Comparative two-dimensional gel analysis and microsequencing identifies gelsolin as one of the most prominent downregulated markers of transformed human fibroblast and epithelial cells.

A systematic comparison of the protein synthesis patterns of cultured normal and transformed human fibroblasts and epithelial cells, using two-dimensional gel protein analysis combined with computerized imaging and data acquisition, identified a 90-kD protein (SSP 5714) as one of the most striking downregulated markers typical of the transformed state. Using the information stored in the comprehensive human cellular protein database, we found this protein strongly expressed in several fetal tissues and one of them, epidermis, served as a source for preparative two-dimensional gel electrophoresis. Partial amino acid sequences were generated from peptides obtained by in situ digestion of the electroblotted protein. These sequences identified the marker protein as gelsolin, a finding that was confirmed by two-dimensional immunoblotting of human MRC-5 fibroblast proteins using specific antibodies and by coelectrophoresis with purified human gelsolin. These results suggest that an important regulatory protein of the microfilament system may play a role in defining the phenotype of transformed human fibroblast and epithelial cells in culture.

A novel class of ectomycorrhiza-regulated cell wall polypeptides in Pisolithus tinctorius.

Development of the ectomycorrhizal symbiosis leads to the aggregation of fungal hyphae to form the mantle. To identify cell surface proteins involved in this developmental step, changes in the biosynthesis of fungal cell wall proteins were examined in Eucalyptus globulus-Pisolithus tinctorius ectomycorrhizas by two-dimensional polyacrylamide gel electrophoresis. Enhanced synthesis of several immunologically related fungal 31- and 32-kDa polypeptides, so-called symbiosis-regulated acidic polypeptides (SRAPs), was observed. Peptide sequences of SRAP32d were obtained after trypsin digestion. These peptides were found in the predicted sequence of six closely related fungal cDNAs coding for ectomycorrhiza up-regulated transcripts. The PtSRAP32 cDNAs represented about 10% of the differentially expressed cDNAs in ectomycorrhiza and are predicted to encode alanine-rich proteins of 28.2 kDa. There are no sequence homologies between SRAPs and previously identified proteins, but they contain the Arg-Gly-Asp (RGD) motif found in cell-adhesion proteins. SRAPs were observed on the hyphal surface by immunoelectron microscopy. They were also found in the host cell wall when P. tinctorius attached to the root surface. RNA blot analysis showed that the steady-state level of PtSRAP32 transcripts exhibited a drastic up-regulation when fungal hyphae form the mantle. These results suggest that SRAPs may form part of a cell-cell adhesion system needed for aggregation of hyphae in ectomycorrhizas.

Direct measurement of ascorbic acid biosynthesis in Arabidopsis cell suspension culture using capillary electrophoresis.

We describe procedures to directly measure the biosynthesis of vitamin C (L-ascorbic acid, L-AA) in crude extracts of an Arabidopsis thaliana cell suspension culture by capillary electrophoresis. Optimal conditions have been established for the quantitation of L-AA formed by the oxidation of three different substrates: L-galactose, L-galactono-1,4-lactone, and L-gulono-1,4-lactone. We also demonstrate that L-galactono-1,4-lactone dehydrogenase activity does not require exogenous cofactor. The minimal sample handling requirements, the high selectivity, and short analysis times represent significant advantages over existing protocols.

Distinct phenotypes generated by overexpression and suppression of S-adenosyl-L-methionine synthetase reveal developmental patterns of gene silencing in tobacco.

S-Adenosyl-L-methionine synthetase (SAM-S) catalyzes the conversion of L-methionine and ATP into S-adenosyl-L-methionine. Tobacco plants that were transformed with a construct allowing high transcription levels of an Arabidopsis sam-s gene could be grouped into two main classes based on their morphology. One class developed yellow-green leaves and had high SAM-S activity and transgene mRNA levels, whereas the other class was stunted and had leather-like leaves, very low SAM-S activity, and suppressed mRNA level of the transgene. Because both overexpression and silencing of transgene expression led to distinct, abnormal phenotypes, the developmental pattern of transgene silencing was visualized. In the lower leaves, the suppressed phenotype was associated with the veins. In successive leaves, the area of the suppressed tissue increased until all newly developed leaves displayed the suppressed phenotype. In this study, a hypothesis is presented for this developmental gene silencing. Furthermore, transgenic plants with suppressed SAM-S activity had a characteristic smell, a consequence of the accumulation of L-methionine that is converted into the volatile methanethiol.

Interpreting peptide mass spectra by VEMS.

Most existing Mass Spectra (MS) analysis programs are automatic and provide limited opportunity for editing during the interpretation. Furthermore, they rely entirely on publicly available databases for interpretation. VEMS (Virtual Expert Mass Spectrometrist) is a program for interactive analysis of peptide MS/MS spectra imported in text file format. Peaks are annotated, the monoisotopic peaks retained, and the b-and y-ion series identified in an interactive manner. The called peptide sequence is searched against a local protein database for sequence identity and peptide mass. The report compares the calculated and the experimental mass spectrum of the called peptide. The program package includes four accessory programs. VEMStrans creates protein databases in FASTA format from EST or cDNA sequence files. VEMSdata creates a virtual peptide database from FASTA files. VEMSdist displays the distribution of masses up to 5000 Da. VEMSmaldi searches singly charged peptide masses against the local database.

Purification and determination of the NH2-terminal amino acid sequence of uracil-DNA glycosylase from human placenta.

Uracil-DNA glycosylase has been purified approximately 130,000-fold from extracts of human placenta. Although all of the uracil-DNA glycosylase activity coeluted through six chromatographic steps, at least four distinct peaks of activity were resolved in the final purification on a Mono S column. Each of the peaks containing uracil-DNA glycosylase activity contained two peptides of Mr = 29,000 and Mr = 26,500, respectively, as analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Experimental evidence indicated that the Mr = 29,000 peptide was the uracil-DNA glycosylase enzyme. The amino-terminal sequence of each peptide was determined after blotting of the peptides from the gel onto Polybrene GF/C paper. The sequences were not related to each other, and neither was any significant homology to other proteins found. Uracil-DNA glycosylase had a molecular turnover number of approximately 600/min and apparent Km value of 2 microM. The enzyme is a basic protein and was stimulated about 10-fold by 60-70 mM NaCl whereas higher concentrations were inhibitory.

Simultaneous high-performance capillary electrophoresis analysis of the reduced and oxidised forms of ascorbate and glutathione.

We describe here a procedure for the simultaneous analysis of the oxidised and reduced forms of the major cellular hydrophillic antioxidants, ascorbic acid (vitamin C) and glutathione (gamma-L-glutamyl-L-cysteinylglycine), by high-performance capillary electrophoresis. Separations are performed in uncoated fused-silica capillaries using 200 mmol/l borate pH 9.0, containing 20% (v/v) acetonitrile as the background electrolyte with fixed-wavelength UV absorbance detection at 185 nm. The influence of pH, organic solvent and other additives on the resolution of these compounds is described and we show that the optimised protocol is capable of simultaneously resolving other thiol components including, N-acetylcysteine and methyl-S-glutathione. The method is suitable for the analysis of these antioxidants in Arabidopsis and Nicotiana leaf tissue and is compatible with the use of the high ionic strength, acidic extraction solvents which are necessary to quench the redox equilibria of these labile components.

Analysis of ascorbate in plant tissues by high-performance capillary zone electrophoresis.

We describe here a simple and rapid capillary electrophoresis method for the determination of ascorbic acid (L-AA) and isoascorbic acid (D-AA) in vegetative tissues. For optimal yields and stabilization, samples are extracted with cold 3% metaphosphoric acid. Hydrophobic contaminants are then removed by passage through a C18 solid-phase extraction cartridge. The analysis itself is performed on a fused silica capillary with 200 mM borate, pH 9, as the carrier electrolyte, using on-line diode array detection over the range 190-350 nm. Quantitation was performed at 260 nm, the uv-absorption maximum for ascorbate at this pH. This method has a minimum detection limit of 84 fmol/injection and linearity of detector response was observed up to at least 12 pmol/injection. We also describe the influence of electrolyte concentration, pH, and the presence of detergent on separations of L-AA, D-AA, and L-galacturonic acid-1,4-lactone. The protocol has been demonstrated to be suitable for the analysis of L-AA in Arabidopsis, parsley, and mushroom. The method has superior resolution to comparable HPLC separations, a comparable analysis time, but lower sensitivity because of the concentration limitations of the detection system.

Antagonistic effects of abscisic acid and jasmonates on salt stress-inducible transcripts in rice roots.

Abscisic acid (ABA) and jasmonates have been implicated in responses to water deficit and wounding. We compared the molecular and physiological effects of jasmonic acid (JA) (< or = 10 microM), ABA, and salt stress in roots of rice. JA markedly induced a cationic peroxidase, two novel 32- and 28-kD proteins, acidic PR-1 and PR-10 pathogenesis-related proteins, and the salt stress-responsive SalT protein in roots. Most JA-responsive proteins (JIPs) from roots also accumulated when plants were subjected to salt stress. None of the JIPs accumulated when plants were treated with ABA. JA did not induce an ABA-responsive group 3 late-embryogenesis abundant (LEA) protein. Salt stress and ABA but not JA induced oslea3 transcript accumulation. By contrast, JA, ABA, and salt stress induced transcript accumulation of salT and osdrr, which encodes a rice PR-10 protein. However, ABA also negatively affected salT transcript accumulation, whereas JA negatively affected ABA-induced oslea3 transcript levels. Endogenous root ABA and methyl jasmonate levels showed a differential increase with the dose and the duration of salt stress. The results indicate that ABA and jasmonates antagonistically regulated the expression of salt stress-inducible proteins associated with water deficit or defense responses.

Three major somatic embryogenesis related proteins in Cichorium identified as PR proteins.

In Cichorium hybrid clone '474' (C. intybus L., var. sativum x C. endivia L., var. latifolia), the direct somatic embryogenesis process in leaf tissues is accompanied by an overall increase in the amount of proteins secreted into the culture medium. Amongst these, three major protein bands of 38 kDa, 32 kDa and 25 kDa were found in the conditioned media. These extracellular protein bands accumulated in the medium of the embryogenic Cichorium hybrid up to 8-fold compared with those in the medium of a nonembryogenic variety. 32 and 25 kDa proteins were purified from the medium and their identities were determined as already described for 38 kDa beta-1,3-glucanases. To investigate their possible function in somatic embryogenesis, peptide sequences, serological relationships or biochemical properties revealed that there were at least two acidic chitinases of 32 kDa and one glycosylated osmotin-like protein of 25 kDa in the embryogenic culture medium. Comparing the amounts of the 38 kDa glucanases, the 32 kDa chitinases, and the 25 kDa osmotin-like protein present in the conditioned media of the embryogenic '474' hybrid and of a non-embryogenic variety, a 2-8-fold higher accumulation of these proteins was observed in the embryogenic hybrid culture medium. This may suggest that part of the accumulation of these three pathogenesis-related (PR) proteins could be correlated with the somatic embryogenesis process. Their possible involvement in this developmental process is discussed.

Molecular and physiological responses to abscisic acid and salts in roots of salt-sensitive and salt-tolerant Indica rice varieties.

The Indica rice (Oryza sativa L.) varieties Pokkali and Nona Bokra are well-known salt tolerance donors in classical breeding. In an attempt to understand the molecular basis of their tolerance, physiological and gene expression studies were initiated. The effect of abscisic acid (ABA) on total proteins in roots from 12-d-old seedlings of Pokkali, Nona Bokra, and the salt-sensitive cultivar Taichung N1 were analyzed on two-dimensional gels. The abundance of ABA-induced proteins was highest in the most tolerant variety, Pokkali. Three ABA-responsive proteins, present at different levels in roots from tolerant and sensitive varieties, were further characterized by partial amino acid analysis. A novel histidine-rich protein and two types of late embryogenesis abundant (LEA) proteins were identified. Protein immunoblotting revealed that the levels of dehydrins and group 3 LEA proteins were significantly higher in roots from tolerant compared with sensitive varieties. Endogenous ABA levels showed a transient increase in roots exposed to osmotic shock (150 mM NaCl). Peak ABA concentrations were 30-fold higher for Nona Bokra and 6-fold higher for Pokkali compared with Taichung N1. Both the salt-induced endogenous ABA levels and a greater molecular response of root tissue to ABA were associated with the varietal differences in tolerance.

Differential effects of elicitors on the viability of rice suspension cells.

We have compared the effects of two elicitors of defense-related processes on rice (Oryza sativa L.) suspension cells. Both chitosan and salicylic acid induced the accumulation of extracellular chitinase, thickening of the cell wall, and a variety of cytological changes in treated cells. Chitosan also induced the production of a brown pigment and cell death. Both of these effects depended on the availability of reactive oxygen species, because the damage was greatly reduced by either catalase or free-radical scavengers. Pretreating cells with salicylic acid also protected them from the cytotoxic effects of chitosan. This type of induced tolerance persisted when salicylic acid was removed and was not simply due to the release of extracellular substances, because salicylic acid-treated cells did not protect untreated cells from chitosan-induced death. Salicylic acid also stimulated the production of a 10-kilodalton subtilisin inhibitor that was not produced by chitosan-treated cells. Most of these changes are associated with the hypersensitive response of many plant species, including monocotyledons, and may serve as an in vitro model for investigating the biochemistry of some diseases.

The homology between the serum proteins PO2 in pig, Xk in horse and alpha 1B-glycoprotein in human.

1. Pig serum Po2 protein and horse Xk protein were purified by FPLC, non-denaturing 2D agarose-PAGE and 2D IPG-PAGE. 2. The separated fractions were electroblotted to poly(4-vinyl-N-methylpyridinium iodide) coated GF/C glass fiber sheets. 3. The partial amino acid sequences and amino acid compositions of different genetic variants of the proteins were determined. 4. The results proved that previously reported polymorphic serum post-albumins in each of these species were homologous to human plasma alpha 1B-glycoprotein.

Alterations in the phenotype of plant cells studied by NH(2)-terminal amino acid-sequence analysis of proteins electroblotted from two-dimensional gel-separated total extracts.

Phenotypic alterations induced by the cytokinin 6-benzylaminopurine in cell suspensions of Nicotiana plumbaginifolia were studied at the level of the NH(2)-terminal sequence of the constituent proteins. Total protein extracts were separated by classical two-dimensional PAGE, and the proteins were recovered by electroblotting onto support materials allowing direct gas-phase sequence analysis of the immobilized proteins. The systems used consist of an efficient electrotransfer buffer (50 mM Tris borate, pH 8.3) in combination with either glass-fiber sheets to which poly(4-vinyl-N-methylpyridinium iodide) is adsorbed or with membranes of polyvinylidene difluoride. The former is an improved version of our previously reported Polybrene-coated glass-fiber sheets and was found to be at least twice as efficient as the polyvinylidene difluoride blots. Thirteen proteins were selected for analysis. They were either induced, repressed, or independent of cytokinin. Ten proteins yielded a sequence, ranging from 10 to 38 residues. Three of the studied Nicotiana proteins show a degree of homology higher than 85% with the amino acid sequences of other eukaryotic proteins-triose-phosphate isomerase, Mn superoxide dismutase, and (1,3)-beta-glucanase. The latter enzyme was repressed by the plant hormone. This study demonstrates that proteins associated with phenotypic variations in cells can now be sequenced by a straightforward procedure involving two-dimensional gel separation of total cellular proteins, recovery by electroblotting, and gas-phase sequence analysis of the immobilized proteins.

Wood formation in poplar: identification, characterization, and seasonal variation of xylem proteins.

Proteins that are preferentially produced in developing xylem may play a substantial role in xylogenesis. To reveal the identity of these proteins, comparative two-dimensional polyacrylamide gel electrophoresis was performed on young differentiating xylem, mature xylem, and bark of poplar (Populus trichocarpa Hook. cv. 'Trichobel') harvested at different times of the year. The most-abundant xylem proteins were identified by microsequence analysis. For 17 of these proteins a putative function could be assigned based on similarity with previously characterized proteins, and for 15 out of these corresponding expressed sequence tags (ESTs) were found in the poplar EST database. The identified xylem-preferential proteins, defined by comparing the protein patterns from xylem and bark, were all involved in the phenylpropanoid pathway: two caffeoyl-coenzyme A O-methyltransferases (CCoAOMT), one phenylcoumaran benzylic ether reductase (PCBER), one bispecific caffeic acid/5-hydroxyferulic acid O-methyltransferase (COMT), five S-adenosyl-L-methionine synthetases, and one homologue of glycine hydroxymethyltransferase (GHMT). Remarkably, the biological function of the two most-abundant xylem-preferential proteins (PCBER and a GHMT homologue) remains unclear. In addition, several housekeeping enzymes were identified: two enolases, two glutamine synthetases, one 70-kDa heat-shock cognate, one calreticulin, and one alpha-tubulin. In comparison to the xylem-preferential proteins, the housekeeping proteins were expressed at significant levels in the bark as well. Also, several additional protein spots were detected for CCoAOMT, PCBER, and COMT by immunoblot. Our data show that for the study of xylogenesis, two-dimensional protein gel comparisons combined with systematic protein sequencing may yield information complementary to that from EST sequencing strategies.

Isolation and characterisation of arcelin-5 proteins and cDNAs.

Arcelins are seed storage proteins present in some wild bean accessions (Phaseolus vulgaris). They are implicated in the resistance phenotype of these wild beans towards the Mexican bean weevil. Arcelin 5, one of six arcelin electrophoretic variants, has been characterised in detail. The purified arcelin-5 protein fraction contained two major polypeptides of 32.2 and 31.5 kDa, designated arcelin 5a and arcelin 5b, respectively, and one minor polypeptide of 30.8 kDa, designated arcelin 5c. The three polypeptides have an identical isoelectric point and are identical for their first nine N-terminal amino acids. Arcelin 5a and arcelin 5b are glycoproteins whereas arcelin 5c is not glycosylated. Native arcelin 5 has a molecular mass corresponding to a dimer form. Using amino acid sequence analysis and PCR techniques, two different arcelin-5 cDNA sequences were obtained, designated arc5-I and arc5-II. Both encode proteins of 261 amino acids with a signal peptide of 21 amino acids. The identity between the two is 99% at the DNA level and 97% at the level of the deduced amino acid sequences. The arc5-I and arc5-II cDNAs encode arcelin 5a and arcelin 5b, respectively. Sequence comparisons and protein characteristics show clearly that arcelin 5 is related to, but distinct from, other arcelin variants and lectins of P. vulgaris.

Maize glutathione-dependent formaldehyde dehydrogenase: protein sequence and catalytic properties.

Glutathione-dependent formaldehyde dehydrogenase (FDH; EC 1.2.1.1) has been purified 3900-fold from maize cell-suspension cultures to a specific activity of 4.68 mumol (mg protein)-1 min-1. The homogeneous enzyme consisted of two identical subunits with a molecular mass of 42 kDa, and an isoelectric point of 5.8. Eight tryptic peptides were sequenced and gave a perfect fit to the protein sequence derived from maize Fdh cDNA (J. Fliegmann and H. Sandermann, 1997, Plant Mol Biol 34: 843-854). There was 62% identity with the eucaryotic FDH consensus sequence. Michaelis constants of approx. 20 microns (formaldehyde), approx. 50 microns (glutathione) and approx. 31 microns (NAD+) were determined for the maize enzyme as well as for FDH partially purified from dog lung. Besides S-hydroxymethylglutathione, pentanol-1, octanol-1, and omega-hydroxy-fatty acids served as substrates for both FDH preparations. The unusual substrate specificity indicates that FDH may be involved in the detoxification of long-chain lipid peroxidation products.

Extracellular beta-1,3-glucanases are induced during early somatic embryogenesis in Cichorium.

In leaf tissues of the Cichorium hybrid clone '474' (C. intybus L. var. sativum x C. endivia L. var. latifolia), the acquisition and expression of embryogenic competence was characterised by the appearance of 15 polypeptides (Boyer et al., 1993, Plant Sci 93: 41-53). The 38-kDa proteins were found to be abundantly present in conditioned embryogenic medium after the first division of the induced cells. These proteins seemed to be glycosylated as indicated by general carbohydrate detection methods. Internal amino-acid sequences obtained after microsequencing tryptic peptides appeared to be 36-57% homologous with plant beta-1,3-endoglucanases. In addition, these 38-kDa proteins were recognised by antibodies raised against the pathogenesis-related tobacco glucanase PR2a and their beta-1,3-glucanase activity was demonstrated by direct detection in polyacrylamide gels after electrophoresis. These results strongly suggested that the 38-kDa somatic-embryogenesis-related (SER) polypeptides are beta-1,3-glucanases. Moreover, the level of glucanase activity was nearly three times higher in the medium of the embryogenic '474' line than in the medium of a non-embryogenic line. The possible involvement of the extracellular 38-kDa proteins in callose degradation during somatic embryogenesis is discussed.

Purification and characterization of peroxidases correlated with lignification in poplar xylem.

Lignin is an integral cell wall component of all vascular plants. Peroxidases are widely believed to catalyze the last enzymatic step in the biosynthesis of lignin, the dehydrogenation of the p-coumaryl alcohols. As the first stage in identifying lignin-specific peroxidase isoenzymes, the classical anionic peroxidases found in the xylem of poplar (Populus trichocarpa Trichobel) were purified and characterized. Five different poplar xylem peroxidases (PXP 1, PXP 2, PXP 3-4, PXP 5, and PXP 6) were isolated. All five peroxidases were strongly glycosylated (3.6% to 4.9% N-glucosamine), with apparent molecular masses between 46 and 54 kD and pI values between pH 3.1 and 3.8. Two of the five isolated peroxidases (PXP 3-4 and PXP 5) could oxidize the lignin monomer analog syringaldazine, an activity previously correlated with lignification in poplar. Because these isoenzymes were specifically or preferentially expressed in xylem, PXP 3-4 and PXP 5 are suggested to be involved in lignin polymerization.

Response of murine cell lines to an IL-1/IL-2-induced factor in a rat/mouse T hybridoma (PC60): differential induction of cytokines by human IL-1 alpha and IL-1 beta and partial amino acid sequence of rat GM-CSF.

We analyzed the proliferative response of the growth factor-dependent murine cell lines FDCp1, DA1-a, 32DC1, Ea3.15, 7TD1, BCL1 and of femural bone marrow cells for their sensitivity to various cytokines, viz. rhIL-1 beta, rhTNF, rhIL-2, mIL-3, rmIL-4, rmIL-5, rhIL-6, rhG-CSF and rmGM-CSF. We also tested for IL-1 and TNF-mediated cytokine secretion by several T cell lines and thymocytes. In all T cell systems, IL-1 alpha and IL-1 beta were equally active in the induction of cytokine production, except for the rat/mouse T cell hybridoma PC60. This cell line exhibited a 10-fold difference in specific activity for the induction of cytokine secretion between rhIL-1 alpha and the other human or murine IL-1 species. Furthermore, IL-1 and IL-2 synergistically induced PC60 cells to produce a factor, which was preferentially active on FDCp1-cells, provisionally called FDCp1-growth factor. SDS-PAGE analysis of partially purified FDCp1-GF showed 19 kDa and 24 kDa-associated biological activities. Amino-terminal and internal amino acid sequences of both bands were determined and on this basis, we identified FDCp1-GF as rat GM-CSF.