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Extraction of Total Proteins from Rice Plant

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Plant Science
Jan 2014



This protocol provides an efficient method for preparation of high-quality proteins from rice leaves and grains. The method involves phenol extraction to separate proteins from the non-protein components such as polysaccharides, lipids and phenolic compounds that are commonly enriched in plant tissues. Following isolation, proteins are precipitated with ammonium acetate/methanol and then solubilized for proteomic analysis. As the protocol is simple, universal, and most importantly compatible with silver staining, it has been applied to our routine protein extraction from rice and many other plant tissues and it even works fine in animal tissues for the requirement of electrophoretic separation.

Keywords: Rice (水稻), Protein extraction (蛋白质的提取), Proteomics (蛋白质组学研究), Two dimentional gel electrophresis (二维凝胶电泳), Staining methods (染色方法)

Materials and Reagents

  1. Tainung 67
    Note: TNG67, an elite japonica type rice variety, has been a leading variety in Taiwan for more than 30 years since it been released in 1978.
  2. SA0420
    Note: An aroma mutant, exhibits an agreeable taro-like flavor, was selected from the TNG67 mutation pool developed via sodium azide mutagenesis.
  3. Liquid nitrogen
  4. Acetone (Merck KGaA, catalog number: 1.00012.4000 )
  5. NH4OAc (Merck KGaA, catalog number: 1.01116.1000 )
  6. DTT (Merck KGaA, catalog number: 1.11474.0001 )
  7. CHAPS (GE Healthcare, catalog number: 17-1314-01 )
  8. HCl (Merck KGaA, catalog number: 1.09063.1000 )
  9. 2-mercaptoethanol (Sigma-Aldrich, catalog number: M6250 )
  10. 2-propanol (Merck KGaA, catalog number: 1.09634.2500 )
  11. Methanol (Merck KGaA, catalog number: 1.06007.4000 )
  12. NaCl (Merck KGaA, catalog number: 7710CN )
  13. NaOH (Merck KGaA, catalog number: 1.06469.1000 )
  14. KCl (Merck KGaA, catalog number: 1.04936.1000 )
  15. PMSF (Merck KGaA, catalog number: 52332 )
  16. Phenol (saturated, pH 6.6/7.9) (AMRESCO, catalog number: 0945 )
  17. PVPP (Merck KGaA, catalog number: 1.07302.0100 )
  18. Seasand (Merck KGaA, catalog number: 107711 )
  19. Sucrose (GERBU Biotechnik GmbH, catalog number: 1366 )
  20. Triton X-100 (GERBU Biotechnik GmbH, catalog number: 2000 )
  21. Tris-base (AMRESCO, catalog number: 0497 )
  22. Urea (AMRESCO, catalog number: 0378 )
  23. Miracloth (Calbiochem®, catalog number: 475855-1R )
  24. Extraction buffer (see Recipes)
  25. Precipitation buffer (see Recipes)
  26. 0.5 M EDTA (see Recipes)
  27. Lysis buffer (see Recipes)
  28. 40 mM PMSF (see Recipes)


  1. Mortar (Φ 9 cm) and pestle (attached with Φ 12 cm mortar) (Figure 1)

    Figure 1. Mortar and pestle

  2. Pipetman (Gilson, model: p5000 , p1000 , p200 , p100 , p20 and p10 )
  3. High-Speed Refrigerated Centrifuges and No.46 Rotor (Hitachi, model: himac CR22F )
  4. 50 ml centrifuge tube (Thermo Fisher Scientific, Nalgene®, model: 3119-0050 )
  5. -20 °C refrigerator (Firstek Scientific, model: F-25 )
  6. SpeedVac system (Thermo Fisher Scientific, model: SPD speed Vac and UVS400 universal vacuum system )
  7. Ultrasonic machine (ULTRASONIC, model: LC130H )
  8. Chemical fume hood (CHUNG FU, model: HAP-090 )


  1. Preparation of protein samples from rice leaves
    1. Cut 0.5 g fresh or -80 °C frozen leaf samples into small pieces, add little sea sand (Figure 2A) and freeze the tissue by pouring liquid nitrogen on the cut leaves in the mortar (Video 1).
    2. Grind the tissue to a fine powder, using a mortar and pestle (Figure 2B, Video 1).
    3. Add 5 ml extraction buffer and immediately grind the sample until foaming (Figure 2C, Video 1).
    4. Add 0.5 g PVPP and grind completely. Then add 5 ml extraction buffer and grind the sample until foaming (Video 1).
    5. Add 250 μl 40 mM PMSF and 5 ml extraction buffer, and then grind the mixture until foaming (Video 1).
    6. Transfer the homogenate into a sterilized 50 ml centrifuge tube (Video 1).
    7. The remaining plant material sticking on mortar and pestle is rescued by carefully rinsing mortar and pestle with 5 ml extraction buffer, and poured into the tube and mixed well with the homogenate (Video 1).
    8. Centrifuge 20 min at 15,000 rpm (in No. 46 Rotor), 4 °C.
    9. Filter the supernatant through 2 layers of Miracloth into another fresh tube (Figure 2F).
    10.  Extract the filtrate with an equal volume of buffer saturated phenol (about 16 ml). Mix well by inversion. Centrifuge 20 min at 15,000 rpm, 4 °C.
    11. Transfer the top layer (phenol phase) into another fresh tube (Figure 2G and 2H).

      Figure 2. Preparation of protein sample. A-E. Leaves were ground and extracted by extraction buffer. F-H. Protein sample was purified by phenol extraction.

    12. Extract the phenol phase with an equal volume of cold extraction buffer twice (1st 14 ml and 2nd 12 ml, respectively). Mix well by inversion. Centrifuge 20 min at 15,000 rpm, 4 °C. Recover the top layer (phenol phase).
    13. Add 3x volume of cooled precipitation buffer to the recovered phenol phase and mix well by inversion.
    14.  Incubate at -20 °C for 4 h (or even overnight) to precipitate the proteins. Then centrifuge 20 min at 15,000 rpm, 4 °C and discard the supernatant.
    15. Wash the pellet with 1.8 ml precipitation buffer twice. Recover the pellet by centrifugation at 8,000 rpm for 5 min.
    16. Wash the pellet with 1 ml of cold 100% acetone containing with 0.7 μl 2-mercaptoethanol (14.3 M). Recover the pellet by centrifugation at 8,000 rpm for 5 min.
    17. Dry the pellet by SpeedVac for about 2-3 min (less than 5 min) and resuspend in an appropriate volume of lysis buffer.
    18. The protein samples can be quantified by Bradford method (Bradford, 1976) and stored at -20 °C.
    19. The obtained protein samples can be used for proteomic analysis (Lin et al., 2014; Liu et al., 2012) or Western blot (Lin and Jeang, 2005) (Figure 3).

      Figure 3. Proteomic analysis and Western blot analysis. A. Proteomic analysis of leaf proteins from various rice varieties. B. Proteomic analysis of taro leaf proteins and western blotting probed with anti-SSSI (Lin and Jeang, 2005).

  2. Preparation of the protein samples from rice grains
    1. Freeze 0.5 g dehulled grains (rice grains without glumes) by liquid nitrogen.
    2. Place the frozen tissue in a mortar containing little seasand and liquid nitrogen. Grind the tissue to a powder with the mortar and pestle.
    3. Add 10 ml extraction buffer, contains with 140 μl 40 mM PMSF. Grind sample for 2 min or to a homogenate and then transfer into a sterilized 50 ml centrifuge tube.
    4. Centrifuge 20 min at 15,000 rpm (in No. 46 Rotor), 4 °C. Transfer the supernatant into another fresh tube.
    5. Add 3x volume of cold 0.1 M NH4OAc/Methanol/10 mM 2-mercaptoethanol to the recovered phenol phase and mix well by inversion.
    6. Incubate at -20 °C for 4 h (or overnight) to precipitate the proteins. Then centrifuge 20 min at 15,000 rpm, 4 °C and discard the supernatant.
    7. Wash the pellet with 1.8 ml 0.1 M NH4OAc/ Methanol/ 10 mM 2-mercaptoethanol twice. Recover the pellet by centrifugation at 8,000 rpm for 5 min.
    8. Wash the pellet with 1 ml of cold 100% acetone containing with 0.7 μl 2-mercaptoethanol (14.3 M). Recover the pellet by centrifugation at 8,000 rpm for 5 min.
    9. Dry the pellet by the SpeedVac system for about 2-3 min (less than 5 min) and resuspend in an appropriate volume of lysis buffer.
    10. The protein samples can be quantified by Bradford method (Bradford, 1976) and stored at -20 °C.
    11. The obtained protein samples can be used for proteomic analysis or Western blot.

Representative data

  1. Video 1. Protein extraction


  1. In this protocol, the critical steps which affect the yield and intactness of protein samples are as follows:
    1. The lyophilized sample is not recommended, because some dehydrated proteins might be difficult to dissolve in the extraction buffer.
    2. The complete homogenization can be achieved by grinding the samples in extraction buffer (see Video 1).
    3. Do not dry the pellet too long in the step B9. It takes about 2-3 min (less than 5 min). The over-dried pellet will be very difficult to resuspend and dissolve completely in the lysis buffer.
    4. Resuspension of protein sample can be achieved by placing the Eppendorf tube containing the protein solution into an ice cold ultrasonication bath (Figure 4).

      Figure 4. The dissolution of protein with ultrasonic vibration. Left panel is the ultrasonic machine. Right panel shows the protein sample is resuspending in the cold bath with ultrasonication.

  2. Phenol waste has to be stored separately in a glass bottle that can be properly sealed. Phenol waste has to be discarded according to the chemical waste regulations of respective institution.


  1. Extraction buffer
    23.96 g Sucrose
    6.05 g Tris-base
    10 ml 0.5 M EDTA (pH 8.0)
    0.75 g KCl
    250 μl HCl
    2 ml 2-mercaptoethanol
    Add dH2O to 100 ml
    Note: This buffer should be prepared freshly and pre-cooled at 4 °C.
  2. Precipitation buffer
    1.54 g NH4OAc
    140 μl 2-mercaptoethanol (14.3 M)
    Add methanol to 200 ml and stored at -20 °C
  3. 0.5 M EDTA (pH 8.0)
    186.1 g EDTA
    800 ml dH2O
    Adjust pH to 8.0 with NaOH (about 20 g NaOH)
    Add dH2O to 1,000 ml, autoclave and store at room temperature
  4. Lysis buffer
    57 g Urea
    4 ml Triton X-100
    4 g CHAPS
    484.4 mg Tris-base
    231.4 mg DTT
    Add dH2O to 100 ml, dispense in 1ml/ tube and stored at -20 °C
  5. 40 mM PMSF
    6.96 mg PMSF
    Add 2-propanol to 1 ml and stored at -20 °C


This protocol was developed by modifying the phenol-methanol method (Hurkman and Tanaka, 1986). The authors acknowledge the financial support from the Council of Agriculture (91-3112-P-055-001-Y) and the National Science Council (NSC 95-2317-B-005 -01, NSC 96-2317-B-005-01) of Taiwan to C. S. Wang. We also thank Miss Yu-Hisn Yeh at the Biotechnology Division, Taiwan Agricultural Research Institute, for helping with the preparation of pictures and videos.


  1. Bradford, M. M. (1976). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72: 248-254.
  2. Hurkman, W. J. and Tanaka, C. K. (1986). Solubilization of plant membrane proteins for analysis by two-dimensional gel electrophoresis. Plant Physiol 81(3): 802-806.
  3. Lin, D. G. and Jeang, C. L. (2005). Cloning, expression, and characterization of soluble starch synthase I cDNA from taro (Colocasia esculenta Var. esculenta). J Agric Food Chem 53(20): 7985-7990.
  4. Lin, D. G., Chou, S. Y., Wang, A. Z., Wang, Y. W., Kuo, S. M., Lai, C. C., Chen, L. J. and Wang, C. S. (2014). A proteomic study of rice cultivar TNG67 and its high aroma mutant SA0420. Plant Sci 214: 20-28.
  5. Liu, C. W., Hsu, Y. K., Cheng, Y. H., Yen, H. C., Wu, Y. P., Wang, C. S. and Lai, C. C. (2012). Proteomic analysis of salt-responsive ubiquitin-related proteins in rice roots. Rapid Commun Mass Spectrom 26(15): 1649-1660.


这个协议提供了一种从稻叶和谷物制备高质量蛋白质的有效方法。 该方法包括酚提取以从通常富含植物组织的非蛋白质组分如多糖,脂质和酚类化合物中分离蛋白质。 分离后,用乙酸铵/甲醇沉淀蛋白质,然后溶解用于蛋白质组分析。 由于协议简单,通用,最重要的是与银染色兼容,它已经应用于我们从水稻和许多其他植物组织的常规蛋白质提取,甚至在动物组织中对于电泳分离的要求很好。

关键字:水稻, 蛋白质的提取, 蛋白质组学研究, 二维凝胶电泳, 染色方法


  1. 台南67
  2. SA0420
    注意:通过 叠氮化钠诱变开发的TNG67突变库中选择了一种芳香突变体,表现出可接受的类芋香味。
  3. 液氮
  4. 丙酮(Merck KGaA,目录号:1.00012.4000)
  5. NH 4 OAc(Merck KGaA,目录号:1.01116.1000)
  6. DTT(Merck KGaA,目录号:1.11474.0001)
  7. CHAPS(GE Healthcare,目录号:17-1314-01)
  8. HCl(Merck KGaA,目录号:1.09063.1000)
  9. 2-巯基乙醇(Sigma-Aldrich,目录号:M6250)
  10. (Merck KGaA,目录号:1.09634.2500)
  11. 甲醇(Merck KGaA,目录号:1.06007.4000)
  12. NaCl(Merck KGaA,目录号:7710CN)
  13. NaOH(Merck KGaA,目录号:1.06469.1000)
  14. KCl(Merck KGaA,目录号:1.04936.1000)
  15. PMSF(Merck KGaA,目录号:52332)
  16. 苯酚(饱和的,pH6.6/7.9)(AMRESCO,目录号:0945)
  17. PVPP(Merck KGaA,目录号:1.07302.0100)
  18. Seasand(Merck KGaA,目录号:107711)
  19. 蔗糖(GERBU Biotechnik GmbH,目录号:1366)
  20. Triton X-100(GERBU Biotechnik GmbH,目录号:2000)
  21. Tris-base(AMRESCO,目录号:0497)
  22. 尿素(AMRESCO,目录号:0378)
  23. Miracloth(Calbiochem ,目录号:475855-1R)
  24. 提取缓冲液(参见配方)
  25. 沉淀缓冲液(参见配方)
  26. 0.5 M EDTA(见配方)
  27. 裂解缓冲液(见配方)
  28. 40 mM PMSF(参见配方)


  1. 砂浆(Φ9cm)和杵(附有Φ12cm砂浆)(图1)


  2. Pipetman(Gilson,型号:p5000,p1000,p200,p100,p20和p10)
  3. 高速冷冻离心机和46转子(日立,型号:himac CR22F)
  4. 50ml离心管(Thermo Fisher Scientific,Nalgene ,型号:3119-0050)
  5. -20℃冰箱(Firstek Scientific,型号:F-25)
  6. SpeedVac系统(Thermo Fisher Scientific,型号:SPD speed Vac和UVS400通用真空系统)
  7. 超声波机(ULTRASONIC,型号:LC130H)
  8. 化学通风橱(CHUNG FU,型号:HAP-090)


  1. 从水稻叶子制备蛋白质样品
    1. 将0.5g新鲜或-80℃冷冻叶样品切成小块,加入 小海沙(图2A),并通过倾倒液体冻结组织 在研钵切割的叶子上的氮气(视频1)
    2. 使用研钵和研杵将组织研磨成细粉末(图2B,视频1)
    3. 加入5毫升提取缓冲液,立即研磨样品直到发泡(图2C,视频1)
    4. 加入0.5g PVPP并完全研磨。 然后加入5毫升提取缓冲液,研磨样品直至发泡(视频1)
    5. 加入250μl40mM PMSF和5ml提取缓冲液,然后研磨混合物直至起泡(视频1)。
    6. 将匀浆转移到无菌的50ml离心管(视频1)。
    7. 剩余的植物材料粘在砂浆和杵上被救出 通过用5ml提取缓冲液小心地冲洗研钵和杵,和 倒入管中并与匀浆充分混合(视频1)
    8. 以15,000rpm离心20分钟(在No.46转子中),4℃。
    9. 将上清液通过2层Miracloth过滤到另一个新管中(图2F)
    10.  用等体积的缓冲液饱和苯酚提取滤液 (约16ml)。 通过反转混合均匀。 以15,000rpm离心20分钟,4   ℃。
    11. 将顶层(苯酚相)转移到另一个新管中(图2G和2H)

      图   2.蛋白质样品的制备。 A-E。 叶被研磨和提取   通过提取缓冲液。 F-H。 蛋白质样品通过苯酚纯化 提取
    12. 用等体积的苯酚相萃取 冷提取缓冲液两次(分别为第一次14ml和第二次12ml)。 通过反转混合均匀。 在15,000rpm,4℃下离心20分钟。 恢复 顶层(苯酚相)。
    13. 向回收的苯酚相中加入3倍体积的冷却的沉淀缓冲液,通过倒置充分混合
    14. 在-20°C孵育4小时(或甚至过夜)以沉淀 蛋白质。 然后在15,000rpm,4℃下离心20分钟并弃去 上清液
    15. 用1.8 ml沉淀缓冲液洗涤沉淀两次。 通过在8,000rpm离心5分钟来回收沉淀
    16. 用1ml含有0.7μl的冷的100%丙酮洗涤沉淀 2-巯基乙醇(14.3M)。 通过离心回收沉淀 8,000 rpm,5分钟。
    17. 通过SpeedVac干燥沉淀约2-3分钟(小于5分钟),并重悬于适当体积的裂解缓冲液中。
    18. 蛋白质样品可以通过Bradford方法(Bradford,1976)定量并储存在-20℃
    19. 获得的蛋白质样品可用于蛋白质组分析(Lin等人,   ,2014; Liu et al。,2012)或Western印迹(Lin和Jeang,2005) (图3)。

      图3.蛋白质组学分析和蛋白质印迹分析 A.来自各种水稻品种的叶蛋白的蛋白质组学分析。 乙。 芋螺叶蛋白的蛋白质组学分析和western blotting探测 与抗SSSI(Lin和Jeang,2005)。

  2. 从米粒制备蛋白质样品
    1. 通过液氮冻结0.5g脱壳谷物(无谷物的谷物)
    2. 将冷冻的组织放在含有少许海水和砂浆的砂浆中 液氮。 使用研钵将组织研磨成粉末 杵
    3. 加入10ml提取缓冲液,含有140μl40mM PMSF。 研磨样品2分钟或匀浆,然后转移到   灭菌的50ml离心管
    4. 以15,000rpm离心20分钟(在No.46转子中),4℃。 将上清液转移到另一个新管中
    5. 向回收的苯酚相中加入3倍体积的冷0.1M NH 4 OAc /甲醇/10mM 2-巯基乙醇,并通过倒置充分混合。
    6. 在-20°C孵育4小时(或过夜)以沉淀蛋白质。 然后在15,000rpm,4℃下离心20分钟,弃去上清液
    7. 用1.8ml 0.1M NH 4 OAc /甲醇/10mM洗涤沉淀 2-巯基乙醇。 通过在8,000离心回收沉淀 rpm,5分钟
    8. 用1ml冷的100%丙酮洗涤沉淀 含有0.7μl2-巯基乙醇(14.3M)。 通过回收丸   在8,000rpm离心5分钟
    9. 干燥颗粒 SpeedVac系统约2-3分钟(少于5分钟)并重悬于 适当体积的裂解缓冲液
    10. 蛋白质样品可以通过Bradford方法(Bradford,1976)定量并储存在-20℃
    11. 获得的蛋白质样品可用于蛋白质组分析或Western印迹。


  1. 视频1.蛋白质提取
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  1. 在本协议中,影响蛋白质样品的产量和完整性的关键步骤如下:
    1. 不建议使用冻干样品,因为有些脱水 蛋白质可能难以溶解在提取缓冲液中
    2. 完全均匀化可以通过在提取缓冲液中研磨样品来实现(见视频1)
    3. 在步骤B9中不要将颗粒干燥太久。 它需要大约2-3分钟 (小于5分钟)。 过度干燥的丸将非常困难 重悬并完全溶解在裂解缓冲液中
    4. 蛋白质样品的重悬可以通过放置Eppendorf来实现 将含有蛋白质溶液的管置于冰冷的超声波处理中 浴(图4)

      图4.用超声波溶解蛋白质 左面板是超声波机。 右面板显示 蛋白质样品在超声波处理的冷浴中重悬。

  2. 苯酚废物必须单独存放在可以正确密封的玻璃瓶中。 苯酚废物必须根据相关机构的化学废物规定进行废弃


  1. 提取缓冲区
    10ml 0.5M EDTA(pH8.0) 0.75克KCl
    2ml 2-巯基乙醇 将dH <2> O添加到100 ml
  2. 降雨缓冲液
    1.54g NH 4 OAc
    140μl2-巯基乙醇(14.3M) 加入甲醇至200ml,贮存于-20℃
  3. 0.5 M EDTA(pH 8.0)
    186.1g EDTA
    800ml dH 2 O
    用NaOH(约20g NaOH)将pH调节至8.0 将dH 2 O加入到1,000ml中,高压灭菌并在室温下贮存
  4. 裂解缓冲液
    4ml Triton X-100 4克CHAPS
    484.4mg Tris-碱
    将dH 2 O加到100ml中,以1ml /管分配并储存在-20℃下。
  5. 40mM PMSF
    6.96mg PMSF


该方案通过改进苯酚 - 甲醇法(Hurkman和Tanaka,1986)开发。作者承认农业理事会(91-3112-P-055-001-Y)和国家科学理事会(NSC 95-2317-B-005 -01,NSC 96-2317-B-005- 01)。我们还感谢台湾农业研究所生物技术部的Yu-Hisn Yeh小姐帮助准备图片和视频。


  1. Bradford,M.M。(1976)。 利用蛋白质染料结合原理的快速灵敏的微克量蛋白定量方法。 Anal Biochem 72:248-254。
  2. Hurkman,W.J.and Tanaka,C.K。(1986)。 通过二维凝胶电泳分析植物膜蛋白的溶解性。植物生理学81(3):802-806。
  3. Lin,D.G。和Jeang,C.L。(2005)。 来自芋头的可溶性淀粉合成酶I cDNA的克隆,表达和表征( Colocasia esculenta Var。 esculenta )。 J Agric Food Chem 53(20):7985-7990。
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引用:Lin, D. and Wang, C. (2014). Extraction of Total Proteins from Rice Plant. Bio-protocol 4(21): e1277. DOI: 10.21769/BioProtoc.1277.



Bianca Oranga
Manila Tytana Colleges
Hi! i am hoping to make a research that includes extraction of proteins from rice. This method is for the rice plant itself or the leaves. So i was wondering, can i use this experiment but on rice grains? To be specific, im doing the research on brown rice and Quinoa
8/26/2018 3:40:10 AM Reply
Chang-Sheng Wang
Department of Agronomy, National Chung-Hsing University, Taiwan

Dear Blanca,
It is okay to use this protocol to extract the proteins from seeds (of rice and Quinoa).
But you have to use the large (>1:10 ~ 1:20) volume of buffer in extraction because seeds contain high protein content.
Good luck!

8/26/2018 5:41:24 PM