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.     

Specific control of messenger translation in Drosophila oocytes and embryos

The distribution of messenger RNA between polysomes and mRNP in oocytes and embryos of Drosophila melanogaster has been studied by in vitro translational analysis. Poly(A)⁺ RNA was purified from polysomes or mRNA from mature oocytes and young embryos. The messenger populations were translated in vitro and the peptides synthesized were separated by two-dimensional electrophoresis. Analysis of the 2D gel patterns enabled the detection of three peptides coded by messengers present predominantly in the mRNA pools of mature oocytes. When DNA-binding peptides were selected from the in vitro translation products, they showed, after separation by two-dimensional electrophoresis, less than 100 spots. The analysis of the 2D gels indicated that three DNA-binding peptides are coded by messengers present only in the mRNP of the oocytes. These messengers are later found in the polysomal fraction of embryos.     

A proteomics study of in vitro cyst germination and appressoria formation in Phytophthora infestans

A proteomics study using two-dimensional gel electrophoresis (2-DE) and mass spectrometry was performed on Phytophthora infestans. Proteins from cysts, germinated cysts and appressoria grown in vitro were isolated and separated by 2-DE. Statistical quantitative analysis of the protein spots from five independent experiments of each developmental stage revealed significant up-regulation of ten spots on gels from germinated cysts compared to cysts. Five spots were significantly up-regulated on gels from appressoria compared to germinated cysts and one of these up-regulated spots was not detectable on gels from cysts. In addition, one spot was significantly down-regulated and another spot not detectable on the gels from appressoria. The corresponding proteins to 13 of these spots were identified with high confidence using tandem mass spectrometry and database searches. The functions of the proteins that were up-regulated in germinated cysts and appressoria can be grouped into the following categories: protein synthesis (e.g. a DEAD box RNA helicase), amino acid metabolism, energy metabolism and reactive oxygen species scavenging. The spot not detected in appressoria was identified as the P. infestans crinkling- and necrosis-inducing protein CRN2. The identified proteins are most likely involved in the establishment of the infection of the host plant.     

Computer analysis of double-labeled two-dimensional electrophoresis gels

A computerized process for the automatic analysis of double-label autoradiography after two-dimensional polyacrylamide gel electrophoresis has been developed. Matching fluorographs and autoradiographs produced from gels containing 3H- and 14C-labeled proteins are digitized by a rotating drum densitometer and analyzed by the Man-computer Interactive Data Analysis System III. This system locates corresponding protein spots in the films with edge-detection algorithms, converts spot density readings to isotopic disintegrations by reference to standard curves, and computes a 3H:14C ratio for each spot in the gels. On the average, calculated ratios are accurate to approximately 9% for test strips of polyacrylamide gel containing uniform mixtures of 3H and 14C. Values obtained for two-dimensional gels containing n protein spots with a known 3H:14C ratio of 8.6 +/- 0.1 are as follows: 8.1 +/- 1.4 (n = 268), 8.8 +/- 2.1 (n = 278), 9.1 +/- 1.7 (n = 245), and 8.8 +/- 2.2 (n = 223). The computer process greatly reduces the time required to precisely compare two complex protein mixtures and has sufficient precision to detect a doubling in the biosynthesis of any individual protein.     

Regulation of Drosophila myosin ATPase activity by phosphorylation of myosin light chains--II. Flightless mfd- fly

1. The Ca2(+)-activated and Mg2+ actin-activated myosin ATPase activities of flightless mfd- mutant Drosophila flight muscle myosin were one-half and one-third of those of the wild-type fly muscle myosin, respectively. 2. In the two-dimensional gel electrophoresis, the spots corresponding to phosphorylated myosin light chains, Lfl and Ltl, were hardly detected in mfd- mutant myosin. 3. These results support not only the conclusion that phosphorylation of myosin light chains regulates Drosophila myosin ATPase activity but also the assumption that the phosphorylation of myosin light chains is directly involved in flight function of the Drosophila fly.     

Analyses of mouse and Drosophila proteins by two-dimensional gel electrophoresis.

Summary Two-dimensional gel electrophoresis was employed for the protein analysis of several different mouse tissues and Drosophila. The number of protein spots detected with conventional protein dye staining techniques ranged from 110 in erythrocyte lysate to 320 in liver homogenate. Strain variation of protein spots on the gels was examined in five different tissues from two strains of inbred mice (DBA/2J and C57BL/6J) and their F₁ hybrids. The protein spots which exhibited strain variation were shown to be autosomally inherited and to follow Mendelian genetics. From these analyses, it was shown that the frequencies of protein variations between these two strains of mice vary from 1 to 5% with the tissue examined. During the course of this study, the protein spots corresponding to nine muscle proteins and three testis enzymes from the mouse as well as two Drosophila enzymes were assigned on two-dimensional gels of their respective homogenates. Radioisotope labelling of Drosophila and autoradiography of the two-dimensional gels were also performed to improve the sensitivity and resolution of the technique. The potential application of two-dimensional gel electrophoresis for mutant screening as well as biochemical genetic studies is discussed.     

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.     

The subunit interface of the Escherichia coli ribosome. Crosslinking of 30 S protein S9 to proteins of the 50 S subunit.

Purified 50 S ribosomal subunits were found to contain significant amounts of protein coincident with the 30 S proteins S9 and/or S11 on two-dimensional polyacrylamide/urea electropherographs. Peptide mapping established that the protein was largely S9 with smaller amounts of S11. Proteins S5 and L6 were nearly coincident on the two-dimensional polyacrylamide/urea electropherographs. Peptide maps of material from the L6 spot obtained from purified 50 S subunits showed the presence of significant amounts of the peptides corresponding to S5. Experiments in which ³⁵S-labelled 30 S subunits and non-radioactive 50 S subunits were reassociated to form 70 S ribosomes showed that some radioactive 30 S protein was transferred to the 50 S subunit. Most of the transferred radioactivity was associated with two proteins, S9 and S5. Sulfhydryl groups were added to the 50 S subunit by amidination with 2-iminothiolane (methyl 4-mercaptobutyrimidate). These were oxidized to form disulfide linkages, some of which crosslinked different proteins of the intact 50 S ribosomal subunit. Protein dimers were partially fractionated by sequential salt extraction and then by electrophoresis of each fraction in polyacrylamide gels containing urea. Slices of the gel were analysed by two-dimensional polyacrylamide/sodium dodecyl sulfate diagonal gel electrophoresis. Final identification of the constituent proteins in each dimer by two-dimensional polyacrylamide/urea gel electrophoresis showed that 50 S proteins L5 and L27 were crosslinked to S9. The evidence suggests that proteins S5, S9, S11, L5 and L27 are located at the interface region of the 70 S ribosome.     

Resolution of basic cellular proteins including histone variants by two-dimensional gel electrophoresis: Evaluation of lysine to arginine ratios and phosphorylation

A procedure is described which resolves histones and other very basic cellular polypeptides from solubilized whole cells by two-dimensional gel electrophoresis. The entry of histones into the gel was apparently quantitative when salt and protamine were added to solubilization buffers containing urea and detergents. Histones and basic polypeptides in the histone region of the gels were identified and characterized by comparison with purified histones and by determining lysine to arginine ratios of individual spots. Phosphorylated derivatives of the nucleosome histones were clearly resolved from stained spots in the charge dimension. Some phosphorylated H1's comgrated with the stained spots and some were retarded in the charge dimension. Acetylated nucleosome histones were nearly coincident with stained spots. The usefulness of this technique for evaluating changes in post-translational modification of histones was illustrated by showing that one H1-like protein increased in ³²P content when C-6 cells were treated with a β-adrenergic agonist.     

Alpha-glycerophosphate dehydrogenase in Drosophila melanogaster: kinetic differences and developmental differentiation of the larval and adult isozymes

The isozymes of α-glycerophosphate dehydrogenase (α-GPDH) differ markedly with respect to their kinetic and stability parameters. Adult-limited GPDH-1 is stable at 50°C but decays at 57°C, while GPDH-3 is labile at 50°C under similar experimental conditions. By extrapolation of the thermal denaturation curves of crude adult extracts, we estimate GPDH-1 to constitute 76 per cent of the adult α-GPDH activity. Substrate kinetic studies revealed that, at pH 9·5, GPDH-3 exhibits an affinity for α-glycerophosphate which is twofold higher than that of GPDH-1, while K_m's for NAD⁺ are indistinguishable. The apparent K_m of GPDH-3 for dihydroxyacetone phosphate is consistently lower than that of GPDH-1 at pH 7·5, whereas at pH 6·7 the latter isozyme's apparent K_m approximates that of GPDH-3 at pH 7·5. Indistinguishable molecular weights of 66,000 were estimated by gel filtration for both GPDH-1 and 3. Gene dosage studies indicate that all three α-GPDH isozymes are simultaneously affected by dosage of the Gdh⁺ locus. These observations support a homomultimeric model of α-GPDH and the isozymes just discussed arise through epigenetic modification of the product of a single structural gene locus.     

Proteins of the brain and body wall in larvae ofDrosophila melanogaster

Proteins of the brain and body wall cells of third instar larvae ofDrosophila melano-gaster have been examined by two-dimensional gel electrophoresis. Out of over 600 [³⁵ S ]-labelled peptide spots seen in brain or body wall extracts, 517 were common to both; 61 spots were unique to brain and 66 unique to muscle. Glycoproteins were identified by soaking the gels in radioactive iodinated Concanavalin-A. Forty four Con-A binding glycoproteins were identifiable in the brain and 41 in the muscle extracts. Out of these, 8 glycoproteins of the brain and 8 of muscles appear to be tissue-specific.     

Partial amino acid sequences of peptidyl-prolyl isomerases ofFusarium sporotrichioides

Peptidyl-proprylyl cis-trans isomerase (PPIase) activity was observed from crude extract ofFusarium sporotrichioides. Proteins from this fungi were separated by two-dimensional polyacrylamide gel electrophoresis and more than one thousand protein spots were separated. Two cytosolic PPIases were found by the N-terminal sequencing from the two separated spots. The N-terminal 41 residues of the major protein spot showed high sequence identity (63.4%) with PPIase fromNeurospora crassa. This protein was designated as PPIase a, having an apparent molecular mass of 20 kD and pI 7.0. The minor other protein spot, having a similar molecular mass but distinguishable pI 6.4, was also sequenced and the N-terminal twenty residues were almost identical to PPIase a and was designated as PPIase b.     

Challenges related to analysis of protein spot volumes from two-dimensional gel electrophoresis as revealed by replicate gels

Assumptions that need to be considered prior to statistical analysis of protein spot volumes from two-dimensional gel electrophoresis (2-DE) data are studied using replicate gels of the same sample. The most important observation is that the data tables of protein spot volumes from 2-DE images contain a large number of missing values, which are not consistent with the presence or absence of the proteins. This implies both loss of information and problems for the subsequent statistical analysis. Challenges with 2-DE protein spot volumes are viewed in light of multiple gel comparisons and multivariate data analysis.     

蛋白负染方法在蛋白质组学中的应用评价

为评价蛋白质负染方法在蛋白质组学分析中的应用,采用负染和考马斯亮蓝染色两种方法对同一样品的双向电泳胶进行染色,取相对应的8对蛋白点,并进行胶内酶解及MALDI-TOF/TOF分析,比较两种方法与质谱的兼容性。图像分析显示,负染方法展示出的蛋白点更多,但三维峰图不如考染明晰;质谱结果显示,8个负染蛋白点中有7个鉴定结果有效,8个考染蛋白点鉴定结果均有效。因此可以得出以下结论:负染的灵敏度高于考染,与质谱的兼容性良好,适用于建立双向电泳参考图谱的研究;但负染后的胶图不适于进行蛋白点丰度对比分析。     

The QUEST system for quantitative analysis of two-dimensional gels

The strategies and methods used by the QUEST system for two-dimensional gel analysis are described, and the performance of the system is evaluated. Radiolabeled proteins, resolved on two-dimensional gels and detected using calibrated exposures to film, are quantified in units of disintegrations per minute or as a fraction of the total protein radioactivity applied to the gel. Spot quantitation and resolution of overlapping spots is performed by two-dimensional gaussian fitting. Pattern matching is carried out for groups of gels called matchsets, and within each matchset every gel is matched to every other gel. During the matching process, spots are automatically added to each pattern at positions where unmatched spots were detected in other patterns. This results in enhanced accuracy for both spot detection and for matching. The spot fitting procedure is repeated after matching. Tests show that up to 97% of spots in each pattern can be matched and that fewer than 1% of the spots are matched inconsistently. Approximately 2000 proteins are detected from typical gels. Of these 1600 are high quality spots. Tests to measure the coefficient of variation of spot quantitation versus spot quality show that the average coefficient of variation for high quality spots is 21%. The intensities of the detected proteins range from 4 to 20,000 ppm of total protein synthesis. The QUEST analysis system has been used to build a quantitative database for the proteins of normal and transformed REF52 cells, as presented in the accompanying reports (Garrels, J., and Franza, B. R., Jr. (1989) J. Biol. Chem. 264, 5283-5298, 5299-5312).     

Computer analysis of two-dimensional gels

New methods and computer programs are described which enable one to analyze autoradiograms produced by two-dimensional gel electrophoresis. These programs are completely automatic with respect to finding spots resolved by such gels and quantitating the radioactivity in them. Semiautomatic programs have also been developed to match the spot patterns of different autoradiograms, and to follow the synthesis of any individual polypeptide through a series of gels.     

A Preliminary Study on Proteome Variations Associated with Gall Formation in <Emphasis Type="Italic">Zizania latifolia</Emphasis> Trucs

Zizania latifolia Trucs is a uniquely flavored aquatic vegetable found in southern and eastern Asia. Several physiology and genetic approaches have been employed to increase our knowledge about the physiological basis of gall formation; however, as yet, data at the proteomic level are not available. Protein yield and sodium dodecyl sulfate-polyacrylamide gel electrophoresis were used to determine the most appropriate protein extraction methods for use in this study. Total proteins were extracted from the culm tissue at three relevant developmental stages and separated by two-dimensional gel electrophoresis. The number and abundance of spots varied among the two-dimensional gel electrophoresis gels at the three stages. Proteins with more than 1.7-fold abundance between the different stages were monitored. We identified 10 well-resolved spots by matrix-assisted laser-desorption ionization/time-of-flight peptide mass fingerprinting and tandem mass spectrometry. Some spots linked to signal transduction of the phytohormone could be identified. The expression volume of these spots transiently increased during the expansion phase. In contrast, the spots linked to phytoene dehydrogenase and methionine synthase or pyrophosphate-dependent phosphofructokinase were more abundant during gall formation, showing an increase in spot intensity during development and maximal abundance in mature gall. Higher intensity was also found in the spots linked to stress response. We discuss protein variations, considering their potential role during gall formation and comparing our results with established variations at metabolite-profiling levels.     

Using standard positions and image fusion to create proteome maps from collections of two-dimensional gel electrophoresis images

Databases for two-dimensional protein gels pose new challenges in extracting meaningful information from large numbers of experiments. In order to create expression profiles, positions of corresponding protein spots across all gel images have to be established. In larger gel sets errors may accumulate rapidly during this spot matching process, effectively limiting the number of samples available for data mining. Here we present a novel approach for organizing spot data based on the concept of a standard position for a protein species. Standard positions are meaningful average positions that are determined using all occurrences of a protein species. They can be extended to spots that are not annotated via interpolation. The standard position of a spot can serve as a unifying index across all gels in a database, thus allowing creation and analysis of expression profiles that span the whole collection. The standard position gives a much more accurate estimation of a spot's position on a gel than can be obtained using theoretical isoelectric point and molecular weight. Positional indexing is a complement to a priori identifications (e.g. by mass spectrometry or Edman degradation). Moreover it can be used in advance to select spots that are worth identifying because they show relevant expression profiles. Furthermore, we show how to combine all spots that occur on any of the gels into one synthetic but nevertheless realistic-looking image. This composite image is produced such that all spots have their standard positions. It can serve as a proteome reference map for an organism. As an application, we have computed a reference map from 23 gel images of Bacillus subtilis, using an enhanced prerelease version of the gel analysis software Delta2D (DECODON, Greifswald, Germany).     

Identification of a Nosema bombycis (Microsporidia) spore wall protein corresponding to spore phagocytosis

Life-cycle stages of the microsporidia Nosema bombycis, the pathogen causing silkworm pebrine, were separated and purified by an improved method of Percoll-gradient centrifugation. Soluble protein fractions of late sporoblasts (spore precursor cells) and mature spores were analysed by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Protein spots were recovered from gels and analysed by mass spectrometry. The most abundant differential protein spot was identified by database search to be a hypothetical spore wall protein. Using immunoelectron microscopy, we demonstrated that HSWP5 is localized to the exospore of mature spores and renamed it as spore wall protein 5 (NbSWP5). Further spore phagocytosis assays indicated that NbSWP5 can protect spores from phagocytic uptake by cultured insect cells. This spore wall protein may function both for structural integrity and in modulating host cell invasion.     

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.