Profile matching and profile subtraction: application of computer-based image analysis system for two-dimensional electrophoresis gels

The microcomputer-based image analysis system IB-1000 (developed by Indiana Biotech, Highland, IN) for two-dimensional electrophoresis gels has been described previously (9). It allows the user to compare protein spots between two profiles and identify those spots that are commonly shared in both profiles. This report describes two applications of the system's global comparison routine-profile matching and profile subtraction. This application is able to subtract commonly shared spots from one profile, creating a new profile made up by the unmatched spots in the other profile. These applications can be employed in a large variety of research projects.     

Identification of Dictyostelium discoideum plasma membrane proteins by cell surface labeling and quantitative two-dimensional gel electrophoresis

Plasma membrane proteins of the cellular slime mold Dictyostelium discoideum were characterized by two-dimensional polyacrylamide gel electrophoresis using a variety of labeling techniques and a microcomputer-based videodensitometer. Algorithms for the determination of molecular weights and isoelectric points were developed to aid in the comparison of polypeptides from different autoradiographs, Coomassie blue-stained gels, and Western blots. Cell homogenates were compared to plasma membranes isolated by a silica density perturbation technique and to cytoskeletons obtained by nonionic detergent extraction. Plasma membrane proteins were distinguished from subcellular contaminants by lactoperoxidase-catalyzed radioiodination, by selective labeling with N-hydroxysuccinimidyl-2-iminobiotin, and by quantitatively determining the enrichments of individual polypeptides from gels of plasma membrane proteins relative to their counterparts in gels of total cell lysate proteins. In contrast to defining plasma membrane purity by measuring a representative marker enzyme activity, the quantitative two-dimensional gel analysis strategy presented allowed for a rigorous evaluation of the enrichments of all detectable polypeptides in the subcellular fraction. Quantitative two-dimensional gel analysis avoided problems encountered with marker enzyme activation or inhibition during subcellular fractionation as enrichments were based solely on polypeptide amounts. It was also capable of identifying a wider spectrum of plasma membrane proteins than any of the labeling techniques employed in this study. A high resolution two-dimensional gel catalog was generated containing information about plasma membrane protein orientation in the bilayer, association with the cytoskeleton, phosphorylation state, glycosylation state, copy number, isoelectric point, and molecular weight.     

A multiple high-resolution mini two-dimensional polyacrylamide gel electrophoresis system: imaging two-dimensional gels using a cooled charge-coupled device after staining with silver or labeling with fluorophore.

A multiple mini two-dimensional electrophoretic method which results in three two-dimensional protein spot patterns being positioned side by side in an individual gel has been developed. Preparation time has been minimized by employing disposable capillary tubes for the isoelectric focusing gels and reducing the number of second-dimensional gels required. Commercially available vertical slab units were used for the second-dimensional electrophoresis. The protein spot patterns were visualized either by staining the second-dimensional gel with silver or fluorescently labeling the focused proteins while present in the isoelectric focusing gel and subsequently electrophoresing them into the second-dimensional gel. The fluorescently labeled second-dimensional gel was imaged while still present in the glass mold immediately following electrophoresis. Two fluorophores were compared: 2-methoxy-2,4-diphenyl-3(2H)-furanone and 5-(4,6-dichlorotriazin-2-yl)aminofluorescein hydrochloride. A rapid imaging system based on a cooled charge-coupled device was used to view both the silver-stained and fluorescently labeled two-dimensional spot patterns. The sensitivity of detection of protein spots in the mini two-dimensional gels was similar for the two types of fluorescently labeled gels and the silver-stained gels.     

Development of a dedicated two-dimensional gel electrophoresis system that provides optimal pattern reproducibility and polypeptide resolution.

The development of a dedicated two-dimensional gel electrophoresis system is described that provides superior performance in terms of high resolving power and enhanced gel-to-gel reproducibility. Isoelectric focusing is performed in a 1-mm capillary tube with a 0.08-mm thread, optimized for this application, incorporated along its length prior to polymerization of the gel matrix. The isoelectric focusing gel is 4% T, 2.6% C to minimize sieving of proteins and promote adhesion of the gel to the thread. The thread incorporated in the isoelectric focusing matrix prevents gel stretching and breakage during its application to the second dimension. An optimum ampholyte pH range has been defined based on 1600 polypeptides present in a transformed fibroblast cell lysate and verified using a variety of other cell types. The length of time required to complete an electrophoretic separation in the second dimension was found to depend on buffer conductivity establishing the importance of high quality electrophoresis grade reagents devoid of contaminating salts. To ensure reproducibility of electrophoretic separations, it is critical to maintain a strict control of temperature during the second dimension separation. This prevents altered migration of some polypeptides relative to neighboring polypeptides that have constant Rfs over a broad temperature range. It was also determined that to obtain the maximum information from a complex protein mixture it is critical to use a large format 22- x 22-cm two-dimensional electrophoretic system. Using the optimized two-dimensional electrophoretic system and computerized gel analysis, it was determined that molecular weight estimates of polypeptides differed by approximately 350 daltons between gels, while isoelectric point estimates differed by approximately 0.03 pH units between gels. Using the two-dimensional electrophoresis system described, approximately 1000 polypeptides can be routinely detected from silver-stained 10% polyacrylamide gels or 1600 polypeptides from autoradiographs of 35S-methionine-labeled polypeptides.     

Dodecyl maltoside-sodium dodecyl sulfate two-dimensional polyacrylamide gel electrophoresis of chloroplast thylakoid membrane proteins

A two-dimensional electrophoretic system has been developed for the separation of chloroplast thylakoid membrane proteins. This system incorporates nondenaturing polyacrylamide gel electrophoresis in the presence of the nonionic detergent dodecyl-beta-D-maltoside in the first dimension and sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the second dimension. Thylakoid membranes isolated from Spinacia oleracea were solubilized in 1.0% dodecyl-beta-D-maltoside and separated in 4-7% linear acrylamide gradient tube gels which contained 0.05% dodecyl-beta-D-maltoside. After electrophoresis, the tube gels were equilibrated with a sodium dodecyl sulfate-containing equilibration buffer and applied to a 12.5-20% acrylamide linear gradient gel. The Lammelli buffer system was used in both dimensions. The two-dimensional gels were analyzed by staining sequentially with 3,3',5,5'-tetramethylbenzidine-H2O2, Coomassie blue, and silver staining. A number of protein components were identified on "Western blots" of these two-dimensional gels by immunological localization. Membrane protein complexes such as the light-harvesting chlorophyll a/b protein complex, photosystem I, photosystem II, the cytochrome b6/f complex and ribulose bisphosphate carboxylase appear to migrate as essentially intact complexes in the first dimension and appear as vertical series of resolved subunits in the second dimension. This technique complements isoelectric focusing/sodium dodecyl sulfate-polyacrylamide gel electrophoresis in providing additional information concerning the subunit composition of membrane protein complexes and may prove to be of general utility for studying the protein composition of other membrane systems.     

Analysis of ultra acidic proteins by the use of anodic acidic gels

Ultra acidic proteins, generated by posttranslational modifications, are becoming increasingly important due to recent evidence showing their function as regulatory elements or as intermediates in degradation pathways in bacteria. Such proteins are important in neurodegenerative diseases and embryonic development, and they include the Alzheimer-related tau (τ) protein (resulting from posttranslational modifications) and the phosphor-storage embryonic proteins. The ultra acidic proteins are difficult to study because standard two-dimensional gel electrophoresis is inadequate for their analysis. Here we describe a novel electrophoresis system of anodic acidic gels that can replace isoelectric focusing as the first dimension of separation in two-dimensional electrophoresis. The system is based on a sodium acetate buffer (pH 4.6), is compatible with traditional stains (e.g., Coomassie blue) as well as novel fluorescent dyes (e.g., Pro-Q Diamond), and is quantitative for the analysis of ultra acidic proteins. The anodic acidic gels were used for the functional classification of the ultra acidic part of the Bacillus subtilis proteome, showing significant improvement over traditional two-dimensional electrophoresis.     

Analyses of genetic variants of l-glycerol-3-phosphate dehydrogenase in Drosophila melanogaster by two-dimensional gel electrophoresis and immunoelectrophoresis

A protein spot corresponding to l-glycerol-3-phosphate dehydrogenase (α-GPDH, E.C. 1.1.1.8, NAD⁺ oxidoreductase) has been identified on a two-dimensional gel (isoelectric focusing-SDS gel) containing up to 150 stained protein spots from a crude Drosophila homogenate. Preliminary identification of the α-GPDH spot was made by including a suitable amount of purified Drosophila α-GPDH in crude fly homogenates prior to electrophoresis and observing an intensity enhancement of the corresponding protein spot on the gels. When three purified electrophoretic variants (slow, fast, and ultrafast) were mixed and analyzed by two-dimensional gel electrophoresis, horizontal displacements of the three protein spots were observed. Immunoprecipitation of the enzyme prior to electrophoresis and gene mapping further confirmed the identity of the α-GPDH protein spot. The α-GPDH spot can also be detected by autoradiography of a two-dimensional gel from a single fly extract, where it has been estimated to constitute 0.5–1% of the total soluble protein. Mutants which express no apparent α-GPDH activity were analyzed by two-dimensional gels and immunoelectrophoresis in an attempt to identify and characterize the inactive proteins. It is suggested that these techniques provide a powerful tool for the analysis of CRM⁺-null activity mutants of a specific gene-enzyme system.     

The resolution of membrane proteins based upon size,charge, and hydrophobicity

Currently available systems for resolving membrane proteins are based only on size and charge differences. Recently, it has been shown that Triton-urea-acetic acid gels which separate proteins on the basis of charge, size and hydrophobicity are capable of resolving proteins differing only by the substitution of a single neutral amino acid. We have applied this new method to the resolution of bacterial envelope proteins. Conditions for optimal resolution of different bacterial envelope proteins were determined by electrophoresis through transverse urea and Triton X-100 gradient gels. We have also correlated the components resolved in this system with those resolved by classical sodium dodecyl sulfate-gel electrophoresis by using two-dimensional slab gels combining the two systems. Furthermore, envelope protein fractions from different species and strains of bacteria were compared to identify specific proteins. This system appears to be a promising method for investigating envelope proteins which are due to missense mutations.     

肝癌亚细胞结构的蛋白质组分比较分析

运用亚细胞蛋白质组学的研究策略,分离纯化亚细胞结构,可以提高低丰度蛋白质在双向电泳中检出的数量。通过对比分析肝癌细胞与正常肝细胞线粒体、细胞核蛋白质组的差异表达情况,为肝癌发病机理的研究提供更多、更有价值的信息。以体外培养的人体肝癌细胞QGY-7703与正常肝细胞LO2为研究模型,通过超离心的方法分离细胞的线粒体和细胞核。双向电泳分离线粒体和细胞核的蛋白质,图像分析筛选差异表达蛋白斑点,MALDI-TOF-MS鉴定蛋白质。从线粒体、细胞核的蛋白质电泳图谱中筛选出54个候选差异表达的蛋白质斑点,质谱鉴定出22种差异表达蛋白质,其中17种在肝癌细胞中表达上调,5种在肝癌细胞中表达下调。筛选出的差异表达蛋白质涉及到细胞的能量代谢、蛋白质合成、细胞骨架与核骨架的改变、mRNA的加工成熟及凋亡调控等许多方面,表明癌变细胞的组织结构和代谢状态都发生了很大的变化。     

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.     

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.     

Two-dimensional zymogram analysis of nucleases in Bacillus subtilis

A two-dimensional zymogram procedure for the analysis of nucleases is described. Isoelectric focusing (IEF) and nonequilibrium pH gradient electrophoresis (NEPHGE) were compared as first dimensions in combination with sodium dodecyl sulfate (SDS) electrophoresis as the second dimension in analyzing nucleases in lysates of Bacillus subtilis. All renaturable nucleases detected following SDS electrophoresis alone were resolved in NEPHGE-SDS electrophoresis gels whereas, in IEF gels, most either were at the basic end or were not present in the second-dimension gels. This method of analysis has revealed a complexity in nuclease species in B. subtilis not previously recognized. Eighty-three discreet nuclease activities have been detected in B. subtilis lysates. Using purified deoxyribonuclease I (bovine pancreas), as little as 10 pg of nuclease can be detected.     

High-throughput Three-dimensional Gel Electrophoresis for Versatile Utilities： A Stacked Slice-gel System for Separation and Reactions （4SR）

Introduction The completion of the Human Genome Project has triggered large-scale screening of genomes (1) and proteomes (2) in aims to find out candidate genes related to diseases (3), perform expression analyses at the mRNA level (4) or at the protein level (5), discover new drugs (6), and analyze molecular in- teractions (7). For such purposes, technologies han- dling a tiny amount of samples should be developed, of which the importance has already been described as the ambient analyte th…     

Detection of human somatic cell structural gene mutations by two-dimensional electrophoresis

The feasibility of detecting human somatic structural gene mutations by two dimensional electrophoresis has been investigated. A lymphoblastoid cell line was grown as a mass culture in the presence of ethylnitrosourea, after which cells were regrown as single cell clones. A total of 257 polypeptide spots were analyzed in gels derived from 186 clones. Four structural mutations were detected by visual analysis of the gels. Computer analysis of gels corresponding to the mutant clones was also undertaken. At a spot size threshold of 200 spots to be matched using a computer algorithm, all four mutant polypeptides were detected. These results indicate the usefulness of the two-dimensional approach for mutagenesis studies at the protein level.     

A procedure for the immunoblotting of proteins separated on isoelectric focusing gels

A method has been devised for performing Western blot assays on proteins resolved by isoelectric focusing. Electrophoretic transfer of proteins directly from isoelectric focusing (IEF) tube gels to nitrocellulose sheets allowed their immunoassay without conventional second dimension SDS gel electrophoresis. The same method can also be used for IEF slab gels. For the immunostaining of nonmuscle actin isoforms in extracts of cultured cells, the resolution of this technique was much improved over that of Western blots of two-dimensional gels.     

Resolution of erythrocyte membrane proteins by two-dimensional electrophoresis.

A two-dimensional electrophoresis method has been developed which solubilizes erythrocyte membrane proteins, and which resolves the components of the band that migrates in detergent gels as if its molecular mass were 95,000 daltons. This method uses gel electrophoresis with sodium dodecyl sulfate in the first dimension and phenol, aqueous urea, and acetic acid in the second dimension. The 95,000 dalton band is known to contain several different membrane proteins, including those associated with anion transport, glucose transport, and (Na+,K+) transport. Two-dimensional electrophoresis resolved this band into one major spot and several minor ones. Pronase digestion of whole erythrocytes, followed by preparation of ghosts and two-dimensional electrophoresis, showed that only the major component of this band was digested by pronase.     

Double-label reductive methylation of tissue proteins for precision two-dimensional polyacrylamide-gel electrophoretic analysis.

Reductive methylation has been used to radioactively label crude-extract proteins with 3H or 14C. The procedure achieved good isotope incorporation and resolution of proteins on two-dimensional polyacrylamide gels. It allows high-precision comparison of tissue samples by double-labelling and should facilitate the study of tissue proteins by two-dimensional gel electrophoresis.     

Functional proteomics using microchannel plate detectors

We describe the development of a novel detection system used for the functional imaging of proteins separated on electrophoretic gels. A microchannel plate detector is used here for real-time imaging of low levels of tritiated protein separated by two-dimensional (2-D) electrophoresis. The system employs radioisotope-free, low noise microchannel plates originally developed for photon counting in X-ray astronomy. Using the detector configuration described here, proteins were resolved on mini gels by either one or two-dimensional electrophoresis, transferred onto polyvinylidene difluoride membranes and directly imaged. Tritiated diisopropylfluorophosphate (DFP) was used as a selective label for the serine hydrolase class of enzymes and their distribution in the central nervous system was examined. This survey revealed approximately 24 protein spots by 2-D electrophoresis. We also investigated the relative sensitivity of these proteins towards DFP and found the peptidase, acylpeptide hydrolase to be the most sensitive brain protein towards this reagent. Using a number of different tritiated standards, it was found that the system can image as little as 0.1 Bq/mm(2) of tritium corresponding to 320 attomol of DFP labelled protein/mm(2). Moreover, the system has a wide dynamic range (>10(6)) allowing samples of high and low activity to be quantified on the same gel.     

Amino-acid sequence homology of a polymorphic cellular protein from human lymphocytes and the chaperonins from Escherichia coli (groEL) and chloroplasts (Rubisco-binding protein)

The human p60 (Mr 60,000) is an abundant protein in the two-dimensional electrophoresis pattern of the cellular proteins of human mitogen-stimulated lymphocytes. The p60 shows as remarkable characteristic a genetic polymorphism with two different alleles. Electrotransfer of this protein from two-dimensional gels onto siliconized glass fiber sheets and subsequent amino-acid sequence analysis has revealed a striking homology to the known bacteria and plant chaperonins, the groEL and the Rubisco-subunit-binding protein. From this sequence homology we conclude that we have identified the human chaperonin homologue.