Search

Loops in the axial channels of ClpAP and other AAA+ proteases bind a short peptide degron connected by a linker to the N- or C-terminal residue of a native protein to initiate degradation. ATP hydrolysis then powers pore-loop movements that translocate these segments through the channel until a native domain is pulled against the narrow channel entrance, creating an unfolding force. Substrate unfolding is thought to depend on strong contacts between pore loops and a subset of amino acids in the unstructured sequence directly preceding the folded domain. Here, we identify such contact sequences that promote grip for ClpAP and use ClpA structures to place these sequences within ClpA's two AAA+ rings. The positions and chemical nature of certain residues within an unstructured segment that are positioned to interact with the D2 ring have major positive effects on substrate unfolding, whereas segments located within the D1 ring have little consequence. Within the D2-bound segment, two short elements are critical for accelerating degradation; one is at the "top" of D2 and consists of at least two properly positioned nonslippery residues. In contrast, the second D2 element, which can be as short as one residue, is positioned to contact pore loops near the "bottom" of this ring. Comparison with similar studies for ClpXP reveals that positioning a wellgripped substrate sequence within the major unfoldase motor is more important than its proximity to the folded domain and that charged, polar, and hydrophobic residues all contribute favorable contacts to substrate grip. [ABSTRACT FROM AUTHOR]

Insulin Receptor Substrate 2 (IRS2) is a signaling adaptor protein for the insulin (IR) and Insulin-like Growth Factor-1 (IGF-1R) receptors. In breast cancer, IRS2 contributes to both the initiation of primary tumor growth and the establishment of secondary metastases through regulation of cancer stem cell (CSC) function and invasion. However, how IRS2 mediates its diverse functions is not well understood.Weused CRISPR/Cas9- mediated gene editing to modify endogenous IRS2 to study the expression, localization, and function of this adaptor protein. A cassette containing an auxin-inducible degradation (AID) sequence, 3x-FLAG tag, and mNeon-green was introduced at the N-terminus of the IRS2 protein to provide rapid and reversible control of IRS2 protein degradation and analysis of endogenous IRS2 expression and localization. Live fluorescence imaging of these cells revealed that IRS2 shuttles between the cytoplasm and nucleus in response to growth regulatory signals in a PI3Kdependent manner. Inhibition of nuclear export or deletion of a putative nuclear export sequence in the C-terminal tail promotes nuclear retention of IRS2, implicating nuclear export in the mechanism by which IRS2 intracellular localization is regulated. Moreover, the acute induction of IRS2 degradation reduces tumor cell invasion, demonstrating the potential for therapeutic targeting of this adaptor protein. Our data highlight the value of our model of endogenously tagged IRS2 as a tool to study IRS2 localization and function. [ABSTRACT FROM AUTHOR]

Prenylcysteine oxidases (PCYOXs) metabolize prenylated cysteines produced by protein degradation. They utilize oxygen as a co-substrate to produce free cysteine, an aldehyde, and hydrogen peroxide through the unusual oxidation of a thioether bond. In this study, we explore the evolution, structure, and mechanism of the two mammalian PCYOXs. A gene duplication event in jawed vertebrates originated in these two paralogs. Both enzymes are active on farnesyl- and geranylgeranylcysteine, but inactive on molecules with shorter prenyl groups. Kinetics experiments outline a mechanism where flavin reduction and re-oxidation occur rapidly without any detectable intermediates, with the overall reaction rate limited by product release. The experimentally determined three-dimensional structure of PCYOX1 reveals long and wide tunnels leading from the surface to the flavin. They allow the isoprene substrate to curl up within the protein and position its reactive cysteine group close to the flavin. A hydrophobic patch on the surface mediates membrane association, enabling direct substrate and product exchange with the lipid bilayer. Leveraging established knowledge of flavoenzyme inhibition, we designed sub-micromolar PCYOX inhibitors. Additionally, we discovered that PCYOXs bind and slowly degrade salisirab, an anti-RAS compound. This activity suggests potential and previously unknown roles of PCYOXs in drug metabolism. [ABSTRACT FROM AUTHOR]

Recent technological advancements, including computer-assisted drug discovery, gene-editing techniques, and high-throughput screening approaches, have greatly expanded the palette of methods for the discovery of peptides available to researchers. These emerging strategies, driven by recent advances in bioinformatics and multi-omics, have significantly improved the efficiency of peptide drug discovery when compared with traditional in vitro and in vivo methods, cutting costs and improving their reliability. An added benefit of peptide-based drugs is the ability to precisely target protein–protein interactions, which are normally a particularly challenging aspect of drug discovery. Another recent breakthrough in this field is targeted protein degradation through proteolysis-targeting chimeras. These revolutionary compounds represent a noteworthy advancement over traditional small-molecule inhibitors due to their unique mechanism of action, which allows for the degradation of specific proteins with unprecedented specificity. The inclusion of a peptide as a protein-of-interest-targeting moiety allows for improved versatility and the possibility of targeting otherwise undruggable proteins. In this review, we discuss various novel wet-lab and computational multi-omic methods for peptide drug discovery, provide an overview of therapeutic agents discovered through these cutting-edge techniques, and discuss the potential for the therapeutic delivery of peptide-based drugs. [ABSTRACT FROM AUTHOR]

Background/Objectives: Cell lines do not faithfully replicate the authentic transcriptomic condition of the disease under study. The HepG2 cell line is widely used for studying hepatocellular carcinoma (HCC), but not all biological processes and genes exhibit congruent expression patterns between cell lines and the actual disease. The objective of this study is to perform a comparative transcriptomic analysis of the HepG2 cell line, HCC, and primary hepatocytes (PH) in order to identify genes suitable for research in HepG2 as a model for PH or HCC research. Methods: We conducted a differential expression analysis between publicly available data from HCC patients, PH, and HepG2. We examined specific overlaps of differentially expressed genes (DEGs) in a pairwise manner between groups in order to obtain a valuable gene list for studying HCC or PH using different parameter filtering. We looked into the function and druggability of these genes. Conclusions: In total, we identified 397 genes for HepG2 as a valuable HCC model and 421 genes for HepG2 as a valuable PH model, and with more stringent criteria, we derived a smaller list of 40 and 21 genes, respectively. The majority of genes identified as a valuable set for the HCC model are involved in DNA repair and protein degradation mechanisms. This research aims to provide detailed guidance on gene selection for studying diseases like hepatocellular carcinoma, primary hepatocytes, or others using cell lines. [ABSTRACT FROM AUTHOR]

Viral infections are one of the principal causes of global primary health crises, with increased rate of infection and mortality demonstrated by the newer progeny of viruses. Viral invasion of the host involves utilization of various cellular machinery. Ubiquitination is one of a few central regulatory systems used by viruses for establishment of the infections in the host. Members of the ubiquitination system are involved in carrying out proteasomal degradation or functional modification of proteins in numerous cellular processes. E3 ubiquitin ligases play a major role in this system through recognition and recruitment of protein substrates and catalyzing the transfer of ubiquitin to these substrates. The versatility of ubiquitin ligases frequently makes them useful tools for the viruses, for either utilizing or degrading other cellular machineries, for carrying out their multiplication or inactivating the defensive strategies of the host. Therefore, these ligases are important targets for aiming at major pathways causing viral protein degradation or functional modification of the infection process. In this review, we have discussed the role and mechanism of different types of ubiquitin ligases in the context of infections of mainly human viruses, highlighting the viral proteins directly interacting with the ligases. Knowledge about these direct interactions is central in understanding the ubiquitin-dependent processes. This comprehensive account may also be beneficial for pharmaceutical exploration of E3 ligase-based broad-spectrum antiviral treatment. [ABSTRACT FROM AUTHOR]

Endoplasmic reticulum (ER) stress is a cellular phenomenon that arises in response to the accumulation of misfolded proteins within the ER. This process triggers the activation of a signalling pathway known as the unfolded protein response (UPR), which aims to restore ER homeostasis by reducing protein synthesis, increasing protein degradation, and promoting proper protein folding. However, excessive ER stress can perturb regular cellular function and contribute to the development of diverse pathological conditions. As is well known, ferroptosis is a kind of programmed cell death characterized by the accumulation of lipid peroxides and iron-dependent reactive oxygen species (ROS), resulting in oxidative harm to cellular structures. In recent years, there has been increasing evidence indicating that ferroptosis occurs in musculoskeletal disorders (MSDs), with emerging recognition of the complex relationship between ER stress and ferroptosis. This review presents a summary of ER stress and the ferroptosis pathway. Most importantly, it delves into the significance of ER stress in the ferroptosis process within diverse skeletal or muscle cell types. Furthermore, we highlight the potential benefits of targeting the correlation between ER stress and ferroptosis in treating degenerative MSDs. [ABSTRACT FROM AUTHOR]

Cereblon (CRBN), a member of the E3 ubiquitin ligase complex, has gained significant attention as a therapeutic target in cancer. CRBN regulates the degradation of various proteins in cancer progression, including transcription factors and signaling molecules. PROTACs (proteolysis‐targeting chimeras) are a novel approach that uses the cell's degradation system to remove disease‐causing proteins selectively. CRBN‐dependent PROTACs work by tagging harmful proteins for destruction through the ubiquitin–proteasome system. This strategy offers several advantages over traditional protein inhibition methods, including the potential to overcome drug resistance. Recent progress in developing CRBN‐based PROTACs has shown promising preclinical results in both hematologic malignancies and solid tumors. Additionally, CRBN‐based PROTACs have enhanced our understanding of CRBN's role in cancer, potentially serving as biomarkers for patient stratification and predicting therapeutic responses. In this review, we delineate the mechanisms of action for CRBN‐dependent PROTACs (CRBN‐PROTACs), summarize recent advances in preclinical and clinical applications, and provide our perspective on future development. [ABSTRACT FROM AUTHOR]

Protein degradation through the ubiquitin proteasome system at the spatial and temporal regulation is essential for many cellular processes. E3 ligases and degradation signals (degrons), the sequences they recognize in the target proteins, are key parts of the ubiquitin-mediated proteolysis, and their interactions determine the degradation specificity and maintain cellular homeostasis. To date, only a limited number of targeted degron instances have been identified, and their properties are not yet fully characterized. To tackle on this challenge, here we develop a novel deep-learning framework, namely MetaDegron, for predicting E3 ligase targeted degron by integrating the protein language model and comprehensive featurization strategies. Through extensive evaluations using benchmark datasets and comparison with existing method, such as Degpred, we demonstrate the superior performance of MetaDegron. Among functional features, MetaDegron allows batch prediction of targeted degrons of 21 E3 ligases, and provides functional annotations and visualization of multiple degron-related structural and physicochemical features. MetaDegron is freely available at http://modinfor.com/MetaDegron/. We anticipate that MetaDegron will serve as a useful tool for the clinical and translational community to elucidate the mechanisms of regulation of protein homeostasis, cancer research, and drug development. [ABSTRACT FROM AUTHOR]

Ubiquitin controls many cellular processes via its posttranslational conjugation onto substrates. Its use is highly variable due to its ability to form poly-ubiquitin chains with various topologies. Among them, linear chains have emerged as important regulators of immune responses and protein degradation. Previous studies in Drosophila melanogaster found that expression of linear poly-ubiquitin that cannot be dismantled into single moieties leads to their ubiquitination and degradation or, alternatively, to their conjugation onto proteins. However, it remains largely unknown which proteins are sensitive to linear poly-ubiquitin. To address this question, here we expanded the toolkit to modulate linear chains and conducted ultra-deep coverage proteomics from flies that express noncleavable, linear chains comprising 2, 4, or 6 moieties. We found that these chains regulate shared and distinct cellular processes in Drosophila by impacting hundreds of proteins, such as the circadian factor Cryptochrome. Our results provide key insight into the proteome subsets and cellular pathways that are influenced by linear poly-ubiquitin chains with distinct lengths and suggest that the ubiquitin system is exceedingly pliable. [ABSTRACT FROM AUTHOR]

In the present study, we investigated the preservative effects of chitosan (CS) coatings, with and without thyme essential oil (TEO), combined with vacuum impregnation (VI) on maintaining the quality of snakehead fillets during chilled storage. The results showed that the VI treatment significantly inhibited drip loss, discoloration, microbial proliferation, and the accumulation of biogenic amines (BAs) in the sneakhead fillets. Compared to the control, the fillets treated with VI of 1% (w/w) CS and 1.5% (w/w) TEO (i.e., CSTEO) showed significant reductions in both psychrophiles and mesophiles, with a 2.66 log CFU/g decrease in total viable count (TVC) on day 3 and a 1.89 log CFU/g decline in TVC on day 9, respectively. In addition, the content of histamine and putrescine in the CSTEO groups was maintained at ∼1.14 and 3.23 mg/kg during the 12‐day chilled storage, respectively. A total of 100 chemical compounds were tentatively identified using untargeted metabolomics approaches. The multivariate analysis further revealed that the combination of VI and CSTEO maintained fish quality mainly through preventing lipid oxidation and protein degradation. Overall, the VI‐CSTEO treatment effectively maintained the fish quality during storage at 4°C, with minimum microbial proliferation and accumulation of BAs. Practical Application: The preservative effect of chitosan coatings containing thyme essential oil combined with vacuum impregnation on snakehead quality during the 12‐day chilled storage was verified, and the underlying mechanisms were deciphered through integrated metabolomics approaches. Our study could provide a promising strategy for the preservation of aquatic products. [ABSTRACT FROM AUTHOR]

Pingyin rose is an edible flower rich in anthocyanins. In this study, antioxidant capacity and color were used as the main evaluation indexes to investigate the effects of common physical and chemical factors on the stability of rose anthocyanin extracts (RAEs). In addition, the physicochemical properties of the whey protein isolate (WPI)‐RAEs complex after spray drying were studied. Vitamin C, temperature, and some metal ions can cause different degrees of discoloration of RAEs solution. More importantly, heat treatment, as well as most metal ions and sugars, had no significant effect on the antioxidant capacity of RAEs solution (p > 0.05). Moreover, compared to spray‐dried pure WPI, the WPI‐RAEs powder was delicate and uniform, and had higher particle size, bulk density, moisture activity, and better gel properties. The release rate of all WPI‐RAEs sol/gel to RAEs reached about 89% in the intestinal digestion stage, but the WPI‐RAEs interaction reduced the digestibility of protein in the intestinal digestion stage. We hope that this study can provide a theoretical basis for the development and utilization of WPI‐RAEs as food ingredients. [ABSTRACT FROM AUTHOR]

Sialodacryoadenitis virus (SDAV) has been identified as the etiological agent responsible for the respiratory system and salivary gland infections in rats. The existing literature on SDAV infections is insufficient to address the topic adequately, particularly in relation to the central nervous system. In order to ascertain how SDAV gains access to neuronal cells and subsequently exits, our attention was focused on the small molecule valosin-containing protein (VCP), which is an ATPase. VCP is acknowledged for its function in the ubiquitin-mediated proteasomal degradation of proteins, including those of viral origin. To ascertain the potential influence of VCP on SDAV replication and egress, high-content screening was employed to determine the viral titer and protein content. Western blot analysis was employed to ascertain the relative expression of VCP. Real-time imaging of SDAV-infected cells and confocal imaging for qualitative morphological analysis were conducted. The Eeyarestatin I (EerI) inhibitor was employed to disrupt VCP involvement in the endoplasmic reticulum-associated protein degradation pathway (ERAD) in both pre- and post-incubation systems, with concentrations of 5 μM/mL and 25 μM/mL, respectively. We demonstrated for the first time that SDAV productively replicates in cultured primary neurons. VCP expression is markedly elevated during SDAV infection. The application of 5 μM/mL EerI in the post-treatment system yielded a statistically significant inhibition of the SDAV yield. It is likely that this modulates the efficacy of virion assembly by arresting viral proteins in the submembrane area. [ABSTRACT FROM AUTHOR]

CycloAnt is an opioid peptide that produces potent and efficacious antinociception with significantly reduced side effects upon systemic administration in mice. To verify its CNS-mediated antinociception, we determined its binding affinity at the opioid receptors, its proteolytic stability in mouse serum, metabolic stability in mouse liver microsomes, and pharmacokinetics in mice. CycloAnt exhibited stability toward proteolytic degradation in serum and resistance against metabolism mediated by cytochrome P450 enzymes (CYP450s) and UDP-glucuronosyl transferases (UGTs) in mouse liver microsomes. A pharmacokinetic study of CycloAnt in mice confirmed that CycloAnt crossed the blood–brain barrier (BBB) with a brain-to-plasma ratio of 11.5%, a high extent of BBB transport for a peptide. To elucidate the structural basis underlying its BBB penetration, we investigated its conformation in water and DMSO using 1H NMR spectroscopy. The results show that CycloAnt displays an extended conformation in water with most amide NHs being exposed, while in less polar DMSO, it adopts a compact conformation with all amide NHs locked in intramolecular hydrogen bonds. The chameleonic property helps CycloAnt permeate the BBB. [ABSTRACT FROM AUTHOR]

The development of novel tools to tackle viral processes has become a central focus in global health, during the COVID-19 pandemic. The spike protein is currently one of the main SARS-CoV-2 targets, owing to its key roles in infectivity and virion formation. In this context, exploring innovative strategies to block the activity of essential factors of SARS-CoV-2, such as spike proteins, will strengthen the capacity to respond to current and future threats. In the present work, we developed and tested novel bispecific molecules that encompass: (i) oligonucleotide aptamers S901 and S702, which bind to the spike protein through its S1 domain, and (ii) hydrophobic tags, such as adamantane and tert-butyl-carbamate-based ligands. Hydrophobic tags have the capacity to trigger the degradation of targets recruited in the context of a proteolytic chimera by activating quality control pathways. We observed that S901-adamantyl conjugates promote the degradation of the S1 spike domain, stably expressed in human cells by genomic insertion. These results highlight the suitability of aptamers as target-recognition molecules and the robustness of protein quality control pathways triggered by hydrophobic signals, and place aptamer-Hytacs as promising tools for counteracting coronavirus progression in human cells. [ABSTRACT FROM AUTHOR]

The production of whey protein concentrates (WPC) from camel milk whey represents an effective approach to valorize this processing byproduct. These concentrates harbor active ingredients with significant bioactive properties. Camel WPC were spray-dried at inlet temperature of 170, 185 and 200°C, or ultrasonicated (US) for 5, 10, and 15 min, then freeze-dried to obtain fine powder. The effect of both treatments on protein degradation was studied by sodium dodecyl sulfate-PAGE and reverse-phase ultraperformance liquid chromatography techniques. Significantly Substantially enhanced protein degradation was observed after US treatment when compared with spray-drying (SPD). Both SPD and US treatments slightly enhanced the WPC samples' antioxidant activities. The US exposure for 15 min exhibited the highest 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) scavenging activity (12.12 mmol Trolox equivalent per gram). Moreover, US treatment for 10 min exhibited the highest in vitro antidiabetic properties (α-amylase and α-glucosidase inhibition), and dipeptidyl peptidase-IV inhibitory activity among all samples. In addition, the US for 10 min and SPD at 170°C showed the lowest median inhibitory concentration (IC 50) values for in vitro antihypercholesterolemic activities in terms of pancreatic lipase and cholesteryl esterase inhibition. Conclusively, these green techniques can be adapted in the preservation and processing of camel milk whey into active ingredients with high bioactive properties. The list of standard abbreviations for JDS is available at adsa.org/jds-abbreviations-24. Nonstandard abbreviations are available in the Notes. [ABSTRACT FROM AUTHOR]

Maintenance of mitochondrial homeostasis requires a plethora of coordinated quality control and adaptations' mechanisms in which mitochondrial proteases play a key role. Their activation or loss of function reverberate beyond local mitochondrial biochemical and metabolic remodelling into coordinated cellular pathways and stress responses that feedback onto the mitochondrial functionality and adaptability. Mitochondrial proteolysis modulates molecular and organellar quality control, metabolic adaptations, lipid homeostasis and regulates transcriptional stress responses. Defective mitochondrial proteolysis results in disease conditions most notably, mitochondrial diseases, neurodegeneration and cancer. Here, it will be discussed how mitochondrial proteases and mitochondria stress signalling impact cellular homeostasis and determine the cellular decision to survive or die, how these processes may impact disease etiopathology, and how modulation of proteolysis may offer novel therapeutic strategies. [ABSTRACT FROM AUTHOR]

Proteins are essential molecular actors in every cellular process. From their synthesis to their degradation, they are subject to continuous quality control mechanisms to ensure that they fulfil cellular needs in proper and timely fashion. Proteostasis is a key process allowing cells or organisms to maintain an appropriate but dynamic equilibrium of their proteome (the ensemble of all their proteins). It relies on multiple mechanisms that together control the level, fate and function of individual proteins, and ensure elimination of abnormal ones. The proteostasis network is essential for development and adaptation to environmental changes or challenges. Its dysfunctions can lead to accumulation of deleterious proteins or, conversely, to excessive degradation of beneficial ones, and are implicated in many diseases such as cancers, neurodegeneration, or developmental and aging disorders. Manipulating this network to control abundance of selected target proteins is therefore a strategy with enormous therapeutic or biotechnological potential. The ProteoCure COST Action gathers more than 350 researchers and their teams (31 countries represented) from the academic, clinical, and industrial sectors, who share the conviction that our understanding of proteostasis is mature enough to develop novel and highly specific therapies based on selective tuning of protein levels. Towards this objective, the Action organizes community-building activities to foster synergies among its participants and reinforce training of the next generation of European researchers. Its ambition is to function as a knowledge-based network and a creative exchange hub on normal and pathologic proteostasis, focusing on developing innovative tools modulating the level of specific protein(s). [Display omitted] • The ProteoCure COST Action gathers European researchers. • More than 350 academic, clinician, and company laboratories join forces. • The focus is in novel therapies manipulating the proteolytic machinery. • COST funds allow organisation of a wide range of networking activities. • ProteoCure's main target: proteostasis malfunctions contributing to human diseases. [ABSTRACT FROM AUTHOR]

Cathepsins, a family of lysosomal peptidases, play a crucial role in maintaining cellular homeostasis by regulating protein turnover and degradation as well as many specific regulatory actions that are important for proper cell function and human health. Alterations in the activity and expression of cathepsins have been observed in many diseases such as cancer, inflammation, neurodegenerative disorders, bone remodelling-related conditions and others. These changes are not exclusively harmful, but rather appear to be a compensatory response on the lack of one cathepsin in order to maintain tissue integrity. The upregulation of specific cathepsins in response to the inhibition or dysfunction of other cathepsins suggests a fine-tuned system of proteolytic balance and understanding the compensatory role of cathepsins may improve therapeutic potential of cathepsin's inhibitors. Selectively targeting one cathepsin or modulating their activity could offer new treatment strategies for a number of diseases. This review emphasises the need for comprehensive research into cathepsin biology in the context of disease. The identification of the specific cathepsins involved in compensatory responses, the elucidation of the underlying molecular mechanisms and the development of targeted interventions could lead to innovative therapeutic approaches. [Display omitted] [ABSTRACT FROM AUTHOR]

The proteostasis network and associated protein quality control (PQC) mechanisms ensure proteome functionality and are essential for cell survival. A distinctive feature of eukaryotic cells is their high degree of compartmentalization, requiring specific and adapted proteostasis networks for each compartment. The nucleus, essential for maintaining the integrity of genetic information and gene transcription, is one such compartment. While PQC mechanisms have been investigated for decades in the cytoplasm and the endoplasmic reticulum, our knowledge of nuclear PQC pathways is only emerging. Recent developments in the field have underscored the importance of spatially managing aberrant proteins within the nucleus. Upon proteotoxic stress, misfolded proteins and PQC effectors accumulate in various nuclear membrane-less organelles. Beyond bringing together effectors and substrates, the biophysical properties of these organelles allow novel PQC functions. In this review, we explore the specificity of the nuclear compartment, the effectors of the nuclear proteostasis network, and the PQC roles of nuclear membrane-less organelles in metazoans. [Display omitted] • The nuclear proteostasis network is spatially organized, safeguarding nuclear functions during adverse conditions. • Biocondensates are crucibles for nuclear protein quality control (PQC), concentrating both substrates and PQC effectors. • The properties of the nucleolus provide multiple PQC functions and mitigate the toxicity of aberrant proteins. • Transient storage into MLOs preserves the nuclear proteostasis network and allows efficient recovery of nuclear functions when the stress subsides. • The nucleus contains a number of non-canonical chaperones reflecting the specificity of this compartment. [ABSTRACT FROM AUTHOR]

PA28γ is a proteasomal interactor whose main and most known function is to stimulate the hydrolytic activity of the 20 S proteasome independently of ubiquitin and ATP. Unlike its two paralogues, PA28α and PA28β, PA28γ is largely present in the nuclear compartment and plays pivotal functions in important pathways such as cellular division, apoptosis, neoplastic transformation, chromatin structure and organization, fertility, lipid metabolism, and DNA repair mechanisms. Although it is known that a substantial fraction of PA28γ is found in the cell in a free form (i.e. not associated with 20 S), almost all of the studies so far have focused on its ability to modulate proteasomal enzymatic activities. In this respect, the ability of PA28γ to strongly stimulate degradation of proteins, especially if intrinsically disordered and therefore devoid of three-dimensional tightly folded structure, appears to be the main molecular mechanism underlying its multiple biological effects. Initial studies, conducted more than 20 years ago, came to the conclusion that among the many biological functions of PA28γ, the immunological ones were rather limited and circumscribed. In this review, we focus on recent evidence showing that PA28γ fulfills significant functions in cell-mediated acquired immunity, with a particular role in attenuating MHC class I antigen presentation, especially in relation to neoplastic transformation and autoimmune diseases. [ABSTRACT FROM AUTHOR]

Cathepsin D (CTSD) is a lysosomal aspartic protease and its inherited deficiency causes a severe pediatric neurodegenerative disease called neuronal ceroid lipofuscinosis (NCL) type 10. The lysosomal dysfunction in the affected patients leads to accumulation of undigested lysosomal cargo especially in none-dividing cells, such as neurons, resulting in death shortly after birth. To explore which proteins are mainly affected by the lysosomal dysfunction due to CTSD deficiency, Lund human mesencephalic (LUHMES) cells, capable of inducible dopaminergic neuronal differentiation, were treated with Pepstatin A. This inhibitor of "acidic" aspartic proteases caused accumulation of acidic intracellular vesicles in differentiating LUHMES cells. Pulse-chase experiments involving stable isotope labelling with amino acids in cell culture (SILAC) with subsequent mass-spectrometric protein identification and quantification were performed. By this approach, we studied the degradation and synthesis rates of 695 and 680 proteins during early and late neuronal LUHMES differentiation, respectively. Interestingly, lysosomal bulk proteolysis was not altered upon Pepstatin A treatment. Instead, the protease inhibitor selectively changed the turnover of individual proteins. Especially proteins belonging to the mitochondrial energy supply system were differentially degraded during early and late neuronal differentiation indicating a high energy demand as well as stress level in LUHMES cells treated with Pepstatin A. [Display omitted] • Cathepsin D (CTSD) expression increased upon in vitro neuronal differentiation of human dopaminergic LUHMES cells. • Data on turnover kinetics of nearly 700 proteins upon CTSD inhibition are reported. • No effect of CTSD inhibition on overall protein turnover in differentiating LUHMES cells. • Yet, upon CTSD inhibition turnover of individual proteins was either decreased or – interestingly-increased. • Specifically, CTSD inhibition stabilized proteins of the vesicular cell compartment in late differentiation. [ABSTRACT FROM AUTHOR]

Many proteins have been identified subject to ubiquitin (Ub)-independent proteasome degradation (UbIPD), a process mediated by Ub-like (UBL) proteins. UBL-conjugates can be processed by 19S proteasomes by mechanisms different from Ub-conjugates and by proteasome activator 28γ, which was previously thought to work as an activator of UbIPD. Ub and UBLs coordinate proteasome degradation to maintain protein homeostasis. UBL proteins, enzymes and modification substrates are tightly associated with proteostasis in muscle and neurodegenerative diseases. Although it is believed that ubiquitin (Ub) modification is required for protein degradation in the proteasome system (UPS), several proteins are subject to Ub-independent proteasome degradation, and in many cases ubiquitin-like (UBL) modifications, including neddylation, FAT10ylation, SUMOylation, ISGylation, and urmylation, are essential instead. In this Review, we focus on UBL-dependent proteasome degradation (UBLPD), on proteasome regulators especially shuttle factors and receptors, as well as potential competition and coordination with UPS. We propose that there is a distinct UBL–proteasome system (UBLPS) that might be underestimated in protein degradation. Finally, we investigate the association of UBLPD with muscle wasting and neurodegenerative diseases in which the proteasome is abnormally activated and impaired, respectively, and suggest strategies to modulate UBLPD for disease therapy. [ABSTRACT FROM AUTHOR]

SUMMARY: Arabidopsis uracil phosphoribosyltransferase (UPP) is an essential enzyme and plants lacking this enzyme are strongly compromised in chloroplast function. Our analysis of UPP amiRNA mutants has confirmed that this vital function is crucial to establish a fully functional photosynthesis as the RIESKE iron sulfur protein (PetC) is almost absent, leading to a block in photosynthetic electron transport. Interestingly, this function appears to be unrelated to nucleotide homeostasis since nucleotide levels were not altered in the studied mutants. Transcriptomics and proteomic analysis showed that protein homeostasis but not gene expression is most likely responsible for this observation and high light provoked an upregulation of protease levels, including thylakoid filamentation temperature‐sensitive 1, 5 (FtsH), caseinolytic protease proteolytic subunit 1 (ClpP1), and processing peptidases, as well as components of the chloroplast protein import machinery in UPP amiRNA lines. Strongly reduced PetC amounts were not only detected by immunoblot from mature plants but in addition in a de‐etiolation experiment with young seedlings and are causing reduced high light‐induced non‐photochemical quenching Φ(NPQ) but increased unregulated energy dissipation Φ(NO). This impaired photosynthesis results in an inability to induce flavonoid biosynthesis. In addition, the levels of the osmoprotectants raffinose, proline, and fumarate were found to be reduced. In sum, our work suggests that UPP assists in stabilization PetC during import, processing or targeting to the thylakoid membrane, or protects it against proteolytic degradation. Significance Statement: The moonlighting enzyme uracil phosphoribosyltransferase from Arabidopsis is an essential protein. By in‐depth analysis of knockdown mutants, we observed disrupted chloroplast proteostasis, characterized by altered amounts of proteins in the categories protein import, processing, folding, and degradation, accompanied by massively reduced amounts of the PetC (Rieske) subunit of the cytochrome b6/f complex. [ABSTRACT FROM AUTHOR]

Developing resistance to cancer treatments is a major challenge, often leading to disease recurrence and metastasis. Understanding the underlying mechanisms of therapeutic resistance is critical for developing effective strategies. O-GlcNAcylation, a post-translational modification that adds GlcNAc from the donor UDP-GlcNAc to serine and threonine residues of proteins, plays a crucial role in regulating protein function and cellular signaling, which are frequently dysregulated in cancer. Similarly, ubiquitination, which involves the attachment of ubiquitin to to proteins, is crucial for protein degradation, cell cycle control, and DNA repair. The interplay between O-GlcNAcylation and ubiquitination is associated with cancer progression and resistance to treatment. This review discusses recent discoveries regarding the roles of O-GlcNAcylation and ubiquitination in cancer resistance, their interactions, and potential mechanisms. It also explores how targeting these pathways may provide new opportunities to overcome cancer treatment resistance in cancer, offering fresh insights and directions for research and therapeutic development. [ABSTRACT FROM AUTHOR]

• HDAC6 expression was higher in endometriotic lesions of deep-infiltrating endometriosis, in both, epithelium and stroma, compared to the other endometriosis subtypes. • In ARID1A negative cases, epithelial expression of HDAC6 was higher in endometriotic lesions compared to eutopic endometrium of women without endometriosis. • There were no significant differences in the stromal expression of HDAC6. Endometriosis is a disease affecting approximately 10% of reproductive age women. Loss of the tumor suppressor gene AT-rich interactive domain-containing protein 1A (ARID1A) occurs in some endometriosis cases. Histone deacetylase 6 (HDAC-6) is an enzyme with implication in several diseases including different cancer types and immunological disorders, where it is involved in protein trafficking and degradation, cell shape, and migration. In ARID1A-deficient ovarian cancer increased HDAC-6 expression lead to apoptosis-inhibiting post-translational modification of p53. It is not known if HDAC-6 expression is also altered in ARID1A-deficient endometriosis. The aim of this study was to assess HDAC-6 expression in endometriotic lesions in correlation to ARID1A-status. Two tissue-microarrays with 168 endometriotic lesions, including ovarian (64/168, 38 %), peritoneal (66/168, 39 %) and deep-infiltrating (38/168, 23 %) subtypes, and 73 endometrium of women without endometriosis were assessed. Mean ARID1A immunoreactivity score (IRS) in endometriosis group was 10.83 (±2.36) and 10.78 (±1.94) in the epithelium and stroma, respectively, while the respective mean HDAC6 IRS were 9.16 (±2.76) and 5.94 (±2.88). The comparison of the HDAC6 expression between endometriosis subtypes showed higher expression in deep-infiltrating endometriosis, in both, epithelium (p = 0.032) and stroma (p = 0.007). In ARID1A negative cases, epithelial expression of HDAC6 was higher in endometriosis compared to women without endometriosis (p = 0.031), and this was also specifically observed in the subset of ovarian endometriosis (p = 0.037). There were no significant differences in the stromal expression of HDAC6. In conclusion, our results demonstrate a complex expression pattern of HDAC6 depending on ARID1A status in different endometriosis subtypes. Further studies on HDAC6 and ARID1A are important to elucidate mechanisms involved in malignant transformation of endometriosis. [ABSTRACT FROM AUTHOR]

Summary: The present study aims to provide an overview of the impact of brown rice protein (BRP) conjugated with microcrystalline cellulose via the Maillard reaction on characteristic features of yoghurt and the bioaccessibility of essential minerals in this dairy product. The confirmation of conjugation was conducted using FTIR spectroscopy. Adding BRP or Maillard conjugate (MC) proved beneficial in enhancing the water‐holding capacity and decreasing the syneresis of samples. Additionally, yoghurt (MCY) containing the Maillard conjugate demonstrated superior performance in these properties. A lower number of pores and a stronger gel network (structural integrity) were identified in MCY compared to the other samples (BRPY: yoghurt containing BRP and PY: plain yoghurt). On the other hand, in general, supplementation of BRP and MC led to slight alteration in the concentration of aroma compounds. Similarly, the impact of BRP and MC on changes in the molecular weight distribution of proteins during in vitro gastrointestinal digestion was negligible. Bioaccessibility values of Ca and Mg in PY were 53.72% and 10.72%, respectively. The improvement in these values was observed in BRPY (Ca: 57.33% and Mg: 15.60%). Moreover, adding MC to yoghurt led to a tighter interface structure (indicating rigid gel), which allowed more minerals to bind, increasing mineral bioaccessibility (Ca: 64.40% and Mg: 31.14%). A higher general acceptability in sensory evaluation was scored for PY followed by MCY and BRPY. Ultimately, the positive effect of ingredients (especially MC) on yoghurt quality was obvious. [ABSTRACT FROM AUTHOR]

Heat stress can impair organismal growth by inducing ubiquitination, proteasome-mediated degradation, and subsequent cellular damage. Vitamin C (VC) has been shown to potentially mitigate the detrimental effects of abiotic stresses on cells. Nevertheless, the impact of heat stress on growth plate chondrocytes remains unclear, and the underlying protective mechanisms of VC in these cells warrant further investigation. In this study, we focused on pig thoracic vertebral chondrocytes (PTVCs) that are crucial for promoting the body's longitudinal elongation and treated them with 41 °C heat stress for 24 h, under varying concentrations of VC. Our findings reveal that, while oxidative stress induced by heat triggers apoptosis and inhibits the ubiquitin-mediated proteolysis pathway, the addition of VC alleviates heat-stress-induced oxidative stress and apoptosis, mitigates cell cycle arrest, and promotes cellular viability. Furthermore, we demonstrate that VC enhances the ubiquitin-proteasome proteolysis pathway by promoting the expression of ubiquitin protein ligase E3A, which thereby stabilizes the ubiquitin-mediated degradation machinery, alleviates the apoptosis, and enhances cell proliferation. Our results suggest the involvement of the ubiquitin-mediated proteolysis pathway in the effects of VC on PTVCs under heat stress, and offer a potential strategy to make use of VC to ensure the skeletal growth of animals under high temperature pressures in summer or in tropical regions. [ABSTRACT FROM AUTHOR]

To uncover the possible role of TRAF3IP3 in the progression of myocardial infarction (MI), clarify its role in mitophagy and mitochondrial function, and explore the underlying mechanism. GEO chip analysis, RT-qPCR, and LDH release assay were used to detect the expression of TRAF3IP3 in tissues and cells and its effects on cell damage. Immunostaining and ATP product assays were performed to examine the effects of TRAF3IP3 on mitochondrial function. Co-IP, CHX assays, Immunoblot and Immunostaining assays were conducted to determine the effects of TRAF3IP3 on mitophagy. TRAF3IP3 was highly expressed in IR rats and HR-induced H9C2 cells. TRAF3IP3 knockdown can alleviate H/R-induced H9C2 cell damage. In addition, TRAF3IP3 knockdown can induce mitophagy, thus enhancing mitochondrial function. We further revealed that TRAF3IP3 can promote the degradation of NEDD4 protein. Moreover, TRAF3IP3 knockdown suppressed myocardial injury in I/R rats. TRAF3IP3 blocks mitophagy to exacerbate myocardial injury induced by I/R via mediating NEDD4 expression. [ABSTRACT FROM AUTHOR]

Background: Researching medical sample storage is crucial for maintaining the integrity of biological specimens and ensuring the accuracy of research investigations and diagnostic tests. Improper storage conditions can lead to sample degradation, compromising the reliability of results. Standardized storage procedures are essential for quality control, particularly in multicenter trials where samples are collected and processed at various locations. Moreover, ethical considerations dictate careful handling of patient samples to uphold privacy and rights. Methods: This study focuses on the surface phenotype of T cells, which is vital for diagnosing immunodeficiency disorders and autoimmune diseases and for monitoring disease activity and treatment efficacy. The effect of storage duration on T cell surface proteins is multifactorial, influenced by factors like protein degradation, cellular metabolism, and cytokine release. Long-term storage can lead to the gradual loss of T cell function, necessitating techniques to preserve cell activity. Changes in surface markers can affect disease diagnosis, emphasizing the importance of accurate sample processing. Results: Findings from this study reveal time-dependent changes in T cell surface markers during storage. CD3 levels declined significantly after the fourth day, with FITC labeling proving superior to APC. CD4 levels remained consistent until the fourth day, contrasting with previous findings on foreskin tissue. HLA-DR levels declined rapidly, indicating unsuitability for storage, consistent with other studies on cryopreserved cells. CD16 and CD8 levels decreased gradually, while CD56 declined rapidly after the third day, consistent with recent research. Conclusions: There were detectable and significant differences after the samples were stored for an improper period, which may have affected the integrity of the results, suggesting that understanding the factors influencing T cell surface protein changes during storage is crucial for maintaining result integrity. [ABSTRACT FROM AUTHOR]

The impact of heat treatment, pH and phytic acid (PA) concentration on the aggregation behavior and digestibility of whey protein isolate (WPI) was investigated. The experimental results indicated that below the isoelectric point of WPI, heat treatment and elevated PA levels significantly increased turbidity and particle size, leading to the aggregation of WPI molecules. No new chemical bonds were formed and the thermodynamic parameters ΔH < 0, ΔS > 0 and ΔG < 0 suggested that the interaction between PA and WPI was primarily a spontaneous electrostatic interaction driven by enthalpy. After the small intestine stage, increasing phytic acid levels resulted in a significant decrease in hydrolysis degree from 16.2 ± 1.5% (PA0) to 10.9 ± 1.4% (0.5% PA). Conversely, above isoelectric point of WPI, there was no significant correlation between the presence of PA and the aggregation behavior or digestion characteristics of WPI. These results were attributed to steric hindrance caused by PA-WPI condensates, which prevented protease binding to hydrolysis sites on WPI. In summary, the effect of PA on protein aggregation behavior and digestive characteristics was not simply dependent on its presence but largely on the aggregation degree of PA-WPI induced by heat treatment, pH and PA concentration. The findings obtained here suggested that phytic acid may be utilized as an agent to modulate the digestion characteristics of proteins according to production requirements. Additionally, the agglomerates formed by heating phytic acid and protein below the isoelectric point could also be utilized for nutrient delivery. [ABSTRACT FROM AUTHOR]

Pulsed electric field (PEF) is one of the emerging technologies that has been applied in many aspects of the food industry. This study examined the impacts of a PEF on the cooking quality, physicochemical properties, nutritional factors, and in vitro protein and starch digestion of two varieties of rice, including Jasmine 105 (white non-glutinous rice) and San Pa Tong 1 (white glutinous rice). Response surface methodology (RSM) and a three-level, three-factor Box–Behnken design were employed to assess the effects of the pulse number, electric field strength, and frequency on cooking time. The findings demonstrated that the number of pulses was a crucial factor influencing cooking time. Under optimal conditions (3347–4345 pulses, electric field strengths of 6–8 kV/cm, and frequencies ranging from 6 to 15 Hz), the rice cooking time was significantly reduced by 40–50% (p < 0.05) when compared to a conventional method. Moreover, PEF-treated rice showed a significant enhancement in in vitro protein and starch digestibility (p < 0.05), as well as retained a higher content of rapidly digestible starch. These results suggested that PEF treatment is a promising green technology for producing a novel quick-cooking rice with an improved eating quality. [ABSTRACT FROM AUTHOR]

Background: Acute and chronic pre-traumatic cigarette smoke exposure increases morbidity and mortality after trauma and hemorrhage. In mice with a genetic deletion of the H2S-producing enzyme cystathione-γ-lyase (CSE−/−), providing exogenous H2S using sodium thiosulfate (Na2S2O3) improved organ function after chest trauma and hemorrhagic shock. Therefore, we evaluated the effect of Na2S2O3 during resuscitation from blunt chest trauma and hemorrhagic shock on CSE−/− mice with pre-traumatic cigarette smoke (CS) exposure. Since H2S is well established as being able to modify energy metabolism, a specific focus was placed on whole-body metabolic pathways and mitochondrial respiratory activity. Methods: Following CS exposure, the CSE−/− mice underwent anesthesia, surgical instrumentation, blunt chest trauma, hemorrhagic shock for over 1 h (target mean arterial pressure (MAP) ≈ 35 ± 5 mmHg), and resuscitation for up to 8 h comprising lung-protective mechanical ventilation, the re-transfusion of shed blood, fluid resuscitation, and continuous i.v. noradrenaline (NoA) to maintain an MAP ≥ 55 mmHg. At the start of the resuscitation, the mice randomly received either i.v. Na2S2O3 (0.45 mg/gbodyweight; n = 14) or the vehicle (NaCl 0.9%; n = 11). In addition to the hemodynamics, lung mechanics, gas exchange, acid–base status, and organ function, we quantified the parameters of carbohydrate, lipid, and protein metabolism using a primed continuous infusion of stable, non-radioactive, isotope-labeled substrates (gas chromatography/mass spectrometry) and the post-mortem tissue mitochondrial respiratory activity ("high-resolution respirometry"). Results: While the hemodynamics and NoA infusion rates did not differ, Na2S2O3 was associated with a trend towards lower static lung compliance (p = 0.071) and arterial PO2 (p = 0.089) at the end of the experiment. The direct, aerobic glucose oxidation rate was higher (p = 0.041) in the Na2S2O3-treated mice, which resulted in lower glycemia levels (p = 0.050) and a higher whole-body CO2 production rate (p = 0.065). The mitochondrial respiration in the heart, kidney, and liver tissue did not differ. While the kidney function was comparable, the Na2S2O3-treated mice showed a trend towards a shorter survival time (p = 0.068). Conclusions: During resuscitation from blunt chest trauma and hemorrhagic shock in CSE−/− mice with pre-traumatic CS exposure, Na2S2O3 was associated with increased direct, aerobic glucose oxidation, suggesting a switch in energy metabolism towards preferential carbohydrate utilization. Nevertheless, treatment with Na2S2O3 coincided with a trend towards worsened lung mechanics and gas exchange, and, ultimately, shorter survival. [ABSTRACT FROM AUTHOR]

Plant-based foods offer a sustainable alternative to meet the growing protein demand. Legumes are the most promising of these, as they contain relatively high concentrations of protein, low digestible starch, and dietary fiber, as well as them possibly featuring low levels of fat. Enzymatically modified legume proteins provide us with tempting perspectives in terms of enhancing foods' biological values. However, their bioavailability and digestibility are generally less sufficient than that of proteins of animal origin, which may be improved by well-tailored enzyme modification. In this study, the efficacy of three plant-based proteases (bromelain, ficin, and papain) were evaluated at two distinct concentrations (2.5% and 10%) and three hydrolysis durations (1, 2, and 12 h) when transforming chickpea and lentil proteins. The degree of hydrolysis (DH), peptide profiles, and free amino acid content were analyzed to determine the efficiency of each enzyme. Results showed significant variations in DH, which was influenced by enzyme type, concentration, and hydrolysis duration. Papain exhibited the highest DH, particularly at a 10% concentration, reaching 27.8% efficiency in chickpea and 34.8% in lentils after 12 h. Bromelain and ficin were proven to be less effective, with ficin showing the least hydrolytic activity. SDS-PAGE analysis revealed substantial protein degradation, especially subsequent to papain treatment, pointing out that most proteins were cleaved into smaller peptides. SEC-HPLC indicated a predominant release of peptides within the 200–1000 Da range, suggesting enhanced bioavailability. Papain and bromelain treatments resulted in a significant release of oligopeptides and dipeptides. UHPLC analysis highlighted a marked post-hydrolysis increase in total free amino acids, with arginine, leucine, and lysine being the most abundant ones. Notably, tryptophan, being undetectable in untreated samples, was released in measurable amounts post-hydrolysis. These findings demonstrate papain's superior performance in protein hydrolysis and its potential in producing bioactive peptides, highlighting its applicability in food processing and the development of both nutraceuticals and functional foods. [ABSTRACT FROM AUTHOR]

Stress granules (SGs) are stress-induced RNA condensates consisting of stalled initiation complexes resulting from translational inhibition. The biochemical composition and function of SGs are highly diverse, and this diversity has been attributed to different stress conditions, signalling pathways involved and specific cell types. Interestingly, mRNA decay components, which are found in ubiquitous cytoplasmic foci known as processing bodies (PB), have also been identified in SG proteomes. A major challenge in current SG studies is to understand the cause of SG diversity, as well as the function of SG under different stress conditions. Trypanosoma brucei is a single-cellular parasite that causes Human African Trypanosomiasis (sleping sickness). In this study, we showed that by varying the supply of extracellular carbon sources during starvation, cellular ATP levels changed rapidly, resulting in SGs of different compositions and dynamics. We identified a subset of SG components, which dissociated from the SGs in response to cellular ATP depletion. Using expansion microscopy, we observed sub-granular compartmentalization of PB- and SG-components within the stress granules. Our results highlight the importance of cellular ATP in SG composition and dynamics, providing functional insight to SGs formed under different stress conditions. Author summary: Stress granules (SGs) and processing bodies (PBs) are cytoplasmic RNA granules containing multiple proteins with functions in translation initiation and mRNA degradation. mRNA and proteins can move between SGs, PBs and translating polysomes, likely regulating gene expression under different cellular conditions. However, little is known about the cellular factors regulating the dynamic behaviour of these RNA granules. In the unicellular Trypanosome parasites, SGs are formed under starvation stress and during differentiation. In this study, we found that in starved T. brucei, the composition and the dynamics of the SGs are distinct, depending on the supply of extracellular carbon sources and subsequent cellular energy (ATP) levels. Using expansion microscopy and super-resolution microscopy, functionally-distinct protein components are found in different sub-granular compartments within the SGs. Our findings emphasized the dynamic changes in SG composition, organization, and potential functions, which are affected by cellular ATP levels that can fluctuate under various stress conditions. [ABSTRACT FROM AUTHOR]

Multivesicular endosomes (MVEs) sequester membrane proteins destined for degradation within intralumenal vesicles (ILVs), a process mediated by the membrane-remodeling action of Endosomal Sorting Complex Required for Transport (ESCRT) proteins. In Arabidopsis, endosomal membrane constriction and scission are uncoupled, resulting in the formation of extensive concatenated ILV networks and enhancing cargo sequestration efficiency. Here, we used a combination of electron tomography, computer simulations, and mathematical modeling to address the questions of when concatenated ILV networks evolved in plants and what drives their formation. Through morphometric analyses of tomographic reconstructions of endosomes across yeast, algae, and various land plants, we have found that ILV concatenation is widespread within plant species, but only prevalent in seed plants, especially in flowering plants. Multiple budding sites that require the formation of pores in the limiting membrane were only identified in hornworts and seed plants, suggesting that this mechanism has evolved independently in both plant lineages. To identify the conditions under which these multiple budding sites can arise, we used particle-based molecular dynamics simulations and found that changes in ESCRT filament properties, such as filament curvature and membrane binding energy, can generate the membrane shapes observed in multiple budding sites. To understand the relationship between membrane budding activity and ILV network topology, we performed computational simulations and identified a set of membrane remodeling parameters that can recapitulate our tomographic datasets. [ABSTRACT FROM AUTHOR]

Trichomes are specialized hair-like structures in the epidermal cells of the above-ground parts of plants and help to protect them from pests and pathogens, and produce valuable metabolites. Chrysanthemum morifolium , which is used in tea products, has both ornamental and medicinal value; however, it is susceptible to infection by the fungus Alternaria alternata , which can result in substantial economic losses. Increasing the density of glandular trichomes enhances disease resistance and improves the production of medicinal metabolites in chrysanthemums, and jasmonate (JA) is known to promote the formation of trichomes in various plants. However, it remains unclear whether glandular trichomes in chrysanthemums are regulated by JA. In addition, grafting, a technique that can improve plant resistance to biotic stresses, has been poorly examined for its impact on glandular trichomes, terpenoids, and disease resistance. In this study, we demonstrate that grafting with Artemisia vulgaris rootstocks improves the resistance of chrysanthemum scions to A. alternata. Heterografted chrysanthemums exhibited higher trichome density and terpenoid content compared to self-grafted counterparts. Transcriptome analysis highlighted the significant role of CmJAZ1-like in disease resistance in heterografted chrysanthemums. Lines overexpressing CmJAZ1-like exhibited sensitivity to A. alternata , and this was characterized by reduced glandular trichome density and limited terpenoid content. Conversely, CmJAZ1-like silenced lines exhibited resistance to A. alternata and showed increased glandular trichome density and terpenoid content. Higher JA content was found in the heterografted chrysanthemum scions compared to self-grafted ones. Furthermore, we established that JA promoted the development of glandular trichomes and the synthesis of terpenoids while also inducing the degradation of CmJAZ1-like proteins in chrysanthemums. Our findings suggest that higher JA increases trichome density and terpenoid content, thereby enhancing resistance to A. alternata by regulating CmJAZ1-like in heterografted chrysanthemums. [ABSTRACT FROM AUTHOR]

ABSTRACT Autophagy is a highly conserved cellular program in eukaryotic cells which mediates the degradation of cytoplasmic components through the lysosome, also named the vacuole in plants. However, the molecular mechanisms underlying the fusion of autophagosomes with the vacuole remain unclear. Here, we report the functional characterization of a rice (Oryza sativa) mutant with defects in storage protein transport in endosperm cells and accumulation of numerous autophagosomes in root cells. Cytological and immunocytochemical experiments showed that this mutant exhibits a defect in the fusion between autophagosomes and vacuoles. The mutant harbors a loss‐of‐function mutation in the rice homolog of Arabidopsis thaliana MONENSIN SENSITIVITY1 (MON1). Biochemical and genetic evidence revealed a synergistic interaction between rice MON1 and AUTOPHAGY‐RELATED 8a in maintaining normal growth and development. In addition, the rice mon1 mutant disrupted storage protein sorting to protein storage vacuoles. Furthermore, quantitative proteomics verified that the loss of MON1 function influenced diverse biological pathways including autophagy and vacuolar transport, thus decreasing the transport of autophagic and vacuolar cargoes to vacuoles. Together, our findings establish a molecular link between autophagy and vacuolar protein transport, and offer insights into the dual functions of the MON1–CCZ1 (CAFFEINE ZINC SENSITIVITY1) complex in plants. [ABSTRACT FROM AUTHOR]

Targeted protein degradation has been widely adopted as a new approach to eliminate both established and previously recalcitrant therapeutic targets. Here, it is reported that the development of small molecule degraders of the envelope (E) protein of dengue virus. Two classes of bivalent E‐degraders are developed by linking two previously reported E‐binding small molecules, GNF‐2, and CVM‐2‐12‐2, to a glutarimide‐based recruiter of the CRL4CRBN ligase to effect proteosome‐mediated degradation of the E protein. ZXH‐2‐107 (based on GNF‐2) is an E‐degrader with ABL inhibitory activity while ZXH‐8‐004 (based on CVM‐2‐12‐2) is a selective and potent E‐degrader. These two compounds provide proof of concept that difficult‐to‐drug targets such as a viral envelope protein can be effectively eliminated using a bivalent degrader and provide starting points for the future development of a new class of direct‐acting antiviral drugs. [ABSTRACT FROM AUTHOR]

Quantitative protein mass spectrometry (MS) is ideally suited for precision diagnostics and for reference standardization of protein analytes. At the Leiden Apolipoprotein Reference Laboratory we apply MS strategies to obtain detailed insight into the protein-to-peptide conversion in order to verify that quantifier peptides are not partly concealed in miscleaved protein backbone.Apolipoprotein(a) (apo(a)) was digested in a non-optimal manner to enhance the number of miscleaved peptides that were identified by high resolution liquid chromatography tandem-MS measurements. The protein-to-peptide conversion was carefully mapped with specific attention for miscleaved peptides that contain an apo(a) quantifier peptide. Four different isotopologues of each apo(a)-quantifier peptide were applied to evaluate linearity of internal peptide standards during measurement of specific real-life samples.Two apo(a) quantifier peptides that were concealed in two different miscleaved peptides were included into a multiple reaction monitoring list in our targeted MS-based apo(a) quantifications to alert for potential protein digestion discrepancies. The presence of miscleaved peptides could be ruled out when applying our candidate reference measurement procedure (RMP) for apo(a) quantification.These data further corroborate the validity of our apo(a) candidate RMP as higher order method for certification of commercial Lp(a) tests that is endorsed by the International Federation of Clinical Chemistry and Laboratory Medicine. MS-based molecular detection and quantification of heterogeneous apo(a) proteoforms will allow manufacturers’ transitioning from confounded lipoprotein(a) [Lp(a)] mass levels into accurate molar apo(a) levels. [ABSTRACT FROM AUTHOR]

Signal peptide peptidase-like 2c (SPPL2c) is a testis-specific aspartyl intramembrane protease that contributes to male gamete function both by catalytic and non-proteolytic mechanisms. Here, we provide an unbiased characterisation of the in vivo interactome of SPPL2c identifying the ER chaperone calnexin as novel binding partner of this enzyme. Recruitment of calnexin specifically required the N-glycosylation within the N-terminal protease-associated domain of SPPL2c. Importantly, mutation of the single glycosylation site of SPPL2c or loss of calnexin expression completely prevented SPPL2c-mediated intramembrane proteolysis of all tested substrates. By contrast and despite rather promiscuous binding of calnexin to other SPP/SPPL proteases, expression of the chaperone was exclusively required for SPPL2c-mediated proteolysis. Despite some impact on the stability of SPPL2c most presumably due to assistance in folding of the luminal domain of the protease, calnexin appeared to be recruited rather constitutively to the protease thereby boosting its catalytic activity. In summary, we describe a novel, highly specific mode of intramembrane protease regulation, highlighting the need to systematically approach control mechanisms governing the proteolytic activity of other members of the aspartyl intramembrane protease family. [ABSTRACT FROM AUTHOR]

The acute exacerbation of chronic obstructive pulmonary disease seriously affects the respiratory system function and quality of life of patients. This study employed 16S rRNA sequencing and metabolomics techniques to analyze the respiratory microbiota and serum metabolites of COPD and AECOPD patients. The results showed that the microbial diversity in the respiratory tract of AECOPD patients was significantly lower than that of COPD patients, and the relative abundance of Bacteroidetes, Prevotella and Neisseria in the respiratory tract of AECOPD patients was significantly lower than that of COPD patients. However, the relative abundance of Haemophilus_D, Veillonella_A and Pseudomonas_E, in AECOPD patients was significantly higher than that of COPD patients, and the ability of respiratory microbiota in AECOPD patients to participate in alanine metabolism was significantly lower than that of COPD patients. Metabolome results further revealed that the serum alanine levels in AECOPD patients were significantly lower than those in COPD patients, and these differential metabolites were mainly involved in linoleic acid metabolism, protein digestion and absorption and regulation of lipolysis in adipocytes. In summary, the structural characteristics of respiratory microbiota in COPD and AECOPD patients are different from those in healthy populations, and their microbiota diversity decreases and microbial community structure and function will also undergo changes when acute exacerbations occur. In addition, the predicted microbial community function and metabolomics results indicate that the onset of AECOPD is mainly related to energy and amino acid metabolism disorders, especially alanine metabolism. [ABSTRACT FROM AUTHOR]

The Golgi apparatus is essential for protein sorting, yet its quality control mechanisms are poorly understood. Here we show that the Dsc ubiquitin ligase complex uses its rhomboid pseudo-protease subunit, Dsc2, to assess the hydrophobic length of α-helical transmembrane domains (TMDs) at the Golgi. Thereby the Dsc complex likely interacts with orphaned ER and Golgi proteins that have shorter TMDs and ubiquitinates them for targeted degradation. Some Dsc substrates will be extracted by Cdc48 for endosome and Golgi associated proteasomal degradation (EGAD), while others will undergo ESCRT dependent vacuolar degradation. Some substrates are degraded by both, EGAD- or ESCRT pathways. The accumulation of Dsc substrates entails a specific increase in glycerophospholipids with shorter and asymmetric fatty acyl chains. Hence, the Dsc complex mediates the selective degradation of orphaned proteins at the sorting center of cells, which prevents their spreading across other organelles and thereby preserves cellular membrane protein and lipid composition. At the Golgi, the Dsc ubiquitin ligase complex targets proteins with shorter transmembrane domains for proteasomal or lysosomal degradation. This quality control at the sorting center of cells restricts the uncontrolled spreading of orphaned proteins. [ABSTRACT FROM AUTHOR]

We prepared novel plasmon-coupled silver (Ag) and silver oxide (Ag2O) nanoparticles using green synthesis and a magnetic stirrer device from lemon juice. Firstly, we prepared six Ag samples from green tea and lemon juice, characterized by XRD, FTIR, UV, and HRTEM. We selected just two samples to apply to MDA-MB-231 cells. The samples entered the cell through endocytosis, showed moderate cytotoxicity and ROS levels, caused cell growth arrest at the G2M phase, exhibited higher inhibition of Cyclin D1, and induced early apoptosis. β-Catenin is an abundant protein in triple-negative breast cancer TNBC. Both samples showed inhibition of the β-catenin proteins pathway. Plasmon-coupled nanoparticles effectively inhibited β-catenin, physically capturing β-catenin and its pathway proteins, mimicking the action of a degradation protein complex due to their geometric properties. The prepared materials could be considered a promising treatment for TNBC that has not responded to chemotherapy and radiotherapy. As they have low toxicity to normal cells; this paves the way for new material designs without strict size limitations. [ABSTRACT FROM AUTHOR]

Liquid–liquid phase separation has emerged as a crucial mechanism driving the formation of membraneless biomolecular condensates, which play important roles in numerous cellular processes. These condensates, found both in the nucleus and cytoplasm, are formed through multivalent, low-affinity interactions between various molecules. P62-containing condensates serve, among other functions, as proteolytic hubs for the ubiquitin–proteasome system. In this study, we investigated the dynamic interplay between nuclear p62 condensates and promyelocytic nuclear bodies (PML-NBs). We show that p62 condensates stabilize PML-NBs under both basal conditions and following exposure to arsenic trioxide which stimulates their degradation. We further show that this effect on the stability of PML-NBs is due to sequestration of their ubiquitin E3 ligase RNF4 in the p62 condensates with subsequent rapid degradation of the ligase. The sequestration of the ligase is made possible by association between the proline-rich domain of the PML protein and the PB1 domain of p62, which results in the formation of a PML-NB shell around the p62 condensates. Importantly, these hybrid structures do not undergo fusion and mixing of their contents which leaves unsolved the mechanism of sequestration of RNF4 in the condensates. These findings suggest an additional possible mechanism of PML-NB as a tumor suppressor which is mediated via interactions between different biomolecular condensates. [ABSTRACT FROM AUTHOR]

Myeloid leukemia factor 1 (Mlf1) was identified as a proto-oncoprotein that affects hematopoietic differentiation in humans. However, its cellular function remains elusive, spanning roles from cell cycle regulation to modulation of protein aggregate formation and participation in ciliogenesis. Given that structurally conserved homologs of Mlf1 can be found across the eukaryotic tree of life, we decided to characterize its cellular role underlying this phenotypic pleiotropy. Using a model of the unicellular eukaryote Giardia intestinalis, we demonstrate that its Mlf1 homolog (GiMlf) mainly localizes to two types of cytosolic foci: microtubular structures, where it interacts with Hsp40, and ubiquitin-rich, membraneless compartments, found adjacent to mitochondrion-related organelles known as mitosomes, containing the 26S proteasome regulatory subunit 4. Upon cellular stress, GiMlf either relocates to the affected compartment or disperses across the cytoplasm, subsequently accumulating into enlarged foci during the recovery phase. In vitro assays suggest that GiMlf can be recruited to membranes through its affinity for signaling phospholipids. Importantly, cytosolic foci diminish in the gimlf knockout strain, which exhibits extensive proteomic changes indicative of compromised proteostasis. Consistent with data from other cellular systems, we propose that Mlf acts in the response to proteotoxic stress by mediating the formation of function-specific foci for protein folding and degradation. Author summary: Giardia intestinalis, a widespread intestinal parasite, has emerged as a valuable model for studying eukaryotic cell biology and host-pathogen interactions. Our study focuses on the Myeloid Leukemia Factor (Mlf) homolog in Giardia (GiMlf), an evolutionarily conserved protein with diverse cellular functions. We demonstrate that GiMlf plays a crucial role in proteostasis by forming two types of cytosolic foci: one associated with microtubular structures and Hsp40, and another comprising ubiquitin-rich, membraneless compartments near mitosomes, containing the 26S proteasome regulatory subunit. Upon cellular stress, GiMlf dynamically relocates, suggesting its involvement in the stress response. Notably, GiMlf knockout leads to extensive proteomic changes and altered encystation rates, indicating its importance in Giardia's life cycle and stress adaptation. Our findings provide insights into how Giardia, and potentially other eukaryotes, maintain proteostasis under various environmental conditions. This research enhances our understanding of fundamental parasite biology and stress response mechanisms, which are critical for pathogen survival in diverse host environments. [ABSTRACT FROM AUTHOR]

Peroxisome proliferator‐activated receptor gamma coactivator 1‐alpha (PGC‐1α) is a key regulator of mitochondrial biogenesis and antioxidative defenses, and it may play a critical role in Parkinson's disease (PD). F‐box/WD repeat domain‐containing protein (FBXW7), an E3 protein ligase, promotes the degradation of substrate proteins through the ubiquitin‐proteasome system (UPS) and leads to the clearance of PGC‐1α. Here, we elucidate a novel post‐translational mechanism for regulating PGC‐1α levels in neurons. We show that enhancing chaperone‐mediated autophagy (CMA) activity promotes the CMA‐mediated degradation of FBXW7 and consequently increases PGC‐1α. We confirm the relevance of this pathway in vivo by showing decreased FBXW7 and increased PGC‐1α as a result of boosting CMA selectively in dopaminergic (DA) neurons by overexpressing lysosomal‐associated membrane protein 2A (LAMP2A) in TH‐Cre‐LAMP2‐loxp conditional mice. We further demonstrate that these mice are protected against MPTP‐induced oxidative stress and neurodegeneration. These results highlight a novel regulatory pathway for PGC‐1α in DA neurons and suggest targeted increasing of CMA or decreasing FBXW7 in DA neurons as potential neuroprotective strategies in PD. [ABSTRACT FROM AUTHOR]

The ubiquitin-proteasome system (UPS) plays crucial roles in cellular processes including plant growth, development, and stress responses. In this study, we report that a pair of E3 ubiquitin ligases, AvrPiz-t-interaction protein 6 (APIP6) and IPA1-interaction protein 1 (IPI1), intricately target early flowering3 (ELF3) paralogous proteins to control rice immunity and flowering. APIP6 forms homo-oligomers or hetero-oligomers with IPI1. Both proteins interact with OsELF3-2, promoting its degradation to positively control resistance against the rice blast fungus (Magnaporthe oryzae). Intriguingly, overexpression of IPI1 in Nipponbare caused significantly late-flowering phenotypes similar to the oself3-1 mutant. Except for late flowering, oself3-1 enhances resistance against M. oryzae. IPI1 also interacts with and promotes the degradation of OsELF3-1, a paralog of OsELF3-2. Notably, IPI1 and APIP6 synergistically modulate OsELF3s degradation, finely tuning blast disease resistance by targeting OsELF3-2, while IPI1 controls both disease resistance and flowering by targeting OsELF3-1. This study unravels multiple functions for a pair of E3 ligases in rice. [Display omitted] • APIP6 forms homo-oligomers with itself and hetero-oligomers with IPI1 • Both APIP6 and IPI1 promote OsELF3-2 degradation to enhance rice immunity • IPI1 targets OsELF3-1 to enhance immunity but negatively controls flowering • APIP6/IPI1 hetero-oligomers facilitate the degradation of ELF3 proteins in rice The pair of E3 ubiquitin ligases, APIP6 and IPI1, positively control rice immunity by promoting the degradation of OsELF3-2, while IPI1 delays flowering by destabilizing OsELF3-1. By forming hetero-oligomers, APIP6 and IPI1 synergistically control ELF3-mediated development and immunity in rice. [ABSTRACT FROM AUTHOR]

Taxadiene is an important precursor of paclitaxel. However, its low yield in eukaryotic systems limits its biosynthesis. This study found that the low yield of taxadiene is likely due to the degradation of expressed taxadiene synthase (TS) in Saccharomyces cerevisiae. The TS expression degradation problem was improved by the knockout of protease PRB1, and the yield of taxadiene was increased by 97% from 19.8 mg L−1 to 39.2 mg L−1. Furthermore, multi-copy integration of the TS gene and enhancement of the geranylgeranyl diphosphate (GGPP) precursor pathway increased the taxadiene titer to 282.4 mg L−1 in a shake flask. Interestingly, enhancing TS expression also decreased the competitive synthesis of geranylgeraniol (GGOH). Finally, the taxadiene titer reached 878.5 mg L−1 after optimising the fed-batch fermentation, which is the highest taxadiene titer reported for eukaryotic microbes. This study alleviated the problems associated with the expression and degradation of heterologous proteins and provided an efficient and green strategy to produce complex natural compounds. [ABSTRACT FROM AUTHOR]

NaCl is the main curing agent in dry-cured meat products, and a large amount of NaCl addition leads to high salt content of final products. Salt content and composition are important factors affecting the activity of endogenous proteases, which in turn could affect proteolysis as well as the quality of dry-cured meat products. With the increasing emphasis on the relationship between diet and health, reducing sodium content without sacrificing quality and safety of products is a great challenge for dry-cured meat industry. In this review, the change of endogenous proteases activity during processing, the potential relationship between sodium reduction strategy, endogenous proteases activity, and quality were summarized and discussed. The results showed that sodium replacement strategy and mediated-curing had a complementary advantage in influencing endogenous proteases activity. In addition, mediated-curing had the potential to salvage the negative effects of sodium substitution by affecting endogenous proteases. Based on the results, a sodium reduction strategy that sodium replacement in conjunction with mediated-curing based on endogenous proteases was proposed for the future perspective. [ABSTRACT FROM AUTHOR]