Search Results (2,468)

ATP-binding cassette (ABC) transporters are one of the largest superfamilies of membrane proteins, but little is known about the structural and evolutionary features of their non-domain regions. To clarify the diversity of these non-canonical regions across evolutionary lineages, we performed an analysis of intrinsically disordered regions, site-specific selection and predicted post-translational modification (PTM) sites among five architectural classes involving 1581 prokaryotic and eukaryotic sequences. Linker and flanking regions were more disordered than transmembrane and nucleotide-binding domains in all architectures. Disorder fraction was significantly different between region types after phylogenetic correction (Pagel’s λ ≈ 0.97). Predicted PTM sites are enriched in disordered non-domain segments, with N-linked glycosylation and phosphoserine showing the strongest positive enrichment. A total of 140 sites satisfied a tiered conservation criterion (MusiteDeep score ≥ 0.5; cross-species conservancy ≥ 30%), including 40 high-confidence or moderate-confidence sites (conservancy ≥ 50%) as well as novel phosphotyrosine candidates in half transporters and NBD-only proteins. Site-specific selection analyses showed pervasive purifying selection across domain cores and architecture-dependent enrichment of episodic positive selection in non-domain regions, with significant non-domain enrichment in full reverse and half forward transporters (Fisher’s exact, BH-adjusted p < 0.05). In summary, these findings establish that non-canonical regions of ABC transporters are evolutionarily dynamic and contain conserved predicted modification sites, supporting the idea that these regions are evolutionary dynamic segments that deserve experimental characterization as candidate regulatory interfaces. Full article

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has greatly impacted public health due to high rates of transmissibility and mutation during the COVID-19 pandemic. Macrodomain 1 (Mac1) of non-structural protein 3 remained well conserved across variants and is critical to suppression of host immune response to infection, making Mac1 a promising target for therapeutic development. Mac1 binds and cleaves the post-translational modification ADP-ribose and is hypothesized to have a downstream effect on the host interferon response, but the exact cellular targets of Mac1 are still unknown. Characterizing the substrates of Mac1 ADP-ribosyl hydrolase activity using a catalytically inactive mutant N40D can reveal critical virus–host interactions to identify protein targets of Mac1 and reveal mechanisms of host interferon suppression. Here, we performed affinity enrichment with WT Mac1 and Mac1 N40D in HEK293T and A549 cells and quantified changes in protein interactions by TMT-multiplexed tandem mass spectrometry. We identified interactions between Mac1 and ADP-ribosylated substrates involved in DNA damage response, cytoskeletal components, and cell cycle regulation. Additionally, several members of the TRiC complex involved in protein folding were selectively enriched with mutant Mac1 from A549 cells. These findings suggest a novel role of Mac1 in regulating host protein folding. Full article

Heat stress (HS) is among the most economically consequential environmental challenges to global dairy production, causing progressive declines in milk yield, compositional quality, and mammary cellular integrity. The temperature–humidity index (THI) is the primary thermal load metric, with performance-impairment thresholds typically beginning at THI 68 in Holstein cattle, with severe impacts manifesting beyond THI 72; breed-specific thresholds for Jersey, Brown Swiss, and Simmental cows differ owing to their lower metabolic heat load and greater inherent thermotolerance. At the molecular level, HS activates heat shock protein networks—notably HSPA1A, HSP90B1, and HSPH1—through HSF1/HSF4 transcriptional activation, while simultaneously suppressing casein genes (CSN1S1, CSN2, CSN3), lipogenic genes (FASN, SCD, CD36), amino acid transporters (SLC7A5, SLC38A2), and mTOR-AKT-STAT5 translational machinery, collectively impairing milk biosynthetic capacity. Pro-apoptotic signaling (BAX, CASP3 upregulation; BCL2 downregulation) and mitochondrial dysfunction further compromise mammary epithelial viability. Post-transcriptional regulation through miRNA, circRNA, and lncRNA competing endogenous RNA networks, alongside epitranscriptomic m6A modifications, adds further regulatory complexity. Genome-wide association studies have identified SNPs in HSP70A1A, HSPA4, TLR4, and PRLR as thermotolerance candidates compatible with sustained milk production. Nutritional supplementation with methionine, arginine, and taurine partially restores cellular synthetic capacity. Integrating multi-trait genomic selection with Bos indicus introgression, precision cooling, and targeted nutrition offers the most viable path toward climate-resilient, high-producing dairy cattle. Full article

Antifungal killer toxins are cytotoxic proteins that have the potential to combat the growing threat of fungi to human health and agriculture. A lack of empirical tertiary structures has limited understanding of their mechanisms of action and their ability to target pathogens. In this study, AlphaFold and molecular dynamics simulations were used to generate tertiary structure models of all canonical Saccharomyces killer toxins and to place them in the context of historical empirical data. These models enabled the prediction of functional domains and posttranslational modifications, including proteolytic cleavage sites and disulfide bonds. They also revealed unexpected homology between Saccharomyces killer toxins, suggesting that all but K28 are likely ionophores. Structural homology to the well-studied killer toxins K1 and K2 enabled the prediction of the antifungal and immunity mechanisms of K1L, K21, K45, K74, and KHS. The understudied killer toxins Klus, KHR, and K62 were found to have homology to bacterial and plant toxins, including members of the aerolysin family and antifungal lectins. These structural similarities provide clues for the mechanisms of killer toxin carbohydrate binding, oligomerization, and membrane attack. This modeling approach will help guide the continued use of the model yeast S. cerevisiae to study killer toxins in the context of the wealth of functional data gathered in the decades since their first discovery. Full article

Transcriptome profiling has been widely used to dissect the molecular mechanisms underlying plant responses to environmental stresses, yet the extent to which RNA changes reflect functional protein levels remains unclear. Here, we performed an integrated multi-omics analysis of the transcriptome, proteome, phosphoproteome, and acetylome in rice during a drought–rewatering cycle. We first identified 5449 differentially expressed genes (DEGs) and 525 differentially expressed proteins (DEPs) under drought stress, followed by 4340 DEGs and 328 DEPs upon rewatering, which underpinned an extensive remodeling of photosynthetic and metabolic pathways. Temporal clustering of transcriptomic and proteomic data then delineated five distinct expression patterns for both transcripts and proteins, uncovering transcriptional and translational strategies ranging from rapid reversal to persistent stress adaptation. Despite the observed coherence in some expression clusters, we nonetheless uncovered widespread transcriptome–proteome discordance, with a substantial fraction of gene–protein pairs exhibiting uncorrelated abundance changes. Remarkably, the observed discordance is quantitatively associated with the dynamic nature of post-translational modifications, including phosphorylation and acetylation, which act as key post-transcriptional tuners to independently regulate protein abundance—particularly for components of photosynthesis and energy metabolism—enabling plants to dynamically balance stress tolerance with the maintenance of core physiological functions. Our research delves into the intricate and often distinct regulatory networks that span transcriptional, translational, and post-translational levels, extending beyond a singular transcriptional focus. Full article

α-Crystallin, the predominant protein of the eye lens, possesses molecular chaperone activity and antioxidative properties, both of which are essential for maintaining lens transparency. Its chaperone function prevents the formation of light-scattering protein aggregates, while its antioxidative activity mitigates oxidative stress through both direct and indirect mechanisms. However, with aging, α-crystallin undergoes cumulative post-translational modifications and oxidative damage, leading to protein crosslinking and a decline in chaperone efficacy. Notably, α-crystallin exhibits free radical-scavenging activity comparable to that of serum albumin, a well-characterized antioxidant protein. In addition, its ability to bind redox-active metal ions and convert them into redox-inactive forms significantly reduces reactive oxygen species (ROS) generation in vivo. α-Crystallin also interacts with key proteins and signaling pathways involved in oxidative stress responses, further enhancing its multifunctional protective role. This review summarizes current evidence on the antioxidative properties of α-crystallin and their relationship to its chaperone function, highlighting its importance in lens homeostasis and age-related cataract formation. Full article

Proteomics has become central to pharmacological research by providing quantitative readouts of protein abundance, post-translational modifications, interactions, and spatial context. However, proteomic datasets are high-dimensional, heterogeneous, and frequently affected by missingness, batch effects, and limited cohort size. Artificial intelligence (AI) and machine learning (ML) can help convert these complex data into decision-relevant outputs for target identification, biomarker discovery, pharmacodynamic monitoring, and drug repurposing. This review critically compares supervised learning, ensemble methods, dimensionality reduction, clustering, deep learning, graph learning, survival modeling, causal inference, and calibration approaches in proteomics-driven drug discovery. We also summarize major software ecosystems for mass-spectrometry processing, targeted assays, spectrum prediction, phosphoproteomics, structure modeling, and reproducible workflows. Emphasis is placed on model selection, benchmarking, missing-data handling, batch correction, interpretability, uncertainty, experimental validation, and translational readiness. Finally, we highlight emerging directions, including contrastive learning, diffusion models, graph-based integration, and federated analytics. Full article

The liver circadian clock coordinates hepatic lipid metabolism, bile acid synthesis, and glucose homeostasis through interlocking transcription–translation feedback loops. Disruption of this temporal organization is increasingly recognized as a shared pathological feature across the chronic liver disease spectrum. Transcriptomic profiling alone cannot capture the full scope of circadian dysregulation. Approximately half of rhythmically abundant hepatic proteins lack correspondingly rhythmic mRNAs. Roughly 25% of hepatic phosphosites oscillate with a 24-h period. Integrating transcriptomics, proteomics, post-translational modification profiling, metabolomics, and emerging single-cell and spatial approaches is therefore necessary for an accurate account of how circadian programs are remodeled in disease. This narrative review delineates the multi-omics landscape of circadian clock dysregulation across six chronic liver disease categories. These encompass metabolic dysfunction-associated fatty liver disease (MAFLD), alcoholic liver disease (ALD), viral hepatitis, hepatocellular carcinoma (HCC), liver fibrosis, and cholestatic disease. Four molecular features recur across these contexts. BMAL1 functional downregulation, REV-ERBα oscillatory output attenuation, NAD⁺ oscillatory amplitude reduction, and gut–liver axis circadian desynchronization together constitute an inferential framework for hepatic circadian failure. These features represent recurring disease-associated motifs rather than an established pan-disease mechanism. The upstream mechanisms and evidence depth differ substantially by disease category. Oncogenic kinase-driven CLOCK post-translational modifications in HCC, phosphoproteomic remodeling in MAFLD, and epigenomic clock disruption persisting after HCV clearance represent findings that transcriptomics alone would not resolve. The near-complete absence of temporally resolved human tissue data remains the principal barrier to translational progress. This evidence gap limits the clinical actionability of current mechanistic findings across all disease categories. Circadian phase inference algorithms and prospective temporally designed cohort studies offer a methodologically grounded path toward clinically actionable circadian hepatology. Full article

Protein lactylation, an emerging post-translational modification (PTM) driven by the metabolite lactate, has surfaced as an important regulatory layer contributing to the crosstalk between metabolic reprogramming and cellular functional plasticity in colorectal cancer (CRC). Within the unique “host–microbiota” symbiotic microenvironment of CRC, the Warburg effect—fueled jointly by oncogene activation and microbial metabolism—provides abundant substrates for lactylation. This modification is dynamically regulated by a complex enzymatic system comprising “Writers” (e.g., p300/CREB-binding protein [p300/CBP], alanyl-tRNA synthetase 1/2 [AARS1/2]) and “Erasers” (e.g., histone deacetylases [HDACs] and Sirtuins). Through intricate crosstalk with other PTMs, such as acetylation and ubiquitination, lactylation exerts critical regulatory effects on both the histone epigenetic landscape and non-histone protein functions. Functionally, lactylation not only drives malignant proliferation, invasion, and metastasis but also systematically remodels the immunosuppressive “cold” tumor microenvironment. Furthermore, it confers broad-spectrum resistance to chemotherapy, radiotherapy, targeted therapy, and immunotherapy by orchestrating a ferroptosis defense network, enhancing DNA damage repair (DDR), and activating protective autophagy. This review systematically synthesizes the regulatory networks and biological functions of lactylation in CRC, deeply elucidating the core mechanisms underlying therapy resistance. Finally, we discuss the clinical translational potential of lactylation as a novel diagnostic/prognostic biomarker and therapeutic target, aiming to provide new theoretical foundations and strategic directions for overcoming current bottlenecks in CRC clinical treatment. Full article

Brassica napus L. is a globally important crop and its productivity is constrained by multiple abiotic stresses (salinity, drought, and heat). Calcineurin B-like proteins (CBLs) act as calcium sensors and play key roles in regulating ion homeostasis and stress-responsive signaling pathways, thereby contributing to plant adaptation under unfavorable environmental conditions. Here, through detailed bioinformatics analyses, the BnCBL gene family has been identified along with its role in tolerance to multiple abiotic stresses. The identified 17 BnCBLs comprised four groups, as in Arabidopsis thaliana. The predicted molecular weights of the CBL proteins ranged from approximately 24.35 kDa (BnCBL3 and -9) to 29.7 kDa (BnCBL5), with protein lengths spanning 213 (BnCBL3, -9, -10, -12 and -15) to 260 amino acids (BnCBL5). Sequence, promoter, and structural analyses showed that BnCBL proteins harbor palmitoylation and myristoylation motifs in their EF-hand domains, contain hormone- and stress-responsive cis-elements, and exhibit characteristic post-translational modification sites and tertiary structures. RNA-seq and RT-qPCR expression analyses showed that several BnCBL genes (BnCBL2, -6, -9, -10, and -15) exhibit differential expression (3~6-fold) under NaCl, drought, and heat stresses, as well as in response to phytohormones (IAA, GA₃, ABA, and JA). In addition, BnCBL2, -3, -6, -8, -9, -11, -12 and -16 showed significant expression (around 7-fold) against biotic stresses (Sclerotinia sclerotiorum (Lib.) de Bary and Plasmodiophora brassicae (Woronin, 1877), indicating their roles in both biotic and abiotic stress tolerance and potential utility in biotechnological breeding of stress-enduring B. napus cultivars. Full article

Ubiquitination is a key post-translational modification regulating cellular signaling and innate immunity, and its reversal by deubiquitinases (DUBs) represents a critical mechanism exploited by pathogens for immune evasion. While ovarian tumor (OTU) domain-containing DUBs are well characterized in viral systems, their roles in fungal pathogens remain largely unexplored. In this study, we investigated two putative OTU domain-containing proteins derived from the plant pathogenic fungi Melampsora larici-populina (MlpOTU, EGG09943.1) and Taphrina deformans (TdOTU, CCG84064.1). Recombinant MlpOTU and TdOTU proteins were successfully expressed and purified from E. coli and exhibited high solubility and proper folding. Functional analyses in HEK293T cells demonstrated that both proteins significantly reduce global ubiquitination levels, confirming their deubiquitinase activity in vivo. Despite this shared enzymatic function, the two proteins displayed markedly distinct effects on host immune gene expression. MlpOTU selectively suppressed key antiviral effectors, most notably MX1, suggesting a targeted immune evasion strategy. In contrast, TdOTU induced robust upregulation of multiple immune-related genes, including type I interferons, indicating a divergent role. Neither MlpOTU nor TdOTU triggered robust apoptosis, supporting their role as modulators of host signaling rather than cytotoxic effectors. Collectively, these findings provide the first functional evidence that fungal OTU domain-containing proteins act as active deubiquitinases and reveal distinct strategies by which plant pathogens may manipulate host immune responses. This study establishes fungal OTU domains as promising targets for antifungal intervention and broadens our understanding of cross-kingdom evasion mechanisms. Full article

Once written off as nothing more than a waste product of glycolysis, lactic acid is now seen as a key signaling molecule that operates across a wide range of physiological and pathological processes, from immune regulation and tumor metabolism to neural function. But its role goes beyond energy metabolism and cell signaling. Recent studies have uncovered a new type of post-translational modification called histone lactylation, in which lactate itself provides the lactoyl group attached to lysine residues on histones. This modification directly ties a cell’s metabolic state to the epigenetic control of gene expression. For example, histone lactylation helps shift macrophages from a pro-inflammatory M1 phenotype to an anti-inflammatory M2 phenotype by fine-tuning gene transcription. In this review, we walk through the discovery and biochemical foundation of histone lactylation; discuss the likely writer and eraser enzymes that manage its dynamic changes; and highlight recent advances in understanding the role of this modification in inflammation, tumorigenesis, neurological disorders, and interactions with gut microbes. We also lay out key unanswered questions and consider why targeting protein lactylation might open up new therapeutic possibilities. Full article

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by memory loss and cognitive decline. Its main pathological features are extracellular plaques composed of aggregated amyloid-β (Aβ) peptides and intracellular neurofibrillary tangles formed by hyperphosphorylated tau. The Aβ hypothesis proposes that Aβ accumulation is a key driver of AD, influencing tau pathology, neuroinflammation, and neurodegeneration. However, therapies that reduce Aβ have shown limited clinical benefits. This suggests that the mechanisms underlying peptide-mediated modulation of AD pathology are much more complex. Both Aβ and tau undergo various post-translational modifications (PTMs) that affect their structure, aggregation, and toxicity. In addition, these abnormal proteins are not efficiently cleared in AD, indicating dysfunction of the protein quality control (PQC) system that maintains proteostasis. Such abnormal PTMs and impaired PQC likely work together to drive disease progression, which may explain the limited success of Aβ-reduction therapies. In this review, we describe how major PTMs, including phosphorylation, ubiquitination, acetylation, glycosylation, and oxidation, regulate the pathological behavior of Aβ and tau. We also discuss the role of the PQC systems in the pathology of AD. We propose that dysregulation of PTMs and PQC constitutes a convergent mechanism underlying AD pathogenesis. Therapeutic strategies targeting these processes may provide more effective and sustained disease modification than approaches focused solely on Aβ reduction. Full article

Plant–pathogen interactions are shaped by dynamic regulatory processes that control immune signaling. Among these, post-translational modifications (PTMs) play central roles in modulating protein activity, stability, and interaction networks. Increasing evidence indicates that Phytophthora effectors target PTM-dependent regulatory systems to suppress host immunity and promote infection. Here, we synthesize current knowledge on how Phytophthora virulence factors manipulate post-translational regulation through two mechanistically distinct strategies: (i) canonical mechanisms, involving direct enzymatic modification of host proteins or the recruitment of host PTM-modifying enzymes, and (ii) non-canonical mechanisms, in which effectors alter the activity, organization, or localization of PTM-associated regulatory systems without directly inducing covalent modification. These processes frequently involve protein–protein interactions and oligomerization-dependent regulation that reshape signaling complexes and enzymatic accessibility. By distinguishing effector-mediated PTM induction from regulatory interference, we provide a mechanistic framework for interpreting how diverse virulence strategies converge on the control of immune signaling pathways, including those governing reactive oxygen species production, transcriptional regulation, hormone signaling, and cell death. We further highlight current limitations in mechanistic understanding and emphasize the need for integrative approaches combining structural biology and proteomics to resolve how effectors reprogram host signaling systems. Full article

Carbonic anhydrases (CAs) efficiently catalyze CO₂ reversible hydration, critical for carbon capture and sequestration (CCS), but naturally low yield limits industrial use. Yarrowia lipolytica, an unconventional yeast, is an ideal heterologous expression host with robust adaptability, post-translational modification capacity, and versatile genetic tools. In this study, 10 α-, β-, and γ-class CAs were successfully expressed in Y. lipolytica, and two top-performing candidates were identified: Methanosarcina mazei γ-CA (MmaCA) and Sulfurihydrogenibium azorense α-CA (SazCA). Their production was further optimized via promoter and gene dosage adjustment, cultural condition optimization and auxiliary protein co-expression. The optimized intracellular MmaCA activity reached 960 U/mL (64.42-fold improvement), and the extracellular SazCA activity peaked at 925 U/mL (70.08-fold enhancement). CO₂ mineralization experiments confirmed both recombinant CAs significantly accelerated CaCO₃ precipitation, demonstrating a promising CCS application potential. To our knowledge, this is the first systematic investigation of CA heterologously expressed in Y. lipolytica, providing a novel strategy for the highly efficient production of CAs to enable their application in industry. Full article