Please use this identifier to cite or link to this item:
標題: 轉譯控制參與阿拉伯芥幼苗光形態發育之分子研究
Molecular assessment of translational control in photomorphogenic Arabidopsis
作者: 劉明容
Liu, Ming-Jung
關鍵字: photomorphogenesis
出版社: 生物科技學研究所
引用: Agresti, A. (1992). A survey of exact inference for contingency tables. Statistical Science 7, 131-177. Alexa, A., Rahnenfuhrer, J., and Lengauer, T. (2006). Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22, 1600-1607. Arava, Y., Wang, Y., Storey, J.D., Liu, C.L., Brown, P.O., and Herschlag, D. (2003). Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 100, 3889-3894. Bailey, T.L., and Elkan, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2, 28-36. Bailey-Serres, J., Sorenson, R., and Juntawong, P. (2009). Getting the message across: cytoplasmic ribonucleoprotein complexes. Trends Plant Sci 14, 443-453. Ballesteros, M.L., Bolle, C., Lois, L.M., Moore, J.M., Vielle-Calzada, J.P., Grossniklaus, U., and Chua, N.H. (2001). LAF1, a MYB transcription activator for phytochrome A signaling. Genes Dev 15, 2613-2625. Branco-Price, C., Kawaguchi, R., Ferreira, R.B., and Bailey-Serres, J. (2005). Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. Ann Bot 96, 647-660. Branco-Price, C., Kaiser, K.A., Jang, C.J., Larive, C.K., and Bailey-Serres, J. (2008). Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. Plant J 56, 743-755. Casal, J.J., and Yanovsky, M.J. (2005). Regulation of gene expression by light. Int J Dev Biol 49, 501-511. Chang, C.S., Maloof, J.N., and Wu, S.H. (2011). COP1-Mediated Degradation of BBX22/LZF1 Optimizes Seedling Development in Arabidopsis. Plant physiology 156, 228-239. Chang, C.S., Li, Y.H., Chen, L.T., Chen, W.C., Hsieh, W.P., Shin, J., Jane, W.N., Chou, S.J., Choi, G., Hu, J.M., Somerville, S., and Wu, S.H. (2008). LZF1, a HY5-regulated transcriptional factor, functions in Arabidopsis de-etiolation. Plant J 54, 205-219. Chattopadhyay, S., Ang, L.H., Puente, P., Deng, X.W., and Wei, N. (1998). Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression. Plant Cell 10, 673-683. Choi, G., Yi, H., Lee, J., Kwon, Y.K., Soh, M.S., Shin, B., Luka, Z., Hahn, T.R., and Song, P.S. (1999). Phytochrome signalling is mediated through nucleoside diphosphate kinase 2. Nature 401, 610-613. Chory, J. (2010). Light signal transduction: an infinite spectrum of possibilities. Plant J 61, 982-991. Davies, E., and Abe, S. (1995). Methods for isolation and analysis of polyribosomes. Methods Cell Biol 50, 209-222. Davis, J.C. (1986). Statistics and Data Analysis in Geology. (New York: John Wiley & Sons). Deshaies, R.J., and Meyerowitz, E. (2000). COP1 patrols the night beat. Nature cell biology 2, E102-104. Dickey, L.F., Petracek, M.E., Nguyen, T.T., Hansen, E.R., and Thompson, W.F. (1998). Light regulation of Fed-1 mRNA requires an element in the 5'' untranslated region and correlates with differential polyribosome association. Plant Cell 10, 475-484. Duncan, R., and McConkey, E.H. (1982). Preferential utilization of phosphorylated 40-S ribosomal subunits during initiation complex formation. Eur J Biochem 123, 535-538. Edgar, R., Domrachev, M., and Lash, A.E. (2002). Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30, 207-210. Fairchild, C.D., Schumaker, M.A., and Quail, P.H. (2000). HFR1 encodes an atypical bHLH protein that acts in phytochrome A signal transduction. Genes Dev 14, 2377-2391. Fankhauser, C., Yeh, K.C., Lagarias, J.C., Zhang, H., Elich, T.D., and Chory, J. (1999). PKS1, a substrate phosphorylated by phytochrome that modulates light signaling in Arabidopsis. Science 284, 1539-1541. Franklin, K.A., Larner, V.S., and Whitelam, G.C. (2005). The signal transducing photoreceptors of plants. The International journal of developmental biology 49, 653-664. Gu, S., Jin, L., Zhang, F., Sarnow, P., and Kay, M.A. (2009). Biological basis for restriction of microRNA targets to the 3'' untranslated region in mammalian mRNAs. Nat Struct Mol Biol 16, 144-150. Helliwell, C.A., Webster, C.I., and Gray, J.C. (1997). Light-regulated expression of the pea plastocyanin gene is mediated by elements within the transcribed region of the gene. Plant J 12, 499-506. Henriques, R., Jang, I.C., and Chua, N.H. (2009). Regulated proteolysis in light-related signaling pathways. Curr Opin Plant Biol 12, 49-56. Holm, M., Ma, L.G., Qu, L.J., and Deng, X.W. (2002). Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis. Genes Dev 16, 1247-1259. Hu, W., Sweet, T.J., Chamnongpol, S., Baker, K.E., and Coller, J. (2009). Co-translational mRNA decay in Saccharomyces cerevisiae. Nature 461, 225-229. Hudson, M., Ringli, C., Boylan, M.T., and Quail, P.H. (1999). The FAR1 locus encodes a novel nuclear protein specific to phytochrome A signaling. Genes Dev 13, 2017-2027. Huq, E., and Quail, P.H. (2002). PIF4, a phytochrome-interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis. Embo J 21, 2441-2450. Huq, E., Al-Sady, B., Hudson, M., Kim, C., Apel, K., and Quail, P.H. (2004). Phytochrome-interacting factor 1 is a critical bHLH regulator of chlorophyll biosynthesis. Science 305, 1937-1941. Ingolia, N.T., Ghaemmaghami, S., Newman, J.R., and Weissman, J.S. (2009). Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218-223. Jiao, Y., and Meyerowitz, E.M. (2010). Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. Mol Syst Biol 6, 419. Jiao, Y., Lau, O.S., and Deng, X.W. (2007). Light-regulated transcriptional networks in higher plants. Nature reviews. Genetics 8, 217-230. Juntawong, P., and Bailey-Serres, J. (2012). Dynamic Light Regulation of Translation Status in Arabidopsis thaliana. Front Plant Sci 3, 66. Kahvejian, A., Roy, G., and Sonenberg, N. (2001). The mRNA closed-loop model: the function of PABP and PABP-interacting proteins in mRNA translation. Cold Spring Harb Symp Quant Biol 66, 293-300. Kami, C., Lorrain, S., Hornitschek, P., and Fankhauser, C. (2010). Light-regulated plant growth and development. Curr Top Dev Biol 91, 29-66. Karniol, B., and Chamovitz, D.A. (2000). The COP9 signalosome: from light signaling to general developmental regulation and back. Curr Opin Plant Biol 3, 387-393. Kawaguchi, R., and Bailey-Serres, J. (2002). Regulation of translational initiation in plants. Curr Opin Plant Biol 5, 460-465. Kawaguchi, R., Girke, T., Bray, E.A., and Bailey-Serres, J. (2004). Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant J 38, 823-839. Kim, B.H., Cai, X., Vaughn, J.N., and von Arnim, A.G. (2007). On the functions of the h subunit of eukaryotic initiation factor 3 in late stages of translation initiation. Genome Biol 8, R60. Kim, J.Y., Song, H.R., Taylor, B.L., and Carre, I.A. (2003). Light-regulated translation mediates gated induction of the Arabidopsis clock protein LHY. Embo J 22, 935-944. Kim, T.H., Kim, B.H., Yahalom, A., Chamovitz, D.A., and von Arnim, A.G. (2004). Translational regulation via 5'' mRNA leader sequences revealed by mutational analysis of the Arabidopsis translation initiation factor subunit eIF3h. Plant Cell 16, 3341-3356. Lackner, D.H., and Bahler, J. (2008). Translational control of gene expression from transcripts to transcriptomes. Int Rev Cell Mol Biol 271, 199-251. Lackner, D.H., Beilharz, T.H., Marguerat, S., Mata, J., Watt, S., Schubert, F., Preiss, T., and Bahler, J. (2007). A network of multiple regulatory layers shapes gene expression in fission yeast. Mol Cell 26, 145-155. Lageix, S., Lanet, E., Pouch-Pelissier, M.N., Espagnol, M.C., Robaglia, C., Deragon, J.M., and Pelissier, T. (2008). Arabidopsis eIF2alpha kinase GCN2 is essential for growth in stress conditions and is activated by wounding. BMC plant biology 8, 134. Lin, J.F., and Wu, S.H. (2004). Molecular events in senescing Arabidopsis leaves. Plant J 39, 612-628. Liu, M.J., Wu, S.H., and Chen, H.M. (2012). Widespread translational control contributes to the regulation of Arabidopsis photomorphogenesis. Mol Syst Biol 8, 566. Ma, X.M., and Blenis, J. (2009). Molecular mechanisms of mTOR-mediated translational control. Nat Rev Mol Cell Biol 10, 307-318. Mahfouz, M.M., Kim, S., Delauney, A.J., and Verma, D.P. (2006). Arabidopsis TARGET OF RAPAMYCIN interacts with RAPTOR, which regulates the activity of S6 kinase in response to osmotic stress signals. Plant Cell 18, 477-490. Matsuura, H., Ishibashi, Y., Shinmyo, A., Kanaya, S., and Kato, K. (2010). Genome-wide analyses of early translational responses to elevated temperature and high salinity in Arabidopsis thaliana. Plant Cell Physiol 51, 448-462. McKim, S.M., and Durnford, D.G. (2006). Translational regulation of light-harvesting complex expression during photoacclimation to high-light in Chlamydomonas reinhardtii. Plant Physiol Biochem 44, 857-865. Mechin, V., Damerval, C., and Zivy, M. (2007). Total protein extraction with TCA-acetone. Methods in molecular biology 355, 1-8. Melamed, D., and Arava, Y. (2007). Genome-wide analysis of mRNA polysomal profiles with spotted DNA microarrays. Methods Enzymol 431, 177-201. Melamed, D., Pnueli, L., and Arava, Y. (2008). Yeast translational response to high salinity: global analysis reveals regulation at multiple levels. RNA 14, 1337-1351. Menand, B., Desnos, T., Nussaume, L., Berger, F., Bouchez, D., Meyer, C., and Robaglia, C. (2002). Expression and disruption of the Arabidopsis TOR (target of rapamycin) gene. Proc Natl Acad Sci U S A 99, 6422-6427. Molina, C., and Grotewold, E. (2005). Genome wide analysis of Arabidopsis core promoters. BMC Genomics 6, 25. Munoz, A., and Castellano, M.M. (2012). Regulation of Translation Initiation under Abiotic Stress Conditions in Plants: Is It a Conserved or Not so Conserved Process among Eukaryotes? Comp Funct Genomics 2012, 406357. Mussgnug, J.H., Wobbe, L., Elles, I., Claus, C., Hamilton, M., Fink, A., Kahmann, U., Kapazoglou, A., Mullineaux, C.W., Hippler, M., Nickelsen, J., Nixon, P.J., and Kruse, O. (2005). NAB1 is an RNA binding protein involved in the light-regulated differential expression of the light-harvesting antenna of Chlamydomonas reinhardtii. Plant Cell 17, 3409-3421. Mustroph, A., Zanetti, M.E., Jang, C.J., Holtan, H.E., Repetti, P.P., Galbraith, D.W., Girke, T., and Bailey-Serres, J. (2009). Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc Natl Acad Sci U S A 106, 18843-18848. Narsai, R., Howell, K.A., Millar, A.H., O''Toole, N., Small, I., and Whelan, J. (2007). Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana. Plant Cell 19, 3418-3436. Ni, M., Tepperman, J.M., and Quail, P.H. (1998). PIF3, a phytochrome-interacting factor necessary for normal photoinduced signal transduction, is a novel basic helix-loop-helix protein. Cell 95, 657-667. Nicolai, M., Roncato, M.A., Canoy, A.S., Rouquie, D., Sarda, X., Freyssinet, G., and Robaglia, C. (2006). Large-scale analysis of mRNA translation states during sucrose starvation in arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control. Plant Physiol 141, 663-673. Osterlund, M.T., Hardtke, C.S., Wei, N., and Deng, X.W. (2000). Targeted destabilization of HY5 during light-regulated development of Arabidopsis. Nature 405, 462-466. Paik, I., Yang, S., and Choi, G. (2012). Phytochrome regulates translation of mRNA in the cytosol. Proc Natl Acad Sci U S A 109, 1335-1340. Parker, R., and Sheth, U. (2007). P bodies and the control of mRNA translation and degradation. Mol Cell 25, 635-646. Petracek, M.E., Dickey, L.F., Huber, S.C., and Thompson, W.F. (1997). Light-regulated changes in abundance and polyribosome association of ferredoxin mRNA are dependent on photosynthesis. Plant Cell 9, 2291-2300. Piques, M., Schulze, W.X., Hohne, M., Usadel, B., Gibon, Y., Rohwer, J., and Stitt, M. (2009). Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Mol Syst Biol 5, 314. Pomeranz, M.C., Hah, C., Lin, P.C., Kang, S.G., Finer, J.J., Blackshear, P.J., and Jang, J.C. (2010). The Arabidopsis tandem zinc finger protein AtTZF1 traffics between the nucleus and cytoplasmic foci and binds both DNA and RNA. Plant Physiol 152, 151-165. Ribeiro, D.M., Araujo, W.L., Fernie, A.R., Schippers, J.H., and Mueller-Roeber, B. (2012). Translatome and metabolome effects triggered by gibberellins during rosette growth in Arabidopsis. J Exp Bot 63, 2769-2786. Roux, P.P., Shahbazian, D., Vu, H., Holz, M.K., Cohen, M.S., Taunton, J., Sonenberg, N., and Blenis, J. (2007). RAS/ERK signaling promotes site-specific ribosomal protein S6 phosphorylation via RSK and stimulates cap-dependent translation. J Biol Chem 282, 14056-14064. Roy, B., Vaughn, J.N., Kim, B.H., Zhou, F., Gilchrist, M.A., and Von Arnim, A.G. (2010). The h subunit of eIF3 promotes reinitiation competence during translation of mRNAs harboring upstream open reading frames. Rna 16, 748-761. Ruvinsky, I., Sharon, N., Lerer, T., Cohen, H., Stolovich-Rain, M., Nir, T., Dor, Y., Zisman, P., and Meyuhas, O. (2005). Ribosomal protein S6 phosphorylation is a determinant of cell size and glucose homeostasis. Genes Dev 19, 2199-2211. Schwechheimer, C., and Deng, X.W. (2000). The COP/DET/FUS proteins-regulators of eukaryotic growth and development. Semin Cell Dev Biol 11, 495-503. Shama, S., and Meyuhas, O. (1996). The translational cis-regulatory element of mammalian ribosomal protein mRNAs is recognized by the plant translational apparatus. Eur J Biochem 236, 383-388. Sherameti, I., Nakamura, M., Yamamoto, Y.Y., Pfannschmidt, T., Obokata, J., and Oelmuller, R. (2002). Polyribosome loading of spinach mRNAs for photosystem I subunits is controlled by photosynthetic electron transport. Plant J 32, 631-639. Sormani, R., Delannoy, E., Lageix, S., Bitton, F., Lanet, E., Saez-Vasquez, J., Deragon, J.M., Renou, J.P., and Robaglia, C. (2011). Sublethal cadmium intoxication in Arabidopsis thaliana impacts translation at multiple levels. Plant Cell Physiol 52, 436-447. Spriggs, K.A., Bushell, M., and Willis, A.E. (2010). Translational regulation of gene expression during conditions of cell stress. Molecular cell 40, 228-237. Tatematsu, K., Ward, S., Leyser, O., Kamiya, Y., and Nambara, E. (2005). Identification of cis-elements that regulate gene expression during initiation of axillary bud outgrowth in Arabidopsis. Plant Physiol 138, 757-766. Tepperman, J.M., Zhu, T., Chang, H.S., Wang, X., and Quail, P.H. (2001). Multiple transcription-factor genes are early targets of phytochrome A signaling. Proc Natl Acad Sci U S A 98, 9437-9442. Tepperman, J.M., Hudson, M.E., Khanna, R., Zhu, T., Chang, S.H., Wang, X., and Quail, P.H. (2004). Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red-light-regulated gene expression during seedling de-etiolation. Plant J 38, 725-739. Tremousaygue, D., Manevski, A., Bardet, C., Lescure, N., and Lescure, B. (1999). Plant interstitial telomere motifs participate in the control of gene expression in root meristems. Plant J 20, 553-561. Turck, F., Kozma, S.C., Thomas, G., and Nagy, F. (1998). A heat-sensitive Arabidopsis thaliana kinase substitutes for human p70s6k function in vivo. Mol Cell Biol 18, 2038-2044. Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98, 5116-5121. Vogel, C., Abreu Rde, S., Ko, D., Le, S.Y., Shapiro, B.A., Burns, S.C., Sandhu, D., Boutz, D.R., Marcotte, E.M., and Penalva, L.O. (2010). Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol 6, 400. Wang, H., and Deng, X.W. (2002). Phytochrome Signaling Mechanism. In CR Somerville, EM Meyerowitz, eds, The Arabidopsis Book. American Society of Plant Biologists, Rockville, MD, doi: 10.1199/tab.0074.1,. Wu, J., Warren, P., Shakey, Q., Sousa, E., Hill, A., Ryan, T.E., and He, T. (2010). Integrating titania enrichment, iTRAQ labeling, and Orbitrap CID-HCD for global identification and quantitative analysis of phosphopeptides. Proteomics 10, 2224-2234. Wu, J.F., Wang, Y., and Wu, S.H. (2008). Two new clock proteins, LWD1 and LWD2, regulate Arabidopsis photoperiodic flowering. Plant Physiol 148, 948-959. Xiong, Y., and Sheen, J. (2012). Rapamycin and glucose-target of rapamycin (TOR) protein signaling in plants. J Biol Chem 287, 2836-2842. Yahalom, A., Kim, T.H., Roy, B., Singer, R., von Arnim, A.G., and Chamovitz, D.A. (2008). Arabidopsis eIF3e is regulated by the COP9 signalosome and has an impact on development and protein translation. Plant J 53, 300-311.
摘要: 植物生長與發育的各個階段都受到環境中『光』訊息的調控,植物會調整體內基因的表現來因應外在光環境的變化;在阿拉伯芥幼苗接受光照的早期,許多基因的表現會增加或減少,讓幼苗可以從暗形態發育 (skotomorphogenesis) 轉為光形態發育 (photomorphogenesis),先前的研究結果顯示這些基因表現的改變可以經由轉錄或蛋白質降解機制來控制,然而,植物體內是否存在其他的調控機制仍有待進一步探討。本論文發現:植物在接受光照數小時之後, 會快速的提高蛋白質轉譯的效率,相較於轉錄控制只調控數百個基因之表現,轉譯控制則作用於數千個基因,使植物可以根據光環境的改變,迅速合成與光合作用或是轉譯機制相關的蛋白質,進而促進植物的生長發育。進一步的分析發現:控制蛋白質轉譯效率的機制與信使核醣核酸 (messenger RNA; mRNA) 本身的結構特性有關,長度短或穩定度高的信使核醣核酸在光照下有較高的轉譯效率;另外,研究也顯示信使核醣核酸 5’ 未轉譯序列 (5’ untranslated region; 5’ UTR) 上的TAGGGTTT順式因子(cis-element)能夠增進信使核糖核酸的轉譯效率。我們更進一步探討在光照中,光訊息接收與傳導因子是否參與調控蛋白質轉譯。研究結果發現光敏素A直接參與遠紅光下轉譯效率的增加,COP1則在暗形態發育時期抑制蛋白質轉譯效率。經由磷酸化蛋白質體實驗, 我們發現光照下,光敏素A會促進核糖體蛋白質RPS6的磷酸化;這個結果顯示光敏素A、COP1以及RPS6可能會共同調控在黑暗與遠紅光下蛋白質轉譯效率的改變。由於之前對光訊息的研究較偏重在轉錄控制和蛋白質降解部分,此論文研究結果為相關領域加入蛋白質轉譯控制的概念,為光訊息傳導的相關研究開啟另一嶄新的方向。
Environmental “light” plays a vital role in regulating plant growth and development. Transcriptomic profiling has been widely used to examine how light regulates mRNA levels on a genome-wide scale, but, the global role of translational regulation in the response to light is unknown. Through a transcriptomic comparison of steady-state and polysome-bound mRNAs, we reveal a clear impact of translational control on thousands of genes, in addition to transcriptomic changes, during photomorphogenesis. Genes encoding ribosomal proteins are preferentially regulated at the translational level, which possibly contributes to the enhanced translation efficiency. We also reveal that mRNAs regulated at the translational level share characteristics of longer half-lives and shorter cDNA length, and that transcripts with a cis-element, TAGGGTTT, in their 5' untranslated region have higher translatability. My research also investigated how light signals modulate the downstream translational machinery for the translational control. By examining the polysome profiling of mutants defective in photoreceptors or light signal components, I revealed that the light-triggered translational activation is impaired in phyA211 mutant under far-red light whereas more mRNAs are actively translated in cop1-4 mutant at the skotomorphogenic stage. Phosphoproteomic analyses further showed that far-red light enhanced the phosphorylation of a translational regulator, ribosomal protein S6 (RPS6), in a phyA-dependent manner. These results implied that phyA, COP1 and RPS6 contribute to the light-triggered translational control. In this study, we discovered a previously neglected aspect of gene expression regulation during Arabidopsis photomorphogenesis. Further mechanistic studies on these signaling components and the molecular signatures associated with the preferentially translated mRNAs will uncover the nature of the light signal cascade on translational control.
其他識別: U0005-2806201210565200
Appears in Collections:生物科技學研究所



Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.