Protein polymorphism in sugarcane revealed by two-dimensional gel analysis

Summary In order to identify molecular markers for the analysis of the sugarcane genome, proteins extracted from apical segments of shoot tissues were resolved by a combination of equilibrium (IEF) and nonequilibrium (NEPHGE) two-dimensional polyacrylamide gel electrophoresis. A number of taxa of the Saccharum complex group (Saccharum species and the related genera of Andropogoneae) with presumed contributions to the sugarcane genome were surveyed. Protein profiles were compared to a reference map consisting of 1,482 protein spots from the noble cane,Saccharum officinarum L. Fifty-three polypeptides, representing about 3.6% of the total resolved spots, showed interspecific variation, whereas 78 polypeptides, about 5.3% of the total, showed intergeneric variation. Of the total polymorphic protein spots, qualitative (presence/absence) variation was more prevalent among the wild than among the cultivated species of the genusSaccharum, but the quantitative (spot intensity) variation was similar for both groups. The population of protein spots showing qualitative and quantitative variations was similar among the related genera of Andropogoneae. These polymorphic proteins can be used in genetic and evolutionary studies of the sugarcane genome.     

Comparative proteomics of leaf,stem, and root tissues of synthetic Brassica napus

Comparative proteomics was applied to three vegetative organs of Brassica napus, the leaf, stem, and root using 2‐DE. Among the >1600 analyzed spots, 43% were found to be common to all three organs, suggesting the existence of a “basal” or ubiquitous proteome composed of housekeeping proteins. The green organs, leaf, and stem, were closely related (～80% common spots) while the root displayed more organ‐specific polypeptides (～10%). Reference maps were established using MS, allowing the identification of 93, 385, and 266 proteins in leaf, stem, and root proteomes, respectively. Bioinformatic analyses were also performed; in silico functional categorization and cellular localization allow obtaining a precise picture of the cell molecular network within vegetative organs. These proteome maps can be explored using the PROTICdb software at the following address: http://bioinformatique.moulon.inra.fr/proticdb/web_view/.     

Floral-specific polypeptides of the Japanese morning glory

Polypeptides from stems, leaves, sepals, corollas, stamens and pistils of the Japanese morning glory (Ipomoea nil Roth (Pharbitis nil Chois.)) were separated by one- and two-dimensional gel electrophoresis and visualized by silver staining. The majority of polypeptides were expressed in two or more organs, while those specific to only one organ were comparatively rate. Among the polypeptides of the former class were two which appeared to be floral-specific. A 46-kDa (kilodalton) polypeptide was expressed in corollas, stamens and pistils, whereas a 32-kDa polypeptide was observed only in extracts prepared from reproductive organs. Polypeptide spots from the various organs were compared with those from leaves, and it was found that sepals and stems shared 40–50% of their polypeptides with leaves, whereas corollas, stamens and pistils shared 20% or less. The latter organs shared 120 polypeptides or roughly 15% of those identified in the floral extracts. Floralorgan-specific polypeptides comprised nearly 10% of the total floral polypeptides identified.Abbreviations kDa kilodalton - PAGE polyacrylamide gel electrophoresis - SDS sodium dodecylsulfate     

Two dimensional gel electrophoresis patterns of total, in vivo labelled and in vitro translated polypeptides from orange flavedo during maturation and following ethylene treatment

Changes in the pattern of silver stained (SS), in vivo [³⁵S]-methionine labelled (IL), and in vitro poly(A⁺)RNA translated (IT) polypeptides from the flavedo of orange fruits [ Citrus sinensis (L). Osbeck cv. Washington Navel] picked at three stages of maturity (mature-green, turning and fully coloured) and treated with different doses of ethylene (0, 1 and 10 μl 1⁻¹) were studied by two dimensional gel electrophoresis (using isoelectric focusing and nonequilibrium pH gradient as a first dimension). More than 500 SS, 300 IL, and 250 IT spots were detected in the gels. During maturation 32 SS, 2 IL and 2 IT spots decreased, whereas 2 SS, 3 IL and 2 IT spots increased. These results indicate that the maturation process is associated with a decrease of many accumulated flavedo proteins and with an increase of a reduced number of specific polypeptides, and that some of them may be regulated at the level of gene expression. All the spots which increased with maturity also increased with ethylene treatment, suggesting a role for this hormone in the maturation process. Ten IT spots which were not affected by maturity increased following ethylene treatment, while only 2 SS and 2 IL spots underwent this pattern of variation. Three spots recognized specifically by tobacco chitinase polyclonal antibodies remained essentially unaltered, whereas one spot whose intensity decreased significantly during maturation and ethylene treatment was identified as the large subunit of ribulose-1,5-bisphosphate carboxylase.     

Seed-protein variation in maritime pine (Pinus pinaster Ait.) revealed by two-dimensional electrophoresis: genetic determinism and construction of a linkage map

Summary Proteins from haploid megagametophytes from 18 trees were studied by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). A total of 222 seeds, an average of 12 per tree, were analysed individually. 150 protein spots appeared to segregate on the polyacrylamide gels in at least tree. Genetic interpretations were made to define the number of loci responsible for the presence versus absence, staining differences or position variation of the segregating spots. The complete covariation observed between some spots could be the result of either the separation of a single gene product into two or more constituents, very close linkage, or the action of a pleiotropic gene. Human genetics techniques were used to map the 84 putative loci detected. Sixty-five loci were organised in 17 linkage groups, whereas 19 remained unlinked.     

Study on nuclear and cytoplasmic genome expression in wheat by two-dimensional gel electrophoresis

Summary Two-dimensional gel electrophoresis of denaturated proteins were performed at five developmental stages or organs (hereafter referred to as stage-organs) on two wheat lines with four different cytoplasms. Five hundred and fifty to 712 reproducible spots were scored depending on the stage-organ. Each stage-organ is unambiguously characterized and several types of control of protein quantity are recorded. Post-translational modifications are hypothetized and may sometimes be stagespecific. Two cytoplasmic patterns are found: one for the euplasmic lines with Triticum aestivum cytoplasm and one for the alloplasmic lines with Aegilops juvenalis, Ae. ventricosa and Ae. kotschyi cytoplasms. Cytoplasmic variation is observed for 28 spots showing position difference, all of which are probably products of the LS gene, and for four spots showing differences for regulation of protein quantity. Nuclear variation between Chinese Spring and Selkirk is found for 20 allelic differences and for 20 regulatory systems, the latter number being probably underestimated.     

Collagen-Induced Changes in the Pattern of Protein Synthesis of Fibroblasts

Cells were cultured on plastic, collagen fibrils or gelatin. General protein synthetic activity of cells did not show any significant, difference among the three substrates, whereas the pattern of protein synthesis was substrate-dependent. Profiles of protein synthesis (polypeptide maps) were obtained by subjecting two-dimensional autoradiograms of poly-acrylamide gel electrophoresis to a computer-assisted image analyzer. Major polypeptide spots expressed on gelatin were rather like those on plastic. Collagen fibrils caused significant changes in the polypeptides map. Fibroblasts on collagen fibrils produced 364 spots of polypeptides, 26% of which were synthesized specifically on collagen fibrils. The remaining was shared by cells on plastic and was categorized into three groups: (1) polypeptides whose synthesis was up-regulated by collagen fibrils (26% of the total); (2) polypeptides that were expressed equally on both plastic and collagen fibrils (51%); and (3) polypeptides down-regulated by'collagen fibrils (23%). A protein with molecular weight of 150 K and an isoelectric point (pI) of 7.3 was one of the collagen-induced and worthy of further analysis. This protein was found to change its pi depending upon the amounts of collagen fibrils and was shown to be located in the mitochondrial fraction.     

Collagen-Induced Changes in the Pattern of Protein Synthesis of Fibroblasts

Cells were cultured on plastic, collagen fibrils or gelatin. General protein synthetic activity of cells did not show any significant, difference among the three substrates, whereas the pattern of protein synthesis was substrate-dependent. Profiles of protein synthesis (polypeptide maps) were obtained by subjecting two-dimensional autoradiograms of poly-acrylamide gel electrophoresis to a computer-assisted image analyzer. Major polypeptide spots expressed on gelatin were rather like those on plastic. Collagen fibrils caused significant changes in the polypeptides map. Fibroblasts on collagen fibrils produced 364 spots of polypeptides, 26% of which were synthesized specifically on collagen fibrils. The remaining was shared by cells on plastic and was categorized into three groups: (1) polypeptides whose synthesis was up-regulated by collagen fibrils (26% of the total); (2) polypeptides that were expressed equally on both plastic and collagen fibrils (51%); and (3) polypeptides down-regulated by'collagen fibrils (23%). A protein with molecular weight of 150 K and an isoelectric point (pI) of 7.3 was one of the collagen-induced and worthy of further analysis. This protein was found to change its pi depending upon the amounts of collagen fibrils and was shown to be located in the mitochondrial fraction.     

Proteomic Analysis of Allergen and Antinutritional Proteins in Wild and Cultivated Soybean Seeds

In this study, profiles of allergen and antinutritional proteins both in wild (Glycine soja) and cultivated (Glycine max) soybean seeds were compared. We used two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) for the separation of proteins at two different pH ranges and applied a combined matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and liquid chromatography mass spectrometry (LC-MS/MS) analysis for the identification of proteins. Although overall distribution patterns of the allergen (Gly m Bd 60K, Gly m Bd 30K, Gly m Bd 28K) and antinutritional proteins (trypsin inhibitors and lectin) appeared similar, there was remarkable variation in the number and intensity of the protein spots between wild and cultivated genotypes. The wild genotype showed fifteen polypeptides of Gly m Bd 60K and three polypeptides of trypsin inhibitors. The cultivated genotypes showed twelve polypeptides of Gly m Bd 60K and two polypeptides of trypsin inhibitors. In contrast, the cultivated genotype showed two polypeptides of Gly m Bd 30K and three polypeptides of lectin and the wild genotype showed two and one polypeptides of Gly m Bd 30K and lectin, respectively. Two polypeptides of Gly m Bd 28K were observed in both genotypes. This is the first study reporting the comparative analysis of allergen and antinutritional proteins in both wild and cultivated soybean genotypes using combined proteomic tools.     

Protein profiles in pin and thrum floral organs of distylous Averrhoa carambola L.

Floral organs (tepal, stamen, style, including stigma, and ovary) from immature and mature (1 day prior to anthesis) flower buds of pin and thrum morphs of Averrhoa carambola were subjected to one and two-dimensional IEF/SDS-PAGE gel electrophoresis and visualized by silver staining. One-dimensional gel electrophoresis of organ extracts from mature floral buds showed a number of protein bands common to all organs in both pin and thrum morphs. In the stamen and style, these bands differed in intensity between the two morphs. Under two-dimensional gels, the differences in protein profiles between the two morphs were more distinct in these organs. When compared with polypeptide spots from leaflets, a total of 14 floral organ-specific polypeptides was detected, the majority appearing in the stamen, followed by the style but none in the ovary. In the stamen, most of these polypeptides were detected in both the pin and thrum morphs. However, in the style, a 72-kDa polypeptide was detected exclusively in the pin morph, and this was also the most abundant floral organ-specific polypeptide. Floral organ-specific polypeptides of 45 kDa (detected in stamens of the thrum morph) and 70 kDa (detected in stamen and style of both morphs) were found to bind concanavalin A.     

Gene expression in normal and virally transformed mouse 3T3B and hamster BHK21 cells

Cell lines 3T3B (mouse), 3T3B-SV40, BHK21 (hamster) and BHK21 polyoma virus (PyY) were labelled with [³⁵S]methionine under conditions in which 500–600 cpm were incorporated per cell during a 20 h incubation period. Two-dimensional gel electrophoresis analysis of the total [³⁵S]methionine-labelled polypeptides from 200–300 cells followed by fluorography revealed about 500 acidic (isoelectric focusing, IEF) and 150 basic polypeptides (non-equilibrium pH gradient electrophoresis, NEPHGE) whose position could be reproducibly assessed. Counting of 33 abundant acidic polypeptides present in both 3T3B and 3T3B-SV40 revealed significant changes in the relative proportion of ten of them. Seven, including the subunit of the 100 Å filaments ‘fibroblast type’ (55K) (1.1% in 3T3B; 0.6% in 3T3B-SV40), three cytoarchitectural proteins and three soluble proteins, corresponded to a decrease of 40% or more in the radioactivity of the spots in transformed cells, and only in three cases was there a significant increase in radioactivity of polypeptides in 3T3B-SV40 cells. Among the polypeptides that show less than 40% variation we have identified total actin (42K) (13% of total label in 3T3B; 10% in 3T3B-SV40), α- and β-tubulin (55K) (1.6% of total label in 3T3B; 2% in 3T3B-SV40), eleven polypeptides present in Triton skeletons, and nine soluble proteins. We have also observed 25 obvious changes in polypeptide intensities (16 acidic and 9 basic) but these were not quantitated. Only three polypeptides were found in transformed cells that were not detected in normal cells. One of these corresponded to the large T antigen and the other two to Triton-soluble proteins of a molecular weight in the range of 52–54K. Similar quantitative studies on the hamster BHK21/BHK21PyY pair confirmed at least the major observations made in 3T3B and 3T3B-SV40.     

Protein synthesis in mitochondria purified from roots, leaves and flowers of sugar beet

Highly purified, intact and functional mitochondria were isolated from roots and leaves of a number of fertile and male-sterile lines of sugar beet ( Beta vulgaris L.). Intact and functional mitochondria were successfully isolated from the flowers of fertile plants, but not from the flowers of male-sterile plants. Several alternative methods for the homogenization of male-sterile flowers were tried. Their failure suggests that the mitochondria from male-sterile flowers are more sensitive to mechanical damage than mitochondria from fertile, or other organs of male-sterile, plants.
In organello protein synthesis was optimized with respect to the total concentration of amino acids, the concentration of [³⁵S]-methionine, pH and respiratory substrate. Inhibitor experiments showed that the mitochondrial preparations contained mitochondrial translational activity only. With the exception of one band, no processing or proteolytic breakdown in either root or leaf mitochondrial protein synthesis products could be detected in pulse-chase experiments. Submitochondrial fractionation experiments showed the presence of two soluble polypeptides, whereas all other polypeptides were membrane bound.
The polypeptide patterns of root, leaf and flower mitochondria were very similar with the exception of 4 polypeptides involved in glycine oxidation. These 4 polypeptides were present in large amounts in leaf mitochondria and just detectable in flower mitochondria. The patterns of polypeptides syntesized in mitochondria isolated from roots, leaves and flowers also showed a number of organ-specific differences. Six qualitative and 6 quantitative differences were found between mitochondria isolated from these three organs. No unique polypeptides were found to be synthesized either by flower mitochondria or by mitochondria from roots and leaves of male-sterile plants compared to their male-fertile counterparts.     

BSP A1/A2-like proteins in ram seminal plasma

The objective of this study was to assess the protein profile of ovine seminal plasma using 2D-PAGE and verify if BSP A1/A2 are present in ovine seminal plasma. Seminal plasma was collected from three mature rams and pooled to eliminate individual differences. Seminal plasma samples were submitted to 2D-PAGE using 12% acrylamide gels. The image analysis software identified 21 protein spots on the air-dried gel, with molecular weight ranging from 15 to 115 kDa and pI 3.2 to 8.7. The most prominent spots were those <30 kDa. The most intensely stained spots were: 3 (18-19 kDa, pI 4.8-5.0), 5 (17-18 kDa, pI 5.0-5.2), 7 (15-16 kDa, pI 6.2-6.4), and 23 (105-108 kDa, pI 6.8-7.0). Three of these spots (spots 3, 5 and 7, respectively) accounted for 41.1% of the relative intensity of the spots of the gels, based on the intensity of the Comassie blue staining. Western blot analysis indicated that spots 3 and 5 were similar to BSP A1/A2 (16.5, pI 4.7-5.0 and 16 kDa, pI 4.9-5.2) identified in Manjunath's studies [Manjunath P, Sairam MR. Purification and biochimical characterization of three major acid proteins (BSP A1, BSP A2 and BSP A3) from bovine seminal plasma. Biochem J 7 (1987) 685-92.], based on the specific reaction of the polyclonal antibody to those spots.     

Relationship between feeding,mating, vitellogenin production and vitellogenesis in the tickDermacentor variabilis

Anti-vitellin IgG directed againstDermacentor variabilis egg vitellin was used in sodium dodecyl sulfate polyacrylamide (SDS-PAGE) gradient gel immunoblots to detect the presence of vitellin and its precursor, vitellogenin, in the organs of feeding adults and in the immature stages of this tick. Vitellin polypeptides were found in the egg, larvae, nymph, and in the unfed adult stages of both sexes. Vitellin polypeptides were first detected in the ovary of mated females during the rapid-engorgement feeding, period. These polypeptides were also present in the ovaries of ovipositing females, unmated females fed for extended periods, and fed unmated females that were detached from the host and held for 12 h before dissection. The same anti-vitellin antibody was used in immunoblots to monitor the appearance of vitellogenin in the organs and hemolymph of female ticks. Immunoreactive peptides of vitellogenin were found in the fat body, midgut, and hemolymph of pre-rapid-engorging mated and unmated females. These polypeptides were not found in fed males nor in Malpighian tubes of feeding or ovipositing females Our data supported the following conclusions: 1) presence of immunoreactive vitellogenin in the adult female fat body, hemolymph, and midgut was, dependent upon feeding; 2) in mated feeding females, we could not detect the uptake of vitellogenin by the ovary until rapid engorgement; 3) in unmated females, vitellogenesis did not, begin unless prolonged feeding occurred; and 4) during the early developmental stages of this tick, vitellin served as an embryonic nutrient reserve and as a reserve against starvation between feedings.     

Changes in the pattern of protein synthesis during differentiation of the Ascomycete Sphaerostilbe repens

The vegetative mycelium of Sphaerostilbe repens Berkeley and Broome (strain CBS 275-60) gives rise, within 48 h, to aggregated organs composed of coremia and rhi-zomorphs. Developmental changes in polypeptide patterns were studied by one- and two-dimensional polyacrylamide gel electrophoresis after cells had been induced to undergo synchronized differentiation. One-dimensional gel electrophoresis revealed only minor changes during the morphogenesis. Of the 300 polypeptides resolved by two-dimensional gel electrophoresis, nearly 12% either increased or decreased during coremium and rhizomorph differentiation. Some polypeptides appeared to be unique to one or the other of the cell preparations and represented apparent qualitative differences. During the first 24 h of differentiation, about 20 polypeptide spots appeared, 6 were enhanced, 4 were reduced and 32 disappeared. Over the next 24 h changes in the population of proteins were less marked: 14 new proteins were revealed and 9 increased in intensity while 15 declined and 9 were no longer detectable. Five proteins which were present at a significant level only during the first stages of differentiation, may therefore, putatively be designated as aggregation-specific polypeptides.     

A comprehensive study of genic variation in natural populations of Drosophila melanogaster. VII. Varying rates of genic divergence as revealed by two-dimensional electrophoresis.

Four sibling species from the melanogaster subgroup (Drosophila melanogaster, D. simulans, D. sechellia, and D. mauritiana) were studied for genetic divergence, by high-resolution two-dimensional protein electrophoresis (2DE) coupled with ultrasensitive silver staining. A total of eight tissues from larval and adult developmental stages representing both gonadal (germ-line) and nongonadal (somatic) tissues were analyzed for protein divergence between species. Close to 400 polypeptides (protein spots) were scored from each tissue and species, and protein divergence was measured on the basis of qualitative differences (presence/absence) of protein spots in pairwise species comparisons. The observed levels of genic divergence varied among tissues and among species. When larval hemolymph proteins (which are known to be highly polymorphic) were excluded, there was no evidence to suggest that either the larval or adult-stage proteins, as a whole, are more diverged than the other; variation between different tissues rather than between developmental stages appears to be the most significant factor affecting genetic divergence between species. The reproductive tissue (testis and accessory gland) showed more divergence than did the nonreproductive tissue; D. melanogaster testis (from both larvae and adult males) showed the highest level of divergence. In view of the previous observation that D. simulans, D. mauritiana, and D. sechellia show similar but significantly less reproductive isolation from each other than from D. melanogaster, the present results suggest a correlation between the levels of reproductive-tract-protein divergence and the degree of reproductive isolation in these species.     

HLA-D region antigen-associated invariant polypeptides as revealed by two-dimensional gel analysis. Glycosylation and structural inter-relationships

Two-dimensional polyacrylamide gel analyses of immunoprecipitates of HLA-D region antigens prepared from [35S]methionine-labeled B lymphoblastoid cells revealed a number of invariant polypeptides (Ii and theta) that co-precipitate with the alpha and beta polypeptides of the class II (Ia) antigens. The invariant polypeptides comprised at least three Ii spots of Mr = 31,000 (Ii1-Ii3) and a series of six theta spots of Mr = 34,000 (theta 1-theta 6). The structural inter-relationships of these polypeptides have been investigated. Tryptic peptide fingerprints showed that Ii and theta have closely related amino acid sequences. In contrast, the fingerprints of the HLA-DR alpha and beta polypeptides clearly differed from those of theta and Ii as well as from each other. Analyses of immunoprecipitates prepared from cells cultured in the presence of tunicamycin revealed the presence of two N-linked oligosaccharides on each invariant polypeptide and suggested that the more acidic theta polypeptides (theta 1 and theta 2) differed from the other invariant polypeptides by the presence of sialic acid on one or both N-linked oligosaccharides. Removal of sialic acid by neuraminidase simplified the pattern of theta spots into three distinct Ii-related polypeptides. Endo-beta-N-acetylglycosaminidase H digestion indicated that the individual theta polypeptides represent stages in carbohydrate processing whereby Ii with two N-linked immature oligosaccharides are converted initially to theta 6-theta 3 with one immature and one complex, but nonsialylated, oligosaccharide and finally to theta 2-theta 1 with two complex oligosaccharides. Digestion of the theta polypeptides with N-acetylgalactosamine oligosaccharidase indicated that the theta spots are also derived by O-glycosylation from the Ii polypeptides. This assignment is supported by results obtained using monensin to block glycosylation within the Golgi. At least three spots persisted after complete removal of the N- and O-linked oligosaccharides, suggesting the presence of a family of invariant polypeptides differing in amino acid sequence.     

Structural relationships between the surface antigens of ground squirrel hepatitis virus and human hepatitis B virus.

Several physical, chemical, and serological properties of surface antigen particles from ground squirrel hepatitis virus (GSHsAg) and human hepatitis B virus (HBsAg) were compared. GSHsAg and HBsAg particles were purified from positive sera by gel chromatography and isopycnic centrifugation. Both antigens consisted mainly of spherical particles with an average diameter of approximately 20 nm and a buoyant density in CsCl of approximately 1.19 g/ml. Their UV absorption spectra indicated the presence of more tryptophane than tyrosine and the absence of detectable nucleic acid. GSHsAg was found to contain two major polypeptides of approximately 23,000 and 27,000 daltons, with electrophoretic migration rates distinctly faster than those of the two major polypeptides of HBsAg particles. After radiolabeling of purified antigen preparations with Bolton-Hunter reagent, the two major polypeptides of GSHsAg showed almost identical tryptic peptide maps. The tryptic peptide map of the major polypeptide from GSHsAg contained 13 of 37 spots also present in the map of the major HBsAg polypeptide, and 13 of 27 spots in the map of the major HBsAg polypeptide were also present in the map of the major GSHsAg polypeptide. This suggests considerable sequence homology between the major surface antigen polypeptides of the two viruses. However, there was only a weak serological cross-reactivity between antigens of the two viruses. Using an anti-HBs-containing serum with a relatively strong cross-reactivity, GSHsAg was found to consist of at least two antigenically different subspecies. The more strongly cross-reacting from had a slightly higher buoyant density than the other antigenic form.     

In vitro biosynthesis of rat sperm outer dense fiber components

Conditions were established for in vitro culture of seminiferous tubules of adult rat testis. Tubules fragments were able to incorporate radioactive amino acids for up to 6 hours of incubation at 32 degrees C in a modified Eagle's minimum media, indicating biosynthetic activity. Addition of D-glucose (11 Mm) increased the incorporation of either [3H] Leucine or [35S] Methionine four-fold in the protein components of seminiferous tubules. Polyclonal antibodies against outer dense fibers (ODF) polypeptides, which represent approximately 30% of the total sperm proteins, immunoprecipitated 5% of the total radioactivity from cultures carried out either in the presence or absence of D-glucose. Moreover, antibodies specific for the 27-30 kilodalton polypeptides of ODF immunoprecipitated 2% of the total radioactivity, showing no differences in the presence and absence of D-glucose. This study indicates that ODF polypeptides can be synthesized in vitro at 32 degrees C with and without D-glucose.