The Dictyostelium discoideum proteome--the SWISS-2DPAGE database of the multicellular aggregate (slug)

Effects of mercury on Dictyostelium discoideum: proteomics reveals the molecular mechanisms of physiological adaptation and toxicity

Dictyostelium discoideum amoebae were exposed to Hg 2 microM corresponding to a sublethal concentration and Hg 10 microM with the first effects on mortality and replication rate. A total of 900 spots were visualized by 2-DE electrophoresis. Two-hundred fifty single proteins were identified by mass spectrometry. Low Hg concentration (2 microM) treatment induced up-regulation of 13 spots, mainly involved in oxidative stress response/detoxification, oxidoreductase activity, and metabolic processes. High Hg concentration (10 microM) treatment showed a different PES with 12 proteins downregulated and only two up-regulated, mainly involved in cellular metabolic processes, metal ion binding, and transferase activity. The analyses for the carbonylation show no changes after 2 microM Hg(2+) treatment and 13 differentially carbonylated proteins after 10 microM Hg(2+) involved in a broad range of cellular processes. Our findings provide insight into the mechanisms of physiological adaptation and toxicity to a low and an high mercury concentration, respectively, of Dictyostelium amoebae.

Large volume sample stacking in capillary zone electrophoresis for the monitoring of the degradation products of metribuzin in environmental samples

A capillary zone electrophoresis (CZE) method with UV-vis detection has been developed for the simultaneous monitoring of the major degradation products of metribuzin, i.e. deaminometribuzin (DA), deaminodiketometribuzin (DADK) and diketometribuzin (DK). The dissociation acid constants have also been estimated by CE and no significant differences have been observed with the values obtained by applying other techniques. Optimum separation has been achieved in less than 9 min in 40 mM sodium tetraborate buffer, pH 9.5 by applying a voltage of 15kV at 25 degrees C and using p-aminobenzoic acid as internal standard. In order to increase sensitivity, large volume sample stacking (LVSS) with polarity switching has been applied as on-line pre-concentration methodology. Detection limits of 10, 10 and 20 ng/mL for DA, DADK and DK, respectively were obtained. The method has been applied to soil samples, after pressurized liquid extraction (PLE). Samples were extracted at high temperature (103 degrees C and 1500 psi) using methanol as extraction solvent and sodium sulphate as drying agent. This PLE procedure was followed by an off-line pre-concentration and sample clean-up procedure by solid-phase extraction (SPE) using a LiChrolut EN sorbent column. These last two procedures were also suitable for the direct treatment of groundwater samples before CE analysis. The combination of both off-line and on-line pre-concentration procedures provided a significant improvement in sensitivity. LVSS provided pre-concentration factors of 4, 36 and 28 for DK, DA and DADK, respectively and with SPE a pre-concentration of 500-fold for the case of water samples and of 2.5-fold in the case of soil samples was obtained. The method is suitable for the monitoring of these residues in environmental samples with high sensitivity, precision and satisfactory recoveries.

Phanerochaete chrysosporium soluble proteome as a prelude for the analysis of heavy metal stress response

A 2-D reference map in pI range 3-10 was constructed for the soluble protein fraction of Phanerochaete chrysosporium growing vegetatively under standard conditions. Functional annotation could be made for 517 spots out of 720 that were subjected to MALDI-TOF-MS analysis, according to the specific accession numbers from the P. chrysosporium genomic database. Further analysis of the data revealed 314 distinct ORFs, 118 of which yielded multiple spots on the master gel. Functional classification of the proteins was made according to the eukaryote orthologous groups defined in the organism's genome website. The functional class of PTMs, protein turnover and chaperones was represented with the highest number (63) of the identified ORFs. Six proteins were assigned to the hypothetical proteins and 29 were predicted to have a signal peptide sequence. Subcellular localization predictions were also made for the identified proteins. Of the protein spots detected on the master gel, 380 were found to be probably phosphorylated and 96 of these matched to the identified proteins. The reference map was efficiently used in the identification of the proteins differentially expressed under cadmium and copper stress. Three new ribosomal proteins as well as zinc-containing alcohol dehydrogenase, glucose-6-phosphate isomerase, flavonol/cinnamoyl-CoA reductase, H+-transporting two-sector ATPase, ribosomal protein S7, ribosomal protein S21e, elongation factor EF-1 alpha subunit were demonstrated as the most strongly induced.

High-resolution peptide mapping of cerebrospinal fluid: a novel concept for diagnosis and research in central nervous system diseases

Peptides, such as many hormones, cytokines and growth factors play a central role in biological processes. Furthermore, as degradation products and processed forms of larger proteins they are part of the protein turnover. Thus, they can reflect disease-related changes in an organism's homeostasis in several ways. Since two-dimensional gel electrophoresis is restricted to analysis and display of proteins with relative molecular masses above 5000, we developed Differential Peptide Display (DPD), a new technology for analysis and visualization of peptides. Here we describe its application to cerebrospinal fluid of three subjects without a disease of the central nervous system (CNS) undergoing routine myelography and of two patients suffering from a primary CNS lymphoma. Peptides with a relative molecular mass below 20000 were extracted and analysed by a combination of chromatography and mass spectrometry. The peptide pattern of a sample was depicted as a multi-dimensional peptide mass fingerprint with each peptide's position being characterized by its molecular mass and chromatographic behaviour. Such a fingerprint of a CNS sample consists of more than 6000 different signals. Data analysis of peptide patterns from patients with CNS lymphoma compared to controls revealed obvious differences regarding the peptide content of the samples. By analysing peptides within a mass range of 750-20000, DPD extends 2D gel electrophoresis, thus offering the chance to investigate CNS diseases on the level of peptides. This represents a new approach for diagnosis and possible therapy.

Proteome map of the human hippocampus

The proteins expressed by a genome have been termed the proteome. By comparing the proteome of a disease-affected tissue with the proteome of an unaffected tissue it is possible to identify proteins that play a role in a disease process. The hippocampus is involved in the processing of short-term memory and is affected in Alzheimer's disease. Any comparative proteome analysis that can identify proteins important in a disease affecting the hippocampus requires the characterization of the normal hippocampal proteome. Therefore, we homogenised normal hippocampal tissue and separated the proteins by two-dimensional polyacrylamide gel electrophoresis (2DE). Seventy-two unique protein spots were collected from Coomassie blue-stained 2DE gels and subjected to in-gel digestion with trypsin, reversed-phase high-pressure liquid chromatography peptide separation, and N-terminal protein sequencing. Sufficient protein sequence was obtained to successfully characterize 66 of the 72 protein spots chosen (92%). Three of the 66 proteins were not present in any database (4.5%). The characterized proteins comprised two dominant functional groups, i.e., enzymes involved in intermediary cellular metabolism (40%), and proteins associated with the cytoskeleton (15%). The identity, molecular mass, isoelectric point, and relative concentration of the characterized proteins are described and constitute a partial proteome map of the normal human hippocampus.

Proteome profiling-pitfalls and progress

In this review we examine the current state of analytical methods in proteomics. The conventional methodology using two-dimensional electrophoresis gels and mass spectrometry is discussed, with particular reference to the advantages and shortcomings thereof. Two recently published methods which offer an alternative approach are presented and discussed, with emphasis on how they can provide information not available via two-dimensional gel electrophoresis. These two methods are the isotope-coded affinity tags approach of Gygi et al. and the two-dimensional liquid chromatography-tandem mass spectrometry approach as presented by Link et al. We conclude that both of these new techniques represent significant advances in analytical methodology for proteome analysis. Furthermore, we believe that in the future biological research will continue to be enhanced by the continuation of such developments in proteomic analytical technology.

Comparative proteome analysis of the hippocampus implicates chromosome 6q in schizophrenia

Comparative brain proteome analysis is a new strategy to discover proteins and therefore genes whose altered expression may underlie schizophrenia. This strategy does not require an a priori theory of the pathogenesis or the mode of inheritance of schizophrenia. Using proteome analysis we previously compared the hippocampal proteome, that is, those proteins expressed by the hippocampal genome, of seven schizophrenic individuals with the hippocampal proteome of seven control individuals, matched for age and post mortem delay.1 We found 18 proteins that were significantly altered in concentration in the schizophrenic hippocampus (P < 0.05), when compared to control tissue. One of these proteins was characterised, by N-terminal sequencing, as diazepam binding inhibitor whose gene maps to 6q12-q21. Here we characterise a further three of the 18 proteins as: manganese superoxide dismutase, 6q25.3, T-complex protein 1, 6q25.3-q26 and collapsin response mediator protein 2, 8p21. That three of these four characterised proteins should map to the long arm of the same chromosome is significant (P < 0.002) and suggests the importance of chromosome 6q in schizophrenia. These results indicate that antioxidant defence is altered in the schizophrenic hippocampus and suggest that segregation distortion, of schizophrenia susceptibility genes, may be a possible causative factor in the high incidence of schizophrenia. Molecular Psychiatry (2000) 5, 85-90.

Peptide mapping of proteins in cerebrospinal fluid utilizing a rapid preparative two-dimensional electrophoretic procedure and matrix-assisted laser desorption/ionization mass spectrometry

A quick two-step procedure involving liquid phase isoelectric focusing in the Rotofor cell in combination with electroelution in the Mini whole cell gel eluter has been used for purification of proteins from human cerebrospinal fluid (CSF). Fractions, each highly enriched in a single protein band and virtually free of other proteins, were selected for characterization by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOFMS). Six CSF proteins, transferrin, alpha1-acid-glycoprotein, Zn-alpha2-glycoprotein, apolipoprotein A1, apolipoprotein E and beta-trace were identified by MALDI-TOFMS analysis of the tryptic digests. These results demonstrate that the combination of liquid phase IEF and electroelution is a rapid preparative two-dimensional separation which can provide single proteins of high purity, in yields sufficient for characterization by MALDI-TOFMS. Characterization of such brain-specific proteins in CSF will be useful in the investigation of the pathophysiology of different brain disorders.

Studies of quantitative analysis of protein expression in Saccharomyces cerevisiae

In the present study amino acid analysis is applied to quantitation of Saccharomyces cerevisiae proteome expression. The quantitation levels obtained are compared to data using densitometric analysis of silver or amido black staining and to the theoretical expression level (codon bias) of the identified proteins determined from their amino acid analysis (AAA). The results show that relative volume ratio (%vol) using Melanie II is a better parameter for spot quantitation than relative optical density ratio (%OD), and amino black staining provides good linearity within the range 1-100 pmol protein. However, AAA shows that theoretical expression levels are not well correlated with actual protein expression level, although there is better correlation when isoforms of the expressed protein are identified and included. It is concluded that amino acid analysis provides accurate protein quantitation and has a continuing role in proteome studies in terms of the rapid and inexpensive quantitation of proteins displayed on proteome maps. We do however recognize that in the context of future clinical applications and large-scale proteome discovery projects, quantitation and post-translational modification need to be analyzed by 'proteomatic' (i.e., proteome automatic bioinformatic analysis directly from the gel) techniques.

Identification of proteins in a human pleural exudate using two-dimensional preparative liquid-phase electrophoresis and matrix-assisted laser desorption/ionization mass spectrometry

Pleural effusion may occur in patients suffering from physical trauma or systemic disorders such as infection, inflammation, or cancer. In order to investigate proteins in a pleural exudate from a patient with severe pneumonia, we used a strategy that combined preparative two-dimensional liquid-phase electrophoresis (2-D LPE), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and Western blotting. Preparative 2-D LPE is based on the same principles as analytical 2-D gel electrophoresis, except that the proteins remain in liquid phase during the entire procedure. In the first dimension, liquid-phase isoelectric focusing allows for the enrichment of proteins in liquid fractions. In the Rotofor cell, large volumes (up to 55 mL) and protein amounts (up to 1-2 g) can be loaded. Several low abundance proteins, cystatin C, haptoglobin, transthyretin, beta2-microglobulin, and transferrin, were detected after liquid-phase isoelectric focusing, through Western blotting analysis, in a pleural exudate (by definition, >25 g/L total protein). Direct MALDI-TOF-MS analysis of proteins in a Rotofor fraction is demonstrated as well. MALDI-TOF-MS analysis of a tryptic digest of a continuous elution sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) fraction confirmed the presence of cystatin C. By applying 2-D LPE, MALDI-TOF-MS, and Western blotting to the analysis of this pleural exudate, we were able to confirm the identity of proteins of potential diagnostic value. Our findings serve to illustrate the usefulness of this combination of methods in the analysis of pathological fluids.

Analysis of intact proteins from cerebrospinal fluid by matrix-assisted laser desorption/ionization mass spectrometry after two-dimensional liquid-phase electrophoresis

A novel combination of methods, two-dimensional liquid-phase electrophoresis (2D-LPE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS), have been used for the analysis of intact brain-specific proteins in cerebrospinal fluid (CSF). 2D-LPE is especially useful for isolating proteins present in low concentrations in complex biological samples. The proteins are separated in the first dimension by liquid-phase isoelectric focusing (IEF) in the Rotofor cell and in the second dimension by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) in the Preparative cell. The removal of SDS by chloroform/methanol/water, followed by sample preparation with the addition of n-octylglucoside, easily interfaced 2D-LPE with MALDI-TOFMS for analysis of intact proteins. Further characterization by proteolytic digestion is also demonstrated. The knowledge of both the molecular weights of the protein and of the proteolytic fragments obtained by peptide mapping increases specificity for protein identification by searching in protein sequence databases. Two brain-specific proteins in human CSF, cystatin C and transthyretin, were isolated in sufficient quantity for determination of the mass of the whole proteins and their tryptic digest by MALDI-TOFMS. This approach simplified the interface between electrophoresis and MALDI-TOFMS.

Proteome analysis: biological assay or data archive?

In this review we examine the current state of proteome analysis. There are three main issues discussed: why it is necessary to study proteomes; how proteomes can be analyzed with current technology; and how proteome analysis can be used to enhance biological research. We conclude that proteome analysis is an essential tool in the understanding of regulated biological systems. Current technology, while still mostly limited to the more abundant proteins, enables the use of proteome analysis both to establish databases of proteins present, and to perform biological assays involving measurement of multiple variables. We believe that the utility of proteome analysis in future biological research will continue to be enhanced by further improvements in analytical technology.

The Australian Proteome Analysis Facility (APAF): assembling large scale proteomics through integration and automation

The field of proteomics opens new possibilities for the mass screening of proteins from many different sources. While genomics is well understood to be a big science field, proteomics is just emerging as such. This paper describes the setting up of the first national proteomics facility. The facility has been funded by the Australian government and this funding has allowed the design of purpose built, integrated laboratories with state of the art equipment for large scale proteome research.

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.