Use of avidin-sepharose to isolate and idenify biotin polypeptides from crude extracts

A method of isolating and identifying biotin polypeptides from crude cellular extracts is described. Protein samples are run on small avidin-Sepharose columns. After washing away nonspecifically bound protein, the biotin enzymes are eluted using an SDS-urea solution. The inactive polypeptides are then electrophoresed on SDS-polyacrylamide gels. The biotin polypeptides in the gels are identified by using fluorescent avidin or by analyzing for radioactive biotin-labeled polypeptides. A sensitive method for assaying biotin using avidin-Sepharose is also described.     

Separation of human erythrocyte membrane associated proteins with one-dimensional and two-dimensional gel electrophoresis followed by identification with matrix-assisted laser desorption/ionization-time of flight mass spectrometry

A classical proteomic analysis was used to establish a reference map of proteins associated with healthy human erythrocyte ghosts. Following osmotic lysis and differential centrifugation, ghost proteins were separated by either one-dimensional gel electrophoresis (1-DE) or two-dimensional gel electrophoresis (2-DE). Selected protein bands or spots were excised and trypsinized before mass spectrometric analyses and data mining was performed using the SWISS-PROT and NCBI nonredundant databases. A total of 102 protein spots from a 2-D gel were successfully identified. These corresponded to 59 distinct polypeptides with the remaining 43 being isoforms. As for the 1-D gel, 44 polypeptides were identified, of which 19 were also found on the 2-D gel. Most of the 19 common polypeptides were membrane cytoskeletal proteins that are often referred to as the "band" proteins. The remaining 25 polypeptides that were found exclusively on 1-D gels were proteins with high hydrophobicity (e.g., sorbitol dehydrogenase and glucose transporter) and high molecular mass (e.g., Kell blood group glycoprotein and Janus-kinase 2). A higher number of signaling proteins was also identified on 1-D gels compared to 2-D gels. These included Ras, cAMP dependent protein kinase and TGF-beta receptor type 1 precursor.     

Analysis of pea chloroplast inner and outer envelope membrane proteins by two-dimensional gel electrophoresis and their comparison with stromal proteins

Analysis of inner and outer pea (Pisum sativum var. Laxtons Progress No. 9) chloroplast envelope membranes by sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that, although the two membranes have distinct polypeptide compositions, there are several comigrating polypeptides in the two membrane fractions. To determine whether these comigrating polypeptides were identical by criteria other than molecular weight, the membrane proteins were analyzed by two-dimensional gel electrophoresis. The results demonstrated that an 86-kilodalton band found in both membranes represents at least two different polypeptides, one an outer membrane protein and the other an inner membrane protein. Several other polypeptide bands found in both membranes appear to be of stromal origin. Two of these polypeptides were shown to be the large and small subunits of ribulose 1,5-bisphosphate carboxylase. The large subunit was identified by two-dimensional electrophoresis of envelope membranes to which stromal proteins were added. Additionally, the large and small subunits of ribulose 1,5-bisphosphate carboxylase were immunologically identified using an electrophoretic transfer procedure coupled with an enzyme-linked immunosorbent assay. Various treatments, including sonication, resulted in no significant loss of the stromal polypeptides from the outer envelope membranes. Based on these results, it is suggested that the stromal proteins are not simply bound to the outer surface of the vesicles.     

Biosynthesis of pigment-protein complex polypeptides in bacteriochlorophyll-less mutant cells of Rhodopseudomonas capsulata YS

Bacteriochlorophyll-less mutant cells of Rhodopseudomonas capsulata YS were capable of synthesizing pigment—protein complex polypeptides under conditions permitting the formation of the photosynthetic apparatus in the wild type. Individual polypeptides were identified by immunoprecipitation. Pulse-chase experiments revealed that the polypeptides did not accumulate in the membranes but underwent rapid degradation. The data suggest that bacteriochlorophyll is needed to stabilize the polypeptides of pigment—protein complexes.     

A 115 kDa calmodulin-binding protein is located in rat liver endosome fractions.

The distribution of calmodulin-binding polypeptides in various rat liver subcellular fractions was investigated. Plasma-membrane, endosome, Golgi and lysosome fractions were prepared by established procedures. The calmodulin-binding polypeptides present in the subcellular fractions were identified by using an overlay technique after transfer from gels to nitrocellulose sheets. Distinctive populations of calmodulin-binding polypeptides were present in all the fractions examined except lysosomes. A major 115 kDa calmodulin-binding polypeptide of pI 4.3 was located to the endosome subfractions, and it emerges as a candidate endosome-specific protein. Partitioning of endosome fractions between aqueous and Triton X-114 phases indicated that the calmodulin-binding polypeptide was hydrophobic. Major calmodulin-binding polypeptides of 140 and 240 kDa and minor polypeptides of 40-60 kDa were present in plasma membranes. The distribution of calmodulin in the various endosome and plasma-membrane fractions was also analysed, and the results indicated that the amounts were high compared with those in the cytosol.     

New insights into the rat spermatogonial proteome: identification of 156 additional proteins

Despite the essential role played by spermatogonia in testicular function, little is known about these cells. To improve our understanding of their biology, our group recently identified a set of 53 spermatogonial proteins using two-dimensional (2-D) gel electrophoresis and mass spectrometry. To continue this work, we investigated a subset of the spermatogonial proteome using narrow range immobilized pH gradients to favor the detection of less abundant proteins. A 2-D reference map of spermatogonia in the pH range 4-9 was created, and protein entities fractionated in a pH 5-6 2-D gel were further processed for protein identification. A new set of 156 polypeptides was identified by peptide mass fingerprinting and tandem mass spectrometry. These polypeptides corresponded to 102 different proteins, which reflect the complexity of post-translational modifications. Seventy-nine of these proteins were identified for the first time in spermatogonia. All identified proteins were classified into functional groups. This work represents a first step toward the establishment of a systematic spermatogonia protein database.     

Identification of polypeptides encoded by the replication of resistance factor R100

Several polypeptides encoded by the resistance factor R100 were synthesized in a DNA-dependent protein synthesis system using a miniplasmid derived from R100 as a template. Nine polypeptides were detected. The locations of the genes for these polypeptides were investigated by using DNA restriction fragments as templates, and also by examining the effect of restriction endonuclease digestion of these templates on the synthesis of the polypeptides. The genes for seven of the polypeptides were identified or located by comparing the results with the known nucleotide sequence and restriction map of this region. Three of the polypeptides appeared to be encoded by the repA1, repA2 and repA3 genes, which are located in the region required for the replication of R100 and the expression of incompatibility. Four of the polypeptides were encoded by regions that are not required for the autonomous replication of R100 in Escherichia coli. One is the gene product of finO, which regulates the expression of the tra genes on R100.The miniplasmid used for these experiments carried one ISI sequence that has three potential genes. However, no polypeptide was detected that could be clearly demonstrated to be encoded by ISI.     

Detection of the interstrain polymorphism of heart muscle proteins in mice using two-dimensional electrophoresis

Cardiac muscle proteins of four inbred murine strains were analyzed by one- and two-dimensional electrophoresis. Of those, 27 and 161 protein fractions were characterized in terms of molecular mass and relative electrophoretic mobility. The protein fractions were identified as corresponding to creatine phosphokinase, myoglobin and an albumin-like protein. Six polypeptides characterized by interlinear polymorphism were identified.     

Comparison of surface proteomes of enterotoxigenic (ETEC) and commensal Escherichia coli strains

Pathogenesis of enterotoxigenic Escherichia coli (ETEC) infections involves colonization of the small intestine mediated by cell-surface fimbriae (CS) or colonization fimbriae antigens (CFA). However, protection against reinfection of ETEC is also conferred by somatic antigens rather than by virulence factors. To discover ETEC specific somatic antigens, the surface proteome of the ETEC H10406 strain was compared with that of non-pathogenic E. coli K12 strains. In this study, we were using stable isotope labelling with amino acids in cell culture (SILAC) technology for the labelling and relative quantification of surface proteins in order to identify polypeptides that are specifically present on ETEC strains. Outer membrane proteins were isolated, separated by gel electrophoresis, and identified by mass spectrometry. Twenty-three differentially expressed cell-surface polypeptides of ETEC were identified and evaluated by bioinformatics for protein vaccine candidates. The combination of being surface-exposed and present differentially makes these polypeptides highly suitable as targets for antibodies and thus for use in passive or active immunisation/vaccination.     

Cell-wall proteins from Sitka spruce xylem are selectively insolubilised during formation of dehydrogenation polymers of coniferyl alcohol

Extracts from the lignifying xylem of Sitka spruce that were enriched in cell-wall-associated glycoproteins contained peroxidase and oxidase activity and readily formed lignin-like water-insoluble dehydrogenation polymers (DHPs) from coniferyl alcohol (CA) when supplied with H2O2. During the formation of DHPs, the abundance of a number of polypeptides in the extracts was diminished. However, these polypeptides were also diminished in control reactions that contained H2O2 but lacked CA. Polypeptides could be recovered from the DHPs by heating in SDS-PAGE sample buffer but no insolubilised polypeptides could be recovered from the + H2O2 reactions. Although most of the DHP-bound polypeptides were easily removed by pre-washing the DHPs, two polypeptides at 125 and 52 kDa remained tightly bound to the DHPs. The abundance of the two DHP-bound polypeptides mirrored the diminution of 120 and 46 kDa polypeptides in the extracts. The N-terminal protein sequences of the 125 and 52 kDa DHP-bound polypeptides were essentially identical to the sequences obtained from the 120 and 46 kDa polypeptides from the extracts, which confirmed that the DHP-bound polypeptides were derived from these soluble polypeptides. The 125-kDa DHP-bound polypeptide yielded an N-terminal protein sequence that was identical to a laccase-type oxidase previously identified in similar extracts from lignifying Sitka xylem. The N-terminal protein sequence of the 46-kDa polypeptide was homologous with a subset of plant peroxidases. The DHPs had tightly bound peroxidase and oxidase activity, which suggested that these polypeptides were active in their insolubilised state. The mechanism and selectivity of insolubilisation of these enzymes is discussed.     

Characterization of the major immediate-early polypeptides encoded by murine cytomegalovirus.

The immediate-early (IE) infected cell proteins induced by the murine cytomegalovirus (Smith strain) were studied. These polypeptides were identified as IE proteins by their synthesis in the presence of actinomycin D after removal from a protein synthesis block mediated by cycloheximide. By using a murine antiserum against murine cytomegalovirus, three abundant polypeptides of 89, 84, and 76 kilodaltons (kd) were immunoprecipitated. The three major proteins are phosphorylated but not glycosylated and share antigenic determinants recognized by monoclonal antibodies. The 84 and 76-kd polypeptides represent post-translational modification products of the 89-kd protein. Accordingly, in vitro translation of IE infected cell RNA revealed only the 89-kd polypeptide. The viral origin of the RNA species directing the synthesis of the major 89-kd IE polypeptide was verified by hybrid selection of IE RNA with DNA fragments representing the region from 0.769 to 0.815 map units of the murine cytomegalovirus genome. IE polypeptides were found to be located in the nuclei and the cytoplasm of infected cells. Studies on the kinetics of IE polypeptide synthesis revealed negative regulatory effects on IE gene expression correlated with the synthesis of early proteins.     

Polypeptide Synthesis in Simian Virus 5-Infected Cells

Polypeptide synthesis in three different cell types infected with simian virus 5 has been examined using high-resolution polyacrylamide slab gel electrophoresis, and all of the known viral polypeptides have been identified above the host cell background. The polypeptides were synthesized in infected cells in unequal proportions, which are approximately the same as they are found in virions, suggesting that their relative rates of synthesis are controlled. The nucleocapsid polypeptide (NP) was the first to be detected in infected cells, and by 12 to 14 h the other virion structural polypeptides were identified, except for the polypeptides comprising the smaller glycoprotein (F). However, a glycosylated precursor (F(0)) with a molecular weight of 66,000 was found in each cell type, and pulse-chase experiments suggested that this precursor was cleaved to yield polypeptides F(1) and F(2). No other proteolytic processing was found. In addition to the structural polypeptides, the synthesis of five other polypeptides, designated I through V, has been observed in simian virus 5-infected cells. One of these (V), with a molecular weight of 24,000, was found in all cells examined and may be a nonstructural viral polypeptide. In contrast, there are polypeptides present in uninfected cells that correspond in size to polypeptides I through IV, and similar polypeptides have also been detected in increased amounts in cells infected with Sendai virus. These findings, and the fact that the synthesis of all four of these polypeptides is not increased in every cell type, suggest that they represent host polypeptides whose synthesis may be enhanced upon infection. When a high salt concentration was used to decrease host cell protein synthesis in infected cells, polypeptides IV and (to a lesser extent) I were synthesized in relatively greater amounts than other cellular polypeptides, as were the viral polypeptides. The possibility that these polypeptides may play some role in virus replication is discussed.     

Biochemical characterization of the structural and nonstructural polypeptides of a porcine group C rotavirus.

Purified virions or radiolabeled lysates of infected MA104 cells were used to characterize the structural and nonstructural polypeptides of a porcine group C rotavirus. At least six structural proteins were identified from purified group C rotavirus by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Of these, two (37,000- and 33,000-molecular-weight polypeptides) were associated with the outer shell, as demonstrated by the ability of EDTA to remove them from the purified virion. The other four polypeptides (molecular weights, 125,000, 93,000, 74,000, and 41,000) were located in the inner shell. The structural or nonstructural nature of a 25,000-molecular-weight protein identified in our studies was unclear. Glycosylation inhibition studies with tunicamycin in infected cells demonstrated that the 37,000- and 25,000-molecular-weight proteins were glycosylated and contained mannose-rich oligosaccharides identified by radiolabeling of the infected cells with [3H]mannose. The 37,000-molecular-weight outer shell glycoprotein was shown by pulse-chase experiments to be posttranslationally processed. The kinetics of viral polypeptide synthesis in infected cells were also studied, and maximal synthesis occurred at 6 to 9 h postinfection. The 41,000-molecular-weight inner capsid polypeptide was the most abundant and was the subunit structure of a 165,000-molecular-weight protein aggregate. Two polypeptides (molecular weights, 39,000 and 35,000) appeared to be nonstructural, as determined by comparison of the protein pattern of radiolabeled infected cell lysates with that of purified virions. Radioimmunoprecipitation was used to examine the serologic cross-reactions between the viral polypeptides of a group C rotavirus with those of a group A rotavirus. No serologic cross-reactivities were detected. The polypeptides of group A and C rotaviruses are compared and discussed.     

Stimulation of actomyosin Mg2+-ATPase activity by a brain microtubule-associated protein fraction. High-molecular-weight actin-binding protein is the stimulating factor

Actomyosin Mg2+-ATPase activity was stimulated by a brain microtubule-associated protein (MAP) fraction. The stimulating activity of the MAP fraction was abolished by boiling and trypsin treatment, suggesting the presence of a protein factor. The factor stimulated actomyosin Mg2+-ATPase activity stoichiometrically by about four times in the optimum conditions (50--75 mM KCl, pH 6.6). The stimulating factor was coprecipitable with actomyosin and was found to be a pair of high-molecular-weight polypeptides (mol wts, 240,000 and 235,000). The polypeptides were not associated with microtubules or myosin, but with fibrous actin. In column chromatographies used for purifying the stimulating factor, the amount of polypeptides coincided with the stimulating activity. Increases in both specific activity and the amount of the paired polypeptides were nearly parallel in the process of the purification. A purified fraction (65% pure with respect to the paired polypeptides) showed a 56-fold increase of the specific stimulating activity as compared with the initial brain supernatant. The two peptides were similar but not identical with filamin and spectrin in terms of electrophoretic mobility. Hence, the pair of polypeptides was identified as an actin-binding protein newly found in brain.     

Specific and azurophilic granules from rabbit polymorphonuclear leukocytes. II. Cell surface localization of granule membrane and content proteins before and after degranulation

The compositional relationship between the cell surface of rabbit polymorphonuclear leukocytes (PMNs) and the membranes of PMN cytoplasmic granules has been investigated. Heterophilic PMNs obtained from peritoneal exudates contained 13 cell surface polypeptides ranging in molecular weight from 220,000 to 12,000 daltons as determined by lactoperoxidase-catalyzed protein iodination and gel electrophoresis. Of these, four polypeptides co-migrated with proteins identified as the major constituents of specific (SpG) and azurophilic (AzG) granule membranes. The most notable of these were cell surface proteins of 145,000 and 96,000 daltons that co-migrated with proteins identified as granule content proteins released from PMNs during exocytosis. Extensive washing did not remove these proteins from the cell surface. Iodination of PMNs after the release of SpG and AzG contents by calcium ionophore- induced exocytosis revealed that there was not a dramatic quantitative change in the proteins on the cell surface. Instead, there were large, quantitative increases in the relative amounts of (125)I that were incorporated into several pre-existing cell surface proteins; all of these cell surface proteins co-migrated as a set with those polypeptides identified as either granule membrane or content proteins. Although nearly all of the major polypeptides of SpG and AzG had counterparts on the cell surface of freshly isolated peritoneal exudates PMNs, there were several polypeptides that were unique to the cell surface. Thus, the PMN has at least three membrane compartments with strikingly different protein compositions.     

Use of antibodies directed against synthetic peptides for identifying cDNA clones, establishing reading frames, and deducing the gene order of measles virus.

A number of cDNA clones complementary to measles virus mRNA and 50S genome RNA have been generated. These clones have been mapped by restriction enzyme analysis and were subsequently sequenced by the method of Maxam and Gilbert (A. M. Maxam and W. Gilbert, Methods Enzymol. 65:499-560, 1980). Computer analysis of these DNA sequences revealed open reading frames which potentially could code for a number of gene products. Portions of these putative polypeptides were synthesized, and rabbit antibodies directed against peptide-hemocyanin conjugates were produced. These antibodies were used to immunoprecipitate virus-specific polypeptides which were identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. For each of the antisera tested, a unique protein was precipitated whose migration on polyacrylamide gels corresponded to standard gene products identified by monoclonal antibodies and antisera against measles virus. By using this method, we were able to assign the coding regions of cDNA clones to specific protein products and, subsequently, to order the genes of the 3'-terminal third of measles genome RNA.     

Effect of epibrassinolide on tyrosine phosphorylation of the calvin cycle enzymes

Two-dimensional electrophoresis was used to separate proteins from crude extracts of pea (Pisum sativum L.) leaves, and thus isolated proteins were subjected to Western blot analysis with monoclonal antibodies against PY20 phosphotyrosine polypeptides. This analysis revealed 44 polypeptides phosphorylated on tyrosine residues. Phosphorylation of some of these proteins was changed under the action of epibrassinolide. Some of these polypeptides were identified by means of MALDI-TOF MS analysis. The results indicate that eight of these proteins belong to the Calvin cycle enzymes, namely, the isoforms of Rubisco large and small subunits, fructose-1,6-phosphate aldolases 1 and 2, and the precursor of α-subunit of Rubisco-binding protein. The observed changes in phosphorylation of these proteins may partly explain the effects of brassinosteroids on photosynthesis. The tyrosine phosphorylation sites were identified in silico for the fragments of polypeptides examined.     

Phosphotransferase-mediated regulation of carbohydrate utilisation in Escherichia coli K12: identification of the products of genes on the specialised transducing phages lambda iex (crr) and lambda gsr (tgs).

The expression of genes adjacent to ptsI was investigated using a series of specialised transducing phages carrying different, overlapping, segments of the cysA-gsr-ptsI-ptsH- iex - cysZ -lig region of the genome of Escherichia coli. The polypeptides were synthesised following the infection of u.v.-irradiated lysogenic and non-lysogenic uvrA recA hosts or a uvrA recA host carrying the lambda cI+ plasmid pKB280 . The polypeptides were identified by SDS-polyacrylamide gel electrophoresis and fluorography. The gsr gene product had a mol. wt. of 23 000. The product of the iex gene was tentatively identified as a protein of mol. wt. of either 33 000 or 21 000. Hpr, the product of the gene ptsH, had a mol. wt. of 9000. The gsr gene appeared to be expressed at a higher level in a non-immune host, which suggests that it was transcribed from lambda promoters. A new lambda host strain, suitable for the detection of small polypeptides (mol. wt. less than 30 000) is described.     

Structure of the cytochrome c oxidase complex of rat liver. 2. Topological orientation of polypeptides in the membrane as studied by proteolytic digestion and immunoblotting

The orientation of the thirteen polypeptides of rat-liver cytochrome c oxidase in the inner mitochondrial membrane was studied by proteolytic digestion of mitoplasts and sonicated particles. After separation by sodium dodecylsulfate gel electrophoresis proteins were transferred on nitrocellulose, and individual polypeptides were identified by incubation with polypeptide-specific antisera, followed by fluorescein-isothiocyanate-conjugated protein A. The three catalytic polypeptides I-III and seven nuclear coded polypeptides (IV, Vb, VIa, VIc, VIIa, VIIb and VIII) were found accessible to proteases from the cytoplasmic phase. Polypeptides II, IV, Va, Vb and VIa were accessible from the matrix phase, indicating a transmembraneous orientation of polypeptides II, IV, Vb and VIa. Together with data on cross-linking and on cytochrome-c-protected labeling of polypeptides, a model of the cytochrome c oxidase complex was developed. It is suggested that the cytochrome c binding site on polypeptide II is surrounded by several nuclear-coded polypeptides, which may modulate the affinity of the enzyme towards cytochrome c.     

Genetic and physiological regulation of intrinsic proteins of the outer membrane of Salmonella typhimurium.

Four major outer membrane polypeptides, accounting for approximately 20% of the total protein of the outer membrane of Salmonella typhimurium, were induced by growth in minimal medium. The polypeptides were tightly bound membrane components. Physiological and genetic evidence indicates that the four polypeptides fall in two separate regulation groups. Synthesis of one of these groups was coordinately regulated by the concentration of iron in the medium, and a mutant strain has been identified in which there is constitutive synthesis of this group of major outer membrane proteins.