Assessment of ProteoExtract subcellular fractionation kit reveals limited and incomplete enrichment of nuclear subproteome from frozen liver and heart tissue

The nuclear fraction of the ProteoExtract subcellular fractionation kit was assessed using frozen rat liver and heart tissue. Fractionation was evaluated by Western blot using protein markers for various subcellular compartments and followed up with LC/MS/MS analysis of the nuclear fractions. Of the proteins identified, nuclear proteins were in the minority (less than 15%) and there was poor representation of the various nuclear substructures when compared with liver nuclear isolations using a classical density‐based centrifugation protocol. The ProteoExtract kit demonstrated poor specificity for the nucleus and offers limited promise for proteomics investigations of the nuclear subproteome in frozen tissue samples.     

Detection of antigen-specific human serum proteins related to the T-cell receptor in infectious disease and in an immune response to milk proteins or chemicals

A monoclonal IgG2 antibody, MG3C9-1 A12, was prepared by immunization of mice with human serum Cohn Fraction III proteins enriched for TCR Ca+ proteins. MG3C9-1 A12 bound to Mr 28,000, antigen-specific TCR Ca+, beta-, and TCR Ca+, beta+ serum proteins associated with TGF-beta1, 2. The IgG2 monoclonal antibody also bound to T-lymphocyte proteins but did not bind to B lymphocyte proteins, human albumin, IgM, IgG, IgA, or TGF-beta1, 2, 3 immunogenic peptides. Monoclonal MG3C9-1 A12 detected TCR-related proteins specific for filarial extract, milk proteins, or benzoic acid in the sera of individuals with chronic or asymptomatic filariasis, milk intolerance, or sensitivity to toluene, respectively. TCR-related serum proteins were also detected intracellularly in mononuclear cells in frozen sections of ileum from a patient with milk intolerance and reactive mesenteric lymph nodes from a patient with a gastric ulcer. The results suggest that antigen-specific TCR-related serum proteins may be elevated during an immune response to oral, environmental, or infectious stimuli.     

The properties of a nuclear acidic protein fraction that binds [6,7-3H]oestradiol-17β

1. Additional evidence was obtained that the nuclear oestradiol-17beta receptor is an acidic protein. Partial purification of the receptor protein was obtained by chromatography on hydroxyapatite and it contains protein-bound phosphate. 2. The nuclear ;5s' and cytoplasmic ;9.5s' and ;5s' receptors from uterus, dimethylbenzanthracene-induced mammary adenocarcinoma and kidney are precipitated together with bound oestradiol-17beta by protamine sulphate. This common property suggests that the nuclear and cytoplasmic receptors are related to each other. 3. The properties of two acidic protein fractions from both liver and dimethylbenzanthracene-induced mammary adenocarcinoma are described. Fraction 1 contains two major components and fraction 2 contains one component, as judged from polyacrylamide-gel electrophoresis. Fraction 2 contains RNA and both fractions contain protein-bound phosphate. 4. These fractions form insoluble complexes with calf thymus histone, protamine sulphate and poly-l-lysine. The formation of these complexes is markedly affected by ionic strength and pH. Ionization of both the in-amino group of lysine and carboxyl group are involved. RNA and DNA do not appear to be involved. The interaction is not affected by EDTA or 1mm-Na(+), -K(+), -Ca(2+), -Mg(2+) or -Mn(2+). Per unit weight, whole histone has 4-5 times as many binding sites for the acidic proteins as the latter have for the former. 5. No convincing evidence was obtained for DNA-acidic protein interaction, but, as judged from precipitation experiments, there was competition between DNA and acidic protein for histone. 6. Relatively large amounts of acidic protein partly relieved the histone inhibition of the template activity of DNA for Escherichia coli RNA polymerase (EC 2.7.7.6).     

Analysis of protein expression in pure cell nuclei populations isolated from human breast cancer tissue by DNA flow cytometric sorting

In this study, cell nuclei from aneuploid breast cancer samples were sorted with respect to DNA content into pure diploid and aneuploid fractions using flow cytometry. The nuclear proteins were then separated by one-dimensional gel electrophoresis (1D-PAGE) and differences in protein expression patterns, between diploid and aneuploid nuclei from the same tumours, were compared. Using a combination of peptide finger printing and peptide identification by MALDI-TOF mass spectrometry, we identified proteins and confirmed that the proteins were of nuclear origins. The results in this study add further information to the knowledge about the breast cancer disease complexity and heterogeneity at molecular level. For some of the tumours studied different nuclei protein patterns were obtained, in the diploid respective aneuploid nuclei populations, whilst other tumours did not show these differences.     

Protein identification of purified particles isolated from spinach thylakoids by deoxycholate electrophoresis

Three thylakoid complexes were isolated by deoxycholate preparative electrophoresis. The protein composition of each fraction was analyzed by SDS analytical electrophoresis. No protein of the PS 1 enriched fraction (fraction 1) was found in the PS 2 enriched fraction (fraction 2) and inversely. The antenna complex (fraction 3) did not have any contamination by proteins of fraction 1 or fraction 2. Fraction 1 was mainly composed of the CP1, the reaction center complex of the PS1, and by low molecular weight proteins, previously found in other PS 1 preparations. Tentative assignments of these proteins are presented; among them are iron sulfur proteins. After analytical SDS electrophoresis of fraction 2, the reaction center complex was dissociated. Nevertheless three proteins of 50 kD, 42 kD and 35 kD were assigned to this complex. Fraction 2 contained also the three cytochromes of the thylakoid membranes: cyt f, cyt b6, cyt b559. Fraction 3 was exclusively composed of one protein pigment complex, CP2.Abbreviations SDS sodium dodecyl sulfate - PS 1 photosystem 1 - PS 2 photosystem 2 - CP1, CP2 protein pigment complexes isolated by SDS electrophoresis - cyt cytochromes - P700 primary electron donor of PS 1 - P680 primary electron donor of PS 2 - DOC deoxycholate - Q primary plastoquinone electron acceptor - CF coupling factor     

Toxoplasma gondii: isolation of tachyzoites rhoptries and incorporation into Iscom

Rhoptries have been isolated from Toxoplasma gondii tachyzoites by subcellular fractionation in isopynic density sucrose gradient. Five bands were observed, and transmission electron microscopy of these indicated that rhoptries were in band 3. This band had a density of 1.17 g/cm(3). Fraction 1 had membrane structures of the parasite. Fraction 2 contained membranes and mitochondria. Fraction 4 had mostly conoid structure and fraction 5 showed ghosts. The electrophoretic and Western blotting analysis of the fractions indicated the presence of a number of proteins. Iscoms were constructed from band 3, which contained the rhoptry structures. Iscom showed a only protein incorporated of 55 kDa. Isolation of the parasite organelles has got in this work is necessary to identification, characterization, and function elucidation of the organelle proteins.     

LaminB1蛋白在食管鳞癌组织中表达的形态学观察

目的探讨laminB1蛋白在食管鳞癌患者的癌组织及上切缘正常粘膜上皮中表达的形态变化。方法制备组织切片原位核基质,应用免疫组化的方法检测核基质制备前后正常粘膜上皮及癌组织中laminB1的表达;同时提取组织核基质蛋白,应用Westen blot检测核基质蛋白中laminB1的表达。结果正常食管粘膜上皮及食管鳞癌组织核基质制备前后laiminB1表达的阳性率分别为:正常粘膜上皮93.3%、正常粘膜上皮核基质86.7%、癌组织96.7%、癌核基质86.7%。正常粘膜上皮laminB1表达阳性细胞从基底层至颗粒层逐渐减少,制备核基质后正常粘膜上皮核基质laminB1表达阳性细胞数目减少、强度明显减弱,阳性细胞集中于基底层,多数细胞整个胞核着色。癌组织laminB1表达阳性细胞散在分布,无规律;癌核基质laminB1表达阳性强度减弱,阳性颗粒在核周较集中。癌核基质laminB1表达的阳性强度比正常粘膜上皮核基质高,差异有显著性(x2=5.042,P<0.05)。Western blot检测显示正常粘膜核基质的laminB1条带比癌核基质弱。结论laminB1蛋白在食管正常粘膜上皮及食管鳞癌组织中广泛存在。制备核基质后,laminB1蛋白在癌核基质的表达比正常粘膜上皮核基质强;且癌核基质中laminB1的分布与正常粘膜上皮核基质存在差异。     

Purification and characterization of a novel protein that is required for degradation of N-alpha-acetylated proteins by the ubiquitin system.

Anion exchange chromatography of reticulocyte lysates revealed that the ubiquitin cell-free system can be resolved into two essential fractions: unadsorbed material (Fraction I) that contains ubiquitin and a high salt eluate (Fraction II) that contains the conjugating enzymes and the conjugate-degrading protease. Many proteins with exposed NH2 termini are degraded in a ubiquitin-supplemented Fraction II. However, this partially purified and reconstituted system does not degrade N-alpha-acetylated proteins. These proteins are degraded in whole lysates in a ubiquitin-dependent manner (Mayer, A. Siegel, N. R., Schwartz, A. L., and Ciechanover, A. (1989) Science 244, 1480-1483). It appears that a protein factor which is specifically required for the degradation of N-alpha-acetylated proteins is removed or inactivated during the fractionation of the lysate. Here we report the purification and characterization of a novel protein that is required along with the protease for the degradation of ubiquitin conjugates of histone H2A, an N-alpha-acetylated protein. The protein is not required for the degradation of ubiquitin conjugates of proteins with free NH2 termini. The protein, which is found in crude Fraction I, was purified approximately 200-fold by (NH4)2SO4 precipitation, Sephadex G-100 gel-filtration chromatography, Mono Q anion exchange chromatography, and an additional Sephadex G-100 gel filtration chromatography step. The protein is removed from Fraction I during the purification of ubiquitin and has not been previously recognized since the majority of the protein substrates evaluated in the cell-free system have free NH2 termini. The protein has an apparent molecular mass of approximately 92 kDa. It is a homodimer that is composed of two identical 46-kDa subunits. Initial analysis of the mechanism of action of this protein revealed that it must interact with the conjugates in order to allow proteolysis to occur. We designated the protein Factor H (Factor Hedva).     

Polypeptide composition of Fraction 1 protein of the somatic hybrid between Petunia parodii and Petunia parviflora

The analysis of the subunit polypeptide composition of Fraction 1 protein provides information on the expression of both chloroplast and nuclear genomes. Fraction 1 protein, isolated from leaves of the somatic hybrid plants derived from the fusion of protoplasts of Petunia parodii and P. parviflora, was analyzed for its subunit polypeptide composition by isoelectric focusing in 8 M urea. The fraction 1 protein enzyme oligomer in the somatic hybrid plants contained small subunits resulting from the expression of both parental nuclear genomes, but probably only one of the parental large subunits, namely that of P. parodii. The relevance of such somatic hybrid material for the study of nucleocytoplasmic interrelationships is discussed, as well as the use of these fraction 1 protein isoelectric focusing patterns for the analysis of taxonomic relationships in Petunia.     

Immunological study of lysates from the cell wall of group A Streptococcus]

The chemical composition and presence of immunogenic components in the lysates of the cell walls of group A Streptococcus, type M29, were studied. The lysates were prepared with the use of muramidase. Fc-Receptors were detected in the lysates. Within the first 30 minutes of cell wall lysis by muramidase, 4 times higher amounts of the protein reacting with fibrinogen excreted than in the subsequent 4 hours. The lysates contained immunogenic proteins. Fraction III isolated by chromatography of the 30-minute lysate on DEAE-trisacryl formed a single precipitation band with lysate antiserum. The lysate Fraction IV forming three precipitation bands contained a protein not specific of the type. The protein was identical to the protein antigen from Triton X-100 extracts of group A Streptococcus, types M1, M12 and M29. The group-specific polysaccharide was detected in the lysate Fraction I and Fraction II of the 4-hour lysate.     

Isolation and partial characterization of soluble alfalfa proteins

Soluble proteins, representing ⋍18% of total plant protein, were extracted from freshly harvested alfalfa. Two fractions based on solubility in one-half saturated (NH₄)₂SO₄—Fraction G (insoluble) and Fraction A (soluble)—were obtained, representing two-thirds and one-third of the extracted protein, respectively. Fraction G contained less hexose-like and more lipid substances than Fraction A which was characterized by an unusually high ash content. Gel electrophoretic patterns revealed greater heterogeneity in Fraction A than in Fraction G, whereas the reverse situation was evident in sedimentation-velocity patterns. The three sedimenting boundaries apparent in Fraction G had S_20,app values of 29.2 (4%), 17.4 (61%) and 3.2 (35%). The S_20,app 3.2 boundary corresponded to the single boundary observed for Fraction A. Moving-boundary electrophoresis revealed a single boundary for each fraction, possessing mobilities of −6.5 (Fraction G) and −7.5 (Fraction A) Tiselius units, respectively.     

Cell-free synthesis and immunological characterization of salivary proteins from Chironomus tentans

We have isolated the salivary proteins of the larva of the harlequin fly Chironomus tentans, and characterized its constituents by gel electrophoresis and immunological techniques. The detailed composition of saliva from individual animals is shown to be very variable, but four main protein groups can be defined. The largest, Fraction A, comprises up to five species, with molecular weights of between 820,000 and 700,000 Daltons. It includes at least two distinct antigenic species. This finding is discussed in the context of the known heterogeneity of the 75S RNA fraction which is transcribed in the Balbiani rings 1 and 2. — The other prominent protein classes in isolated saliva range in size from 230,000 down to less than 20,000 Daltons. — We have also employed antiserum against salivary proteins to investigate the products of in vitro translation of salivary gland RNA in the rabbit reticulocyte lysate system. A broad spectrum of polypeptide species is obtained which are immunologically related to salivary components, including species of over 300,000 Daltons. These latter are interpreted as unfinished Fraction A polypeptides resulting from incomplete translation of 75S RNA from BR1 and BR2. Evidence is presented to demonstrate that other salivary proteins, apart from Fraction A, are faithfully translated in the reticulocyte lysate.     

Cytofluorometric nuclear DNA content analysis of breast tissues after frozen section diagnosis

OBJECTIVE: To establish a suitable method for measurement of nuclear DNA content in breast tissues from frozen storage after frozen section diagnosis. STUDY DESIGN: For fundamental research, rat liver samples preserved in a deep freezer were used. Four protocols were used (1. fixation with 70% ethanol followed by naked nuclei preparation; 2. fixation with 10% neutral buffered formalin followed by naked nuclei preparation; 3. preparation for naked nuclei prior to fixation with 70% ethanol; and 4. preparation for naked nuclei prior to fixation with 70% neutral buffered formalin). For clinical research, 13 separate fresh frozen breast tissue samples were analyzed after frozen section diagnosis. One contained a malignant phyllodes tumor (MPT) consisting of 2 components, benign epithelial cells and malignant stromal cells; 3 were benign tumors containing fibroadenoma; and 9 cases were carcinomas, consisting of 5 scirrhous, 3 papillotubular and 1 mucinous. RESULTS: Protocols 1, 2 and 3 were not suitable methods for our purpose because remaining cytoplasm or cohesive nuclei were observed. In protocol 4 the cytoplasm was completely undetectable, and nuclei were suitably separated for nuclear DNA content measurement. Benign epithelial cell component nuclei presented a diploid pattern, and the malignant stromal cell component nuclei indicated a euploid pattern in MPT. All 3 cases of benign constituents in fibroadenoma showed a diploid pattern, as did the 3 carcinoma cases (1 mucinous, 1 scirrhous and 1 papillary). Four scirrhous and 2 papillary carcinomas showed an aneuploid pattern. CONCLUSION: Our findings show that it is possible to measure nuclear DNA content of human frozen storage tissues after frozen section diagnosis.     

A specific immunoabsorbent for the isolation of fraction I protein

Antibodies produced against pure Fraction I protein (ribulose 1,5-bis-phosphate carboxylase) from Nicotiana tabacum have been covalently linked to a Sepharose 4B matrix. Fraction I protein present in crude extracts of green leaves of higher plants can be absorbed on a column of the immobilised antibody. The Fraction I protein is eluted from the column with 8 M urea and is in the form of dissociated subunits uncontaminated with other proteins. This material is ideal for an examination of the subunit polypeptide composition of the Fraction I protein by isoelectric focusing. By this procedure, Fraction I protein from sugar beet, Beta vulgaris, has been shown to consist of four different types of polypeptides, three large subunit polypeptides and a single small subunit polypeptide.     

Comparative studies on fraction 1 protein from spinach and tobacco leaves

Fraction 1 protein of spinach and tobacco leaves was purifiedby Sephadex G-200 and DEAE-cellulose column chromatography.Immunological comparison of purified preparations of these proteinswas carried out with precipitin analysis using an antiserumof tobacco fraction 1 protein. Two different antigenic activitieswere found in tobacco fraction 1 protein, of which one was commonlyfound in the spinach protein and the other was specific to tobaccofraction 1 protein. The immunological results suggest that fraction 1 protein iscomposed of at least two different structures, one of whichis common to both spinach and tobacco proteins and the otherof which is specific to each of these proteins. This was confirmedfrom a chemical experiment. Fraction 1 protein was divided intolarge and small polypeptide components by sodium dodecyl sulfatetreatment and subsequent Sephadex G-100 column chromatography,then the amino acid compositions of each polypeptide of theseproteins were compared. The amino acid composition of the smallpolypeptide of spinach was different from that of tobacco, whileamino acid compositions of the large polypeptides of those proteinswere similar to each other. (Received July 1, 1968; )     

Characterisation of secreted polysaccharides and (glyco)proteins from suspension cultures of Pyrus communis

High molecular weight material recovered from the culture filtrate of cell suspension cultured Pyrus communis was composed of 81% carbohydrate, 13% protein and 5% inorganic material. This material was separated into three fractions (one neutral (Fraction A) and two acidic (Fractions B and C)), by anion-exchange chromatography on DEAE-Sepharose CL-6B using a gradient of imidazole-HCl at pH 7.0. The monosaccharide and linkage composition of each fraction was determined after carboxyl reduction of uronic acid residues. From the combined results of the carbohydrate analyses, we conclude that the high molecular weight extracellular material consists of three major and two minor polysaccharides: a (fucogalacto)xyloglucan (36%) in the unbound neutral Fraction A; a type II arabinogalactan (as an arabinogalactan-protein, 29%) and an acidic (glucurono)arabinoxylan (2%) in Fraction B; and a galacturonan (33%) and a trace of heteromannan in Fraction C. The main amino acids in the proteins were Glx, Thr, Ser, Hyp/Pro and Gly. Further separation of Fraction B by solvent partition, SDS-PAGE and analysis by LC-MS/MS identified the major proteins as two chitanases, two thaumatin-like proteins, a beta-1,3-glucanase, an extracellular dermal glycoprotein and a pathogenesis-related protein.     

The characterization of the monoclonal antibody Th-10a, specific for a nuclear protein appearing in the S phase of the cell cycle in normal thymocytes and its unregulated expression in lymphoma cell lines

A monoclonal antibody (Th-10a) specific for the nuclear protein appearing in the S phase of the cell cycle in normal mouse thymocytes was derived by immunizing Wistar rats with a murine thymic lymphoma (TIGN), and its isotype was rat IgG_2a and had κ light chain. Immunohistochemical staining of frozen sections of B10.Thy1.1 newborn thymus and embryonic intestine revealed that this monoclonal antibody reacted strongly with the nuclear proteins of subcortical thymocytes and the basal layer of the mucosa, where many cells were dividing, but not with that of the thymic medullary area. To evaluate the expression of the nuclear proteins during the cell cycle in detail, the results of an immunofluorescence analysis of the thymocytes from hydroxyurea-treated B10 mice using Th-10a monoclonal antibody were compared with those of DNA synthesis of these cells with the use of the FITC-conjugated anti-BrdUrd monoclonal antibody. The results indicated that the nuclear protein detected by Th-10a monoclonal antibody was highly expressed in the S phase of normal thymocytes, while the cells in G₁, G₂ and M phases exhibited a low level of the expression. Moreover, the variations in expression of the nuclear proteins in the thymocytes at different times after hydroxyurea treatment were observed to correspond with the frequency of DNA synthesizing cells. In contrast, the high level and unregulated expression of the nuclear protein detected by Th-10a monoclonal antibody was observed throughout the cell cycle of the mouse lymphoma cell lines examined. Since Th-10a monoclonal antibody does not react with the nuclear proteins derived from human, hamster or rat proliferating cells, this antibody may recognize a murine specific epitope of the nuclear protein. To further characteize the nuclear proteins, we extracted them from normal thymocytes or thymic lymphomas, and analysed them by immunoblotting or***     

Cellular factors required for papillomavirus DNA replication.

In vitro replication of papillomavirus DNA has been carried out with a combination of purified proteins and partially purified extracts made from human cells. DNA synthesis requires the viral E1 protein and the papillomavirus origin of replication. The E2 protein stimulates DNA synthesis in a binding site-independent manner. Papillomavirus DNA replication is also dependent on the cellular factors replication protein A, replication factor C, and proliferating-cell nuclear antigen as well as a phosphocellulose column fraction (IIA). Fraction IIA contains DNA polymerase alpha-primase and DNA polymerase delta. Both of these polymerases are essential for papillomavirus DNA replication in vitro. However, unlike the case with T-antigen-dependent replication from the simian virus 40 origin, purified DNA polymerase alpha-primase and delta cannot efficiently replace fraction IIA in the replication reaction. Hence, additional cellular factors seem to be required for papillomavirus DNA replication. Interestingly, replication factor C and proliferating-cell nuclear antigen are more stringently required for DNA synthesis in the papillomavirus system than in the simian virus 40 in vitro system. These distinctions indicate that there must be mechanistic differences between the DNA replication systems of papillomavirus and simian virus 40.     

Biosynthesis of ribosomal proteins by poly(A)-containing mRNAs from rat liver in a wheat germ cell-free system and sizes of mRNAs coding ribosomal proteins

(1) Poly(A)-containing mRNAs from total polysomal RNA of regenerating rat liver were incubated with [3H]leucine in a wheat germ cell-free system. Ribosomal proteins were purified as described previously [1], and with two-dimensional gel electrophoresis. The proteins on the gel except for less basic protein had appreciable radioactivity, whereas the surrounding areas had very low radioactivity. Acetic acid-soluble proteins labeled in this system were subjected to three-dimensional gel electrophoresis [2]. Except for L1 and L2 proteins, each of the ribosomal proteins, including less basic ones, showed a major radioactive peak coinciding with the protein band on SDS gel. Thus, the wheat germ cell-free system completely translates almost all mRNAs for individual ribosomal proteins. Equimolar amounts of almost all ribosomal proteins were synthesized in the presence of the saturating concentration of mRNAs. (2) Free polysomes from regenerating rat liver were fractionated into three sizes. Each class of polysomes was incubated with [3H]leucine. Ribosomal proteins with molecular weights of 40 000 to 21 000 were mainly synthesized by Fraction B (5-14 monomeric ribosomes), L1 and L2 [2] with 60 000 and 54 000, by Fraction C (greater than 15 monomeric ribosomes) and B, and ribosomal proteins smaller than 20 000 by Fractions A (less than pentamer) and B. (3) mRNAs from rat liver total polysomes were fractionated into seven classes by size and each was translated in the wheat germ extract. Ribosomal proteins with molecular weights of 54 000 to 30 000 were mainly synthesized by mRNAs of 12 to 14.5 S, ribosomal proteins of 35 000 to 22 000 by those of 9.5 to 12 S, ribosomal proteins of 22 000 to 13 000 by those of 7 to 9.5 S, and smaller ribosomal proteins by those smaller than 7 S. These results indicate that individual ribosomal proteins are synthesized by monocistronic mRNAs, the lengths of which are proportional to the molecular weights of the corresponding ribosomal proteins.