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UPL5 modulates WHY2 protein distribution in a Kub-site dependent ubiquitination in response to [Ca2+]cyt-induced leaf senescence. iScience 2023; 26:106216. [PMID: 36994183 PMCID: PMC10040967 DOI: 10.1016/j.isci.2023.106216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/08/2023] [Accepted: 02/13/2023] [Indexed: 03/08/2023] Open
Abstract
The translocation of proteins between various compartments of cells is the simplest and most direct way of an/retrograde communication. However, the mechanism of protein trafficking is far understood. In this study, we showed that the alteration of WHY2 protein abundance in various compartments of cells was dependent on a HECT-type ubiquitin E3 ligase UPL5 interacting with WHY2 in the cytoplasm, plastid, and nucleus, as well as mitochondrion to selectively ubiquitinate various Kub-sites (Kub 45 and Kub 227) of WHY2. Plastid genome stability can be maintained by the UPL5-WHY2 module, accompany by the alteration of photosystem activity and senescence-associated gene expression. In addition, the specificity of UPL5 ubiquitinating various Kub-sites of WHY2 was responded to cold or CaCl2 stress, in a dose [Ca2+]cyt-dependent manner. This demonstrates the integration of the UPL5 ubiquitination with the regulation of WHY2 distribution and retrograde communication between organelle and nuclear events of leaf senescence.
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2
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Guharoy M, Lazar T, Macossay-Castillo M, Tompa P. Degron masking outlines degronons, co-degrading functional modules in the proteome. Commun Biol 2022; 5:445. [PMID: 35545699 PMCID: PMC9095673 DOI: 10.1038/s42003-022-03391-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/22/2022] [Indexed: 11/28/2022] Open
Abstract
Effective organization of proteins into functional modules (networks, pathways) requires systems-level coordination between transcription, translation and degradation. Whereas the cooperation between transcription and translation was extensively studied, the cooperative degradation regulation of protein complexes and pathways has not been systematically assessed. Here we comprehensively analyzed degron masking, a major mechanism by which cellular systems coordinate degron recognition and protein degradation. For over 200 substrates with characterized degrons (E3 ligase targeting motifs, ubiquitination sites and disordered proteasomal entry sequences), we demonstrate that degrons extensively overlap with protein-protein interaction sites. Analysis of binding site information and protein abundance comparisons show that regulatory partners effectively outcompete E3 ligases, masking degrons from the ubiquitination machinery. Protein abundance variations between normal and cancer cells highlight the dynamics of degron masking components. Finally, integrative analysis of gene co-expression, half-life correlations and functional relationships between interacting proteins point towards higher-order, co-regulated degradation modules (‘degronons’) in the proteome. Systematic bioinformatics analysis of cooperative degradation of protein complexes indicates that degrons extensively overlap with protein-protein interaction sites, hiding degrons from ubiquitination machinery and suggesting the existence of co-degrading functional modules in the proteome.
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Affiliation(s)
- Mainak Guharoy
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium. .,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium. .,VIB Bioinformatics Core, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium.
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Mauricio Macossay-Castillo
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium. .,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium. .,Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, 1117, Budapest, Hungary.
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Ubiquitin Ligase Redundancy and Nuclear-Cytoplasmic Localization in Yeast Protein Quality Control. Biomolecules 2021; 11:biom11121821. [PMID: 34944465 PMCID: PMC8698790 DOI: 10.3390/biom11121821] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022] Open
Abstract
The diverse functions of proteins depend on their proper three-dimensional folding and assembly. Misfolded cellular proteins can potentially harm cells by forming aggregates in their resident compartments that can interfere with vital cellular processes or sequester important factors. Protein quality control (PQC) pathways are responsible for the repair or destruction of these abnormal proteins. Most commonly, the ubiquitin-proteasome system (UPS) is employed to recognize and degrade those proteins that cannot be refolded by molecular chaperones. Misfolded substrates are ubiquitylated by a subset of ubiquitin ligases (also called E3s) that operate in different cellular compartments. Recent research in Saccharomyces cerevisiae has shown that the most prominent ligases mediating cytoplasmic and nuclear PQC have overlapping yet distinct substrate specificities. Many substrates have been characterized that can be targeted by more than one ubiquitin ligase depending on their localization, and cytoplasmic PQC substrates can be directed to the nucleus for ubiquitylation and degradation. Here, we review some of the major yeast PQC ubiquitin ligases operating in the nucleus and cytoplasm, as well as current evidence indicating how these ligases can often function redundantly toward substrates in these compartments.
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Hickey CM, Breckel C, Zhang M, Theune WC, Hochstrasser M. Protein quality control degron-containing substrates are differentially targeted in the cytoplasm and nucleus by ubiquitin ligases. Genetics 2021; 217:1-19. [PMID: 33683364 PMCID: PMC8045714 DOI: 10.1093/genetics/iyaa031] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/07/2020] [Indexed: 12/21/2022] Open
Abstract
Intracellular proteolysis by the ubiquitin-proteasome system regulates numerous processes and contributes to protein quality control (PQC) in all eukaryotes. Covalent attachment of ubiquitin to other proteins is specified by the many ubiquitin ligases (E3s) expressed in cells. Here we determine the E3s in Saccharomyces cerevisiae that function in degradation of proteins bearing various PQC degradation signals (degrons). The E3 Ubr1 can function redundantly with several E3s, including nuclear-localized San1, endoplasmic reticulum/nuclear membrane-embedded Doa10, and chromatin-associated Slx5/Slx8. Notably, multiple degrons are targeted by more ubiquitylation pathways if directed to the nucleus. Degrons initially assigned as exclusive substrates of Doa10 were targeted by Doa10, San1, and Ubr1 when directed to the nucleus. By contrast, very short hydrophobic degrons-typical targets of San1-are shown here to be targeted by Ubr1 and/or San1, but not Doa10. Thus, distinct types of PQC substrates are differentially recognized by the ubiquitin system in a compartment-specific manner. In human cells, a representative short hydrophobic degron appended to the C-terminus of GFP-reduced protein levels compared with GFP alone, consistent with a recent study that found numerous natural hydrophobic C-termini of human proteins can act as degrons. We also report results of bioinformatic analyses of potential human C-terminal degrons, which reveal that most peptide substrates of Cullin-RING ligases (CRLs) are of low hydrophobicity, consistent with previous data showing CRLs target degrons with specific sequences. These studies expand our understanding of PQC in yeast and human cells, including the distinct but overlapping PQC E3 substrate specificity of the cytoplasm and nucleus.
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Affiliation(s)
- Christopher M Hickey
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Carolyn Breckel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Mengwen Zhang
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - William C Theune
- Department of Biology and Environmental Science, University of New Haven, West Haven, CT 06516, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
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The degradation-promoting roles of deubiquitinases Ubp6 and Ubp3 in cytosolic and ER protein quality control. PLoS One 2020; 15:e0232755. [PMID: 32401766 PMCID: PMC7219781 DOI: 10.1371/journal.pone.0232755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/21/2020] [Indexed: 11/19/2022] Open
Abstract
The quality control of intracellular proteins is achieved by degrading misfolded proteins which cannot be refolded by molecular chaperones. In eukaryotes, such degradation is handled primarily by the ubiquitin-proteasome system. However, it remained unclear whether and how protein quality control deploys various deubiquitinases. To address this question, we screened deletions or mutation of the 20 deubiquitinase genes in Saccharomyces cerevisiae and discovered that almost half of the mutations slowed the removal of misfolded proteins whereas none of the remaining mutations accelerated this process significantly. Further characterization revealed that Ubp6 maintains the level of free ubiquitin to promote the elimination of misfolded cytosolic proteins, while Ubp3 supports the degradation of misfolded cytosolic and ER luminal proteins by different mechanisms.
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Abstract
Nuclear proteins participate in diverse cellular processes, many of which are essential for cell survival and viability. To maintain optimal nuclear physiology, the cell employs the ubiquitin-proteasome system to eliminate damaged and misfolded proteins in the nucleus that could otherwise harm the cell. In this review, we highlight the current knowledge about the major ubiquitin-protein ligases involved in protein quality control degradation (PQCD) in the nucleus and how they orchestrate their functions to eliminate misfolded proteins in different nuclear subcompartments. Many human disorders are causally linked to protein misfolding in the nucleus, hence we discuss major concepts that still need to be clarified to better understand the basis of the nuclear misfolded proteins' toxic effects. Additionally, we touch upon potential strategies for manipulating nuclear PQCD pathways to ameliorate diseases associated with protein misfolding and aggregation in the nucleus.
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Affiliation(s)
- Charisma Enam
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA; ,
| | - Yifat Geffen
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 91904, Israel; ,
| | - Tommer Ravid
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 91904, Israel; ,
| | - Richard G Gardner
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA; ,
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Hickey CM, Xie Y, Hochstrasser M. DNA binding by the MATα2 transcription factor controls its access to alternative ubiquitin-modification pathways. Mol Biol Cell 2018; 29:542-556. [PMID: 29298839 PMCID: PMC6004586 DOI: 10.1091/mbc.e17-10-0589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/19/2017] [Accepted: 12/27/2017] [Indexed: 11/16/2022] Open
Abstract
Like many transcription factors, the yeast protein MATalpha2 (α2) undergoes rapid proteolysis via the ubiquitin-proteasome system (UPS). At least two ubiquitylation pathways regulate α2 degradation: one pathway utilizes the ubiquitin ligase (E3) Doa10 and the other the heterodimeric E3 Slx5/Slx8. Doa10 is a transmembrane protein of the endoplasmic reticulum/inner nuclear membrane, whereas Slx5/Slx8 localizes to the nucleus and binds DNA nonspecifically. While a single protein can often be ubiquitylated by multiple pathways, the reasons for this “division of labor” are not well understood. Here we show that α2 mutants with impaired DNA binding become inaccessible to the Slx5/Slx8 pathway but are still rapidly degraded through efficient shunting to the Doa10 pathway. These results are consistent with the distinct localization of these E3s. We also characterized a novel class of DNA binding-defective α2 variants whose degradation is strongly impaired. Our genetic data suggest that this is due to a gain-of-function interaction that limits their access to Doa10. Together, these results suggest multiple ubiquitin-ligation mechanisms may have evolved to promote rapid destruction of a transcription factor that resides in distinct cellular subcompartments under different conditions. Moreover, gain-of-function mutations, which also occur with oncogenic forms of human transcription factors such as p53, may derail this fail-safe system.
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Affiliation(s)
- Christopher M Hickey
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520
| | - Yang Xie
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520
| | - Mark Hochstrasser
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520
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Engle SM, Crowder JJ, Watts SG, Indovina CJ, Coffey SZ, Rubenstein EM. Acetylation of N-terminus and two internal amino acids is dispensable for degradation of a protein that aberrantly engages the endoplasmic reticulum translocon. PeerJ 2017; 5:e3728. [PMID: 28848693 PMCID: PMC5571791 DOI: 10.7717/peerj.3728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/02/2017] [Indexed: 12/26/2022] Open
Abstract
Conserved homologues of the Hrd1 ubiquitin ligase target for degradation proteins that persistently or aberrantly engage the endoplasmic reticulum translocon, including mammalian apolipoprotein B (apoB; the major protein component of low-density lipoproteins) and the artificial yeast protein Deg1-Sec62. A complete understanding of the molecular mechanism by which translocon-associated proteins are recognized and degraded may inform the development of therapeutic strategies for cholesterol-related pathologies. Both apoB and Deg1-Sec62 are extensively post-translationally modified. Mass spectrometry of a variant of Deg1-Sec62 revealed that the protein is acetylated at the N-terminal methionine and two internal lysine residues. N-terminal and internal acetylation regulates the degradation of a variety of unstable proteins. However, preventing N-terminal and internal acetylation had no detectable consequence for Hrd1-mediated proteolysis of Deg1-Sec62. Our data highlight the importance of empirically validating the role of post-translational modifications and sequence motifs on protein degradation, even when such elements have previously been demonstrated sufficient to destine other proteins for destruction.
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Affiliation(s)
- Sarah M Engle
- Department of Biology, Ball State University, Muncie, IN, United States of America.,Immunology-Translational Science, Eli Lilly and Company, Indianapolis, IN, United States of America
| | - Justin J Crowder
- Department of Biology, Ball State University, Muncie, IN, United States of America.,Center for Medical Education, Indiana University School of Medicine, Muncie, IN, United States of America
| | - Sheldon G Watts
- Department of Biology, Ball State University, Muncie, IN, United States of America.,Marian University College of Osteopathic Medicine, Indianapolis, IN, United States of America
| | | | - Samuel Z Coffey
- Department of Biology, Ball State University, Muncie, IN, United States of America.,Medpace Reference Laboratories, Cincinnati, OH, United States of America
| | - Eric M Rubenstein
- Department of Biology, Ball State University, Muncie, IN, United States of America
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