ijms-logo

Journal Browser

Journal Browser

New Insights into Ubiquitination and Deubiquitination in Plants

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

Deadline for manuscript submissions: 20 September 2025 | Viewed by 553

Special Issue Editor


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,

Numerous important protein components of various cellular processes are post-translationally modified by ubiquitin monomers or polymers of different lengths and linkages. In consequence, ubiquitination regulates these cellular processes by targeting their ubiquitinated components for processes such as proteasome-mediated turnover, endocytosis, autophagy, signal transduction, the recruitment of interacting protein or protein complex, transcriptional activation/suppression, mRNA splicing/export, and chromatin activation/silencing. The assembly of various ubiquitin codes on proteins in all eukaryotic species is performed by a large set of diverged conjugation enzymes including ubiquitin activation (E1), conjugation (E2), and ligation (E3) families; intriguingly, this is delicately modulated by deubiquitinating enzymes that belong to at least seven distinct classes. Due to recent advances in the field of ubiquitination and deubiquitination, this Special Issue welcomes the submission of original research, reviews, and mini-reviews that provide insights into the functional and mechanistic roles of conjugation and deconjugation enzymes, ubiquitin code-binding proteins, and the target substrates of critical components involved in various cellular processes at the cellular and organismic level in plants.

Dr. Hongyong Fu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • ubiquitin
  • E1
  • E2
  • E3
  • deubiquitination
  • proteolysis
  • plants

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (1 paper)

Order results
Result details
Select all
Export citation of selected articles as:

Research

18 pages, 4688 KB  
Article
Biotinylation Interferes with Protein Ubiquitylation and Turnover in Arabidopsis—A Cautionary Insight for Proximity Labeling in Ubiquitylation Proteome Studies
by Yang Li, Peifeng Yu and Zhihua Hua
Int. J. Mol. Sci. 2025, 26(17), 8248; https://doi.org/10.3390/ijms26178248 - 25 Aug 2025
Abstract
Nearly all eukaryotic proteins are turned over by the ubiquitin (Ub)-26S proteasome system (UPS). Despite its broad cellular roles, only a handful of UPS members, particularly the Ub E3 ligases that specifically recognize a protein for ubiquitylation, have been characterized in plants to [...] Read more.
Nearly all eukaryotic proteins are turned over by the ubiquitin (Ub)-26S proteasome system (UPS). Despite its broad cellular roles, only a handful of UPS members, particularly the Ub E3 ligases that specifically recognize a protein for ubiquitylation, have been characterized in plants to date. The challenge arises from the transient recognition and rapid degradation of ubiquitylation substrates by the UPS. To tackle this challenge, the emerging biotinylation-based proximity labeling (PL) offers an exciting tool for enriching transient interactors of Ub E3 ligases. In this study, we examined the efficacy of TurboID in identifying substrates of Arabidopsis Skp1-cullin1-F-box (SCF) ligases. We demonstrate that the Arabidopsis Skp1 Like (ASK)1-TurboID is not fully functioning in planta, which led us to discover a novel antagonism between biotinylation and ubiquitylation in regulating protein stability in vivo. This discovery lowers the effectiveness of PL in ubiquitylome studies. However, using one long-known SCF substrate, phytochrome A, we succeeded to apply its TurboID fusion for complementing the far-red-light response of the phyA-211 null mutant allele, suggesting an efficacy of PL in characterizing single ubiquitylation pathways. This study highlighted a limitation of PL in ubiquitylome studies, discovered a new antagonistic pathway of biotinylation, and developed a theoretical guidance for future PL-based characterization of ubiquitylation pathways. Full article
(This article belongs to the Special Issue New Insights into Ubiquitination and Deubiquitination in Plants)
Back to TopTop