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Ubiquitin Receptors and Associated Mechanisms Involved in Targeting Proteins Modified with Diverged Ubiquitin Signals to Distinct Cellular Processes

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (20 May 2024) | Viewed by 5388

Special Issue Editor

Dr. Hongyong Fu

E-Mail Website
Guest Editor
Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
Interests: ubiquitination; deubiquitination; mediated cellular processes in Arabidopsis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Ubiquitination is a pivotal regulatory mechanism for nearly all major cellular processes. For all eukaryotic organisms, it is essential for the growth and development of and the response to biotic and abiotic stresses. When catalyzing using many conjugation and deconjugation enzymes, the small and evolutionary conserved ubiquitin could be assembled and dynamically modulated on various protein substrates into highly diverged ubiquitin signals: ubiquitin monomer and ubiquitin chains with homogeneous, mixed, or branched linkages of various lengths. Depending on the different ubiquitin signals assembled, the outcomes of modified substrates could be rather distinct such as degradation by 26S proteasome, endocytosis, or the autophagy pathway. Various ubiquitin signals could also provide interfaces for relaying signal transduction pathways or for recruiting epigenetic regulatory and DNA repairing machineries. While the majority of ubiquitination studies focus on conjugation and deconjugation enzyme components and their corresponding physiological functions, little information is available for specific ubiquitin signals assembled on particular substrates in vivo or on corresponding ubiquitin binding factors for deciphering various ubiquitin signals and associated mechanisms en route to various cellular processes. This Special Issue will be focused on ubiquitin signal assembles on specific substrates and ubiquitin binding proteins involved in deciphering various ubiquitin signals for various cellular processes, such as various degradation pathways, signal transduction, epigenetic regulation, and DNA repairing. All related original articles, up-to-date reviews, and methodology papers will all be considered.     

Dr. Hong-yong Fu
Guest Editor

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Keywords

  • ubiquitin
  • ubiquitin signals
  • ubiquitin binding
  • ubiquitin receptor
  • 26S proteasome
  • endocytosis
  • autophagy
  • epigenetic regulation
  • DNA repair

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Published Papers (3 papers)

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Research

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30 pages, 4132 KiB  
Article
The Structural Role of RPN10 in the 26S Proteasome and an RPN2-Binding Residue on RPN13 Are Functionally Important in Arabidopsis
by Shih-Yun Lin, Ya-Ling Lin, Raju Usharani, Ramalingam Radjacommare and Hongyong Fu
Int. J. Mol. Sci. 2024, 25(21), 11650; https://doi.org/10.3390/ijms252111650 - 30 Oct 2024
Viewed by 1234
Abstract
The ubiquitin receptors RPN10 and RPN13 harbor multiple activities including ubiquitin binding; however, solid evidence connecting a particular activity to specific in vivo functions is scarce. Through complementation, the ubiquitin-binding site-truncated Arabidopsis RPN10 (N215) rescued the growth defects of rpn10-2, supporting the [...] Read more.
The ubiquitin receptors RPN10 and RPN13 harbor multiple activities including ubiquitin binding; however, solid evidence connecting a particular activity to specific in vivo functions is scarce. Through complementation, the ubiquitin-binding site-truncated Arabidopsis RPN10 (N215) rescued the growth defects of rpn10-2, supporting the idea that the ubiquitin-binding ability of RPN10 is dispensable and N215, which harbors a vWA domain, is fully functional. Instead, a structural role played by RPN10 in the 26S proteasomes is likely vital in vivo. A site-specific variant, RPN10-11A, that likely has a destabilized vWA domain could partially rescue the rpn10-2 growth defects and is not integrated into 26S proteasomes. Native polyacrylamide gel electrophoresis and mass spectrometry with rpn10-2 26S proteasomes showed that the loss of RPN10 reduced the abundance of double-capped proteasomes, induced the integration of specific subunit paralogues, and increased the association of ECM29, a well-known factor critical for quality checkpoints by binding and inhibiting aberrant proteasomes. Extensive Y2H and GST-pulldown analyses identified RPN2-binding residues on RPN13 that overlapped with ubiquitin-binding and UCH2-binding sites in the RPN13 C-terminus (246–254). Interestingly, an analysis of homozygous rpn10-2 segregation in a rpn13-1 background harboring RPN13 variants defective for ubiquitin binding and/or RPN2 binding supports the criticality of the RPN13–RPN2 association in vivo. Full article
(This article belongs to the Special Issue Ubiquitin Receptors and Associated Mechanisms Involved in Targeting Proteins Modified with Diverged Ubiquitin Signals to Distinct Cellular Processes)
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12 pages, 2764 KiB  
Article
Proximal Co-Translation Facilitates Detection of Weak Protein-Protein Interactions
by Alina Kordonsky, Matan Gabay, Aurelia Rosinoff, Reut Avishid, Amir Flornetin, Noam Deouell, Taimaa Abd Alkhaleq, Noa Efron, Shoham Milshtein, Julia M. Shifman, Maayan Gal and Gali Prag
Int. J. Mol. Sci. 2024, 25(20), 11099; https://doi.org/10.3390/ijms252011099 - 16 Oct 2024
Viewed by 1035
Abstract
Ubiquitin (Ub) signals are recognized and decoded into cellular responses by Ub-receptors, proteins that tether the Ub-binding domain(s) (UBDs) with response elements. Typically, UBDs bind mono-Ub in highly dynamic and weak affinity manners, presenting challenges in identifying and characterizing their binding interfaces. Here, [...] Read more.
Ubiquitin (Ub) signals are recognized and decoded into cellular responses by Ub-receptors, proteins that tether the Ub-binding domain(s) (UBDs) with response elements. Typically, UBDs bind mono-Ub in highly dynamic and weak affinity manners, presenting challenges in identifying and characterizing their binding interfaces. Here, we report the development of a new approach to facilitate the detection of these weak interactions using split-reporter systems where two interacting proteins are proximally co-translated from a single mRNA. This proximity significantly enhances the readout signals of weak protein–protein interactions (PPIs). We harnessed this system to characterize the ultra-weak UBD and ENTH (Epsin N-terminal Homology) and discovered that the yeast Ent1-ENTH domain contains two Ub-binding patches. One is similar to a previously characterized patch on STAM1(signal-transducing adaptor molecule)-VHS (Vps27, Hrs, and STAM), and the other was predicted by AlphaFold. Using a split-CAT selection system that co-translates Ub and ENTH in combination with mutagenesis, we assessed and confirmed the existence of a novel binding patch around residue F53 on ENTH. Co-translation in the split-CAT system provides an effective tool for studying weak PPIs and offers new insights into Ub-receptor interactions. Full article
(This article belongs to the Special Issue Ubiquitin Receptors and Associated Mechanisms Involved in Targeting Proteins Modified with Diverged Ubiquitin Signals to Distinct Cellular Processes)
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Review

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17 pages, 1034 KiB  
Review
Lysine Methylation-Dependent Proteolysis by the Malignant Brain Tumor (MBT) Domain Proteins
by Hong Sun and Hui Zhang
Int. J. Mol. Sci. 2024, 25(4), 2248; https://doi.org/10.3390/ijms25042248 - 13 Feb 2024
Cited by 1 | Viewed by 2342
Abstract
Lysine methylation is a major post-translational protein modification that occurs in both histones and non-histone proteins. Emerging studies show that the methylated lysine residues in non-histone proteins provide a proteolytic signal for ubiquitin-dependent proteolysis. The SET7 (SETD7) methyltransferase specifically transfers a methyl group [...] Read more.
Lysine methylation is a major post-translational protein modification that occurs in both histones and non-histone proteins. Emerging studies show that the methylated lysine residues in non-histone proteins provide a proteolytic signal for ubiquitin-dependent proteolysis. The SET7 (SETD7) methyltransferase specifically transfers a methyl group from S-Adenosyl methionine to a specific lysine residue located in a methylation degron motif of a protein substrate to mark the methylated protein for ubiquitin-dependent proteolysis. LSD1 (Kdm1a) serves as a demethylase to dynamically remove the methyl group from the modified protein. The methylated lysine residue is specifically recognized by L3MBTL3, a methyl-lysine reader that contains the malignant brain tumor domain, to target the methylated proteins for proteolysis by the CRL4DCAF5 ubiquitin ligase complex. The methylated lysine residues are also recognized by PHF20L1 to protect the methylated proteins from proteolysis. The lysine methylation-mediated proteolysis regulates embryonic development, maintains pluripotency and self-renewal of embryonic stem cells and other stem cells such as neural stem cells and hematopoietic stem cells, and controls other biological processes. Dysregulation of the lysine methylation-dependent proteolysis is associated with various diseases, including cancers. Characterization of lysine methylation should reveal novel insights into how development and related diseases are regulated. Full article
(This article belongs to the Special Issue Ubiquitin Receptors and Associated Mechanisms Involved in Targeting Proteins Modified with Diverged Ubiquitin Signals to Distinct Cellular Processes)
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