Roles of SCF and VHL ubiquitin ligases in regulation of cell growth

Protein Homeostasis Networks and the Use of Yeast to Guide Interventions in Alzheimer's Disease

Alzheimer's Disease (AD) is a progressive multifactorial age-related neurodegenerative disorder that causes the majority of deaths due to dementia in the elderly. Although various risk factors have been found to be associated with AD progression, the cause of the disease is still unresolved. The loss of proteostasis is one of the major causes of AD: it is evident by aggregation of misfolded proteins, lipid homeostasis disruption, accumulation of autophagic vesicles, and oxidative damage during the disease progression. Different models have been developed to study AD, one of which is a yeast model. Yeasts are simple unicellular eukaryotic cells that have provided great insights into human cell biology. Various yeast models, including unmodified and genetically modified yeasts, have been established for studying AD and have provided significant amount of information on AD pathology and potential interventions. The conservation of various human biological processes, including signal transduction, energy metabolism, protein homeostasis, stress responses, oxidative phosphorylation, vesicle trafficking, apoptosis, endocytosis, and ageing, renders yeast a fascinating, powerful model for AD. In addition, the easy manipulation of the yeast genome and availability of methods to evaluate yeast cells rapidly in high throughput technological platforms strengthen the rationale of using yeast as a model. This review focuses on the description of the proteostasis network in yeast and its comparison with the human proteostasis network. It further elaborates on the AD-associated proteostasis failure and applications of the yeast proteostasis network to understand AD pathology and its potential to guide interventions against AD.

Modeling and analysis of modular structure in diverse biological networks

Biological networks, like most engineered networks, are not the product of a singular design but rather are the result of a long process of refinement and optimization. Many large real-world networks are comprised of well-defined and meaningful smaller modules. While engineered networks are designed and refined by humans with particular goals in mind, biological networks are created by the selective pressures of evolution. In this paper, we seek to define aspects of network architecture that are shared among different types of evolved biological networks. First, we developed a new mathematical model, the Stochastic Block Model with Path Selection (SBM-PS) that simulates biological network formation based on the selection of edges that increase clustering. SBM-PS can produce modular networks whose properties resemble those of real networks. Second, we analyzed three real networks of very different types, and showed that all three can be fit well by the SBM-PS model. Third, we showed that modular elements within the three networks correspond to meaningful biological structures. The networks chosen for analysis were a proteomic network composed of all proteins required for mitochondrial function in budding yeast, a mesoscale anatomical network composed of axonal connections among regions of the mouse brain, and the connectome of individual neurons in the nematode C. elegans. We find that the three networks have common architectural features, and each can be divided into subnetworks with characteristic topologies that control specific phenotypic outputs.

Isoform-specific regulation of a steroid hormone nuclear receptor by an E3 ubiquitin ligase in Drosophila melanogaster

The steroid hormone 20-hydroxyecdysone (20E) regulates gene transcription through the heterodimeric nuclear receptor composed of ecdysone receptor (EcR) and Ultraspiracle (USP). The EcR gene encodes three protein isoforms--A, B1, and B2--with variant N-terminal domains that mediate tissue and developmental stage-specific responses to 20E. Ariadne-1a is a conserved member of the RING finger family of ubiquitin ligases first identified in Drosophila melanogaster. Loss-of-function mutations at key cysteines in either of the two RING finger motifs, as well as general overexpression of this enzyme, cause lethality in pupae, which suggests a requirement in metamorphosis. Here, we show that Ariadne-1a binds specifically the isoform A of EcR and ubiquitylates it. Co-immunoprecipitation experiments indicate that the full sequence of EcRA is required for this binding. Protein levels of EcRA and USP change in opposite directions when those of ARI-1a are genetically altered. This is an isoform-specific, E3-dependent regulatory mechanism for a steroid nuclear receptor. Further, qRT-PCR experiments show that the ARI-1a levels lead to the transcriptional regulation of Eip78C, Eip74EF, Eip75B, and Br-C, as well as that of EcR and usp genes. Thus, the activity of this enzyme results in the regulation of dimerizing receptors at the protein and gene transcription levels. This fine-tuned orchestration by a conserved ubiquitin ligase is required during insect metamorphosis and, likely, in other steroid hormone-controlled processes across species.

Molecular cloning and characterization of FBXO47, a novel gene containing an F-box domain, located in the 17q12 band deleted in papillary renal cell carcinoma

Genetic alterations of chromosome arm 17q occur in numerous tumor types, including breast and ovarian tumors, suggesting the presence of a tumor-suppressor gene on the long arm of chromosome 17 that is critical for carcinogenesis. Previous studies have shown an allelic imbalance (70% gain or loss) of 17q in papillary renal cell carcinoma (pRCC). In this study, we analyzed 15 cases of pRCC for loss of heterozygosity with the use of 7 microsatellite markers between 17q11 and 17q23. We identified a minimal deleted region in which the D17S250 marker (17q12) was deleted in 50% (7 of 14) of informative cases. We isolated the cDNA of a novel gene named FBXO47, which is near D17S250. Human FBXO47 is composed of 11 exons and spans approximately 30 kb of genomic DNA. FBXO47 cDNA consists of 2,269 bp with a 1,359-bp open-reading frame. Of note is that FBXO47 is preferentially expressed in normal tissue relative to the corresponding tumor tissue, particularly in the kidney, liver, and pancreas and to a lesser extent in the thyroid gland, stomach, and small intestine. The putative protein encoded by this gene is made up of 453 amino acids and belongs to the F-box family, most of whose members, such as SKP2 and FBW7, have been implicated in carcinogenesis. Together, these results indicate that FBX047 has a potential role as a tumor-suppressor gene.

TMF/ARA160 is a BC-box-containing protein that mediates the degradation of Stat3

TMF/ARA160 is a Golgi resident protein whose cellular functions have not been conclusively revealed. Herein we show that TMF/ARA160 can direct the proteasomal degradation of the key cell growth regulator - Stat3. TMF/ARA160 was dispersed in the cytoplasm of myogenic C2C12 cells that were grown under low-serum conditions. The cytoplasmic distribution of TMF/ARA160 was accompanied by its transient association with the tyrosine kinase Fer and with Stat3, which underwent proteasomal degradation under those conditions. Moreover, serum deprivation induced the association of ubiquitinated proteins, with the TMF/ARA160 complex. However, TMF/ARA160 did not bind Stat1, whose cellular levels were increased in serum-starved C2C12 cells. Amino-acid sequence analysis identified a BC-box element in TMF/ARA160 that mediated the binding of this protein to elongin C. Ectopic expression of TMF/ARA160 in serum-starved C2C12 cells drove the ubiquitination and proteasomal degradation of Stat3, an effect that was not caused by TMF/ARA160 devoid of the BC-box motif. Thus, the Golgi apparatus harbors a novel BC-box-containing protein that can direct Stat3 to proteasomal degradation. Interestingly, the level of TMF/ARA160 was significantly decreased in malignant brain tumors, implying a suppressive role of that protein in tumor progression.

Cks1 is degraded via the ubiquitin-proteasome pathway in a cell cycle-dependent manner

BACKGROUND

Recent work has demonstrated the role of cdc kinase subunit 1 (Cks1) in the ubiquitin-proteasome dependent degradation of CDK inhibitor p27Kip1 protein as an essential cofactor for SCFSkp2 ubiquitin ligase. Although over-expression of Cks1 protein as well as it of Skp2 might be associated with tumour progression via p27Kip1 protein degradation, it is unknown how the cellular level of Cks1 is regulated.

RESULTS

Here we show that Cks1 protein is degraded via the ubiquitin-proteasome pathway. Degradation of Cks1 protein was markedly inhibited by proteasome inhibitors. In addition, Cks1 protein was modified with polyubiquitin chains both in vivo and in vitro. Furthermore, we found that degradation of Cks1 protein via the ubiquitin-proteasome pathway was facilitated in M phase during the cell cycle.

CONCLUSION

These observations suggest that the level of expression of Cks1 protein is regulated at not only the transcriptional level but also the post-translational level via the ubiquitin-proteasome pathway in a cell-cycle-dependent manner.