Structural characterization of Dictyostelium discoideum prespore-specific gene D19 and of its product, cell surface glycoprotein PsA.

The Dictyostelium discoideum cell surface antigen PsA is a glycoprotein which first appears in the multicellular stage soon after tip formation and is selectively expressed on prespore cells. The D19 gene encodes an mRNA sequence which is highly enriched in prespore over prestalk cells in the slug stage. We have determined 81 amino acid residues of N-terminal sequence from immunoaffinity-purified PsA protein and shown this sequence to be identical to the predicted sequence of the D19 gene. There are several short repeat elements close to the C terminus, and unequal crossing-over within these is proposed to account for the size polymorphism observed in PsA protein isolated from different D. discoideum strains. The repeats are proline rich and show similarity to the C-terminal region of the D. discoideum cell adhesion molecule, contact sites A. The extreme C terminus, which is also homologous to contact sites A, is characteristic of proteins attached to the plasma membrane via a glycosyl-phosphatidylinositol link. We have marked the PsA gene by insertion of an oligonucleotide encoding an epitope of the human c-myc protein. A construct containing this gene and 990 base pairs of 5'-flanking region directed correct temporal and spatial mRNA accumulation. We found the marked PsA protein, detected with the human c-myc antibody, to be correctly localized on the surface of cells.

High-throughput mass spectrometric discovery of protein post-translational modifications.

The availability of genome sequences, affordable mass spectrometers and high-resolution two-dimensional gels has made possible the identification of hundreds of proteins from many organisms by peptide mass fingerprinting. However, little attention has been paid to how information generated by these means can be utilised for detailed protein characterisation. Here we present an approach for the systematic characterisation of proteins using mass spectrometry and a software tool FindMod. This tool, available on the internet at http://www.expasy.ch/sprot/findmod.html , examines peptide mass fingerprinting data for mass differences between empirical and theoretical peptides. Where mass differences correspond to a post-translational modification, intelligent rules are applied to predict the amino acids in the peptide, if any, that might carry the modification. FindMod rules were constructed by examining 5153 incidences of post-translational modifications documented in the SWISS-PROT database, and for the 22 post-translational modifications currently considered (acetylation, amidation, biotinylation, C-mannosylation, deamidation, flavinylation, farnesylation, formylation, geranyl-geranylation, gamma-carboxyglutamic acids, hydroxylation, lipoylation, methylation, myristoylation, N -acyl diglyceride (tripalmitate), O-GlcNAc, palmitoylation, phosphorylation, pyridoxal phosphate, phospho-pantetheine, pyrrolidone carboxylic acid, sulphation) a total of 29 different rules were made. These consider which amino acids can carry a modification, whether the modification occurs on N-terminal, C-terminal or internal amino acids, and the type of organisms on which the modification can be found. We illustrate the utility of the approach with proteins from 2-D gels of Escherichia coli and sheep wool, where post-translational modifications predicted by FindMod were confirmed by MALDI post-source decay peptide fragmentation. As the approach is amenable to automation, it presents a potentially large-scale means of protein characterisation in proteome projects.

Protein identification with N and C-terminal sequence tags in proteome projects.

Genome sequences are available for increasing numbers of organisms. The proteomes (protein complement expressed by the genome) of many such organisms are being studied with two-dimensional (2D) gel electrophoresis. Here we have investigated the application of short N-terminal and C-terminal sequence tags to the identification of proteins separated on 2D gels. The theoretical N and C termini of 15, 519 proteins, representing all SWISS-PROT entries for the organisms Mycoplasma genitalium, Bacillus subtilis, Escherichia coli, Saccharomyces cerevisiae and human, were analysed. Sequence tags were found to be surprisingly specific, with N-terminal tags of four amino acid residues found to be unique for between 43% and 83% of proteins, and C-terminal tags of four amino acid residues unique for between 74% and 97% of proteins, depending on the species studied. Sequence tags of five amino acid residues were found to be even more specific. To utilise this specificity of sequence tags for protein identification, we created a world-wide web-accessible protein identification program, TagIdent (http://www.expasy.ch/www/tools.html), which matches sequence tags of up to six amino acid residues as well as estimated protein pI and mass against proteins in the SWISS-PROT database. We demonstrate the utility of this identification approach with sequence tags generated from 91 different E. coli proteins purified by 2D gel electrophoresis. Fifty-one proteins were unambiguously identified by virtue of their sequence tags and estimated pI and mass, and a further 11 proteins identified when sequence tags were combined with protein amino acid composition data. We conlcude that the TagIdent identification approach is best suited to the identification of proteins from prokaryotes whose complete genome sequences are available. The approach is less well suited to proteins from eukaryotes, as many eukaryotic proteins are not amenable to sequencing via Edman degradation, and tag protein identification cannot be unambiguous unless an organism's complete sequence is available.

Size polymorphisms due to changes in the number of O-glycosylated tandem repeats in the Dictyostelium discoideum glycoprotein PsA.

The molecular weight polymorphism in the Dictyostelium discoideum cell surface glycoprotein PsA is due to incremental copies of an O-glycosylated tandem tetrapeptide repeat. Allelic variation at the pspA locus results in a PsA glycoprotein with three, four or five tandem copies of Pro-Thr-Val-Thr. The simplest explanation for the origin of this polymorphism is an unequal crossing over event in the ancestral gene containing four copies. Each Thr in the tandem repeat is substituted with carbohydrate, which is completely absent from PsA in strains carrying a glycosylation defective modB mutation. Glycosylated tandem repeats appear to be a common feature of cell surface glycoproteins which are characterized by short domains rich in Pro and Thr or Ser. It is probable that the glycosylated repeat domain acts as a "spacer" peptide that projects the globular domain above the glycocalyx.

Glycoproteins that exhibit extensive size polymorphisms in Dictyostelium discoideum.

Electrophoretic variants which arise from amino acid substitutions, leading to charge differences between proteins are ubiquitous and have been used extensively for genetic analysis. Less well documented are polymorphisms in the size of proteins. Here we report that a group of glycoproteins, which share a common carbohydrate epitope, vary in size in different isolates of the cellular slime mould, Dictyostelium discoideum. One of these proteins, PsA, a developmentally regulated prespore-specific surface glycoprotein, has previously been shown to exist in three size forms due to allelic variation at the pspA locus on linkage group I. In this report, a second glycoprotein, PsB, which is also prespore specific but found inside prespore cells, is studied. PsB maps to linkage group II and exhibits at least four different sizes in the isolates examined. We propose that the size polymorphisms are the product of allelic variation at the pspB locus, due to differences in the number of repeat units.

Genetic Diversity in Cellular Slime Molds: Allozyme Electrophoresis and a Monoclonal Antibody Reveal Cryptic Species among Dictyostelium discoideum Strains.

Cellular slime molds have been classified on the basis of a small number of descriptive criteria such as fruiting body color and morphology, and, in heterothallic species, by assignment to compatible mating groups. However, some isolates which are morphologically classified as conspecific do not fall into a simple mating-type classification; for example some are asexual or homothallic. An increasing interest in inter-strain genetic variation in studies of development and simple behavior has led us to reassess genetic relationships among a number of frequently used isolates. Allozyme electrophoresis of 16 soluble enzymes and use of a monoclonal antibody show that there is relatively little genetic diversity among sexually competent Dictyostelium discoideum isolates, despite considerable variation in geographic origin and time since isolation in the laboratory. In contrast a pair of asexual strains and each of two homothallic strains are genetically quite distinct and differ sufficiently from each other, and from sexually competent isolates, to warrant their recognition as separate species. There are probably four biological species represented in the supposedly D. discoideum isolates studied. This heterogeneity extends to other cellular slime mold species. Each of three isolates of Dictyostelium purpureum is genetically distinct from the others. Limited analysis of other cellular slime molds indicates that the generic distinction of Dictyostelium and Polysphondylium must be questioned. This study emphasizes that caution should be applied in classifying simple organisms on morphological criteria.

Identification of macrophage activation associated proteins by two-dimensional gel electrophoresis and microsequencing.

To understand activation in monocytes and macrophages we have studied changes in protein synthesis using the human monocytoid U937 cell line and two-dimensional polyacrylamide gel electrophoresis (2D PAGE) and protein sequencing. U937 cells that had been metabolically labeled during treatment with PMA, LPS, or IFN-gamma showed appreciable increases or decreases in synthesis of 14 proteins when analyzed by 2D PAGE. Although some 20 proteins are reported to be affected by these agents in U937 cells, none of them correspond with the 14 proteins studied here. Of the 14 observed changes, four spots (p41/65, p35/65, p26/44, p20/53) were up-regulated by PMA only, one (p16/44) by LPS only, five spots (p29/47, p26/45, p26/48, p12/47, p10/45) by both LPS and PMA, and, finally, one (p29/45) by all three agents. Two spots (p20/59 and p20/61) were down-regulated by IFN-gamma and one of these spots (p20/59) was up-regulated by LPS. Only one spot (p20/48) was up-regulated by IFN-gamma. Eleven spots with matching mobilities (both M(r) and pI) to those identified in U937 were observed on 2D PAGE gels from human culture derived macrophages. Ten spots from U937 were sequenced by Edman degradation. Two were could not identified from information contained in the available DNA and protein databases and thus represent novel proteins, whereas a further six of the proteins were N-terminally blocked. The remaining two (29/47 and 12/47, respectively) were identified from existing protein databases as translationally controlled tumor protein (TCTP) and cytokeratin. This is the first report of the presence of TCTP in hemopoietic cells and its modulation by PMA or LPS in any cell type. We believe that 2D PAGE and sequencing is a powerful approach for identifying key proteins in macrophage cellular activation.

What place for polyacrylamide in proteomics?

Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) continues to deliver high quality protein resolution and dynamic range for the proteomics researcher. To remain as the preferred method for protein separation and characterization, several key steps need to be implemented to ensure quality sample preparation and speed of analysis. Here, we describe the progress made towards establishing 2D-PAGE as the optimal separation tool for proteomics research.

A gloverin-like antibacterial protein is synthesized in Helicoverpa armigera following bacterial challenge.

A bacteria inducible antibacterial protein, P2, was isolated from the old world bollworm Helicoverpa armigera. Fifth-instar larvae were injected with live Escherichia coli NCTC 8196. P2 was isolated by HPLC using reversed-phase and size-exclusion columns. In addition, P2 was isolated by an alternative method of sequential cation-exchange and reversed-phase HPLC. The structure of P2 was determined by N-terminal Edman degradation and mass spectrometry. P2 had similar mass (14.1 kDa) structure and activity to gloverin, an inducible glycine-rich antibacterial protein isolated from Hyalophora gloveri [Axén, A.; Carlsson, A.; Engström, A.; Bennich, H. Eur. J. Biochem. 247:614-619; 1997]. At the N-terminus P2 had approximately 60% identity with gloverin. P2 is basic, heat stable, and displayed rapid antibacterial action. P2 was active against the Gram-negative bacteria tested and was inactive against the Gram-positive bacteria, Candida albicans, a bovine turbinate cell line, and pestivirus.

AvGp50, a predominantly axonally expressed glycoprotein, is a member of the IgLON's subfamily of cell adhesion molecules (CAMs).

We have previously reported a 50 kDa glycoprotein (AvGp50) expressed specifically in the chick nervous system [Hancox, K.A., Sheppard, A.M. and Jeffrey, P.L., Characterisation of a novel glycoprotein (AVGP50) in the avian nervous system, with a monoclonal antibody, Dev. Brain Res., 70 (1992) 25-37], and we present its molecular characterization. A PCR fragment was generated following sequencing of peptide and N-terminal fragments derived from purified AvGp50. A 1.58 kb clone (pUEX762) containing the 5'-UTR, the entire coding sequence and a short 3'-UTR was then isolated from a chick embryonic day 18 forebrain library. The deduced amino acid sequence encodes a 338 amino acid peptide containing a 31 amino acid signal peptide at the N-terminal and a 19 amino acid phosphatidylinositol glycan linkage sequence at the C-terminal. The mature protein contains three C2-immunoglobulin-like domains and a glycosyl phosphatidylinositol anchor and shares significant homology to other members of the immunoglobulin superfamily, including neural cell adhesion molecule (N-CAM), myelin-associated glycoprotein (MAG) and the Drosophila protein Amalgam. AvGp50 exhibits highest sequence identity to a recently classified subgroup of the immunoglobulin superfamily (IgLONs - immunoglobulin LAMP, OBCAM and neurotrimin - classified by Pimenta et al. [Pimenta, A.F., Zhukareva, V., Barbe, M.F., Reinoso, B.S., Grimley, C., Henzel, W., Fischer, I. and Levitt, P., The limbic system-associated membrane protein is an Ig superfamily member that mediates selective neuronal growth and axon targeting, Neuron, 15 (1995) 287-297], comprising the opioid binding cell adhesion molecule (OBCAM), neurotrimin and the limbic system-associated membrane protein (LAMP) suggesting that AvGp50 is a member of this subgroup. AvGp50 is expressed predominantly on the cell surface of axons, in particular Purkinje cell and granule cell axons in the cerebellum. In cerebellar and forebrain neuronal cultures, protein expression is exclusively located at the cell surface. Despite its cell surface localization, AvGp50 does not directly influence the outgrowth of neurons from explant cultures from ED8 to ED10 chick forebrain, prompting the suggestion that AvGp50 may act in later maturational events.

Molecular cloning and primary structure of the avian Thy-1 glycoprotein.

We have previously characterised, both biochemically and immunohistochemically, a 23 kDa putative avian Thy-1 protein homologue. In this report we have examined the carbohydrates present on the protein and determined the partial protein sequence of enzymatically and CNBr-produced peptides. The protein sequences enabled us to clone an essentially full-length (1854 bp) cDNA using PCR and colony screening of an embryonic day (ED) 18 forebrain pUEX-1 cDNA library. Analysis of deduced amino acid sequence shows the 23 kDa protein to be 110 amino acids in length compared to mouse (112) and human and rat (111) while still retaining the conserved cysteine residues. The N-glycosylation site at position 61 is the same as that in the human protein, but is different from that in the rodent (position 75). Northern blot analysis of Thy-1 mRNA expression in the forebrain, cerebellum and tectum show that all three tissues have low levels at ED4 (forebrain and tectum) and ED8 (cerebellum), rising most rapidly between ED16 and the first few days post-hatch. Analysis of various tissues at hatch and adult show expression to be predominantly neuronal with very low levels in some other organs, mainly at hatch, indicating the possibility of subsets of cells, which we have also seen in histological sections, in these tissues expressing Thy-1 mRNA. Bone marrow and blood cells were also negative for Thy-1 protein.

Expression, purification and characterisation of secreted recombinant glycoprotein PsA in Dictyostelium discoideum.

Dictyostelium discoideum is a newly developed eukaryotic expression system which is an alternative to tissue cultures for the production of recombinant proteins requiring eukaryotic folding and post-translational modifications. The homologous glycoprotein PsA (prespore specific antigen) is a glycosyl phosphatidylinositol (GPI) anchored membrane protein from D. discoideum. A truncated form of PsA has been expressed in D. discoideum and secreted into a peptone based broth at levels of 10 mg per 1 growth medium. A simple purification protocol for recombinant PsA (rPsA) involved three steps: the concentration of the culture supernatant by ammonium sulfate precipitation, Mono Q anion-exchange chromatography, followed by size exclusion chromatography on Superdex 75. 20 mg of rPsA was purified to 98% purity from 37.1 culture supernatant. Purified rPsA was characterised. The molecular mass of the purified rPsA is 15.6 kDa, which suggests that the molecule is secreted as a monomer and contains 12% (w/w) carbohydrate. The protein sequence of rPsA proved identical to that of the predicted DNA construct. Although the recombinant form of PsA is expressed at a different developmental stage from the native molecule, the same Thr residues that are O-glycosylated in the authentic molecule are glycosylated in the recombinant protein.

Purification of a membrane glycoprotein with an inositol-containing phospholipid anchor from Dictyostelium discoideum.

Large-scale purification of a Dictyostelium discoideum cell surface glycoprotein, which is anchored in the membrane via a glycosylphosphatidylinositol (GPI) moiety, is described. The purification protocol involved four steps: separation of crude cell membranes by low-speed centrifugation, delipidization of these membranes using acetone, extraction of the membrane proteins using the detergent Octyl beta-D-thioglucopyranoside (OTP), and purification of a specific membrane protein by monoclonal antibody immunoaffinity chromatography. The protein purified, PsA (prespore-specific antigen), is a developmentally regulated membrane glycoprotein found on a subset of cells from the cellular slime mould, D. discoideum. The protocol provides an efficient, economical, and technically simple way to purify GPI proteins in sufficient quantities for structural and functional studies. PsA was recovered at a yield of about 60%; with a purity of 97%, the extraction of 1 x 10(10) cells (1.1 g dry weight) yielded about 0.5 mg PsA glycoprotein. Techniques are described for growing kilogram quantities of D. discoideum cells in stainless steel trays at little cost. D. discoideum has considerable potential as a novel expression system for the production of foreign membrane-associated proteins. The purification strategy provides a means of purifying other GPI proteins, including those produced by protein engineering techniques.

Purification by reflux electrophoresis of whey proteins and of a recombinant protein expressed in Dictyostelium discoideum.

Protein purification that combines the use of molecular mass exclusion membranes with electrophoresis is particularly powerful as it uses properties inherent to both techniques. The use of membranes allows efficient processing and is easily scaled up, while electrophoresis permits high resolution separation under mild conditions. The Gradiflow apparatus combines these two technologies as it uses polyacrylamide membranes to influence electrokinetic separations. The reflux electrophoresis process consists of a series of cycles incorporating a forward phase and a reverse phase. The forward phase involves collection of a target protein that passes through a separation membrane before trailing proteins in the same solution. The forward phase is repeated following clearance of the membrane in the reverse phase by reversing the current. We have devised a strategy to establish optimal reflux separation parameters, where membranes are chosen for a particular operating range and protein transfer is monitored at different pH values. In addition, forward and reverse phase times are determined during this process. Two examples of the reflux method are described. In the first case, we described the purification strategy for proteins from a complex mixture which contains proteins of higher electrophoretic mobility than the target protein. This is a two-step procedure, where first proteins of higher mobility than the target protein are removed from the solution by a series of reflux cycles, so that the target protein remains as the leading fraction. In the second step the target protein is collected, as it has become the leading fraction of the remaining proteins. In the second example we report the development of a reflux strategy which allowed a rapid one-step preparative purification of a recombinant protein, expressed in Dictyostelium discoideum. These strategies demonstrate that the Gradiflow is amenable to a wide range of applications, as the protein of interest is not necessarily required to be the leading fraction in solution.

Purification of monoclonal antibodies from ascitic fluid using preparative electrophoresis.

Four monoclonal antibodies (including Ig subclasses, G1, G2a, and G2b) were purified from murine ascitic fluid by a preparative electrophoresis system using a charge- and size-based strategy. Most of the smaller contaminating proteins were removed at pH 8.3 when the ascitic fluid was passed through a cartridge containing a separating membrane with a pore size of M(r) 100,000. After this single step, the immunoglobulin heavy and light chains were the only significant bands present when analysed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. A second step, involving electrophoresis at pH 6.4-7.5 depending on the antibody can be used to remove residual contaminants. For each of the antibodies tested, the recovery of activity at each step was over 80%. As this technology is directly scalable, purification of antibodies by the method described here could be considered a cost effective alternative to protein A chromatography.

Protein phosphorylation: technologies for the identification of phosphoamino acids.

Protein phosphorylation plays a central role in many biological and biomedical phenomena. In this review, while a brief overview of the occurrence and function of protein phosphorylation is given, the primary focus is on studies related to the detection and analysis of phosphorylation both in vivo and in vitro. We focus on phosphorylation of serine, threonine and tyrosine, the most commonly phosphorylated amino acids in eukaryotes. Technologies such as radiolabelling, antibody recognition, chromatographic methods (HPLC, TLC), electrophoresis, Edman sequencing and mass spectrometry are reviewed. We consider the speed, simplicity and sensitivity of tools for detection and identification of protein phosphorylation, as well as quantitation and site characterisation. The limitations of currently available methods are summarised.

Large-scale amino-acid analysis for proteome studies.

Amino-acid analysis is a relatively new method for identification of proteins separated by two-dimensional gel electrophoresis and blotted onto polyvinylidene difluoride (PVDF) membranes. This article describes modified amino-acid analysis methods for this purpose. Streamlined sample handling is a key feature of the process. To minimise sample manipulation, a single vial is used for hydrolysis and the protein hydrolysate on PVDF membrane is extracted by a one-step procedure. The hydrolysate should not be stored for long periods before analysis. Applications of the technique are presented to demonstrate the identification procedure. This approach is the most cost-effective and time-effective first step in mass protein screening for a large-scale proteome project.

Identification and quantitation of cysteine in proteins separated by gel electrophoresis.

A simple technique is introduced to identify and quantitate cysteine (Cys) after acid hydrolysis of protein. The technique involves using 9-fluorenylmethyl chloroformate (Fmoc)-based amino acid analysis that recovers all of the amino acids (asparagine and glutamine are recovered in their acidic forms) except tryptophan. Cys adducts with acrylamide and iodoacetamide have been observed in hydrolysates of gel-separated proteins. To enable quantitation of Cys by amino acid analysis, different conditions of reduction [dithiothreitol (DTT) and tributylphosphine] and alkylation [vinylpyridine, acrylamide and iodoacetamide] were compared. Optimal conditions for on-blot reduction (125 mM of DTT, pH 8.5, at 80 degrees C) and alkylation (0.25 M iodoacetamide, pH 8.5, at 37 degrees C) of proteins which have been separated by gel electrophoresis and blotted onto polyvinylidenedifluoride (PVDF) membrane were established to achieve complete recovery of alkylated Cys. Even with the optimal on-blot iodoacetamide alkylation, there may still be some acrylamide adducts present and these were able to be separated by HPLC along with the other 16 amino acids. The Cys content has been successfully determined by Fmoc-amino acid analysis of PVDF-blotted proteins separated by 1D or 2D gel electrophoresis. Lysine alkylation with iodoacetamide and acrylamide has also been characterised. Protein identification using amino acid composition including Cys has been introduced.

Characterization of human plasma glycoproteins separated by two-dimensional gel electrophoresis.

Purification of protein isoforms for the characterization of post-translational modifications, such as glycosylation, can be laborious and demanding. We report a means of determining monosaccharide composition and the identity of glycoproteins from a single spot on a two-dimensional (2-D) gel. The sensitivity of the method depends on the degree of glycosylation of the protein. We show that bovine fetuin can be analyzed and identified at the level of 100 pmol. 2-D reference maps enable quick identification of glycoprotein isoforms, and the nature of glycosylation differences. Human sera glycoforms were isolated by micropreparative 2-D PAGE using a narrow-range immobilized pH gradient. Single spots excised from one polyvinylidene difluoride blot of a 2-D gel were used sequentially for sialic acid analysis, neutral and amino sugar analysis, and finally amino acid analysis. The glycosylation variations in isoforms of human fetuin and alpha-1-antitrypsin were determined. The amino acid composition, in conjunction with protein pI and MW, successfully identified the glycoproteins.

From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis.

Separation and identification of proteins by two-dimensional (2-D) electrophoresis can be used for protein-based gene expression analysis. In this report single protein spots, from polyvinylidene difluoride blots of micropreparative E. coli 2-D gels, were rapidly and economically identified by matching their amino acid composition, estimated pI and molecular weight against all E. coli entries in the SWISS-PROT database. Thirty proteins from an E. coli 2-D map were analyzed and identities assigned. Three of the proteins were unknown. By protein sequencing analysis, 20 of the 27 proteins were correctly identified. Importantly, correct identifications showed unambiguous "correct" score patterns. While incorrect protein identifications also showed distinctive score patterns, indicating that protein must be identified by other means. These techniques allow large-scale screening of the protein complement of simple organisms, or tissues in normal and disease states. The computer program described here is accessible via the World Wide Web at URL address (http:@expasy.hcuge.ch/).