Metabolic analysis revealed altered amino acid profiles in Lupinus albus organs as a result of boron deficiency

We analysed the changes in the metabolites of Lupinus albus organs (leaf-blades, petioles, apexes, hypocotyls and roots) as a consequence of B deficiency. The deficiency did not affect malate concentration and induced only minor changes in the sugar content, suggesting that the carbohydrate metabolism is little affected by the deficiency. Contrarily, marked changes in the content of free amino acids were observed, with some specific variations associated with the different organs. These changes indicate that various aspects of metabolism implicated in the amino acid accumulation were affected by B deficiency. Most of the detected changes appear to have implications with some stress responses or signalling processes. Asparagine and proline that increase in many stresses also accumulated in petioles, apexes and hypocotyls. Accumulation of γ-aminobutyric acid shunt amino acids, indicative of production of reactive oxygen species, occurs in the same three organs and also the roots. The increase in the branched-chain amino acids, observed in all organs, suggests the involvement of B with the cytoskeleton, whereas glycine decrease in leaf-blades and active growing organs (apexes and roots) could be associated with the proposed role of this amino acids in plant signalling in processes that might be associated with the decreased growth rates observed in B deficiency. Despite the admitted importance of free amino acids in plant metabolism, the available information on this matter is scarce. So our results bring new information concerning the effects of B deficiency in the metabolism of the several L. albus organs.     

A plasma membrane protein is involved in cell contact-mediated regulation of tissue-specific genes in adult hepatocytes

We have identified the liver-regulating protein (LRP), a cell surface protein involved in the maintenance of hepatocyte differentiation when cocultured with rat liver epithelial cells (RLEC). LRP was defined by immunoreactivity to a monoclonal antibody (mAb L8) prepared from RLEC. mAb L8 specifically detected two polypeptides of 85 and 73 kD in immunoprecipitation of both hepatocyte- and RLEC-iodinated plasma membranes. The involvement of these polypeptides, which are integral membrane proteins, in cell interaction-mediated regulation of hepatocytes was assessed by evaluating the perturbing effects of the antibody on cocultures with RLEC. Several parameters characteristic of differentiated hepatocytes were studied, such as liver-specific and house-keeping gene expression, cytoskeletal organization and deposition of extracellular matrix (ECM). An early cytoskeletal disturbance was evidenced and a marked alteration of hepatocyte functional capacity was observed in the presence of the antibody, together with a loss of ECM deposition. By contrast, cell-cell aggregation or cell adhesion to various extracellular matrix components were not affected. These findings suggest that LRP is distinct from an extracellular matrix receptor. The fact that early addition of mAb L8 during cell contact establishment was necessary to be effective may indicate that LRP is a novel plasma membrane protein that plays an early pivotal role in the coordinated metabolic changes which lead to the differentiated phenotype of mature hepatocytes.     

Filamin (280-kDa actin-binding protein) is a caspase substrate and is also cleaved directly by the cytotoxic T lymphocyte protease granzyme B during apoptosis

We used yeast two-hybrid screening to identify the cytoskeletal protein filamin as a ligand for the proapoptotic protease granzyme B, produced by cytotoxic T lymphocytes. Filamin was directly cleaved by granzyme B when target cells were exposed to granzyme B and the lytic protein perforin, but it was also cleaved in a caspase-dependent manner following the ligation of Fas receptors. A similar pattern of filamin cleavage to polypeptides of approximately 110 and 95 kDa was observed in Jurkat cells killed by either mechanism. However, filamin cleavage in response to granzyme B was not inhibited by the caspase inhibitor z-Val-Ala-Asp-fluoromethylketone at concentrations that abolished DNA fragmentation. Filamin staining was redistributed from the cell membrane into the cytoplasm of Jurkat cells exposed to granzyme B and perforin and following ligation of Fas receptors, coincident with the morphological changes of apoptosis. Filamin-deficient human melanoma cells were significantly (although not completely) protected from granzyme B-mediated death compared with isogenic filamin-expressing cells, both in clonogenic survival and (51)Cr release assays, whereas death from multiple other stimuli was not affected by filamin deficiency. Thus, filamin is a functionally important substrate for granzyme B, as its cleavage may account at least partly for caspase-independent cell death mediated by the granzyme.     

Alterations in hepatocyte cytoskeleton caused by redox cycling and alkylating quinones

Quinones may induce toxicity by a number of mechanisms, including alkylation and oxidative stress following redox cycling. The metabolism of quinones by isolated rat hepatocytes is associated with cytoskeletal alterations, plasma membrane blebbing, and subsequent cytotoxicity. The different mechanisms underlying the effects of alkylating (p-benzoquinone), redox cycling (2,3-dimethoxy-1,4-naphthoquinone), and mixed redox cycling/alkylating (2-methyl-1,4-naphthoquinone) quinones on hepatocyte cytoskeleton have been investigated in detail in this study. Analysis of the cytoskeletal fraction extracted from quinone-treated cells revealed a concentration-dependent increase in the amount of cytoskeletal protein and a concomitant loss of protein thiols, irrespective of the quinone employed. In the case of redox cycling quinones, these alterations were associated with an oxidation-dependent actin crosslinking (sensitive to the thiol reductant dithiothreitol). In contrast, with alkylating quinones an oxidation-independent cytoskeletal protein crosslinking (insensitive to thiol reductants) was observed. In addition to these changes, a dose-dependent increase in the relative abundance of F-actin was detected as a consequence of the metabolism of oxidizing quinones in hepatocytes. Addition of dithiothreitol solubilized a considerable amount of polypeptides from the cytoskeletal fraction isolated from hepatocytes exposed to redox cycling but not alkylating quinones. Our findings indicate that the hepatocyte cytoskeleton is an important target for the toxic effects of different quinones. However, the mechanisms underlying cytoskeletal damage differ depending on whether the quinone acts primarily by oxidative stress or alkylation.     

Involvement of mitogen-activated protein kinases in the symbiosis Bradyrhizobium-Lupinus

In plants, mitogen-activated protein kinases (MAPKs) are involved in signalling to hormones, cell cycle regulation, stresses, and plant defence responses. In this work, several MAPKs were detected by immunobloting in roots and nodules of Lupinus albus produced by inoculation with Bradyrhizobium sp. (Lupinus). In vitro kinase assays showed that inoculation of seedling roots with B. sp. (Lupinus) activates salt stress-inducible and stress-activated MAPKs after 5 min of incubation. By contrast, inoculation with dead B. sp. (Lupinus) or the heterologous bacteria Sinorhizobium meliloti did not induce salt stress-inducible and stress-activated MAPK activities. In vivo experiments showed that inoculation with B. sp. (Lupinus) induced the activation of MAPKs in roots. The maximal activation was in the region of the root tip with emerging hairs, which corresponds to the infection zone. The p38 MAPK inhibitors SB 202190 and SB 203580 blocked these kinase activities. Experiments with SB 202190 and the MAPKK inhibitor UO 126 altered the pattern of nodulation in the main root, decreasing the number and weight of nodules produced in the upper sites while increasing the nodule number in the younger lower root zone. These data suggest that MAPK inhibition blocks early events in the susceptible root zone to rhizobial infection, delaying nodulation, and support a role for MAPKs in the infection and nodulation of L. albus by B. sp. (Lupinus).     

How do B cells differ from T cells in terms of gene expression?

As part of an ongoing program to identify the genes that distinguish B cells from T cells, we have analyzed 910 molecular species of polypeptides detectable in mouse lymphocytes by 2D gel electrophoresis. Of these 910 polypeptides, 488 were present in both B and T cells, 185 in B but not T cells, and 237 in T but not B cells. The detected set of polypeptides accounts for more than 95% of the protein mass of lymphocytes. There are about 2000 other polypeptides that are below the threshold of detection. We have started to identify and to retrieve cDNA clones belonging to the B and T cell subset. Dedicated to Professor J. Šterzl on the occasion of his 70th birthday     

Ruminococcus albus 8 mutants defective in cellulose degradation are deficient in two processive endocellulases, Cel48A and Cel9B, both of which possess a novel modular architecture

The cellulolytic bacterium Ruminococcus albus 8 adheres tightly to cellulose, but the molecular biology underpinning this process is not well characterized. Subtractive enrichment procedures were used to isolate mutants of R. albus 8 that are defective in adhesion to cellulose. Adhesion of the mutant strains was reduced 50% compared to that observed with the wild-type strain, and cellulose solubilization was also shown to be slower in these mutant strains, suggesting that bacterial adhesion and cellulose solubilization are inextricably linked. Two-dimensional polyacrylamide gel electrophoresis showed that all three mutants studied were impaired in the production of two high-molecular-mass, cell-bound polypeptides when they were cultured with either cellobiose or cellulose. The identities of these proteins were determined by a combination of mass spectrometry methods and genome sequence data for R. albus 8. One of the polypeptides is a family 9 glycoside hydrolase (Cel9B), and the other is a family 48 glycoside hydrolase (Cel48A). Both Cel9B and Cel48A possess a modular architecture, Cel9B possesses features characteristic of the B(2) (or theme D) group of family 9 glycoside hydrolases, and Cel48A is structurally similar to the processive endocellulases CelF and CelS from Clostridium cellulolyticum and Clostridium thermocellum, respectively. Both Cel9B and Cel48A could be recovered by cellulose affinity procedures, but neither Cel9B nor Cel48A contains a dockerin, suggesting that these polypeptides are retained on the bacterial cell surface, and recovery by cellulose affinity procedures did not involve a clostridium-like cellulosome complex. Instead, both proteins possess a single copy of a novel X module with an unknown function at the C terminus. Such X modules are also present in several other R. albus glycoside hydrolases and are phylogentically distinct from the fibronectin III-like and X modules identified so far in other cellulolytic bacteria.     

Comparative quantitative proteomics to investigate the remodeling of bioenergetic pathways under iron deficiency in Chlamydomonas reinhardtii

The basic question addressed in this study is how energy metabolism is adjusted to cope with iron deficiency in Chlamydomonas reinhardtii. To investigate the impact of iron deficiency on bioenergetic pathways, comparative proteomics was combined with spectroscopic as well as voltametric oxygen measurements to assess protein dynamics linked to functional properties of respiratory and photosynthetic machineries. Although photosynthetic electron transfer is largely compromised under iron deficiency, our quantitative and spectroscopic data revealed that the functional antenna size of photosystem II (PSII) significantly increased. Concomitantly, stress-related chloroplast polypeptides, like 2-cys peroxiredoxin and a stress-inducible light-harvesting protein, LhcSR3, as well as a novel light-harvesting protein and several proteins of unknown function were induced under iron-deprivation. Respiratory oxygen consumption did not decrease and accordingly, polypeptides of respiratory complexes, harboring numerous iron-sulfur clusters, were only slightly diminished or even increased under low iron. Consequently, iron-deprivation induces a transition from photoheterotrophic to primarily heterotrophic metabolism, indicating that a hierarchy for iron allocations within organelles of a single cell exists that is closely linked with the metabolic state of the cell.     

Proteomic analysis of roots growth and metabolic changes under phosphorus deficit in maize (Zea mays L.) plants

Phosphorus (P) deficiency is a major limitation for plant growth and development. Plants can respond defensively to this stress, modifying their metabolic pathways and root morphology, and this involves changes in their gene expression. To better understand the low P adaptive mechanism of crops, we conducted the comparative proteome analysis for proteins isolated from maize roots treated with 1000 microM (control) or 5 microM KH2PO4 for 17 days. The results showed that approximately 20% of detected proteins on 2-DE gels were increased or decreased by two-fold or more under phosphate (Pi) stress. We identified 106 differentially expressed proteins by MALDI-TOF MS. Analysis of these P starvation responsive proteins suggested that they were involved in phytohormone biosynthesis, carbon and energy metabolisms, protein synthesis and fate, signal transduction, cell cycle, cellular organization, defense, secondary metabolism, etc. It could be concluded that they may play important roles in sensing the change of external Pi concentration and regulating complex adaptation activities for Pi deprivation to facilitate P homeostasis. Simultaneously, as a basic platform, the results would also be useful for the further characterization of gene function in plant P nutrition.     

Proteomic alterations of <Emphasis Type="Italic">Brassica napus</Emphasis> root in response to boron deficiency

Boron (B) deficiency is a worldwide problem, and Brassica napus is one of the most sensitive crops to B deficiency. To better understand the B starvation response of Brassica napus, we conducted a comparative proteomic analysis of seedling stage Brassica napus root between B-sufficient and B-limited conditions: 45 differentially expressed proteins were successfully identified by 2-DE coupled with MALDI-TOF/TOF-MS and LTQ-ESI-MS/MS analysis. Among these proteins, 10 were down-regulated and 35 were up-regulated under B-limited condition. Combining GO and KEGG analyses with data from previous reports, proteins were categorized into several functional groups, including antioxidant and detoxification, defense-related proteins, signaling and regulation, carbohydrate and energy metabolism, amino acid and fatty acid metabolism, protein translation and degradation, cell wall structure, and transporter. The genes of selected proteins were analyzed by quantitative RT-PCR. Our results provide novel information for better understanding the physiological and biochemical responses to B deficiency in plants.     

Epstein-Barr virus membrane antigens: characterization, distribution, and strain differences.

The Epstein-Barr virus (EBV)-associated membrane antigen polypeptides (350,000, 220,000, 140,000, and 85,000 daltons) are recognized by a rabbit anti-EBV serum and are present on the plasma membranes of producer cell lines, as we demonstrated previously. In this report, we show that these polypeptides are present on intact virus particles. Subcellular fractionation revealed that these antigens are distributed throughout the cell, except for the 85,000-dalton protein, which was poorly represented in the nuclear fraction. In addition, an EBV-associated protein of 160,000 daltons, which comigrates with a major component of the viral capsid, was detected in the cytoplasmic and nuclear fractions. The immunoprecipitation patterns of 13 different EBV isolates were similar, with two exceptions. First, the 350,000- and 220,000-dalton polypeptides from marmoset cell lines had slightly larger molecular sizes than the corresponding polypeptides from human cell lines. Second, B95-8 virus and B95-8-derived human and marmoset cell lines contained little of the 220,000-dalton protein; however, 883L, the human parent line of B95-8, has a normal amount of the 220,000-dalton protein. Thus, the B95-8 strain of EBV appears to be a structurally defective variant. We have not observed any variation in protein patterns associated with different EBV disease states. The 350,000-, 220,000-, and 85,000-dalton polypeptides were shown to be glycoproteins by incorporation of [3H]mannose and [3H]glucosamine and to contain N-asparagine-linked glycosyl groups by their sensitivity to tunicamycin. To simplify future work, the following nomenclature for these EBV-associated polypeptides is suggested: 350,000 (gp350), 220,000 (gp220), 160,000 (p160), 140,000 (p140), and 85,000 (gp85).     

Molecular control of acid phosphatase secretion into the rhizosphere of proteoid roots from phosphorus-stressed white lupin

White lupin (Lupinus albus) grown under P deficiency displays a suite of highly coordinated adaptive responses. Included among these is secretion of copious amounts of acid phosphatase (APase). Although numerous reports document that plants secrete APases in response to P deficiency, little is known of the biochemical and molecular events involved in this process. Here we characterize the secreted APase protein, cDNA, and gene from white lupin. The secreted APase enzyme is a glycoprotein with broad substrate specificity. It is synthesized as a preprotein with a deduced M(r) of 52,000 containing a 31-amino acid presequence. Analysis of the presequence predicts that the protein is targeted to outside the cell. The processed protein has a predicted M(r) of 49,000 but migrates as a protein with M(r) of 70,000 on sodium dodecyl sulfate gels. This is likely due to glycosylation. Enhanced expression is fairly specific to proteoid roots of P-stressed plants and involves enhanced synthesis of both enzyme protein and mRNA. Secreted APase appears to be encoded by a single gene containing seven exons interrupted by six introns. The 5'-upstream putative promoter of the white lupin-secreted APase contains a 50-base pair region having 72% identity to an Arabidopsis APase promoter that is responsive to P deficiency. The white lupin-secreted APase promoter and targeting sequence may be useful tools for genetically engineering important proteins from plant roots.     

Microgravity alters basal and insulin-mediated metabolic activity of normal and neoplastic cells

In this paper we report the behaviour of normal vascular smooth muscle cells and transformed breast cancer cells under normal versus simulated microgravity conditions by comparing cell proliferation, Glucose transport, Methionine uptake and protein synthesis. Modeled microgravity profoundly affects cell growth (especially in normal cells) and Glucose or Methionine metabolism (although to different extent in the two cell lines). Since both cells own responsive insulin receptors, the comparison was extended to insulin-stimulated versus unstimulated conditions. We report that the detected metabolic changes were strongly enhanced when the cells were simultaneously stimulated with insulin and subjected to modeled microgravity stress. Such observations may have important returns for human health in space; they deserve further attention.     

Analysis of proteomic changes in roots of soybean seedlings during recovery after flooding

A proteomic approach was used to identify proteins involved in post-flooding recovery in soybean roots. Two-day-old soybean seedlings were flooded with water for up to 3 days. After the flooding treatment, seedlings were grown until 7 days after sowing and root proteins were then extracted and separated using two-dimensional polyacrylamide gel electrophoresis (2-DE). Comparative analysis of 2-D gels of control and 3 day flooding-experienced soybean root samples revealed 70 differentially expressed protein spots, from which 80 proteins were identified. Many of the differentially expressed proteins are involved in protein destination/storage and metabolic processes. Clustering analysis based on the expression profiles of the 70 differentially expressed protein spots revealed that 3 days of flooding causes significant changes in protein expression, even during post-flooding recovery. Three days of flooding resulted in downregulation of ion transport-related proteins and upregulation of proteins involved in cytoskeletal reorganization, cell expansion, and programmed cell death. Furthermore, 7 proteins involved in cell wall modification and S-adenosylmethionine synthesis were identified in roots from seedlings recovering from 1 day of flooding. These results suggest that alteration of cell structure through changes in cell wall metabolism and cytoskeletal organization may be involved in post-flooding recovery processes in soybean seedlings.     

Proteomic profiles of thylakoid membranes and changes in response to iron deficiency

The proteomic profile of thylakoid membranes and the changes induced in that proteome by iron deficiency have been studied by using thylakoid preparations from Beta vulgaris plants grown in hydroponics. Two different 2-D electrophoresis approaches have been used to study these proteomes: isoelectrical focusing followed by SDS PAGE (IEF-SDS PAGE) and blue-native polyacrylamide gel electrophoresis followed by SDS PAGE (BN-SDS PAGE). These techniques resolved approximately 110–140 and 40 polypeptides, respectively. Iron deficiency induced significant changes in the thylakoid sugar beet proteome profiles: the relative amounts of electron transfer protein complexes were reduced, whereas those of proteins participating in leaf carbon fixation-linked reactions were increased. A set of polypeptides, which includes several enzymes related to metabolism, was detected in thylakoid preparations from Fe-deficient Beta vulgaris leaves by using BN-SDS PAGE, suggesting that they may be associated with these thylakoids in vivo. The BN-SDS PAGE technique has been proven to be a better method than IEF-SDS PAGE to resolve highly hydrophobic integral membrane proteins from thylakoid preparations, allowing for the identification of complexes and determination of their polypeptidic components.     

Analysis of Lupinus albus Leaf Apoplastic Proteins in Response to Boron Deficiency

Boron is essential for plant development and although its precise functions are not fully understood there is evidence for its importance in the extracellular matrix. So we have analysed by two-dimensional gel electrophoresis the effect of B deficiency in the soluble apoplast proteins of Lupinus albus leaf. Twenty-three polypeptide spots varied significantly between the control and the B deficiency patterns. Of these polypeptides only 9 could be identified by mass spectrometry techniques: PR-1 like protein, β-1,3-glucanases, class III chitinases, thaumatin like proteins and an expansin-like protein, all of them being involved in plant defence mechanisms. Only PR-1 like protein was de novo expressed under B deficiency, while the remaining proteins also responded to water stress. Although general response mechanisms seem to be triggered by both B and water stress, the pattern of protein expression was distinct, suggesting that under B deficiency specific regulatory mechanisms may be induced.     

Responses to Nickel in the Proteome of the Hyperaccumulator Plant <Emphasis Type="BoldItalic">Alyssum lesbiacum</Emphasis>

A proteomic analysis of the Ni hyperaccumulator plant Alyssum lesbiacum was carried out to identify proteins that may play a role in the exceptional degree of Ni tolerance and accumulation characteristic of this metallophyte. Of the 816 polypeptides detected in root tissue by 2D SDS-PAGE, eleven increased and one decreased in abundance relative to total protein after 6-week-old plants were transferred from a standard nutrient solution containing trace concentrations of Ni to a moderately high Ni treatment (0.3 mM NiSO₄) for 48 h. These polypeptides were identified by tandem mass spectrometry and the majority were found to be involved in sulphur metabolism (consistent with a re-allocation of sulphur towards cysteine and glutathione), protection against reactive oxygen species, or heat-shock response. In contrast, very few polypeptides were found to change in abundance in root or shoot tissue after plants were exposed for 28 days to 0.03 mM NiSO₄, a concentration representing the optimum for growth of this species but sufficient to lead to hyperaccumulation of Ni in the shoot. Under these conditions, constitutively expressed genes in this highly Ni-tolerant species may be sufficient to allow for effective chelation and sequestration of Ni without the need for additional protein synthesis.