Tandem Mass Tag-10plex (TMT-10plex) phosphoproteomics dataset for comprehensive analysis of active compounds with tyrosine kinase inhibition activity.

Bioactive compounds derived from natural products demonstrate a wide range of beneficial properties in cancer treatment. One popular approach to inhibiting cancer cell growth is by stimulating apoptosis. Interestingly, our research has discovered that traditional mushroom and isolated compounds from traditional herbs can induce apoptosis in A549 cells while inhibiting tyrosine kinase activities. We have identified two extracts from traditional mushrooms, Phallus indusiatus and Fomes rimosus (Berk.) Cooke, which exhibit promising abilities to activate apoptotic events in cells. Additionally, isolated compounds such as Chamuangone, Cannabigerol (CBG), Cannabidiol (CBD), and NP1-cyclic peptide have also demonstrated significant apoptotic activation capabilities. To further our understanding, we analyzed phosphoprotein changes in A549 cells exposed to these extracts and compounds, both with and without epidermal growth factor (EGF) stimulation. Our positive controls were two known drugs, Afatinib and Osimertinib, which are tyrosine kinase inhibitors with apoptotic stimulation abilities. In order to enrich our understanding of the kinase pathway, we conducted phosphoprotein enrichment analysis and identified altered phosphoproteins using LC-MS/MS. Across these testing conditions, we found that 1228 phosphoproteins were altered, providing valuable insights into the biochemical mechanisms underlying cell apoptosis in A549 cells through post-translational modifications of proteins. Furthermore, our findings not only shed light on the mechanisms of cell apoptosis in A549 cells but also offer promising avenues for future research and therapeutic development.

Charting the importance of filamin A posttranslational modifications.

Filamin A is an essential protein in the cell cytoskeleton because of its actin binding properties and unique homodimer rod-shaped structure, which organises actin into three-dimensional orthogonal networks imperative to cell motility, spreading and adhesion. Filamin A is subject to extensive posttranslational modification (PTM) which serves to co-ordinate cellular architecture and to modulate its large protein-protein interaction network which is key to the protein's role as a cellular signalling hub. Characterised PTMs include phosphorylation, irreversible cleavage, ubiquitin mediated degradation, hydroxylation and O-GlcNAcylation, with preliminary evidence of tyrosylation, carbonylation and acetylation. Each modification and its relation to filamin A function will be described here. These modifications are often aberrantly applied in a range of diseases including, but not limited to, cancer, cardiovascular disease and neurological disease and we discuss the concept of target specific PTMs with novel therapeutic modalities. In summary, our review represents a topical 'one-stop-shop' that enables understanding of filamin A function in cell homeostasis and provides insight into how a variety of modifications add an extra level of Filamin A control.

Androgen receptor post-translational modifications and their implications for pathology.

A major mechanism to modulate the biological activities of the androgen receptor (AR) involves a growing number of post-translational modifications (PTMs). In this review we summarise the current knowledge on the structural and functional impact of PTMs that affect this major transcription factor. Next, we discuss the cross-talk between these different PTMs and the presence of clusters of modified residues in the AR protein. Finally, we discuss the implications of these covalent modifications for the aetiology of diseases such as spinal and bulbar muscular atrophy (Kennedy's disease) and prostate cancer, and the perspectives for pharmacological intervention.

Insight into the regulatory mechanism of ß-arrestin2 and its emerging role in diseases.

ß-arrestin2, a member of the arrestin family, mediates the desensitization and internalization of most G protein-coupled receptors (GPCRs) and functions as a scaffold protein in signalling pathways. Previous studies have demonstrated that ß-arrestin2 expression is dysregulated in malignant tumours, fibrotic diseases, cardiovascular diseases and metabolic diseases, suggesting its pathological roles. Transcription and post-transcriptional modifications can affect the expression of ß-arrestin2. Furthermore, post-translational modifications, such as phosphorylation, ubiquitination, SUMOylation and S-nitrosylation affect the cellular localization of ß-arrestin2 and its interaction with downstream signalling molecules, which further regulate the activity of ß-arrestin2. This review summarizes the structure and function of ß-arrestin2 and reveals the mechanisms involved in the regulation of ß-arrestin2 at multiple levels. Additionally, recent studies on the role of ß-arrestin2 in some major diseases and its therapeutic prospects have been discussed to provide a reference for the development of drugs targeting ß-arrestin2.

Predictive modeling for ubiquitin proteins through advanced machine learning technique.

Ubiquitination is an essential post-translational modification mechanism involving the ubiquitin protein's bonding to a substrate protein. It is crucial in a variety of physiological activities including cell survival and differentiation, and innate and adaptive immunity. Any alteration in the ubiquitin system leads to the development of various human diseases. Numerous researches show the highly reversibility and dynamic of ubiquitin system, making the experimental identification quite difficult. To solve this issue, this article develops a model using a machine learning approach, tending to improve the ubiquitin protein prediction precisely. We deeply investigate the ubiquitination data that is proceed through different features extraction methods, followed by the classification. The evaluation and assessment are conducted considering Jackknife tests and 10-fold cross-validation. The proposed method demonstrated the remarkable performance in terms of 100 %, 99.88 %, and 99.84 % accuracy on Dataset-I, Dataset-II, and Dataset-III, respectively. Using Jackknife test, the method achieves 100 %, 99.91 %, and 99.99 % for Dataset-I, Dataset-II and Dataset-III, respectively. This analysis concludes that the proposed method outperformed the state-of-the-arts to identify the ubiquitination sites and helpful in the development of current clinical therapies. The source code and datasets will be made available at Github.

[Lysine Succinylation:A New Perspective in the Treatment of Cardiovascular Diseases].

With the continuous development of identification technologies such as mass spectrometry,omics,and antibody technology,post-translational modification (PTM) has demonstrated increasing potential in medical research.PTM as a novel chemical modification method provides new perspectives for the research on diseases.Succinylation as a novel modification has aroused the interest of more and more researchers.The available studies about succinylation mainly focus on a desuccinylase named sirtuin 5.This enzyme plays a key role in modification and has been preliminarily explored in cardiovascular studies.This paper summarizes the influencing factors and regulatory roles of succinylation and the links between succinylation and other PTMs and reviews the research progress of PTMs in the cardiovascular field,aiming to deepen the understanding about the role of this modification and give new insights to the research in this field.

TGF­ß/Smad signaling in chronic kidney disease: Exploring post­translational regulatory perspectives (Review).

The TGF­ß/Smad signaling pathway plays a pivotal role in the onset of glomerular and tubulointerstitial fibrosis in chronic kidney disease (CKD). The present review delves into the intricate post­translational modulation of this pathway and its implications in CKD. Specifically, the impact of the TGF­ß/Smad pathway on various biological processes was investigated, encompassing not only renal tubular epithelial cell apoptosis, inflammation, myofibroblast activation and cellular aging, but also its role in autophagy. Various post­translational modifications (PTMs), including phosphorylation and ubiquitination, play a crucial role in modulating the intensity and persistence of the TGF­ß/Smad signaling pathway. They also dictate the functionality, stability and interactions of the TGF­ß/Smad components. The present review sheds light on recent findings regarding the impact of PTMs on TGF­ß receptors and Smads within the CKD landscape. In summary, a deeper insight into the post­translational intricacies of TGF­ß/Smad signaling offers avenues for innovative therapeutic interventions to mitigate CKD progression. Ongoing research in this domain holds the potential to unveil powerful antifibrotic treatments, aiming to preserve renal integrity and function in patients with CKD.

Lectins as a promising therapeutic agent for breast cancer: A review.

Efficient treatment of cancer has been a subject of research by scientists for many years. Current treatments for cancer, such as radiotherapy, chemotherapy and surgery have been used in traditional combination therapy, but they have major setbacks like non-specificity, non-responsiveness in certain cancer types towards treatment, tumor recurrence, etc. Epidemiological data has shown that breast cancer accounts for 14% of cancer cases occurring in Indian women. In recent years, scientists have started to focus on the use of natural compounds like lectins obtained from various sources to counter the side effects of traditional therapy. Lectins like Sambucus nigra Agglutinin, Maackia amurensis lectin, Okra lectins, Haliclona caerulea lectin, Sclerotium rolfsii lectin, etc., have been discovered to have both diagnostic and therapeutic potential for breast cancer patients. Lectins have been found to have inhibitory effects on various cancer cell activities such as neo-angiogenesis, causing cell cycle arrest at the G1 phase, and inducing apoptosis. The major idea behind the use of lectins in cancer diagnostics and therapeutics is their capability to bind to glycosylated proteins that are expressed on the cell surface. This review focuses on an exploration of the roles of post-translational modification in cancer cells, especially glycosylation, and the potential of lectins in cancer diagnosis and therapeutics.

Progress in Core-Shell Magnetic Mesoporous Materials for Enriching Post-Translationally Modified Peptides.

Endogenous peptides, particularly those with post-translational modifications, are increasingly being studied as biomarkers for diagnosing various diseases. However, they are weakly ionizable, have a low abundance in biological samples, and may be interfered with by high levels of proteins, peptides, and other macromolecular impurities, resulting in a high limit of detection and insufficient amounts of post-translationally modified peptides in real biological samples to be examined. Therefore, separation and enrichment are necessary before analyzing these biomarkers using mass spectrometry. Mesoporous materials have regular adjustable pores that can eliminate large proteins and impurities, and their large specific surface area can bind more target peptides, but this may result in the partial loss or destruction of target peptides during centrifugal separation. On the other hand, magnetic mesoporous materials can be used to separate the target using an external magnetic field, which improves the separation efficiency and yield. Core-shell magnetic mesoporous materials are widely utilized for peptide separation and enrichment due to their biocompatibility, efficient enrichment capability, and excellent recoverability. This paper provides a review of the latest progress in core-shell magnetic mesoporous materials for enriching glycopeptides and phosphopeptides and compares their enrichment performance with different types of functionalization methods.

The role of redox-active small molecules and oxidative protein post-translational modifications in seed aging.

Seed vigor is a crucial indicator of seed quality. Variations in seed vigor are closely associated with seed properties and storage conditions. The vigor of mature seeds progressively declines during storage, which is called seed deterioration or aging. Seed aging induces a cascade of cellular damage, including impaired subcellular structures and macromolecules, such as lipids, proteins, and DNA. Reactive oxygen species (ROS) act as signaling molecules during seed aging causing oxidative damage and triggering programmed cell death (PCD). Mitochondria are the main site of ROS production and change morphology and function before other organelles during aging. The roles of other small redox-active molecules in regulating cell and seed vigor, such as nitric oxide (NO) and hydrogen sulfide (H2S), were identified later. ROS, NO, and H2S typically regulate protein function through post-translational modifications (PTMs), including carbonylation, S-glutathionylation, S-nitrosylation, and S-sulfhydration. These signaling molecules as well as the PTMs they induce interact to regulate cell fate and seed vigor. This review was conducted to describe the physiological changes and underlying molecular mechanisms that in seed aging and provides a comprehensive view of how ROS, NO, and H2S affect cell death and seed vigor.

Smad7 palmitoylation by the S-acyltransferase zDHHC17 enhances its inhibitory effect on TGF-ß/Smad signaling.

Intracellular signaling by the pleiotropic cytokine transforming growth factor-ß (TGF-ß) is inhibited by Smad7 in a feedback control mechanism. The activity of Smad7 is tightly regulated by multiple post-translational modifications. Using resin-assisted capture and metabolic labeling methods, we show here that Smad7 is S-palmitoylated in mammary epithelial cell models that are widely studied because of their strong responses to TGF-ß and their biological relevance to mammary development and tumor progression. S-palmitoylation of Smad7 is mediated by zDHHC17, a member of a family of 23 S-acyltransferase enzymes. Moreover, we identified four cysteine residues (Cys202, Cys225, Cys415, and Cys417) in Smad7 as palmitoylation acceptor sites. S-palmitoylation of Smad7 on Cys415 and Cys417 promoted the translocation of Smad7 from the nucleus to the cytoplasm, enhanced the stability of the Smad7 protein, and enforced its inhibitory effect on TGF-ß-induced Smad transcriptional response. Thus, our findings reveal a new post-translational modification of Smad7, and highlight an important role of S-palmitoylation to enhance inhibition of TGF-ß/Smad signaling by Smad7.

Lactate and lactylation in macrophage metabolic reprogramming: current progress and outstanding issues.

It is commonly known that different macrophage phenotypes play specific roles in different pathophysiological processes. In recent years, many studies have linked the phenotypes of macrophages to their characteristics in different metabolic pathways, suggesting that macrophages can perform different functions through metabolic reprogramming. It is now gradually recognized that lactate, previously overlooked as a byproduct of glycolytic metabolism, acts as a signaling molecule in regulating multiple biological processes, including immunological responses and metabolism. Recently, lactate has been found to mediate epigenetic changes in macrophages through a newfound lactylation modification, thereby regulating their phenotypic transformation. This novel finding highlights the significant role of lactate metabolism in macrophage function. In this review, we summarize the features of relevant metabolic reprogramming in macrophages and the role of lactate metabolism therein. We also review the progress of research on the regulation of macrophage metabolic reprogramming by lactylation through epigenetic mechanisms.

Shining Light on Plant Growth: Recent Insights into Phytochrome Interacting Factors.

Light serves as a pivotal environmental cue regulating various aspects of plant growth and development, including seed germination, seedling de-etiolation, and shade avoidance. Within this regulatory framework, the basic helix-loop-helix transcription factors known as PHYTOCHROME INTERACTING FACTORS (PIFs) play an essential role in orchestrating responses to light stimuli. Phytochromes, acting as red/far-red light receptors, initiate a cascade leading to the degradation of PIFs (except PIF7), thereby triggering transcriptional reprogramming to facilitate photomorphogenesis. Recent research has unveiled multiple post-translational modifications that regulate the abundance and/or activity of PIFs, including phosphorylation, dephosphorylation, ubiquitination, deubiquitination and SUMOylation. Moreover, intriguing findings indicate that PIFs can influence chromatin modifications. These include modulation of Histone 3 Lysine-9 acetylation (H3K9ac), as well as occupancy of histone variants such as H2A.Z (associated with gene repression) and H3.3 (associated with gene activation), thereby intricately regulating downstream gene expression in response to environmental cues. This review summarizes recent advances in understanding PIFs' role in regulating various signaling pathways with a major focus on photomorphogenesis.

Dysregulation of protein succinylation and disease development.

As a novel post-translational modification of proteins, succinylation is widely present in both prokaryotes and eukaryotes. By regulating protein translocation and activity, particularly involved in regulation of gene expression, succinylation actively participates in diverse biological processes such as cell proliferation, differentiation and metabolism. Dysregulation of succinylation is closely related to many diseases. Consequently, it has increasingly attracted attention from basic and clinical researchers. For a thorough understanding of succinylation dysregulation and its implications for disease development, such as inflammation, tumors, cardiovascular and neurological diseases, this paper provides a comprehensive review of the research progress on abnormal succinylation. This understanding of association of dysregulation of succinylation with pathological processes will provide valuable directions for disease prevention/treatment strategies as well as drug development.

Corrigendum: SUMOylation of OsPSTOL1 is essential for regulating phosphate starvation responses in rice and Arabidopsis.

[This corrects the article DOI: 10.3389/fpls.2024.1274610.].

Microglial activation induces nitric oxide signalling and alters protein S-nitrosylation patterns in extracellular vesicles.

Neuroinflammation is an underlying feature of neurodegenerative conditions, often appearing early in the aetiology of a disease. Microglial activation, a prominent initiator of neuroinflammation, can be induced through lipopolysaccharide (LPS) treatment resulting in expression of the inducible form of nitric oxide synthase (iNOS), which produces nitric oxide (NO). NO post-translationally modifies cysteine thiols through S-nitrosylation, which can alter function of the target protein. Furthermore, packaging of these NO-modified proteins into extracellular vesicles (EVs) allows for the exertion of NO signalling in distant locations, resulting in further propagation of the neuroinflammatory phenotype. Despite this, the NO-modified proteome of activated microglial EVs has not been investigated. This study aimed to identify the protein post-translational modifications NO signalling induces in neuroinflammation. EVs isolated from LPS-treated microglia underwent mass spectral surface imaging using time of flight-secondary ion mass spectrometry (ToF-SIMS), in addition to iodolabelling and comparative proteomic analysis to identify post-translation S-nitrosylation modifications. ToF-SIMS imaging successfully identified cysteine thiol side chains modified through NO signalling in the LPS treated microglial-derived EV proteins. In addition, the iodolabelling proteomic analysis revealed that the EVs from LPS-treated microglia carried S-nitrosylated proteins indicative of neuroinflammation. These included known NO-modified proteins and those associated with LPS-induced microglial activation that may play an essential role in neuroinflammatory communication. Together, these results show activated microglia can exert broad NO signalling changes through the selective packaging of EVs during neuroinflammation.

Expanding the horizons of targeted protein degradation: A non-small molecule perspective.

Targeted protein degradation (TPD) represented by proteolysis targeting chimeras (PROTACs) marks a significant stride in drug discovery. A plethora of innovative technologies inspired by PROTAC have not only revolutionized the landscape of TPD but have the potential to unlock functionalities beyond degradation. Non-small-molecule-based approaches play an irreplaceable role in this field. A wide variety of agents spanning a broad chemical spectrum, including peptides, nucleic acids, antibodies, and even vaccines, which not only prove instrumental in overcoming the constraints of conventional small molecule entities but also provided rapidly renewing paradigms. Herein we summarize the burgeoning non-small molecule technological platforms inspired by PROTACs, including three major trajectories, to provide insights for the design strategies based on novel paradigms.

Distinctive tumorigenic significance and innovative oncology targets of SUMOylation.

Protein SUMOylation, a post-translational modification, intricately regulates diverse biological processes including gene expression, cell cycle progression, signaling pathway transduction, DNA damage response, and RNA metabolism. This modification contributes to the acquisition of tumorigenicity and the maintenance of cancer hallmarks. In malignancies, protein SUMOylation is triggered by various cellular stresses, promoting tumor initiation and progression. This augmentation is orchestrated through its specific regulatory mechanisms and characteristic biological functions. This review focuses on elucidating the fundamental regulatory mechanisms and pathological functions of the SUMO pathway in tumor pathogenesis and malignant evolution, with particular emphasis on the tumorigenic potential of SUMOylation. Furthermore, we underscore the potential therapeutic benefits of targeting the SUMO pathway, paving the way for innovative anti-tumor strategies by perturbing this dynamic and reversible modifying process.

Physiological roles of α-synuclein serine-129 phosphorylation - not an oxymoron.

α-Synuclein (αS) is an abundant presynaptic protein that regulates neurotransmission. It is also a key protein implicated in a broad class of neurodegenerative disorders termed synucleinopathies, including Parkinson's disease (PD) and Lewy body dementia (LBD). Pathological αS deposits in these diseases, Lewy bodies (LBs)/neurites (LNs), contain about 90% of αS in its phospho-serine129 (pS129) form. Therefore, pS129 is widely used as a surrogate marker of pathology. However, recent findings demonstrate that pS129 is also physiologically triggered by neuronal activity to positively regulate synaptic transmission. In this opinion article, we contrast the literature on pathological and physiological pS129, with a special focus on the latter. We emphasize that pS129 is ambiguous and knowledge about the context is necessary to correctly interpret changes in pS129.

Phosphorylation of mammalian cytosolic and mitochondrial malate dehydrogenase: insights into regulation.

Malate dehydrogenase (MDH) is a key enzyme in mammalian metabolic pathways in cytosolic and mitochondrial compartments. Regulation of MDH through phosphorylation remains an underexplored area. In this review we consolidate evidence supporting the potential role of phosphorylation in modulating the function of mammalian MDH. Parallels are drawn with the phosphorylation of lactate dehydrogenase, a homologous enzyme, to reveal its regulatory significance and to suggest a similar regulatory strategy for MDH. Comprehensive mining of phosphorylation databases, provides substantial experimental (primarily mass spectrometry) evidence of MDH phosphorylation in mammalian cells. Experimentally identified phosphorylation sites are overlaid with MDH's functional domains, offering perspective on how these modifications could influence enzyme activity. Preliminary results are presented from phosphomimetic mutations (serine/threonine residues changed to aspartate) generated in recombinant MDH proteins serving as a proof of concept for the regulatory impact of phosphorylation. We also examine and highlight several approaches to probe the structural and cellular impact of phosphorylation. This review highlights the need to explore the dynamic nature of MDH phosphorylation and calls for identifying the responsible kinases and the physiological conditions underpinning this modification. The synthesis of current evidence and experimental data aims to provide insights for future research on understanding MDH regulation, offering new avenues for therapeutic interventions in metabolic disorders and cancer.