Transformation-sensitive and Growth-related Changes of Protein Synthesis in REF52 Cells

Advances in shotgun proteomics and the analysis of membrane proteomes

The emergence of shotgun proteomics has facilitated the numerous biological discoveries made by proteomic studies. However, comprehensive proteomic analysis remains challenging and shotgun proteomics is a continually changing field. This review details the recent developments in shotgun proteomics and describes emerging technologies that will influence shotgun proteomics going forward. In addition, proteomic studies of integral membrane proteins remain challenging due to the hydrophobic nature in integral membrane proteins and their general low abundance levels. However, there have been many strategies developed for enriching, isolating and separating membrane proteins for proteomic analysis that have moved this field forward. In summary, while shotgun proteomics is a widely used and mature technology, the continued pace of improvements in mass spectrometry and proteomic technology and methods indicate that future studies will have an even greater impact on biological discovery.

Description of an ultrathin multiwire proportional chamber-based detector and application to the characterization of theSpraguea lophii(Microspora) two-dimensional genome fingerprint

Multiwire proportional chamber is a useful technology to build detectors that supersede the lack of interactivity of autoradiography in molecular biology experiments. Some drawbacks still limited the diffusion of existing instruments in biological laboratories. The major competitors are storage phosphor imaging systems. The simplified description of a radio-chromato-imager prototype (RCI) based on an original ultrathin multiwire proportional chamber is presented. It combines the advantage of the different existing technologies to present competitive properties in terms of efficiency, spatial resolution, robustness, manipulation easiness and production cost. Application of the RCI detector to molecular biology was performed by the analysis of karyotype and restriction display two-dimensional pulsed-field gel electrophoresis (KARD 2-D PFGE) data which are used to describe small eukaryotic genome structures. The comparative analysis with autoradiography was performed with the PDQuest software on Spraguea lophii (Microspora) genome fingerprints. The spot detection procedure applied to the different images leads to a similar conclusion considering the genome structure of S. lophii which appeared to be composed of 15 chromosomes for 13 karyotypic bands (200-880 kbp).

Stage-Dependent Effects of Oocytes and Growth Differentiation Factor 9 on Mouse Granulosa Cell Development: Advance Programming and Subsequent Control of the Transition from Preantral Secondary Follicles to Early Antral Tertiary Follicles1

The development of an ovarian follicle requires a complex set of reciprocal interactions between the oocyte and granulosa cells in order for both types of cells to develop properly. These interactions are largely orchestrated by the oocyte via paracrine factors such as growth differentiation factor 9 (GDF9). To examine these interactions further, a study was conducted of the effects of oocytes at different stages of development on proteins synthesized by mouse granulosa cells during the transition of granulosa cells (GCs) from preantral, secondary (2 degrees ) follicles (2 degrees GCs) to mural granulosa cells (3 degrees GCs) of antral tertiary (3 degrees ) follicles. The ability of recombinant GDF9 to mimic the effects of oocytes was also determined. Effects were evaluated by high- resolution, two-dimensional protein gel electrophoresis coupled to computer-assisted, quantitative gel image analysis. Coculture of the 2 degrees GCs with growing oocytes (GOs) from 2 degrees follicles brought about many of the changes in granulosa cell phenotype associated with the 2 degrees to 3 degrees follicle transition. GDF9 likewise brought about many of these changes, but only a subset of GDF9-affected protein spots were also affected by coculture with GOs. Coculture of 2 degrees GCs with the nearly fully grown oocytes (FGOs) from 3 degrees follicles had a reduced effect on 2 degrees GC phenotype, in comparison with coculture with GOs. For some proteins, oocyte coculture or GDF9 treatment appeared to have opposite effects on 2 degrees GCs and 3 degrees GCs. Additional effects of GDF9 and oocytes were seen in cultures of 2 degrees GCs for proteins other than those that differed between untreated control 2 degrees and 3 degrees GCs. These results indicate that GOs and GDF9 can each induce 2 degrees GCs to shift their phenotype toward that of 3 degrees GCs. The ability of the oocyte to produce this effect is diminished with oocyte development. The transition in the GC phenotype promoted by oocytes appears stable because differences in 2 degrees GCs promoted by oocytes and GDF9 were observed in untreated 3 degrees GCs. We conclude that the influence of the oocyte on GCs changes with the progression of their development, and so too does the response of the GCs to the oocyte. Moreover, by acting on the 2 degrees GCs, GOs are able to influence stably the phenotype of 3 degrees GCs. Thus, at or near the 2 degrees to 3 degrees follicle transition, signals from the growing oocyte contribute to the development of the mural GC phenotype.

A mass spectrometric journey into protein and proteome research

It is a frequently debated question whether technology drives biology or whether biology drives the development of new technologies. This issue is discussed in this manuscript as an account that covers approximately a decade during which mass spectrometry and protein biochemistry have intersected. It is shown that the capabilities of the mass spectrometric methods, initially developed to address the specific need to identify proteins reliably and at high sensitivity soon transcended the intended task. The rapid development of mass spectrometric technologies applied to protein research has catalyzed entirely new experimental approaches and opened up new types of biological questions to experimentation, culminating in the field of proteomics. Some conclusions from this case study relating to technological research and the environment in which it is carried out are also discussed.

Proteomics: the first decade and beyond

Proteomics is the systematic study of the many and diverse properties of proteins in a parallel manner with the aim of providing detailed descriptions of the structure, function and control of biological systems in health and disease. Advances in methods and technologies have catalyzed an expansion of the scope of biological studies from the reductionist biochemical analysis of single proteins to proteome-wide measurements. Proteomics and other complementary analysis methods are essential components of the emerging 'systems biology' approach that seeks to comprehensively describe biological systems through integration of diverse types of data and, in the future, to ultimately allow computational simulations of complex biological systems.

Rice proteomics: a step toward functional analysis of the rice genome

The technique of proteome analysis with two-dimensional PAGE has the power to monitor global changes that occur in the protein expression of tissues and organisms and/or expression that occurs under stresses. In this study, the catalogues of the rice proteome were constructed, and a functional characterization of some of these proteins was examined. Proteins extracted from tissues of rice and proteins extracted from rice under various kinds of stress were separated by two-dimensional PAGE. An image analyzer was used to reveal a total of 10,589 protein spots on 10 kinds of two-dimensional PAGE gels stained by Coomassie Brilliant Blue. The separated proteins were electroblotted onto a polyvinylidene difluoride membrane, and the N-terminal amino acid sequences of 272 of 905 proteins were determined. The internal amino acid sequences of 633 proteins were determined using a protein sequencer or mass spectrometry after enzyme digestion of the proteins. Finally, a data file of rice proteins that included information on amino acid sequences and sequence homologies was constructed. The major proteins involved in the growth and development of rice can be identified using the proteome approach. Some of these proteins, including a calcium-binding protein that turned out to be calreticulin and a gibberellin-binding protein, which is ribulose-1,5-bisphosphate carboxylase/oxygenase activase in rice, have functions in the signal transduction pathway. The information thus obtained from the rice proteome will be helpful in predicting the function of the unknown proteins and will aid in their molecular cloning.

Differential proteome analysis of replicative senescence in rat embryo fibroblasts

Normal somatic cells undergo a finite number of divisions and then cease dividing whereas cancer cells are able to proliferate indefinitely. To identify the underlying mechanisms that limit the mitotic potential, a two-dimensional differential proteome analysis of replicative senescence in serially passaged rat embryo fibroblasts was undertaken. Triplicate independent two-dimensional gels containing over 1200 spots each were run, curated, and analyzed. This revealed 49 spots whose expression was altered more than 2-fold. Of these, 42 spots yielded positive protein identification by mass spectrometry comprising a variety of cytoskeletal, heat shock, and metabolic proteins, as well as proteins involved in trafficking, differentiation, and protein synthesis, turnover, and modification. These included gelsolin, a candidate tumor suppressor for breast cancer, and alpha-glucosidase II, a member of the family of glucosidases that includes klotho; a defect in klotho expression in mice results in a syndrome that resembles human aging. Changes in expression of TUC-1, -2, -4, and -4 beta, members of the TUC family critical for neuronal differentiation, were also identified. Some of the identified changes were also shown to occur in two other models of senescence, premature senescence of REF52 cells and replicative senescence of mouse embryo fibroblasts. The majority of these candidate proteins were unrecognized previously in replicative senescence. They are now implicated in a new role.

Comparison of protein synthesis patterns in mouse cumulus cells and mural granulosa cells: effects of follicle-stimulating hormone and insulin on granulosa cell differentiation in vitro

Successful development of mammalian oocytes requires correct interactions between developing oocytes and associated granulosa cells. Development of oocyte-granulosa cell complexes from preantral follicles in vitro does not produce oocytes competent to develop to blastocysts at the same frequency as for oocytes that develop in vivo. Addition of either FSH or insulin to cultures of oocyte-granulosa cell complexes does not improve the frequency of blastocyst development, and the combination of both insulin and FSH is deleterious. Here, high-resolution 2-dimensional PAGE (2D-PAGE) and computerized gel image analysis were used to compare patterns of protein synthesis in cumulus cells and mural granulosa cells of small antral follicles, and then to assess effects of FSH and insulin on the differentiation of oocyte-associated granulosa cells (OAGCs) in vitro. Culture of OAGCs without FSH or insulin resulted in failure to synthesize many proteins at rates characteristic of cumulus cells. Either hormone used alone caused many cumulus cell proteins that were decreased in control cultures to be synthesized at nearly normal cumulus cell rates, and also caused the synthesis of other proteins to be increased or decreased. The two hormones added together produced the greatest change in protein synthetic pattern, including overexpression or underexpression of many proteins not affected by either hormone alone. Addition of these hormones to culture media thus appeared insufficient to elicit a normal cumulus cell phenotype in OAGCs and could lead to complex changes in protein synthesis that may be deleterious to oocyte development. The high-resolution 2D-PAGE approach described here should be a valuable tool in studies on oocyte and granulosa cell development in vitro, since phenotype can be evaluated globally through the display of over 1000 newly synthesized proteins rather than relying upon the expression of just a few genes.

Application of two-dimensional protein gels in biotechnology

The optimal use of biological systems for technologically developed products will not be achieved until biological systems are completely defined in biochemical terms. Two-dimensional polyacrylamide gel electrophoresis, 2-D gels, are contributing to this goal. These gels separate complex mixtures of proteins into individual polypeptide species. The ultimate use of 2-D gels is the construction of cellular 2-D gel databases which identify the proteins on the gels and catalog their responses to different environmental conditions. In addition to these global analyses, many applications for 2-D gels in basic, applied and clinical research have been shown.

Down-regulated proteins of mesenchymal tumor cells

To identify proteins that are lost during the establishment of the transformed phenotype of a tumor cell, we have prepared a subtracted cDNA library with mRNA from normal human fibroblasts and from their matched SV40 transformed counterparts. More than 40 clones were obtained that showed a dramatic reduction in their relative expression after oncogenic transformation. The proteins encoded by these clones could be grouped into four distinct classes: extracellular matrix proteins (fibronectin, beta ig-h3, collagen VI), enzymes (collagenase, urokinase), cytoskeletal proteins (vinculin, SM22) and regulatory proteins (beta-glycan, integrin-associated protein, myosin kinase, IGFBP-5). Six novel gene products were discovered during these experiments, including a novel serine protease, a zyxin-like protein, an ankyrin-like protein and a GTP-binding protein. Only four of all the transformation-sensitive cDNAs were consistently down-regulated when a variety of cell lines derived from spontaneous mesenchymal tumors was investigated: beta ig-h3, collagen VI, the novel ankyrin-like protein, and IGFBP-5. It is likely that these gene products play an important role in the maintenance of the normal phenotype.

A novel negative imaging technique for accurate localization of stainable proteins on complex two-dimensional autoradiograms

This paper describes a fast, simple, and accurate method for localization of protein antigens in complex two-dimensional (2-D) autoradiograms where the precise position and identity of the protein is required. The method involves the creation of negative images on an autoradiogram through arrangement of image-intensifying screens. By placing a chromogenically stained 2-D gel or blot between the intensifying screen and the film, photons emitted from the intensifying screen are obstructed by the stained spots, thus creating a negative image on the film. The technique can be used in autoradiograms of proteins labeled with either 32P or (125)I radioisotopes. The technique permits analysis of radiolabeled, gold-stained and immunoreacted proteins on a single film and offers versatility by combining analysis of total protein patterns with specific identification of radiolabeled and/or immunoreacted protein spots. The technique is especially useful when selecting a subset of specifically radiolabeled proteins from the total protein pattern in 2-D gels or membranes for microsequencing.

Analysis of polypeptide expression in benign and malignant human breast lesions

Results of two-dimensional electrophoresis (2-DE) analyses of human breast carcinoma are described. Tumor cells were extracted and purified from breast carcinomas with different proliferative indeces and degrees of genomic stability. Cells purified from fibroadenoma tissue served as controls for benign cells. The following results were observed: (i) Analysis of samples from different areas of the same tumor showed a high degree of similarity in the pattern of polypeptide expression. Similarly, analysis of two tumors and their metastases revealed similar 2-DE profiles. (ii) In contrast, large variations were observed between different lesions with comparable histological characteristics. Larger differences in polypeptide expression were observed between potentially highly malignant carcinomas compared to comparisons of less malignant lesions. These differences were in the same order of magnitude as those observed comparing a breast carcinoma to a lung carcinoma. (iii) The levels of all cytokeratin forms resolved (CK7, CK8, CK15, and CK18) were significantly lower in carcinomas compared to fibroadenomas. (iv) The levels of high molecular weight tropomyosins (1-3) were lower in carcinomas compared to fibroadenomas. The expression of tropomyosin-1 was found to be 1.7-fold higher in primary tumors with metastatic spread to axillar lymph nodes compared to primary tumors with no evidence of metastasis (p < 0.05). (v) The expression of proliferating cell nuclear antigen (PCNA) and some members of the stress protein family (pHSP60, HSP90, and calreticulin) were higher in carcinomas. We conclude that malignant progression of breast carcinomas results in large heterogeneity in polypeptide expression between different tumors, but that some common themes such as decreased expression of cytokeratin and tropomyosin polypeptides can be discerned.

Determining selectivity of drugs by quantitative two-dimensional gel analysis. A study of tenidap, piroxicam, and dexamethasone

In vitro pharmacologic measures of drug specificity are well established, i.e. drug interaction with a specific target such as an enzyme, receptor, or ion channel. However, in vitro measures of drug selectivity, defined as effects on secondary targets, are lacking. Two-dimensional gel electrophoresis (2-D gel) was examined as a measure of drug selectivity by comparing the effects of three drugs, tenidap, piroxicam, and dexamethasone, on the synthesis of intracellular proteins in lipopolysaccharide (LPS)-stimulated murine macrophages. A set of 902 35S-methionine-labeled proteins were separated consistently, identified by their coordinates of apparent isoelectric point and molecular weight, and quantified. LPS altered the concentrations of 45 proteins. Tenidap, at 10 microM, affected a total of five proteins (suppressed three; stimulated two), whereas piroxicam, at 10 microM, suppressed two proteins. Dexamethasone at 0.01 microM suppressed eight proteins and stimulated one. Thus, none of the drugs reversed the LPS-induced changes. Two of the eight proteins suppressed by dexamethasone were also suppressed by tenidap and were identified as proIL-1 alpha and proIL-1 beta. Since the subset of affected proteins provided a unique protein "fingerprint" for each drug, the three drugs were mechanistically differentiated by 2-D gel analysis. Compared to LPS (5% affected proteins), all three drugs were selective (< or = 1% affected) with piroxicam > tenidap > dexamethasone. With identification of affected proteins, this technique can provide a useful in vitro assessment of drug selectivity.

Federated two-dimensional electrophoresis database: a simple means of publishing two-dimensional electrophoresis data

While a two-dimensional electrophoresis (2-DE) database is a relatively old concept, in recent years it generated renewed interest within the 2-DE community due to two main factors: (i) The high reproducibility of the current 2-DE method allows 2-DE images to be exchanged and compared between laboratories. (ii) The recent development of faster and more powerful techniques for protein identification such as microsequencing, matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) and amino acid composition makes the production of reference protein maps and 2-DE databases cost- and time-effective. Additionally, the Internet network's current increase in popularity, combined with the rapid growth of Internet-connected laboratories, provides a straightforward means of publishing and sharing 2-DE data. While a small number of laboratories have already successfully published their data over the net, the increasing number of 2-DE database servers that are currently being set up will sooner or later require some kind of standardization. Unfortunately, standardization can be a long and cumbersome process inevitably leading to undesirable compromises. A federated database offers a simple and efficient way to publish and share 2-DE data without the need for standardization. Taking advantage of Internet protocols such as World Wide Web, they allow each laboratory to maintain their own database and to interconnect it with other similar databases through the use of active cross-references. This paper first presents guidelines for building a federated 2-DE database that may easily be followed by most laboratories. It then briefly reviews the state-of-the-art in networked 2-DE databases, and finally describes the SWISS-2DPAGE database which fully implements the concept of a federated 2-DE database.

Analysis of rat placental plasma membrane proteins by two-dimensional gel electrophoresis

The placenta plays an essential role in fetal growth and the maintenance of pregnancy and its functions are strictly controlled in a stage-specific manner. To gain an insight into placental functions and their regulation, we analyzed the plasma membrane proteins of rat placenta by two-dimensional polyacrylamide gel electrophoresis (2D/E). Plasma membrane fractions of the placenta obtained on days 12, 14, 16, 18 and 20 of pregnancy were purified by Percoll gradient centrifugation, and subjected to 2D/E analysis. After the proteins on the 2D/E gels had been visualized by silver staining, the patterns on the gels at different stages of pregnancy were compared using image analysis software. Proteins within an isoelectric point (pI) range of 4.0 to 7.0 and a molecular weight (Mw) range of 20-100 kDa were analyzed in detail, and about 800 proteins on average were recognized on each gel. Of these, the expression of 150 proteins was found to change dramatically according to the stage of pregnancy. According to their expression patterns, these proteins were categorized into two groups, Group I and Group II. The proteins belonging to Group I showed a higher intensity of expression on day 12 and disappeared on day 20. They included 119 plasma membrane proteins and were divided into five subgroups. Group II, which consisted of three subgroups, included 31 proteins showing a low or negligible expression on day 12 and higher expression on day 20. Most of the other membrane proteins (about 600) were expressed constantly during pregnancy. On the basis of our data, we constructed a database for plasma membrane proteins of the rat placenta.

The human keratinocyte two-dimensional gel protein database (update 1995): mapping components of signal transduction pathways

The master two-dimensional (2-D) gel database of human keratinocytes currently lists 3154 cellular proteins (2224 isoelectric focusing, IEF; and 930 nonequilibrium pH gradient electrophoresis, NEPHGE), many of which correspond to post-translational modifications. 1082 polypeptides have been identified (protein name, organelle components, etc.) using a procedure or a combination of procedures that include (i) comigration with known human proteins, (ii) 2-D gel immunoblotting using specific antibodies, (iii) microsequencing of Coomassie Brilliant Blue stained proteins, (iv) mass spectrometry, (v)vaccinia virus expression of full length cDNAs, and (vi) in vitro transcription/translation of full-length cDNAs. This year, special emphasis has been given to the identification of signal transduction components by using 2-D gel immunoblotting of crude keratinocyte lysates in combination with enhanced chemoluminescence (ECL) detection. Identified proteins are listed both in alphabetical order and with increasing SSP number, together with their M(r), pI, cellular localization and credit to the investigator(s) that aided in the identification. Ultimately, the aim of the comprehensive database is to gather--through a systematic study of ekeratinocytes--qualitative and quantitative information on proteins and their genes that may allow us to identify abnormal patterns of gene expression and to pinpoint signaling pathways and components affected in various skin diseases, cancer included.

Protein analysis on a genomic scale

Methods for protein analysis, such as chromatography, electrophoresis, enzyme tests, receptor assays and immunological tests, have always been aimed in a classical reductionistic manner at investigating single proteins isolated from the complex protein composition of biological compartments. The complexity of the protein composition in biological systems was first visualized by two-dimensional electrophoresis (2-DE). Using 2-DE like a molecular microscope, protein variations between different biological situations may be detected by subtractive 2-DE analyses. Combining 2-DE with microsequencing, amino acid analysis and mass spectrometry protein spots on 2-DE gels may be identified. The sequence information can be used to find the gene. However, by 2-DE not only single protein changes can be detected and investigated on the gene level, but also complex changes of many proteins on a genomic scale.

Spermatocytes and round spermatids of rat testis: protein patterns

Spermatogenesis is a process in the testis that involves meiotic cell division and spermiogenesis. The mechanisms of regulation and its associated proteins are mostly unknown. This publication shows the two-dimensional (2-D) gel electrophoresis protein map obtained from rat testis using nonlinear 3.5-10 immobilized pH gradients for the first-dimensional separation. Eighteen proteins were successfully identified in the SWISS-PROT protein database using amino acid analysis of proteins recovered from polyvinylidene difluoride (PVDF) membranes and verified for one of them by comparison with Anderson's rat liver reference map. Fourteen new polypeptides were identified and four were previously known. Two of these new proteins were closely related to the spermatogenetic process. T-complex protein 1 is expressed in large amounts in germ cells. Androgen-dependent sperm-coating glycoprotein is secreted by epididymal cells. In order to detect changes in protein expression during meiosis and spermiogenesis, spermatocytes and round spermatid cell populations were purified by centrifugal elutriation and compared. In this way several proteins not found in the spermatocyte 2-D images could be high-lighted. The sperm-coating glycoprotein was thus shown to be present in large amounts in round spermatids.

Protein mutations revealed by two-dimensional electrophoresis

High-resolution two-dimensional electrophoresis (2DE) can resolve many hundreds of proteins present in complex mixtures depending on the method of detection. These proteins can be characterised qualitatively, with respect to their electrophoretic mobilities (i.e. charge and apparent molecular mass) and quantitatively, using densitometry, to determine their amounts. There has been a widespread application of 2DE in the analysis and characterisation of protein mutations for a range of organisms. This review presents examples of the use of 2DE to study naturally occurring protein mutations and polymorphisms as well as the characterisation of induced protein mutations in prokaryotes and eukaryotes. Examples are presented to illustrate the use of 2DE to detect mutations affecting the electrophoretic mobility and biosynthesis of individual proteins as well as mutations leading to global alterations in cellular protein synthesis. The advantages and disadvantages of 2DE in the detection of protein mutations are discussed.

The expression of carbohydrate blood group antigens correlates with heat resistance

Recent data indicate that cells may resist heat shock via more than one route: heat shock protein synthesis and other still ill-defined mechanisms. We investigated this phenomenon using four types of cells derived from a single rat colon carcinoma: clones REGb and PROb; PRO A+, a glycosylation variant of PROb selected for its high expression of blood group A antigen; and Ph8, a thermoresistant variant of PROb selected by repeated sublethal heat treatments. Basal heat resistance was clearly associated with the level of cell surface expression of blood group H and A antigens. Biosynthesis of these carbohydrate structures requires two glycosyltransferases, H and A enzymes, whose activities are also correlated with basal heat resistance. In addition, heat sensitive REGb cells were rendered more resistant by transfection with the gene encoding for H enzyme, allowing expression of H antigen. Thus, these terminal glycosylations could play a role as cellular protectors against heat treatment. Blood group carbohydrate antigens were mainly located on O-linked carbohydrate chains of a major glycoprotein of 200 kDa and to a lesser extent on N-linked chains. Only trace amounts were present as glycolipids.

Down-regulation of collagen XII in transformed mesenchymal cells

Collagen XII is a complex multidomain protein associated with the surface of interstitial collagen fibrils. This protein is produced in large amounts by fibroblasts cultivated in vitro. However, it is completely absent from cells transformed by the oncogene v-myc or v-src and from cells derived from a methylcholanthrene-induced fibrosarcoma. Since all these cells lack any mRNA for collagen, XII, it seems likely that the synthesis is blocked at the transcriptional level. Experiments with a temperature-sensitive mutant of Rous sarcoma virus demonstrated that a single oncogene product is sufficient to inhibit the synthesis. A reduction in the expression of collagen XII might have profound effects on the stability of the extracellular matrix of transformed cells.

The human keratinocyte two-dimensional protein database (update 1994): towards an integrated approach to the study of cell proliferation, differentiation and skin diseases

The master two-dimensional (2-D) gel database of human keratinocytes currently lists 3087 cellular proteins (2168 isoelectric focusing, IEF; and 919 none-quilibrium pH gradient electrophoresis, NEPHGE), many of which correspond to posttranslational modifications, 890 polypeptides have been identified (protein name, organelle components, etc.) using one or a combination of procedures that include (i) comigration with known human proteins, (ii) 2-D gel immunoblotting using specific antibodies (iii) microsequencing of Coomassie Brilliant Blue stained proteins, (iv) mass spectrometry and (v) vaccinia virus expression of full length cDNAs. These are listed both in alphabetical order and with increasing SSP number, together with their M(r), pI, cellular localization and credit to the investigator(s) that aided in the identification. Furthermore, we list 239 microsequenced proteins recorded in the database. We also report a database of proteins recovered from the medium of noncultured, unfractionated keratinocytes. This database lists 398 polypeptides (309 IEF; 89 NEPHGE) of which 76 have been identified. The aim of the comprehensive databases is to gather, through a systematic study of keratinocytes, qualitative and quantitative information on proteins and their genes that may allow us to identify abnormal patterns of gene expression and, ultimately, to pinpoint signaling pathways and components affected in various skin diseases, cancer included.

REF52 on Global Gel Navigator: an internet-accessible two-dimensional gel electrophoresis database

Until recently, the REF52 2-D gel database of experiments with rat cell lines was accessible only with special software. This database has now been made available to all investigators with access to the Internet, using the World Wide Web (WWW) technology. The package which delivers the database through the WWW has been named the Global Gel Navigator and can be used to explore the data by several methods, including the direct selection of proteins in the displayed gel using the mouse.

EGTA induces the synthesis in Escherichia coli of three proteins that cross-react with calmodulin antibodies

Escherichia coli mutants, (verA, dilA) specifically resistant to the Ca2+ channel inhibitors verapamil and diltiazem, respectively, are hypersensitive to EGTA and BAPTA. We have shown, using 1-D and 2-D gel electrophoresis, that the synthesis of at least 25 polypeptides in the mutants was enhanced by treatment with Ca2+ chelators and the synthesis of at least 11 polypeptides was repressed. This pattern of induction was not observed in heat- or SDS-treated cells and therefore does not appear to be a general stress response. The majority of the induced proteins are low molecular weight, extremely heat stable and acidic, characteristic properties of calmodulin. Moreover, of the major induced species, three with apparent molecular masses of 12, 18, and 34 kDa all cross-reacted with polyclonal and monoclonal antibodies to eukaryote calmodulins or calerythrin, a heat-resistant Ca(2+)-binding protein from Saccharopolyspora erythraea. The verA, dilA mutants, in being hypersensitive to EGTA and to the Ca2+ ionophore A23187 + Ca2+, may be defective in the regulation of the level of free intracellular Ca2+.

Phenotypic change and altered protein expression in X-ray and methylcholanthrene-transformed C3H10T1/2 fibroblasts

The morphology, growth properties and cellular protein patterns from parent and two transformed C3H10T1/2 cell lines were analyzed to associate the phenotypic and protein differences with cell transformation. Transformed 10T1/2 cells were obtained by colony isolation after exposure of parent 10T1/2 cells to methylcholanthrene (MCA-1 cell line) or X-ray irradiation (XR-III cell line). Compared to parent 10T1/2 and MCA-1 cells, XR-III cells were much smaller in size and exhibited the highest growth rate, greatest cell saturation density, increased plating efficiency and greater expression of proliferating cell nuclear antigen. MCA-1 cells showed intermediate characteristics between parent and XR-III cells. Among the three cell lines, only XR-III cells showed anchorage-independent growth in soft agar. When [35S]methionine-labeled whole cell lysate proteins were separated by two-dimensional polyacrylamide gel electrophoresis, computer comparison algorithms revealed a 97% similarity in protein profiles among almost 800 proteins detected from each cell line. However, comparison of proteins patterns of the transformed cell lines to that of parent 10T1/2 cells showed that 30 and 20 proteins were induced or repressed in XR-III cells and MCA-1 cells, respectively. Similarly, 81 and 24 proteins showed significant quantitative changes (threefold or greater) in XR-III and MCA-1 cells, respectively, as compared with parent 10T1/2 cell proteins. The anchorage-independent growth and increased proliferation properties of XR-III cells suggest a later stage of transformation compared to MCA-1 cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Induced expression of p52(PAI-1) in normal rat kidney cells by the microfilament-disrupting agent cytochalasin D

In established normal rat kidney (NRK) cells, synthesis of the 52 kDa type-1 inhibitor of plasminogen activator [p52(PAI-1)] is stimulated by the cell shape-modulating fungal metabolite cytochalasin D (CD). Induction paralleled the time course of morphologic change and reflected relatively specific increases in saponin-resistant p52(PAI-1) protein accumulation (approximating ten- to thirty-fold over control) and mRNA abundance (seven- to nine-fold). Augmented p52 (PAI-1) mRNA levels closely correlated with increases in 43 kDa p52(PAI-1) core protein biosynthesis. Sensitivity to tunicamycin indicated that N-linked post-translational modifications to this 43 kDa core species generated the full complement of 50 kDa (intermediate) and 52 kDa (mature) p52(PAI-1) glycosylated isoforms. CD-induced p52(PAI-1) expression occurred efficiently in quiescent NRK cells maintained under serum-free conditions as well as in fully serum-supplemented actively growing cultures. While 8-bromo-cAMP reduced both constitutive and transforming growth factor-beta-induced p52(PAI-1) synthesis by > 50%, no such inhibition was evident in short-term (4 h) CD-stimulated cultures. Long-term (24 h) exposure of NRK/CD cells to 8-bromo-cAMP did result in an approximately 34% reduction in stimulated p52(PAI-1) expression, however, levels expressed by NRK/CD+cAMP populations remained markedly elevated relative to control values. These data suggest the existence of a cell shape-dependent aspect of p52(PAI-1) expression control distinct from both the constitutive and growth factor-mediated pathways of gene regulation.

A qualitative and quantitative protein database approach identifies individual and groups of functionally related proteins that are differentially regulated in simian virus 40 (SV40) transformed human keratinocytes: an overview of the functional changes associated with the transformed phenotype

A qualitative and quantitative two-dimensional (2-D) gel database approach has been used to identify individual and groups of proteins that are differentially regulated in simian virus 40 (SV40) transformed human keratinocytes (K14). Five hundred and sixty [35S]methionine-labeled proteins (462 isoelectric focusing, IEF; 98 nonequilibrium pH gradient electrophoresis, NEPHGE), out of the 3038 recorded in the master keratinocyte database, were excised from dry, silver-stained gels of normal proliferating primary keratinocytes and K14 cells and the radioactivity was determined by liquid scintillation counting. Two hundred and thirty five proteins were found to be either up- (177) or down-regulated (58) in the transformed cells by 50% or more, and of these, 115 corresponded to known proteins in the keratinocyte database (J.E. Celis et al., Electrophoresis 1993, 14, 1091-1198). The lowest abundance acidic protein quantitated was present in about 60,000 molecules per cell, assuming a value of 10(8) molecules per cell for total actin. The results identified individual, and groups of functionally related proteins that are differentially regulated in K14 keratinocytes and that play a role in a variety of cellular activities that include general metabolism, the cytoskeleton, DNA replication and cell proliferation, transcription and translation, protein folding, assembly, repair and turnover, membrane traffic, signal transduction, and differentiation. In addition, the results revealed several transformation sensitive proteins of unknown identity in the database as well as known proteins of yet undefined functions. Within the latter group, members of the S100 protein family--whose genes are clustered on human chromosome 1q21--were among the highest down-regulated proteins in K14 keratinocytes. Visual inspection of films exposed for different periods of time revealed only one new protein in the transformed K14 keratinocytes and this corresponded to keratin 18, a cytokeratin expressed mainly by simple epithelia. Besides providing with the first global overview of the functional changes associated with the transformed phenotype of human keratinocytes, the data strengthened previous evidence indicating that transformation results in the abnormal expression of normal genes rather than in the expression of new ones.

Two-dimensional polyacrylamide gel electrophoresis in experimental hepatocarcinogenesis studies

High resolution two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) in combination with computer-assisted densitometry was used to analyze sequential changes in polypeptide expression during chemically (aflatoxin Bl; AFB), spontaneously, and oncogene (v-Ha-ras, v-raf, and v-raflv-myc)-induced experimental rat hepatocarcinogenesis. Two-dimensional mapping of [35S]methionine and [32P]orthophosphate-labeled whole cell lysate and nuclear polypeptides revealed subsets of polypeptides specific for each transformation modality in the in vitro rat liver epithelial (RLE) transformation model. Many of the observed changes in whole cell lysate preparations were localized to specific subcellular organelles. Significant alterations in the expression of the extracellular matrix protein, fibronectin, as well as tropomyosin- and intermediate filament-related polypeptides (vimentin, beta-tubulin, cytokeratins 8, 14, and 18, and actin) were observed among the various transformant cell lines. Whereas alterations in the tropomyosin isoforms appeared to be transformation specific, concomitant modulation of intermediate filament expression was related more to the differentiation state of the individual cell lines than to the transformed phenotype. To integrate protein and DNA information of polypeptides believed to be critically involved during cellular transformation, N-terminal amino acid microsequencing of selected nuclear polypeptides was performed. Preliminary results suggest that N-terminal blockage of rat liver epithelial nuclear proteins to be minor (approximately 20%) with sequencing sensitivity of one pmol. These studies extend our on-going efforts toward the establishment of computerized database of rat liver epithelial cellular proteins (Wirth et al., Electrophoresis, 1991, 12, 931-954) to aid in the delineation of polypeptides critically involved in cellular growth and differentiation as well as transformation.

Characterization of gene expression in clinical lung cancer materials by two-dimensional polyacrylamide gel electrophoresis

Fourteen human lung tumors of various histopathological types were subjected to two-dimensional gel electrophoresis (2-DE). Samples were prepared for 2-DE using a nonenzymatic sample preparation (NESP) technique recently established in our laboratory. Variations in the expression of some polypeptides were observed between tumors of different histopathological types. To this end, high expression of beta-tubulin, heat shock proteins 73 and 90, lamin B, and proliferating cell nuclear antigen (PCNA) were observed in small cell lung carcinomas (SCLC). One polypeptide of unknown identity (35 kDa, pI 5.5) was significantly overexpressed in primary lung adenocarcinomas compared with SCLC, squamous cell lung carcinomas, metastatic lung adenocarcinomas from colon and rectum, and normal tissue. The amino acid composition of this polypeptide is presented. In summary, combining the NESP technique and 2-DE is an effective approach to define tumor-specific markers.

Expression of the 100-kda glucose-regulated protein (GRP100/endoplasmin) is associated with tumorigenicity in a model of rat colon adenocarcinoma

Resistance to glucose starvation and expression of glucose-regulated proteins (grp) were studied in a model of rat colon carcinoma. In this model, various clones originating from the same parental tumor showed distinct tumorigenic potential in syngeneic hosts. Some clones were tumorigenic while others were rejected by an immune-based mechanism. It appeared that the more tumorigenic clones were more resistant to glucose starvation and able to synthesize larger amounts of grp100 than non-tumorigenic clones in response to either glucose starvation or tunicamycin treatment. In contrast, there was no difference in the induced levels of synthesis of grp78 between tumorigenic and non-tumorigenic clones. These results suggest that the ability of cells to synthesize large amounts of the stress protein grp100 might allow them to resist marginal conditions imposed by fully immunocompetent hosts, thus conferring greater tumorigenicity.

Preliminary characterization of a transformed cell strain derived from human trabecular meshwork

Cells isolated from the trabecular meshwork (TM) of a male glaucoma patient were transformed by transfection with an origin defective mutant of SV40 virus. Transformation dramatically increased the growth rate of these cells (designated HTM-3 cells), allowing biochemical and pharmacological characterization. The HTM-3 cells had cytoskeletal components that were reported to be present in TM tissue and non-transformed TM cells. Vimentin, tubulin and smooth muscle specific alpha-actin, but not desmin, were localized in these cells by immunocytochemistry. The extracellular matrix components collagen types I, III and IV, fibronectin and laminin were found in HTM-3 cells as well as their non-transformed parental cells. As predicted, the protein profile of the HTM-3 cells revealed by two-dimensional gel electrophoresis was different from that of the non-transformed cells, probably due to the enhanced growth characteristics of these cells. Furthermore, HTM-3 cells had various intracellular second messenger systems that responded to pharmacological agents. Forskolin, prostaglandin E2, beta-adrenergic and adenosine A2 agonists stimulated the adenylyl cyclase in these cells, whereas muscarinic, serotonergic, dopaminergic and other agonists were ineffective. Sodium nitroprusside increased the intracellular concentration of cGMP, demonstrating the presence of a functional guanylyl cyclase. Phospholipase C activity in these cells was also detected. Muscarinic agonists, histamine and bradykinin, but not adrenergic, serotonergic agonists or prostaglandins, increased phosphoinositide turnover. These drug responses of HTM-3 cells agree with published data on primary TM cells and TM tissues, suggesting that the transformed cells may be a valid substitute for certain pharmacological studies of TM.

SWISS-2DPAGE: a database of two-dimensional gel electrophoresis images

This publication presents the SWISS-2DPAGE database which gathers data on proteins identified on various two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) maps. Each SWISS-2DPAGE entry contains data on one protein, including mapping procedures, physiological and pathological data and bibliographical references, as well as several 2-D PAGE images showing the protein location. Links are also provided to other databases such as SWISS-PROT, EMBL, PROSITE and OMIM. The database has been set up on a server which may be accessed from any computer connected to the internet and it also makes it possible to display the theoretical location of proteins, the positions of which are not yet known on the 2-D PAGE.

The human keratinocyte two-dimensional gel protein database: update 1993

The master two-dimensional gel database of human keratinocytes currently lists 3038 cellular proteins (2127 isoelectric focusing, IEF; and 911 nonequilibrium pH gradient electrophoresis, NEPHGE) many of which correspond to post-translational modifications. 763 proteins have been identified (protein name, organelle components, etc.) and they are listed both in alphabetical order and with increasing SSP number, together with their M(r), pI, cellular localization and credit to the investigator(s) that aided in the identification. Furthermore we have listed 176 proteins that have been microsequenced so far and that are recorded in this database. We also include synthetic images depicting some interesting sets of proteins identified so far; these include components of hnRNP's, proteasomes or prosomes, ribosomes, as well as assorted organelle markers, GTP-binding proteins, calcium binding proteins, stress proteins, autoantigens, differentiation markers and psoriasis upregulated proteins. The aim of the comprehensive database is to gather, through a systematic study of keratinocytes, qualitative and quantitative information on proteins and their genes that may allow us to identify abnormal patterns of gene expression and ultimately to pinpoint signaling pathways and components affected in various skin diseases, cancer included.

The rat liver epithelial (RLE) cell nuclear protein database

The master two-dimensional computer database of rat liver epithelial (RLE) cellular proteins (Wirth et al., Electrophoresis 1991, 12, 931-954) has been expanded to include detailed information concerning 1100 nucleoplasmic (cytosolic) and 850 particulate associated [35S]methionine labeled as well as 215 nucleoplasmic and 269 particulate associated [32P]orthophosphate labeled RLE nuclear polypeptides, respectively. The RLE nuclear protein database developed using the Elsie 5 gel analysis system contains both qualitative and quantitative annotations including polypeptide identification number, protein name (if known), molecular weight and pI information, quantitation and polypeptide spot shape, subcellular location, as well as specific information regarding transformation (chemical and spontaneous) and growth-related characteristics. Microsequencing of polypeptides directly from two-dimensional (2-D) blotted membranes has recently been established in our laboratory and provides a highly efficient and rapid means of polypeptide identification in the absence of specific antibodies. At present the RLE protein database is still in the developmental stage and is continually being updated as additional information is obtained. Nonetheless, it is anticipated that knowledge obtained concerning the identification and characterization of specific transformation and/or growth regulatory proteins in the RLE in vitro cell system will not only have direct application to other rodent and human 2-D protein databases currently under development but will also complement them.

A rice protein library: a data-file of rice proteins separated by two-dimensional electrophoresis

Proteins extracted from embryos, endosperms and leaves of rice were separated by two-dimensional electrophoresis and relative molecular weights and isoelectric points were determined. The separated proteins were electroblotted onto a polyvinylidene difluoride membrane and 85 electroblotted proteins were analyzed by a gas-phase protein sequencer. The N-terminal amino-acid sequences of 27 out of 85 proteins were determined in this manner. The N-terminal regions of the remaining proteins could not be sequenced and they were inferred to have a blocking group at the N-terminus. Among proteins, 11 could be sequenced after deblocking by in situ treatment with pyroglutamyl peptidase. The internal amino-acid sequences of 23 proteins were determined by sequence analysis of peptides obtained by Cleveland peptide mapping. The amino-acid sequences determined here were compared with those of known plant and animal proteins. The concanavalin A-peroxidase method was used to determine whether the 85 proteins were glycosylated and the diagonal electrophoresis method was used to determine whether they contained disulphide bonding. Finally, we constructed a data-file of rice proteins including information on relative molecular weight, isoelectric point, amino-acid sequence, sequence homology, glycosylation, and the presence of disulphide bonding.

Quantitative analysis of protein synthesis in mouse embryos. II: Differentiation of endoderm, mesoderm, and ectoderm

The changes in protein synthesis that occur during differentiation of the primitive germ layers were examined by high-resolution, two-dimensional gel electrophoresis of proteins synthesized in 6.5 and 7.5 days postcoitum (d.p.c.) mouse embryos. For 6.5 d.p.c. embryos, protein synthesis patterns were compared between whole extraembryonic and embryonic regions and between embryonic visceral endoderm and embryonic ectoderm. For 7.5 d.p.c. embryos, comparisons were made between extraembryonic and embryonic regions and between isolated embryonic endoderm, mesoderm, and ectoderm. Each of the isolated 7.5 d.p.c. germ layers was divided into anterior and posterior fragments in order to evaluate possible regional differences in gene expression along the anterior-posterior axis. Comparisons of protein synthesis patterns revealed the greatest difference between isolated endoderm and ectoderm, indicating that by as early as 6.5 d.p.c. patterns of gene expression differ significantly between these tissues. The greatest similarities were found between ectoderm and whole embryonic regions and between endoderm and whole extraembryonic regions, which most likely reflects the overall cellular compositions of the embryonic and extraembryonic regions. Based on their patterns of synthesis, four groups of proteins were identified that were preferentially synthesized in either endoderm or ectoderm. These provide useful markers for studying differentiation in these tissues. One other protein, migrating at the position expected for vimentin, was synthesized at an elevated rate in isolated mesoderm. We also observed differences in rates of synthesis of alpha-tubulin and tropomyosin-5 indicative of potential differences in cytoskeletal composition among the germ layers beyond those previously described. The difference in overall protein synthesis patterns between anterior and posterior regions was greatest in the embryonic endoderm, indicating that differentiation along the anterior-posterior axis may be initiated sooner or may proceed more rapidly in the endoderm than in the other germ layers. These data provide the first quantitative evaluation of the degree to which differentiation of the three primitive germ layers affects protein synthesis patterns and reveal potentially useful markers of endoderm and ectoderm differentiation.

Evolution of coxsackie B virus during in vitro persistent infection: detection of protein mutations using two-dimensional polyacrylamide gel electrophoresis

Serotype 5 coxsackie B virus (CBV5) can establish in vitro persistent infections in human rhabdomyosarcoma (RD) cells. This paper describes the characterisation of the virus released from the persistently infected RD cell line designated piRD-3673. Although infectious virus was released for 42 sequential passages of piRD-3673 cells, no gross virus-specific cytopathic effect was detected when the cells were examined by light microscopy. Two-dimensional polyacrylamide gel electrophoresis was used to compare the virus released from piRD-3673 cells with the CBV5 isolate (CBV-3673) used to initiate the persistent virus infection. Two of the virus intracellular proteins (apparent molecular weights 33,000 and 39,000, designated p33 and p39, respectively) increased in their net basic charge for the virus released from piRD-3673 cells compared to CBV-3673; a reduction in the apparent molecular weights of p33 and p39 was also observed. The charge alteration for both p33 and p39 was a two-stage process, the accumulative effect of which resulted in p33 increasing in pI from 6.14 to 6.53 and p39 increasing in pI from 6.29 to 6.63. The first mutation of p33 and p39 occurred between passages 7 and 10 of piRD-3673 cells and affected both the charge and apparent molecular weight of these two proteins. The second mutation at passage 15 of piRD-3673 cells caused only a change in the charge of p33 and p39. Two other virus proteins (p54 and p75) showed no evidence of mutation over the same passage history of piRD-3673 cells. The virus released from piRD-3673 cells also differed from CBV-3673 by two further criteria, a reduction in plaque-forming efficiency in HEp-2 cells and increased virus replication in RD cells. These data on virus evolution are discussed in relation to the maintenance of persistent CBV infections and the presence of naturally occurring CBV variants.

Quantitative two-dimensional gel electrophoresis analysis of human fibroblasts transformed by ras oncogenes

Quantitative two-dimensional gel electrophoresis was used to compare the cellular protein patterns of a normal foreskin-derived human fibroblasts cell line (LG1) and three immortal derivatives of LG1. One derivative, designated MSU-1.1 VO, was selected for its ability to grow in the absence of serum and is non-tumorigenic in athymic mice. The other two strains were selected for focus-formation following transfection with either Ha-ras or N-ras oncogenes and form high grade malignant tumors. Correspondence and cluster analysis provided a nonbiased estimate of the relative similarity of the different two-dimensional patterns. These techniques separated the gel patterns into three distinct classes: LG1, MSU-1.1 VO, and the ras transformed cell strains. The MSU-1.1 VO cells were more closely related to the parental LG1 than to the ras-transformed cells. The differences between the three classes were primarily quantitative in nature: 16% of the spots demonstrated statistically significant changes (P < 0.01, T test, mean ratio of intensity > 2) in the rate of incorporation of radioactive amino acids. The patterns from the two ras-transformed cell strains were similar, and variations in the expression of proteins that occurred between the separate experiments obscured consistent differences between the Ha-ras and N-ras transformed cells. However, while only 9 out of 758 spots were classified as different (1%), correspondence analysis could consistently separate the two ras transformants. One of these spots was five times more intense in the Ha-ras transformed cells than the N-ras.(ABSTRACT TRUNCATED AT 250 WORDS)

Metabolic labelling and quantitation of proteins synthesized by single chick cochleas

Molecular studies of the peripheral auditory system are made difficult by the small quantities of tissue available and by their relative inaccessibility. In addition, the cochlea and other hair cell-containing receptor organs are composed of both hair cells and supporting cells, as well as several other cell types. The identification of known proteins and the characterization of specific and novel protein molecules from these tissues require the use of sensitive techniques and a consideration of the complex histology. The chick cochlea was selected as an experimental system since the cochlea is relatively accessible in the bird, the receptor neuroepithelium contains a large number of hair cells compacted in a small area, and the physiology of the auditory periphery has been studied extensively. A general procedure is described for the metabolic radiolabelling of proteins from single cochleas followed by their solubilization, separation by high-resolution two-dimensional gel electrophoresis, and accurate quantitation. The method is highly reproducible and sensitive, and should prove useful in studies of proteins from the specialized cell types of the chick cochlea, including the identification of those whose rates of synthesis are modified in response to acoustic stimulation and sound damage or recovery.

Two-dimensional electrophoretic analysis of transformation-sensitive polypeptides during chemically, spontaneously, and oncogene-induced transformation of rat liver epithelial cells

Recently, we described the establishment of a computerized database of rat liver epithelial (RLE) cellular polypeptides (Wirth et al., Electrophoresis, 1991, 12, 931-954). This database has now been expanded to include the analysis of cellular polypeptide alterations during chemically (aflatoxin B1; AFB), spontaneously, and oncogene (v-Ha-ras, v-raf, and v-myc/v-raf)-induced transformation of RLE cells. Two-dimensional mapping of [35S]methionine-labeled whole cell lysate, cell-free in vitro translation products and [32P]orthophosphate-labeled polypeptides revealed subsets of polypeptides specific for each transformation modality. A search of the RLE protein database indicated the specific subcellular location for the majority of these transformation-sensitive proteins. Significant alterations in the expression of the extracellular matrix protein, fibronectin, as well as tropomyosin- and intermediate filament-related polypeptides (vimentin, beta-tubulin, the cytokeratins, and actin) were observed among the various transformant cell lines. Immunoprecipitation and Western immunoblot analysis of tropomyosin expression in four individual AFB-, as well as four spontaneously induced, and each of the oncogene-transformed cell lines indicated that five major tropomyosin (Tm 1-5) isoforms were variably expressed in the various cell lines, including one polypeptide tentatively identified as Tm6. Whereas alterations in tropomyosin expression appeared to be transformation-specific, alterations in the individual intermediate filament polypeptides were related more to the differentiation state of the individual cell lines rather than to the transformation phenotype. These studies extend our earlier efforts toward the establishment of a comprehensive computerized database of RLE cellular proteins and demonstrates how such a database may serve as a useful source for studies concerning the regulation of growth and differentiation as well as transformation of RLE cells.

Non-cytopathic infection of rhabdomyosarcoma cells by coxsackie B5 virus

Infection of rhabdomyosarcoma (RD) cells by coxsackie B5 virus (CBV5) was non-cytopathic, although low titres of infectious virus were produced after 24 h post-infection. The extent of CBV5 replication in RD cells increased after sequential passage of the virus in these cells. The RD cells from the first cycle of CBV5 infection were recovered and maintained in culture for 3 months (equivalent to 21 passages) releasing infectious virus throughout this period; these cells were considered to be persistently infected with CBV5 and were designated piRD cells. Coxsackie virus antigen was demonstrated in a small proportion of piRD cells by immunofluorescence staining. High resolution two-dimensional polyacrylamide gel electrophoresis was used to analyse the intracellular proteins prepared from piRD cells, three proteins were detected which were absent in uninfected RD cells. These new proteins were similar in charge to virus proteins induced during CBV5 lytic infection of HEp-2 cells. Quantitative densitometry of 2-dimensional protein profiles of piRD and uninfected cells showed no significant disruption of RD cell protein synthesis by the persistent virus infection. Three cloned cell lines were recovered from piRD cells, none of which showed evidence of infectious virus or virus-induced protein synthesis suggesting that the parental cell line was a carrier culture for CBV5.

Effect of various detergents on protein migration in the second dimension of two-dimensional gels

Two-dimensional gel electrophoresis (2D)1 is a powerful technique used to separate complex protein mixtures. The technique involves the separation of proteins by charge in the first dimension and by molecular weight in the second dimension. The effect of substituting various detergents for sodium dodecyl sulfate (SDS) in the second dimension (PAGE) was investigated. Individual C-10 through C-14 alkyl sulfates, C-11 through C-14 alkyl sulfonates, sodium N-lauroyl-N-methyl-taurine, N-lauroylsarcosine, sodium laurate, or benzyldimethyl-n-hexadecylammonium chloride were substituted for SDS in equilibration buffer, gel buffer, and upper running buffer. The cationic benzyldimethyl-n-hexadecylammonium chloride system was run with reversed polarity. Dramatic effects on protein migration from human mesothelial cell extracts were observed when different detergents were utilized. The C-12 (SDS) through C-14 alkyl sulfates and sulfonates resulted in anomalous migration of the simple epithelial keratins. Unlike SDS, the C-10 and C-11 alkyl sulfates and C-11 sulfonate resulted in gels in which the keratins were separated accurately with respect to their gene sequence-determined molecular weights. However, with these shorter chain alkyl sulfates and sulfonate, resolution was compromised, especially with respect to the high-molecular-weight polypeptides. The C-12 alkyl sulfate (SDS) and alkyl sulfonate provided the best resolution of polypeptides. Mixtures of C-11 sulfate and SDS resulted in gels with better sequence molecular weight estimates and high resolution. In addition, trace amounts of sodium tetradecyl sulfate/sodium heptadecyl sulfate in commercial SDS preparations had an effect on polypeptide resolution.

Utility of protein electrophoretic analysis in the characterization of malignant tissues

High-resolution electrophoresis of samples from malignant tissues and tumour cells has developed from a simple analytical tool to a high-tech system requiring a lot of satellite techniques. Though this developmental history now demands additional expensive instrumentation and a detailed knowledge of protein chemistry, the usefulness of this technique in tumour biology has been dramatically enhanced. Consequently, electrophoretic techniques combined with additional high-resolution and sensitive analytical tools can now be used to elucidate a particular phenotype of a cancer cell; moreover, the chemical nature of this phenotype can be revealed. The way from the protein backwards to the gene is now open!

The molecular basis for tropomyosin isoform diversity

The tropomyosins are a family of actin filament binding proteins. In multicellular animals, they exhibit extensive cell type specific isoform diversity. In this essay we discuss the genetic mechanisms by which this diversity is generated and its possible significance to cellular function.

Tris-tricine and Tris-borate buffer systems provide better estimates of human mesothelial cell intermediate filament protein molecular weights than the standard Tris-glycine system

Human mesothelial cells contain a number of well defined intermediate filament proteins (IFs) that have been completely sequenced including vimentin and the cytokeratins (K7, K8, K18, and K19). The electrophoretic migration of these IFs was monitored as a function of second dimension gel buffer composition using various systems including Tris-glycine (pH 8.3 or 9.2), Tris-glycine with 20% methanol, Tris-borate, Tris-tricine, and sodium phosphate. All of the second dimension buffer chemistries yielded patterns of sufficient resolution to identify the major cytoskeletal proteins but differed in the relative mobilities of the IFs. Using gene sequence calculated molecular weight data, the major cytoskeletal polypeptides of human mesothelial cells were ranked from highest molecular weight to lowest molecular weight. This rank order of sequence calculated molecular weights was then compared to the rank order determined form the actual migration of the polypeptides in the different gel systems. With the Tris-tricine and the Tris-borate gel systems as well as gene sequence data, KS = vimentin greater than beta-tubulin = K7 greater than K18 greater than K19 greater than actin. With the pH 8.3 and 9.2 Tris-glycine systems, as well as the sodium phosphate gel system, the rank order of the polypeptides did not correspond to gene sequence data. Adding 20% methanol to the Tris-glycine system resulted in IF migration that more closely corresponded to the gene sequence derived data. Migration position of the IFs depended upon the temperature of the second dimension separation as well. In mesothelial cells, the migration of a total of 15-25% of the polypeptides was influenced by differing buffer systems.(ABSTRACT TRUNCATED AT 250 WORDS)