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      The E3 ubiquitin ligase UBR 5 interacts with the H/ ACA ribonucleoprotein complex and regulates ribosomal RNA biogenesis in embryonic stem cells

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          Abstract

          UBR5 is an E3 ubiquitin ligase involved in distinct processes such as transcriptional regulation and development. UBR5 is highly upregulated in embryonic stem cells (ESCs), whereas its expression decreases with differentiation, suggesting a role for UBR5 in ESC function. However, little is known about how UBR5 regulates ESC identity. Here, we define the protein interactome of UBR5 in ESCs and find interactions with distinct components of the H/ACA ribonucleoprotein complex, which is required for proper maturation of ribosomal RNA (rRNA). Notably, loss of UBR5 induces an abnormal accumulation of rRNA processing intermediates, resulting in diminished ribosomal levels. Consequently, lack of UBR5 triggers an increase in p53 levels and a concomitant decrease in cellular proliferation rates. Thus, our results indicate a link between UBR5 and rRNA maturation.

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          RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts.

          Jack Keene, Jordan Komisarow, Matthew B Friedersdorf (2006)
          RNA targets of multitargeted RNA-binding proteins (RBPs) can be studied by various methods including mobility shift assays, iterative in vitro selection techniques and computational approaches. These techniques, however, cannot be used to identify the cellular context within which mRNAs associate, nor can they be used to elucidate the dynamic composition of RNAs in ribonucleoprotein (RNP) complexes in response to physiological stimuli. But by combining biochemical and genomics procedures to isolate and identify RNAs associated with RNA-binding proteins, information regarding RNA-protein and RNA-RNA interactions can be examined more directly within a cellular context. Several protocols--including the yeast three-hybrid system and immunoprecipitations that use physical or chemical cross-linking--have been developed to address this issue. Cross-linking procedures in general, however, are limited by inefficiency and sequence biases. The approach outlined here, termed RNP immunoprecipitation-microarray (RIP-Chip), allows the identification of discrete subsets of RNAs associated with multi-targeted RNA-binding proteins and provides information regarding changes in the intracellular composition of mRNPs in response to physical, chemical or developmental inducements of living systems. Thus, RIP-Chip can be used to identify subsets of RNAs that have related functions and are potentially co-regulated, as well as proteins that are associated with them in RNP complexes. Using RIP-Chip, the identification and/or quantification of RNAs in RNP complexes can be accomplished within a few hours or days depending on the RNA detection method used.
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            Signaling to p53: ribosomal proteins find their way.

            Yanping Zhang, Hua Lu (2009)
            Inherently disparate cell growth and division, which are intimately coupled through a delicate network of intracellular and extracellular signaling, require ribosomal biogenesis. A number of events imparting instability to ribosomal biogenesis can cause nucleolar stress. In response to this stress, several ribosomal proteins bind to MDM2 and block MDM2-mediated p53 ubiquitination and degradation, resulting in p53-dependent cell cycle arrest. By doing so, the ribosomal proteins play a crucial role in connecting deregulated cell growth with inhibition of cell division. The ribosomal protein-MDM2-p53 signaling pathway provides a molecular switch that may constitute a surveillance network monitoring the integrity of ribosomal biogenesis.
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              The post-transcriptional steps of eukaryotic ribosome biogenesis.

              A K Henras, J Soudet, M Gerus … (2008)
              One of the most important tasks of any cell is to synthesize ribosomes. In eukaryotes, this process occurs sequentially in the nucleolus, the nucleoplasm and the cytoplasm. It involves the transcription and processing of pre-ribosomal RNAs, their proper folding and assembly with ribosomal proteins and the transport of the resulting pre-ribosomal particles to the cytoplasm where final maturation events occur. In addition to the protein and RNA constituents of the mature cytoplasmic ribosomes, this intricate process requires the intervention of numerous protein and small RNA trans-acting factors. These transiently interact with pre-ribosomal particles at various stages of their maturation. Most of the constituents of pre-ribosomal particles have probably now been identified and research in the field is starting to unravel the timing of their intervention and their precise mode of action. Moreover, quality control mechanisms are being discovered that monitor ribosome synthesis and degrade the RNA components of defective pre-ribosomal particles.
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                Author and article information

                Journal
                Title: FEBS Letters
                Abbreviated Title: FEBS Lett
                Publisher: Wiley
                ISSN (Print): 0014-5793
                ISSN (Electronic): 1873-3468
                Publication date Created: August 08 2019
                Publication date Created: January 2020
                Publication date (Electronic): August 08 2019
                Publication date (Print): January 2020
                Volume: 594
                Issue: 1
                Pages: 175-188
                Affiliations
                [1 ]Institute for Genetics and Cologne Excellence Cluster for Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Germany
                [2 ]Institute for Genetics Department of Biology University of Cologne Germany
                [3 ]Max Planck Institute for Biology of Ageing Cologne Germany
                [4 ]Section of Bioinformatics and Systems Cardiology Department of Internal Medicine III and Klaus Tschira Institute for Computational Cardiology, University Hospital Heidelberg Germany
                Article
                DOI: 10.1002/1873-3468.13559
                PubMed ID: 31365120
                SO-VID: 75d63393-6e4f-46c0-806c-c203b2ad666b
                Copyright © © 2020
                License:

                http://creativecommons.org/licenses/by/4.0/

                http://doi.wiley.com/10.1002/tdm_license_1.1

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