進階搜尋


   電子論文尚未授權公開,紙本請查館藏目錄
(※如查詢不到或館藏狀況顯示「閉架不公開」,表示該本論文不在書庫,無法取用。)
系統識別號 U0026-1708201417465700
論文名稱(中文) 利用轉錄體分析水稻根部對環境逆境的反應
論文名稱(英文) Transcriptome analysis of rice root response to environmental stress
校院名稱 成功大學
系所名稱(中) 生命科學系
系所名稱(英) Department of Life Sciences
學年度 102
學期 2
出版年 103
研究生(中文) 黃醴嶢
研究生(英文) Li-Yao Huang
學號 l56014081
學位類別 碩士
語文別 英文
論文頁數 57頁
口試委員 指導教授-黃浩仁
口試委員-蔣鎮宇
口試委員-張文粲
口試委員-朱信
口試委員-林財富
中文關鍵字 轉錄體  環境逆境  生物標記  植物賀爾蒙  能量代謝 
英文關鍵字 transcriptome  environmental stress  biomarker  phytohormone  energy metabolism 
學科別分類
中文摘要 植物對於逆境的反應仍是重要的研究課題。隨著高通量技術(生物晶片、次世代定序)發展以來,現已被大量應用於此研究領域上,其可用於探討植物在逆境中的轉錄體變化。然而,大多數研究皆只針對單一逆境的反應進行探討。在此篇研究中,比較轉錄體學(comparative transcriptom)的方法被應用於研究水稻面對不同環境壓力時所產生的轉錄體變化。我們研究了水稻在處理六種金屬/類金屬汙染物:砷、鎘、鉻、銅、釩、汞以及兩種植物相剋化合物: 阿魏酸及胡桃酮後的轉錄體變化。我們將八個環境逆境下表現量皆大於兩倍的基因定義為一般壓力誘導反應(GSIR)基因。經過分析後,我們找到了539個GSIR基因,其中我們發現水稻在面臨環境壓力時,初期具有三個核心反應。第一個為植物賀爾蒙的變化。產生乙烯、離層酸及茉莉酸的基因表現量會上升。同時,將細胞分裂素、生長素以及吉貝素去活化的基因表現量亦會上升。第二個為能量的代謝,參與糖解作用的基因以及生產γ-氨基丁酸的基因會上升。第三個為負責生產木質素及木栓質的基因表現量上升,進而影響水稻根部細胞結構的改變。除此之外,本研究發現水稻對於砷以及胡桃酮有著類似的反應,尤其在解毒機制相關的基因上有相似的表現趨勢。除了GSIR基因,本研究亦找到了在單一逆境下被獨特調控的基因,這些基因具有發展成為生物標記的潛力,可以用於偵測環境中是否有特定汙染物存在。在這些基因中,本研究發現其中一個基因,暫時命名為OsCadM1,未來或許可做為偵測環境中鎘汙染之生物標記。此基因只有環境中存在鎘離子時才會有高基因表現量,在其他環境汙染下則不會有此現象。本研究的結果對於水稻在面對環境逆境時的反應提供了新的見解,未來植物逆境等相關研究可先將GSIR基因排除,進而找出該逆境下特有的分子防禦機制。此研究亦指出了利用比較轉錄體學發展新生物標記的潛力。
英文摘要 Comparative transcriptome analysis was performed to explore transcriptional response
of rice (Oryza sativa L. cv. TN-67) to a variety of environmental stresses. Global response
of rice to eight stress conditions: arsenate, copper, cadmium, mercury, chromate, vanadate,
ferulic acid and juglone, were analyzed using DNA microarrays. There were 539 genes
defined as general stress induced response (GSIR) genes as being induced at least two fold
change under all stress conditions. A total of 61 transcription factors (TFs) were found in
GSIR genes, and most of their Arabidopsis homologs were also generally induced under
different stresses, indicating functional conservation of these TFs in stress signaling. Three
central aspects in the early response of rice to environmental stress were discovered after
analyzing GSIR genes. These aspects includes 1) biosynthesis of ethylene, jasmonate acid
and abscisic acid as well as deactivation of gibberellin, indole-3-acetic acid and cytokinin;
2) alternation in energy metabolism such as biosynthesis of γ-aminobutyric acid (GABA); 3)
biosynthesis of lignin and suberin in the root. In addition, rice exhibited similar
transcriptional response to arsenate and juglone, especially in genes related to xenobiotic
metabolism. Genes that were specifically induced by single stress in our data, might hold
potential to be developed as a biomarker for specific environment contamination. In this
study, we discovered a candidate biomarker to detect cadmium contamination in the
environment. Our results provide insights into understanding of molecular response of rice
to environmental stresses and also demonstrated the potential of using comparative
transcriptome analysis to discover new biomarkers.
論文目次 Table of Contents
Abstract I
Acknowledgments III
List of tables V
List of figures VI
Abbreviations VII
Introduction 1
Material and Methods
Plant materials 4
Data source and analysis 4
Experiment design for verifying candidate biomarker 5
Preparation of total RNA and qRT-PCR analysis 5
Gene ontology (GO) analysis 6
Results
Overview 7
GSIR genes 8
Signal transduction and transcription factors 9
Hormone and Energy Metabolism 9
Cell wall modification 10
Similar response to arsenate and juglone in rice 11
Candidate biomarker in detecting cadmium contamination 12
Discussion 13
Conclusion 17
References 18
參考文獻 1. Achard P and Genschik P. Releasing the brakes of plant growth: how GAs shutdown
DELLA proteins. Journal of experimental botany 60: 1085-1092, 2009.
2. Agarwal P, Arora R, Ray S, Singh AK, Singh VP, Takatsuji H, Kapoor S, and Tyagi
AK. Genome-wide identification of C2H2 zinc-finger gene family in rice and their
phylogeny and expression analysis. Plant molecular biology 65: 467-485, 2007.
3. Apel K and Hirt H. Reactive oxygen species: metabolism, oxidative stress, and signal
transduction. Annual review of plant biology 55: 373-399, 2004.
4. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW,
and Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic acids
research 37: W202-208, 2009.
5. Bouche N and Fromm H. GABA in plants: just a metabolite? Trends in plant science
9: 110-115, 2004.
6. Bruinsma M, Posthumus MA, Mumm R, Mueller MJ, van Loon JJ, and Dicke M.
Jasmonic acid-induced volatiles of Brassica oleracea attract parasitoids: effects of time
and dose, and comparison with induction by herbivores. Journal of experimental botany
60: 2575-2587, 2009.
7. Bundy JG, Keun HC, Sidhu JK, Spurgeon DJ, Vendsen CS, Kille P, and Morgan
AJ. Metabolic Profile Biomarkers of Metal Contamination in a Sentinel Terrestrial
Species Are Applicable Across Multiple Sites. Environ Sci Technol 4458-4464, 2007.
8. Chen D, Toone WM, Mata J, Lyne R, Burns G, Kivinen K, Brazma A, Jones N,
and Bahler J. Global transcriptional responses of fission yeast to environmental stress.
Molecular biology of the cell 14: 214-229, 2003.
9. Chen L, Song Y, Li S, Zhang L, Zou C, and Yu D. The role of WRKY transcription
factors in plant abiotic stresses. Biochimica et biophysica acta 1819: 120-128, 2012.
27
10. Chen T, Cai X, Wu X, Karahara I, Schreiber L, and Lin J. Casparian strip
development and its potential function in salt tolerance. Plant signaling & behavior 6:
1499-1502, 2011.
11. Cheng MC, Hsieh EJ, Chen JH, Chen HY, and Lin TP. Arabidopsis RGLG2,
functioning as a RING E3 ligase, interacts with AtERF53 and negatively regulates the
plant drought stress response. Plant physiology 158: 363-375, 2012.
12. Ciftci-Yilmaz S and Mittler R. The zinc finger network of plants. Cellular and
molecular life sciences : CMLS 65: 1150-1160, 2008.
13. De Domenico S, Bonsegna S, Horres R, Pastor V, Taurino M, Poltronieri P, Imtiaz
M, Kahl G, Flors V, Winter P, and Santino A. Transcriptomic analysis of oxylipin
biosynthesis genes and chemical profiling reveal an early induction of jasmonates in
chickpea roots under drought stress. Plant physiology and biochemistry : PPB / Societe
francaise de physiologie vegetale 61: 115-122, 2012.
14. Depuydt S and Hardtke CS. Hormone signalling crosstalk in plant growth regulation.
Current biology : CB 21: R365-373, 2011.
15. Fujita Y, Fujita M, Shinozaki K, and Yamaguchi-Shinozaki K. ABA-mediated
transcriptional regulation in response to osmotic stress in plants. Journal of plant
research 124: 509-525, 2011.
16. Greco M, Chiappetta A, Bruno L, and Bitonti MB. In Posidonia oceanica cadmium
induces changes in DNA methylation and chromatin patterning. Journal of
experimental botany 63: 695-709, 2012.
17. Gremion F, Chatzinotas A, Kaufmann K, Von Sigler W, and Harms H. Impacts of
heavy metal contamination and phytoremediation on a microbial community during a
twelve-month microcosm experiment. FEMS microbiology ecology 48: 273-283, 2004.
18. Gruber V, Blanchet S, Diet A, Zahaf O, Boualem A, Kakar K, Alunni B, Udvardi
28
M, Frugier F, and Crespi M. Identification of transcription factors involved in root
apex responses to salt stress in Medicago truncatula. Molecular genetics and genomics :
MGG 281: 55-66, 2009.
19. Haferburg G and Kothe E. Metallomics: lessons for metalliferous soil remediation.
Applied microbiology and biotechnology 87: 1271-1280, 2010.
20. Hummel I, Pantin F, Sulpice R, Piques M, Rolland G, Dauzat M, Christophe A,
Pervent M, Bouteille M, Stitt M, Gibon Y, and Muller B. Arabidopsis plants
acclimate to water deficit at low cost through changes of carbon usage: an integrated
perspective using growth, metabolite, enzyme, and gene expression analysis. Plant
physiology 154: 357-372, 2010.
21. Bundy JG, Spurgeon DJ, Svendsen C, Hankard PK, Weeks JM, Osborn D, Lindon
JC, and Nicholson JK. Environmental Metabonomics: Applying Combination
Biomarker Analysis in Earthworms at a Metal Contaminated Site. Ecotoxicology 13:
797-806,2005.
22. Karahara I, Ikeda A, Kondo T, and Uetake Y. Development of the Casparian strip
in primary roots of maize under salt stress. Planta 219: 41-47, 2004.
23. Keltjens WG and Beusichem MLv. Phytochelatins as biomarkers for heavy metal
stress inmaize (Zea mays L.) and wheat (Triticum aestivum L.): combined effects of
copper and
cadmium. Plant and Soil 119-126, 1998.
24. Kieffer P, Dommes J, Hoffmann L, Hausman JF, and Renaut J. Quantitative
changes in protein expression of cadmium-exposed poplar plants. Proteomics 8: 2514-
2530, 2008.
25. Kielbowicz-Matuk A. Involvement of plant C(2)H(2)-type zinc finger transcription
factors in stress responses. Plant science : an international journal of experimental
29
plant biology 185-186: 78-85, 2012.
26. Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C,
Bornberg-Bauer E, Kudla J, and Harter K. The AtGenExpress global stress
expression data set: protocols, evaluation and model data analysis of UV-B light,
drought and cold stress responses. The Plant journal : for cell and molecular biology
50: 347-363, 2007.
27. Kim C, Meskauskiene R, Zhang S, Lee KP, Lakshmanan Ashok M, Blajecka K,
Herrfurth C, Feussner I, and Apel K. Chloroplasts of Arabidopsis are the source and
a primary target of a plant-specific programmed cell death signaling pathway. The Plant
cell 24: 3026-3039, 2012.
28. Korasick DA, Enders TA, and Strader LC. Auxin biosynthesis and storage forms.
Journal of experimental botany 64: 2541-2555, 2013.
29. Kosova K, Vitamvas P, Prasil IT, and Renaut J. Plant proteome changes under
abiotic stress--contribution of proteomics studies to understanding plant stress response.
Journal of proteomics 74: 1301-1322, 2011.
30. Kovalchuk O, Titov V, Hohn B, and Kovalchuk aI. A sensitive transgenic plant
system to detect toxic inorganic compounds in the environment. Nature biotechnology
19: 568-572, 2001.
31. Lee SB, Jung SJ, Go YS, Kim HU, Kim JK, Cho HJ, Park OK, and Suh MC. Two
Arabidopsis 3-ketoacyl CoA synthase genes, KCS20 and KCS2/DAISY, are
functionally redundant in cuticular wax and root suberin biosynthesis, but differentially
controlled by osmotic stress. The Plant journal : for cell and molecular biology 60:
462-475, 2009.
32. Luo X, Bai X, Zhu D, Li Y, Ji W, Cai H, Wu J, Liu B, and Zhu Y. GsZFP1, a new
Cys2/His2-type zinc-finger protein, is a positive regulator of plant tolerance to cold and
30
drought stress. Planta 235: 1141-1155, 2012.
33. Møller IM. Plant mitochondria and oxidative stress: electron transport, NADPH
turnover, and metabolism of reactive oxygen species. Plant Mol Biol 561-591.
34. Maere S, Heymans K, and Kuiper M. BiNGO: a Cytoscape plugin to assess
overrepresentation of gene ontology categories in biological networks. Bioinformatics
21: 3448-3449, 2005.
35. Perrot-Rechenmann C. Cellular responses to auxin: division versus expansion. Cold
Spring Harbor perspectives in biology 2: a001446, 2010.
36. Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K,
Seki M, Shinozaki K, and Yamaguchi-Shinozaki K. Monitoring expression profiles
of rice genes under cold, drought, and high-salinity stresses and abscisic acid
application using cDNA microarray and RNA gel-blot analyses. Plant physiology 133:
1755-1767, 2003.
37. Renault H, Bassard JE, Hamberger B, and Werck-Reichhart D. Cytochrome P450-
mediated metabolic engineering: current progress and future challenges. Current
opinion in plant biology 19C: 27-34, 2014.
38. Rizhsky L, Liang H, Shuman J, Shulaev V, Davletova S, and Mittler R. When
defense pathways collide. The response of Arabidopsis to a combination of drought and
heat stress. Plant physiology 134: 1683-1696, 2004.
39. Luchi S, Kobayashi M, Taji T, Naramoto M, Seki M, Kato T, Tabata S, Kakubari
Y, Yamaguchi-Shinozaki K, and Shinozaki K. Regulation of drought tolerance by
gene manipulation of 9-cis-epoxycarotenoid dioxygenase, a key enzyme in abscisic
acid biosynthesis in Arabidopsis. Plant J 27(4): 325-333, 2001.
40. Sakakibara H. Cytokinins: Activity,Biosynthesis, and Translocation. Annu Rev Plant
Biol 431-449, 2006.
31
41. Sarry JE, Kuhn L, Ducruix C, Lafaye A, Junot C, Hugouvieux V, Jourdain A,
Bastien O, Fievet JB, Vailhen D, Amekraz B, Moulin C, Ezan E, Garin J, and
Bourguignon J. The early responses of Arabidopsis thaliana cells to cadmium
exposure explored by protein and metabolite profiling analyses. Proteomics 6: 2180-
2198, 2006.
42. Satoh K, Saji S, Ito S, Shimizu H, Saj H, and Kikuchi1* S. Gene response in rice
plants treated with continuous fog influenced by pH, was similar to that treated with
biotic stress. Rice 7: 2014.
43. Skirycz A, Claeys H, De Bodt S, Oikawa A, Shinoda S, Andriankaja M, Maleux K,
Eloy NB, Coppens F, Yoo SD, Saito K, and Inze D. Pause-and-stop: the effects of
osmotic stress on cell proliferation during early leaf development in Arabidopsis and a
role for ethylene signaling in cell cycle arrest. The Plant cell 23: 1876-1888, 2011.
44. Skirycz A, and Inze D. More from less: plant growth under limited water. Current
opinion in biotechnology 21: 197-203, 2010.
45. Suzuki N, Koussevitzky S, Mittler R, and Miller G. ROS and redox signalling in the
response of plants to abiotic stress. Plant, cell & environment 35: 259-270, 2012.
46. Sweetlove LJ, Heazlewood JL, Herald V, Holtzapffel R, Day DA, Leaver CJ, and
Millar  AH. The impact of oxidative stress on Arabidopsis mitochondria. Plant J 32: 891-904, 2002.
47. Takahashi F, Mizoguchi T, Yoshida R, Ichimura K, and Shinozaki K. Calmodulindependent
activation of MAP kinase for ROS homeostasis in Arabidopsis. Molecular
cell 41: 649-660, 2011.
48. Tamasloukht B, Wong Quai Lam MS, Martinez Y, Tozo K, Barbier O, Jourda C,
Jauneau A, Borderies G, Balzergue S, Renou JP, Huguet S, Martinant JP, Tatout
C, Lapierre C, Barriere Y, Goffner D, and Pichon M. Characterization of a
32
cinnamoyl-CoA reductase 1 (CCR1) mutant in maize: effects on lignification, fibre
development, and global gene expression. Journal of experimental botany 62: 3837-
3848, 2011.
49. Vescovi M, Zaffagnini M, Festa M, Trost P, Lo Schiavo F, and Costa A. Nuclear
accumulation of cytosolic glyceraldehyde-3-phosphate dehydrogenase in cadmiumstressed
Arabidopsis roots. Plant physiology 162: 333-346, 2013.
50. Walia H, Wilson C, Wahid A, Condamine P, Cui X, and Close TJ. Expression
analysis of barley (Hordeum vilgare L.) during salinity stress. Funct Integr Genomics
143-156, 2006.
51. Wasternack C. Jasmonates: an update on biosynthesis, signal transduction and action
in plant stress response, growth and development. Annals of botany 100: 681-697, 2007.
52. Wasternack C, and Hause B. Jasmonates: biosynthesis, perception, signal
transduction and action in plant stress response, growth and development. An update to
the 2007 review in Annals of Botany. Annals of botany 111: 1021-1058, 2013.
53. Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, and Provart NJ. An
"Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale
biological data sets. PloS one 2: e718, 2007.
54. Zhang FQ, Wang YS, Lou ZP, and Dong JD. Effect of heavy metal stress on
antioxidative enzymes and lipid peroxidation in leaves and roots of two mangrove plant
seedlings (Kandelia candel and Bruguiera gymnorrhiza). Chemosphere 67: 44-50, 2007.
55. Zhang L, Zhao G, Jia J, Liu X, and Kong X. Molecular characterization of 60
isolated wheat MYB genes and analysis of their expression during abiotic stress.
Journal of experimental botany 63: 203-214, 2012.
56. Zhang L, Zhao G, Xia C, Jia J, Liu X, and Kong X. A wheat R2R3-MYB gene,
TaMYB30-B, improves drought stress tolerance in transgenic Arabidopsis. Journal of
33
experimental botany 63: 5873-5885, 2012.
57. Zhang W, Swarup R, Bennett M, Schaller GE, and Kieber JJ. Cytokinin induces
cell division in the quiescent center of the Arabidopsis root apical meristem. Current
biology : CB 23: 1979-1989, 2013.
論文全文使用權限
  • 同意授權校內瀏覽/列印電子全文服務,於2019-09-09起公開。


  • 如您有疑問,請聯絡圖書館
    聯絡電話:(06)2757575#65773
    聯絡E-mail:etds@email.ncku.edu.tw