Alkaline urea solubilization, two-dimensional electrophoresis and lectin staining of mammalian cell plasma membrane and plant seed proteins

Integrated metabolomic and transcriptomic analyses of two peanut (Arachis hypogaea L.) cultivars differing in amino acid metabolism of the seeds

Peanut is an important economic crop worldwide. The content of amino acids, especially essential amino acids, is an important nutritional quality trait of peanut seeds. However, the regulation of amino acid metabolism in peanut seeds is poorly understood. Here, two peanut cultivars, Zhonghuahei 1 and Zhongkaihua 151, with high and low free amino acids in mature seeds, respectively, were selected to investigate the regulatory mechanisms of amino acids during seed development. Zhonghuahei 1 is composed of significantly higher arginine (Arg), asparagine (Asn), and glutamate (Glu) contents than Zhongkaihua 151. However, the metabolomic analyses indicated that the contents of most amino acids were significantly lower in Zhonghuahei 1 at the early developmental stage, while they were reverse at the middle and late stages. Transcriptomic analyses also revealed that the differentially expressed genes between the two cultivars during different stages were enriched in multiple pathways associated with amino acid metabolism. Among them, the Arg biosynthesis pathway showed different regulatory profiles between the two cultivars according to the temporal analysis of gene expression patterns. Subsequent gene co-expression network analysis showed that the gene module darkorange was significantly correlated with Arg content, with an enriched Arg biosynthesis pathway. Accordingly, a gene regulatory network for Arg biosynthesis and metabolism, including key genes (ALDH, ASS1, OTC, and GAD) and transcription factors (GATA, HEX, and ATF), was constructed. These findings provide insights into the regulatory network of amino acid metabolism in peanuts and provide candidate genes that can be applied to facilitate peanut breeding with desirable seeds.

Trichocyst ribbons of a cryptomonads are constituted of homologs of R-body proteins produced by the intracellular parasitic bacterium of Paramecium

Trichocysts are ejectile organelles found in cryptomonads, dinoflagellates, and peniculine ciliates. The fine structure of trichocysts differs considerably among lineages, and their evolutionary relationships are unclear. The biochemical makeup of the trichocyst constituents has been studied in the ciliate Paramecium, but there have been no investigations of cryptomonads and dinoflagellates. Furthermore, morphological similarity between the contents of cryptomonad trichocysts and the R-bodies of the endosymbiotic bacteria of Paramecium has been reported. In this study, we identified the proteins of the trichocyst constituents in a red cryptomonad, Pyrenomonas helgolandii, and found their closest relationships to be with rebB that comprises the R-bodies of Caedibacter taeniospiralis (gammaproteobacteria), which is an endosymbiont of Paramecium. In addition, the biochemical makeups of the trichocysts are entirely different between cryptomonads and peniculine ciliates, and therefore, cryptomonad trichocysts have an evolutionary origin independent from the peniculine ciliate trichocysts.

Native phytochrome: Inhibition of proteolysis yields a homogeneous monomer of 124 kilodaltons from Avena

Phytochrome purified from Avena as the red-absorbing form, Pr, by an established immunoaffinity column procedure is heterogeneous. Two major polypeptides and one minor polypeptide with apparent molecular masses of 118, 114, and 112 kilodaltons (kDal), respectively, are observed on NaDodSO(4)/polyacrylamide gel electrophoresis. In contrast, only a single band of 124 kDal is obtained when phytochrome is rapidly immunoprecipitated after extraction either (i) as the far-red absorbing form, Pfr, in detergent-free buffer or (ii) in either spectral form in a 100 degrees C NaDodSO(4)-containing buffer. On two-dimensional gel electrophoresis the three column-purified species have pIs of 5.8, 6.0, and 6.0, whereas 124-kDal phytochrome is a single spot with a pI of 5.9. Incubation as Pr in extracts causes progressive conversion of the 124-kDal polypeptide to the 118- and 114-kDal species. This process is inhibited by phenylmethylsulfonyl fluoride, suggesting that Pr is susceptible and Pfr resistant to limited proteolysis during extraction. These data, and the fact that the cell-free translation product of phytochrome mRNA is also 124 kDal [Bolton, G. W. & Quail, P. H. (1982) Planta, in press], indicate that the native monomer from Avena is a single species of 124 kDal. Thus the heterogeneous preparations of slightly lower molecular weight ("large" or "120-kilodalton" phytochrome) previously extensively characterized appear to have consisted of a mixture of partially degraded molecules that have undergone limited proteolysis during purification as Pr, as is established practice. A reexamination of the molecular properties of phytochrome appears necessary.

Solubilization of proteins in 2DE: an outline

Protein solubilization for two-dimensional electrophoresis (2DE) has to break molecular interactions to separate the biological contents of the material of interest into isolated and intact polypeptides. This must be carried out in conditions compatible with the first dimension of 2DE, namely isoelectric focusing. In addition, the extraction process must enable easy removal of any nonprotein component interfering with the isoelectric focusing. The constraints brought in this process by the peculiar features of isoelectric focusing are discussed, as well as their consequences in terms of possible solutions and limits for the solubilization process.

Membrane proteins and proteomics: un amour impossible?

Proteome analysis implies the ability to separate proteins as a first step prior to characterization. Thus, the overall performance of the analysis strongly depends on the performance of the separation tool, usually two-dimensional electrophoresis. This review shows how two-dimensional electrophoresis performs with membrane proteins from bacteria or animal or vegetable cells and tissues, the recent progress in this field, and it examines future prospects in this area.

Use of thiourea to increase the solubility of membrane proteins in two-dimensional electrophoresis

The separation of membrane proteins by high-resolution two-dimensional electrophoresis was carried out. At high loads, these proteins are prone to precipitation, resulting in poor resolution. It is shown here that the use of thiourea, previously described for focusing in immobilized pH gradients, can be extended to conventional isoelectric focusing. As thiourea inhibits acrylamide polymerization, a modified photopolymerization system must be used. These modifications result in higher solubility of proteins during IEF, thereby increasing the resolution and capacity of the two-dimensional gels.

Improvement of the solubilization of proteins in two-dimensional electrophoresis with immobilized pH gradients

Membrane and nuclear proteins of poor solubility have been separated by high resolution two-dimensional (2-D) gel electrophoresis. Isoelectric focusing with immobilized pH gradients leads to severe quantitative losses of proteins in the resulting 2-D map, although the resolution is usually high. Protein solubility could be improved by using denaturing solutions containing various detergents and chaotropes. Best results were obtained with a denaturing solution containing urea, thiourea, and detergents (both nonionic and zwitterionic). The usefulness of thiourea-containing denaturing mixtures is shown for microsomal and nuclear proteins as well as for tubulin, a protein highly prone to aggregation.

Two-dimensional electrophoresis of membrane proteins: a current challenge for immobilized pH gradients

Membrane proteins were separated by high resolution two-dimensional (2-D) electrophoresis. On isoelectric focusing (IEF) with immobilized pH gradients severe protein losses in the resulting 2-D map were observed when compared with carrier ampholyte-based IEF. This has been noticed for two different biological systems, namely the chloroplast envelope of spinach and the endocytic vesicles from Dictyostelium discoideum. The possible mechanisms of these losses on immobilized pH gradients are discussed.

Optimizing a method of protein extraction for two-dimensional electrophoretic separation of proteins from planarians (Platyhelminthes, Turbellaria)

Different procedures for microscale extraction of proteins from small amounts of tissue of planarians (Platyhelminthes, Turbellaria) to be analyzed by two-dimensional gel electrophoresis (2-D PAGE) are compared. Three extraction methods were assessed: (i) extraction of soluble proteins with nondenaturing Tris buffers, (ii) extraction with Tris buffer containing the anionic detergent sodium dodecyl sulfate (SDS), and (iii) denaturing extraction under reducing conditions in the presence of urea and Nonidet P-40 (NP-40) with or without SDS. Buffers combining minute concentrations of SDS (0.01%), denaturing concentrations of urea (8M) and alkaline pH solubilized the greatest number of proteins without detectable proteolysis. Neither the presence of protease inhibitors nor higher concentrations of SDS improved protein extraction. We have applied this method to planarians to detect proteins specific to the pharynx. The resulting two-dimensional pattern shows a larger number of specific spots than in previous extraction methods.

Systematic analysis of the total proteins of a mammalian organism: principles, problems and implications for sequencing the human genome

High-resolution two-dimensional electrophoresis (2-DE) has reached a technological level that allows us to resolve most of the numerous unknown protein species of a mammalian organism if appropriate strategies are used. We will discuss the problems of classification and characterization of proteins and propose a systematic approach to the analysis of the total protein complex. Both a comprehensive as well as a pragmatic approach towards systematic analysis have been considered. A "complex protein database" is suggested and considered with regard to various uses. A systematic analysis of the mouse proteins has been started and some of the preliminary results are summarized here. In particular, genetic properties of the proteins were investigated and are presented in order to demonstrate the significance of a systematic analysis of proteins for research and practical application (e.g. mutagenicity testing). A concept is presented for sequencing the coding DNA of mouse and man, starting with a systematic analysis of mouse proteins and then using two recently developed methods - microsequencing of proteins from spots of 2-DE protein patterns, and utilization of the relatively short N-terminal sequences obtained - to produce the corresponding cDNA's of these proteins.

Extraction of plant proteins for two-dimensional electrophoresis

Three different extraction procedures for two-dimensional electrophoresis of plant proteins are compared: (i) extraction of soluble proteins with a nondenaturing Tris-buffer, (ii) denaturing extraction in presence of sodium dodecyl sulfate at elevated temperature allowing the solubilization of membrane proteins in addition to a recovery of soluble proteins, and (iii) a trichloroacetic acid-acetone procedure allowing the direct precipitation of total proteins.

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.

Seminal plasma proteins of fertile and infertile men analyzed by two-dimensional electrophoresis

Sperm-free seminal plasma from seminal fluid ejaculate of fertile and infertile men obtained in the presence and absence of aprotinin (500 kallikrein inhibitor units per milliliter) was analyzed by two-dimensional electrophoresis followed by silver staining. To evaluate postliquefaction proteolytic breakdown of seminal plasma proteins, protease inhibitors were added to the semen at 15, 30, and 60 minutes after ejaculation. Most seminal plasma proteins in normospermic men (n = 4) had molecular weights of 30,000 to 70,000 and were similar to those present in serum. The major non-serum protein in seminal plasma of all men was a basic product with an approximate molecular weight of 40,000. A group of proteins (molecular weights = 20,000 to 23,000) in seminal plasma analyzed immediately after liquefaction was detected in oligospermic men (n = 4) but not in normospermic men (n = 4) or azoospermic men (n = 4). When protease inhibitor was added to normospermic semen at greater than or equal to 15 minutes after liquefaction, these proteins (molecular weight = 20,000 to 23,000) and another group of proteins (molecular weights = 40,000 to 43,000) were readily identifiable but were further enhanced in the absence of protease inhibitors. These findings suggest that oligospermic men may have accelerated proteolysis of sperm or seminal plasma proteins that may contribute to subfertility.

Two-dimensional gel electrophoresis of proteins

The high-resolution capacity of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) makes it an excellent tool for the analysis and characterisation of complex protein mixtures. The evolution of two-dimensional electrophoresis is briefly described. The various steps involved in 2-D PAGE, the identification and characterization of proteins separated by 2-D PAGE and the quantitative and qualitative analysis of 2-D patterns are discussed in detail and some new approaches are described. In the final section a brief outline of some of the biomedical applications of 2-D PAGE to screening of body fluids, genetic diseases, inborn errors of metabolism, cancer and neoplastic transformation are discussed.

Production of monospecific antibodies to a low-abundance hepatic membrane protein using nitrocellulose immobilized protein as antigen

Membrane proteins from primary cultures of rat hepatocytes were separated by two-dimensional polyacrylamide gel electrophoresis. The proteins were transferred to nitrocellulose paper which was then dissolved in dimethyl sulfoxide and this mixture was used as a primary immunogen in rabbits. Subsequent immunizations were performed using nonsolubilized protein immobilized on nitrocellulose paper. A monospecific polyclonal antibody was generated against a specific mitochondrial membrane protein (MP-73) for which de novo synthesis appeared to be induced by amino acid starvation of the hepatocytes. A minimum of 15-20 micrograms of protein antigen was required to elicit significant antibody production. Serum antibody titer was sufficient to allow detection of MP-73 at a serum dilution of 1:2000.

Cell surface glycoproteins of CHO cells. I. Internalization and rapid recycling

The major cell surface proteins of Chinese hamster ovary (CHO) cells have been investigated after reacting cells at 4 degrees C with the membrane-impermeant reagent, trinitrobenzenesulfonate (TNBS). Immunoprecipitation and subsequent two-dimensional, sodium-dodecyl sulfate, polyacrylamide gel electrophoresis (SDS-PAGE) of proteins from derivatized cells that had been labelled previously with [3H]D-glucosamine or [3H]L-leucine showed that TNBS reacted with most of the high molecular weight (HMW) acidic glycoproteins that became labelled with iodine by the lactoperoxidase technique and that bind the lectin, wheat germ agglutinin (WGA). After warming the cells to allow endocytosis to proceed, molecules haptenized with trinitrophenol (TNP) groups were followed radiochemically by means of [125I]anti-DNP antibodies. The half-life for internalization of proteins tagged with either [125I]anti-DNP IgG or Fab averaged about 5 min. A similar result was obtained when a monoclonal antibody directed against a single plasma membrane glycoprotein was used, or when the rate of surface loss of TNP groups unoccupied by antibodies was measured. Within 15 min at 37 degrees C, a steady-state between surface and cytoplasmic label was reached, with about 65% of the hapten located internally. Recycling of internalized TNP groups back to the cell surface also occurred rapidly (t 1/2 approximately 5 min). Most of the intracellular radioactivity was associated with a membrane fraction of density similar to that of the plasma membrane. Over a 4-h period, there was no significant entry of labeled molecules into lysosomes. By contrast, the fluid-phase marker, horseradish peroxidase, became associated with the lysosomes within 1 h. Our results are consistent with the view that the majority of plasma membrane glycoproteins are continuously being internalized and recycled at a high rate.

Rapid isolation of monoclonal antibodies specific for cell surface differentiation antigens

Two immunization procedures were compared for their ability to yield monoclonal antibodies that react with plasma membrane-bound differentiation antigens of Dictyostelium. In the first method, hybridomas prepared from BALB/c mice immunized with aggregating amoebae produced monoclonal antibodies that recognized antigens present on both growing and aggregating Dictyostelium amoebae. None of the monoclonal antibodies reacted with only the injected aggregation-stage cell type. In contrast, monoclonal antibodies that reacted with differentiation antigens were easily obtained by primary immunization of BALB/c mice with living aggregation-stage cells, followed by secondary immunization with a preparation of plasma membrane from aggregating cells or intact aggregating cells mixed with polyclonal BALB/c antiserum raised against undifferentiated cells. By this method, approximately 20% of all anti-Dictyostelium monoclonal antibodies obtained in a fusion are specific for differentiation antigens. The properties and developmental regulation of several of these antigens are described. The possible uses of this immunological method to detect unique determinants on other kinds of cells and the likely immune mechanisms that make it successful are discussed.

Skin test, RAST and clinical reactions to peanut allergens in children

One-hundred-and-four children were skin-tested with four peanut-allergen preparations, a commercial extract, extracts of raw and roast peanuts prepared by NH4HCO3 extraction, and a wheatgerm lectin-reactive glycoprotein obtained by affinity chromatography. The presence of symptoms after ingestion of peanut or peanut products was also recorded. The roast allergen extract provided the greatest specificity with eight symptomatic children having a positive skin test and only one positive skin-test reaction in an asymptomatic child in the group of 104 children tested. Despite differences in the incidence of skin-test reactions there was a strong correlation between raw, roast and commercial RAST suggesting common allergens were being identified by circulating IgE. Clinical sensitivity was observed particularly in younger children with 75% of the children being under 4 years of age. A positive roast skin test or a RAST test adds confirmation to the clinical history of allergic reactions to peanuts.

Solubilization of plasma membranes in anionic, non-ionic and zwitterionic surfactants for iso-dalt analysis: a critical evaluation

A critical study has been made of the solubilizing properties of anionic, nonionic and zwitterionic surfactants to be used in the first dimension of two-dimensional isoelectric focusing-sodium dodecyl sulphate (IF-SDS) maps. Excess of SDS is a powerful solubilizing agent, but prevents proteins from entering the IF gel. Nonidet P-40 (NP-40)-urea mixtures are mediocre solubilizing agents, but are compatible with the IF dimension. Zwitterionic detergents (zwittergents) appear to exhibit a well balanced solubilizing power and are able to generate sharp two-dimensional maps, with round spots and minimal vertical and horizontal streaking. SB3-12 and SB3-14 appear to have the best solubilizing properties; shorter surfactants (SB3-8) exhibit a poor solubilization efficiency, while longer detergents (SB3-16) bind too strongly to hydrophobic regions in proteins. The random performance of non-ionic detergents has been attributed to their ability to form mixed micelles with the carrier ampholytes used in the IF step: depending on the relative ratio of NP-40 to Ampholines, different types of micelles would be formed, which, when reaching appropriate stoichiometries and charge densities, would mimic the behaviour of natural zwittergents. Acceptable two-dimensional maps can be obtained when the sample is lysed in limiting amounts of SDS (SDS:protein = 1:3), suggesting that excess of free SDS in solution is deleterious to the IF process.

Isolation and characterization of the crystallins of the normal and cataractous canine lens

The lens crystallins were analyzed in normal dogs and Miniature offSchnauzer dogs with congenital cataract formation. There was an increase in the relative proportions of alpha and beta L-crystallin and a decrease in the beta H and gamma-crystallin with increasing age in the noncataractous lens. These trends were advanced in the age-matched cataractous lenses. "Advanced aging" trends were also noted in various polypeptide components of beta-crystallin. Specifically, the appearance of a 29K band as well as a reversal of the 26K to 27.6K ratio occurred at an earlier age in the cataractous lens than in the clear lens. Three subunits of approximately 19K, 20K, and 21.5K were present on SDS-PAGE for alpha-crystallin from the cataractous lens as opposed to only two of 19K and 21.5K from the clear lens. However, if the protein was not heated following resolubilization in buffer containing 2% SDS and 5% 2-mercaptoethanol, only two subunits of 20K and 21.5K were evident in both clear and cataractous lenses. The electrophoretic behavior observed for both alpha and gamma-crystallins did not appear to be age related.

Uteroferrin has N-asparagine-linked high-mannose-type oligosaccharides that contain mannose 6-phosphate

Uteroferrin is an iron-containing, progesterone-induced, acid phosphatase that is secreted in large amounts by the uterine endometrium of pigs. During pregnancy, it transports iron across the chorioallantois (placenta) for use in fetal hematopoiesis. In this paper, it is reported that uteroferrin synthesized by cultured endometrial explants possesses N-linked, high-mannose, oligosaccharide chains that contain 6- phosphomannose units. The latter is regarded as a possible recognition marker whereby acid hydrolases are targeted to the lysosome. On uteroferrin, however, the majority of the phosphate is in single diester linkages between the mannose and a covering N-acetylglucosamine. It is suggested that uteroferrin is a lysosomal enzyme that has assumed a role in iron transport and metabolism and is secreted because the covering N-acetylglucosamine is not removed.

The H protein isolated from tobacco mosaic virus reassociates with virions reconstituted in vitro

Virions of two strains of tobacco mosaic virus (U1 and Cc) have associated with them a small amount of a minor protein called H protein (A. Asselin and M. Zaitlin, 1978, Virology 91, 173-181), now known to be related to the viral coat protein (C.W. Collmer, V.M. Vogt, and M. Zaitlin, 1983, Virology 126, 429-448.). In the present study, a quantification technique involving disruption of virions followed by direct analysis of the component parts on SDS polyacrylamide gels was used to confirm an average of one molecule of H protein per virion for U1 TMV. H protein was separated from coat protein and purified by electrofocusing in a flatbed of granulated gel under stringent dissociating conditions. When assayed in the presence of urea, H protein has a pI of approximately 5.4, coat protein has a pI of approximately 4.9. Proteinase K-treated TMV RNA and H-protein-free TMV coat protein were reconstituted in vitro with or without H protein and the resulting virions were analyzed. A small amount of H protein reassociated with virions reconstituted in vitro (less than 10% of the amount found in native virions) and became resistant to degradation by trypsin, but such virions were no different from virions reconstituted without H protein in terms of yield of reconstituted particles or infectivity. In mixed reconstitution experiments with RNA and coat protein from strains U1 and Cc in all four possible combinations and with U1 H protein, the H protein always associated with the U1 coat protein. This demonstrated U1-H protein affinity for a specific coat protein rather than a specific RNA. It is unlikely that H protein functions in the early stages of viral infection, although the possibility of its having some other role in the life cycle of TMV remains.

Isolation of a domain of the plasma membrane in Chinese hamster ovary cells which contains iodinatable, acidic glycoproteins of high molecular weight

A light vesicle fraction, apparently derived from the plasma membrane, was obtained following breakage of Chinese hamster ovary (CHO) cells by means of a fluid pump disrupting device. The final preparation was enriched approx. 40-fold over the homogenate in K+,Na+-stimulated ATPase and phosphodiesterase I, but only approx. 10-fold in 125I specific radioactivity after lactoperoxidase-catalyzed iodination. This preparation was compared with another plasma membrane fraction purified as large sheets via a two-phase centrifugation procedure. Two-dimensional polyacrylamide gel electrophoresis followed by Coomassie blue staining indicated that both fractions were fairly similar in polypeptide composition, although a few consistent differences were evident. However, staining of glycoproteins by the periodic acid-Schiff technique or by overlaying with 125I-labeled concanavalin A showed that the vesicle fraction was highly enriched in groups of high molecular weight, acidic glycoproteins which stain only weakly with Coomassie blue. These glycoproteins also bound 125I-labeled ricin I agglutinin and wheat germ agglutinin. They appear to be the major receptors for wheat germ agglutinin on the CHO cell surface. After surface labeling of cells by the 125I-lactoperoxidase technique, the membrane sheet fraction contained a large number of iodinated polypeptides, whereas labeling in the vesicle fraction was restricted almost entirely to the high molecular weight, acidic glycoproteins. It is proposed that the vesicle fraction constitutes a specific domain of the cell surface which is coated on its exterior by this group of glycoproteins. These components probably mask underlying proteins of the plasma membrane from external labeling.