iCysMod: an integrative database for protein cysteine modifications in eukaryotes

Systematic analysis of the global characteristics and reciprocal effects of S-nitrosylation and S-persulfidation in the human proteome

Gasotransmitter-mediated cysteine post-translational modifications, including S-nitrosylation (SNO) and S-persulfidation (SSH), play crucial roles and interact in various biological processes. However, there has been a delay in appreciating the interactional rules between SNO and SSH. Here, all human S-nitrosylated and S-persulfidated proteomic data were curated, and comprehensive analyses from multiple perspectives, including sequence, structure, function, and exact protein impacts (e.g., up-/down-regulation), were performed. Although these two modifications collectively regulated a wide array of proteins to jointly maintain redox homeostasis, they also exhibited intriguing differences. First, SNO tended to be more accessible and functionally clustered in pathways associated with cell damage repair and other protein modifications, such as phosphorylation and ubiquitination. Second, SSH preferentially targeted cysteines in disulfide bonds and modulated tissue development and immune-related pathways. Finally, regardless of whether SNO and SSH occupied the same position of a given protein, their combined effect tended to be suppressive when acting synergistically; otherwise, SNO likely inhibited while SSH activated the target protein. Indeed, a side-by-side comparison of SNO and SSH shed light on their globally reciprocal effects and provided a reference for further research on gasotransmitter-mediated biological effects.

Protein S-Nitrosylation: A Chemical Modification with Ubiquitous Biological Activities

Nitric oxide (NO) induces protein posttranslational modification (PTM), known as S-nitrosylation, which has started to gain attention as a critical regulator of thousands of substrate proteins. However, our understanding of the biological consequences of this emerging PTM is incomplete because of the limited number of identified S-nitrosylated proteins (S-NO proteins). Recent advances in detection methods have effectively contributed to broadening the spectrum of discovered S-NO proteins. This article briefly reviews the progress in S-NO protein detection methods and discusses how these methods are involved in characterizing the biological consequences of this PTM. Additionally, we provide insight into S-NO protein-related diseases, focusing on the role of these proteins in mitigating the severity of infectious diseases.

Oxidative Cysteine Post Translational Modifications Drive the Redox Code Underlying Neurodegeneration and Amyotrophic Lateral Sclerosis

Redox dysregulation, an imbalance between oxidants and antioxidants, is crucial in the pathogenesis of various neurodegenerative diseases. Within this context, the "redoxome" encompasses the network of redox molecules collaborating to maintain cellular redox balance and signaling. Among these, cysteine-sensitive proteins are fundamental for this homeostasis. Due to their reactive thiol groups, cysteine (Cys) residues are particularly susceptible to oxidative post-translational modifications (PTMs) induced by free radicals (reactive oxygen, nitrogen, and sulfur species) which profoundly affect protein functions. Cys-PTMs, forming what is referred to as "cysteinet" in the redox proteome, are essential for redox signaling in both physiological and pathological conditions, including neurodegeneration. Such modifications significantly influence protein misfolding and aggregation, key hallmarks of neurodegenerative diseases such as Alzheimer's, Parkinson's, and notably, amyotrophic lateral sclerosis (ALS). This review aims to explore the complex landscape of cysteine PTMs in the cellular redox environment, elucidating their impact on neurodegeneration at protein level. By investigating specific cysteine-sensitive proteins and the regulatory networks involved, particular emphasis is placed on the link between redox dysregulation and ALS, highlighting this pathology as a prime example of a neurodegenerative disease wherein such redox dysregulation is a distinct hallmark.

Chemistry and biology of enzymes in protein glutathionylation

Protein S-glutathionylation is emerging as a central oxidation that regulates redox signaling and biological processes linked to diseases. In recent years, the field of protein S-glutathionylation has expanded by developing biochemical tools for the identification and functional analyses of S-glutathionylation, investigating knockout mouse models, and developing and evaluating chemical inhibitors for enzymes involved in glutathionylation. This review will highlight recent studies of two enzymes, glutathione transferase omega 1 (GSTO1) and glutaredoxin 1 (Grx1), especially introducing their glutathionylation substrates associated with inflammation, cancer, and neurodegeneration and showcasing the advancement of their chemical inhibitors. Lastly, we will feature protein substrates and chemical inducers of LanC-like protein (LanCL), the first enzyme in protein C-glutathionylation.

Reversible Redox-Dependent Conformational Switch of the C-Terminal α-Helical Lid of Human Hsp70 Observed by In-Cell NMR

Glutathionylation of human stress-inducible Hsp70 (hHsp70) under oxidative stress conditions has been suggested to act as an on/off switch of hHsp70 chaperone activity and thus transfer redox signals to hHsp70 clients through a change in conformation. The mechanism of this switch involves unfolding of the C-terminal α-helical lid, SBDα, upon glutathionylation, which then binds to and blocks the hHsp70 substrate-binding site. This process is reversible and redox-regulated and has been demonstrated for purified protein in solution. Here, we found that this redox-regulated reversible process also occurs in the cellular environment. Using Escherichia coli as a model system, in-cell NMR data clearly indicate that hHsp70 SBDα undergoes a conformational transition from ordered to disordered after diamide stimulation. The disordered SBDα could spontaneously recover back to the helix bundle conformation over time. This oxidative-stress induced process also occurred in cell lysate, with a similar unfolding rate as in cells, but the refolding rate was significantly slower in cell lysate. Increased temperature accelerates this process. Under heat stress alone, unfolding of the SBDα could not be detected in cells. Our in-cell NMR results provide direct support for the molecular switch model of hHsp70 redox regulation and also demonstrate the power of in-cell NMR for real-time study of protein structures during biological processes in living cells.

Multi-Omics Approach Reveals Redox Homeostasis Reprogramming in Early-Stage Clear Cell Renal Cell Carcinoma

Clear cell renal cell carcinoma (ccRCC) is a malignant tumor originating from proximal tubular epithelial cells, and despite extensive research efforts, its redox homeostasis characteristics and protein S-nitrosylation (or S-nitrosation) (SNO) modification remain largely undefined. This serves as a reminder that the aforementioned features demand a comprehensive inspection. We collected tumor samples and paracancerous normal samples from five patients with early-stage ccRCC (T1N0M0) for proteomic, SNO-proteome, and redox-targeted metabolic analyses. The localization and functional properties of SNO proteins in ccRCC tumors and paracancerous normal tissues were elucidated for the first time. Several highly useful ccRCC-associated SNO proteins were further identified. Metabolic reprogramming, redox homeostasis reprogramming, and tumorigenic alterations are the three major characteristics of early-stage ccRCC. Peroxidative damage caused by rapid proliferation coupled with an increased redox buffering capacity and the antioxidant pool is a major mode of redox homeostasis reprogramming. NADPH and NADP⁺, which were identified from redox species, are both effective biomarkers and promising therapeutic targets. According to our findings, SNO protein signatures and redox homeostasis reprogramming are valuable for understanding the pathogenesis of ccRCC and identifying novel topics that should be seriously considered for the diagnosis and precise therapy of ccRCC.

Emerging chemistry and biology in protein glutathionylation

Protein S-glutathionylation serves a regulatory role in proteins and modulates distinct biological processes implicated in health and diseases. Despite challenges in analyzing the dynamic and reversible nature of S-glutathionylation, recent chemical and biological methods have significantly advanced the field of S-glutathionylation, culminating in selective identification and detection, structural motif analysis, and functional studies of S-glutathionylation. This review will highlight emerging studies of protein glutathionylation, beginning by introducing biochemical tools that enable mass spectrometric identification and live-cell imaging of S-glutathionylation. Next, it will spotlight recent examples of S-glutathionylation regulating physiology and inflammation. Lastly, we will feature two emerging lines of glutathionylation research in cryptic cysteine glutathionylation and protein C-glutathionylation.

DLF-Sul: a multi-module deep learning framework for prediction of S-sulfinylation sites in proteins

Protein S-sulfinylation is an important posttranslational modification that regulates a variety of cell and protein functions. This modification has been linked to signal transduction, redox homeostasis and neuronal transmission in studies. Therefore, identification of S-sulfinylation sites is crucial to understanding its structure and function, which is critical in cell biology and human diseases. In this study, we propose a multi-module deep learning framework named DLF-Sul for identification of S-sulfinylation sites in proteins. First, three types of features are extracted including binary encoding, BLOSUM62 and amino acid index. Then, sequential features are further extracted based on these three types of features using bidirectional long short-term memory network. Next, multi-head self-attention mechanism is utilized to filter the effective attribute information, and residual connection helps to reduce information loss. Furthermore, convolutional neural network is employed to extract local deep features information. Finally, fully connected layers acts as classifier that map samples to corresponding label. Performance metrics on independent test set, including sensitivity, specificity, accuracy, Matthews correlation coefficient and area under curve, reach 91.80%, 92.36%, 92.08%, 0.8416 and 96.40%, respectively. The results show that DLF-Sul is an effective tool for predicting S-sulfinylation sites. The source code is available on the website https://github.com/ningq669/DLF-Sul.

Peroxisome-Derived Hydrogen Peroxide Modulates the Sulfenylation Profiles of Key Redox Signaling Proteins in Flp-In T-REx 293 Cells

The involvement of peroxisomes in cellular hydrogen peroxide (H₂O₂) metabolism has been a central theme since their first biochemical characterization by Christian de Duve in 1965. While the role of H₂O₂ substantially changed from an exclusively toxic molecule to a signaling messenger, the regulatory role of peroxisomes in these signaling events is still largely underappreciated. This is mainly because the number of known protein targets of peroxisome-derived H₂O₂ is rather limited and testing of specific targets is predominantly based on knowledge previously gathered in related fields of research. To gain a broader and more systematic insight into the role of peroxisomes in redox signaling, new approaches are urgently needed. In this study, we have combined a previously developed Flp-In T-REx 293 cell system in which peroxisomal H₂O₂ production can be modulated with a yeast AP-1-like-based sulfenome mining strategy to inventory protein thiol targets of peroxisome-derived H₂O₂ in different subcellular compartments. By using this approach, we identified more than 400 targets of peroxisome-derived H₂O₂ in peroxisomes, the cytosol, and mitochondria. We also observed that the sulfenylation kinetics profiles of key targets belonging to different protein families (e.g., peroxiredoxins, annexins, and tubulins) can vary considerably. In addition, we obtained compelling but indirect evidence that peroxisome-derived H₂O₂ may oxidize at least some of its targets (e.g., transcription factors) through a redox relay mechanism. In conclusion, given that sulfenic acids function as key intermediates in H₂O₂ signaling, the findings presented in this study provide valuable insight into how peroxisomes may be integrated into the cellular H₂O₂ signaling network.

Hsp70 in Redox Homeostasis

Cellular redox homeostasis is precisely balanced by generation and elimination of reactive oxygen species (ROS). ROS are not only capable of causing oxidation of proteins, lipids and DNA to damage cells but can also act as signaling molecules to modulate transcription factors and epigenetic pathways that determine cell survival and death. Hsp70 proteins are central hubs for proteostasis and are important factors to ameliorate damage from different kinds of stress including oxidative stress. Hsp70 members often participate in different cellular signaling pathways via their clients and cochaperones. ROS can directly cause oxidative cysteine modifications of Hsp70 members to alter their structure and chaperone activity, resulting in changes in the interactions between Hsp70 and their clients or cochaperones, which can then transfer redox signals to Hsp70-related signaling pathways. On the other hand, ROS also activate some redox-related signaling pathways to indirectly modulate Hsp70 activity and expression. Post-translational modifications including phosphorylation together with elevated Hsp70 expression can expand the capacity of Hsp70 to deal with ROS-damaged proteins and support antioxidant enzymes. Knowledge about the response and role of Hsp70 in redox homeostasis will facilitate our understanding of the cellular knock-on effects of inhibitors targeting Hsp70 and the mechanisms of redox-related diseases and aging.

qPTMplants: an integrative database of quantitative post-translational modifications in plants

As a crucial molecular mechanism, post-translational modifications (PTMs) play critical roles in a wide range of biological processes in plants. Recent advances in mass spectrometry-based proteomic technologies have greatly accelerated the profiling and quantification of plant PTM events. Although several databases have been constructed to store plant PTM data, a resource including more plant species and more PTM types with quantitative dynamics still remains to be developed. In this paper, we present an integrative database of quantitative PTMs in plants named qPTMplants (http://qptmplants.omicsbio.info), which hosts 1 242 365 experimentally identified PTM events for 429 821 nonredundant sites on 123 551 proteins under 583 conditions for 23 PTM types in 43 plant species from 293 published studies, with 620 509 quantification events for 136 700 PTM sites on 55 361 proteins under 354 conditions. Moreover, the experimental details, such as conditions, samples, instruments and methods, were manually curated, while a variety of annotations, including the sequence and structural characteristics, were integrated into qPTMplants. Then, various search and browse functions were implemented to access the qPTMplants data in a user-friendly manner. Overall, we anticipate that the qPTMplants database will be a valuable resource for further research on PTMs in plants.

The Modus Operandi of Hydrogen Sulfide(H2S)-Dependent Protein Persulfidation in Higher Plants

Protein persulfidation is a post-translational modification (PTM) mediated by hydrogen sulfide (H₂S), which affects the thiol group of cysteine residues from target proteins and can have a positive, negative or zero impact on protein function. Due to advances in proteomic techniques, the number of potential protein targets identified in higher plants, which are affected by this PTM, has increased considerably. However, its precise impact on biological function needs to be evaluated at the experimental level in purified proteins in order to identify the specific cysteine(s) residue(s) affected. It also needs to be evaluated at the cellular redox level given the potential interactions among different oxidative post-translational modifications (oxiPTMs), such as S-nitrosation, glutathionylation, sulfenylation, S-cyanylation and S-acylation, which also affect thiol groups. This review aims to provide an updated and comprehensive overview of the important physiological role exerted by persulfidation in higher plants, which acts as a cellular mechanism of protein protection against irreversible oxidation.