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標題: Proteomic Analysis of Glutinous Rice and Improvement of Mass Spectrometric Approach for Identification of Phosphopeptides
作者: 劉志偉
Liu, Chih-Wei
關鍵字: 糯稻;glutinous rice;澱粉生合成;質譜儀;電子轉移裂解;starch biosynthesis;Mass Spectrometry;electron-transfer dissociation
出版社: 分子生物學研究所
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Rice (Oryza sativa) is one of the most important cereals in the world. The grains of the rice are the important source of starch, and starch biosynthesis is the major metabolic pathway in the developing grains. Starch consists of the amylose and amylopectin. The starch reserves of the rice grains generally contain more than 75% amylopectin; however, the abundance of amylose can affect the properties of starch in the grains. The amylase contents in the grains are usually used to evaluate the quality of rice. Therefore, the mechanisms of starch biosynthesis (especially amylase) are widely discussed and studied recently. In this study, we use the Tainung 67 (TNG67) and its sodium azide-induced mutant SA0419 as the investigated materials. The low amylose content in SA0419 grains (8%) is apparently different from TNG67 grains (20%). Moreover, the superior efficiency of starch biosynthesis and shorter developing period are observed in SA419. We want to resolve the regulated mechanisms of starch biosynthesis in rice endosperm from protein expression level and to provide the useful information for further agriculture breeding and gene study.
Endosperm proteome of the grains of 14 days after anthesis (DAA) were extracted and separated by 2D-PAGE (pI 4-7). MS-based protein identification strategy was used to analyze the total proteome and differential-expression proteome of TNG67 and SA0419. The qualitative database of endosperm soluble proteome in TNG67 grains was established, and 620 out of 726 protein spots were successful identified. Endosperm proteome major involved in carbohydrate metabolic process, and the final products of α-D-glucose-1P were produced and as the substrates for starch biosynthesis. Moreover, total 121 protein spots were determined as the differential-expression proteome between TNG67 and SA0419 after software analysis. The higher abundance of enzymes in SA0419 were used to produce the more α-D-glucose-1P, and high level of starch biosynthesis enzyme ( were generated to produce the ADP-glucose and to accelerate the accumulations of starch. Furthermore, lack of granule-bound starch synthase (GBSS) in SA0419 is the major key factor to cause the low amylose content. Overall, the starch biosynthesis model in the rice endosperm was presented in this study. The increased in gluconeogenesis pathway and reduction of the other metabolism pathway in SA0419 elevated the substrate contents for starch biosynthesis. The enzymes of, and debranching enzyme (PUL) was highly expressed to accelerate the accumulation of starch and shorten the developing periods.
In the past decade, tandem mass spectrometry (MS/MS) has played a major role in the bottom-up approach of protein identification and post-translational modifications (PTMs) analysis. Collision-induced dissociation (CID) is the most widely used peptide fragmentation technique in protein identification; however, it has the limitations for PTMs analysis. The emerging ion activation method, electron-transfer dissociation (ETD), has been shown to be useful for investigating PTMs and identifying large peptides and small proteins. There are specific problems in double-charged phosphopeptides identification by CID and ETD methods, and lack of the unsuitable searching algorithms. Thus, in this study, we demonstrated that the ET/CID fragmentation is powerful for sequencing of doubly-charged phosphopeptides without spectra-processing and successfully improves the applications of ETD technique in phosphorylation analysis.

水稻是世界上最重要的穀類作物之一。水稻的澱粉儲存器官-穀粒(種子),是重要的澱粉來源,榖粒之充實內容物以澱粉為主。澱粉可分為直鏈性澱粉(amylose)與支鏈性澱粉(amylopectin),amylopectin是澱粉的主要成分,通常佔有75%以上。然而,amylose的含量可決定澱粉的特性,高含量amylose會造成飯粒之柔軟度、黏著度、色澤、光澤等食味品性質之下降,amylose含量亦常被用來作為米質之評估指標,所以,對於澱粉(特別是直鏈性澱粉)之合成因子廣受研究與探討。本研究以水稻台農67號(TNG67)及其糯性突變株SA0419作為研究材料,SA0419穀粒內的amylose含量只有8%;相對於TNG67穀粒所含20% amylose,具有明顯差異;另一方面,SA0419發育期的穀粒澱粉充實速率相對於TNG67較快速,且成熟期提早一星期。於此,欲從蛋白質表現層次解析、了解水稻胚乳澱粉生合成與調控的機制,以利後續的水稻育種與基因研究。
萃取抽穗後第14天的穀粒胚乳蛋白質體,透過二維凝膠電泳分離蛋白質點,對TNG67與SA0419的蛋白質體與差異表現蛋白質體進行全面的定性,建構TNG67穀粒胚乳可溶性蛋白質體全定性資料庫,共定性726個蛋白質點,其中620個蛋白質點可成功鑑定其身分,此結果可幫助後人在研究其他水稻突變體胚乳差異表現蛋白質體,能快速得知其身分,作為參考資料庫使用。胚乳蛋白質體所參與的胚乳生理反應,主要是參與醣類相關代謝路徑,再細分這些牽涉路徑發現,酵素主要往α-D-glucose-1P的生成反應,可作為澱粉生合成的受質,供給澱粉生合成酵素使用。透過比對軟體判定SA0419的表現蛋白質體,共121個蛋白質點被判定為具有差異表現量,發現SA0419表現更多的酵素可幫助累積α-D-glucose-1P;且SA0419具有更高的澱粉生合成酵素表現量(幫助合成ADP-glucose,加速澱粉累積。另外,SA0419缺少GBSS表現,是影響SA0419直鏈性澱粉含量偏低的主因。最後透過人工重新判定所有參與醣類生合成酵素的表現量,提出水稻穀粒胚乳澱粉生合成路徑模型,分析SA0419具有比TNG67較快的澱粉充實速率、較短充實期的特性,是由於SA0419提升gluconeogenesis的生合成反應,並減低其他代謝路徑的表現,使得供給澱粉生合成的受質相對提升含量,再加上2.7.7.27、與debranching enzyme(PUL)較強烈的表現,使澱粉累積加快,縮短充實期,並且不影響SA0419的總澱粉含量。
近年來,以質譜為基礎的蛋白質體學發展快速,其中,蛋白質身分鑑定與後轉譯修飾分析為質譜在蛋白質體學領域的主要研究內容,目前常用的碰撞引致裂解(collision-induced dissociation,CID),是最常應用於蛋白質身分鑑定分析,但對於後轉譯修飾分析上,仍存在許多缺點;電子轉移裂解(electron-transfer dissociation,ETD)雖是新興的片段化方法,較適合用於大片段的胜肽與後轉譯修飾研究,然而,碰撞引致裂解與電子轉移裂解對於正二價磷酸化鑑定分析仍有其各自缺陷,且有電腦比對演繹法軟體無法完全適應的問題,常造成正二價磷酸化胜肽鑑定上的困難,在本實驗,我們提出的ET/CID裂解策略,可以很容易鑑定到正二價磷酸化胜肽的身分,且不需任何圖譜處理,成功改善正二價磷酸化鑑定的效率,提升電子轉移裂解對於正二價磷酸化分析的應用性。
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