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      Control of protein stability by post-translational modifications

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          Abstract

          Post-translational modifications (PTMs) can occur on specific amino acids localized within regulatory domains of target proteins, which control a protein’s stability. These regions, called degrons, are often controlled by PTMs, which act as signals to expedite protein degradation (PTM-activated degrons) or to forestall degradation and stabilize a protein (PTM-inactivated degrons). We summarize current knowledge of the regulation of protein stability by various PTMs. We aim to display the variety and breadth of known mechanisms of regulation as well as highlight common themes in PTM-regulated degrons to enhance potential for identifying novel drug targets where druggable targets are currently lacking.

          Abstract

          Here the authors summarize current knowledge of the regulation of protein stability by various post-translational modifications (PTMs) including methylation and phosphorylation. PTM-regulated degrons act as signals for protein degradation or stabilization.

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          Global quantification of mammalian gene expression control.

          Björn Schwanhäusser, Dorothea Busse, Na Li … (2011)
          Gene expression is a multistep process that involves the transcription, translation and turnover of messenger RNAs and proteins. Although it is one of the most fundamental processes of life, the entire cascade has never been quantified on a genome-wide scale. Here we simultaneously measured absolute mRNA and protein abundance and turnover by parallel metabolic pulse labelling for more than 5,000 genes in mammalian cells. Whereas mRNA and protein levels correlated better than previously thought, corresponding half-lives showed no correlation. Using a quantitative model we have obtained the first genome-scale prediction of synthesis rates of mRNAs and proteins. We find that the cellular abundance of proteins is predominantly controlled at the level of translation. Genes with similar combinations of mRNA and protein stability shared functional properties, indicating that half-lives evolved under energetic and dynamic constraints. Quantitative information about all stages of gene expression provides a rich resource and helps to provide a greater understanding of the underlying design principles.
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            HIFalpha targeted for VHL-mediated destruction by proline hydroxylation: implications for O2 sensing.

            M Ivan, K Kondo, H. Yang … (2001)
            HIF (hypoxia-inducible factor) is a transcription factor that plays a pivotal role in cellular adaptation to changes in oxygen availability. In the presence of oxygen, HIF is targeted for destruction by an E3 ubiquitin ligase containing the von Hippel-Lindau tumor suppressor protein (pVHL). We found that human pVHL binds to a short HIF-derived peptide when a conserved proline residue at the core of this peptide is hydroxylated. Because proline hydroxylation requires molecular oxygen and Fe(2+), this protein modification may play a key role in mammalian oxygen sensing.
            Article 0 comments Cited 1047 times – based on 0 reviews     Review now
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              CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.

              Luke A Gilbert, Matthew Larson, Leonardo Morsut … (2013)
              The genetic interrogation and reprogramming of cells requires methods for robust and precise targeting of genes for expression or repression. The CRISPR-associated catalytically inactive dCas9 protein offers a general platform for RNA-guided DNA targeting. Here, we show that fusion of dCas9 to effector domains with distinct regulatory functions enables stable and efficient transcriptional repression or activation in human and yeast cells, with the site of delivery determined solely by a coexpressed short guide (sg)RNA. Coupling of dCas9 to a transcriptional repressor domain can robustly silence expression of multiple endogenous genes. RNA-seq analysis indicates that CRISPR interference (CRISPRi)-mediated transcriptional repression is highly specific. Our results establish that the CRISPR system can be used as a modular and flexible DNA-binding platform for the recruitment of proteins to a target DNA sequence, revealing the potential of CRISPRi as a general tool for the precise regulation of gene expression in eukaryotic cells. Copyright © 2013 Elsevier Inc. All rights reserved.
              Article 0 comments Cited 705 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Sung Hee Baek:
                ORCID: http://orcid.org/0000-0002-0588-8243
                sbaek@snu.ac.kr
                Journal
                Journal ID (nlm-ta): Nat Commun
                Journal ID (iso-abbrev): Nat Commun
                Title: Nature Communications
                Publisher: Nature Publishing Group UK (London )
                ISSN (Electronic): 2041-1723
                Publication date (Electronic): 13 January 2023
                Publication date PMC-release: 13 January 2023
                Publication date Collection: 2023
                Volume: 14
                Electronic Location Identifier: 201
                Affiliations
                [1 ]GRID grid.37172.30, ISNI 0000 0001 2292 0500, Graduate School of Medical Science & Engineering, , Korea Advanced Institute of Science and Technology, ; Daejeon, 34141 Korea
                [2 ]GRID grid.4709.a, ISNI 0000 0004 0495 846X, Genome Biology Unit, , European Molecular Biology Laboratory, ; 69117 Heidelberg, Germany
                [3 ]GRID grid.31501.36, ISNI 0000 0004 0470 5905, Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, , Seoul National University, ; Seoul, 08826 Korea
                Author information
                http://orcid.org/0000-0003-2978-2440
                http://orcid.org/0000-0003-2011-9247
                http://orcid.org/0000-0002-0588-8243
                Article
                Publisher ID: 35795
                DOI: 10.1038/s41467-023-35795-8
                PMC ID: 9839724
                PubMed ID: 36639369
                SO-VID: f5fe826b-919f-4702-92f3-574f6f9508ce
                Copyright © © The Author(s) 2023
                License:

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                Date received : 22 April 2021
                Date accepted : 2 January 2023
                Categories
                Subject: Review Article
                Custom metadata
                issue-copyright-statement © The Author(s) 2023

                ScienceOpen disciplines: Uncategorized
                Keywords: biochemistry,post-translational modifications
                Data availability:
                ScienceOpen disciplines: Uncategorized
                Keywords: biochemistry, post-translational modifications

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