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研究生：	黃明德 Huang, Ming-Der
論文名稱：	利用生物資訊泛基因體選殖及功能分析阿拉伯芥離層酸調控基因 Genome-wide in silico identification and functional characterization of abscisic acid-regulated genes in Arabidopsis
指導教授：	吳文鑾 Wu, Wen-Luan
學位類別：	博士 Doctor
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：	2007
畢業學年度：	95
語文別：	英文
論文頁數：	84
中文關鍵詞：	阿拉伯芥、離層酸調控序列、離層酸調控基因、環境逆境、離層酸
外文關鍵詞：	ABA-responsive element, Arabidopsis, ABA-regulated gene, abiotic stress, Abscisic acid
相關次數：	點閱：79 下載：3
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離層酸(abscisic acid, ABA)為重要的植物荷爾蒙，其廣泛地影響植物生長及發育。受離層酸所調控的基因其啟動子多具有一高度保留的轉錄調控序列-ABRE (ABA responsive element)，該序列可被一群具有bZIP結構的轉錄調控因子(transcription factor)所辨認。目前雖已有部份離層酸調控基因被發現，但離層酸訊息調控路徑則仍未清楚，因此本研究希望以阿拉伯芥(Arabidopsis thaliana)為材料，利用生物資訊學(bioinformatics)的方式找出新的離層酸調控基因，並探討其於植物生理所扮演的角色。
首先利用電腦程式針對阿拉伯芥基因組序列(genomic sequence)進行搜尋，在阿拉伯芥26,207個基因中，共有137個基因含有兩個以上的ABREs，其中31個基因產物為未知蛋白(unknown protein)。利用RT-PCR檢測16個離層酸調控候選基因，共有12個基因於離層酸處理後有較高表現。以北方墨點法進一步分析離層酸調控基因於環境逆境下的表現，這些離層酸調控基因於鹽害、滲透壓及寒冷逆境下的表現量增加，顯示這些基因可能和環境逆境有關。利用轉殖阿拉伯芥，進一步研究這些基因於植物中所扮演的角色。其中TMAC1 (two or more ABREs containing gene 1)為一PMP22 (22-kDa peroxisomal membrane protein)相似蛋白，其表現除了受離層酸、鹽及冷處理所誘導，於物理傷害(wounding)下表現量亦增加，顯示其功能應和這些逆境有關。此外，TMAC1表現亦受到H2O2所誘導，且其不論在野生株或離層酸缺失株(ABA-deficient mutant)中均可受到物理傷害誘導，顯示H2O2在TMAC1於物理傷害表現時扮演重要的角色。TMAC2為一未知蛋白，於離層酸、鹽處理下會大量表現。過量表現TMAC2於阿拉伯芥不僅造成植株對離層酸及鹽處理不敏感，亦使植物開花時間延長、根變短及葉子澱粉堆積增加，顯示TMAC2在這些植物生理上都是扮演著負向調控的角色。綜合上述，本研究提供一個在後基因體時代有效且快速的基因功能研究策略。

Abscisic acid (ABA) is a key phytohormone which regulates plant development and growth in many aspects. Functional analysis of the ABA-regulated gene promoter reveals a conserved ABA-responsive element (ABRE), which is recognized by a group of transcription factors with a bZIP domain. Although some ABA-regulated genes have been reported, the molecular mechanism of ABA signaling remained unknown. To facilitate the identification of ABA-regulated genes, we identify novel ABA-regulated genes in Arabidopsis thaliana using a bioinformatics approach.
A computational search revealed that 137 of 26,207 genes possess two or more ABREs in Arabidopsis, and 31 genes encode unknown proteins. In an attempt to monitor the expression of these candidate genes in response to ABA, we selected 16 genes were and examined their expression by RT-PCR. Among these 16 genes, 12 candidates were up-regulated by ABA. In addition, Northern blot analysis indicated that some candidates were further shown to differentially respond to various stresses. To explore the functions of these ABA-regulated genes, we generated the transgenic Arabidopsis plants. One of these genes, TMAC1 (two or more ABREs containing gene 1), which encodes a PMP22-like protein, was up-regulated by ABA, salt, cold and wounding stresses; the results indicated that TMAC1 is a stress-related gene. Additionally, TMAC1 transcript rapidly increased in response to wounding in both wild-type and ABA-deficient mutant leaves and exogenous hydrogen peroxide (H2O2) stimulated TMAC1 expression. Thus, the signaling molecule ROS, rather than ABA, may be the intermediate of the signal transduction pathway leading to TMAC1 expression by wounding. TMAC2, which encodes a protein with no domains of known function, was highly induced by ABA and salt. Constitutive overexpression of TMAC2 in transgenic plants resulted in insensitivity of the plants to ABA and salt; the results suggested that TMAC2 plays a negative role in ABA and salt stress responses. Furthermore, TMAC2-overexpressing plants exhibited the phenotypes of short roots, late flowering and starch-excess leaves. Taken together, these results show that in silico identification of ABA-regulated genes by using data mining of Arabidopsis genome sequence is a fast and reliable approach to dissecting the function of these genes.

中 文 摘 要	i
Abstract	ii
Table of contents	iii
Table of tables	vi
Table of figures	vii
Abbreviation	viii
Introduction	1
1. History of abscisic acid (ABA)	1
2. ABA biosynthesis	1
3. Functions of ABA	2
3.1. Seed development, dormancy and germination	3
3.2. Stress adaptation	3
4. ABA signaling pathway	4
5. ABA-responsive element (ABRE)	5
6. 22-kDa peroxisomal membrane protein (PMP22)	7
7. Research objectives	7
Materials and methods	9
1. Computational identification of ABA-regulated candidate genes in Arabidopsis genome	9
2. Plant materials	9
3. ABA and stress treatments	10
4. RT-PCR analyses	10
5. Northern blot	11
6. Transgene constructs and Arabidopsis transformation	12
7. Histochemical GUS staining	13
8. Subcellular localization of TMAC2-GFP fusion protein	13
9. Stomatal aperture measurements	14
10. Starch measurement	15
11. Yeast two-hybrid experiment	15
Results	17
1. Genome-wide in silico identification of ABA-regulated genes	17
1.1. In silico analysis of ABA-regulated candidate genes	17
1.2. Experimental analysis of computational identified ABA-candidate genes in response to ABA	19
1.3. Expression patterns of ABA-regulated genes in response to abiotic stress	20
2. TMAC1, an ABA- and stress-regulated PMP22-like protein	21
2.1. Identification and characterization of TMAC1 cDNA	21
2.2. Tissue, stresses and ABA regulation of TMAC1 gene expression	22
2.3. Expression analysis of TMAC1 promoter in transgenic Arabidopsis	23
2.4. TMAC1 gene expression in response to wounding and ROS treatment	23
3. TMAC2, a novel protein with pleiotropic effects in Arabidopsis	24
3.1. Cloning and characterization of TMAC2	24
3.2. Tissue expression pattern of TMAC2	25
3.3. Subcellular localization of TMAC2 protein	26
3.4. TMAC2-overexpressing plants show insensitive to ABA and salinity	26
3.5. The effect of TMAC2 on root elongation	28
3.6. Overexpression of TMAC2 causes late flowering in transgenic Arabidopsis plants	29
3.7. TMAC2-overexpressing plants exhibit the starch-excess phenotype	29
3.8. Protein-protein interaction of TMAC2 and ABI5	30
Discussion	32
1. Genome-wide in silico identification of ABA-regulated genes is a fast and reliable method	32
2. TMAC1 encodes a ABA-, abiotic stress- and wounding-regulated PMP22-like protein	34
3. TMAC2 is a negative regulator of ABA and salt signaling, flowering time control, root growth and starch metabolism in Arabidopsis	36
References	40
Table 1. In silico defined ABA-regulated candidate genes in Arabidopsis genome	53
Table 2. ABA-regulated candidate genes used for test in the thesis	62
Table 3. List of the primers used for RT-PCR analyses and promoter amplification	63
Figure 1. Distribution of ABREs location sites.	64
Figure 2. Transcriptional level of ABA-regulated candidate genes.	65
Figure 3. Expression level of ABA-regulated genes treated with various stresses and ABA in Arabidopsis.	66
Figure 4. TMAC1 encodes a member of Arabidopsis PMP22 family.	68
Figure 5. Stress and tissue regulation of TMAC1 gene expression.	69
Figure 6. The TMAC1 promoter-driven GUS expression pattern.	71
Figure 7. Accumulation of TMAC1 in response to wounding and ROS.	72
Figure 8. Northern blot analysis of TMAC2 expression.	73
Figure 9. Alignment of TMAC2 amino acid sequence with its homologous proteins.	74
Figure 10. Histochemical GUS staining in the TMAC2::GUS transgenic Arabidopsis.	75
Figure 11. Fluorescence microscopy of subcellular localization of TMAC2-GFP fusion protein in Arabidopsis mesophyll protoplasts.	76
Figure 12. Construction of TMAC2 overexpression and RNAi transgenic plants.	77
Figure 13. Inhibition of ABA and salt responses in 35S::TMAC2 transgenic plants.	79
Figure 14. The effects of TMAC2 on root elongation.	80
Figure 15. Alteration of flowering time in 35S::TMAC2 transgenic plants.	81
Figure 16. Starch-excess phenotype of TAMC2-overexpressed transgenic plants.	82
Figure 17. Expression patterns of TMAC2 in response to starvation and glucose treatment.	83
Figure 18. Detection of interaction between ABI5 and TMAC2 by using the yeast two-hybrid assay.	84
                                    

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