CTLs, a new class of RING-H2 ubiquitin ligases uncovered by YEELL, a motif close to the RING domain that is present across eukaryotes

Structural Dynamics, Evolutionary Significance, and Functions of Really Interesting New Gene Proteins in Ubiquitination and Plant Stress: A Review

Abiotic stress causes major crop losses worldwide. Plants have evolved complex intricate signaling network involving transcriptional regulators and posttranslational modifications (PTMs). Ubiquitination-a key PTM-regulates protein degradation through the ubiquitin-proteasome system (UPS). The UPS plays a pivotal role in detecting and modulating plant responses to environmental fluctuations. The E3 ligase family in plants is extensive, offering high substrate specificity and playing a vital role in signaling and protein turnover. Really Interesting New Gene (RING) proteins primarily function as E3 ubiquitin ligases, their functional diversity facilitates the transfer of ubiquitin molecules to specific target proteins. Plants possess abscisic acid (ABA)-dependent and ABA-independent stress-signaling pathways. RING-type E3 ligases regulate ABA signaling either negatively or positively in response to stress by regulating protein degradation, modulating transcription factors, ABA biosynthesis, and degradation. This dynamic interaction between ABA and E3 ligase proteins helps plants to adapt to environmental stress. Negative regulators, such as AIP2 and OsDSG1, target ABI3 for degradation. Keep on going (KEG) ubiquitinates ABI5, ABF1, and ABF3, though KEG itself is subject to feedback regulation by ABA levels, leading to its degradation. Positive regulators include SDIR1, OsSDIR1, AIRP1, RHA2b/RHA2a, and XERICO, along with its maize orthologs ZmXerico1 and ZmXerico2. Additionally, SINAT5 and BOI regulate auxin and gibberellin signaling, integrating hormonal responses to stress. The functional diversity of RING-type E3 ligases offers promising targets for genetic engineering to enhance crop resilience under adverse environmental conditions. Understanding these molecular mechanisms could lead to the development of climate-resilient crops, crucial for sustaining global food security.

ATL Protein Family: Novel Regulators in Plant Response to Environmental Stresses

Plants actively develop intricate regulatory mechanisms to counteract the harmful effects of environmental stresses. The ubiquitin-proteasome pathway, a crucial mechanism, employs E3 ligases (E3s) to facilitate the conjugation of ubiquitin to specific target substrates, effectively marking them for proteolytic degradation. E3s play critical roles in many biological processes, including phytohormonal signaling and adaptation to environmental stresses. Arabidopsis Toxicosa en Levadura (ATL) proteins, belonging to a subfamily of RING-H2 E3s, actively modulate diverse physiological processes and plant responses to environmental stresses. Despite studies on the functions of certain ATL family members in rice and Arabidopsis, most ATLs still need more comprehensive study. This review presents an overview of the ubiquitin-proteasome system (UPS), specifically focusing on the pivotal role of E3s and associated enzymes in plant development and environmental adaptation. Our study seeks to unveil the active modulation of plant responses to environmental stresses by E3s and ATLs, emphasizing the significance of ATLs within this intricate process. By emphasizing the importance of studying the roles of E3s and ATLs, our review contributes to developing more resilient plant varieties and promoting sustainable agricultural practices while establishing a research roadmap for the future.

SCFOsFBK1 E3 ligase mediates jasmonic acid-induced turnover of OsATL53 and OsCCR14 to regulate lignification of rice anthers and roots

The rice F-box protein OsFBK1, which mediates the turnover of a cinnamoyl CoA-reductase, OsCCR14, has previously been shown to regulate anther and root lignification. Here, we identify OsATL53, a member of the ATL family of RING-H2 proteins that interacts with OsCCR14 in the cytoplasm. OsATL53 was identified in the same yeast two-hybrid library screening as reported previously for OsCCR14, and we show it to have cytoplasmic localization and E3 ligase ubiquitination properties. SCFOsFBK1 mediates turnover of OsATL53 in the cytoplasm and the nucleus, and that of OsCCR14 only in the nucleus, as shown by cell-free degradation assays. Confocal fluorescence lifetime imaging microscopy analyses demonstrate that in presence of jasmonic acid (JA), which plays a role in anther dehiscence, OsATL53-OsCCR14 undergoes conformational changes that trigger the complex to accumulate around the nuclear periphery and signals OsFBK1 to initiate degradation of the proteins in the respective cellular compartments. OsATL53 decreases the enzymatic activity of OsCCR14 and sequesters it in the cytoplasm, thereby regulating the lignification process. Transgenic rice with knockdown of OsATL53 display increased lignin deposition in the anthers and roots compared to the wild type, whilst knockdown of OsCCR14 results in decreased lignin content. Our results show that OsATL53 affects the activity of OsCCR14, and that their JA-induced degradation by SCFOsFBK1 regulates lignification of rice anthers and roots.

EMR, a cytosolic-abundant ring finger E3 ligase, mediates ER-associated protein degradation in Arabidopsis

Investigation of the endoplasmic reticulum-associated degradation (ERAD) system in plants led to the identification of ERAD-mediating RING finger protein (EMR) as a plant-specific ERAD E3 ligase from Arabidopsis. EMR was significantly up-regulated under endoplasmic reticulum (ER) stress conditions. The EMR protein purified from bacteria displayed high E3 ligase activity, and tobacco leaf-produced EMR mediated mildew resistance locus O-12 (MLO12) degradation in a proteasome-dependent manner. Subcellular localization and coimmunoprecipitation analyses showed that EMR forms a complex with ubiquitin-conjugating enzyme 32 (UBC32) as a cytosolic interaction partner. Mutation of EMR and RNA interference (RNAi) increased the tolerance of plants to ER stress. EMR RNAi in the bri1-5 background led to partial recovery of the brassinosteroid (BR)-insensitive phenotypes as compared with the original mutant plants and increased ER stress tolerance. The presented results suggest that EMR is involved in the plant ERAD system that affects BR signaling under ER stress conditions as a novel Arabidopsis ring finger E3 ligase mainly present in cytosol while the previously identified ERAD E3 components are typically membrane-bound proteins.

Repertoire of plant RING E3 ubiquitin ligases revisited: New groups counting gene families and single genes

E3 ubiquitin ligases of the ubiquitin proteasome system (UPS) mediate recognition of substrates and later transfer the ubiquitin (Ub). They are the most expanded components of the system. The Really Interesting New Gene (RING) domain contains 40-60 residues that are highly represented among E3 ubiquitin ligases. The Arabidopsis thaliana E3 ubiquitin ligases with a RING finger primarily contain RING-HC or RING-H2 type domains or less frequently RING-v, RING-C2, RING-D, RING-S/T and RING-G type domains. Our previous work on three E3 ubiquitin ligase families with a RING-H2 type domain, ATL, BTL, and CTL, suggested that a phylogenetic distribution based on the RING domain allowed for the creation a catalog of known domains or unknown conserved motifs. This work provided a useful and comprehensive view of particular families of RING E3 ubiquitin ligases. We updated the annotation of A. thaliana RING proteins and surveyed RING proteins from 30 species across eukaryotes. Based on domain architecture profile of the A. thaliana proteins, we catalogued 4711 RING finger proteins into 107 groups, including 66 previously described gene families or single genes and 36 novel families or undescribed genes. Forty-four groups were specific to a plant lineage while 41 groups consisted of proteins found in all eukaryotic species. Our present study updates the current classification of plant RING finger proteins and reiterates the importance of these proteins in plant growth and adaptation.