Detection and quantification of protein disulfides in biological tissues a fluorescence-based proteomic approach

Polysulfides promote protein disulfide bond formation in microorganisms growing under anaerobic conditions

Polysulfides commonly occur in anaerobic, microbial active environments, where they play key roles in sulfur cycling and redox transformations. Anaerobic survival of microorganisms requires the formation of protein disulfide bond (DSB). The relationship between polysulfides and anaerobic DSB formation has not been studied so far. Herein, we discovered that polysulfides can efficiently mediate protein DSB formation of microorganisms under anaerobic conditions. We used polysulfides to treat proteins, including roGFP2, Trx1, and DsbA, under anaerobic conditions and found that all three proteins formed intramolecular DSB in vitro. Under anaerobic conditions, Escherichia coli ΔdsbB displayed reduced growth and decreased intracellular protein DSB levels, but polysulfide treatment restored both growth and DSB content. Similarly, polysulfide treatment of E. coli ΔdsbA promoted periplasmic roGFP2 DSB formation and recovered growth under anaerobic conditions. Furthermore, treating Schizosaccharomyces pombe and Cupriavidus pinatubonensis JMP134 with polysulfides increased their intracellular protein DSB content. Collectively, these findings demonstrate that polysulfides can promote DSB formation independently of known enzymatic DSB-mediated systems and the presence of oxygen, thereby benefiting the survival of microorganisms in anaerobic habitats.IMPORTANCEHow polysulfides enhance the adaption of microorganisms to anaerobic environments remains unclear. Our study reveals that polysulfides efficiently facilitate protein DSB formation under anaerobic conditions. Polysulfides contain zero-valent sulfur atoms (S0), which can be transferred to the thiol group of cysteine residue. This S0 atom then accepts two electrons from two cysteine residues and is reduced to H2S, leaving the two cysteines linked by a disulfide bond. Anaerobic growth of microorganisms benefits from the formation of DSB. These findings pave the way for a deeper understanding of the intricate relationship between polysulfides and microorganisms in various environmental contexts.

D6PK plasma membrane polarity requires a repeated CXX(X)P motif and PDK1-dependent phosphorylation

D6 PROTEIN KINASE (D6PK) is a polarly localized plasma-membrane-associated kinase from Arabidopsis thaliana that activates polarly distributed PIN-FORMED auxin transporters. D6PK moves rapidly to and from the plasma membrane, independent of its PIN-FORMED targets. The middle D6PK domain, an insertion between kinase subdomains VII and VIII, is required and sufficient for association and polarity of the D6PK plasma membrane. How D6PK polarity is established and maintained remains to be shown. Here we show that cysteines from repeated middle domain CXX(X)P motifs are S-acylated and required for D6PK membrane association. While D6PK S-acylation is not detectably regulated during intracellular transport, phosphorylation of adjacent serine residues, in part in dependence on the upstream 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE, promotes D6PK transport, controls D6PK residence time at the plasma membrane and prevents its lateral diffusion. We thus identify new mechanisms for the regulation of D6PK plasma membrane interaction and polarity.

Redox Post-translational Modifications of Protein Thiols in Brain Aging and Neurodegenerative Conditions-Focus on S-Nitrosation

Reactive oxygen species and reactive nitrogen species (RONS) are by-products of aerobic metabolism. RONS trigger a signaling cascade that can be transduced through oxidation-reduction (redox)-based post-translational modifications (redox PTMs) of protein thiols. This redox signaling is essential for normal cellular physiology and coordinately regulates the function of redox-sensitive proteins. It plays a particularly important role in the brain, which is a major producer of RONS. Aberrant redox PTMs of protein thiols can impair protein function and are associated with several diseases. This mini review article aims to evaluate the role of redox PTMs of protein thiols, in particular S-nitrosation, in brain aging, and in neurodegenerative diseases. It also discusses the potential of using redox-based therapeutic approaches for neurodegenerative conditions.

Redox and global interconnected proteome changes in mice exposed to complex environmental hazards surrounding Doñana National Park

Natural environments are receiving an increasing number of contaminants. Therefore, the evaluation and identification of early responses to pollution in these complex habitats is an urgent and challenging task. Doñana National Park (DNP, SW Spain) has been widely used as a model area for environmental studies because, despite its strictly protected core, it is surrounded by numerous threat sources from agricultural, mining and industrial activities. Since many pollutants often induce oxidative stress, redox proteomics was used to detect redox-based variations within the proteome of Mus spretus mice captured in DNP and the surrounding areas. Functional analysis showed that most differentially oxidized proteins are involved in the maintenance of homeostasis, by eliciting mechanisms to respond to toxic substances and oxidative stress, such as antioxidant and biotransformation processes, immune and inflammatory responses, and blood coagulation. Furthermore, changes in the overall protein abundance were also analysed by label-free quantitative proteomics. The upregulation of phase I and II biotransformation enzymes in mice from Lucio del Palacio may be an alert for organic pollution in the area located at the heart of DNP. Metabolic processes involved in protein turnover (proteolysis, amino acid catabolism, new protein biosynthesis and folding) were activated in response to oxidative damage to these biomolecules. Consequently, aerobic respiratory metabolism increased to address the greater ATP demands. Alterations of cholesterol metabolism that could cause hepatic steatosis were also detected. The proteomic detection of globally altered metabolic and physiological processes offers a complete view of the main biological changes caused by environmental pollution in complex habitats.

Subcellular Redox Targeting: Bridging in Vitro and in Vivo Chemical Biology

Networks of redox sensor proteins within discrete microdomains regulate the flow of redox signaling. Yet, the inherent reactivity of redox signals complicates the study of specific redox events and pathways by traditional methods. Herein, we review designer chemistries capable of measuring flux and/or mimicking subcellular redox signaling at the cellular and organismal level. Such efforts have begun to decipher the logic underlying organelle-, site-, and target-specific redox signaling in vitro and in vivo. These data highlight chemical biology as a perfect gateway to interrogate how nature choreographs subcellular redox chemistry to drive precision redox biology.

Proteomic approaches to quantify cysteine reversible modifications in aging and neurodegenerative diseases

Cysteine is a highly reactive amino acid and is subject to a variety of reversible post-translational modifications (PTMs), including nitrosylation, glutathionylation, palmitoylation, as well as formation of sulfenic acid and disulfides. These modifications are not only involved in normal biological activities, such as enzymatic catalysis, redox signaling, and cellular homeostasis, but can also be the result of oxidative damage. Especially in aging and neurodegenerative diseases, oxidative stress leads to aberrant cysteine oxidations that affect protein structure and function leading to neurodegeneration as well as other detrimental effects. Methods that can identify cysteine modifications by type, including the site of modification, as well as the relative stoichiometry of the modification can be very helpful for understanding the role of the thiol proteome and redox homeostasis in the context of disease. Cysteine reversible modifications however, are challenging to investigate as they are low abundant, diverse, and labile especially under endogenous conditions. Thanks to the development of redox proteomic approaches, large-scale quantification of cysteine reversible modifications is possible. These approaches cover a range of strategies to enrich, identify, and quantify cysteine reversible modifications from biological samples. This review will focus on nongel-based redox proteomics workflows that give quantitative information about cysteine PTMs and highlight how these strategies have been useful for investigating the redox thiol proteome in aging and neurodegenerative diseases.

Fluorescence-Based Approaches for Quantitative Assessment of Protein Carbonylation, Protein Disulfides, and Protein Conformation in Biological Tissues

Protein oxidation and misfolding have been considered as key players for progression of aging and etiology of various pathological conditions. However, few attempts have been made to develop sensitive and reproducible assays to quantify the changes in protein oxidation and alteration in structure. Here we describe three distinct fluorescence-based assays to quantify changes in protein oxidation, namely carbonylation and disulfides and alteration in protein surface hydrophobicity as a reporter for protein conformation. These techniques will provide investigators the opportunity to address important biological questions in their experimental models.

Redox proteomics as biomarker for assessing the biological effects of contaminants in crayfish from Doñana National Park

Despite its environmental relevance and sensitivity, Doñana National Park (DNP) is under high ecological pressure. In crayfish (Procambarus clarkii), the utility of redox proteomics as a novel biomarker was evaluated in the aquatic ecosystems of DNP and its surroundings, where agricultural activity is a serious concern. After fluorescence labeling of reversibly oxidized Cys and 2-DE separation, the total density of proteins with reversibly oxidized thiols was found to be much higher in animals from the Matochal (MAT) and Rocina (ROC) streams, while no difference was found in crayfish from Partido (PAR) stream compared to those from the DNP core at Lucio del Palacio (the negative control). The 2-DE analysis revealed 35 spots with significant differences in thiol oxidation, among which 19 proteins were identified via MALDI-TOF/TOF. While 3 spots, identified as ferritin, showed higher oxidation levels in ROC, other identified proteins were more intense at MAT than at ROC (superoxide dismutase, protein disulfide isomerase and actin) or were overoxidized only in MAT (nucleoside diphosphate kinase, fructose-biphosphate aldolase, fatty acid-binding protein, phosphopyruvate hydratase). For most of the identified proteins, spots corresponding to different Cys oxidized forms were detected, and the native forms, without oxidized thiol groups were also found in some of them. Evidence of reversible oxidation was found for specific Cys residues, including Cys13 in ferritin as well as Cys76 and Cys108 in nucleoside diphosphate kinase. The identified thiol-oxidized proteins provide information about the metabolic pathways and/or physiological processes affected by pollutant-elicited oxidative stress.

Elevated protein carbonylation and oxidative stress do not affect protein structure and function in the long-living naked-mole rat: a proteomic approach

The 'oxidative stress theory of aging' predicts that aging is primarily regulated by progressive accumulation of oxidized macromolecules that cause deleterious effects to cellular homeostasis and induces a decline in physiological function. However, our reports on the detection of higher level of oxidized protein carbonyls in the soluble cellular fractions of long-living rodent naked-mole rats (NMRs, lifespan ~30yrs) compared to short-lived mice (lifespan ~3.5yrs) apparently contradicts a key tenet of the oxidative theory. As oxidation often inactivates enzyme function and induces higher-order soluble oligomers, we performed a comprehensive study to measure global protein carbonyl level in different tissues of age-matched NMRs and mice to determine if the traditional concept of oxidation mediated impairment of function and induction of higher-order structures of proteins are upheld in the NMRs. We made three intriguing observations with NMRs proteins: (1) protein carbonyl is significantly elevated across different tissues despite of its exceptional longevity, (2) enzyme function is restored despite of experiencing higher level of protein carbonylation, and (3) enzymes show lesser sensitivity to form higher-order non-reducible oligomers compared to short-living mouse proteins in response to oxidative stress. These observations were made based on the global analysis of protein carbonyl and identification of two heavily carbonylated proteins in the kidney, triosephosphate isomerase (TPI) and cytosolic peroxiredoxin (Prdx1). These un-expected intriguing observations thus strongly suggest that oxidative modification may not be the only criteria for impairment of protein and enzyme function; cellular environment is likely be the critical determining factor in this process and may be the underlying mechanism for exceptional longevity of NMR.

The redoxome: Proteomic analysis of cellular redox networks

Redox-regulated proteins play fundamentally important roles not only during the defense of organisms against oxidative stress conditions but also as targets of cellular signaling events. This realization has spurred the development of proteomic techniques geared towards characterizing the redoxome; proteins with highly reactive cysteine residues, whose thiol oxidation state controls the function of the proteins, and by extension, the pathways they are part of. We will here summarize the most recent advances made in the field of redox proteomic analysis, aimed to elucidate the cellular redox networks that appear to control prokaryotic and eukaryotic organisms.