriptional changes during cold acclimation in Arabidopsis. PLoS ONE 5, e14101.
Fang, C., Li, K., Wu, Y., Wang, D., Zhou, J., Liu, X., Li, Y., Jin, C., Liu, X., Mur, L.A.J., et al. (2019). OsTSD2-mediated cell wall modification affects ion homeostasis and salt tolerance. Plant Cell Environ 42, 1503–1512.
Farré, E.M., and Kay, S.A. (2007). Prr7 protein levels are regulated by light and the circadian clock in Arabidopsis. Plant J 52, 548–560.
Farré, E.M., and Weise, S.E. (2012). The interactions between the circadian clock and primary metabolism. Curr Opin Plant Biol 15, 293–300.
Fernie, A.R., and Stitt, M. (2012). On the discordance of metabolomics with proteomics and transcriptomics: coping with increasing complexity in logic, chemistry, and network interactions scientific correspondence. Plant Physiol 158, 1139–1145.
Ferrari, C., Proost, S., Janowski, M., Becker, J., Nikoloski, Z., Bhattacharya, D., Price, D., Tohge, T., Bar-Even, A., Fernie, A., et al. (2019). Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida. Nat Commun 10, 737.
Filichkin, S.A., Breton, G., Priest, H.D., Dharmawardhana, P., Jaiswal, P., Fox, S.E., Michael, T.P., Chory, J., Kay, S.A., and Mockler, T.C. (2011). Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules. PLoS ONE 6, e16907.
Gibon, Y., Blaesing, O.E., Hannemann, J., Carillo, P., Hohne, M., Hendriks, J.H.M., Palacios, N., Cross, J., Selbig, J., and Stitt, M. (2004). Arobot-based platform to measure multiple enzyme activities in Arabidopsis using a set of cycling assays: comparison of changes of enzyme activities and transcript levels during diurnal cycles and in prolonged darkness. Plant Cell 16, 3304–3325.
Goodspeed, D., Chehab, E.W., Covington, M.F., and Braam, J. (2013). Circadian control of jasmonates and salicylates. Plant Signal Behav 8, e23123.
Graf, A., Coman, D., Uhrig, R.G., Walsh, S., Flis, A., Stitt, M., and Gruissem, W. (2017). Parallel analysis of Arabidopsis circadian clock mutants reveals different scales of transcriptome and proteome regulation. Open Biol 7, 160333.
Greenham, K., Guadagno, C.R., Gehan, M.A., Mockler, T.C., Weinig, C., Ewers, B.E., and McClung, C.R. (2017). Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa. eLife 6, e29655.
Greenham, K., and McClung, C.R. (2015). Integrating circadian dynamics with physiological processes in plants. Nat Rev Genet 16, 598–610.
Harmer, S.L. (2009). The circadian system in higher plants. Annu Rev Plant Biol 60, 357–377.
Harmer, S.L., Hogenesch, J.B., Straume, M., Chang, H.S., Han, B., Zhu, T., Wang, X., Kreps, J.A., and Kay, S.A. (2000). Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290, 2110–2113.
Haydon, M.J., Mielczarek, O., Robertson, F.C., Hubbard, K.E., and Webb, A.A.R. (2013). Photosynthetic entrainment of the Arabidopsis thaliana circadian clock. Nature 502, 689–692.
Heintzen, C., Nater, M., Apel, K., and Staiger, D. (1997). AtGRP7, a nuclear RNA-binding protein as a component of a circadian-regulated negative feedback loop in Arabidopsis thaliana. Proc Natl Acad Sci USA 94, 8515–8520.
Higashi, T., Aoki, K., Nagano, A.J., Honjo, M.N., and Fukuda, H. (2016). Circadian oscillation of the lettuce transcriptome under constant light and light-dark conditions. Front Plant Sci 7.
Hu, Y., Jiang, L., Wang, F., and Yu, D. (2013). Jasmonate regulates the INDUCER OF CBF EXPRESSION-C-REPEAT BINDING FACTOR/DRE BINDING FACTOR1 cascade and freezing tolerance in Arabidopsis. Plant Cell 25, 2907–2924.
Hu, Y., Jiang, Y., Han, X., Wang, H., Pan, J., and Yu, D. (2017). Jasmonate regulates leaf senescence and tolerance to cold stress: crosstalk with other phytohormones. J Exp Bot 68, 1361–1369.
Hughes, M.E., Hogenesch, J.B., and Kornacker, K. (2010). JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets. J Biol Rhythms 25, 372–380.
Hurley, J.M., Jankowski, M.S., De Los Santos, H., Crowell, A.M., Fordyce, S.B., Zucker, J.D., Kumar, N., Purvine, S.O., Robinson, E.W., Shukla, A., et al. (2018). Circadian proteomic analysis uncovers mechanisms of post-transcriptional regulation in metabolic pathways. Cell Syst 7, 613–626.e5.
Hwang, H., Cho, M.H., Hahn, B.S., Lim, H., Kwon, Y.K., Hahn, T.R., and Bhoo, S.H. (2011). Proteomic identification of rhythmic proteins in rice seedlings. Biochim Biophys Acta 1814, 470–479.
Ito, S., Nakamichi, N., Kiba, T., Yamashino, T., and Mizuno, T. (2007). Rhythmic and light-inducible appearance of clock-associated pseudoresponse regulator protein PRR9 through programmed degradation in the dark in Arabidopsis thaliana. Plant Cell Physiol 48, 1644–1651.
Jin, C., Fang, C., Zhang, Y., Fernie, A.R., and Luo, J. (2021). Plant metabolism paves the way for breeding crops with high nutritional value and stable yield. Sci China Life Sci 64, 2202–2205.
Kim, J.A., Kim, H.S., Choi, S.H., Jang, J.Y., Jeong, M.J., and Lee, S.I. (2017). The importance of the circadian clock in regulating plant metabolism. Int J Mol Sci 18, 2680.
Ko, D.K., Rohozinski, D., Song, Q., Taylor, S.H., Juenger, T.E., Harmon, F. G., and Chen, Z.J. (2016). Temporal shift of circadian-mediated gene expression and carbon fixation contributes to biomass heterosis in maize hybrids. PLoS Genet 12, e1006197.
Krishnaiah, S.Y., Wu, G., Altman, B.J., Growe, J., Rhoades, S.D., Coldren, F., Venkataraman, A., Olarerin-George, A.O., Francey, L.J., Mukherjee, S., et al. (2017). Clock regulation of metabolites reveals coupling between transcription and metabolism. Cell Metab 25, 1206.
Kubota, A., Shim, J.S., and Imaizumi, T. (2015). Natural variation in transcriptional rhythms modulates photoperiodic responses. Trends Plant Sci 20, 259–261.
Langfelder, P., and Horvath, S. (2008). WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9, 559.
Lee, H.G., Mas, P., and Seo, P.J. (2016). Myb96 shapes the circadian gating of aba signaling in Arabidopsis. Sci Rep 6, 17754.
Litthauer, S., Chan, K.X., and Jones, M.A. (2018). 3′-Phosphoadenosine 5′-phosphate accumulation delays the circadian system. Plant Physiol 176, 3120–3135.
López-Ibáñez, J., Pazos, F., and Chagoyen, M. (2016). Mbrole 2.0—functional enrichment of chemical compounds. Nucleic Acids Res 44, W201–W204.
Luo, J. (2015). Metabolite-based genome-wide association studies in plants. Curr Opin Plant Biol 24, 31–38.
Martinière, A., Shvedunova, M., Thomson, A.J.W., Evans, N.H., Penfield, S., Runions, J., and McWatters, H.G. (2011). Homeostasis of plasma membrane viscosity in fluctuating temperatures. New Phytol 192, 328–337.
Matsuzaki, J., Kawahara, Y., and Izawa, T. (2015). Punctual transcriptional regulation by the rice circadian clock under fluctuating field conditions. Plant Cell 27, 633–648.
McClung, C.R. (2006). Plant circadian rhythms. Plant Cell 18, 792–803.
McClung, C.R. (2019). The plant circadian oscillator. Biology 8, 14.
Michael, T.P., Mockler, T.C., Breton, G., McEntee, C., Byer, A., Trout, J. D., Hazen, S.P., Shen, R., Priest, H.D., Sullivan, C.M., et al. (2008). Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet 4, e14.
Missra, A., Ernest, B., Lohoff, T., Jia, Q., Satterlee, J., Ke, K., and von Arnim, A.G. (2015). The circadian clock modulates global daily cycles of mRNA ribosome loading. Plant Cell 27, 2582–2599.
Müller, N.A., Wijnen, C.L., Srinivasan, A., Ryngajllo, M., Ofner, I., Lin, T., Ranjan, A., West, D., Maloof, J.N., Sinha, N.R., et al. (2016). Domestication selected for deceleration of the circadian clock in cultivated tomato. Nat Genet 48, 89–93.
Murakami, M., Tago, Y., Yamashino, T., and Mizuno, T. (2007). Comparative overviews of clock-associated genes of Arabidopsis thaliana and Oryza sativa. Plant Cell Physiol 48, 110–121.
Nagel, D.H., Doherty, C.J., Pruneda-Paz, J.L., Schmitz, R.J., Ecker, J.R., and Kay, S.A. (2015). Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. Proc Natl Acad Sci USA 112, E4802–E4810.
Ni, Z., Kim, E.D., Ha, M., Lackey, E., Liu, J., Zhang, Y., Sun, Q., and Chen, Z.J. (2009). Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457, 327–331.
Noguchi, R., Kubota, H., Yugi, K., Toyoshima, Y., Komori, Y., Soga, T., and Kuroda, S. (2013). The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns. Mol Syst Biol 9, 664.
Nohales, M.A., and Kay, S.A. (2016). Molecular mechanisms at the core of the plant circadian oscillator. Nat Struct Mol Biol 23, 1061–1069.
Prusty, M.R., Bdolach, E., Yamamoto, E., Tiwari, L.D., Silberman, R., Doron-Faigenbaum, A., Neyhart, J.L., Bonfil, D., Kashkush, K., Pillen, K., et al. (2021). Genetic loci mediating circadian clock output plasticity and crop productivity under barley domestication. New Phytol 230, 1787–1801.
Rawat, R., Takahashi, N., Hsu, P.Y., Jones, M.A., Schwartz, J., Salemi, M. R., Phinney, B.S., and Harmer, S.L. (2011). Reveille8 and pseudo-reponse regulator5 form a negative feedback loop within the Arabidopsis circadian clock. PLoS Genet 7, e1001350.
Rey, G., Valekunja, U.K., Feeney, K.A., Wulund, L., Milev, N.B., Stangherlin, A., Ansel-Bollepalli, L., Velagapudi, V., O’Neill, J.S., and Reddy, A.B. (2016). The pentose phosphate pathway regulates the circadian clock. Cell Metab 24, 462–473.
Robertson, F.C., Skeffington, A.W., Gardner, M.J., and Webb, A.A.R. (2009). Interactions between circadian and hormonal signalling in plants. Plant Mol Biol 69, 419–427.
Robles, M.S., Cox, J., and Mann, M. (2014). In-vivo quantitative proteomics reveals a key contribution of post-transcriptional mechanisms to the circadian regulation of liver metabolism. PLoS Genet 10, e1004047.
Sanchez-Villarreal, A., Shin, J., Bujdoso, N., Obata, T., Neumann, U., Du, S.X., Ding, Z., Davis, A.M., Shindo, T., Schmelzer, E., et al. (2013). TIME FOR COFFEE is an essential component in the maintenance of metabolic homeostasis in Arabidopsis thaliana. Plant J 76, 188–200.
Seaton, D.D., Graf, A., Baerenfaller, K., Stitt, M., Millar, A.J., and Gruissem, W. (2018). Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism. Mol Syst Biol 14, e7962.
Shalit-Kaneh, A., Kumimoto, R.W., Filkov, V., and Harmer, S.L. (2018). Multiple feedback loops of the Arabidopsis circadian clock provide rhythmic robustness across environmental conditions. Proc Natl Acad Sci USA 115, 7147–7152.
Slotte, T., Holm, K., McIntyre, L.M., Lagercrantz, U., and Lascoux, M. (2007). Differential expression of genes important for adaptation in Capsella bursa-pastoris (Brassicaceae). Plant Physiol 145, 160–173.
Smolen, P., Baxter, D.A., and Byrne, J.H. (1999). Effects of macromolecular transport and stochastic fluctuations on dynamics of genetic regulatory systems. Am J Physiol 277, C777–C790.
Song, H.R., and Noh, Y.S. (2012). Rhythmic oscillation of histone acetylation and methylation at the Arabidopsis central clock loci. Mol Cells 34, 279–287.
Song, Q., Huang, T.Y., Yu, H.H., Ando, A., Mas, P., Ha, M., and Chen, Z.J. (2019). Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in Arabidopsis. Genome Biol 20, 170.
Spensley, M., Kim, J.Y., Picot, E., Reid, J., Ott, S., Helliwell, C., and Carre, I.A. (2009). Evolutionarily conserved regulatory motifs in the promoter of the Arabidopsis clock gene LATE ELONGATED HYPOCOTYL. Plant Cell 21, 2606–2623.
Spoel, S.H., and van Ooijen, G. (2014). Circadian redox signaling in plant immunity and abiotic stress. Antioxid Redox Signal 20, 3024–3039.
Steed, G., Ramirez, D.C., Hannah, M.A., and Webb, A.A.R. (2021). Chronoculture, harnessing the circadian clock to improve crop yield and sustainability. Science 372.
Sun, Y., Shi, Y., Liu, G., Yao, F., Zhang, Y., Yang, C., Guo, H., Liu, X., Jin, C., and Luo, J. (2020). Natural variation in the OsbZIP18 promoter contributes to branched-chain amino acid levels in rice. New Phytol 228, 1548–1558.
Uhrig, R.G., Schläpfer, P., Roschitzki, B., Hirsch-Hoffmann, M., and Gruissem, W. (2019). Diurnal changes in concerted plant protein phosphorylation and acetylation in Arabidopsis organs and seedlings. Plant J 99, 176–194.
Vogel, C., and Marcotte, E.M. (2012). Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet 13, 227–232.
Wang, F., Han, T., Song, Q., Ye, W., Song, X., Chu, J., Li, J., and Chen, Z.J. (2020). The rice circadian clock regulates tiller growth and panicle development through strigolactone signaling and sugar sensing. Plant Cell 32, 3124–3138.
Wang, W., Barnaby, J.Y., Tada, Y., Li, H., Tör, M., Caldelari, D., Lee, D., Fu, X.D., and Dong, X. (2011). Timing of plant immune responses by a central circadian regulator. Nature 470, 110–114.
Webb, A.A.R., Seki, M., Satake, A., and Caldana, C. (2019). Continuous dynamic adjustment of the plant circadian oscillator. Nat Commun 10, 550.
Xu, W., Yang, R., Li, M., Xing, Z., Yang, W., Chen, G., Guo, H., Gong, X., Du, Z., Zhang, Z., et al. (2011). Transcriptome phase distribution analysis reveals diurnal regulated biological processes and key pathways in rice flag leaves and seedling leaves. PLoS ONE 6, e17613.
Zhang, F., Guo, H., Huang, J., Yang, C., Li, Y., Wang, X., Qu, L., Liu, X., and Luo, J. (2020). A UV-B-responsive glycosyltransferase, OsUGT706C2, modulates flavonoid metabolism in rice. Sci China Life Sci 63, 1037–1052.
Zhang, N., Meng, Y., Li, X., Zhou, Y., Ma, L., Fu, L., Schwarzländer, M., Liu, H., and Xiong, Y. (2019). Metabolite-mediated TOR signaling regulates the circadian clock in Arabidopsis. Proc Natl Acad Sci USA 116, 25395–25397.
Zhao, Z., Zhang, Z., Ding, Z., Meng, H., Shen, R., Tang, H., Liu, Y.G., and Chen, L. (2020). Public-transcriptome-database-assisted selection and validation of reliable reference genes for qRT-PCR in rice. Sci China Life Sci 63, 92–101.
Zhou, Z., Dang, Y., Zhou, M., Li, L., Yu, C.H., Fu, J., Chen, S., and Liu, Y. (2016). Codon usage is an important determinant of gene expression levels largely through its effects on transcription. Proc Natl Acad Sci USA 113, E6117–E6125.
Zvonic, S., Floyd, Z.E., Mynatt, R.L., and Gimble, J.M. (2007). Circadian rhythms and the regulation of metabolic tissue function and energy homeostasis. Obesity 15, 539–543.
Zwighaft, Z., Aviram, R., Shalev, M., Rousso-Noori, L., Kraut-Cohen, J., Golik, M., Brandis, A., Reinke, H., Aharoni, A., Kahana, C., et al. (2015). Circadian clock control by polyamine levels through a mechanism that declines with age. Cell Metab 22, 874–885.
This work was supported by the Hainan Major Science and Technology Project (ZDKJ202002), the State Key Program of National Natural Science Foundation of China (31530052), the Key Research and Development Program of Hainan (ZDYF2020066), the Hainan Academician Innovation Platform (HD-YSZX-202003 and HD-YSZX-202004), and the Hainan University Startup Fund (KYQD(ZR)1866).
Compliance and ethics
The author(s) declare that they have no conflict of interest.
Electronic supplementary material
Integration of rhythmic metabolome and transcriptome provides insight into the transmission of rhythm fluctuations and temporal diversity of metabolism in rice
Table S1. The scheduled MRM transitions for widely targeted metabolite analysis in leaf of rice (Oryza sativa L.) varieties.
Rights and permissions
About this article
Cite this article
Zhou, J., Liu, C., Chen, Q. et al. Integration of rhythmic metabolome and transcriptome provides insights into the transmission of rhythmic fluctuations and temporal diversity of metabolism in rice. Sci. China Life Sci. 65, 1794–1810 (2022). https://doi.org/10.1007/s11427-021-2064-7
- Oryza sativa
- diurnal cycle
- time delay
- rhythmic diversity