High-throughput screening of cellular redox sensors using modern redox proteomics approaches

Cancer cells are characterized by higher levels of intracellular reactive oxygen species (ROS) due to metabolic aberrations. ROS are widely accepted as second messengers triggering pivotal signaling pathways involved in the process of cell metabolism, cell cycle, apoptosis, and autophagy. However, the underlying cellular mechanisms remain largely unknown. Recently, accumulating evidence has demonstrated that ROS initiate redox signaling through direct oxidative modification of the cysteines of key redox-sensitive proteins (termed redox sensors). Uncovering the functional changes underlying redox regulation of redox sensors is urgently required, and the role of different redox sensors in distinct disease states still remains to be identified. To assist this, redox proteomics has been developed for the high-throughput screening of redox sensors, which will benefit the development of novel therapeutic strategies for cancer treatment. Highlighted here are recent advances in redox proteomics approaches and their applications in identifying redox sensors involved in tumor development.     

ReviewPTPs versus PTKs: The redox side of the coin

The phosphorylation of tyrosine, and to a lesser extent threonine and serine, plays a key role in the regulation of signal transduction during a plethora of eukaryotic cell functions, including cell activation, cell-cycle progression, cytoskeletal rearrangement and cell movement, differentiation, apoptosis and metabolic homeostasis. In vivo, tyrosine phosphorylation is reversible and dynamic; the phosphorylation states are governed by the opposing activities of protein tyrosine kinases (PTKs)² and protein tyrosine phosphatases (PTPs). Reactive oxygen species (ROS) act as cellular messengers in cellular processes such as mitogenic signal transduction, gene expression, regulation of cell proliferation, senescence and apoptosis. Redox regulated proteins include PTPs and PTKs, although with opposite regulation of enzymatic activity. Transient oxidation of thiols in PTPs leads to their inactivation by the formation of either an intramolecular S–S bridge or a sulfenyl–amide bond. Conversely, oxidation of PTKs leads to their activation, either by direct SH modification or, indirectly, by concomitant inhibition of PTPs that guides to sustained activation of PTKs. This review focuses on the redox regulation of both PTPs and PTKs and the interplay of their specular regulation.     

Amyloidogenic domains, prions and structural inheritance: rudiments of early life or recent acquisition?

Amyloids are self-assembled fibre-like beta-rich protein aggregates. Amyloidogenic prion proteins propagate amyloid state in vivo and transmit it via infection or in cell divisions. While amyloid aggregation may occur in the absence of any other proteins, in vivo propagation of the amyloid state requires chaperone helpers. Yeast prion proteins contain prion domains which include distinct aggregation and propagation elements, responsible for these functions. Known aggregation and propagation elements are short in length and composed of relatively simple sequences, indicating possible ancient origin. Prion-like self-assembled structures could be involved in the initial steps of biological compartmentalization in early life.     

Taking aim at a moving target: designing drugs to inhibit drug-resistant HIV-1 reverse transcriptases

HIV undergoes rapid genetic variation; this variation is caused primarily by the enormous number of viruses produced daily in an infected individual. Because of this variation, HIV presents a moving target for drug and vaccine development. The variation within individuals has led to the generation of diverse HIV-1 subtypes, which further complicates the development of effective drugs and vaccines. In general, it is more difficult to hit a moving target than a stationary target. Two broad strategies for hitting a moving target (in this case, HIV replication) are to understand the movement and to aim at the portions that move the least. In the case of anti-HIV drug development, the first option can be addressed by understanding the mechanism(s) of drug resistance and developing drugs that effectively inhibit mutant viruses. The second can be addressed by designing drugs that interact with portions of the viral machinery that are evolutionarily conserved, such as enzyme active sites.     

Redox regulation of cellular functions

Maintenance of normal intracellular redox status plays an important role in such processes as DNA synthesis, gene expression, enzymatic activity, and others. In addition, it is clear that changes in the redox status of intracellular content and individual molecules, resulting from stress or intrinsic cellular activity, are involved in the regulation of different processes in cells. Small changes in intracellular levels of reactive oxygen species participate in intracellular signaling. Thiol-containing molecules, such as glutathione, thioredoxins, glutaredoxins, and peroxiredoxins, also play an important role in maintaining redox homeostasis and redox regulation. This review attempts to summarize the current knowledge about redox regulation in different cell types.     

Light-regulated nuclear localization of phytochromes

Phytochrome is a soluble protein that regulates various responses of plants to light. Not all but most of the phytochrome responses are accompanied by changes in the pattern of gene expression. Upon light activation, phytochrome is imported into the nucleus by the nuclear localization activity of the carboxy-terminal half of the molecule. In darkness, the amino-terminal chromophoric domain suppresses this activity to retain the molecule in the cytoplasm. In the nucleus, light-activated phytochrome forms speckles whose biological function remains unclear.     

SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State–Dependent Redox-Sensitive Cysteines

Proteinaceous cysteine residues act as privileged sensors of oxidative stress. As reactive oxygen and nitrogen species have been implicated in numerous pathophysiological processes, deciphering which cysteines are sensitive to oxidative modification and the specific nature of these modifications is essential to understanding protein and cellular function in health and disease. While established mass spectrometry-based proteomic platforms have improved our understanding of the redox proteome, the widespread adoption of these methods is often hindered by complex sample preparation workflows, prohibitive cost of isotopic labeling reagents, and requirements for custom data analysis workflows. Here, we present the SP3-Rox redox proteomics method that combines tailored low cost isotopically labeled capture reagents with SP3 sample cleanup to achieve high throughput and high coverage proteome-wide identification of redox-sensitive cysteines. By implementing a customized workflow in the free FragPipe computational pipeline, we achieve accurate MS1-based quantitation, including for peptides containing multiple cysteine residues. Application of the SP3-Rox method to cellular proteomes identified cysteines sensitive to the oxidative stressor GSNO and cysteine oxidation state changes that occur during T cell activation.     

Small GTPases in vesicle trafficking

Plant small GTPases belonging to the Rop, Arf, and Rab families are regulators of vesicle trafficking. Rop GTPases regulate actin dynamics and modulate H(2)O(2) production in polar cell growth and pathogen defence. A candidate Rop GDP to Rop GTP exchange factor (RopGEF) SPIKE1 is involved in the morphogenesis of leaf epidermal cells. The ArfGEF GNOM regulates the endosomal recycling of the PIN proteins, which are involved in polar auxin transport. Intracellular localisation of small GTPases and functional studies using dominant mutant versions of Arf and Rab GTPases are defining novel plant-specific membrane compartments, especially those that participate in endosomal vesicle trafficking.     

Assessing the regulation of leaf redox status under water stress conditions in Arabidopsis thaliana: Col-0 ecotype (wild-type and vtc-2), expressing mitochondrial and cytosolic roGFP1

Using Arabidopsis plants Col-0 and vtc2 transformed with a redox sensitive green fluorescent protein, (c-roGFP) and (m-roGFP), we investigated the effects of a progressive water stress and re-watering on the redox status of the cytosol and the mitochondria. Our results establish that water stress affects redox status differently in these two compartments, depending on phenotype and leaf age, furthermore we conclude that ascorbate plays a pivotal role in mediating redox status homeostasis and that Col-0 Arabidopsis subjected to water stress increase the synthesis of ascorbate suggesting that ascorbate may play a role in buffering changes in redox status in the mitochondria and the cytosol, with the presumed buffering capacity of ascorbate being more noticeable in young compared with mature leaves. Re-watering of water-stressed plants was paralleled by a return of both the redox status and ascorbate to the levels of well-watered plants. In contrast to the effects of water stress on ascorbate levels, there were no significant changes in the levels of glutathione, thereby suggesting that the regeneration and increase in ascorbate in water-stressed plants may occur by other processes in addition to the regeneration of ascorbate via the glutathione. Under water stress in vtc2 lines it was observed stronger differences in redox status in relation to leaf age, than due to water stress conditions compared with Col-0 plants. In the vtc2 an increase in DHA was observed in water-stressed plants. Furthermore, this work confirms the accuracy and sensitivity of the roGFP1 biosensor as a reporter for variations in water stress-associated changes in redox potentials.     

Redox signaling

Reactive oxygen species (ROS) and reactive nitrogen species (RNS) have recently been shown to be involved in a multiplicity of physiological responses through modulation of signaling pathways. Some of the specific signaling components altered by reactive oxygen and nitrogen species (RONS) have begun to be identified. We will discuss RONS signaling by detailing the chemistry of signaling, the roles of antioxidant enzymes as signaling components, thiol chemistry in the specificity of RONS signaling, NO-heme interactions, and some do's and don'ts of redox signal research. The principal points raised are that: (1) as with classic signaling pathways, signaling by RONS is regulated; (2) antioxidant enzymes are essential 'turn-off' components in signaling; (3) spatial relationships are probably more important in RONS signaling than the overall 'redox state' of the cell; (4) deprotonation of cysteines to form the thiolate, which can react with RONS, occurs in specific protein sites providing specificity in signaling; (5) although multiple chemical mechanisms exist for producing nitrosothiols, their formation in vivo remains unclear; and (6) caution should be taken in the use of 'antioxidants' in signal transduction.     

Selecting the signals for a brain-machine interface

Brain-machine interfaces are being developed to assist paralyzed patients by enabling them to operate machines with recordings of their own neural activity. Recent studies show that motor parameters, such as hand trajectory, and cognitive parameters, such as the goal and predicted value of an action, can be decoded from the recorded activity to provide control signals. Neural prosthetics that use simultaneously a variety of cognitive and motor signals can maximize the ability of patients to communicate and interact with the outside world. Although most studies have recorded electroencephalograms or spike activity, recent research shows that local field potentials (LFPs) offer a promising additional signal. The decode performances of LFPs and spike signals are comparable and, because LFP recordings are more long lasting, they might help to increase the lifetime of the prosthetics.     

Selective Sensitization of Zinc Finger Protein Oxidation by Reactive Oxygen Species through Arsenic Binding

Cysteine oxidation induced by reactive oxygen species (ROS) on redox-sensitive targets such as zinc finger proteins plays a critical role in redox signaling and subsequent biological outcomes. We found that arsenic exposure led to oxidation of certain zinc finger proteins based on arsenic interaction with zinc finger motifs. Analysis of zinc finger proteins isolated from arsenic-exposed cells and zinc finger peptides by mass spectrometry demonstrated preferential oxidation of C3H1 and C4 zinc finger configurations. C2H2 zinc finger proteins that do not bind arsenic were not oxidized by arsenic-generated ROS in the cellular environment. The findings suggest that selectivity in arsenic binding to zinc fingers with three or more cysteines defines the target proteins for oxidation by ROS. This represents a novel mechanism of selective protein oxidation and demonstrates how an environmental factor may sensitize certain target proteins for oxidation, thus altering the oxidation profile and redox regulation.     

Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry

Living cells rival computers in their ability to process external information and make complex behavioral decisions. Many of these decisions are made by networks of interacting signaling proteins. Ongoing structural, biochemical and cell-based studies have begun to reveal several common principles by which protein components are used to specifically transmit and process information. Recent engineering studies demonstrate that these relatively simple principles can be used to rewire signaling behavior in a process that mimics the evolution of new phenotypic responses.     

Membrane raft redox signalosomes in endothelial cells

Abstract

Membrane rafts (MRs) are specialized microdomains in the cell membrane with an altered lipid composition. Upon various stimulations, MRs can be clustered to aggregate or recruit NADPH oxidase sub-units and related proteins to form MR redox signalosomes in the membrane of cells like vascular endothelial cells (ECs). Multiple protein complexes, like MR redox signalosomes, are now considered to play a crucial role in the regulation of cell function and in the development of different cell dysfunctions. To form such redox signalosomes, ceramide will be generated from the hydrolysis of sphingomyelin by lysosomal acid sphingomyelinase that has been translocated via lysosome fusion to the MR area. In this brief review, current information is provided to help understand the occurrence and function of MR redox signalosomes. This may increase enthusiasm of the scientific community for further studies on the molecular mechanisms and the functional significance of forming such MR redox signalosomes.     

Glutamate-induced metabolic changes influence the cytoplasmic redox state of hippocampal neurons

Brain cell metabolism is intimately associated with intracellular oxidation–reduction (redox) balance. Glutamatergic transmission is accompanied with changes in substrate preference in neurons. Therefore, we studied cytoplasmatic redox changes in hippocampal neurons in culture exposed to glutamate. Neurons were transfected with HyPer, a genetically encoded redox biosensor for hydrogen peroxide which allows real-time imaging of the redox state. The rate of fluorescence decay, corresponding to the reduction of the biosensor was found to be augmented by low doses of glutamate (10 μM) as well as by pharmacological stimulation of NMDA glutamate receptors. Acute chelation of extracellular Ca²⁺ abolished the glutamate-induced effect observed on HyPer fluorescence. Additional experiments indicated that mitochondrial function and hence energetic substrate availability commands the redox state of neurons and is required for the glutamate effect observed on the biosensor signal. Furthermore, our results implicated astrocytic metabolism in the changes of neuronal redox state observed with glutamate.     

Functional microcircuitry in the accumbens underlying drug addiction: insights from real-time signaling during behavior

An understanding of the neurobiological basis of drug addiction requires examination of real-time (subsecond) cellular and chemical responses in the brain reward system during drug-seeking and drug-taking behavior. Electrophysiological and electrochemical studies in the rodent nucleus accumbens have examined changes in cell firing and rapid dopamine signaling during crucial periods of behavioral responding for drugs, and show the associative nature of those signals. These findings are considered with respect to the functional microcircuitry in the nucleus accumbens that underlies goal-directed behavior and the role of this circuit in drug addiction.     

Cell polarity, intercellular signalling and morphogenetic cell movements in Myxococcus xanthus

In Myxococcus xanthus morphogenetic cell movements constitute the basis for the formation of spreading vegetative colonies and fruiting bodies in starving cells. M. xanthus cells move by gliding and gliding motility depends on two polarly localized engines, type IV pili pull cells forward, and slime extruding nozzle-like structures appear to push cells forward. The motility behaviour of cells provides evidence that the two engines are localized to opposite poles and that they undergo polarity switching. Several proteins involved in regulating polarity switching have been identified. The cell surface-associated C-signal induces the directed movement of cells into nascent fruiting bodies. Recently, the molecular nature of the C-signal molecule was elucidated and the motility parameters regulated by the C-signal were identified. From the effect of the C-signal on cell behaviour it appears that the C-signal inhibits polarity switching of the two motility engines. This establishes a connection between cell polarity, signalling by an intercellular signal and morphogenetic cell movements during fruiting body formation.     

Tuning of functional heme reduction potentials in Shewanella fumarate reductases

The fumarate reductases from S. frigidimarina NCIMB400 and S. oneidensis MR-1 are soluble and monomeric enzymes located in the periplasm of these bacteria. These proteins display two redox active domains, one containing four c-type hemes and another containing FAD at the catalytic site. This arrangement of single-electron redox co-factors leading to multiple-electron active sites is widespread in respiratory enzymes. To investigate the properties that allow a chain of single-electron co-factors to sustain the activity of a multi-electron catalytic site, redox titrations followed by NMR and visible spectroscopies were applied to determine the microscopic thermodynamic parameters of the hemes. The results show that the redox behaviour of these fumarate reductases is similar and dominated by a strong interaction between hemes II and III. This interaction facilitates a sequential transfer of two electrons from the heme domain to FAD via heme IV.