Fluorescent labeling of disulfide proteins on 2D gel for screening allergens: a preliminary study

Redox-mediated activation of ATG3 promotes ATG8 lipidation and autophagy progression in Chlamydomonas reinhardtii

Autophagy is one of the main degradative pathways used by eukaryotic organisms to eliminate useless or damaged intracellular material to maintain cellular homeostasis under stress conditions. Mounting evidence indicates a strong interplay between the generation of reactive oxygen species and the activation of autophagy. Although a tight redox regulation of autophagy has been shown in several organisms, including microalgae, the molecular mechanisms underlying this control remain poorly understood. In this study, we have performed an in-depth in vitro and in vivo redox characterization of ATG3, an E2-activating enzyme involved in ATG8 lipidation and autophagosome formation, from 2 evolutionary distant unicellular model organisms: the green microalga Chlamydomonas (Chlamydomonas reinhardtii) and the budding yeast Saccharomyces cerevisiae. Our results indicated that ATG3 activity from both organisms is subjected to redox regulation since these proteins require reducing equivalents to transfer ATG8 to the phospholipid phosphatidylethanolamine. We established the catalytic Cys of ATG3 as a redox target in algal and yeast proteins and showed that the oxidoreductase thioredoxin efficiently reduces ATG3. Moreover, in vivo studies revealed that the redox state of ATG3 from Chlamydomonas undergoes profound changes under autophagy-activating stress conditions, such as the absence of photoprotective carotenoids, the inhibition of fatty acid synthesis, or high light irradiance. Thus, our results indicate that the redox-mediated activation of ATG3 regulates ATG8 lipidation under oxidative stress conditions in this model microalga.

Reducing Allergenicity to Arginine Kinase from Mud Crab Using Site-Directed Mutagenesis and Peptide Aptamers

The mud crab ( Scylla paramamosain) is widely consumed but can cause a severe food allergic reaction. To reduce allergenicity to arginine kinase (AK), site-directed mutagenesis was used to destroy disulfide bonds or mutate critical amino acids of conformational epitopes. Three hypoallergenic mutant AKs (mAK1, mAK2, and mAK3) were generated, with the immunoreactivity decreasing by 54.2, 40.1, and 71.4%, respectively. In comparison to recombinant AK (rAK), the structure of mAKs was clearly changed. Additionally, antisense peptides were designed on the basis of linear epitopes and pepsin-cutting sites of AK. Five peptide aptamers were screened by molecular docking and then analyzed by the immunoglobulin E inhibition enzyme-linked immunosorbent assay and human Laboratory of Allergic Diseases 2 mast cell degranulation assay. The peptide aptamers could significantly inhibit allergenicity of rAK and mAKs, and the inhibitory effect of peptide aptamer 3 was slightly better than the others. These results provide synergistic methods to reduce allergenicity to AK, which could be applied to other shellfish allergens.

Chemical Probes for Redox Signaling and Oxidative Stress

SIGNIFICANCE

Cellular reactive oxygen species (ROS) mediate redox signaling cascades that are critical to numerous physiological and pathological processes. Analytical methods to monitor cellular ROS levels and proteomic platforms to identify oxidative post-translational modifications (PTMs) of proteins are critical to understanding the triggers and consequences of redox signaling. Recent Advances: The prevalence and significance of redox signaling has recently been illuminated through the use of chemical probes that allow for sensitive detection of cellular ROS levels and proteomic dissection of oxidative PTMs directly in living cells.

CRITICAL ISSUES

In this review, we provide a comprehensive overview of chemical probes that are available for monitoring ROS and oxidative PTMs, and we highlight the advantages and limitations of these methods.

FUTURE DIRECTIONS

Despite significant advances in chemical probes, the low levels of cellular ROS and low stoichiometry of oxidative PTMs present challenges for accurately measuring the extent and dynamics of ROS generation and redox signaling. Further improvements in sensitivity and ability to spatially and temporally control readouts are essential to fully illuminate cellular redox signaling.

Comparative studies on sulfhydryl determination of soy protein using two aromatic disulfide reagents and two fluorescent reagents

In this study, the sulfhydryl (SH) contents of unheated and heated (90 °C, 5 min) soy protein were detected under different conditions (pH, reagent addition order, SDS/GuHCl concentration, EDTA) using two aromatic disulfide reagents: 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) and 4,4'-dithiodipyridine (DPS). Two fluorescent alkylating reagents, monobromobimane (mBBr) and N-(1-pyrenyl)maleimide (NPM), were chosen due to their high sensitivity and were also used. Amino acid analysis was used to detect the SH (cysteine) contents of unheated (7.51 ± 0.45 μmol SH/g protein) and heated (1.47 ± 0.10 μmol SH/g protein) soy protein, and similar results were obtained using enzymatic hydrolysis-assisted DPS. The SH content detected by DTNB was affected by pH, denaturant species, and denaturant concentration, and the best results were obtained at pH 7.0 when 6 M GuHCl was added after DTNB. These results were lower than that of the amino acid analysis, however. The SH detected by DPS was not as affected as that of DTNB by pH, denaturant species, and denaturant concentration. Additionally, the results of the amino acid analysis were similar to that of DPS at pH 7.0 in 2% SDS and 4-6 M GuHCl when SDS and GuHCl were added after DPS. EDTA did not have a significant effect on SH detection when DTNB and DPS were added before SDS and GuHCl. Finally, although mBBr and NPM can detect SH in low protein concentrations ((1)/10 of that required for DTNB and DPS), mBBr and NPM overestimated the SH content of soy protein. Therefore, using DPS at pH 7.0 when it is added before SDS and GuHCl is the most reliable method for detecting the SH content of soy protein.

Proteome screens for Cys residues oxidation: the redoxome

The oxidation of the cysteine (Cys) residue to sulfenic (-S-OH), disulfide (-S-S-), or S-nitroso (S-NO) forms are thought to be a posttranslational modifications that regulate protein function. However, despite a few solid examples of its occurrence, thiol-redox regulation of protein function is still debated and often seen as an exotic phenomenon. A systematic and exhaustive characterization of all oxidized Cys residues, an experimental approach called redox proteomics or redoxome analysis, should help establish the physiological scope of Cys residue oxidation and give clues to its mechanisms. Redox proteomics still remains a technical challenge, mainly because of the labile nature of thiol-redox reactions and the lack of tools to directly detect the modified residues. Here we consider recent technical advances in redox proteomics, focusing on a gel-based fluorescent method and on the shotgun OxICAT technique.

Dominant-negative inhibitors of the Clostridium perfringens epsilon-toxin

The Clostridium perfringens epsilon-toxin is responsible for a severe, often lethal intoxication. In this study, we characterized dominant-negative inhibitors of the epsilon-toxin. Site-specific mutations were introduced into the gene encoding epsilon-toxin, and recombinant proteins were expressed in Escherichia coli. Paired cysteine substitutions were introduced at locations predicted to form a disulfide bond. One cysteine in each mutant was introduced into the membrane insertion domain of the toxin; the second cysteine was introduced into the protein backbone. Mutant proteins with cysteine substitutions at amino acid positions I51/A114 and at V56/F118 lacked detectable cytotoxic activity in a MDCK cell assay. Cytotoxic activity could be reconstituted in both mutant proteins by incubation with dithiothreitol, indicating that the lack of cytotoxic activity was attributable to the formation of a disulfide bond. Fluorescent labeling of the cysteines also indicated that the introduced cysteines participated in a disulfide bond. When equimolar mixtures of wild-type epsilon-toxin and mutant proteins were added to MDCK cells, the I51C/A114C and V56C/F118C mutant proteins each inhibited the activity of wild-type epsilon-toxin. Further analysis of the inhibitory activity of the I51C/A114C and V56C/F118C mutant proteins indicated that these proteins inhibit the ability of the active toxin to form stable oligomeric complexes in the context of MDCK cells. These results provide further insight into the properties of dominant-negative inhibitors of oligomeric pore-forming toxins and provide the basis for developing new therapeutics for treating intoxication by epsilon-toxin.

Thioredoxin target proteins in chloroplast thylakoid membranes

In recent years, impressive progress has been made in the identification of thioredoxin-linked proteins. However, due to technical difficulties inherent in working with hydrophobic proteins, identifications so far have been restricted to proteins in the soluble fraction. Thus, our knowledge of redox regulated membrane proteins is quite limited. To gain information in this area, the authors have applied an adaptation of the approach based on the fluorescent thiol probe monobromobimane (mBBr) to identify redox-linked proteins of chloroplast thylakoids. By application of this procedure, 14 potential membrane-bound thioredoxin target proteins were identified, including seven new candidates functional in processes associated with photosynthetic electron flow, ATP synthesis, and Photosystem II/Photosystem I state transitions.

A complete ferredoxin/thioredoxin system regulates fundamental processes in amyloplasts

A growing number of processes throughout biology are regulated by redox via thiol-disulfide exchange. This mechanism is particularly widespread in plants, where almost 200 proteins have been linked to thioredoxin (Trx), a widely distributed small regulatory disulfide protein. The current study extends regulation by Trx to amyloplasts, organelles prevalent in heterotrophic plant tissues that, among other biosynthetic activities, catalyze the synthesis and storage of copious amounts of starch. Using proteomics and immunological methods, we identified the components of the ferredoxin/Trx system (ferredoxin, ferredoxin-Trx reductase, and Trx), originally described for chloroplasts, in amyloplasts isolated from wheat starchy endosperm. Ferredoxin is reduced not by light, as in chloroplasts, but by metabolically generated NADPH via ferredoxin-NADP reductase. However, once reduced, ferredoxin appears to act as established for chloroplasts, i.e., via ferredoxin-Trx reductase and a Trx (m-type). A proteomics approach in combination with affinity chromatography and a fluorescent thiol probe led to the identification of 42 potential Trx target proteins, 13 not previously recognized, including a major membrane transporter (Brittle-1 or ADP-glucose transporter). The proteins function in a range of processes in addition to starch metabolism: biosynthesis of lipids, amino acids, and nucleotides; protein folding; and several miscellaneous reactions. The results suggest a mechanism whereby light is initially recognized as a thiol signal in chloroplasts, then as a sugar during transit to the sink, where it is converted again to a thiol signal. In this way, amyloplast reactions in the grain can be coordinated with photosynthesis taking place in leaves.

Disulfide proteome yields a detailed understanding of redox regulations: A model study of thioredoxin-linked reactions in seed germination

Accumulating evidence suggests that redox regulations play important roles in a broad spectrum of biological processes. Recently, Yano et al. developed a disulfide proteome technique that comprehensively visualizes redox change in proteins. In this paper, using the disulfide proteome, we examined rice bran and identified fragments of embryo-specific protein and dienelactone hydrolase as putative targets of thioredoxin. Also, monitoring of the endogenous and recombinant effects of thioredoxin on rice bran proteins and supporting in vivo observations propose a mechanism of redox regulation in seed germination, in which thioredoxin activates cysteine protease with a concurrent unfolding of its substrate, the embryo-specific protein. Our findings suggest that thioredoxin controls the lifetime of specific proteins effectively by regulating the redox reactions coordinately. The model study demonstrates that the disulfide proteome technique is useful not only for identifying targets of thioredoxin, but also for clarify the detailed mechanism of redox regulation.

Genetic approaches to reducing losses of stored grain to insects and diseases

Insects and diseases devour or damage a fifth or more of stored food grains each year in many parts of the world. Modern breeding and genomics promise progress in characterizing the resistance to the pests responsible for these losses that is present in the vast and diverse gene pool of cereals, as well as advances in incorporating this resistance into productive and acceptable crop varieties. The impact of such varieties could be dramatic in developing countries, where grain infestations are most common and harmful, and where surging populations require affordable food.

Thioredoxin targets of developing wheat seeds identified by complementary proteomic approaches

The role of thioredoxin in wheat starchy endosperm was investigated utilizing two proteomic approaches. Thioredoxin targets were isolated from total KCl-soluble extracts of endosperm and flour and separated by 2-DE following (1) reduction of the extract by the NADP/thioredoxin system and labeling the newly generated sulfhydryl (SH) groups with monobromobimane (mBBr), and, in parallel, (2) trapping covalently interacting proteins on an affinity column prepared with mutant thioredoxin h in which one of the active site cysteines was replaced by serine. The two procedures were complementary: of the total targets, one-third were observed with both procedures and one-third were unique to each. Altogether 68 potential targets were identified; almost all containing conserved cysteines. In addition to confirming known interacting proteins, we identified 40 potential thioredoxin targets not previously described in seeds. A comparison of the results obtained with young endosperm (isolated 10 days after flowering) to those with mature endosperm (isolated 36 days after flowering) revealed a unique set of proteins functional in processes characteristic of each developmental stage. Flour contained 36 thioredoxin targets, most of which have been found in the isolated developing endosperm.

Thioredoxin links redox to the regulation of fundamental processes of plant mitochondria

Mitochondria contain thioredoxin (Trx), a regulatory disulfide protein, and an associated flavoenzyme, NADP/Trx reductase, which provide a link to NADPH in the organelle. Unlike animal and yeast counterparts, the function of Trx in plant mitochondria is largely unknown. Accordingly, we have applied recently devised proteomic approaches to identify soluble Trx-linked proteins in mitochondria isolated from photosynthetic (pea and spinach leaves) and heterotrophic (potato tubers) sources. Application of the mitochondrial extracts to mutant Trx affinity columns in conjunction with proteomics led to the identification of 50 potential Trx-linked proteins functional in 12 processes: photorespiration, citric acid cycle and associated reactions, lipid metabolism, electron transport, ATP synthesis/transformation, membrane transport, translation, protein assembly/folding, nitrogen metabolism, sulfur metabolism, hormone synthesis, and stress-related reactions. Almost all of these targets were also identified by a fluorescent gel electrophoresis procedure in which reduction by Trx can be observed directly. In some cases, the processes targeted by Trx depended on the source of the mitochondria. The results support the view that Trx acts as a sensor and enables mitochondria to adjust key reactions in accord with prevailing redox state. These and earlier findings further suggest that, by sensing redox in chloroplasts and mitochondria, Trx enables the two organelles of photosynthetic tissues to communicate by means of a network of transportable metabolites such as dihydroxyacetone phosphate, malate, and glycolate. In this way, light absorbed and processed by means of chlorophyll can be perceived and function in regulating fundamental mitochondrial processes akin to its mode of action in chloroplasts.