|
|
拟南芥光周期开花路径的建模与分析
|
Abstract:
植物开花机制是一个复杂而精密的调控网络。组学分析表明，几乎所有光周期开花途径的相关基因或蛋白的昼夜节律性表达都受到生物钟的调控，其中一些关键基因，CYCLING DOF FACTOR 1 (CDF1)、CONSTANS (CO)和FLOWERING LOCUS T (FT)等在光周期条件下发挥着重要作用。本研究根据拟南芥生物钟对开花相关基因的调控关系，建立光周期开花路径的微分方程模型。模拟结果表明，在长日照下开花相关基因保持着昼夜节律振荡，FT积累到一定阈值，植物才能开花。此外，基于模型残差的平稳性和纯随机性检验的修正模型，再现了FT的积累量的变化趋势，为预测开花时间提供了一个可靠的分析工具。
Plant flowering mechanism is a complex and sophisticatedregulatory network. Omics analysis showed that the circadian rhythmicexpression of almost all genes or proteins related to photoperiodic flowering pathway is regulated by the circadianclock, and some key genes, CYCLING DOF FACTOR 1 (CDF1), CONSTANS (CO) and FLOWERING LOCUS T (FT) play important rolesunder photoperiodic conditions. In this study, adifferential equationmodel for photoperiodic flowering pathway was developed based on the regulatory relationship of flowering genes in Arabidopsis thaliana. The simulation results showed that the flowering related genes maintained circadian oscillations under long-day. FT must accumulate to a certain threshold before plants could flower. In addition, the modified model based on the stationarity and pure randomness test of model residuals simulated the trend of FT accumulation, which provided a reliable analytical tool for predicting flowering time.
| [1] | 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, eabc9141. https://doi.org/10.1126/science.abc9141 |
| [2] | Creux, N. and Harmer, S. (2019) Circadian Rhythms in Plants. Cold Spring Harbor Perspectives in Biology, 11, a034611. https://doi.org/10.1101/cshperspect.a034611 |
| [3] | Adams, S., Manfield, I., Stockley, P. and Carré, I.A. (2015) Revised Morning Loops of the Arabidopsis Circadian Clock Based on Analyses of Direct Regulatory Interactions. PLOS ONE, 10, e0143943. https://doi.org/10.1371/journal.pone.0143943 |
| [4] | Kamioka, M., Takao, S., Suzuki, T., Taki, K., Higashiyama, T., Kinoshita, T. and Nakamichi, N. (2016) Direct Repression of Evening Genes by CIRCADIAN CLOCK-ASSOCIATED1 in the Arabidopsis Circadian Clock. Plant Cell, 28, 696-711. https://doi.org/10.1105/tpc.15.00737 |
| [5] | Lu, S.X., Webb, C.J., Knowles, S.M., Kim, S.H.J., Wang, Z. and Tobin, E.M. (2012) CCA1 and ELF3 Interact in the Control of Hypocotyl Length and Flowering Time in Arabidopsis. Plant Physiology, 158, 1079-1088. https://doi.org/10.1104/pp.111.189670 |
| [6] | Locke, J.C.W., Millar, A.J. and Turner, M.S. (2005) Modelling Genetic Networks with Noisy and Varied Experimental Data: The Circadian Clock in Arabidopsis Thaliana. Journal of Theoretical Biology, 234, 383-393. https://doi.org/10.1016/j.jtbi.2004.11.038 |
| [7] | Kikis, E.A., Khanna, R. and Quail, P.H. (2005) ELF4 Is a Phytochrome-Regulated Component of a Negative-Feedback Loop Involving the Central Oscillator Components CCA1 and LHY: ELF4 and Rc Induction of the Circadian Clock. The Plant Journal, 44, 300-313. https://doi.org/10.1111/j.1365-313X.2005.02531.x |
| [8] | Hazen, S.P., Schultz, T.F., Pruneda-Paz, J.L., Borevitz, J.O., Ecker, J.R. and Kay, S.A. (2005) LUX ARRHYTHMO Encodes a Myb Domain Protein Essential for Circadian Rhythms. Proceedings of the National Academy of Sciences, 102, 10387-10392. https://doi.org/10.1073/pnas.0503029102 |
| [9] | Nakamichi, N., Kiba, T., Henriques, R., Mizuno, T., Chua, N.-H. and Sakakibara, H. (2010) PSEUDO-RESPONSE REGULATORS 9, 7, and 5 Are Transcriptional Repressors in the Arabidopsis Circadian Clock. Plant Cell, 22, 594-605. https://doi.org/10.1105/tpc.109.072892 |
| [10] | Gendron, J.M., Pruneda-Paz, J.L., Doherty, C.J., Gross, A.M., Kang, S.E. and Kay, S.A. (2012) Arabidopsis Circadian Clock Protein, TOC1, Is a DNA-Binding Transcription Factor. Proceedings of the National Academy of Sciences, 109, 3167-3172. https://doi.org/10.1073/pnas.1200355109 |
| [11] | Huang, W., Pérez-García, P., Pokhilko, A., Millar, A.J., Antoshechkin, I., Riechmann, J.L. and Mas, P. (2012) Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator. Science, 336, 75-79. https://doi.org/10.1126/science.1219075 |
| [12] | Ito, S., Kawamura, H., Niwa, Y., Nakamichi, N., Yamashino, T. and Mizuno, T. (2009) A Genetic Study of the Arabidopsis Circadian Clock with Reference to the TIMING OF CAB EXPRESSION 1 (TOC1) Gene. Plant and Cell Physiology, 50, 290-303. https://doi.org/10.1093/pcp/pcn198 |
| [13] | Mizuno, T., Nomoto, Y., Oka, H., Kitayama, M., Takeuchi, A., Tsubouchi, M. and Yamashino, T. (2014) Ambient Temperature Signal Feeds into the Circadian Clock Transcriptional Circuitry through the EC Night-Time Repressor in Arabidopsis Thaliana. Plant and Cell Physiology, 55, 958-976. https://doi.org/10.1093/pcp/pcu030 |
| [14] | Song, Y.H., Shim, J.S., Kinmonth-Schultz, H.A. and Imaizumi, T. (2015) Photoperiodic Flowering: Time Measurement Mechanisms in Leaves. Annual Review of Plant Biology, 66, 441-464. https://doi.org/10.1146/annurev-arplant-043014-115555 |
| [15] | Imaizumi, T. (2010) Arabidopsis Circadian Clock and Photoperiodism: Time to Think about Location. Current Opinion in Plant Biology, 13, 83-89. https://doi.org/10.1016/j.pbi.2009.09.007 |
| [16] | Song, Y.H., Kubota, A., Kwon, M.S., Covington, M.F., Lee, N., Taagen, E.R., LaboyCintrón, D., Hwang, D.Y., Akiyama, R., Hodge, S.K., Huang, H., Nguyen, N.H., Nusinow, D.A., Millar, A.J., Shimizu, K.K. and Imaizumi, T. (2018) Molecular Basis of Flowering under Natural Long-Day Conditions in Arabidopsis. Nature Plants, 4, 824-835. https://doi.org/10.1038/s41477-018-0253-3 |
| [17] | Locke, J.C.W., Kozma-Bognár, L., Gould, P.D., Fehér, B., Kevei, é., Nagy, F., Turner, M.S., Hall, A. and Millar, A.J. (2006) Experimental Validation of a Predicted Feedback Loop in the Multi-Oscillator Clock of Arabidopsis Thaliana. Molecular Systems Biology, 2, 59. https://doi.org/10.1038/msb4100102 |
| [18] | Pokhilko, A., Hodge, S.K., Stratford, K., Knox, K., Edwards, K.D., Thomson, A.W., Mizuno, T. and Millar, A.J. (2010) Data Assimilation Constrains New Connections and Components in a Complex, Eukaryotic Circadian Clock Model. Molecular Systems Biology, 6, 416. https://doi.org/10.1038/msb.2010.69 |
| [19] | Pokhilko, A., Fernández, A.P., Edwards, K.D., Southern, M.M., Halliday, K.J. and Millar, A.J. (2012) The Clock Gene Circuit in Arabidopsis Includes a Repressilator with Additional Feedback Loops. Molecular Systems Biology, 8, 574. https://doi.org/10.1038/msb.2012.6 |
| [20] | Pokhilko, A., Mas, P. and Millar, A.J. (2013) Modelling the Widespread Effects of TOC1 Signalling on the Plant Circadian Clock and Its Outputs. BMC Systems Biology, 7, Article No. 23. https://doi.org/10.1186/1752-0509-7-23 |
| [21] | De Caluwé, J., Xiao, Q., Hermans, C., Verbruggen, N., Leloup, J.-C. and Gonze, D. (2016) A Compact Model for the Complex Plant Circadian Clock. Frontiers in Plant Science, 7, Article No. 74. https://doi.org/10.3389/fpls.2016.00074 |
| [22] | Greenwood, M., Tokuda, I.T. and Locke, J.C.W. (2022) A Spatial Model of the Plant Circadian Clock Reveals Design Principles for Coordinated Timing. Molecular Systems Biology, 18, e10140. https://doi.org/10.15252/msb.202010140 |
| [23] | Jaeger, K.E., Pullen, N., Lamzin, S., Morris, R.J. and Wigge, P.A. (2013) Interlocking Feedback Loops Govern the Dynamic Behavior of the Floral Transition in Arabidopsis. The Plant Cell, 25, 820-833. https://doi.org/10.1105/tpc.113.109355 |
| [24] | Leal Valentim, F., Mourik, S., van Posé, D., Kim, M.C., Schmid, M., van Ham, R.C.H.J., Busscher, M., Sanchez-Perez, G.F., Molenaar, J., Angenent, G.C., Immink, R.G.H. and van Dijk, A.D.J. (2015) A Quantitative and Dynamic Model of the Arabidopsis Flowering Time Gene Regulatory Network. PLOS ONE, 10, e0116973. https://doi.org/10.1371/journal.pone.0116973 |
| [25] | Kinmonth-Schultz, H.A., MacEwen, M.J.S., Seaton, D.D., Millar, A.J., Imaizumi, T. and Kim, S.-H. (2019) An Explanatory Model of Temperature Influence on Flowering through Whole-Plant Accumulation of FLOWERING LOCUS T in Arabidopsis Thaliana. In Silico Plants, 1, diz006. https://doi.org/10.1093/insilicoplants/diz006 |
| [26] | Niwa, Y., Ito, S., Nakamichi, N., Mizoguchi, T., Niinuma, K., Yamashino, T. and Mizuno, T. (2007) Genetic Linkages of the Circadian Clock-Associated Genes, TOC1, CCA1 and LHY, in the Photoperiodic Control of Flowering Time in Arabidopsis Thaliana. Plant and Cell Physiology, 48, 925-937. https://doi.org/10.1093/pcp/pcm067 |
| [27] | Nakamichi, N., Kiba, T., Kamioka, M., Suzuki, T., Yamashino, T., Higashiyama, T., Sakakibara, H. and Mizuno, T. (2012) Transcriptional Repressor PRR5 Directly Regulates Clock-Output Pathways. Proceedings of the National Academy of Sciences, 109, 17123-17128. https://doi.org/10.1073/pnas.1205156109 |
| [28] | Sawa, M., Nusinow, D.A., Kay, S.A. and Imaizumi, T. (2007) FKF1 and GIGANTEA Complex Formation Is Required for Day-Length Measurement in Arabidopsis. Science, 318, 261-265. https://doi.org/10.1126/science.1146994 |
| [29] | Lazaro, A., Valverde, F., Pi？eiro, M. and Jarillo, J.A. (2012) The Arabidopsis E3 Ubiquitin Ligase HOS1 Negatively Regulates CONSTANS Abundance in the Photoperiodic Control of Flowering. Plant Cell, 24, 982-999. https://doi.org/10.1105/tpc.110.081885 |
| [30] | Song, Y.H., Smith, R.W., To, B.J., Millar, A.J. and Imaizumi, T. (2012) FKF1 Conveys Timing Information for CONSTANS Stabilization in Photoperiodic Flowering. Science, 336, 1045-1049. https://doi.org/10.1126/science.1219644 |
| [31] | Laubinger, S., Marchal, V. and Gentilhomme, J. (2006) Arabidopsis SPA Proteins Regulate Photoperiodic Flowering and Interact with the Floral Inducer CONSTANS to Regulate Its Stability. Development, 133, 4608-4608. https://doi.org/10.1242/dev.02691 |
| [32] | Helton, J.C. and Davis, F.J. (2003) Latin Hypercube Sampling and the Propagation of Uncertainty in Analyses of Complex Systems. Reliability Engineering & System Safety, 81, 23-69. https://doi.org/10.1016/S0951-8320(03)00058-9 |
| [33] | Mockler, T.C., Michael, T.P., Priest, H.D., Shen, R., Sullivan, C.M., Givan, S.A., McEntee, C., Kay, S.A. and Chory, J. (2007) The Diurnal Project: Diurnal and Circadian Expression Profiling, Model-Based Pattern Matching, and Promoter Analysis. Cold Spring Harbor Symposia on Quantitative Biology, 72, 353-363. https://doi.org/10.1101/sqb.2007.72.006 |
| [34] | Kinmonth-Schultz, H.A., Tong, X., Lee, J., Song, Y.H., Ito, S., Kim, S. and Imaizumi, T. (2016) Cool Night-Time Temperatures Induce the Expression of CONSTANS and FLOWERING LOCUS T to Regulate Flowering in Arabidopsis. New Phytologist, 211, 208-224. https://doi.org/10.1111/nph.13883 |
| [35] | Cryer, J.D. and Chan, K.S. (2008) Time Series Analysis: With Applications in R. 2nd Edition, Springer, New York, 128-130, 183-185. |
| [36] | Smith, H. (1982) Light Quality, Photoperception, and Plant Strategy. Annual Review of Plant Physiology, 33, 481-518. https://doi.org/10.1146/annurev.pp.33.060182.002405 |
| [37] | Huang, T., Shui, Y., Wu, Y., Hou, X. and You, X. (2022) Red Light Resets the Expression Pattern, Phase, and Period of the Circadian Clock in Plants: A Computational Approach. Biology, 11, Article No. 1479. https://doi.org/10.3390/biology11101479 |
