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研究生：	阮黃清風 Phong, Nguyen Huynh Thanh
論文名稱：	類囊體膜瓦解形成油粒體過程中的葉片老化相關轉錄因子功能研究 Function study of senescence-associated transcription factors in plastoglobuli formation during thylakoid membrane disassembly
指導教授：	李瑞花 Lee,Ruey-Hua
共同指導教授:	吳文鑾 Wu, Wen-Luan
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：	2017
畢業學年度：	105
語文別：	英文
論文頁數：	104
中文關鍵詞：	阿拉伯芥、基因調控、葉片老化、類囊膜瓦解、PAP-fibrillin 、plastoglobuli
外文關鍵詞：	Arabidopsis thaliana, gene regulation, leaf senescence, thylakoid membrane degradation, PAP-fibrillin, plastoglobuli
相關次數：	點閱：100 下載：2
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葉綠體瓦解時，類囊膜是最早受瓦解的胞器內結構，而且可以觀察到葉綠體內部大量形成plastoglobule且數目及大小隨著瓦解程度的增加變多及變大Plastoglobule是單膜結構主要成分為半乳糖酯，並有蛋白質(如PAP-fibrillins)崁鑲在單膜表面上，PAP-fibrillins 被認為扮演穩定plastoglobule的結構型態、新陳代謝物運輸及抵抗逆境功能，為了瞭解發育及環境網絡如何調控PAP-fibrillin族群基因的表現，本研究利用阿拉伯芥為模式植物，探討14個PAP-fibrillin族群基因在葉片發育及老化不同發育時期的表現模式，分析PAP-fibrillin族群基因的promoter DNA序列，我們初步有分離40個引子基因可能扮演調控PAP-fibrillin族群基因表現的腳色，我們更進一步探討AtWRKY71 (At1g29860), AtNAC21/22 (AT1G56010), AtMYB2 (AT2G47190)和AtbZIP37/ABF3 (AT4G34000)老化相關引子在調控PAP-fibrillin基因表現所扮演的功能，從分析CREST-T表現異株，發現這些基因剃除植株有延緩葉片老化的現象，線已經建構基因大量表現轉植株及Promoter-GUS表現轉植株，這些植物材料可用為探討這幾個引子在調控PAP-fibrillin族群基因應對生長發育及環境逆境所扮演的腳色

Degradation of the thylakoid membrane is the first step for chloroplast breakdown during leaf senescence and is masked by increase number and size of plastoglobuli. Plastoglobuli consist of an outer galactolipid monolayer studded with PAP-fibrillin on the surface of plastoglobuli. PAP-fibrillin suggested playing roles in maintaining the structural stability of plastoglobuli, metabolite transport and against biotic and abiotic stresses. We are interested in dissecting the regulatory network of PAP-fibrillin genes in response to developmental and environmental signals during leaf senescence in Arabidopsis. In this study, we have analyzed expression profiles of 14 PAP-fibrillin genes during different stages of leaf growth and senescence. Based on promoter sequences of these PAP-fibrillin genes, we have previously identified 40 putative transcription factors. In this study, we isolated CREST-T mutants AtWRKY71 (At1g29860), AtNAC21/22 (AT1G56010), AtMYB2 (AT2G47190) and AtbZIP37/ABF3 (AT4G34000). Null mutants for these transcription factors showed delayed senescence. We also generate over-expression transgenic plants for these transcription factors. Promoter-GUS expression constructs also prepared by cloning 2 kb promoter regions of these transcription factors. Function studies of these CREST-T mutants and over-expression transgenic plants, and examining the tissue specificities of gene expression will enable us better understanding of these transcription factors in the regulation of PAP-fibrillin genes expression in response to developmental and environmental signals.

1. INTRODUCTION	1
1.1.	Leaf senescence	1
1.1.1. Gene expression during leaf senescence	2
1.1.2. Chlorophyll and Protein degradation during leaf senescence	3
1.1.3. Why study leaf senescence?	4
1.2.	Structure and function of chloroplast	4
1.2.1. Structure of chloroplast	4
1.2.2. Function of chloroplast	5
1.3.	Thylakoid membranes	6
1.3.1. Composition of thylakoid membranes	6
1.3.2. Structural function of thylakoid membrane	7
1.4. Chloroplast degradation during leaf senescence	8
1.4.1.Cellular view	9
1.4.2. Degradation of thylakoid membrane	10
1.5. Formation of plastioglobules is a hallmark of chloroplast degradation	11
1.5.1. Structure and composition of plastioglobules	12
1.5.2. Function of plastioglobules	13
1.5.3. PAPs/fibrillin family proteins	13
1.6. Transcriptional regulation during leaf senescence	14
1.6.1. NAC transcription factor family	15
1.6.2. WRKY transcription factor family	17
1.6.3. MYB transcription factor family	20
1.6.4. bZIP transcription factor family	23
1.6. Research aim	24
2. MATERIALS AND METHODS	25
2.1. Growth and maintenance of Arabidopsis plant	25
2.2. Total RNA extraction and quantitation	25
2.3. Non-denaturing RNA and DNA agarose gel electrophoresis	26
2.4. Total chlorophyll extraction and quantitation	26
2.5. Retrieval of PAP-fibrillin cDNA, gDNA, promoter and amino acid sequences and phylogenetic analysis	27
2.6. Sequence analysis	27
2.7. Semi-Quantitative Reverse Transcription-PCR (RT-PCR)	28
2.8. Construction of transgenic plants	28
2.8.1 Preparation of chemically competent E. coli DH5α	28
2.8.2. Preparation of TF-ORFs cDNA flanking with SfiI sites	29
2.8.3. Subcloning of the TF-ORFs cDNA into the pENTR223.1-Sfi vector	29
2.8.4. Bacterials Transformation by heat shock	30
2.8.3. Colony PCR	30
2.8.4. Plasmid DNA isolation	31
2.8.5. Preparation of Escherichia coli glycerol stocks	31
2.8.6. Gateway cloning (LR reactions)	32
2.8.7. Sequencing	32
2.8.8. Generation of chemically competent Agrobacteria tumefaciens	32
2.8.9. Transformation of Agrobacteria tumefaciens ( freeze-thraw method)	33
2.8.10. Preparing Agrobacteria solution for plant transformation	33
2.8.11. Plant transformation	34
2.8.12 Selection of BASTA resistant Arabidopsistransformants in soil.	34
2.9. Confirmation of CRES-T mutant for senescence-associated transcription factor	35
2.9.1. Genotyping	35
2.9.2. Dark treatment	35
3. RESULTS	36
3.1. DNA and amino acid sequence analysis	36
3.2. The chlorophyll levels during different stages of leaf growth and senescence	37
3.3. Expression profiles of PAPs/fibrillins genes during different stages of leaf growth and senescence.	38
3.4. Expression profiles of putative transcription factors during different stages of leaf growth and senescence	38
3.5. Genotyping of CRES-T mutants for transcription factors	38
3.6. Constructing over-expression transgenic plants using pEarley103 Gateway vector	39
3.7. Constructing Gus-fusion transgenic plants using pCAMBIA1281Z expression vector	40
4. DISCUSSION	41
5. CONCLUSION	46
LIST OF TABLES AND FIGURES	47
Table 1. List of PAP-fibrillin family genes in Arabidopsis thaliana.	48
Table 2. List of primers used for studying expression level of 14 PAP-fibrillin genes by RT-PCR.	49
Table 3. List of five senescence-associated transcription factors in Arabidopsis thaliana 	50
Table 4. List of primers used for studying expression level of five senescence-associated TFs by RT-PCR.	51
Table 5. PAP/fibrillin genes twin-peak expression during both young stage of senescent stages of leaf development and senescence	52
Table 6. List of primers used for constructing transgenic plants	53
Table 7. List of primers used for amplification of 2 kb promoter regions in four transctiption factors.	54
Figure 1. Phylogenetic analysis of Arabidopsis PAP-fibrillin proteins. A phylogenetic tree was generated by using iTOL (http://itol.embl.de/upload.cgi) software.	55
Figure 2. Phylogenetic analysis of the PAP-fibrillin family proteins in different plants. A phylogenetic tree was generated by using iTOL (http://itol.embl.de/upload.cgi) software.	56
Figure 3. Structures of 14 PAP-fibrillin genes in Arabidopsis thaliana	57
Figure 4. Conserved motif in PAP-fibrillin family proteins in Arabidopsis showing PAP-fibrillin conserved motif (red underline); Serine/threonine kinase motif (green underline); ATP binding site (black underline) and unknown conserved motif (blue box)	58
Figure 5 Putative cis-elements of AtWRKY71 transcription factor A) cis-elements logo, B) percentage of nucleotide type for each position and C) alignment of putative cis-elements showing core sequences for AtWRKY71 binding to DNA.	59
Figure 6. Putative cis-elements of AtNAC21-22 transcription factor. A) putative cis-elements logo, B) percentage of nucleotide type for each position and C) putative cis-elements of AtNAC21-22	60
Figure 7. Putative cis-elements of AtMYB2 transcription factor, A) cis-elements logo, B) percentage of nucleotide type for each position and C) alignment of putative cis-elements showing core sequences for AtMYB2 binding to DNA.	61
Figure 8. Putative cis-elements of AtbZIP37/AtABF3 transcription factor, A) cis-elements logo, B) percentage of nucleotide type for each position and C) alignment of putative cis-elements showing core sequences for AtbZIP37/AtABF3 binding to DNA.	62
Figure 9. Putative binding sites for AtWRKY transcription factors on 1KB promoter of 14 PAP-fibrillin genes. The putative binding sites were prepared using AthaMap (http://www.athamap.de/).	63
Figure 10. Putative binding sites for AtNAC transcription factors on 1KB promoter of 14	64
Figure 11. Putative binding sites for AtMYB transcription factors on 1KB promoter of 14 PAP-fibrillin genes. The putative binding sites were prepared using AthaMap (http://www.athamap.de/).	65
Figure 12. Putative binding sites for AtbZIP transcription factors on 1KB promoter of 14 PAP-fibrillin genes. The putative binding sites were prepared using AthaMap (http://www.athamap.de/).	66
Figure 13. Phylogenetic analysis of AtWRKY71 (At1g29860) homologus, paralogous and orthologous proteins in Arabidopsis, Oryza sativa, Sorghum bicolor, Vitis vinifera, Selaginella moellendorffii and Physcomitrella patens. Phylogenetic analysis was carried out SALAD 3.0 program (http://salad.dna.affrc.go.jp/salad/en/ ).	67
Figure 14. Phylogenetic analysis of AtNAC21-22 (AT1G56010) homologus, paralogous and orthologous proteins in Arabidopsis, Oryza sativa, Sorghum bicolor, Vitis vinifera, Selaginella moellendorffii and Physcomitrella patens. Phylogenetic analysis was carried out with SALAD 3.0 program (http://salad.dna.affrc.go.jp/salad/en/ ).	68
Figure 15. Phylogenetic analysis of AtMYB2 (AT2G47190) homologus, paralogous and orthologous proteins in Arabidopsis, Oryza sativa, Sorghum bicolor, Vitis vinifera and Selaginella moellendorffii. Phylogenetic analysis was carried out with SALAD 3.0 program (http://salad.dna.affrc.go.jp/salad/en/ ).	69
Figure 16. Phylogenetic analysis of AtbZIP37/ABF3 (AT4G34000) homologus, paralogous and orthologous proteins in Arabidopsis, Oryza sativa, Sorghum bicolor, Vitis vinifera and Selaginella moellendorffii. Phylogenetic analysis was carried out with SALAD 3.0 program (http://salad.dna.affrc.go.jp/salad/en/ ).	70
Figure 17. A phylogenetic tree of 90 WRKY transcription factors in Arabidopsis was generated by using iTOL (http://itol.embl.de/upload.cgi) software.	71
Figure 18. A phylogenetic tree of 110 NAC transcription factors in Arabidopsis was generated by using iTOL (http://itol.embl.de/upload.cgi) software.	72
Figure19. A phylogenetic tree of 168 MYB transcription factors in Arabidopsis was generated by using iTOL (http://itol.embl.de/upload.cgi) software	73
Figure 20. A phylogenetic tree of 127 bZIP transcription factors in Arabidopsis was generated by using iTOL (http://itol.embl.de/upload.cgi) software.	74
Figure 21. Leaves were harvested from plants after 6 to 14 weeks of sowing. a) plant growth, b) leaf samples and c) 1 µg of total RNA electrophoresed on a 1% agarose gel.	75
Figure 22. Total chlorophyll contents at different stages of leaf growth and development after 6 to 14 weeks of sowing. Numbers above the bars are mean total chlorophyll contents in mg for per gram leaf tissues calculated from three replicates.	76
Figure 23A. Expression patterns and levels of gene expression for PAP-fibrillin genes detected by RT-PCR.	77
Figure 23B. Expression patterns of PAP-fibrillin genes are divided into five groups during different stages of leaf growth and senescence.	78
Figure 24. Expression patterns of different transcription factors during different stages of leaf growth and senescence. At1g29860, AtWRKY71; AT1G56010.1, AtNAC21; AT1G56010.2, AtNAC22; AT2G47190, AtMYB2; AT4G34000, AtbZIP37/ABF3.	79
Figure 25. Vector construct for CRES-T mutants.	80
Figure 26. Genotyping and expression levels transcription factors in T4 CRES-T mutants.	81
Figure 27. Plant growth of the wild type and CRES-T mutants after 6 weeks of plant growth.	82
Figure 28. Senescence phenotype of the wild type and CRES-T mutants after 35 days of continuous dark treatment.	83
Figure 29. Work flow for construction over-expression transgenic plants for transcription factors.	84
Figure 30. RT-PCR amplification of ORFs for AtWRKY71 (At1g29860), AtNAC21 (AT1G56010.1), AtNAC22 (AT1G56010.2), AtMYB2 (AT2G47190) and AtbZIP37/ABF3 (AT4G34000).	85
Figure 31. Transcription factor ORFs were subcloned into pENTR223.1-Sfi as entry vector for LR Gateway reaction into pEarley103 destination vector	86
Figure 32. Restriction enzyme digestion for checking transcription factor ORFs DNA fragments in pEarley103.	87
Figure 33. Arabidopsis plant transformation by floral dip.	88
Figure 34. Herbicide selection (BASTA) for transgenic plants using 120 mg/L phosphinothricin after 0 day (0D) and 9 days (9D) treatments.	89
Figure 35. PCR amplification of 2 kb promoter DNA fragments upstream of start codons for AtWRKY71 (At1g29860), AtNAC21/22 (AT1G56010), AtMYB2 (AT2G47190) and AtbZIP37/ABF3 (AT4G34000) genes.	90
Figure 36. Constructing promoter GUS-fusion constructs. pCAMBIA1281Z GUS expression vector is used (upper panel). Restriction enzyme digestion shows presence of transgenes in the vector (lower panel).	91
Figure 35. Work flow for generation of promoter-GUS fusion transgenic plants used in studying tissue specificity of gene expression.	92
Figure 38. Antibiotics and cloning vectors used for this study.	93
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