Protein Degradation Research Articles

Sensoproteomic Characterization of Lactobacillus Johnsonii-Fermented Pea Protein-Based Beverage: A Promising Strategy for Enhancing Umami and Kokumi Sensations while Mitigating Bitterness.

This study investigated the mechanism underlying the flavor improvement observed during fermentation of a pea protein-based beverage using Lactobacillus johnsonii NCC533. A combination of sensomics and sensoproteomics approach revealed that the fermentation process enriched or generated well-known basic taste ingredients, such as amino acids, nucleotides, organic acids, and dipeptides, besides six new taste-active peptide sequences that enhance kokumi and umami notes. The six new umami and kokumi enhancing peptides, with human recognition thresholds ranging from 0.046 to 0.555 mM, are produced through the degradation of Pisum sativum's storage protein. Our findings suggest that compounds derived from fermentation enhance umami and kokumi sensations and reduce bitterness, thus improving the overall flavor perception of pea proteins. In addition, the analysis of intraspecific variations in the proteolytic activity of L. johnsonii and the genome-peptidome correlation analysis performed in this study point at cell-wall-bound proteinases such as PrtP and PrtM as the key genes necessary to initiate the flavor improving proteolytic cascade. This study provides valuable insights into the molecular mechanisms underlying the flavor improvement of pea protein during fermentation and identifies potential future research directions. The results highlight the importance of combining fermentation and senso(proteo)mics techniques in developing tastier and more palatable plant-based protein products.

The Role of Ubiquitination in Osteosarcoma Development and Therapies

The ubiquitin–proteasome system (UPS) maintains intracellular protein homeostasis and cellular function by regulating various biological processes. Ubiquitination, a common post-translational modification, plays a crucial role in the regulation of protein degradation, signal transduction, and other physiological and pathological processes, and is involved in the pathogenesis of various cancers, including osteosarcoma. Osteosarcoma, the most common primary malignant bone tumor, is characterized by high metastatic potential and poor prognosis. It is a refractory bone disease, and the main treatment modalities are surgery combined with chemotherapy. Increasing evidence suggests a close association between UPS abnormalities and the progression of osteosarcoma. Due to the complexity and pleiotropy of the ubiquitination system, each step in the ubiquitination process can be targeted by drugs. In recent years, research and development of inhibitors targeting the ubiquitin system have increased gradually, showing great potential for clinical application. This article reviews the role of the ubiquitination system in the development and treatment of osteosarcoma, as well as research progress, with the hope of improving the therapeutic effects and prognosis of osteosarcoma patients by targeting effective molecules in the ubiquitination system.

P-442 Genome edition in endometrial stroma cells leading to decreased expression of UDP-glucuronic acid decarboxylase I (UXS1) alters the molecular interactions of the implantation area

Abstract Study question Does UDP-glucuronic acid decarboxylase 1 (UXS1) expression in endometrial stroma cells have a direct effect on the early stages of implantation? Summary answer Decreased expression of UXS1 was found to alter adhesion, invasion, development and function related genes of implantation in 3D cultures in a time dependent manner. What is known already The implantation process is governed by a complex interaction of genes and molecular pathways. Some of those genes are well-defined, however, as fertility problems increase with escalating rates of recurrent implantation failure or abortions, with an effort to reveal those genes that may be more significant than known for implantation RNA-seq analyses are used. UDP-glucuronic acid decarboxylase 1 (UXS1) is an enzyme involved in the detoxification and conversion of UDP-glucuronic acid to UDP-xylose. Loss of UXS1 led to defective glycosylation, increased protein degradation, and decreased overall protein levels, but no direct relation to has been stated before. Study design, size, duration Two different Matrigel based 3D culture systems were constructed with labeled mouse endometrium epithelial cells, stroma cells and blastocysts for 24-72 hours (n = 24). Sorted cells were sequenced for RNA for determination of differentially expressed genes. Of over 4000 genes, a highly expressed one was UXS1 in the endometrial stroma cells, The gene was knocked out via CRISPR/Cas9. The impact of decline of UXS1 in stroma cells on implantation parameters has been evaluated. Participants/materials, setting, methods CB6F1 female mice were superovulated. Blastocysts were obtained, endometrium was used for isolation of epithelial and stroma cells. 3D cultures were constructed for RNA-seq analysis. Three gRNAs were designed for CRISPR/Cas9 experiments. Cultures were constructed with knock out stroma and wild epithelial cells, wild blastocysts. On hours 24 and 72 of culture, gene and protein expression analyses for e-cadherin, MMP9, entactin, LIF; Hoxa10, Wnt4, ESR1, PR, fibronectin have been accomplished. Supported by TUBITAK 118S676. Main results and the role of chance All adherence molecules tested (e-cadherin, entactin, fibronectin) have shown significant increase compared to non targeted (the cell has Cas9, but no gRNA) groups (p < 0.00001). As e-cadherin has decreased detrimentally from 24 to 72 hours, fibronectin has continued to increase. LIF, an important gene for embryo-blastocyst interphase, has increased steeply and then decreased in the long term culture (p < 0.00001). ESR1 and PR (estrogen and progesterone receptors) increased compared to non-targeted groups but they were lower than the control groups with no genome edition (p < 0.01). The invasion gene MMP9 has increased steeply in the first 24 hours, then declined suddenly at hour 72 (p < 0.0001). The developmental genes Wnt4 and Hoxa10 were also affected significantly, as Wnt4 has decreased and Hoxa10 has increased compared to non-targeted groups (p < 0.001, p < 0.0001 respectively), however the expressions did not change from 24 to 72 hours. These findings were mostly supported by the protein expressions depicted by IF staining. The data can be interpreted as UXS1 has some fundamental effects during the implantation process as its decreased expression changes the adhesion and invasion patterns with unexpectedly high and low pattern, and it deteriorates differential expression of LIF during the critical interaction of endometrial cells and the blastocyst. Limitations, reasons for caution - This is a 3D in vitro implantation model constructed with mouse cells, so it cannot reflect in vivo process perfectly. - The genome edition of primary cells can show lower yield than cell lines. - There are numerous parameters of implantation, more tests can always be added. Wider implications of the findings - Data arising from various RNAseq analyses for implantation is accumulating and it is possible to find new genes and their connections and contribution can be revealed. - The new genes tested in vitro can further be re-examined in knock out mouse models or can be scanned in the abortus materials. Trial registration number not applicable

ATBS1-INTERACTING FACTOR 2 Positively Regulates Freezing Tolerance via INDUCER OF CBF EXPRESSION 1/C-REPEAT BINDING FACTOR-Induced Cold Acclimation Pathway.

The INDUCER OF CBF EXPRESSION 1/C-REPEAT BINDING FACTOR (ICE1/CBF) pathway plays a crucial role in plant responses to cold stress, impacting growth and development. Here, we demonstrated that ATBS1-INTERACTING FACTOR 2 (AIF2), a non-DNA-binding basic helix-loop-helix transcription factor, positively regulates freezing tolerance through the ICE1/CBF-induced cold tolerance pathway in Arabidopsis. Cold stress transcriptionally upregulated AIF2 expression and induced AIF2 phosphorylation, thereby stabilizing the AIF2 protein during early stages of cold acclimation. The AIF2 loss-of-function mutant, aif2-1, exhibited heightened sensitivity to freezing before and after cold acclimation. In contrast, ectopic expression of AIF2, but not the C-terminal-deleted AIF2 variant, restored freezing tolerance. AIF2 enhanced ICE1 stability during cold acclimation and promoted the transcriptional expression of CBFs and downstream cold-responsive genes, ultimately enhancing plant tolerance to freezing stress. MITOGEN-ACTIVATED PROTEIN KINASES 3 and 6 (MPK3/6), known negative regulators of freezing tolerance, interacted with and phosphorylated AIF2, subjecting it to protein degradation. Furthermore, transient co-expression of MPK3/6 with AIF2 and ICE1 downregulated AIF2/ICE1-induced transactivation of CBF2 expression. AIF2 interacted preferentially with BIN2 and MPK3/6 during the early and later stages of cold acclimation, respectively, thereby differentially regulating AIF2 activity in a cold acclimation time-dependent manner. Moreover, AIF2 acted additively in a gain-of-function mutant of BRASSINAZOLE-RESISTANT 1 (BZR1; bzr1-1D) and a triple knockout mutant of BRASSINOSTEROID-INSENSITIVE 2 (BIN2) and its homologs (bin2bil1bil2) to induce CBFs-mediated freezing tolerance. This suggests that cold-induced AIF2 coordinates freezing tolerance along with BZR1 and BIN2, key positive and negative components, respectively, of brassinosteroid signaling pathways.

P-606 Maintenance of telomere length through autophagy and androgen receptor inhibition in infertile individuals with differences of sex development (DSD)

Abstract Study question What are the molecular mechanisms underlying genome instability concomitant with increased telomere length (TL) in individuals with DSD? Summary answer Low autophagy activity and androgen receptor signaling stabilize GAR1, a telomerase-specific protein, leading to an increase in TL in DSD cells. What is known already Increased genome instability is linked to infertility, and compromised telomere maintenance is associated with genome instability. Individuals with DSD, characterized by dysgenic gonads and a high risk of Germ Cell Tumor (GCT) development, exhibit concurrent genome instability, increased TL, and deregulated Androgen Receptor (AR) signaling. Telomeric DNA damage promotes autophagy, which induces cell death and prevents propagation of replication crisis and tumorigenesis. We previously demonstrated that inhibition of autophagy, a conservative process of protein degradation, led to TL increase in cell lines derived from individuals with DSD, but the underlying mechanisms remain unclear. Study design, size, duration 112 individuals with DSD, including Swyer syndrome (46,XY females), Complete Androgen Insensitivity Syndrome (CAIS 46,XY females), Turner (45,X0 females), and Mixed Gonadal Dysgenesis (MGD 45,X0/46,XY females and males) were enrolled into study during routine praxis in our clinic. The samples were collected with written patients consent. A control group included fertile women and men, when appropriate, of comparable age. Samples underwent standard genetic and histological characterization. Lymphoblastoid cell lines were used for functional studies. Participants/materials, setting, methods Study groups comprised individuals with CAIS (n = 19); Swyer (n = 8); MGD (n = 12); Turner (n = 23) with mosaic (n = 12), with chr. X/Y deletions (n = 8), with X-isochr./idiocentric/marker chr. (n = 23) syndromes. Blood samples were collected for DNA, RNA and protein isolation from leukocytes. Additionally, individuals with DSD who underwent gonadectomy formed an additional group with histologically proven GCT (DSD-GCT, n = 7). Gonadal tissue was provided by the tissue bank. Samples were analyzed using quantitative real-time PCR (qRT-PCR), immunoblotting, and mass spectrometry. Main results and the role of chance Leukocytes from Swyer (p = 0,0069), Turner (p = 0,0064), and MGD without GCT (p = 0,05) groups exhibited a 1,5-folds increase in TL, diminished with GCT (p = 0,003). The RNA component of telomerase, TERC, was inhibited two times in Swyer (p = 0,0417). Proteomic analysis identified a telomerase protein GAR1 accumulation in Swyer, but downregulated in GCT group together with AR upregulation (p = 0,0379). Immunoblotting confirmed a two-fold increase of GAR1 in Swyer (p = 0,0022) and Turner (p = 0,0401), while GAR1 decreased in all DSD samples (p = 0,0455). GAR1 protein increased stability, not due to upregulated transcription, and promoted TL since we illustrated GAR1 accumulation within 72h of BafilomycinA1 treatment inhibiting autophagy. This treatment induced telomerase activity within 24h. Further autophagy inhibition caused accumulation of DNA damage in DSD cells, measured by γH2AX levels labeling double strand brakes (p = 0,0286). Dysgenic gonadal tissue analysis also showed a negative correlation between autophagy and TL-specific gene expression, with LC3 (p = 0,0341) and P62 (p = 0,0342) increased in all DSD samples, and proteins LC3 (p = 0,0298) and P62 (p = 0,0237) upregulated, and GAR1 (p = 0,0432) inhibited exclusively in Swyer group. Inhibition of AR increased TL (p = 0,0357) together with GAR1 (p = 0,0125) in DSD group at 19h, which was associated with a consecutive γH2AX upregulation (p = 0,0489) at 24h with Enzalutamide. Limitations, reasons for caution This study is based on a limited number of samples from the individuals with rare genetic syndromes, some observed only in 1 out of 10,000 clinical cases. Therefore, in vitro study models are recommended for further research. Wider implications of the findings The study reveals gene expression patterns and molecular regulatory mechanisms associated with DSD and GCT risk. The data suggest possibilities for prophylactic treatment of DSD individuals and new diagnostic approaches of GCT using peripheral blood. The study also emphasizes the importance of addressing genome integrity in infertility research. Trial registration number NA

Effects of Centella asiatica Extracts on Rumen In Vitro Fermentation Characteristics and Digestibility.

Two in vitro experiments were conducted to evaluate the effects of Centella asiatica extract (CAE) supplementation on the rumen's in vitro fermentation characteristics. In the first experiment, CAE with five concentrations (C: 0%; T1: 3.05%; T2: 6.1%; T3: 12.2%; and T4: 24.4% CAE in diet) was supplemented in the rumen fluid and incubated for 6, 24, and 48 h to determine the optimal dosage. The total gas and methane production increased in all incubation times, and the total volatile fatty acids increased at 6 and 48 h. Ammonia nitrogen, branched chain volatile fatty acids, acetate, and butyrate were increased by CAE supplementation. T1 was chosen as the optimal dosage based on the total volatile fatty acids, branched chain volatile fatty acids, and ammonia nitrogen production. The CAE with the identified optimal dosage (T1) was incubated to identify its effect on the rumen's in vitro degradability in the second experiment. The CAE supplementation did not influence the in vitro dry matter, crude protein, or neutral detergent fiber degradability. In conclusion, CAE has no CH4 abatement or digestion promotion effects. However, CAE could be utilized as a feed additive to increase the rumen's total volatile fatty acid production without an adverse effect on the in vitro dry matter, crude protein, or neutral detergent fiber degradability.

A novel variant in GAS2 is associated with autosomal dominant nonsyndromic hearing impairment in a Chinese family

Knockout of GAS2 (growth arrest-specific protein 2), causes disorganization and destabilization of microtubule bundles in supporting cells of the cochlear duct, leading to hearing loss in vivo. However, the molecular mechanism through which GAS2 variant results in hearing loss remains unknown. By Whole-exome sequencing, we identified a novel heterozygous splicing variant in GAS2 (c.616–2 A > G) as the only candidate mutation segregating with late-onset and progressive nonsyndromic hearing loss (NSHL) in a large dominant family. This splicing mutation causes an intron retention and produces a C-terminal truncated protein (named GAS2mu). Mechanistically, the degradation of GAS2mu via the ubiquitin-proteasome pathway is enhanced, and cells expressing GAS2mu exhibit disorganized microtubule bundles. Additionally, GAS2mu further promotes apoptosis by increasing the Bcl-xS/Bcl-xL ratio instead of through the p53-dependent pathway as wild-type GAS2 does, indicating that GAS2mu acts as a toxic molecule to exacerbate apoptosis. Our findings demonstrate that this novel variant of GAS2 promotes its own protein degradation, microtubule disorganization and cellular apoptosis, leading to hearing loss in carriers. This study expands the spectrum of GAS2 variants and elucidates the underlying pathogenic mechanisms, providing a foundation for future investigations of new therapeutic strategies to prevent GAS2-associated progressive hearing loss.

Effect of distillery wastewater on chemical composition and microbial community of Sorghum propinquum silage during micro-permeation of air

The aim of this study was to investigate the effect of distillery wastewater (DWW) on the nutrient composition, fermentation quality and microbial community of Sorghum propinquum silage during the micro-permeation of air. S. propinquum without (CK) or with L. buchneri, (LAB), distillery wastewater yellow serofluid (Y) and distillery spent wash (S) was ensiled for 60 days, and then subjected to a micro-permeation stability of air test for 6 days. After 60 days of storage, treatments with DWW and LAB decreased the loss of DM, inhibited the degradation of protein and reduced the production of ammonia nitrogen in silage relative to the control. In particular, S. propinquum silage treated with yellow serofluid sustained higher levels. Moreover, the addition of DWW resulted in higher levels of acetic and propionic acid than the other treatments. During the micro-permeation of air, the addition of DWW was effective in inhibiting the reduction of lactic acid content, and unique genera Roseburia and Faecalibacterium, which are beneficial for livestock production, discovered in DWW-treated S. propinquum silage. In conclusion, the addition of DWW was efficacious in improving the nutritional composition and microbial community of S. propinquum silage during the micro-permeation of air.

Intrinsic signaling pathways modulate targeted protein degradation

Targeted protein degradation is a groundbreaking modality in drug discovery; however, the regulatory mechanisms are still not fully understood. Here, we identify cellular signaling pathways that modulate the targeted degradation of the anticancer target BRD4 and related neosubstrates BRD2/3 and CDK9 induced by CRL2VHL- or CRL4CRBN -based PROTACs. The chemicals identified as degradation enhancers include inhibitors of cellular signaling pathways such as poly-ADP ribosylation (PARG inhibitor PDD00017273), unfolded protein response (PERK inhibitor GSK2606414), and protein stabilization (HSP90 inhibitor luminespib). Mechanistically, PARG inhibition promotes TRIP12-mediated K29/K48-linked branched ubiquitylation of BRD4 by facilitating chromatin dissociation of BRD4 and formation of the BRD4–PROTAC–CRL2VHL ternary complex; by contrast, HSP90 inhibition promotes BRD4 degradation after the ubiquitylation step. Consequently, these signal inhibitors sensitize cells to the PROTAC-induced apoptosis. These results suggest that various cell-intrinsic signaling pathways spontaneously counteract chemically induced target degradation at multiple steps, which could be liberated by specific inhibitors.

Loss-of-function mutation of REV1 (p.R704Q) mediates cetuximab primary resistance by activating autophagy in RAS-wild type metastatic colorectal cancer

Cetuximab in combination with FOLFIRI/FOLFOX is the standard first-line treatment for patients with RAS wild-type metastatic colorectal cancer (mCRC). However, some patients experience rapid tumor progression after treatment with cetuximab (primary resistance). Our previous research identified a gene mutation, REV1 p.R704Q, which may be a key biomarker for primary cetuximab resistance. This study aimed to study the mechanism of cetuximab resistance caused by REV1 p.R704Q mutation and reveal a novel mechanism to induce cetuximab resistance. Sanger sequencing and multivariate clinical prognostic analysis of 208 patients with mCRC showed that REV1 p.R704Q mutation is an independent risk factor for tumor progression after treatment with cetuximab in patients with RAS wild-type mCRC (Hazard ratio=2.481, 95% Confidence interval: 1.389–4.431, P = 0.002). The sensitivity of REV1 p.R704Q mutant cell lines to cetuximab decreased in vitro Cell Counting Kit-8 assay and in vivo subcutaneous tumor model. In vitro, we observed that decreased stability and accelerated degradation of REV1 mutant protein results in REV1 dysfunction, which activated autophagy and mediated cetuximab resistance. These findings suggested that REV1 p.R704Q mutation could predict cetuximab primary resistance in mCRC. REV1 p.R704Q mutation caused decreased stability and degradation of REV1 protein, as well as dysfunction of p.R704Q protein. REV1 p.R704Q mutation activates autophagy and mediates cetuximab resistance; further, inhibition of autophagy could reverse cetuximab resistance.

Therapeutic effects of exendin-4 on spinal cord injury via restoring autophagy function and decreasing necroptosis in neuron.

Necroptosis is one of programmed death that may aggravate spinal cord injury (SCI). We aimed to investigate the effect and mechanism of exendin-4 (EX-4) on the recovery of motor function and necroptosis after SCI. The SD rats with left hemisection in the T10 spinal cord as SCI model were used. The behavior tests were measured within 4 weeks. The effects of EX-4 on necroptosis-associated proteins and autophagy flux were explored. In addition, the SHSY5Y cell model was introduced to explore the direct effect of EX-4 on neurons. The effect of lysosome was explored using mTOR activator and AO staining. EX-4 could improve motor function and limb strength, promote the recovery of autophagy flux, and accelerate the degradation of necroptosis-related protein at 3 d after injury in rats. EX-4 reduced lysosome membrane permeability, promoted the recovery of lysosome function and autophagy flux, and accelerated the degradation of necroptosis-related proteins by inhibiting the phosphorylation level of mTOR in the SHSY5Y cell model. Our results demonstrated that EX-4 may improve motor function after SCI via inhibiting mTOR phosphorylation level and accelerating the degradation of necroptosis-related proteins in neurons. Our findings may provide new therapeutic targets for clinical treatment after SCI.

Exercise Attenuate Diaphragm Atrophy in COPD Mice via Inhibiting the RhoA/ROCK Signaling.

Exercise is an indispensable component of pulmonary rehabilitation with strong anti-inflammatory effects. However, the mechanisms by which exercise prevents diaphragmatic atrophy in COPD (chronic obstructive pulmonary disease) remain unclear. Forty male C57BL/6 mice were assigned to the control (n=16) and smoke (n=24) groups. Mice in the smoke group were exposed to the cigarette smoke (CS) for six months. They were then divided into model and exercise training groups for 2 months. Histological changes were observed in lung and diaphragms. Subsequently, agonist U46639 and antagonist Y27632 of RhoA/ROCK were subjected to mechanical stretching in LPS-treated C2C12 myoblasts. The expression levels of Atrogin-1, MuRF-1, MyoD, Myf5, IL-1β, TNF-α, and RhoA/ROCK were determined by Western blotting. Diaphragmatic atrophy and increased RhoA/ROCK expression were observed in COPD mice. Exercise training attenuated diaphragmatic atrophy, decreased the expression of MuRF-1, and increased MyoD expression in COPD diaphragms. Exercise also affects the upregulation of RhoA/ROCK and inflammation-related proteins. In in vitro experiments with C2C12 myoblasts, LPS remarkably increased the level of inflammation and protein degradation, whereas Y27632 or combined with mechanical stretching prevented this phenomenon considerably. RhoA/ROCK plays an important role in the prevention of diaphragmatic atrophy in COPD.

Exploring the correlation of microbial community diversity and succession with protein degradation and impact on the production of volatile compounds during cold storage of grouper (Epinephelus coioides)

Microorganisms, proteins, and lipids play crucial and intricate roles in the aroma generation of aquatic products. To explore the impact of the interaction between microorganisms and proteins on the volatile compounds (VOCs) in grouper, this study employed whey protein isolate (WPI) to inhibit lipid oxidation and reduce mutual interference. Changes in bacterial profiles, metabolites, and VOCs were detected. Eighteen key VOCs associated with the overall flavor of grouper were identified, and the potential relationships among microorganisms, proteins, and VOCs were explored using a correlation network. Five microorganisms (Vibrio, Vagococcus, Pseudomonas, Psychrobacter, and Shewanella) closely related to characteristic flavor compounds were identified. Additionally, 30 differential metabolites related to proteins and six metabolic pathways were screened. Therefore, this study unveils the potential interaction between microorganisms and proteins in flavor formation and provides new insights into the relationships among microorganisms, proteins, and VOCs.

SYNAPTOTAGMIN 4 is expressed mainly in the phloem and participates in abiotic stress tolerance in Arabidopsis.

Plant synaptotagmins structurally resemble animal synaptotagmins and extended-synaptotagmins. Animal synaptotagmins are well-characterized calcium sensors in membrane trafficking, and extended-synaptotagmins mediate lipid transfer at the endoplasmic reticulum-plasma membrane contact sites. Here, we characterize SYNAPTOTAGMIN 4 (SYT4), which belongs to the six-member family in Arabidopsis. Fluorometric GUS assay showed that the SYT4 promoter was strongest in roots and the least active in rosettes and cauline leaves, which was confirmed by qPCR. In seedlings, promoter activity was influenced by several factors, such as plant growth regulators, mannitol, sucrose, polyethylene glycol and cold. GUS histochemistry revealed SYT4 promoter activity in the phloem of all organs and even almost exclusively in sieve element precursors and differentiating sieve elements. Accordingly, the SYT-GFP fusion protein also accumulated in these cells with maximal abundance in sieve element precursors. The protein formed a network in the cytoplasm, but during sieve tube differentiation, it deposited at the cell periphery and disappeared from mature tubes. Using photoconvertible fluorescence technology, we showed that a high abundance of SYT4 protein in meristematic protophloem cells was due to its extensive synthesis. SYT4 protein synthesis was interrupted in differentiating sieve elements, but protein degradation was also reduced. In addition to phloem, the fusion protein was detected in shoot and root stem cell niche as early as the late heart stage of the embryo. We isolated and molecularly and biologically characterized five syt4 T-DNA insertion alleles and subjected them to phenotype analysis. The allele with the C2B domain interrupted by an T-DNA insertion exhibits increased sensitivity to factors such as auxins, osmotics, salicylic acid, sodium chloride, and the absence of sucrose in the root growth test.

Ubiquitin: Not just a one-way ticket to the proteasome, but a therapeutic dial to fine-tune the molecular landscape of disease.

Recently, there is a rise in studies that recognize the importance of targeting ubiquitin and related molecular machinery in various therapeutic contexts. Here we briefly discuss the history of ubiquitin, its biological roles in protein degradation and beyond, as well as the current state of ubiquitin-targeting therapeutics across diseases. We conclude that targeting ubiquitin machinery is approaching a renaissance, and tapping its full potential will require embracing a wholistic perspective of ubiquitin's multifaceted roles.

Caspase-3 interactins with calpain and cathepsin L: implications for protein stability and quality in fish fillets during postmortem storage

The degradation of structural proteins during fish postmortem storage is a critical factor affecting meat quality, leading to economic losses in the seafood industry. The complex interplay between caspase-3 and structural protein stability during fish postmortem storage remains largely unexplored. By treating grass carp fillets with a caspase-3 inhibitor, we establish a model for inhibiting apoptosis, delineating the role of caspase-3 in protein degradation. The effect of caspase-3 on grass carp proteins following postmortem storage and its cascade interaction with calpain and cathepsin L was further investigated. The result demonstrated that the destabilisation of the mitochondrial membrane during apoptosis led to modifications in the B-cell lymphoma (Bcl) family proteins, subsequently triggered the activation of caspase-9/caspase-3. Additionally, caspase-3 reduced the expression of the calpastatin and lysosomal membrane protein 1 (LAMP-1) gene, resulting in increased calpain and cathepsin L activity. SDS-PAGE and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis indicated that caspase-3 inhibitor treatment reduced actin fractures and preserved critical structural proteins. This investigation unveils the molecular mechanisms through which caspase-3 affects protein degradation in fish fillets during storage, providing valuable insights into the postmortem degradation processes.

Multiple strategy for antibacterial effect via copper porphyrin doping polyphenolic aldehydes based covalent organic framework

Microbial infections continue to be one of the cosmopolitan safety hazards to humankind. To achieve effective sterilization, it is urgent to develop non-antibiotic strategies or integrating multiple antimicrobial methods. Organic photo-antimicrobials (OPAMs) has attracted attention in fighting against bacteria by reactive oxygen species (ROS) or heat without triggering drug resistance. In our work, a copper-porphyrin doping donor-acceptor (D-A) type covalent organic framework (COF), named CTF-BTA2OH-Por(Cu), is constructed to achieve synergistic antibacterial effects by ROS generation and protein degradation. Copper-porphyrin doping improves ROS generation of D-A COF, showing great photocatalytic antibacterial activity (>90% within 1h). Additionally, the polyphenolic aldehydes of BTA2OH can interact with protein strongly and cause degradation, resulting inhibition of bacteria growth without light. Thus, CTF-BTA2OH-Por(Cu) showed antibacterial activity under both light and dark conditions. These findings give inspiration for COF multifunctional design for antimicrobials strategy and its application in supplies anti-infection or preservation.

Effect of Zanthoxylum bungeanum extract on the quality and cathepsin L activity of Niuganba

Niuganba (NGB) is a traditional fermented beef product. Protease activity typically significantly affects the quality of NGB. Some natural food extracts may markedly influence NGB's protease activity and performance. This study aims to investigate the effect of Zanthoxylum bungeanum extract (ZBE) on the quality and cathepsin L activity of NGB. Following ZBE treatment, the myofibril fragmentation index (MFI), the content of TCA-soluble peptides, surface hydrophobicity, disulfide bond content, and cathepsin L activity of NGB significantly decrease. The content of free thiol groups and β-sheet significantly increases. Scanning electron microscopy (SEM) reveals that the arrangement of muscle fibers in the cross-section of NGB is more compact after ZBE treatment. The research results indicate that ZBE effectively inhibits cathepsin L activity, alleviates the degradation of myofibrillar proteins, improves the physicochemical characteristics of NGB, and enhances its structural stability.

P-NADs: PUX-based NAnobody degraders for ubiquitin-independent degradation of target proteins

Targeted protein degradation (TPD) allows cells to maintain a functional proteome and to rapidly adapt to changing conditions. Methods that repurpose TPD for the deactivation of specific proteins have demonstrated significant potential in therapeutic and research applications. Most of these methods are based on proteolysis targeting chimaeras (PROTACs) which link the protein target to an E3 ubiquitin ligase, resulting in the ubiquitin-based degradation of the target protein. In this study, we introduce a method for ubiquitin-independent TPD based on nanobody-conjugated plant ubiquitin regulatory X domain-containing (PUX) adaptor proteins. We show that the PUX-based NAnobody Degraders (P-NADs) can unfold a target protein through the Arabidopsis and human orthologues of the CDC48 unfoldase without the need for ubiquitination or initiating motifs. We demonstrate that P-NAD plasmids can be transfected into a human cell line, where the produced P-NADs use the endogenous CDC48 machinery for ubiquitin-independent TPD of a 143 kDa multidomain protein. Thus, P-NADs pave the road for ubiquitin-independent therapeutic TPD approaches. In addition, the modular P-NAD design combined with in vitro and cellular assays provide a versatile platform for elucidating functional aspects of CDC48-based TPD in plants and animals.

Physicochemical characteristics and microbial diversity of sous vide scallops (Chlamys farreri) during chilled storage

This study investigated the impact of sous vide (SV) cooking methods on the physical and chemical characteristics as well as the microbial composition of scallops (Chlamys farreri) over a 30 days period of refrigerated storage. Scallop treatments were divided into two groups: CS (scallops vacuum-packed and then steamed for 30 min at 75 °C) and CK (scallops steamed for 15 min at 100 °C). With the increase in refrigeration time, the total volatile basic nitrogen (TVBN), pH, cooking loss, microbial content, and malondialdehyde (MDA) content gradually increased, while the water-soluble protein extraction rate and the myofibrillar protein (MP) extraction rate of the CS and CK samples significantly decreased. Notably, the SV steaming treatment effectively reduced microbial degradation of proteins, improved water retention of scallop samples, and maintained high MP extraction as compared to CK samples (MP content ranged from 1.09% to 2.50% in the CK group and 1.75%–3.33% in the CS group). During the late stages of refrigeration, conventionally cooked scallops (CK) were dominated by Pseudomonas and Psychrobacter, with the ability to produce biogenic amines, while SV steamed scallops were dominated by Psychrobacillus. Furthermore, a link was discovered between the microbial community and the physicochemical parameters.