Identification of proteins of potential diagnostic value for bovine paratuberculosis

Previously we showed that Mycobacterium paratuberculosis culture filtrates (CFs) contain more antigens that react with sera from infected cattle than do cellular extracts of the organism. The goal of the present study was to identify proteins of potential diagnostic value among these CF proteins. Proteins of potential interest were first separated by 2-DE. Roughly 240 CF protein spots were detected on CBB-stained gels using Phoretix 2D software. Of these, 83% reacted with serum from M. paratuberculosis-infected cattle in immunoblots. When bovine serum was absorbed with M. phlei antigens, however, only 37 of these antigenic protein spots were reactive. Twenty-four of these spots were selected for identification based on their immunoblot staining intensity and differences in pI and mass. A total of 14 proteins were ultimately identified by MS and BLAST searches as ModD, PepA, ArgJ, CobT, Antigen 85C, and nine hypothetical proteins. N-terminal peptide analysis of PepA, Antigen 85C, ModD, MAP1693c, MAP2168c, and MAP1022c showed that each protein has 27-39 amino acids that may function as a signal sequence suggesting they are secreted through a Sec-dependent pathway. These 14 proteins from M. paratuberculosis CF are strong candidates for use as antigens for improved serodiagnostic tests for bovine paratuberculosis.     

不同浓度和梯度的SDS-PAGE胶对双向电泳中蛋白分离的影响

目的：探讨双向电泳中不同浓度和梯度的SDS-PAGE胶对肠道菌蛋白分离效果的影响。方法：制备弗氏2a志贺菌2457T野生株37℃晚期全菌蛋白质样品,进行不同浓度及梯度的SDS-PAGE,研究分离肠道菌蛋白最适宜的SDS-PAGE胶浓度。结果：获得了3个不同浓度（10%、12.5%和15%）的均一胶电泳图谱和3个不同梯度（4%～15%、10%～20%和12%～14%）的电泳图谱,并比较了这些图谱的分离效果;同时,为了分析肠道菌天然表达蛋白的相对分子质量范围,鉴定了8个极端相对分子质量蛋白。结论：对于肠道菌蛋白质的分离来说,12.5%的均一胶或12%～14%的梯度胶较为适宜。     

Sensitivity of Mycoplasma hominis cultures isolated from clinical material to certain antibiotics]

Sensitivity to II antibiotics of 80 strains of M. hominis isolated from patients with various inflammatory processes of the urogenital tract was studied by the method of suppressing the metabolic activity. Inhibition of the arginine metabolism of mycoplasma was used as a test for determination of the growth suppression. All the strains tested were highly sensitive to tetracycline and lincomycin. Kanamycin and neomycin were less active against M. hominis. All the strains tested were resistant to erythromycin, oleandomycin, ristomycin, novobiocin and streptomycin. The inhibitory effect of tetracycline and lincomycin on M. hominis decreased by the 5th day.     

Electrophoretic analysis of proteins from Mycoplasma capricolum and related serotypes using extracts from intact cells and from minicells containing cloned mycoplasma DNA

The acidic proteins of six different mycoplasma serotypes causing bovine or caprine pleuropneumonia were compared by two-dimensional gel electrophoresis of extracts of 35S-labelled cells. The organisms investigated were Mycoplasma mycoides subsp. mycoides (PG1), M. mycoides subsp. mycoides (Y-goat), M. mycoides subsp. capri (PG3), M. capricolum (California kid), the unclassified bovine serogroup 7 of Leach (PG50) and the F38-like group (F38). The results suggested a close relationship between M. capricolum and F38 and a similarly close relationship between the different M. mycoides subspecies, whereas the two M. mycoides subspecies appeared to be quite distant from M. capricolum and F38. The representative strain of the bovine serogroup 7 of Leach was equally distant from F38, M. capricolum and the three strains of M. mycoides. Strikingly, all six mycoplasma strains apparently shared six proteins in the two-dimensional gels. In Escherichia coli minicells, DNA from strain PG50 cloned in the vector pBR325 gave rise to incorporation of radioactive label into proteins which were identified as mycoplasma proteins by two-dimensional electrophoresis and immunoprecipitation.     

Proteome analysis of rat hippocampal neurons by multiple large gel two-dimensional electrophoresis

The goal of the present study was to detect as many protein spots as possible in mammalian cells using two-dimensional gel electrophoresis (2-DE). For proteome analysis, it is of importance to reveal as many proteins as possible. A single standard 2-DE gel (pH 3-10, 18 cm x 20 cm, 13.5% gel) could detect 853 spots from proteins of cultured rat hippocampal neurons when visualized by silver staining. To increase the resolution of the separation and the number of detectable proteins by 2-DE, we utilized seven different narrow pH range immobilized pH gradients in the first dimension. In the second dimension, fourteen long SDS polyacrylamide gels were used: seven 7.5% gels for the separation of high molecular mass proteins (> or = 40 kDa) and seven 13.5% gels for the separation of low molecular mass proteins (< or = 40 kDa). Three hundred and sixty microg of proteins from cultured hippocampal neurons were loaded on to individual gels and visualized by silver staining. All 14 gel images were assembled into a 70 cm x 67 cm cybergel that contained 6677 protein spots, thereby indicating that the utilization of the present strategy led to a 783% increase in the number of detected spots in comparison to the standard procedure. Loading double the amount (720 microg) of proteins on to a 13.5% gel led to a 184% increase in the number of detected spots, thereby indicating that the present strategy has a potential to display more protein spots in the cybergels.     

Exploring Early and Late Toxoplasma gondii Strain RH Infection by Two-Dimensional Immunoblots of Chicken Immunoglobulin G and M Profiles

Toxoplasma gondii is an intracellular apicomplexan parasite infecting warm-blooded vertebrate hosts, with only early infection stage being contained with drugs. But diagnosis differencing early and late infection was not available. In the present investigation, 2-dimensional immunobloting was used to explore early and late infections in chickens. The protein expression of T. gondii was determined by image analysis of the tachyzoites proteome separated by standard-one and conventional two-dimentional gel polyacrylamide electrophoresis (2D- PAGE). Pooled gels were prepared from tachyzoites of T. gondii. A representative gel spanning a pH range of 3-10 of the tachyzoite proteome consisted of 1306 distinct polypeptide spots. Two-dimensional electrophoresis (2-DE) combined with 2-DE immunoblotting was used to resolve and compare immunoglobulins (Igs) M & G patterns against Toxoplasma gondii strain RH (mouse virulent strain). Total tachyzoite proteins of T. gondii were separated by two-dimensional gel electrophoresis and analyzed by Western blotting for their reactivity with the 7 and 56 days post-infection (dpi) SPF chicken antisera. Different antigenic determinant patterns were detected during analysis with M and G immunoglobulins. Of the total number of polypeptide spots analyzed (1306 differentially expressed protein spots), 6.97% were identified as having shared antigenic polypeptide spots on immunoblot profiles with IgG and IgM antibodies regardless the time after infection. Furthermore, some of the immunoreactive polypeptide spots seemed to be related to the stage of infection. Interestingly, we found natural antibodies to toxoplasmic antigens, in addition to the highly conserved antigenic determinants that reacted with non-specific secondary antibody; goat anti-chicken IgG antibodies conjugated with horseradish peroxidase. In conclusion, unique reactive polypeptide spots are promising candidates for designation of molecular markers to discriminate early and late chicken infection.     

Electrophoretic elution of proteins from polyacrylamide gel slices

A method for electrophoretic elution of proteins from polyacrylamide gel slices is described. Eluted proteins were retained by a discontinuous conductivity gradient (M. Otto and M. Snejdárková, Anal. Biochem. 111, 111-114 (1981)). The method has been adapted to slices from slab gels and gels that have been stained and destained. Proteins were eluted as their sodium dodecyl sulfate complexes. Minute amounts of proteins (0.1 microgram) were recovered in high yield (85-95%) in 2 h in less than 0.1 ml volume.     

Two-dimensional protein profiles of cultured stromal and epithelial cells from hyperplastic human prostate

Studies were undertaken to compare and contrast the two-dimensional protein profiles of epithelial and stromal cells from hyperplastic human prostate to establish the protein composition of the two major cellular components of the prostate. Epithelial and stromal cells were isolated from human prostate obtained from patients undergoing open prostatectomy for benign prostatic hyperplasia (BPH). Proteins, isolated from the two cell populations and separated by two-dimensional (2D) electrophoresis, were analyzed by silver staining, fluorography of [35S]-methionine-labeled proteins, and immunoprotein blotting. Isolated prostatic epithelial cells, but not stromal cells, contained cytokeratin polypeptides 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, and 19. Although vimentin could not be identified in silver stained 2D gels and fluorographs of cultured prostatic epithelial cells, a low level of immunoreactivity was noted following immunoblot analysis of epithelial cells proteins by the use of an anti-vimentin polyclonal. Vimentin was prominently expressed in cultured prostatic stromal cells and could be identified on silver stained 2D gels, fluorographs, and immunoblots of stroma-derived proteins. In addition, stromal marker proteins SM1, SM2, and SM3 were identified in 2D gels of stromal cells to distinguish them from epithelial cells. These studies demonstrate (1) the two-dimensional protein profile and cytokeratin polypeptide composition of cultured epithelial cells from hyperplastic human prostate and (2) the 2D protein profile of cultured prostatic stromal cells and identification of specific stromal marker proteins.     

Integral and peripheral association of proteins and protein complexes with <Emphasis Type="Italic">Yersinia pestis</Emphasis> inner and outer membranes

Yersinia pestis proteins were sequentially extracted from crude membranes with a high salt buffer (2.5 M NaBr), an alkaline solution (180 mM Na₂CO₃, pH 11.3) and membrane denaturants (8 M urea, 2 M thiourea and 1% amidosulfobetaine-14). Separation of proteins by 2D gel electrophoresis was followed by identification of more than 600 gene products by MS. Data from differential 2D gel display experiments, comparing protein abundances in cytoplasmic, periplasmic and all three membrane fractions, were used to assign proteins found in the membrane fractions to three protein categories: (i) integral membrane proteins and peripheral membrane proteins with low solubility in aqueous solutions (220 entries); (ii) peripheral membrane proteins with moderate to high solubility in aqueous solutions (127 entries); (iii) cytoplasmic or ribosomal membrane-contaminating proteins (80 entries). Thirty-one proteins were experimentally associated with the outer membrane (OM). Circa 50 proteins thought to be part of membrane-localized, multi-subunit complexes were identified in high M_r fractions of membrane extracts via size exclusion chromatography. This data supported biologically meaningful assignments of many proteins to the membrane periphery. Since only 32 inner membrane (IM) proteins with two or more predicted transmembrane domains (TMDs) were profiled in 2D gels, we resorted to a proteomic analysis by 2D-LC-MS/MS. Ninety-four additional IM proteins with two or more TMDs were identified. The total number of proteins associated with Y. pestis membranes increased to 456 and included representatives of all six β-barrel OM protein families and 25 distinct IM transporter families.     

Induction of specific proteins in cultured skeletal muscle cells by 1,25-dihydroxyvitamin D-3

The presence in myoblasts of an intracellular receptor specific for 1,25-dihydroxyvitamin D-3 [1,25(OH)2D3) and 1,25(OH)2D3-dependent changes in myoblast Ca2+ transport and phospholipid metabolism which are suppressed by RNA and protein synthesis inhibitors have been shown. In agreement with these observations, incubation of chick embryo myoblasts, precultured for 24 h in a medium containing low levels of vitamin D-3 metabolites, with 1,25(OH)2D3 at conditions which induce maximum cell responses (10(-10) M, 24 h) markedly stimulated the incorporation of [3H]leucine into total cell proteins and this effect was abolished when sterol treatment was performed in the presence of cycloheximide or puromycin. To investigate whether 1,25(OH)2D3 selectively stimulates the de novo synthesis of muscle cell proteins, mixtures of myoblast proteins from control and sterol-treated cultures labelled with [14C]leucine and [3H]leucine, respectively, were separated by SDS-polyacrylamide gel electrophoresis and isoelectric focussing. Examination of 3H/14C ratios in gel fractions revealed that 1,25-(OH)2D3 stimulates the production of proteins of molecular masses (isoelectric points) of 9 kDa (4.1 and 8.5), 17 kDa (7.5), 30 kDa (7.2), 40 kDa (5.5), 55 kDa (4.5) and 100 kDa (8.6). Cell fractionation studies showed the following subcellular distribution: 9 kDa (85% cytosol, 15% microsomes); 17 and 100 kDa (100%, 1200 X g pellet); 30 kDa (65% cytosol, 35% mitochondria); 40 kDa (100% microsomes); 55 kDa (65% microsomes, 35% mitochondria). Marker enzyme data indicated that this distribution is not due to cross-contamination between fractions. Affinity chromatography of double-labelled myoblast proteins on an immobilized lectin showed that the 55 kDa protein contains carbohydrate. Labelling of myoblast proteins with 45CaCl2 after their separation on SDS-polyacrylamide gels showed in addition that the 1,25(OH)2D3-dependent proteins of 9, 17, 40 and 100 kDa are major Ca2+-binding components of the cells. Synthesis of these proteins may mediate the effects of the sterol on myoblast calcium metabolism.     

A clinical study on the association of Trichomonas vaginalis and Mycoplasma hominis infections in women attending a sexually transmitted disease (STD) outpatient clinic

Swabs from the posterior vaginal fornix were obtained from 804 consecutive female patients visiting a large Dutch sexually transmitted diseases (STD) outpatient clinic. A detailed clinical history was obtained and complaints concerning the lower genital tract, such as vaginal discharge or vulval and vaginal irritation, were recorded. Patients were examined and the presence of non-physiological vaginal secretions was established by speculum examination. The swabs were monitored for bacterial vaginosis (BV) or Candida albicans infection. PCR diagnosis of Chlamydia trachomatis and Trichomonas vaginalis was performed as well. Four groups of patients (n=14-21) with BV or single infections caused by one of these three pathogens and a control group with no pathogens were selected and Mycoplasma hominis PCR was performed additionally. At clinical presentation, controls and single-infected patient groups were comparable with regard to complaints of the lower genital tract and sexual risk behavior defined as having prior STDs and/or admitted prostitution. Only in the T. vaginalis-positive group significantly more women reporting sexual risk behavior were found than in controls. In agreement with former in vitro observations, an in vivo association between the PCR-detected presence of M. hominis and T. vaginalis was established. In 79% of all samples positive for T. vaginalis, M. hominis could be detected, as compared to only 6% in control samples (P=0.0004). However, since single infections by either of the two pathogens were regularly observed, there does not seem to be an exclusive association between the species, as the bacterium is also more frequently found in cases of BV (P=0.026). Co-infection of M. hominis with C. albicans (11%) or C. trachomatis (0%) did not differ significantly from controls (6%). M. hominis did not associate with complaints of the lower genital tract. However, if all groups were combined there appears to be a very significant association between the presence of M. hominis and sexual risk behavior (P=0.0004). M. hominis and sexual risk behavior were more closely associated than M. hominis and T. vaginalis. No indications were found for an enhanced pathogenicity by either of the symbionts.     

Deoxyribonucleic Acid Homology and Relative Genome Size in Mycoplasma

The deoxyribonucleic acid homologies of Mycoplasma laidlawii type A and type B, M. pulmonis (#47 and #63), and M. hominis were determined by membrane methodology. The homology data revealed a difference in genome size between M. laidlawii type A and type B. This difference also held with stringent conditions of annealing (high temperature). Little or negligible homology was shown to exist between the M. laidlawii strains type A and type B and M. pulmonis strains 47 and 63 and M. hominis. M. hominis showed less than 10% homology to the M. pulmonis and M. laidlawii strains. Neither of the M. laidlawii strains showed more than 2% annealing to the M. pulmonis strains. Reaction rate studies are suggested as a means of demonstrating the phylogenetic relationship between the Mycoplasma and other microorganisms.     

Acidic ribosomal proteins of Dictyostelium discoideum that show electrophoretic similarity to Escherichia coli proteins L7 and L12

This study documents the presence of three acidic proteins, A1 (pI 4.95), A2 (pI 4.85), and A3 (pI 4.70), in Dictyostelium discoideum ribosomes. All three proteins showed an apparent molecular mass of 13,000 by two-dimensional, sodium dodecyl sulfate gel electrophoresis. They were selectively released by treatment of ribosomes with 50% ethanol -1 M NH4Cl. The amino acid composition of A1, A2, and A3 were identical and indicated a predominant amount of alanine. All the above properties are shared by Escherichia coli proteins L7 and L12 and acidic ribosomal proteins in many eukaryotes. Unlike other eukaryotic systems, the acidic proteins of D. discoideum were found associated with the 40S rather than the 60S ribosomal subunit. Acidic proteins analogous in size and electrophoretic mobility to those of D. discoideum were also detected in several other cellular slime mold strains. Not one of the cellular slime mold acidic proteins reacted with antibodies to E. coli proteins L7 and L12 in immunodiffusion tests. In D. discoideum, the distribution of acidic proteins was altered during development. Amoebae contained all three proteins. In spores, A1 was absent and the relative amounts of A2 and A3 were lower than in amoebae. In addition, nine other acidic ribosomal proteins exhibited differences between vegetative amoebae and spores.     

Conditions for reproducible detection of calmodulin and S100 beta in immunoblots

The conditions used in some immunoblot procedures can fail to detect calmodulin, S100 proteins, and other proteins with similar physical properties. We describe here some of the basis of this difficulty, and provide an immunoblot protocol that allows the rapid and reproducible detection of calmodulin and S100 beta in crude biological samples. These proteins are rapidly transferred from sodium dodecyl sulfate-polyacrylamide gels to membrane matrices, and retention on the matrix is enhanced by a glutaraldehyde fixation step. Either nitrocellulose or a positively charged membrane filter (ZetaProbe) can be used as the immobilizing matrix. By combining microslab gel electrophoresis, 30 min electrophoretic transfer, and glutaraldehyde fixation of nitrocellulose paper, an immunoblot analysis can be done in an 8-hr day.     

Outer Membrane Protein Heterogeneity within Pseudomonas fluorescens and P. putida and Use of an OprF Antibody as a Probe for rRNA Homology Group I Pseudomonads

The electrophoretic patterns of outer membrane proteins of strains representing the biovars of Pseudomonas fluorescens and Pseudomonas putida were analyzed by gel electrophoresis. The outer membrane protein profiles were variable, and they were not useful for assigning strains to a specific biovar. However, three or four predominant outer membrane proteins migrating at 42 to 46 kDa, 33 to 38 kDa, and 20 to 22 kDa were conserved among the strains. They could be tentatively identified as OprE (44 kDa), OprF (38 kDa), OprH (21 kDa), and OprL (20.5 kDa), which are known proteins from Pseudomonas aeruginosa. A 37-kDa OprF-like protein was purified from P. fluorescens DF57 and used to raise a polyclonal antibody. In Western blot (immunoblot) analysis, this antibody reacted with OprF proteins from members of Pseudomonas rRNA homology group I but not with proteins from nonpseudomonads. The heterogeneity in M(infr) of OprF was greater among P. fluorescens strains than among P. putida strains. Immunofluorescence microscopy of intact cells demonstrated that the antibody recognized epitopes that were accessible only after unmasking by EDTA treatment. The antibody was used in a colony blotting assay to determine the percentage of rRNA homology group I pseudomonads among bacteria from the rhizosphere of barley. The bacteria were isolated on 10% tryptic soy agar, King's B agar, and the pseudomonad-specific medium Gould S1 agar. The estimate of OprF-containing CFU in rhizosphere soil obtained by colony blotting on 10% tryptic soy agar was about 2 and 14 times higher than the values obtained from King's agar and Gould S1 agar, respectively, indicating that not all fluorescent pseudomonads are scored on more specific media. The colonies reacting with the OprF antibody were verified as being rRNA homology group I pseudomonads by using the API 20NE system.     

Large-scale identification of novel mitosis-specific phosphoproteins

Systematic identification of phosphoproteins is essential for understanding cellular signalling pathways since phosphorylation plays important roles in cellular regulation. Monoclonal antibody MPM-2 recognizes a discrete set of mitosis-specific phosphoproteins and constitutes a specific tool to investigate the significance of phosphorylation in cell cycle. However, due to the difficulties in identifying antigens revealed on immunoblot membrane, only minority of MPM-2 antigens have been identified. Here we originated proteomics approaches for large-scale identification of MPM-2 phosphoproteins. Mitotic extracts were run on several two-dimensional gel electrophoresis (2D) in parallel, and stained by Coomassie Blue. Each individual spot on one of the gels was excised, and proteins in it were further resolved by regular SDS-electrophoresis and blotted on membrane for MPM-2 stain. Counterparts of the positive proteins were selected on another parallel 2D gel and identified by mass-spectrometry. Using this strategy, 100 spots were excised from Coomassie-stained 2D gel and screened by 1D immunoblots for MPM-2 reactivity, and 22 proteins containing potential MPM-2 epitope were identified in addition to a known MPM-2 antigen, laminin-binding protein. These results were further validated by immunofluorescence, co-immunoprecipitation and in vitro phosphorylation assay. The identification of an unprecedented number of potential MPM-2 phosphoprotein antigens gives new insight into the range of proteins involved in the regulation of the early stages of cell division. Meanwhile, this strategy could be used wherever unknown antigens are explored, especially for antibodies that can recognize more than one antigen.     

Solubilization of proteins from human lymph node tissue and two-dimensional gel storage

In the present study, we compared six different solubilization buffers and optimized two-dimensional electrophoresis (2-DE) conditions for human lymph node proteins. In addition, we developed a simple protocol for 2-D gel storage. Efficient solubilization was obtained with lysis buffers containing (a) 8 M urea, 4% CHAPS (3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate), 40 mM Tris base, 65 mM DTT (dithiothreitol) and 0.2% carrier ampholytes; (b) 5 M urea, 2 M thiourea, 2% CHAPS, 2% SB 3-10 (N-decyl-N,N-dimethyl-3-ammonio-1-propanesulfonate), 40 mM Tris base, 65 mM DTT and 0.2% carrier ampholytes or (c) 7 M urea, 2 M thiourea, 4% CHAPS, 65 mM DTT and 0.2% carrier ampholytes. The optimal protocol for isoelectric focusing (IEF) was accumulated voltage of 16,500 Vh and 0.6% DTT in the rehydration solution. In the experiments conducted for the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), best results were obtained with a doubled concentration (50 mM Tris, 384 mM glycine, 0.2% SDS) of the SDS electrophoresis buffer in the cathodic reservoir as compared to the concentration in the anodic reservoir (25 mM Tris, 192 mM glycine, 0.1% SDS). Among the five protocols tested for gel storing, success was attained when the gels were stored in plastic bags with 50% glycerol. This is the first report describing the successful solubilization and 2D-electrophoresis of proteins from human lymph node tissue and a 2-D gel storage protocol for easy gel handling before mass spectrometry (MS) analysis.     

Two dimensional electrophoresis of the exo-proteome produced from community acquired methicillin resistant Staphylococcus aureus belonging to clonal complex 80

Two-dimensional electrophoresis (2DE) combined with mass spectrometry was used to characterize the exo-proteome secreted by two strains (ER13 and ER21) representing community acquired methicillin resistant Staphylococcus aureus (CA-MRSA) belonging to clonal complex 80 (CC80). Common spots were detected between the 2 gels using the Progenesis SameSpots software. Two hundred and fifty-one and 312 spots from the exo-proteome of ER13 and ER21 were resolved, respectively. 2DE overlap comparison showed that 59 spots were shared. LC–MS/MS analysis identified 57 proteins from these spots comprising about 21% extracellular, 48% cytoplasmic, 2% cytoplasmic membrane, 2% cell wall, and 26% with unknown localization. The identified proteins were classified with respect to their Gene Ontology (GO) annotation as ～24% virulence determinants and toxins, ～17% involved in carbohydrate metabolism, ～14% involved in environmental stress, and ～12% associated with cell division. The identification of the enterotoxin B from the exo-products of both strains used in our study, as belonging to CC80 was interesting.