De‐ubiquitinases on the move: an emerging field in plant biology

Abstract

A balance between the synthesis and degradation of active proteins governs diverse cellular processes in plants, spanning from cell‐cycle progression and circadian rhythm to the outcome of several hormone signalling pathways. Ubiquitin‐mediated post‐translational modification determines the degradative fate of the target proteins, thereby altering the output of cellular processes. An equally important, and perhaps under‐appreciated, aspect of this pathway is the antagonistic process of de‐ubiquitination. De‐ubiquitinases (DUBs), a group of processing enzymes, play an important role in maintaining cellular ubiquitin homeostasis by hydrolyzing ubiquitin poly‐proteins and free poly‐ubiquitin chains into mono‐ubiquitin. Further, DUBs rescue the cellular proteins from 26S proteasome‐mediated degradation to their active form by cleaving the poly‐ubiquitin chain from the target protein. Any perturbation in DUB activity is likely to affect proteostasis and downstream cellular processes. This review illustrates recent findings on the biological significance and mechanisms of action of the DUBs in Arabidopsis thaliana, with an emphasis on ubiquitin‐specific proteases (UBPs), the largest family among the DUBs. We focus on the putative roles of various protein–protein interaction interfaces in DUBs and their generalized function in ubiquitin recycling, along with their pre‐eminent role in plant development.

Deubiquitination of BES1 by UBP12/UBP13 promotes brassinosteroid signaling and plant growth

“…Although plant DUBs have not been as extensively investigated as ubiquitin E3 ligases, nonetheless, results to date show that these enzymes play crucial roles in plant growth and development ( Majumdar and Nath, 2020 ). The functionally redundant UBP12 and UBP13 are expressed at a reasonably high level throughout the plant life cycle.…”

The DUB family in Populus: identification, characterization, evolution and expression patterns

“…org/search#tabview=tab1) and confirmed by searching the Conserved Domain Database (CDD) of the National Center for Biotechnology Information (NCBI; https:// www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) [59]. The protein sequences of Arabidopsis DUB family members were obtained from the TAIR database on the basis of the gene ID [19,60,61]. The protein sequences of rice DUB family members were downloaded from the Rice Genome Annotation Project (http://rice.plantbiology.…”

Met1-specific motifs conserved in OTUB subfamily of green plants enable rice OTUB1 to hydrolyse Met1 ubiquitin chains

“…In contrast, the catalytic centre and the overall structure of RavD do not undergo visible conformational changes upon binding to Met1-diUb, leading to the conclusion that the full activity of RavD is not predicated on substrate assistance 9 . In plants, physiological roles of Met1 chains and directly correlated DUBs have rarely been reported 15 – 17 . With the exception of Arabidopsis , no DUBs digesting Met1 chains have been reported in other plants.…”