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The Not4 ubiquitin ligase utilizes its conserved RNA binding domains to regulate global proteostasis and RNA polymerase II-dependent transcription

ABSTRACT: The conserved Ccr4-Not complex regulates all aspects of the RNA polymerase II (Pol II) gene expression pathway, while it also controls proteasome assembly and function. The Not4 RING domain ubiquitin ligase is a core subunit that also contains an RNA recognition motif (RRM) and C3H1 domain (collectively referred to as the RRM-C) whose function is unknown. Herein, we demonstrate that the Not4 RRM-C contributes to both Not4-dependent regulation of the proteasome and Pol II. Disruption of both Not4 ligase activity and the RRM-C domain simultaneously replicates the proteasome-dependent deubiquitylation and catalytic activity misregulation found in Not4-deficient cells. Transcriptome analysis reveals that the Not4 RRM-C affects a subset of Pol II-dependent genes involved in specific biological functions, including transcription elongation, cyclin-dependent kinase regulated nutrient responses, and ribosomal biogenesis. At these genes, the Not4 RRM-C negatively regulates Pol II binding. While Not4 RRM-C disruption modestly increases between Ccr4-Not and Pol II, a Not4 ligase mutant decreases Ccr4-Not association with Pol II, thus implicating Not4-dependent ubiquitylation in mediating Ccr4-Not interaction with Pol II. Collectively, our results suggests the cellular RNA environment may integrate control of global proteostasis and Pol II transcription through the Not4 ubiquitin ligase.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE102192 | GEO | 2017/08/03

SECONDARY ACCESSION(S): PRJNA396954

REPOSITORIES: GEO

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Project description:Proctor2007 - Age related decline of proteolysis, ubiquitin-proteome system This is a stochastic model of the ubiquitin-proteasome system for a generic pool of native proteins (NatP), which have a half-life of about 10 hours under normal conditions. It is assumed that these proteins are only degraded after they have lost their native structure due to a damage event. This is represented in the model by the misfolding reaction which depends on the level of reactive oxygen species (ROS) in the cell. Misfolded proteins (MisP) are first bound by an E3 ubiquitin ligase. Ubiquitin (Ub) is activated by E1 (ubiquitin-activating enzyme) and then passed to E2 (ubiquitin-conjugating enzyme). The E2 enzyme then passes the ubiquitin molecule to the E3/MisP complex with the net effect that the misfolded protein is monoubiquitinated and both E2 and E3 are released. Further ubiquitin molecules are added in a step-wise manner. When the chain of ubiquitin molecules is of length 4 or more, the polyubiquitinated misfolded protein may bind to the proteasome. The model also includes de-ubiquitinating enzymes (DUB) which cleave ubiquitin molecules from the chain in a step-wise manner. They work on chains attached to misfolded proteins both unbound and bound to the proteasomes. Misfolded proteins bound to the proteasome may be degraded releasing ubiquitin. Misfolded proteins including ubiquitinated proteins may also aggregate. Aggregates (AggP) may be sequestered (Seq_AggP) which takes them out of harm's way or they may bind to the proteasome (AggP_Proteasome). Proteasomes bound by aggregates are no longer available for protein degradation. Figure 2 and Figure 3 has been simulated using Gillespie2. This model is described in the article: An in silico model of the ubiquitin-proteasome system that incorporates normal homeostasis and age-related decline. Proctor CJ, Tsirigotis M, Gray DA. BMC Syst Biol 2007; 1: 17 Abstract: BACKGROUND: The ubiquitin-proteasome system is responsible for homeostatic degradation of intact protein substrates as well as the elimination of damaged or misfolded proteins that might otherwise aggregate. During ageing there is a decline in proteasome activity and an increase in aggregated proteins. Many neurodegenerative diseases are characterised by the presence of distinctive ubiquitin-positive inclusion bodies in affected regions of the brain. These inclusions consist of insoluble, unfolded, ubiquitinated polypeptides that fail to be targeted and degraded by the proteasome. We are using a systems biology approach to try and determine the primary event in the decline in proteolytic capacity with age and whether there is in fact a vicious cycle of inhibition, with accumulating aggregates further inhibiting proteolysis, prompting accumulation of aggregates and so on. A stochastic model of the ubiquitin-proteasome system has been developed using the Systems Biology Mark-up Language (SBML). Simulations are carried out on the BASIS (Biology of Ageing e-Science Integration and Simulation) system and the model output is compared to experimental data wherein levels of ubiquitin and ubiquitinated substrates are monitored in cultured cells under various conditions. The model can be used to predict the effects of different experimental procedures such as inhibition of the proteasome or shutting down the enzyme cascade responsible for ubiquitin conjugation. RESULTS: The model output shows good agreement with experimental data under a number of different conditions. However, our model predicts that monomeric ubiquitin pools are always depleted under conditions of proteasome inhibition, whereas experimental data show that monomeric pools were depleted in IMR-90 cells but not in ts20 cells, suggesting that cell lines vary in their ability to replenish ubiquitin pools and there is the need to incorporate ubiquitin turnover into the model. Sensitivity analysis of the model revealed which parameters have an important effect on protein turnover and aggregation kinetics. CONCLUSION: We have developed a model of the ubiquitin-proteasome system using an iterative approach of model building and validation against experimental data. Using SBML to encode the model ensures that it can be easily modified and extended as more data become available. Important aspects to be included in subsequent models are details of ubiquitin turnover, models of autophagy, the inclusion of a pool of short-lived proteins and further details of the aggregation process. This model is hosted on BioModels Database and identified by: BIOMD0000000105. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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The Not4 ubiquitin ligase utilizes its conserved RNA binding domains to regulate global proteostasis and RNA polymerase II-dependent transcription

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