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Purification and analysis of RTI40, a type I alveolar epithelial cell apical membrane protein.

RTI40 is a 40-42 kDa protein that, within the lung, is specific to the apical plasma membrane of the rat alveolar type I cell. Type I cells cover greater than 95% of the internal surface area of the lung. In this report, we describe some of the physical properties of RTI40, and its purification to homogeneity. By liquid phase isoelectric focusing, the pI of the protein is 3.0+/-0.5. In two-dimensional immunoblots, there is a 1.0 pH unit charge train, suggesting post-translational modification of the protein. We have purified the protein to homogeneity by the following method. A membrane preparation from perfused rat lungs was extracted with detergent and applied to an ion-exchange column. Immunoreactive fractions from the column were pooled, dialyzed and further fractionated by reverse phase high performance liquid chromatography (HPLC). Essentially all the antigenicity was recovered in one protein peak that was homogeneous both by spectral analysis and silver-stained polyacrylamide gels. Because the purified protein was N terminus blocked, we cleaved the protein with CNBr and fractionated peptide fragments by reverse phase HPLC. Fractions were pooled and concentrated. Direct amino acid sequencing of the major peptide fragment yielded a 15 amino acid peptide homologous to a mouse osteoblast protein, OTS-8. Analysis of purified RTI40 shows that the protein contains glycan, some of which is sialic acid. Characterization of RTI40 should facilitate future studies of the functional properties of RTI40.

Amino Acid Sequence↗

Fibrous protein of human epidermis.

The fibrous proteins of the malpighian layer of human epidermis (prekeratin) have been isolated with citrate buffer, pH 2.65, and shown to consist of 7 polypeptide chains varying in molecular weight from 45,000 daltons to 67,000. Some variation in the number and amount of the components was observed in prekeratin prepared from the epidermis of different individuals. The fibrous proteins of the stratum corneum were isolated with Tris buffer, pH 9.0, containing 6 M urea and 0.1 M mercapto-ethanol and were found to have a pattern similar to prekeratin but not identical to it. However, fibrous protein isolated from the superficial layers of the stratum showed a considerably different pattern indicating that there was post-translational modification of the protein in the late stages of keratinization. These data show that human keratin has the same heterogeneity which was observed previously in cow epidermis. This was further confirmed by studying the polypeptide chain content of prekeratin from a large number of lesions showing benign epidermal hyperplasia, where considerable variation in composition was observed.

Animals↗

Differential protein profiles reflect the different lifestyles of symbiotic and aposymbiotic Anthopleura elegantissima, a sea anemone from temperate waters

Mutualistic associations are prevalent in virtually all environments yet relatively little is known about their complex biochemical and molecular integration and regulation. The endosymbiosis between cnidarians such as the sea anemone Anthopleura elegantissima and the photosynthetic dinoflagellate Symbiodinium californium, in which the algal symbionts are housed in vacuoles within animal endodermal cells, is an ideal model for the study of highly integrated associations at the biochemical and molecular levels. This study describes differential protein synthesis between symbiotic A. elegantissima, collected from environments with high levels of light in the intertidal zone and A. elegantissima that naturally lack symbionts (aposymbiotic), collected from nearby deep-shade habitats. Two-dimensional gel electrophoresis profiles of both steady-state and newly synthesized proteins were compared between the two types of animals using scanning densitometry and image analysis. Symbiotic and aposymbiotic animals share a majority of proteins; however, striking differences in several abundant proteins in steady-state profiles occur. Two proteins are unique to symbiotic animals, one at 32 kDa with an isoelectric point (pI) of 7.9 and another at 31 kDa, pI 6.3. Levels of six proteins with an apparent molecular mass of 25 kDa and pI values ranging from 4.8 to 5.5 are greatly enhanced in aposymbiotic animals. Furthermore, profiles of newly synthesized proteins from symbiotic animals contain a unique cluster of proteins ranging from 25 to 30 kDa and pI 6.6 to 6.9. These marked differences in protein profiles must be a reflection either of underlying differences in the regulation of gene expression or in post-translational modification of common proteins. Identifying the symbiosis-specific products present in A. elegantissima and identifying the inter-partner signaling and cues that result in differential expression will provide an insight into the understanding of these highly integrated associations.

Journal Article↗

Characterization of a novel heterodimeric cathepsin L-like protease and cDNA encoding the catalytic subunit of the protease in embryos of Artemia franciscana.

Embryos and larvae of the brine shrimp, Artemia franciscana, contain a novel cathepsin L-like cysteine protease (ACP) composed of 28.5- and 31.5-kDa subunits. Both subunits of the ACP are glycosylated, and seven isoforms of the protease were identified by isoelectric focusing with pI values ranging from 4.6 to 6.2. Several clones containing sequences coding for the 28.5-kDa subunit of the ACP were isolated from an Artemia embryo cDNA library in lambda ZAP II. One clone of 1229 bp, with an open reading frame of 1014 bp, was sequenced and found to contain 50-65% amino acid sequence identity with several members of the cathepsin L subfamily of cysteine proteases. The mature protein predicted from this sequence consisted of 217 amino acids with a mass of 23.5 kDa prior to post-translational modifications. The mature protein showed 68.6% amino acid sequence identity with human cathepsin L and 73.9% identity with cathepsin L-like proteases from Sarcophaga. peregrina and Drosophila melanogaster. The full-length cDNA clone analyzed in this study (pCP-3b) was renamed AFCATL1 (A. franciscana Cathepsin L1) and the sequence has been deposited in the Genbank database, accession number AF147207. Northern blot analyses identified a single transcript of about 1.4 kb in both embryos and young larvae of Artemia. Southern blot analyses of Artemia genomic DNA treated with various restriction endonucleases indicated a single gene for the ACP. The catalytic subunit of the ACP was tightly associated with a 31.5-kDa protein, which may localize the protease to nonlysosomal sites in embryos and larvae.

Amino Acid Sequence↗

Ubiquitination-mediated protein degradation and modification: an emerging theme in plant-microbe interactions.

Post-translational modification is central to protein stability and to the modulation of protein activity. Various types of protein modification, such as phosphorylation, methylation, acetylation, myristoylation, glycosylation, and ubiquitination, have been reported. Among them, ubiquitination distinguishes itself from others in that most of the ubiquitinated proteins are targeted to the 26S proteasome for degradation. The ubiquitin/26S proteasome system constitutes the major protein degradation pathway in the cell. In recent years, the importance of the ubiquitination machinery in the control of numerous eukaryotic cellular functions has been increasingly appreciated. Increasing number of E3 ubiquitin ligases and their substrates, including a variety of essential cellular regulators have been identified. Studies in the past several years have revealed that the ubiquitination system is important for a broad range of plant developmental processes and responses to abiotic and biotic stresses. This review discusses recent advances in the functional analysis of ubiquitination-associated proteins from plants and pathogens that play important roles in plant-microbe interactions.

Models, Biological↗

Identification of methylation and acetylation sites on mouse histone H3 using matrix-assisted laser desorption/ionization time-of-flight and nanoelectrospray ionization tandem mass spectrometry.

Covalent modifications to histone proteins are well documented in the literature. Specific modification sites are correlated with chromatin structure and transcriptional activity. The histone code is very complex, and includes several types of covalent modifications such as acetylation, methylation, phosphorylation, and ubiquitination of at least 20 possible sites within the histone proteins. The final chromatin structure "read-out" is a result of the cooperation between these many sites of covalent modifications. Methylation and acetylation sites of histone H3 from many different species have been previously identified. However, a full post-translational modification status on histone H3 from mouse has not yet been reported. Here we demonstrate the use of high-accuracy matrix-assisted laser desorption/ionization time-of-flight and nanoelectrospray ionization tandem mass spectrometry to identify the methylation and acetylation sites of the mouse histone H3. In addition to the sites previously identified from other species, one unique methylation site, Lys-122, from mouse histone H3 was identified. The reported mass spectrometric method provides an efficient and sensitive way for analyzing post-translational modifications of histone proteins.

Acetylation↗

Heterologous protein production using the Pichia pastoris expression system.

The Pichia pastoris expression system is being used successfully for the production of various recombinant heterologous proteins. Recent developments with respect to the Pichia expression system have had an impact on not only the expression levels that can be achieved, but also the bioactivity of various heterologous proteins. We review here some of these recent developments, as well as strategies for reducing proteolytic degradation of the expressed recombinant protein at cultivation, cellular and protein levels. The problems associated with post-translational modifications performed on recombinant proteins by P. pastoris are discussed, including the effects on bioactivity and function of these proteins, and some engineering strategies for minimizing unwanted glycosylations. We pay particular attention to the importance of optimizing the physicochemical environment for efficient and maximal recombinant protein production in bioreactors and the role of process control in optimizing protein production is reviewed. Finally, future aspects of the use of the P. pastoris expression system are discussed with regard to the production of complex membrane proteins, such as G protein-coupled receptors, and the industrial and clinical importance of these proteins.

Bioreactors↗

PRMT 3, a type I protein arginine N-methyltransferase that differs from PRMT1 in its oligomerization, subcellular localization, substrate specificity, and regulation.

Methylation is one of the many post-translational modifications that modulate protein function. Although asymmetric NG,NG-dimethylation of arginine residues in glycine-arginine-rich domains of eucaryotic proteins, catalyzed by type I protein arginine N-methyltransferases (PRMT), has been known for some time, members of this enzyme class have only recently been cloned. The first example of this type of enzyme, designated PRMT1, cloned because of its ability to interact with the mammalian TIS21 immediate-early protein, was then shown to have protein arginine methyltransferase activity. We have now isolated rat and human cDNA orthologues that encode proteins with substantial sequence similarity to PRMT1. A recombinant glutathione S-transferase (GST) fusion product of this new rat protein, named PRMT3, asymmetrically dimethylates arginine residues present both in the designed substrate GST-GAR and in substrate proteins present in hypomethylated extracts of a yeast rmt1 mutant that lacks type I arginine methyltransferase activity; PRMT3 is thus a functional type I protein arginine N-methyltransferase. However, rat PRMT1 and PRMT3 glutathione S-transferase fusion proteins have distinct enzyme specificities for substrates present in both hypomethylated rmt1 yeast extract and hypomethylated RAT1 embryo cell extract. TIS21 protein modulates the enzymatic activity of recombinant GST-PRMT1 fusion protein but not the activity of GST-PRMT3. Western blot analysis of gel filtration fractions suggests that PRMT3 is present as a monomer in RAT1 cell extracts. In contrast, PRMT1 is present in an oligomeric complex. Immunofluorescence analysis localized PRMT1 predominantly to the nucleus of RAT1 cells. In contrast, PRMT3 is predominantly cytoplasmic.

Amino Acid Sequence↗

Age-related changes in the protein and mRNA levels of CYP2E1 and CYP3A isoforms as well as in their hepatic activities in Wistar rats. What role for oxidative stress?

Drug biotransformation and its therapeutic effect may be modified during ageing. Among different causative factors of ageing, the impairment of normal cellular functions by free radicals has been evoked as playing a critical role. The effect of age on the expression and activity of CYP2E1 and CYP3A was investigated in male Wistar rats of 3, 8, 11 and 18 months old. The total cytochrome P450 as well as the expression and the activity (midazolam oxidation) of CYP3A isoforms did not change until 18 months of age. Chlorzoxazone hydroxylation (CYP2E1 activity) increased from 3 to 8 months, remained constant between 8 and 11 months and then progressively decreased until 18 months. Interestingly, CYP2E1 microsomal protein followed the same enzyme activity profile from 3 to 8 months, but remained constant thereafter. The level of CYP2E1 mRNA did not change over the whole period. While the amount of proteins did not change after 8 months, their functionality may be affected by oxidative stress (increase in thiobarbituric acid reactive substances, decrease in reduced glutathione level). However, no changes in carbonyl protein content were observed. The decrease in CYP2E1 activity in rats after 11 months is most probably due to post-translational modifications of CYP2E1 proteins. Indeed, it may be correlated with an accumulation of oxidative damage. Since no change was observed in CYP3A activity or in their protein and mRNA content, it seems that such isoforms should be less affected by oxidative stress.

Age Factors↗

Characterization of post-translationally modified recombinant protein using liquid chromatography/mass spectrometry.

Post-translational modification plays an important role in the biological functions of many proteins. Characterization of such modifications is crucial in the development of recombinant protein-based vaccines. Liquid Chromatography coupled with Mass Spectrometry (LC/MS) provides a powerful tool with high resolution and accuracy to characterize proteins and their post-translational modifications. The technique was applied to characterization of a Lyme vaccine protein rOspA (recombinant Outer surface protein A). The results demonstrate that LC/MS could be used to resolve and characterize various forms of post-translational lipidation of the protein. It was this detailed structural information that made it possible to validate a method for quantitative determination of the lipidation forms of rOspA.

Bacterial Outer Membrane Proteins↗

Proteomic identification of the wt-p53-regulated tumor cell secretome.

Tumor-stroma interactions play a major role in tumor development, maintenance and progression. Yet little is known on how the genetic alterations that underlie cell transformation elicit cell extrinsic changes modulating heterotypic cell interactions. We hypothesized that these events involve a modification in the complement of secreted proteins by the cell, acting as mediators of intercellular communication. To test this hypothesis, we examined the role of wt-p53, a major tumor suppressor, on the tumor microenvironment through its regulation of secreted factors. Using a combination of 2-DE and cICAT proteomic techniques, we found a total of 111 secreted proteins, 39 of which showed enhanced and 21 inhibited secretion in response to wt-p53 expression. The majority of these were not direct targets of p53 transcription factor activity, suggesting a novel role for wt-p53 in the control of intracellular protein trafficking and/or secreted protein stability. Evidence for p53-controlled post-translational modifications on nine secreted proteins was also found. These findings will enhance our understanding of wt-p53 modulated interactions of the tumor with its environment.

Cell Line, Tumor↗

Identification of the bull sperm p80 protein as a PH-20 ortholog and its modification during the epididymal transit.

We have identified an 80 kDa protein in ejaculated bull spermatozoa (p80) which is found in acrosomal and post-acrosomal areas of the head. It has a hyaluronidase activity and shares homologies with PH-20, a sperm surface glycoprotein involved in sperm-egg interaction. The aim of the present study was to characterize bull sperm p80 protein at the nucleic and amino acid levels to determine whether it is the bovine PH-20 ortholog. The complete nucleotide sequence determined by RT-PCR, 3' and 5' RACE show that bull p80, displays identity with the PH-20 nucleotide and amino acid sequences. Messenger RNA and protein expressions determined by Northern blot and immunohistochemistry revealed that the protein is testicular (expressed in spermatocytes and spermatids). The localization of p80 on spermatozoa, determined by indirect immunofluorescence using a monoclonal antibody, shows the protein in acrosomal and post acrosomal areas of the head with an increase in the signal intensity as sperm progress through the epididymis. Post-translational modifications of the protein were investigated during the epididymal maturation by Western blot on protein extracts from sperm collected in the caput, corpus and cauda portions of bull epididymis. Glycolysation status of sperm p80 protein on proteins from ejaculated and epididymidal sperm was investigated. Result show that the glycosylation status is modified as spermatozoa migrate through the epididymis. Hyaluronidase activity evaluated in protein extracts from spermatozoa of the three different epididymal sections revealed that the activity is higher at pH 7 than 4 and is not affected by epididymal maturation. These data strongly suggest that p80 is the bovine PH-20.

Amino Acid Sequence↗

A cell-permeable, activity-based probe for protein and lipid kinases.

Protein and lipid kinases are two important classes of biomedically relevant enzymes. The expression and activity of many kinases are known to be dysregulated in a variety of diseases, and proteomic tools that can assess the presence and activity of these enzymes are likely to be useful for their evaluation. Because many of the mechanisms by which protein kinases can become unregulated involve post-translational modifications or changes in protein localization, they can only be detected by examining protein activity, sometimes within the context of the living cell. Wortmannin is a steroid-derived fungal metabolite that covalently inhibits both protein and lipid kinases. Here we describe the synthesis of three wortmannin derivatives, biotin-wortmannin, BODIPY-wortmannin, and tetramethylrhodamine-wortmannin. We demonstrate that these reagents exhibit reactivity similarly as wortmannin and react with members of the phosphatidylinositol 3-kinase and PI3-kinase related kinase families in cellular lysates. Moreover, in some cases these reagents can differentiate between the active and inactive forms of the enzyme, indicating that they are activity-based probes. The reagents also exhibit complementary properties. The biotin-wortmannin reagent is effective in the isolation of labeled proteins; all three can be used for protein labeling, and BODIPY-wortmannin is cell-permeable and can be used to label proteins within cells.

Androstadienes↗

Post-translational modification and evoked release of two large surface proteins of sympathetic neurons.

Two high molecular weight glycoproteins, exposed on the surface of sympathetic neurons, are modified after they have been translated, glycosylated, and inserted in the plasma membrane. B1 (apparent Mr = 230,000 by electrophoresis in sodium dodecyl sulfate) and B3 (Mr approximately 200,000) are each modified to give proteins of lower apparent molecular weight: B2 (Mr approximately 215,000) and B4 (Mr approximately 185,000). B1 and B3 are derived from two precursors, P1 (Mr approximately 210,000) and P3 (Mr approximately 185,000) which are nonsialylated, mannose-rich proteins not exposed on the cell surface. In unstimulated cells, B1 and B3 are converted to B2 and B4 with a half-life of 4 to 6 hr. In cells which have been treated chemically to evoke the release of neurotransmitter, the modification appears to be accelerated, and B2 and B4 are shed into the medium in soluble form (S2 and S4). This evoked release of protein is calcium dependent and is detected only in conditions which favor the rapid release of neurotransmitter. In the absence of exogenous calcium, however, transmitter release can be evoked without the accompanying release of protein. Thus the release of protein is not an essential step of transmitter release, but may follow it. B1, its precursor, and derivatives are immunologically related to the NILE (nerve growth factor-inducible, large external) glycoprotein of pheochromocytoma PC12 cells (McGuire, J. C., L. A. Greene, and A. V. Furano (1978) Cell 15: 357-365). B3 does not cross-react with B1 or NILE antigenically, but otherwise is synthesized, processed, and released in a similar manner.

Animals↗

A novel mass spectrometry-based assay for GSK-3beta activity.

BACKGROUND: As a component of the progression from genomic to proteomic analysis, there is a need for accurate assessment of protein post-translational modifications such as phosphorylation. Traditional kinase assays rely heavily on the incorporation of gamma-P32 radiolabeled isotopes, monoclonal anti-phospho-protein antibodies, or gel shift analysis of substrate proteins. In addition to the expensive and time consuming nature of these methods, the use of radio-ligands imposes restrictions based on the half-life of the radionucleotides and pose potential health risks to researchers. With the shortcomings of traditional assays in mind, the aim of this study was to develop a high throughput, non-radioactive kinase assay for screening Glycogen Synthase Kinase-3beta (GSK-3beta) activity. RESULTS: Synthetic peptide substrates designed with a GSK-3beta phosphorylation site were assayed with both recombinant enzyme and GSK-3beta immunoprecipitated from NIH 3T3 fibroblasts. A molecular weight shift equal to that of a single phosphate group (80 Da.) was detected by surface enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF-MS) in a GSK-3beta target peptide (2B-Sp). Not only was there a dose-dependent response in molecular weight shift to the amount of recombinant GSK-3beta used in this assay, this shift was also inhibited by lithium chloride (LiCl), in a dose-dependent manner. CONCLUSION: We present here a novel method to sensitively measure peptide phosphorylation by GSK-3beta that, due to the incorporation of substrate controls, is applicable to either purified enzyme or cell extracts. Future studies using this method have the potential to elucidate the activity of GSK-3beta in vivo, and to screen enzyme activity in relation to a variety of GSK-3beta related disorders.

Glycogen Synthase Kinase 3↗

Carbonylation of glycolytic proteins is a key response to drug-induced oxidative stress and apoptosis.

Recent work has highlighted the importance of protein post-translational modifications such as phosphorylation (enzymatic) and nitrosylation (nonenzymatic) in the early stages of apoptosis. In this study, we have investigated the levels of protein carbonylation, a nonenzymatic protein modification that occurs in conditions of cellular oxidative stress, during etopside-induced apoptosis of HL60 cells. Within 1 h of VP16 treatment, a number of proteins underwent carbonylation due to oxidative stress. This was inhibited by the antioxidant N-acetyl-L-cysteine. Among the proteins found to be carbonylated were glycolytic enzymes. Subsequently, we found that the rate of glycolysis was significantly reduced, probably due to a carbonylation mediated reduction in enzymatic activity of glycolytic enzymes. Our work demonstrates that protein carbonylation can be rapidly induced through cytotoxic drug treatment and may specifically inhibit the glycolytic pathway. Given the importance of glycolysis as a source of cellular ATP, this has severe implications for cell function.

Acetylcysteine↗

Exercise affects energy metabolism and neural plasticity-related proteins in the hippocampus as revealed by proteomic analysis.

Studies were conducted to evaluate the effect of a brief voluntary exercise period on the expression pattern and post-translational modification of multiple protein classes in the rat hippocampus using proteomics. An analysis of 80 protein spots of relative high abundance on two-dimensional gels revealed that approximately 90% of the proteins identified were associated with energy metabolism and synaptic plasticity. Exercise up-regulated proteins involved in four aspects of energy metabolism, i.e. glycolysis, ATP synthesis, ATP transduction and glutamate turnover. Specifically, we found increases in fructose-bisphosphate aldolase C, phosphoglycerate kinase 1, mitochondrial ATP synthase, ubiquitous mitochondrial creatine kinase and glutamate dehydrogenase 1. Exercise also up-regulated specific synaptic-plasticity-related proteins, the cytoskeletal protein alpha-internexin and molecular chaperones (chaperonin-containing TCP-1, neuronal protein 22, heat shock 60-kDa protein 1 and heat shock protein 8). Western blot was used to confirm the direction and magnitude of change in ubiquitous mitochondrial creatine kinase, an enzyme essential for transducing mitochondrial-derived ATP to sites of high-energy demand such as the synapse. Protein phosphorylation visualized by Pro-Q Diamond fluorescent staining showed that neurofilament light polypeptide, glial fibrillary acidic protein, heat shock protein 8 and transcriptional activator protein pur-alpha were more intensely phosphorylated with exercise as compared with sedentary control levels. Our results, together with the fact that most of the proteins that we found to be up-regulated have been implicated in cognitive function, support a mechanism by which exercise uses processes of energy metabolism and synaptic plasticity to promote brain health.

Animals↗

Effects of oxidative stress on the cardiac myocyte proteome: modifications to peroxiredoxins and small heat shock proteins.

Endogenous oxidative stress is a likely cause of cardiac myocyte death in vivo. We examined the early (0-2 h) changes in the proteome of isolated cardiac myocytes from neonatal rats exposed to H2O2 (0.1 mM), focussing on proteins with apparent molecular masses of between 20 and 30 kDa. Proteins were separated by two-dimensional gel electrophoresis (2DGE), located by silver-staining and identified by mass spectrometry. Incorporation of [35S]methionine or 32Pi was also studied. For selected proteins, transcript abundance was examined by reverse transcriptase-polymerase chain reaction. Of the 38 protein spots in the region, 23 were identified. Two families showed changes in 2DGE migration or abundance with H2O2 treatment: the peroxiredoxins and two small heat shock protein (Hsp) family members: heat shock 27 kDa protein 1 (Hsp25) and alphaB-crystallin. Peroxiredoxins shifted to lower pI values and this was probably attributable to 'over-oxidation' of active site Cys-residues. Hsp25 also shifted to lower pI values but this was attributable to phosphorylation. alphaB-crystallin migration was unchanged but its abundance decreased. Transcripts encoding peroxiredoxins 2 and 5 increased significantly. In addition, 10 further proteins were identified. For two (glutathione S-transferase pi, translationally-controlled tumour protein), we could not find any previous references indicating their occurrence in cardiac myocytes. We conclude that exposure of cardiac myocytes to oxidative stress causes post-translational modification in two protein families involved in cytoprotection. These changes may be potentially useful diagnostically. In the short term, oxidative stress causes few detectable changes in global protein abundance as assessed by silver-staining.

Amino Acid Sequence↗