成功大學博碩士論文系統

簡易檢索 / 詳目顯示

回結果列表

研究生：	盧提文 Lu, Ti-Wen
論文名稱：	以數學模式探討蝴蝶蘭小丑花之花色色素圖案形成機制 A mathematical approach for analyzing the mechanisms of pigmentation patterning of harlequin Phalaenopsis orchids
指導教授：	陳虹樺 Chen, Hong-Hwa
學位類別：	碩士 Master
系所名稱：	生物科學與科技學院 - 生命科學系 Department of Life Sciences
論文出版年：	2023
畢業學年度：	111
語文別：	英文
論文頁數：	69
中文關鍵詞：	蝴蝶蘭小丑花、MYB11 、花色色素圖案形成、HORT1 反轉錄轉座子、微小 RNA (microRNA) 、圖靈圖騰、系統生物學
外文關鍵詞：	harlequin Phalaenopsis, MYB11, pigmentation patterning, retrotransposon HORT1, microRNA (miRNA), Turing patterns, systems biology
相關次數：	點閱：125 下載：2
分享至:	分享至facebook 分享至twitter

查詢本校圖書館目錄查詢臺灣博碩士論文知識加值系統勘誤回報

小丑花蝴蝶蘭（小丑花）始於蝴蝶蘭科組織培養時產生的個體變異，以前所未見的斑駁紫色色塊和多變的花色色素圖案而聞名，也為蝴蝶蘭花色色素圖案形成的研究開闢了一個新的課題。小丑花紫色和白色區域之間明顯的界限使其為研究蝴蝶蘭花青素生合成調控機制的好材料。MYB 轉錄因子 PeMYB11 在小丑花的紫色區域表達量很高。而且 Harlequin Orchids Retrotransposon 1 (HORT1) 反轉錄轉座子插入到小丑花 PeMYB11 的啟動子中增強小丑花花青素的積累。此外，花青素抑制子 PeMYBx 在紫色區域為白色區域之基因表達量的 96.9 倍。根據以上信息，提出斑點色素沉著圖案形成有關的假設。受圖靈擴散理論的啟發，構建了 PeMYB11 系統促進 PeMYBx 系統激活的生物學模型。通過數學建模和模擬，結果表明 PeMYB11系統和 PeMYBx 系統之間的相互作用模式是斑點產生的原因。根據已測試的生物模型，開始了小丑花色素圖案形成的研究工作。PeMYB11 生合成的速率在模型中被調整到不同的水平，以模擬 HORT1 對 PeMYB11 轉錄的影響。斑點的直徑隨著參數值的增加而增加。然而，這些斑點並不會融合，也沒有形成斑駁的紫色色塊。進一步，前人研究指出 miR858 的表現量在紫色區域比起白色區域低。microRNA (miRNA) 以降解 mRNA 方式下調基因表達。且 miR858 之標的降解基因為 PeMYB11。因此，將 PeMYB11 mRNA 降解因素一併考慮到 PeMYB11-PeMYBx 之數學模型中。令人驚訝的，加入 miR858 後，原來的斑點即融合在一起，更接近於小丑花性狀之觀察。由此可知，減少的 miR858 表達量擴大了 HORT1 所誘導之大斑點邊界。總結，在數學模擬和生物學觀察相結合的幫助下，發現 HORT1 和 miR858 對小丑花色素圖案形成的影響模式不同。因此，不同比例的 HORT1 和 miR858 的組合效果可能是蝴蝶蘭小丑花多變花色的造成原因。

Harlequin Phalaenopsis is derived from the somaclonal variants during the micropropagation of Phalaenopsis orchids, and well-known for unprecedented clownish purple spots and changeful pigmentation patterning. It opens a new subject for the studying of regulation of pigmentation patterning of Phalaenopsis. Moreover, the distinct boundaries between purple and white regions make harlequin Phalaenopsis one of nice materials for studying anthocyanin biosynthesis mechanisms in Phalaenopsis. A MYB transcription factor PeMYB11, is highly expressed in the purple regions on the flowers of harlequin Phalaenopsis, and Harlequin Orchids Retrotransposon 1 (HORT1) is inserted in the promoter region of PeMYB11. The insertion of HORT1 contributes to the enhancement of anthocyanin accumulation of harlequin Phalaenopsis. In addition, PeMYBx, an inhibitor of anthocyanin biosynthesis, also shows high expression levels in the purple regions of harlequin flowers. With above information, the PeMYB11 system, the PeMYBx system and their interactions were hypothesized to be related to the formation of spotted pigmentation patterning. Inspired by the Turing’s reaction-diffusion theory, the biological model which states that the activation of the PeMYBx system is promoted by the PeMYB11 system was constructed. By mathematical modeling and simulation, the results show that the interaction between the PeMYB11 system and the PeMYBx system is causal for the generation of spots in Phalaenopsis. Based on the PeMYB11-PeMYBx interaction model, a few investigations on the pigmentation patterning of harlequin Phalaenopsis were discussed. The generation rate of PeMYB11 biosynthesis was adjusted up to different levels in the model to simulate the effect of HORT1 on PeMYB11 transcription. The diameter of the spots increased upon parameter value increased. However, the spots did not have apparent fusion and no clownish purple spots was formed. Furthermore, miR858 in the purple regions is less than that in the white regions of the harlequin flowers. microRNA (miRNA) downregulate gene expression by degrading mRNA, and the target gene of miR858 is PeMYB11. The regulation of PeMYB11 targeted by miR858 was then added to the PeMYB11-PeMYBx interaction model. Amazingly, the spots fused together which was further close to the biological observations of harlequin flowers. Reduced miR858 expression plays a role in expanding boundaries of the big spots induced by HORT1. In conclusion, aided by mathematical simulations combined with biological observations, the ways HORT1 and miR858 contribute to the harlequin-type pigmentation patterning were found to be different. Therefore, the combinatorial effects of HORT1 and miR858 in different ratios may be a causal reason that brings changeful pigmentation patterning to harlequin Phalaenopsis.

摘要 I
Abstract III
致謝 V
Table of contents VI
List of figure X
List of appendix figure XI
Abbreviations XII
A concise introduction to this study	1
1 Motivation of my study 1
2 Turing patterns, a widely accepted mathematical model for explaining the formation of natural patterns 1
3 Transcriptional regulation of pigmentation patterning in flowers 2
3.1 A MYB transcription factor is involved in the formation of splatter-type spots on the flower of Asiatic hybrid lilies 2
3.2 Three distinct pigmentation patterning in Phalaenopsis spp. are regulated by respective MYB transcription factors 3
3.3 The self-organizing reaction-diffusion system including an R2R3-MYB transcription activator and an R3-MYB transcription repressor generates spotted pigmentation patterning in monkeyflowers (Mimulus) 3
4 Significant features of harlequin Phalaenopsis: exotic pigmentation patterning and ambiguous genetic rules 4
5 Retrotransposon HORT1 and microRNA miR858 are related to the formation of dark purple dots of harlequin Phalaenopsis 5
6 Aim 6
Background 7
1 An introduction to harlequin Phalaenopsis orchids 7
1.1 Diverse pigmentation patterning of harlequin Phalaenopsis 7
1.2 The breeding history of harlequin Phalaenopsis 7
2 Molecular mechanisms involved in regulation of anthocyanin biosynthesis pathway 8
2.1 The biosynthesis pathway of anthocyanin 8
2.2 Transcriptional regulation of anthocyanin biosynthesis 8
2.2.1	The MBW complex-mediated regulation of anthocyanin biosynthesis 8
2.2.2	MYB transcription repressors 9
2.2.3	Transposon-mediated regulation of anthocyanin biosynthesis 10
2.2.4	miRNA as regulators of anthocyanin biosynthesis 11
3 Mathematical descriptions of pattern formation mechanisms 12
3.1 Basic concepts and necessary conditions for pattern formation in self-organizing reaction-diffusion systems 12
3.2 The Gierer-Meinhardt model 13
4 An introduction to numerical analysis of differential equations 14
4.1 Explicit and implicit methods 14
4.2 Stiff differential equations 15
Materials and Methods 16
1 Plant materials and growth condition 16
2 Methods 16
2.1 Identification and organization of molecular mechanisms for spotted pigmentation patterning of Phalaenopsis orchids: Construction of the PeMYB11-PeMYBx interaction model 16
2.2 Mathematical description of the PeMYB11-PeMYBx interaction model 18
2.3 Implementation of computational simulations of the PeMYB11-PeMYBx interaction model 18
2.3.1	Simulation of typical spotted patterning by the PeMYB11-PeMYBx interaction model 18
2.3.2	Increased levels of PeMYB11 transcriptional activity induced by the solo-LTR of HORT1 20
2.3.3	Reduced degradation rate of PeMYB11 caused by reduction of miR858 expression 20
2.3.4	Comprehensive consideration of the heterogeneous spatial distribution of full-length HORT1 and the solo-LTR of HORT1 21
2.4 Visualization of the simulated PeMYB11, PeMYBx concentration 22
Results 23
1 Anthocyanin spots formation in Phalaenopsis is controlled not only by PeMYB11 but also by PeMYBx 23
2 The deformation of typical spotted pigmentation patterning of Phalaenopsis orchids 24
2.1 Solo-LTR of HORT1, an enhancer of PeMYB11, increases the size of each spot of the spotted patterning of Phalaenopsis 24
2.2 Differential miR858 expression disrupts the formation of spotted patterning of Phalaenopsis 25
2.3 Solo-LTR of HORT1 and differential miR858 expression are indispensable factors causal for the generation of fusion dark purple spots of harlequin Phalaenopsis 26
3 Spatially heterogeneous insertion of full-length HORT1 or the solo-LTR of HORT1 in PeMYB11 promoter is a key factor for generating the dark purple patches of harlequin Phalaenopsis Yushan Little Pearl 26
Discussion 28
1 Applications of the self-organizing reaction-diffusion system in floral pigmentation patterning 28
2 Proposed molecular mechanisms of the interactions among MYB activators and repressors 30
3 Detailed characterization of possible mechanisms causal for “random” fusion of harlequin Phalaenopsis spots 30
4 Benefits of mathematical modeling and simulation in biology 31
Conclusions & Perspectives 33
References 35
                                    

Achkar, N. P., Cambiagno, D. A., & Manavella, P. A. (2016). miRNA biogenesis: a dynamic pathway. Trends in Plant Science, 21, 1034-1044.
Albert, N. W., Davies, K. M., Lewis, D. H., Zhang, H., Montefiori, M., Brendolise, C., ... & Schwinn, K. E. (2014). A conserved network of transcriptional activators and repressors regulates anthocyanin pigmentation in eudicots. The Plant Cell, 26, 962-980.
Andrejek, L., Chou, C. S., & Husbands, A. Y. (2021). A robust mathematical model of adaxial–abaxial patterning. in silico Plants, 3, diaa015.
Bhattacharya, A., Kunz, M. (2013). Target Identification, microRNA. In W. W. Dubitzky, Encyclopedia of Systems Biology (pp. 2138-2142). Springer, New York, NY.
Burden, R. L., Faires, J. D., & Burden, A. M. (2015). Numerical analysis. Cengage learning.
Butelli, E., Garcia-Lor, A., Licciardello, C., Las Casas, G., Hill, L., Recupero, G. R., ... & Martin, C. (2017). Changes in anthocyanin production during domestication of Citrus. Plant Physiology, 173, 2225-2242.
Butelli, E., Licciardello, C., Zhang, Y., Liu, J., Mackay, S., Bailey, P., ... & Martin, C. (2012). Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. The Plant Cell, 24, 1242-1255.
Campo, S., Sánchez‐Sanuy, F., Camargo‐Ramírez, R., Gómez‐Ariza, J., Baldrich, P., Campos‐Soriano, L., ... & San Segundo, B. (2021). A novel Transposable element‐derived microRNA participates in plant immunity to rice blast disease. Plant Biotechnology Journal, 19, 1798-1811.
Chen, T. C., Lin, Y. Y., & Chen, W. H. (2021). Breeding of Harlequin Flowers in Phalaenopsis Orchid. In Orchid Biotechnology IV, pp.15-41.
Cotterell, J., Robert-Moreno, A., & Sharpe, J. (2015). A local, self-organizing reaction-diffusion model can explain somite patterning in embryos. Cell systems, 1, 257-269.
Ding, B., Patterson, E. L., Holalu, S. V., Li, J., Johnson, G. A., Stanley, L. E., Greenlee, A. B., Peng, F., Bradshaw, Jr., H.D., Blinov, M. L., Blackman, B. K., Yuan, Y. W. (2020). Two MYB proteins in a self-organizing activator-inhibitor system produce spotted pigmentation patterns. Current Biology, 30, 802-814.
Du, H., Feng, B. R., Yang, S. S., Huang, Y. B., & Tang, Y. X. (2012). The R2R3-MYB transcription factor gene family in maize. PloS one, 7, e37463.
Gierer, A., & Meinhardt, H. (1972). A theory of biological pattern formation. Kybernetik, 12, 30-39.
Hsu, C. C., Chen, Y. Y., Tsai, W. C., Chen, W. H., & Chen, H. H. (2015). Three R2R3-MYB transcription factors regulate distinct floral pigmentation patterning in Phalaenopsis spp. Plant physiology, 168, 175-191.
Hsu, C. C., Su, C. J., Jeng, M. F., Chen, W. H., & Chen, H. H. (2019). A HORT1 retrotransposon insertion in the PeMYB11 promoter causes harlequin/black flowers in Phalaenopsis orchids. Plant physiology, 180, 1535-1548.
Iserles, A. (2009). A first course in the numerical analysis of differential equations (No. 44). Cambridge university press.
Kobayashi, S., Goto-Yamamoto, N., & Hirochika, H. (2004). Retrotransposon-induced mutations in grape skin color. Science, 304, 982.
Kreuzaler, F., & Hahlbrock, K. (1975). Enzymatic synthesis of aromatic compounds in higher plants: Formation of Bis-noryangonin (4-Hydroxy-6 [4-hydroxystyryl] 2-pyrone) from p-coumaroyl-CoA and malonyl-CoA. Archives of biochemistry and biophysics, 169, 84-90.
Landge, A. N., Jordan, B. M., Diego, X., & Müller, P. (2020). Pattern formation mechanisms of self-organizing reaction-diffusion systems. Developmental biology, 460, 2-11.
Lee, Y. I., Tseng, Y. F., Lee, Y. C., & Chung, M. C. (2020). Chromosome constitution and nuclear DNA content of Phalaenopsis hybrids. Scientia Horticulturae, 262, p. 109089.
Li, Y., Wang, J., & Hou, X. (2017). Stripe and spot patterns for the Gierer–Meinhardt model with saturated activator production. Journal of Mathematical Analysis and Applications, 449, 1863-1879.
Liu, Y., Tikunov, Y., Schouten, R. E., Marcelis, L. F., Visser, R. G., & Bovy, A. (2018). Anthocyanin biosynthesis and degradation mechanisms in Solanaceous vegetables: A review. Frontiers in Chemistry, 6, 52.
Long, S. P. (2019). Making our plant modelling community more than the sum of its parts: a personal perspective. in silico Plants, 1, diy002.
Marita, J. M., Hatfield, R. D., Rancour, D. M., & Frost, K. E. (2014). Identification and suppression of the p‐coumaroyl CoA: hydroxycinnamyl alcohol transferase in Zea mays L. The Plant Journal, 78, 850-864.
Meinhardt, H., & Gierer, A. (2000). Pattern formation by local self‐activation and lateral inhibition. Bioessays, 22, 753-760.
Nagashima, Y., Tsugawa, S., Mochizuki, A., Sasaki, T., Fukuda, H., & Oda, Y. (2018). A Rho-based reaction-diffusion system governs cell wall patterning in metaxylem vessels. Scientific Reports, 8, 1-17.
Pearson, J. E. (1993). Complex patterns in a simple system. Science, 261, 189-192.
Petrik, D. L., Karlen, S. D., Cass, C. L., Padmakshan, D., Lu, F., Liu, S., ... & Sedbrook, J. C. (2014). p‐Coumaroyl‐C o A: monolignol transferase (PMT) acts specifically in the lignin biosynthetic pathway in Brachypodium distachyon. The Plant Journal, 77, 713-726.
Ringham, L., Owens, A., Cieslak, M., Harder, L. D., & Prusinkiewicz, P. (2021). Modeling flower pigmentation patterns. ACM Transactions on Graphics (TOG), 40, 1-14.
Schaff, J., Fink, C. C., Slepchenko, B., Carson, J. H., & Loew, L. M. (1997). A general computational framework for modeling cellular structure and function. Biophysical journal, 73, 1135-1146.
Sharma, D., Tiwari, M., Pandey, A., Bhatia, C., Sharma, A., & Trivedi, P. K. (2016). MicroRNA858 is a potential regulator of phenylpropanoid pathway and plant development. Plant physiology, 171, 944-959.
Skopelitis, D. S., Benkovics, A. H., Husbands, A. Y., & Timmermans, M. C. (2017). Boundary formation through a direct threshold-based readout of mobile small RNA gradients. Developmental cell, 43, 265-273.
Skopelitis, D. S., Hill, K., Klesen, S., Marco, C. F., von Born, P., Chitwood, D. H., & Timmermans, M. C. (2018). Gating of miRNA movement at defined cell-cell interfaces governs their impact as positional signals. Nature communications, 9, 1-10.
Turing, A. M. (1990). The chemical basis of morphogenesis. Bulletin of mathematical biology, 52, 153-197.
Yamagishi, M., & Sakai, M. (2020). The microRNA828/MYB12 module mediates bicolor pattern development in Asiatic hybrid lily (Lilium spp.) flowers. Frontiers in plant science, 11, 590791.
Yamagishi, M., Toda, S., & Tasaki, K. (2014). The novel allele of the LhMYB12 gene is involved in splatter‐type spot formation on the flower tepals of Asiatic hybrid lilies (Lilium spp.). New Phytologist, 20, 1009-1020.
Yan, H., Pei, X., Zhang, H., Li, X., Zhang, X., Zhao, M., ... & Zhao, X. (2021). MYB-mediated regulation of anthocyanin biosynthesis. International journal of molecular sciences, 22, 3103.
Yang, J., Meng, J., Liu, X., Hu, J., Zhu, Y., Zhao, Y., ... & Yuan, T. (2021). Integrated mRNA and small RNA sequencing reveals a regulatory network associated with flower color in oriental hybrid lily. Plant Physiology and Biochemistry, 166, 103-114.
Zhang, L., Hu, J., Han, X., Li, J., Gao, Y., Richards, C. M., ... & Cong, P. (2019). A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nature communications, 10, 1-13.
Zhang, X., Xu, Z., Wang, W., Mu, D., Meng, X., Lu, M., & Li, C. (2022). Advances on the Coloring Mechanism of Double-color Flowers in Plants. HortScience, 57, 1120-1127.
Zhao, A., Cui, Z., Li, T., Pei, H., Sheng, Y., Li, X., ... & Wang, J. (2019). mRNA and miRNA expression analysis reveal the regulation for flower spot patterning in Phalaenopsis ‘Panda’. International journal of molecular sciences, 20, 4250.

校內：2025-02-06公開
校外：2025-02-06公開

簡易檢索 / 詳目顯示

相關論文