Autophagy-mediated Protein Degradation Research Articles

Regional and age-dependent changes in ubiquitination in cellular and mouse models of spinocerebellar ataxia type 3.

Spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph disease, is the most common dominantly inherited ataxia. SCA3 is caused by a CAG repeat expansion in the ATXN3 gene that encodes an expanded tract of polyglutamine in the disease protein ataxin-3 (ATXN3). As a deubiquitinating enzyme, ATXN3 regulates numerous cellular processes including proteasome- and autophagy-mediated protein degradation. In SCA3 disease brain, polyQ-expanded ATXN3 accumulates with other cellular constituents, including ubiquitin (Ub)-modified proteins, in select areas like the cerebellum and the brainstem, but whether pathogenic ATXN3 affects the abundance of ubiquitinated species is unknown. Here, in mouse and cellular models of SCA3, we investigated whether elimination of murine Atxn3 or expression of wild-type or polyQ-expanded human ATXN3 alters soluble levels of overall ubiquitination, as well as K48-linked (K48-Ub) and K63-linked (K63-Ub) chains. Levels of ubiquitination were assessed in the cerebellum and brainstem of 7- and 47-week-old Atxn3 knockout and SCA3 transgenic mice, and also in relevant mouse and human cell lines. In older mice, we observed that wild-type ATXN3 impacts the cerebellar levels of K48-Ub proteins. In contrast, pathogenic ATXN3 leads to decreased brainstem abundance of K48-Ub species in younger mice and changes in both cerebellar and brainstem K63-Ub levels in an age-dependent manner: younger SCA3 mice have higher levels of K63-Ub while older mice have lower levels of K63-Ub compared to controls. Human SCA3 neuronal progenitor cells also show a relative increase in K63-Ub proteins upon autophagy inhibition. We conclude that wild-type and mutant ATXN3 differentially impact K48-Ub- and K63-Ub-modified proteins in the brain in a region- and age-dependent manner.

Functional genome-wide short hairpin RNA library screening identifies key molecules for extracellular vesicle secretion from microglia

SUMMARYActivated microglia release extracellular vesicles (EVs) as modulators of brain homeostasis and innate immunity. However, the molecules critical for regulating EV production from microglia are poorly understood. Here we establish a murine microglial cell model to monitor EV secretion by measuring the fluorescence signal of tdTomato, which is linked to tetraspanin CD63. Stimulation of tdTomato+ cells with ATP induces rapid secretion of EVs and a reduction in cellular tdTomato intensity, reflecting EV secretion. We generate a GFP+ tdTomato+ cell library expressing TurboGFP and barcoded short hairpin RNAs for genome-wide screening using next-generation sequencing. We identify Mcfd2, Sepp1, and Sdc1 as critical regulators of ATP-induced EV secretion from murine microglia. Small interfering RNA (siRNA-based) silencing of each of these genes suppresses lipopolysaccharide- and ATP-induced inflammasome activation, as determined by interleukin-1β release from primary cultured murine microglia. These molecules are critical for microglial EV secretion and are potential therapeutic targets for neuroinflammatory disorders.

Carbamazepine promotes surface expression of mutant Kir6.2-A28V ATP-sensitive potassium channels by modulating Golgi retention and autophagy

Pancreatic β-cells express ATP-sensitive potassium (KATP) channels, consisting of octamer complexes containing four sulfonylurea receptor 1 (SUR1) and four Kir6.2 subunits. Loss of KATP channel function causes persistent hyperinsulinemic hypoglycemia of infancy (PHHI), a rare but debilitating condition if not treated. We previously showed that the sodium-channel blocker carbamazepine (Carb) corrects KATP channel surface expression defects induced by PHHI-causing mutations in SUR1. In this study, we show that Carb treatment can also ameliorate the trafficking deficits associated with a recently discovered PHHI-causing mutation in Kir6.2 (Kir6.2-A28V). In human embryonic kidney 293 or INS-1 cells expressing this mutant KATP channel (SUR1 and Kir6.2-A28V), biotinylation and immunostaining assays revealed that Carb can increase surface expression of the mutant KATP channels. We further examined the subcellular distributions of mutant KATP channels before and after Carb treatment; without Carb treatment, we found that mutant KATP channels were aberrantly accumulated in the Golgi apparatus. However, after Carb treatment, coimmunoprecipitation of mutant KATP channels and Golgi marker GM130 was diminished, and KATP staining was also reduced in lysosomes. Intriguingly, Carb treatment also simultaneously increased autophagic flux and p62 accumulation, suggesting that autophagy-dependent degradation of the mutant channel was not only stimulated but also interrupted. In summary, our data suggest that surface expression of Kir6.2-A28V KATP channels is rescued by Carb treatment via promotion of mutant KATP channel exit from the Golgi apparatus and reduction of autophagy-mediated protein degradation.

Combined Inhibition of p38MAPK and PIKfyve Synergistically Disrupts Autophagy to Selectively Target Cancer Cells

In nutrient-poor conditions, autophagy buffers metabolic stress and counteracts the effects of chemotherapy and radiation on cancer cells, which depend on autophagy for survival. However, clinical trials targeting autophagy have failed to produce successful anticancer treatments using currently available inhibitors. Recent studies have shown that PIKfyve kinase inhibitors disrupt lysosome function in autophagy and can selectively kill certain cancer cells. Analysis of biochemical changes caused by PIKfyve inhibition revealed that resistant cells contain significantly higher levels of cellular p38MAPK protein and phosphorylation. Expression of the lysosomal protein, lysosomal-associated membrane protein 2, carrying phosphomimetic mutations of the p38MAPK phosphorylation sites prevented all effects caused by PIKfyve inhibition-induced lysosome dysfunction. Thus, the activation of p38MAPK in response to PIKfyve inhibition revealed a novel compensatory role in maintaining lysosome function in autophagy. The functional cooperation between the cellular PIKfyve and p38MAPK pathways in regulating lysosome homeostasis was especially important in cancer cells. Combined inhibition of PIKfyve and p38MAPK activities synergistically blocked autophagy-mediated protein degradation, prevented cathepsin maturation, and markedly reduced the viability of multiple cancer cell types without affecting the viability of normal cells. Furthermore, combined PIKfyve and p38MAPK inhibitors synergistically reduced tumor growth in mice bearing xenografts of human colorectal adenocarcinoma, suggesting a novel way to target cancer cells by prolonged inhibition of autophagy using lower drug concentrations. SIGNIFICANCE: This study demonstrates that PIKfyve and p38MAPK cooperate to regulate lysosome homeostasis and their combined inhibition synergistically blocks autophagy to reduce cancer cell viability in vitro and in vivo.

Host Plant Strategies to Combat Against Viruses Effector Proteins.

Viruses are obligate parasites that exist in an inactive state until they enter the host body. Upon entry, viruses become active and start replicating by using the host cell machinery. All plant viruses can augment their transmission, thus powering their detrimental effects on the host plant. To diminish infection and diseases caused by viruses, the plant has a defence mechanism known as pathogenesis-related biochemicals, which are metabolites and proteins. Proteins that ultimately prevent pathogenic diseases are called R proteins. Several plant R genes (that confirm resistance) and avirulence protein (Avr) (pathogen Avr gene-encoded proteins [effector/elicitor proteins involved in pathogenicity]) molecules have been identified. The recognition of such a factor results in the plant defence mechanism. During plant viral infection, the replication and expression of a viral molecule lead to a series of a hypersensitive response (HR) and affect the host plant’s immunity (pathogen-associated molecular pattern–triggered immunity and effector-triggered immunity). Avr protein renders the host RNA silencing mechanism and its innate immunity, chiefly known as silencing suppressors towards the plant defensive machinery. This is a strong reply to the plant defensive machinery by harmful plant viruses. In this review, we describe the plant pathogen resistance protein and how these proteins regulate host immunity during plant–virus interactions. Furthermore, we have discussed regarding ribosome-inactivating proteins, ubiquitin proteasome system, translation repression (nuclear shuttle protein interacting kinase 1), DNA methylation, dominant resistance genes, and autophagy-mediated protein degradation, which are crucial in antiviral defences.

BAG5 Promotes Alpha-Synuclein Oligomer Formation and Functionally Interacts With the Autophagy Adaptor Protein p62.

Molecular chaperones are critical to maintaining intracellular proteostasis and have been shown to have a protective role against alpha-synuclein-mediated toxicity. Co-chaperone proteins regulate the activity of molecular chaperones and connect the chaperone network to protein degradation and cell death pathways. Bcl-2 associated athanogene 5 (BAG5) is a co-chaperone that modulates proteostasis by inhibiting the activity of Heat shock protein 70 (Hsp70) and several E3 ubiquitin ligases, resulting in enhanced neurodegeneration in models of Parkinson’s disease (PD). Here we identify a novel interaction between BAG5 and p62/sequestosome-1 (SQSTM1), suggesting that BAG5 may bridge the chaperone network to autophagy-mediated protein degradation. We found that BAG5 enhanced the formation of pathogenic alpha-synuclein oligomers and regulated the levels and subcellular distribution of p62. These results extend the role of BAG5 in alpha-synuclein processing and intracellular proteostasis.

The Role of Selective Protein Degradation in the Regulation of Iron and Sulfur Homeostasis in Plants.

Plants are able to synthesize all essential metabolites from minerals, water, and light to complete their life cycle. This plasticity comes at a high energy cost, and therefore, plants need to tightly allocate resources in order to control their economy. Being sessile, plants can only adapt to fluctuating environmental conditions, relying on quality control mechanisms. The remodeling of cellular components plays a crucial role, not only in response to stress, but also in normal plant development. Dynamic protein turnover is ensured through regulated protein synthesis and degradation processes. To effectively target a wide range of proteins for degradation, plants utilize two mechanistically-distinct, but largely complementary systems: the 26S proteasome and the autophagy. As both proteasomal- and autophagy-mediated protein degradation use ubiquitin as an essential signal of substrate recognition, they share ubiquitin conjugation machinery and downstream ubiquitin recognition modules. Recent progress has been made in understanding the cellular homeostasis of iron and sulfur metabolisms individually, and growing evidence indicates that complex crosstalk exists between iron and sulfur networks. In this review, we highlight the latest publications elucidating the role of selective protein degradation in the control of iron and sulfur metabolism during plant development, as well as environmental stresses.

Autophagy promotes osteoclast podosome disassembly and cell motility athrough the interaction of kindlin3 with LC3

Osteoclasts are responsible for bone resorption and play an important role in physiological and pathological bone metabolism. Osteoclast migration across bone surfaces is essential for bone resorption, and a previous study demonstrated the role of autophagy in osteoclastogenesis and acid secretion. However, the role of autophagy in osteoclast migration remains unclear. Osteoclast migration requires the successive and rapid assembly and disassembly of podosome rings. In this study, we show that kindlin3, an important adaptor protein in the podosome, can interact with LC3B and undergo autophagy-mediated protein degradation to promote the disassembly of the podosome.Moreover, further analyses showed that the inhibition of autophagy increased kindlin3 levels and enhanced the interaction between kindlin3 and integrin β3. The over activation of integrins inhibits the disassembly of obsolete podosome rings, resulting in disorganization of the actin cytoskeleton and impaired migration in osteoclasts. Our results show that LC3B affects osteoclast migration and FAK/AKT activation by modulating integrin activation via a kindlin3-mediated inside-out signal from the extracellular matrix. Based on these results, we propose that LC3 is an important target for regulating osteoclast migration.

Multilayered Control of Protein Turnover by TORC1 and Atg1

The target of rapamycin complex 1 (TORC1) is a master regulator of cell homeostasis, which promotes anabolic reactions and synchronously inhibits catabolic processes such as autophagy-mediated protein degradation. Its prime autophagy target is Atg13, a subunit of the Atg1 kinase complex that acts as the gatekeeper of canonical autophagy. To study whether the activities of TORC1 and Atg1 are coupled through additional, more intricate control mechanisms than simply this linear pathway, we analyzed the epistatic relationship between TORC1 and Atg1 by using quantitative phosphoproteomics. Our invivo data, combined with targeted invitro TORC1 and Atg1 kinase assays, not only uncover numerous TORC1 and Atg1 effectors, but also suggest distinct bi-directional regulatory feedback loops and characterize Atg29 as a commonly regulated downstream target of both TORC1 and Atg1. Thus, an exquisitely multilayered regulatory network appears to coordinate TORC1 and Atg1 activities to robustly tune autophagy in response to nutritional cues.

Everolimus induces G1 cell cycle arrest through autophagy-mediated protein degradation of cyclin D1 in breast cancer cells.

Everolimus inhibits mammalian target of rapamycin complex 1 (mTORC1) and is known to cause induction of autophagy and G1 cell cycle arrest. However, it remains unknown whether everolimus-induced autophagy plays a critical role in its regulation of the cell cycle. We, for the first time, suggested that everolimus could stimulate autophagy-mediated cyclin D1 degradation in breast cancer cells. Everolimus-induced cyclin D1 degradation through the autophagy pathway was investigated in MCF-10DCIS.COM and MCF-7 cell lines upon autophagy inhibitor treatment using Western blot assay. Everolimus-stimulated autophagy and decrease in cyclin D1 were also tested in explant human breast tissue. Inhibiting mTORC1 with everolimus rapidly increased cyclin D1 degradation, whereas 3-methyladenine, chloroquine, and bafilomycin A1, the classic autophagy inhibitors, could attenuate everolimus-induced cyclin D1 degradation. Similarly, knockdown of autophagy-related 7 (Atg-7) also repressed everolimus-triggered cyclin D1 degradation. In addition, everolimus-induced autophagy occurred earlier than everolimus-induced G1 arrest, and blockade of autophagy attenuated everolimus-induced G1 arrest. We also found that everolimus stimulated autophagy and decreased cyclin D1 levels in explant human breast tissue. These data support the conclusion that the autophagy induced by everolimus in human mammary epithelial cells appears to cause cyclin D1 degradation resulting in G1 cell cycle arrest. Our findings contribute to our knowledge of the interplay between autophagy and cell cycle regulation mediated by mTORC1 signaling and cyclin D1 regulation.

The Tug-of-War between Plants and Viruses: Great Progress and Many Remaining Questions.

Plants are persistently challenged by various phytopathogens. To protect themselves, plants have evolved multilayered surveillance against all pathogens. For intracellular parasitic viruses, plants have developed innate immunity, RNA silencing, translation repression, ubiquitination-mediated and autophagy-mediated protein degradation, and other dominant resistance gene-mediated defenses. Plant viruses have also acquired diverse strategies to suppress and even exploit host defense machinery to ensure their survival. A better understanding of the defense and counter-defense between plants and viruses will obviously benefit from the development of efficient and broad-spectrum virus resistance for sustainable agriculture. In this review, we summarize the cutting edge of knowledge concerning the defense and counter-defense between plants and viruses, and highlight the unexploited areas that are especially worth investigating in the near future.

Abstract P6-04-01: Rapalog everolimus induces G1 cell cycle arrest through autophagy-mediated protein degradation of cyclin D1 in breast cancer cells

Abstract Rapamycin analogs (rapalogs) inhibit mammalian target of rapamycin (mTOR) and are known to cause induction of autophagy and G1 cell cycle arrest. However, it remains unknown whether rapalog-induced autophagy plays a critical role in its regulation of cell cycle. We, for the first time, found that rapalog everolimus could stimulate autophagy-mediated Cyclin D1 degradation in breast cancer cells. Inhibiting mTOR with everolimus rapidly increased the degradation of Cyclin D1 in MCF-10DCIS.COM and MCF-7 cells. 3-Methyladenine (3-MA), a classic autophagy inhibitor, could attenuate everolimus-induced Cyclin D1 degradation. Furthermore, knockdown of autophagy related gene 7 (Atg-7) could also repress everolimus-triggered degradation of Cyclin D1 in MCF-10DCIS.COM. Moreover, everolimus-induced autophagy occurred earlier than its induction of G1 arrest and cell death. Blockade of autophagy attenuated everolimus-induced G1 cell cycle arrest. These preliminary data support the conclusion that the autophagy induced by rapalogs in breast cancer cells appears to cause Cyclin D1 protein degradation resulting in G1 cell cycle arrest. Our findings contribute to our knowledge of the interplay between autophagy and cell cycle regulation mediated by mTOR signaling and Cyclin D1 regulation. Citation Format: Chen G, Ding X-F, Bouamar H, Pressley K, Yang J, Sun L-Z. Rapalog everolimus induces G1 cell cycle arrest through autophagy-mediated protein degradation of cyclin D1 in breast cancer cells [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P6-04-01.

Role of Ubiquilins in Neurodegenerative Diseases

Ubiquilin (Ubqln) proteins, including Ubqln1-4, are a family of ubiquitin-like (UBL) proteins that structurally contain anN-terminalubiquitin-like domain, a C-terminalubiquitin-associated (UBA) domain, and aninternal variable number of Stil repeat motifs. Unlike those small molecule ubiquitin-like proteins, Ubqln proteins cannot be covalently tagged to the proteins that are targeted to the proteasome for degradation. Instead, this family of proteins binds to thepolyubiquitinated proteins via the UBA domain and delivers them to the proteasome for degradation, despite their involving in autophagy-mediated protein degradation. Increasing studies have suggested that Ubqln proteins play important roles in mediating the degradation of damaged/misfolded proteins and thus theirinsufficiencies or dysfunctionsare frequently associated with different neurodegenerative disorders. This review summarizes the role of Ubqln proteins in several neurodegenerative disorders.

Insulin and IGF-1 receptors regulate FoxO-mediated signaling in muscle proteostasis.

Diabetes strongly impacts protein metabolism, particularly in skeletal muscle. Insulin and IGF-1 enhance muscle protein synthesis through their receptors, but the relative roles of each in muscle proteostasis have not been fully elucidated. Using mice with muscle-specific deletion of the insulin receptor (M-IR-/- mice), the IGF-1 receptor (M-IGF1R-/- mice), or both (MIGIRKO mice), we assessed the relative contributions of IR and IGF1R signaling to muscle proteostasis. In differentiated muscle, IR expression predominated over IGF1R expression, and correspondingly, M-IR-/- mice displayed a moderate reduction in muscle mass whereas M-IGF1R-/- mice did not. However, these receptors serve complementary roles, such that double-knockout MIGIRKO mice displayed a marked reduction in muscle mass that was linked to increases in proteasomal and autophagy-lysosomal degradation, accompanied by a high-protein-turnover state. Combined muscle-specific deletion of FoxO1, FoxO3, and FoxO4 in MIGIRKO mice reversed increased autophagy and completely rescued muscle mass without changing proteasomal activity. These data indicate that signaling via IR is more important than IGF1R in controlling proteostasis in differentiated muscle. Nonetheless, the overlap of IR and IGF1R signaling is critical to the regulation of muscle protein turnover, and this regulation depends on suppression of FoxO-regulated, autophagy-mediated protein degradation.

Aneuploidy-induced cellular stresses limit autophagic degradation.

An unbalanced karyotype, a condition known as aneuploidy, has a profound impact on cellular physiology and is a hallmark of cancer. Aneuploid cells experience a number of stresses that are caused by aneuploidy-induced proteomic changes. How the aneuploidy-associated stresses affect cells and whether cells respond to them are only beginning to be understood. Here we show that autophagosomal cargo such as protein aggregates accumulate within lysosomes in aneuploid cells. This causes a lysosomal stress response. Aneuploid cells activate the transcription factor TFEB, a master regulator of autophagic and lysosomal gene expression, thereby increasing the expression of genes needed for autophagy-mediated protein degradation. Accumulation of autophagic cargo within the lysosome and activation of TFEB-responsive genes are also observed in cells in which proteasome function is inhibited, suggesting that proteotoxic stress causes TFEB activation. Our results reveal a TFEB-mediated lysosomal stress response as a universal feature of the aneuploid state.

The different roles of selective autophagic protein degradation in mammalian cells.

Autophagy is an intracellular pathway for bulk protein degradation and the removal of damaged organelles by lysosomes. Autophagy was previously thought to be unselective; however, studies have increasingly confirmed that autophagy-mediated protein degradation is highly regulated. Abnormal autophagic protein degradation has been associated with multiple human diseases such as cancer, neurological disability and cardiovascular disease; therefore, further elucidation of protein degradation by autophagy may be beneficial for protein-based clinical therapies. Macroautophagy and chaperone-mediated autophagy (CMA) can both participate in selective protein degradation in mammalian cells, but the process is quite different in each case. Here, we summarize the various types of macroautophagy and CMA involved in determining protein degradation. For this summary, we divide the autophagic protein degradation pathways into four categories: the post-translational modification dependent and independent CMA pathways and the ubiquitin dependent and independent macroautophagy pathways, and describe how some non-canonical pathways and modifications such as phosphorylation, acetylation and arginylation can influence protein degradation by the autophagy lysosome system (ALS). Finally, we comment on why autophagy can serve as either diagnostics or therapeutic targets in different human diseases.

Abstract 154: Immunological significance of p62/SQSTM1 accumulation in oral squamous cell carcinoma

Abstract Introduction: Autophagy is a prosurvival function that facilitates cellular response to stress by cleaning damaged proteins and organelles, and provides energy to the cells during starvation. p62/SQSTM1, which is a multifunctional, multi-domain scaffolding protein that has been implicated in various cell signaling pathways including autophagy-mediated protein degradation. In autophagy, an accumulation of ubiquitinated proteins retains p62/SQSTM1 in the cell, resulting in an increase of selective autophagy, whereas autophagy impairment can accumulate p62/SQSTM1. To date, evidence has accumulated that, in the tumor microenvironment, autophagy is known to play an important role in tumorigenesis, but also influences immune response to tumor cells. However, it still remains unknown how this autophagy-regulated protein, p62/SQSTM1 in tumor cells takes part in antitumor immune responses. To clarify the relation between the p62/SQSTM1 accumulation and antitumor immunity, we investigated the expression of p62/SQSTM1 and immune cell infiltration in tumor tissues obtained from patients with oral squamous cell carcinoma (OSCC). Patients and methods: Seventy-four patients with OSCC who underwent curative surgical resection were included in this study. Tumor sections were stained by immunohistochemistry for p62/SQSTM1; dendritic cells (CD1a); T cells (CD3); NK cells (CD56); HLA class I heavy chain; HLA class II; Ki-67; p53. Each expression level was evaluated, and the association with clinicopathological factors was also determined. Results: p62/SQSTM1 accumulation was observed in 24 of 74 (32.4 %) OSCC examined. The p62/SQSTM1 accumulation in tumor cells showed statistically significant positive correlation to HLA class I expression on tumor cells. Interestingly, in tumor margin regions, expression of p62/SQSTM1 in tumor cells was significantly associated with CD3+T cell infiltration, suggesting that anti-tumor specific T cells may infiltrate and recognize tumor cells as target cells. Moreover, p62/SQSTM1 accumulation in tumor cells was also significant correlated with vessel invasion by tumor cells. Conclusion: In OSCC, p62/SQSTM1 accumulation in tumor cells was likely to associate with increase of tumor antigenicity, resulting in the mobilization of T cells toward cancer nest. On the other hand, p62/SQSTM1 accumulation in tumor cells may also contribute malignant potential in OSCC. Further elucidation of the role of p62/SQSTM1 in antitumor immunity through autophagy is currently underway. Citation Format: Hideyuki Takahashi, Koichi Sakakura, Kyoichi Kaira, Minoru Toyoda, Tetsunari Oyama, Kazuaki Chikamatsu. Immunological significance of p62/SQSTM1 accumulation in oral squamous cell carcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 154. doi:10.1158/1538-7445.AM2014-154

An ethanolic extract of Artemisia dracunculus L. regulates gene expression of ubiquitin–proteasome system enzymes in skeletal muscle: Potential role in the treatment of sarcopenic obesity

ObjectiveObesity is linked to insulin resistance, a primary component of metabolic syndrome and type 2 diabetes. The problem of obesity-related insulin resistance is compounded when age-related skeletal muscle loss, called sarcopenia, occurs with obesity. Skeletal muscle loss results from elevated levels of protein degradation and prevention of obesity-related sarcopenic muscle loss will depend on strategies that target pathways involved in protein degradation. An extract from Artemisia dracunculus, termed PMI 5011, improves insulin signaling and increases skeletal muscle myofiber size in a rodent model of obesity-related insulin resistance. The aim of this study was to examine the effect of PMI 5011 on the ubiquitin–proteasome system, a central regulator of muscle protein degradation. MethodsGastrocnemius and vastus lateralis skeletal muscle was obtained from KK-Ay obese diabetic mice fed a control or 1% (w/w) PMI 5011-supplemented diet. Regulation of genes encoding enzymes of the ubiquitin–proteasome system was determined using real-time quantitative reverse transcriptase polymerase chain reaction. ResultsAlthough MuRF-1 ubiquitin ligase gene expression is consistently down-regulated in skeletal muscle, atrogin-1, Fbxo40, and Traf6 expression is differentially regulated by PMI 5011. Genes encoding other enzymes of the ubiquitin–proteasome system ranging from ubiquitin to ubiquitin-specific proteases are also regulated by PMI 5011. Additionally, expression of the gene encoding the microtubule-associated protein-1 light chain 3 (LC3), a ubiquitin-like protein pivotal to autophagy-mediated protein degradation, is down-regulated by PMI 5011 in the vastus lateralis. ConclusionPMI 5011 alters the gene expression of ubiquitin–proteasome system enzymes that are essential regulators of skeletal muscle mass. This suggests that PMI 5011 has therapeutic potential in the treatment of obesity-linked sarcopenia by regulating ubiquitin–proteasome-mediated protein degradation.

Multi-omic Data Integration Links Deleted in Breast Cancer 1 (DBC1) Degradation to Chromatin Remodeling in Inflammatory Response

This study investigated the dynamics of ubiquitinated proteins after the inflammatory stimulation of RAW 264.7 macrophage-like cells with bacterial lipopolysaccharide. Ubiquitination is a common protein post-translational modification that regulates many key cellular functions. We demonstrated that levels of global ubiquitination and K48 and K63 polyubiquitin chains change after lipopolysaccharide stimulation. Quantitative proteomic analysis identified 1199 ubiquitinated proteins, 78 of which exhibited significant changes in ubiquitination levels following stimulation. Integrating the ubiquitinome data with global proteomic and transcriptomic results allowed us to identify a subset of 88 proteins that were targeted for degradation after lipopolysaccharide stimulation. Using cellular assays and Western blot analyses, we biochemically validated DBC1 (a histone deacetylase inhibitor) as a degradation substrate that is targeted via an orchestrated mechanism utilizing caspases and the proteasome. The degradation of DBC1 releases histone deacetylase activity, linking lipopolysaccharide activation to chromatin remodeling in caspase- and proteasome-mediated signaling.

The Cdc48 Protein and Its Cofactor Vms1 Are Involved in Cdc13 Protein Degradation

Vms1 is a newly identified Cdc48-binding protein. The biological function of Vms1 remains obscure. Here, we show that both Cdc48 and Vms1, but not Cdc48 cofactors Ufd1 and Ufd2, are crucial for the degradation of Cdc13, a telomere regulator. Interestingly, both autophagy and the proteasome are involved in Cdc13 turnover. Toxicity associated with accumulation of large amounts of Cdc13 in vms1Δ or autophagy mutants underscores the significance of the proteolytic regulation of Cdc13. Because few ubiquitylated yeast proteins are known to be degraded by autophagy under non-stress conditions, the identification of Cdc13 as a target of autophagy provides a valuable tool to unravel the mechanism of autophagy-mediated selective protein degradation.