Evidence that the Arabidopsis Ubiquitin C-terminal Hydrolases 1 and 2 associate with the 26S proteasome and the TREX-2 complex

Plant deubiquitinases: from structure and activity to biological functions

This article attempts to provide comprehensive review of plant deubiquitinases, paying special attention to recent advances in their biochemical activities and biological functions. Proteins in eukaryotes are subjected to post-translational modifications, in which ubiquitination is regarded as a reversible process. Cellular deubiquitinases (DUBs) are a key component of the ubiquitin (Ub)-proteasome system responsible for cellular protein homeostasis. DUBs recycle Ub by hydrolyzing poly-Ub chains on target proteins, and maintain a balance of the cellular Ub pool. In addition, some DUBs prefer to cleave poly-Ub chains not linked through the conventional K48 residue, which often alter the substrate activity instead of its stability. In plants, all seven known DUB subfamilies have been identified, namely Ub-binding protease/Ub-specific protease (UBP/USP), Ub C-terminal hydrolase (UCH), Machado-Joseph domain-containing protease (MJD), ovarian-tumor domain-containing protease (OTU), zinc finger with UFM1-specific peptidase domain protease (ZUFSP), motif interacting with Ub-containing novel DUB family (MINDY), and JAB1/MPN/MOV34 protease (JAMM). This review focuses on recent advances in the structure, activity, and biological functions of plant DUBs, particularly in the model plant Arabidopsis.

UBP12 and UBP13 deubiquitinases destabilize the CRY2 blue light receptor to regulate Arabidopsis growth

Light is a crucial exogenous signal sensed by cryptochrome (CRY) blue light receptors to modulate growth and the circadian clock in plants and animals. However, how CRYs interpret light quantity to regulate growth in plants remains poorly understood. Furthermore, CRY2 protein levels and activity are tightly regulated in light to fine-tune hypocotyl growth; however, details of the mechanisms that explain precise control of CRY2 levels are not fully understood. We show that in Arabidopsis, UBP12 and UBP13 deubiquitinases physically interact with CRY2 in light. UBP12/13 negatively regulates CRY2 by promoting its ubiquitination and turnover to modulate hypocotyl growth. Growth and development were explicitly affected in blue light when UBP12/13 were disrupted or overexpressed, indicating their role alongside CRY2. UBP12/13 also interacted with and stabilized COP1, which is partially required for CRY2 turnover. Our combined genetic and molecular data support a mechanistic model in which UBP12/13 interact with CRY2 and COP1, leading to the stabilization of COP1. Stabilized COP1 then promotes the ubiquitination and degradation of CRY2 under blue light. Despite decades of studies on deubiquitinases, the knowledge of how their activity is regulated is limited. Our study provides insight into how exogenous signals and ligands, along with their receptors, regulate deubiquitinase activity by protein-protein interaction. Collectively, our results provide a framework of cryptochromes and deubiquitinases to detect and interpret light signals to control plant growth at the most appropriate time.

Towards Understanding Plant Calcium Signaling through Calmodulin-Like Proteins: A Biochemical and Structural Perspective

Ca2+ ions play a key role in a wide variety of environmental responses and developmental processes in plants, and several protein families with Ca2+-binding domains have evolved to meet these needs, including calmodulin (CaM) and calmodulin-like proteins (CMLs). These proteins have no catalytic activity, but rather act as sensor relays that regulate downstream targets. While CaM is well-studied, CMLs remain poorly characterized at both the structural and functional levels, even if they are the largest class of Ca2+ sensors in plants. The major structural theme in CMLs consists of EF-hands, and variations in these domains are predicted to significantly contribute to the functional versatility of CMLs. Herein, we focus on recent advances in understanding the features of CMLs from biochemical and structural points of view. The analysis of the metal binding and structural properties of CMLs can provide valuable insight into how such a vast array of CML proteins can coexist, with no apparent functional redundancy, and how these proteins contribute to cellular signaling while maintaining properties that are distinct from CaM and other Ca2+ sensors. An overview of the principal techniques used to study the biochemical properties of these interesting Ca2+ sensors is also presented.

Plant Deubiquitinases and Their Role in the Control of Gene Expression Through Modification of Histones

Selective degradation of proteins in the cell occurs through ubiquitination, which consists of post-translational deposition of ubiquitin on proteins to target them for degradation by proteases. However, ubiquitination does not only impact on protein stability, but promotes changes in their functions. Whereas the deposition of ubiquitin has been amply studied and discussed, the antagonistic activity, deubiquitination, is just emerging and the full model and players involved in this mechanism are far from being completely understood. Nevertheless, it is the dynamic balance between ubiquitination and deubiquitination that is essential for the development and homeostasis of organisms. In this review, we present a detailed analysis of the members of the deubiquitinase (DUB) superfamily in plants and its division in different clades. We describe current knowledge in the molecular and functional characterisation of DUB proteins, focusing primarily on Arabidopsis thaliana. In addition, the striking function of the duality between ubiquitination and deubiquitination in the control of gene expression through the modification of chromatin is discussed and, using the available information of the activities of the DUB superfamily in yeast and animals as scaffold, we propose possible scenarios for the role of these proteins in plants.

The plant nuclear envelope and regulation of gene expression

The nuclear envelope (NE) separates the key mechanisms of transcription and translation, and as such is a critical control point in all eukaryotic cells. In plants, the proteins of the NE influence a number of processes including the control of nucleo-cytoplasmic transport of RNA and protein, chromatin localization to the nuclear periphery, and direct chromatin binding by members of the nuclear pore complex (NPC). In this review I attempt to bring these roles under the umbrella of their effect on gene expression, even though the complex nature of this cellular environment means there is considerable overlap of effects. Although the volume of research in plant cells has greatly improved over recent years, it is clear that our understanding of how the components of the NE either directly or indirectly influence gene expression is still in its infancy.