Entamoeba histolytica: analysis of the trophozoite proteome by two-dimensional polyacrylamide gel electrophoresis

The Entamoeba histolytica genome project carried out at TIGR and the Sanger Institute has produced a near-complete set of deduced open reading frame sequences. These data provide strong support for the identification of signals from proteomic analyses such as two-dimensional electrophoresis by protein sequencing and/or mass spectrometric methods. To carry out an initial investigation of the E. histolytica proteome, appropriate sample preparation and silver staining protocols were adapted. After preparation of protein extracts from E. histolytica HM-1:IMSS trophozoites, solubilized proteins were separated in the first dimension in IPG (immobilized pH gradient) strips depending on their pI and subsequently in the second dimension according to their molecular weight by SDS-polyacrylamide gel electrophoresis. Of the more than 1500 protein spots visualized, several landmark spots were isolated from the gels and identified by either tryptic cleavage and subsequent MALDI-TOF mass spectrometry or by protein sequencing.     

Subpicogram analysis of sweat proteins using two-dimensional polyacrylamide gel electrophoresis

Sweat collected from six normal volunteers was analyzed to determine if reproducible protein patterns could be obtained using two-dimensional polyacrylamide gel electrophoresis of ¹²⁵I-labeled sweat proteins. This method has the capability of easily detecting picogram quantities of protein. Once the methods of collection of the sweat had been standardized, reproducible patterns were obtained from these volunteers. Over 100 discrete spots were revealed by a combination of fluorography and rare earth screen radioautography of dried two-dimensional gels. This method will allow analysis of sweat for qualitative and quantitative variations in protein content in pathologic conditions such as cystic fibrosis, renal failure, and diabetes.     

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.     

Separation of t-RNAs by two-dimensional polyacrylamide gel electrophoresis

A pH 5.8 polyacrylamide gel electrophoresis buffer is described. Electrophoresis in this MES-citrate system at pH 5.8 separates E. coli transfer RNAs into 15 bands using 15% acrylamide gels. Polyacrylamide gel electrophoresis in a second dimension at pH 8.3 further resolves E. coli t-RNAs into 20 spots.     

Modification of commerical and custom-built slab gel electrophoresis units for two-dimensional polyacrylamide gel electrophoresis

Many commercial and custom-built slab gel electrophoresis units can be modified to function as two-dimensional polyacrylamide gel electrophoresis units with the insertion of Plexiglas adapters. These adapters can be made for about $50 a pair and can be used for either temporary or permanent modification of the slab gel units. The physical dimensions of the adapters can be varied to permit great flexibility in the diameter of cylinder gels and the thickness of slab gels that can be run together. For example, proteins from 6-mm cylinder gels can be easily separated on 1-mm slab gels, which can then be dried for autoradiography.     

Identification of mitochondrial protein complexes inArabidopsis using two-dimensional blue-native polyacrylamide gel electrophoresis

Mitochondria fulfill a wide range of functions in the plant cell, including producing ATP, providing carbon skeletons for biosynthesis, and biosynthesizing vitamins and cofactors. Recently, mitochondria have been implicated in the pathway of programmed cell death in plant cells. In addition, mutations in the mitochondrial genome have been shown to be causally related to cytoplasmic male sterility—the failure to produce functional pollen in a range of crop plants. Proteomics has been used to attempt to catalogue mitochondrial proteins and extend our understanding of this essential organelle. Conventional proteomics based on isoelectric focusing and SDS-PAGE is unsuitable for hydrophobic proteins and therefore does not allow the identification of many components of the respiratory complexes. To identify such proteins, we have used blue-native PAGE to fractionate protein complexes in their native state, followed by SDS-PAGE to separate component subunits of each complex. A total of 40 protein spots were reproducibly resolved, and 29 were identified by means of mass spectrometry, thus giving a map of the most abundant complexes in plant mitochondria. Chaperones; transporters; novel proteins; and proteins involved in the respiratory chain, the citric acid cycle, amino acid and carbon metabolist, and stress response were identified. This study gives new insight on the role and functioning of well-characterised and recently identified mitochondrial proteins by localising them to specific complexes. It also identifies novel proteins in plant mitochondria.     

Preparative two-dimensional polyacrylamide gel electrophoresis of 32 P-labeled RNA

Complex mixtures of RNA molecules may be separated by two-dimensional electrophoresis on polyacrylamide gel slabs. The first dimension of the separation is carried out on acid gels in the presence of a high urea concentration, the second on more concentrated gels buffered at pH 8. The method has been applied to the complete separation of RNA fractions obtained after a preliminary gel electrophoresis of partial enzymic digests of ³²P-labeled bacteriophage RNA. Another application is the fractionation of partial digests as obtained in sequence determination of RNA molecules. Spots are detected by autoradiography and extracted by a simple micro procedure which yields the material in a concentrated form suitable for sequence analysis by fingerprinting.     

Genetic analysis of gliadin components in winter wheat using two-dimensional polyacrylamide gel electrophoresis

Summary Blocks of gliadin components found both in a number of varieties and in single F₂ grains of winter wheat intervarietal hybrids have been studied by two-dimensional electrophoresis combining electrophoresis in acidic aluminium-lactate buffer (pH3.1) and SDS-electrophoresis. Gliadin components (spots) have been shown to be inherited as linked groups (blocks), codominantly and in accordance with a gene dosage in triploid endosperm. Blocks include components differing in their electrophoretic mobility and molecular weight. Some allelic variants of blocks differ only in presence of few additional components or in the electrophoretic mobility of components with similar molecular weights; other variants may contain no similar components. Apparently, in the course of evolution, mutations in individual genes of gliadin-coding loci and processes changing the number of expressing genes and the sizes of their structural part occurred.     

Double-beam flying spot scanner for two-dimensional polyacrylamide gel electrophoresis

The construction of a double-beam photometer in which the light source is a cathode ray oscilloscope is described. The light spot from the oscilloscope was focused and reduced in size at the gel plane to give a diameter of less than 0.15 mm and make it possible to scan over a 50 X 59-mm rectangle; using reduced spatial resolution (spot less than 0.2 mm) the area scanned becomes 70 X 90 mm. The light from the CRT was divided into two beams; one was directed through the transparent object to a photomultiplier and the other to a reference photomultiplier. The signals from these two detectors were converted to the logarithm of the ratio by a logging amplifier to give a direct measure of absorbance. Positioning of the spot, control of light intensity, and measurement of absorbance were carried out through an interface to a 16-bit computer. The relationship between measured and actual absorbance was linear over the range of absorbance 0 to 2, which could be raised to 1 to 3 by placing a neutral filter in the reference beam. The system generated an image containing 256 X 256 pixels in about 5 min, the scanning speed was determined by the persistence time of the P4 phosphor on the cathode ray tube, and faster scans can be made using A6 phosphor.     

Improved comparative proteome analysis based on two-dimensional gel electrophoresis

The purpose of this study was to test the extent to which differences in spot intensity can be reliably recognized between two groups of two-dimensional electrophoresis gels (pH 4-7, visualized with ruthenium fluorescent stain) each loaded with different amounts of protein from rat brain (power analysis). Initial experiments yielded only unsatisfactory results: 546 spots were matched from two groups of 6 gels each loaded with 200 microg and 250 microg protein, respectively. Only 72 spots were higher (p<0.05), while 58 spots were significantly lower in the 250-microg group. The construction of new apparatuses that allowed the simultaneous processing of 24 gels throughout all steps between rehydration and staining procedure considerably lowered the between-gel variation. This resulted in the detection of significant differences in spot intensities in 77-90% of all matched spots on gel groups with a 25% difference in protein load. This applied both when protein from 24 biological replicates was loaded onto two groups of 12 gels and when two pooled tissue samples were each loaded onto 6 gels. At a difference of 50% in protein load, more than 90% of all spots differed significantly between two experimental groups.     

Characterization of proteins associated with nuclear ribonucleoprotein particles by two-dimensional polyacrylamide gel electrophoresis.

Rat liver nuclear ribonucleoprotein particles were prepared by two different methods and defined as 40S ribonucleoprotein (40S RNP) and heterogeneous nuclear ribonucleoprotein (HnRNP) particles. The RNP particles were either solubilized in 8 M urea--6 mM 2-mercaptoethanol--20 mM glycine--20 mM Tris--HCl (pH 8.4) or subjected to removal of RNA by phenol extraction prior to solubilizing the proteins in the urea buffer. The proteins associated with 40S RNP and HnRNP were heterogeneous and very similar in their electrophoretic patterns when analyzed by two-dimensional PAGE, except a protein with molecular weight of 62 000 and an isoelectric point (pI) of 6.2 was present only in HnRNP particles. At least 12 major and 22 minor components could be identified in both preparations. The major proteins were found at pI values varying from 6.0 to 8.5 and with molecular weights from 32 000 to 42 000, and a group of proteins with molecular weight approximately 65 000 were more prominent in HnRNP than in 40S RNP. The other components were found mainly at pI ranges from 5.0 to 6.5 with molecular weights from 43 000 to 65 000. The phenol method extracted essentially all proteins associated with either 40S RNP and HnRNP, but was less effective in extracting a group of proteins with pI values from 5.0 to 5.5 and more efficient for proteins with pI values from 7.5 to 8.5. When chromatin proteins isolated by phenol extraction were compared with HnRNP particle proteins isolated by the same method, the electrophoretic mobilities of the HnRNP particle proteins were found to be identical with a fraction nonhistone chromatin proteins. The 40S RNP particles were further purified by metrizamide isopycnic density gradient centrifugation. The electrophoretic patterns of these proteins were very similar to those prepared by sucrose density gradient centrifugation. Therefore, we concluded that the proteins of RNP particles constituted part of the chromatin proteins.     

Removal of artifactual bands associated with the presence of 2-mercaptoethanol in two-dimensional polyacrylamide gel electrophoresis

A method for eliminating artifactual bands due to the presence of 2-mercaptoethanol in two-dimensional gels is described. The method is based on a modification of the procedure of application of the first dimension gel to the SDS slab gel. 2-Mercaptoethanol is removed during equilibration and replaced by iodoacetamide. The use of iodoacetamide improves the recovery of proteins and results in a better detection of them.     

Mapping of bovine skeletal muscle proteins using two-dimensional gel electrophoresis and mass spectrometry

The large individual variation in meat quality seen both within and between animals is not fully understood. Consequently, our long-term goal is to identify reliable proteins which control or determine bovine meat quality. Using a proteomic approach, bovine skeletal muscle samples were analyzed by two-dimensional gel electrophoresis (2-DE) using an immobilized pH 4-7 gradient in the first dimension and mass spectrometry. We first tested the reproducibility of the method. These experiments showed slightly greater intersample than intrasample variability. In order to evaluate the type of visualized proteins in 2-DE, we initiated the construction of a protein reference map of bovine Semitendinosus muscle. In total, 129 protein spots corresponding to 75 different gene products were identified. Of these proteins, the largest portion is involved in metabolism (25.5%), cell structure (17%), cell defense (16%) and contractile apparatus (14.5%). One quarter of the identified proteins are represented by two or several protein spots and multiple isoforms of troponin T are present. Peptide mass fingerprint results indicate that these isoforms are partly generated by alternative splicing. The data presented here are an important step for further proteome analyses on bovine muscle. This may lead to progress in understanding the mechanisms controlling postmortem muscle metabolism and meat quality.     

Analytical and biological variances associated with proteomic studies of Medicago truncatula by two-dimensional polyacrylamide gel electrophoresis

Two-dimensional polyacrylamide gel electrophoresis (2-DE) and mass spectrometry are being used as proteomic tools in an integrated functional genomics program focused on the model legume Medicago truncatula. Due to the perceived high levels of indeterminate error associated with 2-DE we deemed it necessary to quantify the coefficient of variance (or relative standard deviation) for both analytical and biological sources associated with 2-DE of Medicago truncatula leaf protein extracts. Leaf protein extracts were chosen because of their biological significance and due to the more challenging nature of green tissues. Analytical variance was calculated for fifty proteins from ten replicate 2-DE gels of the same protein extract. Biological variance was calculated for the same fifty proteins from ten independent 2-DE gel analyses of ten independent but similar plants grown under identical conditions. Average analytical and biological variances were calculated for both data sets and represent the average variance of approximately 500 independent measurements of protein concentration. Analytical variance was determined to be 16.2% and biological variance was determined to be 24.2%. These average variances provide a quantified and statistical basis for evaluation of protein expression changes in future comparative proteomic investigations. It is proposed that 2-DE measured protein expression levels should differ by a minimum of 3.92sigma (i.e. /+/-2sigma/ and sigma = standard deviation), or 94.7% based on our measured variances, for the difference to be significant at the 95% confidence level.     

An optical comparator for measuring two-dimensional polyacrylamide gel electrophoresis records using an on-line microcomputer

A comparator which makes it possible to compare two wet gels or photographic negatives or autoradiograms through a flickering light system has been built. The system consists of two special-purpose projectors which combine the images on a digitizing platform. When the lights are switched On and off out of phase, the positions of the common components remain unchanged, whereas those that are spatially displaced appear to jump from side to side and those present in one image but not the other switch on and off. This produces a flickering image in which differences are readily seen. Commercial camera lenses were used to construct the projectors and the overall specifications for the system are given. The coordinates of both the displaced components, as well as the selected standards from the two images, are digitized and entered automatically into an on-line microcomputer. By using an iterative procedure for collecting records from several superimposable records of the gel, it is possible to compensate for the lack of total reproducibility over the whole gels. These coordinates are then normalized and superimposed on a master map through a television display using a curser to adjust the coordinates. The whole procedure can be repeated for many gels using a common reference gel in the comparator, and the result is a set of normalized coordinates which can be plotted on a single map to provide a final record of the experiments.     

Aldosterone-induced proteins in toad urinary bladders. Identification and characterization using two-dimensional polyacrylamide gel electrophoresis

Aldosterone-stimulated Na+ transport is mediated by new protein synthesis, but the identification of specific aldosterone-induced proteins (AIPs) has proven difficult and the cellular function of such proteins is unknown. Using high resolution two-dimensional polyacrylamide gel electrophoresis and autoradiography we have identified AIPs of similar isoelectric points (5.8 to 6.4) and molecular weights (70,000 to 80,000) in membrane-rich and cytosolic subcellular fractions of epithelial cells derived from single toad urinary bladders. The ability of actinomycin D to inhibit both AIP synthesis and aldosterone-induced Na+ transport is consistent with a role for these proteins in the natriferic action of aldosterone. In addition, since non-natriferic concentrations of cortisol did not induce similar proteins, AIP synthesis appears to be mineralocorticoid-specific. The relationship of AIP synthesis to Na+ transport was also studied. Since amiloride, which blocks Na+ transport in high resistance epithelia, did not affect the synthesis of these proteins, Na+ transport is not required for their synthesis. In addition, similar proteins were not induced when Na+ transport was stimulated by antidiuretic hormone and theophylline. Consequently, AIP synthesis is not merely a nonspecific consequence of the cellular metabolic changes associated with Na+ transport.     

Improvement of two-dimensional gel electrophoresis proteome maps of the haloarchaeon Haloferax volcanii

Proteins of haloarchaea are remarkably unstable in low-ionic-strength solvents and tend to aggregate under standard two-dimensional (2-D) gel electrophoresis conditions, causing strong horizontal streaking. We have developed a new approach to generate 2-D maps of halophilic proteins which included washing cells with 1.5 M Tris-HCl buffer. In addition, proteins were precipitated with acetone, solubilized with urea and thiourea in the presence of the sulfobetaine detergent 3-[(3-cholamidopropyl)dimethylamino]-1-propanesulfonate (CHAPS), reduced with tributylphosphine (TBP), and separated with microrange strips of immobilized pH gradients (pH 3.9-5.1). This combination enabled the construction of highly reproducible 2-D maps of Haloferax volcanii proteins.