Protein Degradation Processes Research Articles

Temporal and Spatial Characterization of CUL3KLHL20-driven Targeted Degradation of BET family, BRD Proteins by the Macrocycle-based Degrader BTR2004.

Targeted protein degradation (TPD) is a promising new therapeutic modality that leverages the endogenous cellular protein degradation machinery of the ubiquitin-proteasome system (UPS) to degrade selected proteins. Recently, we developed a synthetic macrocycle ligand to recruit CUL3KLHL20 E3 ligase for TPD. Using this KLHL20 ligand, we constructed the PROTAC BTR2004, which demonstrated potent degradation of BET family proteins BRD 2, 3, and 4. As the TPD field expands, it is important to understand the cellular and biochemical properties of all utilized E3 ligases. Herein we report the temporal and spatial processes of BTR2004-facilitated BET family protein degradation by KLHL20: The target protein degradation kinetics, BTR2004 intracellular activity half-life, and the onset of BTR2004 cell permeabilization. Employing proximity ligation and confocal microscopy techniques, we also illustrate the subcellular location of the ternary complex assembly upon BTR2004 treatment. These characterizations provide further insight into the processes that govern TPD and features that could be incorporated when designing future PROTAC molecules.

SITP: A single cell bioinformatics analysis flow captures proteasome markers in the development of breast cancer

Single cell sequencing and related databases have been widely used in the exploration of cancer occurrence and development, but there is still no in-depth explanation of specific and complicated cellular protein modification processes. Ubiquitin-Proteasome System (UPS), as a specific and precise protein modification and degradation process, plays an important role in the biological functions of cancer cell proliferation and apoptosis. Proteasomes, vital multi-catalytic proteinases in eukaryotic cells, play a crucial role in protein degradation and contribute to tumor regulation. The 26S proteasome, part of the ubiquitin–proteasome system. In this study, we have enrolled a common SITP process including analysis of single cell sequencing to elucidate a flow that can capture typical proteasome markers in the oncogenesis and progression of breast cancer. PSMD11, a key component of the 26S proteasome regulatory particle, has been identified as a critical survival factor in cancer cells. Results suggest that PSMD11’s rapid degradation is linked to acute apoptosis in cancer cells, making it a potential target for cancer treatment. Our study explored the potential mechanisms of PSMD11 in breast cancer development. The findings revealed the feasibility of disclosing ubiquitinating biomarkers from public database, as well as presented new evidence supporting PSMD11 as a potential therapeutic biomarker for breast cancer.

Integrative study of skeletal muscle mitochondrial dysfunction in a murine pancreatic cancer-induced cachexia model

Pancreatic ductal adenocarcinoma (PDAC), the most common pancreatic cancer, is a deadly cancer, often diagnosed late and resistant to current therapies. PDAC patients are frequently affected by cachexia characterized by muscle mass and strength loss (sarcopenia) contributing to patient frailty and poor therapeutic response. This study assesses the mechanisms underlying mitochondrial remodeling in the cachectic skeletal muscle, through an integrative exploration combining functional, morphological, and omics-based evaluation of gastrocnemius muscle from KIC genetically engineered mice developing autochthonous pancreatic tumor and cachexia. Cachectic PDAC KIC mice exhibit severe sarcopenia with loss of muscle mass and strength associated with reduced muscle fiber’s size and induction of protein degradation processes. Mitochondria in PDAC atrophied muscles show reduced respiratory capacities and structural alterations, associated with deregulation of oxidative phosphorylation and mitochondrial dynamics pathways. Beyond the metabolic pathways known to be altered in sarcopenic muscle (carbohydrates, proteins, and redox), lipid and nucleic acid metabolisms are also affected. Although the number of mitochondria per cell is not altered, mitochondrial mass shows a twofold decrease and the mitochondrial DNA threefold, suggesting a defect in mitochondrial genome homeostasis. In conclusion, this work provides a framework to guide toward the most relevant targets in the clinic to limit PDAC-induced cachexia.

Integrative study of skeletal muscle mitochondrial dysfunction in a murine pancreatic cancer-induced cachexia model.

Pancreatic ductal adenocarcinoma (PDAC), the most common pancreatic cancer, is a deadly cancer, often diagnosed late and resistant to current therapies. PDAC patients are frequently affected by cachexia characterized by muscle mass and strength loss (sarcopenia) contributing to patient frailty and poor therapeutic response. This study assesses the mechanisms underlying mitochondrial remodeling in the cachectic skeletal muscle, through an integrative exploration combining functional, morphological, and omics-based evaluation of gastrocnemius muscle from KIC genetically engineered mice developing autochthonous pancreatic tumor and cachexia. Cachectic PDAC KIC mice exhibit severe sarcopenia with loss of muscle mass and strength associated with reduced muscle fiber's size and induction of protein degradation processes. Mitochondria in PDAC atrophied muscles show reduced respiratory capacities and structural alterations, associated with deregulation of oxidative phosphorylation and mitochondrial dynamics pathways. Beyond the metabolic pathways known to be altered in sarcopenic muscle (carbohydrates, proteins, and redox), lipid and nucleic acid metabolisms are also affected. Although the number of mitochondria per cell is not altered, mitochondrial mass shows a twofold decrease and the mitochondrial DNA threefold, suggesting a defect in mitochondrial genome homeostasis. In conclusion, this work provides a framework to guide toward the most relevant targets in the clinic to limit PDAC-induced cachexia.

Nedl1 knockout impaired the learning and memory of mice

BackgroundProtein ubiquitination is a common post-translational modification involved in protein degradation and various life processes in cells. NEDL1 is a ubiquitin ligase that is highly expressed primarily in the brain. However, the functions of NEDL1 in social approach/novelty preference, anxiety, learning and memory remain poorly understood. MethodsNedl1 knockout mice (Nedl1−/−) and wild-type mice (Nedl1+/+) were tested using three-chamber test, elevated plus maze, and Barnes maze. Then, brain tissue was stained, and blood was collected for metabolic analysis. ResultsCompared with Nedl1+/+ mice, Nedl1−/− mice showed no differences in social approach/novelty preference and anxiety behavior. Nedl1−/− mice displayed impaired learning and memory. Nedl1 knockout did not affect the number of neurons and oligodendrocytes in the hippocampus. Astrocytes proliferated in the hippocampus of Nedl1−/− mice. The amino acid metabolism of Nedl1+/+and Nedl1−/− mice is different, especially the increase in proline and tryptophan. ConclusionThis study showed that Nedl1 knockout impaired learning and memory, which may be related to astrocyte proliferation and amino acid metabolism change. Nedl1 knockout did not affect social style/novelty preference and anxiety behavior in mice. The preliminary study of NEDL1 in neurobehavioral function could help understand the role of NEDL1 in the nervous system.

The essential function of cathepsin X of the orange-spotted grouper, Epinephelus coioides during SGIV infection

Cathepsin X, a class of cysteine proteases in the lysosome, involved in intracellular protein degradation processes. Numerous reports revealed that many kinds of cysteine proteases played a crucial role in pathogen invasion. To investigate the relationship between cathepsin X of teleost fish and virus infection, EcCX was cloned and characterized in the orange-spotted grouper, Epinephelus coioides. The open reading frame (ORF) of EcCX included 909 nucleotides and encoded a protein consisting of 302 amino acids, which shared 75% and 56% identity with zebrafish and humans, respectively. The protein EcCX mainly consisted of a signal peptide (1–19 aa), a pro-pre-peptide region (20–55 aa), and a mature cysteine protease region (56–302 aa). Subcellular localization analysis showed that EcCX was mainly distributed in the cytoplasm, but EcCX ectoped to the vicinity of apoptotic vesicles in FHM cells during SGIV infection. Following stimulation with SGIV or Poly (dA:dT), there was a notable rise in the expression levels of EcCX. EcCX overexpression facilitated virus infection, upregulated the production of inflammatory factors, and induced the activation of the NF-κB promoter. Furthermore, the overexpression of EcCX also accelerated the process of SGIV-induced apoptosis, potentially by enhancing the promoter activity of P53 and AP-1. Overall, our findings demonstrated a correlation between the function of EcCX and SGIV infection, providing a new understanding of the mechanisms involved in fish virus infection.

The Dual Role of NRF2 in Colorectal Cancer: Targeting NRF2 as a Potential Therapeutic Approach.

Colorectal cancer (CRC), as the third most common bisexual cancer worldwide, requires urgent research on its underlying mechanisms and intervention methods. NRF2 is an important transcription factor involved in the regulation of redox homeostasis, protein degradation, DNA repair, and other cancer processes, playing an important role in cancer. In recent years, the complex role of NRF2 in CRC has been continuously revealed: on the one hand, it exhibits a chemopreventive effect on cancer by protecting normal cells from oxidative stress, and on the other hand, it also exhibits a protective effect on malignant cells. Therefore, this article explores the dual role of NRF2 and its related signaling pathways in CRC, including their chemical protective properties and promoting effects in the occurrence, development, metastasis, and chemotherapy resistance of CRC. In addition, this article focuses on exploring the regulation of NRF2 in CRC ferroptosis, as well as NRF2 drug modulators (activators and inhibitors) targeting CRC, including natural products, compounds, and traditional Chinese medicine formulations.

Protein degradation in the stratum corneum.

The stratum corneum (SC), the outermost epidermal layer, plays a pivotal role in skin barrier function. This review delves into the intricate process of protein degradation within the stratum corneum, elucidating the roles of specific enzymes, regulatory mechanisms and the consequent impact on various skin conditions. Protein degradation is a finely tuned process, orchestrated by a suite of proteolytic enzymes like kallikreins. These enzymes are responsible for the breakdown of corneodesmosomes and the orderly desquamation of corneocytes, a process essential for skin homeostasis. Another critical enzymatic process is the breakdown of proteins like filaggrin and the generation of amino acids and their derivatives, required in the physiological water-handling properties of the SC. Regulation of these proteolytic activities is complex, involving a balance between endogenous inhibitors and other factors like pH, hydration and environmental stressors. Dysregulation of protease activity is linked to a spectrum of skin conditions, ranging from xerosis to inflammatory diseases like atopic dermatitis and psoriasis. Aberrant protein degradation can lead to compromised skin barrier function, increased tissue water loss and heightened susceptibility to infections and allergens. Understanding the factors affecting protein degradation can inform the development of targeted skincare products. Advances in biochemistry and dermatology have paved the way for the search for active ingredients designed to modulate protease activity. Such innovations may offer promising therapeutic avenues for enhancing skin barrier function and treating skin disorders. This review underscores the significance of enzymatic protein degradation in the SC and its regulatory mechanisms. It provides insights into the pathophysiology of skin diseases and outlines the potential for novel skincare interventions. By bridging the gap between fundamental research and practical applications, this article aims to inspire further investigation for better understanding of skin physiology and innovation in the realm of skincare product development.

Lysineless HiBiT and NanoLuc Tagging Systems as Alternative Tools for Monitoring Targeted Protein Degradation.

Target protein degradation (TPD) has emerged as a revolutionary approach in drug discovery, leveraging the cell's intrinsic machinery to selectively degrade disease-associated proteins. Nanoluciferase (nLuc) fusion proteins and the NanoBiT technology offer two robust and sensitive screening platforms to monitor the subtle changes in protein abundance induced by TPD molecules. Despite these advantages, concerns have arisen regarding potential degradation artifacts introduced by tagging systems due to the presence of lysine residues on them, prompting the development of alternative tools. In this study, we introduce HiBiT-RR and nLucK0, variants devoid of lysine residues, to mitigate such artifacts. Our findings demonstrate that HiBiT-RR maintains a similar sensitivity and binding affinity with the original HiBiT. Moreover, the comparison between nLucWT and nLucK0 constructs reveals variations in degradation patterns induced by certain TPD molecules, emphasizing the importance of choosing appropriate tagging systems to ensure the reliability of experimental outcomes in studying protein degradation processes.

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

USP38 exacerbates pressure overload-induced left ventricular electrical remodeling

BackgroundUbiquitin-specific protease 38 (USP38), belonging to the USP family, is recognized for its role in controlling protein degradation and diverse biological processes. Ventricular arrhythmias (VAs) following heart failure (HF) are closely linked to ventricular electrical remodeling, yet the specific mechanisms underlying VAs in HF remain inadequately explored. In this study, we examined the impact of USP38 on VAs in pressure overload-induced HF.MethodsCardiac-specific USP38 knockout mice, cardiac-specific USP38 transgenic mice and their matched control littermates developed HF induced by aortic banding (AB) surgery. After subjecting the mice to AB surgery for a duration of four weeks, comprehensive investigations were conducted, including pathological analysis and electrophysiological assessments, along with molecular analyses.ResultsWe observed increased USP38 expression in the left ventricle of mice with HF. Electrocardiogram showed that the USP38 knockout shortened the QRS interval and QTc, while USP38 overexpression prolonged these parameters. USP38 knockout decreased the susceptibility of VAs by shortening action potential duration (APD) and prolonging effective refractory period (ERP). In addition, USP38 knockout increased ion channel and Cx43 expression in ventricle. On the contrary, the increased susceptibility of VAs and the decreased expression of ventricular ion channels and Cx43 were observed with USP38 overexpression. In both in vivo and in vitro experiments, USP38 knockout inhibited TBK1/AKT/CAMKII signaling, whereas USP38 overexpression activated this pathway.ConclusionOur data indicates that USP38 increases susceptibility to VAs after HF through TBK1/AKT/CAMKII signaling pathway, Consequently, USP38 may emerge as a promising therapeutic target for managing VAs following HF.

A BRD4‐Targeting Photothermal Agent for Controlled Protein Degradation

AbstractBRD4 protein plays a pivotal role in cell cycle regulation and differentiation. Disrupting the activity of BRD4 has emerged as a promising strategy for inhibiting the growth and proliferation of cancer cells. Herein, we introduced a BRD4‐targeting photothermal agent for controlled protein degradation, aiming to enhance low‐temperature photothermal therapy (PTT) for cancer treatment. By incorporating a BRD4 protein inhibitor into a cyanine dye scaffold, the photothermal agent specifically bond to the bromodomain of BRD4. Upon low power density laser irradiation, the agent induced protein degradation, directly destroying the BRD4 structure and inhibiting its transcriptional regulatory function. This strategy not only prolonged the retention time of the photothermal agent in cancer cells but also confined the targeted protein degradation process solely to the tumor tissue, minimizing side effects on normal tissues through the aid of exogenous signals. This work established a simple and feasible platform for future PTT agent design in clinical cancer treatment.

A BRD4-Targeting Photothermal Agent for Controlled Protein Degradation.

BRD4 protein plays a pivotal role in cell cycle regulation and differentiation. Disrupting the activity of BRD4 has emerged as a promising strategy for inhibiting the growth and proliferation of cancer cells. Herein, we introduced a BRD4-targeting photothermal agent for controlled protein degradation, aiming to enhance low-temperature photothermal therapy (PTT) for cancer treatment. By incorporating a BRD4 protein inhibitor into a cyanine dye scaffold, the photothermal agent specifically bond to the bromodomain of BRD4. Upon low power density laser irradiation, the agent induced protein degradation, directly destroying the BRD4 structure and inhibiting its transcriptional regulatory function. This strategy not only prolonged the retention time of the photothermal agent in cancer cells but also confined the targeted protein degradation process solely to the tumor tissue, minimizing side effects on normal tissues through the aid of exogenous signals. This work established a simple and feasible platform for future PTT agent design in clinical cancer treatment.

An Epigenetic Manifestation of Alzheimer's Disease: DNA Methylation.

Alzheimer's disease (AD), the most common form of dementia, has a complex pathogenesis. The number of AD patients has increased in recent years due to population aging, while a trend toward a younger age of onset has arisen, imposing a substantial burden on society and families, and garnering extensive attention. DNA methylation has recently been revealed to play an important role in AD onset and progression. DNA methylation is a critical mechanism regulating gene expression, and alterations in this mechanism dysregulate gene expression and disrupt important pathways, including oxidative stress responses, inflammatory reactions, and protein degradation processes, eventually resulting in disease. Studies have revealed widespread changes in AD patients' DNA methylation in the peripheral blood and brain tissues, affecting multiple signaling pathways and severely impacting neuronal cell and synaptic functions. This review summarizes the role of DNA methylation in the pathogenesis of AD, aiming to provide a theoretical basis for its early prevention and treatment.

Proteomic profiling of peanut hairy root culture unveils distinctive adaptive responses induced by elicitor treatment across diverse time intervals

Plants employ a diverse array of responses to counteract and defend against stressors. Utilizing quantitative proteomic analysis allows for the exploration of global proteomic dynamics in cells and tissues at specific time points. In order to comprehend the intricate mechanisms underlying plant responses, we conducted a proteomic investigation of peanut hairy root cultures induced with a combination of chitosan (CHT), methyl jasmonate (MeJA), and cyclodextrin (CD) at multiple time points. The study identified 292, 317, and 327 differentially expressed proteins (DEPs) in hairy root tissues at 24-, 48-, and 72 h intervals post-elicitation, respectively. Principal component analysis (PCA) distinctly clustered each timepoint of treatment and the control group. Gene ontology (GO) enrichment analysis highlighted terms such as "responding to biotic stimuli" and "defense response" during the early response, with the upregulation of Heat shock cognate 70 kDa protein, Wound-induced protein 1, and Disease resistance-like protein. The 72 h time point specifically showed an upregulation of superoxide dismutase (SOD) and auxin response factor, indicating a delayed response and illustrating how hairy roots adapt to stress in later stages. Furthermore, GO enrichment at later stages implicated alterations in protein production, involving both synthesis and degradation processes. Proteolytic enzymes, including those in the ubiquitin/proteasome pathway, were identified as facilitating protein degradation. The detection of small molecular weight (MW) peptides in the culture medium of elicited hairy roots suggested their origin from the proteolytic cleavage of precursor proteins. The GO enrichment of culture medium peptides pointed towards involvement in signaling pathways. The suggested signaling cascade acts as a potential link that connects the recognition of stress to the initiation of appropriate response to external stressors. This approach delves into dynamic changes in protein expression and secretion patterns over various intervals, providing insights into the plant's adaptive response to external stress.

Nm-Nano: a machine learning framework for transcriptome-wide single-molecule mapping of 2´-O-methylation (Nm) sites in nanopore direct RNA sequencing datasets

ABSTRACT 2´-O-methylation (Nm) is one of the most abundant modifications found in both mRNAs and noncoding RNAs. It contributes to many biological processes, such as the normal functioning of tRNA, the protection of mRNA against degradation by the decapping and exoribonuclease (DXO) protein, and the biogenesis and specificity of rRNA. Recent advancements in single-molecule sequencing techniques for long read RNA sequencing data offered by Oxford Nanopore technologies have enabled the direct detection of RNA modifications from sequencing data. In this study, we propose a bio-computational framework, Nm-Nano, for predicting the presence of Nm sites in direct RNA sequencing data generated from two human cell lines. The Nm-Nano framework integrates two supervised machine learning (ML) models for predicting Nm sites: Extreme Gradient Boosting (XGBoost) and Random Forest (RF) with K-mer embedding. Evaluation on benchmark datasets from direct RNA sequecing of HeLa and HEK293 cell lines, demonstrates high accuracy (99% with XGBoost and 92% with RF) in identifying Nm sites. Deploying Nm-Nano on HeLa and HEK293 cell lines reveals genes that are frequently modified with Nm. In HeLa cell lines, 125 genes are identified as frequently Nm-modified, showing enrichment in 30 ontologies related to immune response and cellular processes. In HEK293 cell lines, 61 genes are identified as frequently Nm-modified, with enrichment in processes like glycolysis and protein localization. These findings underscore the diverse regulatory roles of Nm modifications in metabolic pathways, protein degradation, and cellular processes. The source code of Nm-Nano can be freely accessed at https://github.com/Janga-Lab/Nm-Nano.

Lon1 Inactivation Downregulates Autophagic Flux and Brassinosteroid Biogenesis, Modulating Mitochondrial Proportion and Seed Development in Arabidopsis.

Mitochondrial protein homeostasis is crucially regulated by protein degradation processes involving both mitochondrial proteases and cytosolic autophagy. However, it remains unclear how plant cells regulate autophagy in the scenario of lacking a major mitochondrial Lon1 protease. In this study, we observed a notable downregulation of core autophagy proteins in Arabidopsis Lon1 knockout mutant lon1-1 and lon1-2, supporting the alterations in the relative proportions of mitochondrial and vacuolar proteins over total proteins in the plant cells. To delve deeper into understanding the roles of the mitochondrial protease Lon1 and autophagy in maintaining mitochondrial protein homeostasis and plant development, we generated the lon1-2atg5-1 double mutant by incorporating the loss-of-function mutation of the autophagy core protein ATG5, known as atg5-1. The double mutant exhibited a blend of phenotypes, characterized by short plants and early senescence, mirroring those observed in the individual single mutants. Accordingly, distinct transcriptome alterations were evident in each of the single mutants, while the double mutant displayed a unique amalgamation of transcriptional responses. Heightened severity, particularly evident in reduced seed numbers and abnormal embryo development, was observed in the double mutant. Notably, aberrations in protein storage vacuoles (PSVs) and oil bodies were evident in the single and double mutants. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of genes concurrently downregulated in lon1-2, atg5-1, and lon1-2atg5-1 unveiled a significant suppression of genes associated with brassinosteroid (BR) biosynthesis and homeostasis. This downregulation likely contributes to the observed abnormalities in seed and embryo development in the mutants.

Role of autophagy-related genes in liver cancer prognosis

Autophagy, a highly conserved process of protein and organelle degradation, has emerged as a critical regulator in various diseases, including cancer progression. In the context of liver cancer, the predictive value of autophagy-related genes remains ambiguous. Leveraging chip datasets from the TCGA and GTEx databases, we identified 23 differentially expressed autophagy-related genes in liver cancer. Notably, five key autophagy genes, PRKAA2, BIRC5, MAPT, IGF1, and SPNS1, were highlighted as potential prognostic markers, with MAPT showing significant overexpression in clinical samples. In vitro cellular assays further demonstrated that MAPT promotes liver cancer cell proliferation, migration, and invasion by inhibiting autophagy and suppressing apoptosis. Subsequent in vivo studies further corroborated the pro-tumorigenic role of MAPT by suppressing autophagy. Collectively, our model based on the five key genes provides a promising tool for predicting liver cancer prognosis, with MAPT emerging as a pivotal factor in tumor progression through autophagy modulation.

Skeletal muscle ULK1 and ULK2 modulate protein synthesis impacting fiber size

Maintenance of skeletal muscle homeostasis is largely influenced by the processes of protein synthesis and degradation. However, the regulation of these processes remains incompletely understood particularly in a tissue or cell type-specific manner. We have previously demonstrated that Unc-51 like autophagy activating kinases 1 and 2 (Ulk1/2) are among the top 5 mostly enriched putative autophagy genes in skeletal muscle when compared to >90 other mouse tissues and cell lines (Fuqua et al., FASEB J, 2019). However, because protein kinases commonly have several downstream targets, here we hypothesized that skeletal muscle ULK1 and ULK2 redundantly modulate other important cellular processes. To begin to address this question, we generated mice with skeletal muscle-specific knockout of ULK1 and ULK2 (i.e., ULK1/2 skmDKO) and studied those at different ages. Muscle basal autophagy flux was impaired in ULK1/2 skmDKO mice. However, contrary to other models of autophagy impairment, which commonly leads to muscle atrophy, adult ULK1/2 skmDKO mice had increased muscle size (15-25%, P≤0.01). Hypertrophy occurred in all fiber types (6-20% increase in fiber diameter, P≤0.05) and in response to an acute (4-week) deficiency of ULK1/2 (via electroporations of plasmids encoding ULK1/2miR), where TA fiber diameter increased by 9% (p<0.05). Further studies using D2O labeling and cellular fractionation revealed that ULK1/2 skmDKO mice have increased myofibrillar protein synthesis rates (~5%/day, p<0.05). Examination of the molecular mechanisms involved suggests that ULK1/2 skmDKO mice have enhanced mTORC1-dependent signaling, particularly in the fed state. Altogether, our findings reveal for the first time that ULK1 and ULK2 collectively stimulate protein degradation and inhibit protein synthesis in skeletal muscle potentially impacting muscle mass and function in conditions of muscle atrophy and hypertrophy. Supported by the University of Iowa Fraternal Order of Eagles Diabetes Research Center (UIowa FOEDRC). This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Erasing marks: Functions of plant deubiquitylating enzymes in modulating the ubiquitin code.

Plant cells need to respond to environmental stimuli and developmental signals accurately and promptly. Ubiquitylation is a reversible posttranslational modification that enables the adaptation of cellular proteostasis to internal or external factors. The different topologies of ubiquitin linkages serve as the structural basis for the ubiquitin code, which can be interpreted by ubiquitin-binding proteins or readers in specific processes. The ubiquitylation status of target proteins is regulated by ubiquitylating enzymes or writers, as well as deubiquitylating enzymes (DUBs) or erasers. DUBs can remove ubiquitin molecules from target proteins. Arabidopsis (A. thaliana) DUBs belong to 7 protein families and exhibit a wide range of functions and play an important role in regulating selective protein degradation processes, including proteasomal, endocytic, and autophagic protein degradation. DUBs also shape the epigenetic landscape and modulate DNA damage repair processes. In this review, we summarize the current knowledge on DUBs in plants, their cellular functions, and the molecular mechanisms involved in the regulation of plant DUBs.