Search Results (3,293)

Multi-omics technologies enable parallel quantification of proteomic and metabolomic layers, yet enzyme abundance often shows weak or nonlinear correspondence under diverse biological conditions. This apparent discordance has been attributed to both technical limitations—such as dynamic range compression in LC-MS/MS, metabolite derivatization artifacts, and missing values in proteomic measurements—as well as intrinsic biological properties of metabolic network architecture. While technical factors contribute to cross-omic mismatch, accumulating evidence suggests that constraint-driven network behavior plays a major role in shaping this decoupling. Enzyme abundance constrains catalytic capacity; however, realized flux is selected within this capacity under distributed flux control, as formalized by flux control coefficients in metabolic control analysis, and is further modulated by enzyme kinetics (e.g., km and Vmax), post-translational modifications, substrate availability, and thermodynamic constraints. Metabolite pools, in turn, reflect the physicochemical state of the system, while specific metabolites can also act as regulatory effectors that modulate enzymatic activity and cellular signaling. Because metabolic networks are underdetermined, multiple flux configurations can satisfy identical protein abundance and metabolite concentration data. Static cross-layer correlation is therefore insufficient for mechanistic inference. We synthesize biological mechanisms—including post-translational regulation, allostery, thermodynamic buffering, spatial compartmentalization, feedback amplification, and redox gating—that weaken linear abundance–metabolite expectations. We further outline a constraint-based interpretation framework in which proteomics imposes capacity bounds, metabolomics informs reaction directionality and metabolite pool constraints, and flux-informed approaches reduce solution degeneracy by providing additional information on pathway activity. Moving beyond correlation requires integrating perturbation, temporal resolution, and constraint-aware modeling. Proteome–metabolome discordance should therefore be interpreted not as inconsistency, but as indicative of constraint-driven state selection within high-dimensional biochemical systems. Full article

Glycation is a type of post-translational protein modification that affects antigen self-recognition, cell signaling, the proteasomal degradation of proteins, protein solubility, and the mechanical properties of tissues. Some glycation products are able to cross-link proteins. Serum concentrations of the cross-linking GOLD (glyoxal lysine dimer) and MOLD (methylglyoxal lysine dimer), and the non-cross-linking MG-H1 (methylglyoxal-derived hydroimidazolone isomer 1) in patients with psoriasis (n = 63) and in healthy controls (n = 35) were examined using the LC-Orbitrap-MS/MS (liquid chromatography–Orbitrap tandem mass spectrometry) technique. The following indices were assessed in the patients: BSA (body surface area), PASI (psoriasis area and severity index), and DLQI (Dermatology Life Quality Index). Serum concentrations of GOLD, MOLD, and MG-H1 were found to be significantly lower in psoriasis patients compared with healthy individuals. The concentrations of GOLD, MOLD, and MG-H1 did not correlate with the indices of disease activity and severity. These results may reflect the complexity of metabolic dysregulation accompanying immune-mediated inflammatory diseases such as psoriasis. Full article

Background: Translational regulation constitutes a critical layer of gene expression control in plants, yet the contribution of endogenous 5′ untranslated regions (5′ UTRs) to translational efficiency remains incompletely defined. While viral and synthetic leader sequences have been widely used to enhance protein production, comparatively few native plant 5′ UTRs have been systematically characterised. The objective of this study was to identify and functionally evaluate endogenous plant 5′ UTR elements that promote translation through post-transcriptional mechanisms. Methods: A 79-nucleotide fragment (CYSTM α) derived from the 5′ UTR of Arabidopsis thaliana CYSTM1 (AT1G05340) was cloned upstream of reporter genes and assessed using dual-luciferase assays in transient expression systems (Nicotiana benthamiana and A. thaliana) and in stable transgenic Arabidopsis lines. Translational activity was further evaluated in monocot wheat germ extract and in Escherichia coli. Transcript abundance was quantified by qRT-PCR. Publicly available ribosome profiling and m⁶A datasets were analysed to assess translational efficiency and RNA modification status. Results: In N. benthamiana and A. thaliana, CYSTM α increases reporter protein production 3–7 fold relative to the control and 30–130% above the benchmark Tobacco Mosaic Virus (TMV) Ω leader, without altering mRNA abundance. The CYSTM α sequence also enhances luciferase translation in monocot wheat germ extract and elevates translation 5-fold in E. coli. CYSTM α contains three motifs that may promote translation, namely three CAA repeats that are associated with translation initiation, an AMAYAA motif that is associated with eIF3 binding, and two N6-adenosine DRACH sites that are associated with cap-independent translation. Additionally, ribosome profiling revealed high translational efficiency (TE = 3.25) of native CYSTM1. Conclusions: CYSTM α represents a compact endogenous 5′ UTR element that enhances translation across multiple experimental systems. These findings expand the repertoire of plant-derived translational enhancers and provide insight into sequence features associated with efficient mRNA translation in plants. Full article

The proteolytic processing of the amyloid precursor protein (APP) is a core pathological event in Alzheimer’s disease (AD) pathogenesis, yet the global genetic regulatory networks modulating this process have not been fully characterized. To systematically identify novel regulators of APP cleavage, we performed a genome-wide CRISPR/Cas9 knockout screen utilizing an optimized UAS-GAL4-based cellular reporter, and identified genetic modulators governing amyloidogenic and non-amyloidogenic processing. The screen uncovered distinct functional gene clusters regulating the APP, prominently involving cellular metabolism, protein modification, and vesicular trafficking. Specifically, LDHB, PIAS2, CCDC53, and TRIM61 emerged as novel functional modulators. Biochemical validation confirmed that ablating these genes significantly alters the metabolic balance between sAPPα and amyloid-β (Aβ) production. Finally, integration with human AD transcriptomic datasets demonstrated that these identified modulators undergo significant dysregulation in clinics. Together, these findings establish a reporter-based functional screening framework for APP processing and identify candidate regulatory nodes linked to metabolism, protein modification, and vesicular trafficking. These candidates provide a resource for future mechanistic investigation and validation in more disease-relevant AD models. Full article

Excessive activation of the sympathetic nervous system is a prominent contributor linked to heart failure (HF) progression. Pathological remodeling of the central nervous system represents a plausible upstream event associated with central sympathetic hyperactivity, whereas dysfunction of the brain–heart axis may act as a pivotal hub involved in this pathological process. This review systematically summarizes the functional characteristics of major sympathetic regulatory nuclei under HF, including the subfornical organ (SFO), paraventricular nucleus of the hypothalamus (PVN), rostral ventrolateral medulla (RVLM), and nucleus tractus solitarius (NTS). Following the pathological logic from upstream initiation to inter-organ closed-loop responses, seven interconnected pathological mechanisms are analyzed: glial cell activation and neuroinflammation, endoplasmic reticulum stress, renin–angiotensin system (RAS) imbalance, abnormal signaling pathways and transcription factors, impaired neuronal microenvironment homeostasis, dysregulated post-transcriptional and post-translational modifications, and extracellular vesicle-mediated inter-organ signal transmission. Their cross-regulation and positive feedback amplification effects are highlighted. Multidimensional central-targeted intervention strategies established on this basis possess important fundamental significance and translational potential. This review also discusses current scientific challenges and prospects for interdisciplinary frontiers, providing theoretical references and practical insights for central regulation research in HF and its precise clinical translation. Full article

Osmotic stress limits rice productivity, yet the crosstalk between hydrogen sulfide signaling and redox regulation remains incompletely understood. We previously showed that redox-dependent oligomerization of the basic (region) leucine zippers transcription factor bZIP68 at Cys245 confers osmotic tolerance. However, the role of an adjacent cysteine, Cys171, was undefined. Here, we demonstrate that osmotic stress induces persulfidation of bZIP68 specifically at Cys171. This modification facilitates Cys245-mediated oxidation-dependent oligomerization, thereby enhancing bZIP68 transcriptional activity toward COLD-REGULATED413-THYLAKOID MEMBRANE1 (COR413-TM1). Transgenic complementation and physiological assays confirmed that Cys171 persulfidation is essential for full bZIP68 function in osmotic adaptation. Transcriptomic analysis further revealed that Cys171 is required for bZIP68-driven transcriptional reprogramming under stress. Our findings establish a hierarchical redox cascade wherein persulfidation primes bZIP68 for oxidative activation, highlighting a regulatory crosstalk between distinct post-translational modifications. These mechanistic insights expand our understanding of H₂S signaling and identify the bZIP68 cysteine network as a potential target for improving crop stress resilience. Full article

The sodium-taurocholate cotransporting polypeptide (NTCP) plays a critical dual role in liver function: maintaining bile acid (BA) enterohepatic circulation and acting as a receptor for the entry of hepatitis B and D viruses into hepatocytes. This review outlines the impact of various post-translational modifications (PTMs) of NTCP—including phosphorylation, oligomerization, ubiquitination, and glycosylation—on its dynamic regulatory network. These modifications coordinate the modulation of NTCP’s membrane localization, stability, conformational state, and protein interactions, precisely controlling its functions in BA uptake and viral invasion. Targeting this PTM network presents a promising strategy for next-generation therapies that selectively inhibit viral infection while preserving BA transport, overcoming the limitations of conventional inhibitors that indiscriminately disrupt virus–NTCP interactions. By synthesizing recent insights into NTCP PTM research, this article highlights its role as a central regulator of its bifunctional properties and reveals potential avenues for precision therapies in viral hepatitis, cholestasis, and related liver diseases. However, most existing evidence is derived from in vitro or cell-based models, whereas in vivo studies and clinical validation remain limited; thus, the translational feasibility of strategies targeting post-translational modifications of NTCP still requires further investigation. Full article

Sucrose synthase (SUS) is a key enzyme in plant carbon metabolism, catalyzing the reversible interconversion between sucrose + uridine diphosphate (UDP) and UDP-glucose (UDP-Glc) + fructose. It plays a central role in carbon flux allocation, cell wall and starch synthesis, as well as plant development and stress responses. SUS is encoded by a multigene family whose members exhibit significant functional diversification and expression specificity across species, tissues, and subcellular compartments. This review systematically summarizes the physiological functions of SUS in source–sink regulation, seed filling, and rapidly growing tissues; describes the organ-specific expression patterns and diverse subcellular localizations of different isoenzymes in Arabidopsis and major crops; and elucidates the phylogenetic pattern of the SUS gene family into three evolutionary clades—SUS I, SUS II, and SUS III—based on a comparative analysis of selected angiosperm species. Furthermore, it integrates the multi-level regulatory mechanisms of SUS, including transcriptional and post-transcriptional regulation, as well as the dynamic control of enzyme activity, stability, and subcellular localization through post-translational modifications such as phosphorylation and ubiquitination and protein interactions. Finally, this study identifies gaps in current research regarding ubiquitination mechanisms, metabolic network integration, and crop applications. It envisions SUS-centered molecular breeding strategies, informed by integrative regulatory genomics, multi-omics, and genome editing, to redirect crop carbon fluxes and thereby enhance yield, improve quality traits, and increase stress tolerance. Full article

Recent advances in mass spectrometry, data-independent acquisition, proteoform-resolving workflows, and multi-omics integration have significantly expanded the scale and scope of proteomics. However, the reuse and translational application of these datasets are limited by inconsistent standards, insufficient metadata, and inadequate computational interoperability. Proteoform-centric approaches provide higher molecular resolution by capturing intact protein variants and patterns of post-translational modification. Computational methods, including selected applications of machine learning and large language models (LLMs), are increasingly used for tasks such as spectral prediction and pattern discovery in clinical proteomics datasets. Despite these advancements, FAIR (Findable, Accessible, Interoperable, and Reusable) data practices, proteoform biology, and AI analytics are often pursued independently. This work presents an integrated framework for next-generation proteomics in which standardization and FAIR (Findable, Accessible, Interoperable, and Reusable) principles establish machine-actionable foundations for proteoform-resolved analysis and computational inference. It examines community efforts to promote data sharing and interoperability, as well as strategies for characterizing proteoforms using bottom-up, middle-down, and top-down approaches. It also highlights emerging AI and ML applications within the proteomics workflow. The framework emphasizes the importance of treating proteoforms as primary computational entities and adopting FAIR practices during data collection to enable reproducible and interpretable modeling. Finally, it introduces an architectural model that integrates FAIR infrastructures and proteoform resolution. In addition, practical recommendations for making AI-ready proteomics, including a minimal community checklist to support reproducibility, benchmarking, and translational scalability, are provided. Full article

Background/Objectives: Bone-targeted drug delivery systems hold great promise for treating skeletal diseases, yet the optimal strategy for functionalizing lipid nanoparticles (LNPs) with bone-homing ligands remains insufficiently explored. Herein, we compared two alendronate sodium (Alen) modification approaches (pre-conjugation and post-conjugation) for constructing bone-targeted LNPs capable of delivering mRNA to skeletal tissues. Methods: LNPs were fabricated via microfluidic mixing, and the 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-polyethylene glycol-alendronate conjugate (DSPE-PEG-Alen) required for the pre-conjugation method was synthesized. The bone-targeting ability of LNPs prepared by the two Alen modification strategies was evaluated using an in vitro hydroxyapatite (HAP) binding assay. Furthermore, the physicochemical properties, bone-targeting performance, mRNA delivery efficiency, and biosafety of the LNPs prepared by the post-conjugation method were assessed through cellular uptake, in vivo imaging, and other methods. Results: Hydroxyapatite binding assays revealed that the post-conjugation strategy afforded significantly superior bone affinity compared to the pre-conjugation approach. In addition, ex vivo bone fragment binding experiments further confirmed that the bone-targeting LNPs prepared by the post-conjugation method exhibited stronger bone-binding capability compared to unmodified LNPs. The optimized Alen-LNPs demonstrated efficient cellular uptake and functional mRNA translation in bone marrow mesenchymal stem cells with negligible cytotoxicity. In vivo studies in mice confirmed the preferential accumulation of Alen-LNPs in bone tissues, with successful green fluorescent protein (GFP) mRNA translation detected in bone tissue sections. Histopathological analysis confirmed the biosafety of the formulation. Conclusions: This study establishes the post-conjugation strategy as the superior approach for Alen functionalization of LNPs, providing a robust and reproducible platform for bone-targeted mRNA therapeutics. Full article

Vibrio alginolyticus is a common pathogenic bacterium and can cause diseases in aquaculture animals. Lysine lactylation (Kla) is a novel post-translational modification (PTM) that has been confirmed to play critical roles in key biological processes. However, the modification landscape and functions of Kla in V. alginolyticus remain unclear. In this study, lactylation modification profiles of the bacterial pathogen V. alginolyticus were first systematically characterized; a total of 9308 lactylation sites on 2155 proteins were successfully identified. The lactylation of cAMP receptor protein (CRP) and triosephosphate isomerase (TPI) was verified by Co-immunoprecipitation (Co-IP) and Western blot to validate the lactylome data. Bioinformatic analysis of the Kla sites revealed 32 conserved sequence motifs surrounding the modified residues. Kla proteins were mainly involved in central metabolic pathways, including glycolysis/gluconeogenesis and ribosome biogen regulators were found to contain Kla modification sites. To investigate crosstalk among lysine acylations in V. alginolyticus, we integrated Kla, lysine acetylation (Kac), and lysine succinylation (Ksuc) profiles and identified 337 co-modified proteins and 5 co-modified sites. Additionally, phylogenetic analysis of Vibrio alginolyticus CobQ based on protein sequence alignment revealed no homology to the known delactylase CobB. Combined in vitro and in vivo functional validation identified VaCobQ as a candidate delactylase with potential NAD⁺-independent activity. This study establishes a lysine lactylation landscape in V. alginolyticus, providing a resource for exploring Kla functions in bacterial metabolism and its possible connections to virulence. Full article

Background: Autism Spectrum Disorder (ASD) is a complex neurodevelopmental condition marked by heterogeneous behavioral symptoms and systemic comorbidities, including immune and gastrointestinal dysfunctions. Emerging studies suggest that glycosylation—a fundamental post-translational modification regulating cellular communication and immune responses—may play a role in ASD pathophysiology, yet its contribution remains underexplored. Methods: In this study, we developed an integrative transcriptomic and network analysis framework to investigate glycosylation-related gene expression changes and their functional associations in ASD. Using publicly available datasets from bulk and single-cell RNA sequencing of brain and blood tissues, we focused on four prior-knowledge gene subsets: glycogenes, extracellular matrix glycoproteins, immune response genes, and autism risk genes. Results: Differential expression and pathway enrichment analyses revealed consistent dysregulation of glycosylation pathways, including mucin-type O-glycan biosynthesis, glycosaminoglycan metabolism, GPI-anchor formation, and sialylation, across ASD tissues. These transcriptional changes were functionally linked to altered immune signaling (e.g., IL-17, Toll-like receptor, and complement pathways) and synaptic development pathways, forming a distinct glyco-immune axis. Network analysis identified key glycogenes such as GALNT10, NEU1, LMAN2L, and CHST1 as central molecular nodes, interacting with immune and neuronal regulators. Linkage disequilibrium analysis further revealed ASD-associated SNPs influencing the expression of these glycogenes in both blood and brain tissues. Conclusions: Together, these findings support a model in which disrupted glycosylation contributes to ASD pathophysiology by mediating immune dysregulation and altered neuronal connectivity. This study offers a systems-level framework to understand the molecular complexity of ASD and highlights glycogenes as potential biomarkers and targets for future therapeutic exploration. Full article

Autoimmune diseases arise from the failure of self-tolerance. The recognition of self-antigen peptide–MHC (pMHC) complexes by the T-cell receptor (TCR) is the fundamental event triggering autoimmune pathogenesis. While traditional immunosuppressants provide broad systemic effects, they often compromise global immunity. Emerging molecular strategies aim to selectively disrupt the trimolecular complex—comprising the TCR, the antigenic peptide, and the MHC molecule—to induce antigen-specific tolerance. This review highlights the pMHC–TCR interaction as the primary molecular checkpoint for antigen-specific intervention. We discuss the structural basis of these interactions and their potential to redefine the therapeutic landscape for autoimmune diseases (ADs). We examine the molecular drivers of tolerance breakdown—including genetic susceptibility, molecular mimicry, post-translational modifications (PTMs), and ectopic MHC II expression—that shape the autoreactive T-cell landscape. This review examines current advancements in biological and pharmacological interventions, such as pMHC-decorated nanoparticles and soluble pMHC, to reprogram pathogenic T-cell response. We also explored CAR-T therapy strategies for autoimmune diseases, such as CAR-Treg, designed to precisely modulate pMHC-TCR signaling. Collectively, these precision interventions in immunological synapse assembly during autoimmune response are considered the basis for safer, antigen-specific immunotherapy capable of restoring self-tolerance without global immunosuppression. Full article

Metabolic reprogramming plays a critical role in the pathogenesis of cardiovascular diseases. Historically regarded as a metabolic waste product, lactate has recently emerged as a critical regulator of vascular biology, exerting both metabolic and signaling functions. Moreover, the discovery of protein lactylation, a novel post-translational modification derived from lactate, has revealed a direct link between metabolic flux and gene regulation. This review provides a comprehensive overview of the evolving roles of lactate and lactylation in cardiovascular physiology and disease, offering insights into potential therapeutic interventions. It first provides a historical perspective of lactate and lactylation, followed by an overview of lactate metabolism, lactate shuttle theory and signaling pathways. It then discusses the mechanism and regulation of lactylation, focusing on its writers, erasers, and readers. Finally, this review summarizes clinical implications of lactate and lactylation in various cardiovascular diseases, including atherosclerosis, pulmonary hypertension, myocardial infarction, heart failure, and diabetic vascular complications. A deeper understanding of the mechanisms underlying the lactate–lactylation axis may facilitate the development of new therapeutic strategies to prevent or treat cardiovascular diseases. Full article

Aging is one of the most complex biological processes, which leads to a gradual decline in the function of organs, tissues and cells, and significant increases in the risks of many age-associated diseases, including cancer, neurodegenerative disorders, and cardiovascular diseases. Protein biomarkers have attracted increasing attention in research on aging and age-related diseases. Considering the fact that proteins are large heterogenous biomolecules due to coding polymorphisms, alternative RNA splicing and post-translational modifications (PTMs), including glycosylation, phosphorylation, and methylation, mass spectrometry (MS)-based top-down proteomics (TDP) is a powerful technology that allows for measuring proteins without proteolysis, thus characterizing intact forms of proteins, which provides information on primary sequences, including their modifications. This review provides an overview of TDP technologies, with a particular focus on the separation, ionization, and fragmentation of intact proteins and introduces the most recent applications of TDP to the discovery of proteoform-resolved biomarkers associated with aging and age-related diseases. Full article