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The Ubiquitin Code in Cellular Signaling and Homeostasis
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The Ubiquitin Code in Cellular Signaling and Homeostasis

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

Deadline for manuscript submissions: closed (30 January 2020) | Viewed by 18877

Special Issue Editors

Dr. Enrico Bracco

E-Mail Website
Guest Editor
Department of Oncology, University of Turin, 10043 Turin, Italy
Interests: signal transduction; G-protein; GPCR; ubiquitin; peroxisome; lipid; Dictyostelium
Special Issues, Collections and Topics in MDPI journals
Dr. Barbara Pergolizzi

E-Mail Website
Guest Editor
Department of Oncology, University of Turin, 10043 Turin, Italy
Interests: ubiquitination system; chemotaxis and aerotaxis; omics science; simple model; leukemia and cancer
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Ubiquitylation has long been implicated in proteasomal degradation, though many of its non-proteolytic functions are key regulators of cellular homeostasis.

The ubiquitylation of a protein, as well as the synthesis of free polyubiquitin chains, is a process involving the action of three classes of enzymes: E1, E2, and E3. The E3 ligases, responsible for substrate specificity, are classified as RING, RBR, or HECT. Conversely, ubiquitin removal is catalyzed by deubiquitylating enzymes (DUBs). Ubiquitin conjugates adopt distinct conformational ensembles that can be recognized by effector proteins that recognize ubiquitin via specific ubiquitin-binding domains (UBDs). Thus, ubiquitin—either as monomer or as chains—can encode information that is deciphered by UBDs to trigger specific biological outcomes.

This Special Issue aims to include contributions from scientists with a long-standing interest in ubiquitination as a central player in regulating cell signaling and homeostasis.

Dr. Enrico Bracco
Dr. Barbara Pergolizzi
Guest Editors

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Published Papers (4 papers)

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Research

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18 pages, 3573 KiB  
Article
Diversifying Evolution of the Ubiquitin-26S Proteasome System in Brassicaceae and Poaceae
by Zhihua Hua and Peifeng Yu
Int. J. Mol. Sci. 2019, 20(13), 3226; https://doi.org/10.3390/ijms20133226 - 30 Jun 2019
Cited by 15 | Viewed by 3744
Abstract
Genome amplification and sequence divergence provides raw materials to allow organismal adaptation. This is exemplified by the large expansion of the ubiquitin-26S proteasome system (UPS) in land plants, which primarily rely on intracellular signaling and biochemical metabolism to combat biotic and abiotic stresses. [...] Read more.
Genome amplification and sequence divergence provides raw materials to allow organismal adaptation. This is exemplified by the large expansion of the ubiquitin-26S proteasome system (UPS) in land plants, which primarily rely on intracellular signaling and biochemical metabolism to combat biotic and abiotic stresses. While a handful of functional genomic studies have demonstrated the adaptive role of the UPS in plant growth and development, many UPS members remain unknown. In this work, we applied a comparative genomic study to address the functional divergence of the UPS at a systematic level. We first used a closing-target-trimming annotation approach to identify most, if not all, UPS members in six species from each of two evolutionarily distant plant families, Brassicaceae and Poaceae. To reduce age-related errors, the two groups of species were selected based on their similar chronological order of speciation. Through size comparison, chronological expansion inference, evolutionary selection analyses, duplication mechanism prediction, and functional domain enrichment assays, we discovered significant diversities within the UPS, particularly between members from its three largest ubiquitin ligase gene families, the F-box (FBX), the Really Interesting New Gene (RING), and the Bric-a-Brac/Tramtrack/Broad Complex (BTB) families, between Brassicaceae and Poaceae. Uncovering independent Arabidopsis and Oryza genus–specific subclades of the 26S proteasome subunits from a comprehensive phylogenetic analysis further supported a diversifying evolutionary model of the UPS in these two genera, confirming its role in plant adaptation. Full article
(This article belongs to the Special Issue The Ubiquitin Code in Cellular Signaling and Homeostasis)
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12 pages, 2099 KiB  
Article
Reversible Regulation of Polyubiquitin Gene UBC via Modified Inducible CRISPR/Cas9 System
by Seung-Woo Han, Byung-Kwon Jung, So-Hyun Park and Kwon-Yul Ryu
Int. J. Mol. Sci. 2019, 20(13), 3168; https://doi.org/10.3390/ijms20133168 - 28 Jun 2019
Cited by 5 | Viewed by 3838
Abstract
Ubiquitin is required under both normal and stress conditions. Under stress conditions, upregulation of the polyubiquitin gene UBC is essential to meet the requirement of increased ubiquitin levels to confer stress resistance. However, UBC upregulation is usually observed only under stress conditions and [...] Read more.
Ubiquitin is required under both normal and stress conditions. Under stress conditions, upregulation of the polyubiquitin gene UBC is essential to meet the requirement of increased ubiquitin levels to confer stress resistance. However, UBC upregulation is usually observed only under stress conditions and not under normal conditions. Therefore, it has not been possible to upregulate UBC under normal conditions to study the effect of excess ubiquitin on cellular machinery. Recently, the CRISPR/Cas9 system has been widely used in biological research as a useful tool to study gene disruption effects. In this study, using an inducible CRISPR/Cas9 variant, a dCas9–VP64 fusion protein, combined with a single guide RNA (sgRNA) containing MS2 aptamer loops and MS2-p65-HSF1, we developed a system to increase the ubiquitin pool via upregulation of UBC. Although it is challenging to upregulate the expression of a gene that is already expressed at high levels, the significance of our system is that UBC upregulation can be induced in an efficient, reversible manner that is compatible with cellular processes, even under normal conditions. This system can be used to study ubiquitin pool dynamics and it will be a useful tool in identifying the role of ubiquitin under normal and stress conditions. Full article
(This article belongs to the Special Issue The Ubiquitin Code in Cellular Signaling and Homeostasis)
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Review

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26 pages, 861 KiB  
Review
The Role of Ubiquitination in Regulating Embryonic Stem Cell Maintenance and Cancer Development
by Dian Wang, Fan Bu and Weiwei Zhang
Int. J. Mol. Sci. 2019, 20(11), 2667; https://doi.org/10.3390/ijms20112667 - 30 May 2019
Cited by 19 | Viewed by 5530
Abstract
Ubiquitination regulates nearly every aspect of cellular events in eukaryotes. It modifies intracellular proteins with 76-amino acid polypeptide ubiquitin (Ub) and destines them for proteolysis or activity alteration. Ubiquitination is generally achieved by a tri-enzyme machinery involving ubiquitin activating enzymes (E1), ubiquitin conjugating [...] Read more.
Ubiquitination regulates nearly every aspect of cellular events in eukaryotes. It modifies intracellular proteins with 76-amino acid polypeptide ubiquitin (Ub) and destines them for proteolysis or activity alteration. Ubiquitination is generally achieved by a tri-enzyme machinery involving ubiquitin activating enzymes (E1), ubiquitin conjugating enzymes (E2) and ubiquitin ligases (E3). E1 activates Ub and transfers it to the active cysteine site of E2 via a transesterification reaction. E3 coordinates with E2 to mediate isopeptide bond formation between Ub and substrate protein. The E1-E2-E3 cascade can create diverse types of Ub modifications, hence effecting distinct outcomes on the substrate proteins. Dysregulation of ubiquitination results in severe consequences and human diseases. There include cancers, developmental defects and immune disorders. In this review, we provide an overview of the ubiquitination machinery and discuss the recent progresses in the ubiquitination-mediated regulation of embryonic stem cell maintenance and cancer biology. Full article
(This article belongs to the Special Issue The Ubiquitin Code in Cellular Signaling and Homeostasis)
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16 pages, 1401 KiB  
Review
Revisiting Bacterial Ubiquitin Ligase Effectors: Weapons for Host Exploitation
by Antonio Pisano, Francesco Albano, Eleonora Vecchio, Maurizio Renna, Giuseppe Scala, Ileana Quinto and Giuseppe Fiume
Int. J. Mol. Sci. 2018, 19(11), 3576; https://doi.org/10.3390/ijms19113576 - 13 Nov 2018
Cited by 14 | Viewed by 5311
Abstract
Protein ubiquitylation plays a central role in eukaryotic cell physiology. It is involved in several regulatory processes, ranging from protein folding or degradation, subcellular localization of proteins, vesicular trafficking and endocytosis to DNA repair, cell cycle, innate immunity, autophagy, and apoptosis. As such, [...] Read more.
Protein ubiquitylation plays a central role in eukaryotic cell physiology. It is involved in several regulatory processes, ranging from protein folding or degradation, subcellular localization of proteins, vesicular trafficking and endocytosis to DNA repair, cell cycle, innate immunity, autophagy, and apoptosis. As such, it is reasonable that pathogens have developed a way to exploit such a crucial system to enhance their virulence against the host. Hence, bacteria have evolved a wide range of effectors capable of mimicking the main players of the eukaryotic ubiquitin system, in particular ubiquitin ligases, by interfering with host physiology. Here, we give an overview of this topic and, in particular, we detail and discuss the mechanisms developed by pathogenic bacteria to hijack the host ubiquitination system for their own benefit. Full article
(This article belongs to the Special Issue The Ubiquitin Code in Cellular Signaling and Homeostasis)
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