Sequential solubilization of proteins precipitated with trichloroacetic acid in acetone from cultured Catharanthus roseus cells yields 52% more spots after two-dimensional electrophoresis

Sample preparation is still the most critical step in two-dimensional gel electrophoresis (2-DE), and needs to be optimized for each type of sample. To analyze the proteome of the medicinal plant Catharanthus roseus, we developed and evaluated a sequential solubilization procedure for the solubilization of proteins after precipitation in trichloroacetic acid and acetone. The procedure includes solubilization with a conventional urea buffer followed by a stronger solubilizing buffer containing thiourea. The sequential solubilization of the precipitated proteins results in very different spot patterns following 2-DE. The number of protein spots which could be detected in both samples of the sequential solubilization was only about 10% of the total number of spots. Compared to solubilization in a single step, the total number of spots that could be detected in the sequential solubilization procedure was increased by 52%. The method described is simple and is applicable to different types of plant tissue.     

Solubilization of plant membrane proteins for analysis by two-dimensional gel electrophoresis

A plasma membrane-enriched fraction prepared from barley roots was analyzed by two-dimensional gel electrophoresis. Four methods of sample solubilization were assessed on silver stained gels. When membranes were solubilized with 2% sodium dodecyl sulfate followed by addition of Nonidet P-40, gels had high background staining and few proteins because of incomplete solubilization. Gels of membranes solubilized in urea and Nonidet P-40 had a greater number of proteins but proteins with molecular weights greater than 85,000 were absent and proteins with low molecular weights were diffuse. High molecular weight proteins were present in gels of membranes solubilized in 4% sodium dodecyl sulfate followed by acetone precipitation but background staining and streaking remained a problem. Gels of the best quality were obtained when membrane proteins were extracted with phenol and precipitated with ammonium acetate in methanol; background staining and streaking were diminished and proteins were clearly resolved. This method makes possible the resolution required for meaningful qualitative and quantitative comparisons of protein patterns on two-dimensional gels of plant membrane proteins.     

Solubilization of membrane proteins for two-dimensional gel electrophoresis: identification of sarcoplasmic reticulum membrane proteins

Solubilization of membrane proteins for two-dimensional electrophoresis (2DE) is very difficult. In this study, we report the use of 1,2-diheptanoyl-sn-glycero-3-phosphatdiyl choline (DHPC) as a detergent to solubilize integral membrane proteins for 2DE. Rat ventricular microsomal fractions enriched with sarco(endo)plasmic reticulum (SR) membrane proteins were used as a model system. Compatibility of DHPC with a high concentration of urea increases the solubility of proteins compared with sulphobetaines or ASB-14. Peptide mass analysis assisted in the identification of key SR membrane proteins including SR Ca(2+) ATPase and other membrane proteins, which have not previously been reported on 2DE. These results suggest that DHPC is a better detergent for solubilizing membrane proteins and may be useful in generating proteomic maps for most complex organelles including SR.     

Solubility of peptides in trichloroacetic acid (TCA) solutions. Hypothesis on the precipitation mechanism

The assessment of proteolysis levels is often achieved by global quantification of the peptides soluble at different TCA concentrations, but little information is available on the features of this precipitation mechanism. Peptic, tryptic and chymotryptic digests of alpha s1, beta, and kappa caseins have been prepared and fractionated by RP-HPLC and each isolated peptide was identified. Each digest was precipitated by adding TCA to different final concentrations (2, 4, 8, and 12%). The soluble fraction was analysed by RP-HPLC. Relationships have been searched between the properties of 75 peptides obtained in this way, and their solubilities in TCA. The best correlation was found with the peptide retention time in RP-HPLC, which can be regarded as the experimental measure of peptide hydrophobicity. We concluded that TCA, by interacting with peptides, induces an increase of the hydrophobicity of peptides which can lead to aggregation through hydrophobic interactions.     

三氯乙酸(TCA)提取法与微波提取法检测活性污泥中三磷酸腺苷(ATP)

【目的】针对活性污泥法中的重要参数ATP进行研究分析,通过在不同条件下检测污泥的活性,得出以ATP为指标的污泥活性状态,为准确判定活性污泥的活性提供依据。【方法】分别运用三氯乙酸(TCA)提取法及微波提取法检测活性污泥中的ATP,并对检测ATP的影响因素(TCA浓度、冰浴时间、p H、微波频率及时间等)进行探讨与优化。【结果】运用TCA提取法检测ATP时,在1.0%-7.0%的TCA体积百分数内,活性污泥中TCA最佳体积百分数为2.5%;在2-60 min的冰浴时间内,最佳冰浴时间为10 min;三羟甲基丙烷-乙二胺四乙酸(Tris-EDTA)缓冲液的最佳p H 7.5;运用微波提取法检测ATP适宜的微波辐射条件为:功率800 W,辐射时间15 s。【结论】TCA提取法和微波提取法均可以检测活性污泥中的ATP,但与微波提取法相比,TCA提取法更能保证从细胞内释放出来的ATP的完整性,因此TCA提取法更适合用于检测活性污泥中的ATP。     

Solubilization of fish proteins using immobilized microbial cells

Cells of Bacillus megaterium, Aeromonas hydrophila, and Pseudomonas marinoglutinosa were immobilized in calcium alginate. The immobilized cells secreted protease when held in fish meat suspension in water. The enzyme synthesis by the entrapped cells was supported by small amounts of soluble nutrients present in the meat. The secreted protease solubilized the fish meat, solubilization being optimum at pH range of 7.5 to 9.5 and at 50 degrees C. Under these conditions immobilized B. megaterium was most efficient giving 30% solubilization of the meat, followed by A. hydrophila (18%), while immobilized P. marinoglutinosa was less effective. The optimum ratio of fish meat to beads was about 4:3 for B. megaterium and A. hydrophila. The beads had a storage life of 30 days at 4 degrees C. The results suggested potential for use of immobilized microbial cells having extracellular protease activity to enhance solubility of waste proteins. A prototype reactor with beads holding assembly was fabricated which could recover the beads from the meat slurry after the treatment.     

High-resolution two-dimensional electrophoresis of plant proteins

A technique for the analysis of plant proteins from seed, leaf, root, and coleoptile tissues by high resolution two-dimensional electrophoresis is described. This technique is based primarily on the procedure of P. O'Farrell (1975, J. Biol. Chem. 250, 4007-4021); however, a number of improvements and simplifications have been introduced. We have found that resolution of polypeptides from a range of plant tissues is improved if the concentrations of nonionic detergent and ampholytes used in the isoelectric focusing (IEF) step are increased to 4 and 5% (w/v), respectively. Further increase in the concentrations of these two components results in gels of decreased resolution and low mechanical strength. We have also found that substitution of n-octyl beta-D-glucopyranoside or 3-[(cholamidopropyl)dimethylammonio]-1-propanesulfonate for Triton X-100 or Nonidet-P40 in the IEF dimension significantly increases the resolution of polypeptides in these gels. This technique also allows minor polypeptide differences between closely related cultivars of plants to be identified.     

Synthesis of chiral arogenic acid via immobilized microbial proteins

Although l-(8S)-arogenate has been recognized as a potential precursor of l-phenylalanine or l-tyrosine biosynthesis for only a few years, it is widely distributed in nature. The biochemical formation of arogenate has involved its isolation from the culture supernatant of a mutant strain of Neurospora crassa, a lengthy procedure of 20-day duration. We now report an improved approach using immobilized crude enzyme extracts from a cyanobacterium. The starting materials, chorismic acid or prephenic acid, are readily available, and overall yields ranging from 40 to 60% are obtained. The whole procedure takes only 1 day. Crude, unfractionated enzyme extracts from Synechocystis sp. ATCC 29108 are immobilized on a phenoxyacetyl cellulose solid support. The hydrophobic binding of the extract proteins did not denature chorismate mutase or prephenate aminotransferase, the enzymes catalyzing the conversion of chorismate to prephenate and prephenate to arogenate, respectively. This microbial system was ideally suited for preparation of arogenate, since other enzyme activities which might compete for prephenate or chorismate as substrates, or which might further metabolize arogenate, were absent or inactive under the conditions used. In addition to the substrates prephenate or chorismate, pyridoxal-5′-phosphate (the coenzyme required for transamination), as well as leucine (amino donor for transamination of prephenate), was added. The reaction product, arogenate, was separated from the starting materials by preparative thin-layer chromatography.     

Assay of plant proteins with bicinchoninic acid for high resolution two-dimensional polyacrylamide gel electrophoresis

A method is described for estimating proteins in the same plant tissue sample that is solubilized for separation by two-dimensional polyacrylamide gel electrophoresis. The method uses a modified bicinchoninic acid (BCA) protein assay procedure and a modified standard urea solubilization buffer to estimate microgram values of unknown protein concentration, in the presence of 9 M urea and 4% Nonidet P-40, from a linear standard curve. A method for a quantitative determination of protein concentration by BCA in a sample containing 9 M urea and 4% Nonidet P-40 is also described. This method is effective for the determination of proteins in minute non-green and green plant tissue, and is especially designed for vegetative and floral shoot apices, and the primordia of inflorescences.     

A method for the two-dimensional electrophoresis of leaf proteins

Proteins extracted from green leaves of tobacco were subjected to analysis by two-dimensional electrophoresis. It was found that electrophoretic separations were unsatisfactory when leaf extracts were analyzed directly without prior extraction of pigments, phenols, and lipids by acetone treatment. The plant pigments and several phenolic compounds present in leaves presumably interacted with the proteins and created charge heterogeneity, streaking, and other artifacts. It was found that these problems could be overcome by treatment of leaf extracts with acetone followed by solubilization and electrophoresis of the acetone-treated proteins. Leaf extracts were prepared by grinding deribbed leaf disks in a buffer containing 5 mm potassium carbonate, 9.5 m urea, 0.5 dithiothreitol, 2% Nonidet P-40 detergent, 500 μg/ml l-lysine, and 2% Ampholines. The extracts, after centrifugation to remove cell debris and insoluble material, were treated several times with ice-cold acetone. The acetone-precipitated proteins were treated with nucleases, reprecipitated with cold acetone, and then resuspended in the above grinding buffer. The presence of l-lysine and Ampholines were required for good electrophoretic separations. The resuspended proteins were subjected to two-dimensional electrophoresis and proteins detected by staining and or fluorography. At least 300 distinct proteins could be recognized in radioactive samples. The method gives reproducible patterns even after repeated freezing and thawing of the samples.     

Highly-resolving two-dimensional electrophoresis for the study of insect proteins

In this paper, we describe methods for isolation, purification and solubilization of insect proteins from various tissues, including lipid-rich fat body. An Australian locust, Oedaleus australis, and its associated dipteran parasite, Trichopsidea oestracea, provided the protein samples. Protein samples of locust fat body, haemolymph and body wall as well as parasite whole-body extracts were isolated and purified of lipids and salts using chloroform-methanol extraction. Proteins were solubilized using two types of enhanced solubilizing solutions and arrayed using two-dimensional electrophoresis. We demonstrated substantial differences between the body wall protein spectra of normal locusts and those parasitized by T. oestracea. Proteins more abundant in parasitized locusts include two 70 kDa proteins with an isoelectric point (pI) of about 5.5, one approximately 55 kDa protein cluster with a pI of about 4.7 and three 40 kDa proteins with pI values of around 5.6. Proteins that decreased in parasitized locusts include a group of 45 kDa proteins with pI values between 6 and 6.8, and a cluster of 22 to 23 kDa proteins with pI values of approximately 5.4 and 5.6.     

Identification of tissue proteins by amino acid analysis after purification by two-dimensional electrophoresis

Mouse brain proteins were separated by two-dimensional electrophoresis (2-DE). The proteins of a section of the 2-DE pattern were blotted onto hydrophobic membranes and 43 of them were excised and hydrolyzed by liquid-phase hydrolysis. The amino acid composition of these proteins was determined by orthophthaldialdehyde precolumn derivatization and compared with the compositions of known proteins stored in the NBRF sequence database. An identification program named ASA was developed for this purpose. The ASA program includes correction and weighting factors, data reduction by molecular weight windows, and exclusion or inclusion of certain organisms as desired. As a control, eight test proteins and five well-known proteins from mouse brain, all separated by 2-DE, were correctly identified by the program. Out of the 43 brain proteins selected, 19 were identified with high confidence.     

Fast method for two-dimensional electrophoresis of proteins from biological samples

The method for two-dimensional gel electrophoresis of J. Klose and M. Feller [(1981) Electrophoresis 2, 12-24] has been simplified by reducing the thickness of the gels from 3.5 to 1.1 mm for isoelectric focusing gels and from 3.5 to 0.84 mm for sodium dodecyl sulfate slab gels. Thin gels need less reagents and smaller sample volumes. Cooling of the thin gels during electrophoresis is more effective, which allows the use of higher electric power. Therefore, less time is required for an electrophoretic run (approx 4 h). The resolution increases due to the smaller size of the spots. The time required for staining the gels is reduced from at least 3 days to about 1 h. The method has been tested with a protein sample from the filamentous fungus Fusarium solani.     

Preparation of membrane proteins for analysis by two-dimensional gel electrophoresis

In order to separate hydrophobic membrane proteins, we have developed a novel two-dimensional electrophoresis system. For the iso-electric focusing, agarose was used as a supporting matrix and n-dodecyl-beta-D-maltopyranoside was used as a surfactant. In combination with a previously developed Tris/MES electrophoresis system in the second dimension, distinct spots were reproducibly detected from hydrophobic membrane proteins whose grand average hydropathicity (GRAVY) exceed 0.3. In contrast to the immobilized pH gradient system, c-type heme was also visualized in this system.     

Micro-scale two-dimensional polyacrylamide gel electrophoresis of ribosomal proteins

Summary A specially designed apparatus and conditions are described for the rapid analysis of ribosomal proteins by two-dimensional gel electrophoresis on a micro scale. The resolution of proteins in electropherograms is comparable to that obtained with other systems, but because of miniaturization, only 0.5 to 1 g of each protein is required, and the entire procedure, including electrophoresis in both dimensions, and staining and destaining can be completed in 6 to 7 hours.     

A method for two-dimensional electrophoresis of proteins from green plant tissues

A method of extraction of proteins from green plant tissues for two-dimensional electrophoresis is presented. The method is demonstrated on barley and potato leaves and on spruce needles for use in isoelectric focusing as well as in nonequilibrium pH gradient electrophoresis. The following three-step procedure was used: (i) The tissue was ground in liquid nitrogen and then in a pH 5.0 buffer with thiourea added to inhibit phenoloxidase and polyvinylpyrrolidone to bind phenolic compounds. (ii) The proteins were precipitated with acetone at -20 degrees C. (iii) The proteins were dialyzed. Protease activity was generally not a problem during this procedure.     

Efficient extraction of proteins from woody plant samples for two-dimensional electrophoresis

Protein extraction from plant samples is usually challenging due to the low protein content and high level of contaminants. Therefore, the 2-DE pattern resolution is strongly influenced by the procedure of sample preparation. Efficient solubilization of proteins strictly depends on the chaotrope and detergent in the extraction buffer. Despite the large number of detergents that have been developed for the use in protein extraction and IEF, there is no single compound able to efficiently extract proteins from any source. Hence, optimization has to be performed for each type of sample. We tested several chaotrope/detergent combinations to achieve optimal solubilization and separation of proteins from Norway spruce [Picea abies (L.) H. Karst.] needles and European beech (Fagus sylvatica L.) leaves and roots. The same chaotrope mixture (7 M urea, 2 M thiourea) was found to be suitable for the extraction and separation of proteins from all samples. Nonetheless, the efficiency of the surfactants tested varied between samples so that optimal extraction and separation was achieved with different detergents or combination of detergents for each sample. The 2-DE separation of spruce needle proteins was optimal in a mixture of two zwitterionic detergents (2% CHAPS and 2% decyl dimethylammonio propanesulfonate). Beech proteins were best separated in buffers containing sugar-based detergents (2% n-octyl beta-D-glucopiranoside in the case of leaf samples and 2% dodecyl maltoside for the root samples). IEF was performed in buffers with the same composition as the extraction buffer except for the root proteins that were better focused in a buffer containing 2% CHAPS.     

A novel system for the two-dimensional electrophoresis of membrane proteins.

Membrane proteins were resolved in two dimensions by a novel technique that uses discontinuous electrophoresis in both directions. After electrophoresis in the first direction in chloral hydrate, the membrane proteins were further resolved by a novel system that used organic-base dodecyl sulphates to stack and then resolve them. This latter system has several advantages over conventional electrophoresis in sodium dodecyl sulphate, notably that it avoids the production of artifacts generated by other systems.     

The determination of similarities in amino acid composition among proteins separated by two-dimensional gel electrophoresis

A simple and rapid procedure has been developed to determine similarities in amino acid composition among cellular proteins separated by two-dimensional gel electrophoresis. Cells in tissue culture are simultaneously labeled with two different amino acids each tagged with a different radioisotope. The proteins are then separated on two-dimensional gels and their location on the gels determined by Coomassie-blue staining or autoradiography. Elution of the protein from the appropriate region of the gel followed by liquid scintillation counting yields an isotope ratio which reflects the ratio of the two amino acids in the protein. Examples of the use of this technique in analyzing mutant proteins, proteins altered by carbamylation, and cell proteins with similar amino acid composition (e.g., actin and tubulin) are given.