Evaluation of Protein Extraction Methods for Vitis vinifera Leaf and Root Proteome Analysis by Two-Dimensional Electrophoresis

An efficient protein extraction method is crucial to ensure successful separation by two-dimensional electrophoresis(2-DE)for recalcitrant plant species, in particular for grapevine(Vitis vinifera L.). Trichloroacetic acid-acetone(TCA-acetone)and phenol extraction methods were evaluated for proteome analysis of leaves and roots from the Tunisian cultivar 'Razegui'. The phenol-based protocol proved to give a higher protein yield,a greater spot resolution, and a minimal streaking on 2-DE gels for both leaf and root tissues compared with the TCA-based protocol. Furthermore, the highest numbers of detected proteins on 2-DE gels were observed using the phenol extraction from leaves and roots as compared with TCA-acetone extraction.     

Evaluation of sample extraction methods for proteomic analysis of coniferous seeds

In this study, three methods of protein extraction from the seeds of the Chinese fir were compared by examining the quality (including the number of protein spots observed) in the two-dimensional gel electrophoresis (2-DE), obtained by isoelectric focusing and sodium dodecyl sulfate polyacrylamide gel electrophoresis of the total released protein. Three protein extraction methods were: TCA-acetone precipitation, SDS extraction/acetone precipitation, and phenol extraction methanol/ammonium acetate precipitation. The results showed that TCA-acetone precipitation was the most effective method for protein extraction; it gave the highest yield of total protein (8.9 mg protein per g seed weight) and the greatest number of proteins spots (1,034 spots) on the 2-DE gel. Further, several proteins were identified by liquid chromatography mass spectrometry (LC MS/MS), which are legumin-like storage protein, similar to AMP binding/acetate-CoA ligase, similar to 40S ribosomal protein S20, actin, ascorbate peroxidase, Similar to cysteine synthase, and unknown protein. These data demonstrates that TCA-acetone precipitation followed by 2-DE and LC MS/MS is a suitable method for proteomic analysis of coniferous species, such as Chinese fir and provides a valuable starting point for similar proteomic analysis of other coniferous tree species.     

建立和优化双向电泳分析柱花草根系蛋白谱的方法

本研究以柱花草根系为材料,比较了不同蛋白质提取方法和蛋白上样量等因素对双向电泳方法分析根系蛋白图谱的影响。结果表明,在苯酚法提取蛋白中,加入0.7mol·L-1NaCl和20%乙醇,并在蛋白沉淀过程中加入1/10倍体积5mol·L-1NaCl,能够有效去除组织样品中的非蛋白成分,结合使用pH4～7范围的IPG胶条,1mg根系蛋白可以在双向电泳图谱上分辨出较多蛋白点,图谱背景清晰,该体系适合柱花草根系蛋白质的双向电泳分析。     

Method development for analysis of proteins extracted from the leaves of Orthosiphon aristatus

Orthosiphon aristatus is a traditionally used medicinal plant. In order to study the proteome of the plant, we have developed a simple plant protein extraction method by direct extraction of protein using a modified 2D-gel compatible tris-sucrose buffer followed by a double TCA-acetone precipitation. This method omitted the use of toxic phenol which is widely used in the studies of plants proteins. Moreover, it shortens the lengthy extraction procedure of phenol extraction and back-extraction method and therefore reduced the extraction time (by 2h) while increased in protein yields (by 50%). Comparison of the 2D-gel images of the two extracts revealed that >60 extra protein spots were detected in the extract of our current method. The method was applied on the leaves of O. aristatus collected from six geographical areas in Malaysia. The correlation coefficient of each replicate gels from the six areas ranged from 0.70 to 0.90 indicating good reproducibility of the method.     

Evaluation of three different protocols of protein extraction for Arabidopsis thaliana leaf proteome analysis by two-dimensional electrophoresis

This work was performed to compare three precipitation protocols of protein extraction for 2-DE proteomic analysis using Arabidopsis leaf tissue: TCA-acetone, phenol, and TCA-acetone-phenol. There were no statistically significant differences in protein yield between the three methods. Samples were subjected to 2-DE in the 5 to 8 pH and 14-80 kDa ranges. The TCA-acetone-phenol protocol provided the best results in terms of spot focusing, resolved spots, spot intensity, unique spots detected, and reproducibility. In all, 93 qualitative or quantitative statistically significant differential spots were found between the three protocols. The 2-DE map of TCA-acetone-phenol extracts presented more resolved spots above 40 kDa, with no pI-dependent differences observed between the three protocols. 54 spots were selected for trypsin digestion, and the peptides were analyzed by MALDI-TOF-TOF MS. After database search using peptide mass fingerprinting, and MS/MS combined search, 30 proteins were identified, the proteins from chloroplastic photosynthetic and carbohydrate metabolism being those most highly represented. From these data, we were able to conclude that each extraction protocol had its main features. Considering this, the workflow of any standard comparative proteomic experiment should include the optimization and adaptation of the protein extraction protocol to the plant tissue and to the particular objective pursued.     

蝴蝶兰叶片蛋白质双向电泳方法初探

针对蝴蝶兰叶片蛋白质含量少且含有大量色素和酚等干扰物质的特点,通过对总蛋白提取方法、银染方法的改进,以及双向电泳实验条件的比较选择,初步建立一套适用于蝴蝶兰叶片蛋白质组分析的双向电泳技术。     

用于双向凝胶电泳分析的奶牛乳清蛋白样品制备方法的比较

为建立适用于双向凝胶电泳分析的奶牛乳清蛋白的制备方法,分别比较了直接裂解法、三氯乙酸-丙酮法,Trizol法和2-D clean up kit法对奶牛乳清蛋白提取效率和双向凝胶电泳图谱的影响.用2-D Quant Kit试剂盒测定蛋白浓度,分别用十二烷基磺酸钠 聚丙烯酰胺凝胶电泳和双向凝胶电泳进行奶牛乳清蛋白的分离.蛋白定量结果表明,2-D clean up kit法产率最高,直接裂解法、三氯乙酸-丙酮法次之,trizol法产率最低;十二烷基磺酸钠-聚丙烯酰胺凝胶电泳结果表明,2- D clean up kit法提取的蛋白质量最高;双向电泳图谱分析表明,2-D clean up kit法得到的蛋白图谱与另外3种方法相比,检测到的蛋白点最多,图谱背景清晰,分辨率最高.结果提示,2-D clean-up法相对最适合于双向凝胶电泳分析奶牛乳清蛋白样品的制备,尤其对一些低丰度高分子量蛋白的分离效果较为明显.     

红肉蜜柚汁胞蛋白质双向电泳体系优化研究

为建立适合红肉蜜柚发育过程中汁胞蛋白质组学的研究体系,以着色初始时期的红肉蜜柚汁胞为试材,摸索最适合的蛋白质双向电泳体系参数。结果表明,酚提取法比TCA-丙酮法更适合于红肉蜜柚汁胞总蛋白质的提取,提取得率高,双向电泳图谱清晰。采取18 cm、线性pH 3～10 和18 cm、线性pH 4～7 相结合的分析策略,可获得更为完整的蛋白质组信息,其第一向等电聚焦最佳参数（总伏小时数）分别为30 000 Vhs和43 000 Vhs。     

蝴蝶兰叶片蛋白质提取及双向电泳体系优化

通过对蛋白质提取、IPG胶条选择、上样量、水化方式、聚焦条件等方面的优化,建立蝴蝶兰叶片蛋白质的双向电泳体系。结果表明,采用酚抽提法提取蝴蝶兰叶片蛋白质的纯度较高,复溶较完全;双向电泳优化体系选用24 cm pH 3～10 NL的IPG胶条,被动水化,上样量为1.35 mg,B1程序进行等电聚焦,12%分离胶进行第二向电泳,考马斯亮蓝G-250染色。该方法获得分辨率较高、重复性较好的蝴蝶兰叶片双向电泳图谱,蛋白数点多达1163个,可以满足蝴蝶兰蛋白质组学研究和分析。     

灵芝子实体原基双向电泳和总蛋白质提取方法的建立

比较了Tris-饱和酚法和三氯乙酸(TCA)/丙酮沉淀法对灵芝子实体原基总蛋白质的提取效果。用Image Master 2D Platinum6.0软件分析两种方法所提蛋白质的双向电泳图谱,分别得到565和273个蛋白质点;(TCA)/丙酮沉淀法在碱性端低分子量区域有些蛋白质斑点存在拖尾现象,Tris-饱和酚法能有效去除样品中的盐分,使蛋白质的聚焦效果更好,蛋白点数增加。Tris-饱和酚法可做为灵芝子实体原基总蛋白质的提取方法并为其他药用真菌总蛋白质的提取提供参考,同时为本实验室后续研究灵芝双向性固体发酵雷公藤的蛋白差异表达奠定了基础。     

适用于盐生植物的双向电泳样品制备方法

比较了三氯乙酸,丙酮沉淀法（TCA）、三氯乙酸沉淀法（E-TCA）和酚抽法（Phe）3种方法对盐生植物盐角草（Salicornia europaea L．）总蛋白的提取效果。3种方法分别得到579、343和535个蛋白点;TCA和E-TCA法所得图谱均存在严重的横向纹理,Phe法所得图谱则背景干净,基本上没有纹理。说明Phe法不仅能很好地提取盐角草蛋白,而且能有效去除样品中的盐分。对Phe法的提取液进行了改进,所得图谱背景更加清晰,蛋白点数增加。为其他盐生植物以及嗜盐微生物蛋白质的提取提供了重要参考。     

适用于双向电泳分析的水稻悬浮细胞外分泌蛋白提取方法

目的:建立适用于双向电泳分析的水稻悬浮细胞外分泌蛋白提取方法。方法:采用酚抽提结合甲醇醋酸铵沉淀法、三氯乙酸-丙酮沉淀法和硫酸铵沉淀等3种方法制备水稻悬浮细胞外分泌蛋白,并进行双向电泳分析;利用Western印迹对候选方法提取的外分泌蛋白进行纯度检测。另外,还利用质谱技术对从双向电泳胶上随机挑选的9个蛋白点进行测定,并用SignalP 3.0 Server对测定的蛋白点进行信号肽预测。结果:酚抽提结合甲醇醋酸铵沉淀法提取的外分泌蛋白得率最高,且双向电泳图谱清晰,并能检测到最多的蛋白点;Western印迹表明利用该法所提取的外分泌蛋白未被细胞内蛋白质污染。利用质谱技术鉴定了随机挑选的9个蛋白点,SignalP 3.0 Server分析表明其中6个蛋白含有信号肽。结论:酚抽提结合甲醇醋酸铵沉淀法是一种适用于双向电泳分析的水稻悬浮细胞外分泌蛋白提取方法。     

Comparison of Different Protein Extraction Methods for Gel-Based Proteomic Analysis of <Emphasis Type="Italic">Ganoderma</Emphasis> spp.

Ganoderma species are a group of fungi that have the ability to degrade lignin polymers and cause severe diseases such as stem and root rot and can infect economically important plants and perennial crops such as oil palm, especially in tropical countries such as Malaysia. Unfortunately, very little is known about the complex interplay between oil palm and Ganoderma in the pathogenesis of the diseases. Proteomic technologies are simple yet powerful tools in comparing protein profile and have been widely used to study plant–fungus interaction. A critical step to perform a good proteome research is to establish a method that gives the best quality and a wide coverage of total proteins. Despite the availability of various protein extraction protocols from pathogenic fungi in the literature, no single extraction method was found suitable for all types of pathogenic fungi. To develop an optimized protein extraction protocol for 2-DE gel analysis of Ganoderma spp., three previously reported protein extraction protocols were compared: trichloroacetic acid, sucrose and phenol/ammonium acetate in methanol. The third method was found to give the most reproducible gels and highest protein concentration. Using the later method, a total of 10 protein spots (5 from each species) were successfully identified. Hence, the results from this study propose phenol/ammonium acetate in methanol as the most effective protein extraction method for 2-DE proteomic studies of Ganoderma spp.     

中枢神经蛋白质组分析中双向电泳技术的建立

建立和优化了中枢神经组织蛋白质组分析所需的双向电泳及相关技术.由于中枢神经组织结构的特殊性,样品处理非常困难.对样品液组成、样品处理、上样方式、上样量、IPG胶条和SDS-聚丙烯酰胺凝胶电泳染色方法和保存等相关技术进行了比较研究和条件优化后,以固相pH梯度等电聚焦为第一向和SDS均一胶（T=12.5%）的水平电泳为第二向,成功地得到了神经组织双向电泳图谱.     

DMSO, an Organic Cleanup Solvent for TCA/Acetone-Precipitated Proteins, Improves 2-DE Protein Analysis of Rice Roots

Protein extraction is a critical step in a two-dimensional electrophoresis (2-DE)-based proteomic analysis. Dimethyl sulfoxide (DMSO), a small organic molecule, is widely used as a solvent in biological sciences. In this study, we modified the cleanup step of the commonly used trichloroacetic acid (TCA)/acetone method of protein extraction by using 20?% DMSO/acetone as a solvent to wash TCA?Cacetone-precipitated pellets. The improved protocol (TCA/acetone?CDMSO) was compared with the TCA/acetone and phenol extraction method based on the protein yield, the number of spots, and resolution on 2-DE maps. TCA/acetone?CDMSO washing increased protein yield, and improved the resolution in 2-DE with less background, streaking, and smearing. This method also produced the highest number of protein spots. To our knowledge, the present study is the first to use DMSO as a cleanup solvent for TCA/acetone-precipitated proteins to enhance their quality prior to 2-DE.     

A Comparison of Protein Extraction Methods Suitable for Gel-Based Proteomic Studies of Aphid Proteins

Protein extraction methods can vary widely in reproducibility and in representation of the total proteome, yet there are limited data comparing protein isolation methods. The methodical comparison of protein isolation methods is the first critical step for proteomic studies. To address this, we compared three methods for isolation, purification, and solubilization of insect proteins. The aphid Schizaphis graminum, an agricultural pest, was the source of insect tissue. Proteins were extracted using TCA in acetone (TCA-acetone), phenol, or multi-detergents in a chaotrope solution. Extracted proteins were solubilized in a multiple chaotrope solution and examined using 1-D and 2-D electrophoresis and compared directly using 2-D Difference Gel Electrophoresis (2-D DIGE). Mass spectrometry was used to identify proteins from each extraction type. We were unable to ascribe the differences in the proteins extracted to particular physical characteristics, cell location, or biological function. The TCA-acetone extraction yielded the greatest amount of protein from aphid tissues. Each extraction method isolated a unique subset of the aphid proteome. The TCA-acetone method was explored further for its quantitative reliability using 2-D DIGE. Principal component analysis showed that little of the variation in the data was a result of technical issues, thus demonstrating that the TCA-acetone extraction is a reliable method for preparing aphid proteins for a quantitative proteomics experiment. These data suggest that although the TCA-acetone method is a suitable method for quantitative aphid proteomics, a combination of extraction approaches is recommended for increasing proteome coverage when using gel-based separation techniques.     

果实蛋白质组学研究的实验方法

双向电泳技术是蛋白质组学研究的基本方法之一。果实由于富含糖、多酚、单宁和有机酸等物质,蛋白质的提取比其它植物组织更加困难。本文主要介绍不同果实蛋白质的提取、等电聚焦系统和凝胶染色技术,并建立了一套适用于桃、樱桃、苹果、芒果和冬枣等多种果实蛋白质组学的研究方法。结果表明,采用匀浆法和酚抽提法提取果实的蛋白质,裂解缓冲液2溶解蛋白质,并用固相pH梯度进行等电聚焦,可以获得背景清晰和分辨率高的凝胶图谱,具有较好的重复性,可用于果实蛋白质组学的研究。我们的研究结果显示,固相干胶条与IEF管胶相比,具有更加明显的优势。而不同的染色方法,对结果影响不大。     

2-DE-based proteomic analysis of common bean (Phaseolus vulgaris L.) seeds

Common bean (Phaseolus vulgaris L.) is the most important grain legume for direct human consumption. Proteomic studies in legumes have increased significantly in the last years but few studies have been performed to date in P. vulgaris. We report here a proteomic analysis of bean seeds by two-dimensional electrophoresis (2-DE). Three different protein extraction methods (TCA-acetone, phenol and the commercial clean-up kit) were used taking into account that the extractome can have a determinant impact on the level of quality of downstream protein separation and identification. To demonstrate the quality of the 2-DE analysis, a selection of 50 gel spots was used in protein identification by mass spectrometry (MALDI-TOF MS and MALDI-TOF/TOF). The results showed that a considerable proportion of spots (70%) were identified in spite of incomplete genome/protein databases for bean and other legume species. Most identified proteins corresponded to storage protein, carbohydrate metabolism, defense and stress response, including proteins highly abundant in the seed of P. vulgaris such as the phaseolin, the phytohemagglutinin and the lectin-related α-amylase inhibitor.     

棉花纤维蛋白质3种提取及二维电泳方法的比较

高质量的蛋白样品制备是进行二维电泳的先决条件.棉花纤维中含有纤维素、多酚、多糖等严重干扰二维电泳的物质, 增加了蛋白提取和二维电泳的难度.分别采用3种提取植物组织蛋白的方法(水法、酚法和尿素法), 提取棉纤维总蛋白, 进而进行了二维电泳分析.在蛋白产量、蛋白纯度和电泳图谱等方面对3种方法进行了比较, 结果采用酚法提取的样品取得了较好的电泳图谱, 有望成为从棉纤维样品中提取总蛋白的可选方法.     

柑橘叶片和果皮总蛋白质提取及双向电泳体系的建立

以春甜橘(Citrus reticulata Blanco‘Chuntianju’)果皮和叶片为材料,分别用Tris-HCl、尿素/硫脲(Thi/Urea)、三氯乙酸/丙酮(TCA)和酚(Phe)等4种方法提取柑橘总蛋白质,从蛋白质产量、单向SDS-PAGE和双向电泳等方面进行比较。结果表明,4种方法的分离效果存在较大差异,不论是以柑橘叶片还是果皮为材料,均以TCA法最好,且双向电泳图谱分辨率较好,蛋白点清晰、均匀、基本没有条纹,且蛋白点多。这说明TCA法不仅能很好地去除柑橘果皮、叶片中存在的大量干扰物质,而且还能得到稳定的蛋白点。