請用此 Handle URI 來引用此文件：
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/33793完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 林讚標 | |
| dc.contributor.author | Yen-Heng Lin | en |
| dc.contributor.author | 林延衡 | zh_TW |
| dc.date.accessioned | 2021-06-13T05:46:15Z | - |
| dc.date.available | 2006-07-18 | |
| dc.date.copyright | 2006-07-18 | |
| dc.date.issued | 2006 | |
| dc.date.submitted | 2006-07-11 | |
| dc.identifier.citation | Alonso-Blanco, C., Gomez-Mena, C., Llorente, F., Koornneef, M., Salinas, J., and Martı´nez-Zapater, J.M. (2005). Genetic and molecular analyses of natural variation indicate CBF2 as a candidate gene for underlying a freezing tolerance quantitative trait locus in Arabidopsis. Plant Physiol. 139, 1304-1312.
Bamshad, M.J., Mummidi, S., Gonzalez, E., Ahuja, S.S., Dunn, D.M., Watkins, W.S., Wooding, S., Stone, A.C., Jorde, L.B., Weiss, R.B., and Ahuja, S.K. (2002). A strong signature of balancing selection in the 5’ cis-regulatory region of CCR5. Proc. Natl. Acad. Sci. USA 99, 10539-10544. Barkman, T.J. (2003). Evidence for positive selection on the floral scent gene isoeugenol-O-methyltransferase. Mol. Biol. Evol. 20, 168-172. Bielawski, J.P., and Yang, Z. (2003). Maximum likelihood methods for detecting adaptive evolution after gene duplication. J. Struct. Funct. Genomics 3, 201-212. Buskirk, H.A.V., and Thomashow, M.F. (2006). Arabidopsis transcription factors regulating cold acclimation. Physiol. Plantarum 126, 72-80. Caicedo, A.L., Stinchcombe, J.R., Olsen, K.M., Schmitt, J., and Purugganan, M.D. (2004). Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait. Proc. Natl. Acad. Sci. USA 101, 15670-15675. Chinnusamy, V., Ohta, M., Kanrar, S., Lee, B.H., Hong, X., Agarwal, M., and Zhu, J.K. (2003). ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev. 17, 1043–1054 Cook, D., Fowler, S., Fiehn, O., and Thomashow, M.F. (2004). A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis. Proc. Natl. Acad. Sci. USA 101, 15243-15248. Doyle, J.J. and Doyle, J.L. (1990). Isolation of plant DNA from fresh tissue. Focus 12, 13-15. Endo, T., Ikeo, K., and Gojobori, T. (1996). Large-scale search for genes on which positive selection may operate. Mol. Biol. Evol. 13, 685-690. Fay, J.C., and Wu, C.I. (2000). Hitchhiking under positive Darwinian selection. Genetics 155, 1405-1413. Fowler, S., and Thomashow, M.F. (2002). Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14, 1675-1690. Fowler, S.G., Cook, D., and Thomashow, M.F. (2005). Low temperature induction of Arabidopsis CBF1, 2, and 3 is gated by the circadian clock. Plant Physiol. 137, 961-968. Frankel, N., Hasson, E., Iusem, N.D. and Rossi, M.S. (2003). Adaptive evolution of the water stress-induced gene Asr2 in Lycopersicon species dwelling in arid habitats. Mol. Biol. Evol. 20, 1955-1962. Gilmour, S.J., Fowler, S.G., and Thomashow, M.F. (2004). Arabidopsis transcriptional activators CBF1, CBF2, and CBF3 have matching functional activities. Plant Mol. Biol. 54, 767–781. Gilmour, S.J., Zarka, D.G., Stockinger, E.J., Salazar, M.P., Houghton, J.M., and Thomashow, M.F. (1998). Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J. 16, 433–442. Haake, V., Cook, D., Riechmann, J.L., Pineda, O., Thomashow, M.F., and Zhang, J.Z. (2002). Transcription factor CBF4 is a regulator of drought adaptation in Arabidopsis. Plant Physiol. 130, 639-648. Haldane, J.B.S. (1932). The causes of evolution. Princeton University Press, Princeton, N.J. Higo, K., Ugawa, Y., Iwamoto, M., and Higo, H. (1998). PLACE: a database of plant cis-acting regulatory DNA elements. Nucleic Acids Res. 26, 358-359. Jackson, M.W., Stinchcombe, J.R., Korves, T.M., and Schmitt, J. (2004). Costs and benefits of cold tolerance in transgenic Arabidopsis thaliana. Mol. Ecol. 13, 3609-3615. Kimura, M. (1968). Evolutionary rate at the molecular level. Nature 217, 624-626. King, J.L., and Jukes, T.H. (1969). Non-Darwinian evolution. Science 164, 788-798. Kreitman, M. (2000). Methods to detect selection in populations with applications to the human. Annu. Rev. Genomics Hum. Genet. 1, 539-559. Kumar, S., Tamura, K., and Nei, M. (2004). MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinformatics 5, 150-163. Liu, Q., Kasuga, M., Sakuma, Y., Abe, H., Miura, S., Yamaguchi-Shinozaki, K., and Shinozaki, K. (1998). Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell 10, 1391–1406. Maruyama, K., Sakuma, Y., Kasuga, M., Ito, Y., Seki, M., Goda, H., Shimada, Y., Yoshida, S., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2004). Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems. Plant J. 38, 982–993. McDonald, J. H. (1998). Improved tests for heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. Mol. Biol. Evol. 15, 377–384. Meaux, J., Goebel, U., Pop, A., and Mitchell-Olds, T. (2005). Allele-specific assay reveals functional variation in the Chalcone Synthase promoter of Arabidopsis thaliana that is compatible with neutral evolution. Plant Cell 17, 676-690. Medina, J., Bargues, M., Terol, J., Perez-Alonso, M., and Salinas, J. (1999). The Arabidopsis CBF gene family is composed of three genes encoding AP2 domain-containing proteins whose expression is regulated by low temperature but not by abscisic acid or dehydration. Plant Physiol. 119, 463–470. Moore, R.C., Grant, S.R., and Purugganan, M.D. (2005). Molecular population genetics of redundant floral-regulatory genes in Arabidopsis thaliana. Mol. Biol. Evol. 22, 91-103. Nei, M. (2005). Selectionism and neutralism in molecular evolution. Mol. Biol. Evol. 22, 2318-2342. Nei, M., and Gojobori, T. (1986). Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418-426. Nielsen, R., and Yang, Z. (1998). Likelihood models for detecting positively selected amino acids and applications to the HIV-1 envelope gene. Genetics 148, 929-936. Novillo, F., Alonso, J.M., Ecker, J.R., and Salinas, J. (2004). CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis. Proc. Natl. Acad. Sci. USA 101, 3985–3990. Olsen, K.M., Womack, A., Garrett, A.R., Suddith, J.I. and Purugganan, M.D. (2002). Contrasting evolutionary forces in the Arabidopsis thaliana floral developmental pathway. Genetics 160, 1641-1650. Rose, L.E., Bittner-Eddy, P.D., Langley, C.H., Holub, E.B., Michelmore, R.W., and Beynon, J.L. (2004). The maintenance of extreme amino acid diversity at the disease resistance gene, RPP13, in Arabidopsis thaliana. Genetics 166, 1517-1527. Rozas, J., Sanchez-DelBarrio, J.C., Messeguer, X., and Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496-2497. Shinwari, Z.K., Nakashima, K., Miura, S., Kasuga, M., Seki, M., Yamaguchi-Shinozaki, K., and Shinozaki, K. (1998). An Arabidopsis gene family encoding DRE/CRT binding proteins involved in low-temperature-responsive gene expression. Biochem. Biophys. Res. Commun. 250, 161–170. Stahl, E.A., Dwyer, G., Mauricio, R., Kreitman, M., and Bergelson, J. (1999). Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis. Nature 400, 667-671. Stockinger, E.J., Gilmour, S.J., and Thomashow, M.F. (1997). Arabidopsis thaliana CBF1 encodes an AP2 domain containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc. Natl. Acad. Sci. USA 94, 1035–1040. Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595. Vasemagi, A., and Primmer, C.R. (2005). Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies. Mol. Ecol. 14, 3623-3642. Vogel, J.T., Zarka, D.G., Buskirk, H.A.V., Fowler, S.G., and Thomashow, M.F. (2005). Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J. 41, 195–211. Wang, Z., Triezenberg, S.J., Thomashow, M.F., and Stockinger, E.J. (2005). Multiple hydrophobic motifs in Arabidopsis CBF1 COOH-terminus provide functional redundancy in transactivation. Plant Mol. Biol. 58, 543–559. Wray, G.A., Hahn, M.W., Abouheif, E., Balhoff, J.P., Pizer, M., Rockman, M.V., and Romano, L.A. (2003). The evolution of transcriptional regulation in eukaryotes. Mol. Biol. Evol. 20, 1377-1419. Yan, H., and Zhou, W. (2004). Allelic variations in gene expression. Curr. Opin. Oncol. 16, 39-43. Yang, Z. (1998). Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15, 568-573. Yang, Z., Nielsen, R., Goldman, N., and Pederson, A.M.K., W.J. (2000). Codon-substitution models for heterogeneous selection pressures among sites classes. Genetics 155, 431-449. Yoshida, K., Kamiya, T., Kawabe, A., and Miyashita, N.T. (2003). DNA polymorphism at the ACAULIS5 locus of the wild plant Arabidopsis thaliana. Genes Genet. Syst. 78, 11-21. Zarka, D.G., Vogel, J.T., Cook, D., and Thomashow, M.F. (2003). Cold induction of Arabidopsis CBF genes involves multiple ICE (inducer of CBF expression) promoter elements and a cold-regulatory circuit that is desensitized by low temperature. Plant Physiol. 133, 910–918. Zuckerkandl, E., and Pauling, L. (1962). Molecular disease, evolution, and genetic heterogeneity. Pp. 189-225 in M. Kasha and B. Pullman, eds. Horizons in biochemistry. Academic Press, New York. _____. (1965). Evolutionary divergence and convergence in proteins. Pp. 97-166 in V. Bryson and H.J. Vogel, eds. Evolving genes and proteins. Academic Press, New York. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/33793 | - |
| dc.description.abstract | 我們以28個生態型的阿拉伯芥研究受冷誘導基因，CBF3的功能性演化。 CBF3是受冷調控的訊息傳導路徑上重要的“開關”。我們以不同的軟體分析了1297-bp長的啟動子區域序列以及909-bp轉錄區域序列。經過4oC，1.5小時冷處理後，我們以real-rime PCR測量不同生態型之CBF3表現差異，並將此表現差異和以啟動子序列建構之親緣樹互相對照，試圖找出決定該基因表現之重要序列。大部分啟動子及轉錄區域的序列變異符合中性演化，然而藉由sliding window method of Tajima’s D test，我們偵測到不同形式的天擇存在。雖然啟動子上一段區域可能受到balancing selection，然而此一結果之生物上的意義仍未知。我們也在transcriptional activation domain的C端偵測到以低頻率存在之alleles，此一現象也可能由天擇決定。在蛋白質序列的演化上，CBF3大致受到purifying selection作用。然而跟高度保守的AP2 domain相較，Ka/Ks的比值在transcriptional activation domain有劇烈的波動。我們在此區域找到Ka/Ks比值超過1的區段。經由codeml程式(PAML package)的檢測，我們在此區段中偵測到ㄧ個可能是受到positive selection作用的胺基酸(151E)。此胺基酸在7個生態型中被置換為alanine。根據前人對於CBF1之transcriptional activation domain的研究，此一胺基酸(151E)若被取代為alanine，則其活化下游基因表現之能力會增強。我們因此推斷positive selection選擇此一突變，以增加阿拉伯芥植株對於冷的耐受性。經由研究對偶基因特異性表現(allele-specific expression)的策略，我們在啟動子上找到2個核苷酸序列與CBF3低表現量相關。我們也找到ㄧ個天然的CBF3 knockout line，Kas-2。此一發現可供我們進一步釐清CBF3在植物抗冷中扮演的角色。 | zh_TW |
| dc.description.abstract | We are interested in functional evolution of CBF3, one of the “master switches” in cold-regulated pathways, in 28 ecotypes of Arabidopsis thaliana. We analyzed sequence polymorphism of 1297-bp promoter and 909-bp transcriptional unit (TU) regions with the aids of different software. After 1.5h chilling treatment (4oC), the CBF3 expression levels were measured by real-time PCR, and the expression variations were mapped to the phylogeny tree constructed according to promoter sequences polymorphisms. The promoter and TU evolution are compatible with neutral evolution while heterogeneity of natural selection was also detected by the sliding window method of Tajima’s D test. A region in promoter was possibly subject to balancing selection, however, the meaning of this is not clear at present. We also found selection against low frequency alleles in C-terminal transcriptional activation domain. In protein sequence evolution, the CBF3 is under strong purifying selection which is against deleterious substitution. However, in contrast to highly conserved AP2 domain, the Ka/Ks ratio fluctuated in transcriptional activation domain in paired comparisons among CBF paralogs. A region with ω more than one was found. The amino acid residue within this region, 151E, was identified by codeml (PAML package) as positively selected site. 151E was substituted by 151A in seven ecotypes we have studied. According to a previous report of trans-activation assay in the transcriptional activation domain, this substitution led to stronger trans-activity. We believe this substitution was favored by positive selection to acquire better cold-tolerance for Arabidopsis in the wild. Using the allele-specific expression approach, we identified two nucleotide sites that are related to low expression of CBF3 after chilling treatment. Kas-2, a CBF3 natural knockout line, was found in this study and will be useful to evaluate the roles of CBF3 in freezing tolerance in Arabidopsis. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-13T05:46:15Z (GMT). No. of bitstreams: 1 ntu-95-R93b42007-1.pdf: 2536625 bytes, checksum: 23beb04f3769d53f9919349e2f22f95a (MD5) Previous issue date: 2006 | en |
| dc.description.tableofcontents | Abstract 1
中文摘要 2 INTRODUCTION 3 Molecular evolution and statistics to detect evolutionary process 3 Advantages of using natural variation to predict functional sequences 4 The necessity of searching the link of genotype-phenotype 5 In protein evolution 5 Allele-specific expression approach 6 CBF gene family in Arabidopsis thaliana 7 Divergence of CBF paralogs 8 Strategies and goals of CBF functional evolution research 10 Objectives that have been obtained in this report: 10 MATERIALS AND METHODS 12 Arabidopsis thaliana ecotypes 12 DNA extraction, PCR, and Sequencing 12 Molecular evolution and population genetic analysis 13 Cold-treatment and sampling procedure 14 RNA extraction and cDNA synthesis 14 Real-time PCR analysis 15 RESULTS 17 Sequence polymorphism in CBF3 (AT4G25480) 17 The evolutionary distances among CBF paralogs 18 CBF3 nucleotide diversity is compatible with neutral evolution while heterogeneity of selection strength was also detected 19 A probable selective sweep occurred in both promoter and coding sequence but no significant heterogeneity of polymorphism to divergence ratios was identified 19 The CBF3 protein is under strong purifying selection but significant differences of selection constraints were detected in different functional domains 20 A positively selected site was identified within transcriptional activation domain 21 CBF3 expressions in ecotypes after chilling treatment 22 Real-time PCR data calibration 22 Variation of CBF3 expression levels in different ecotypes 23 DISCUSSION 25 The technical bias in real-time PCR and sampling 25 The sequence polymorphism in CBF3 gene 25 The link of coding sequence diversity to previous functional assay 27 Positive selection in CBF3 protein sequence 28 Matching the expression levels with phylogeny constructed according to promoter sequences 29 FIGURES and TABLES 31 REFERENCES 46 Appendix 50 | |
| dc.language.iso | zh-TW | |
| dc.subject | 阿拉伯芥 | zh_TW |
| dc.subject | 天擇 | zh_TW |
| dc.subject | 中性演化 | zh_TW |
| dc.subject | 功能性演化 | zh_TW |
| dc.subject | 冷誘導基因 | zh_TW |
| dc.subject | Arabidopsis thaliana | en |
| dc.subject | natural selection | en |
| dc.subject | neutral evolution | en |
| dc.subject | functional evolution | en |
| dc.subject | real-time PCR | en |
| dc.subject | positive selection | en |
| dc.subject | CBF3 | en |
| dc.title | 阿拉伯芥之受冷誘導基因，CBF3的功能性演化 | zh_TW |
| dc.title | Functional Evolution of a Cold-induced Gene, CBF3, in Arabidopsis thaliana Ecotypes | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 94-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 蔣鎮宇,黃士穎,何國傑 | |
| dc.subject.keyword | 阿拉伯芥,冷誘導基因,功能性演化,中性演化,天擇, | zh_TW |
| dc.subject.keyword | CBF3,Arabidopsis thaliana,real-time PCR,functional evolution,neutral evolution,natural selection,positive selection, | en |
| dc.relation.page | 59 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2006-07-13 | |
| dc.contributor.author-college | 生命科學院 | zh_TW |
| dc.contributor.author-dept | 植物科學研究所 | zh_TW |
| 顯示於系所單位： | 植物科學研究所 | |
文件中的檔案：
| 檔案 | 大小 | 格式 | |
|---|---|---|---|
| ntu-95-1.pdf 未授權公開取用 | 2.48 MB | Adobe PDF |
系統中的文件，除了特別指名其著作權條款之外，均受到著作權保護，並且保留所有的權利。