CUL3 E3 ligases in plant development and environmental response

Abstract

Thirty years of research have revealed the fundamental role of the ubiquitin-proteasome system in diverse aspects of cellular regulation in eukaryotes. The ubiquitin-protein ligases or E3s are central to the ubiquitin-proteasome system since they determine the specificity of ubiquitylation. The cullin-RING ligases (CRLs) constitute one large class of E3s that can be subdivided based on the cullin isoform and the substrate adapter. SCF complexes, composed of CUL1 and the SKP1/F-box protein substrate adapter, are perhaps the best characterized in plants. More recently, accumulating evidence has demonstrated the essential roles of CRL3 E3s, consisting of a CUL3 protein and a BTB/POZ substrate adaptor. In this Review, we describe the variety of CRL3s functioning in plants and the wide range of processes that they regulate. Furthermore, we illustrate how different classes of E3s may cooperate to regulate specific pathways or processes.

Fig. 1 |. Subunit composition of CRLs in plants.

a, CUL1 E3 ligases utilize SKP1 to bind CUL1 and F-box proteins to target substrates. b, In CUL3 E3 ligases, BTB/POZ proteins interact with both CUL3 and substrates. c E3 ligases use DAMAGE-SPECIFIC DNA-BINDING PROTEIN 1 (DDB1) to bind CUL4 and WD40 domain-containing DWD proteins for target recognition. d, The APC contains 11 or more subunits. APC2 and APC11 function is similar to cullins and RBX1, respectively, while CDC20, CDH1 and APC10 function as substrate adaptors.

Fig. 2 |. Phylogenetic analysis of the BtB/POZ protein family from Arabidopsis.

A total of 80 BTB/POZ sequences from Arabidopsis were aligned using Clustal W and their BTB domains were used to generate the tree. Phylogenetic trees were inferred using MrBayes version 3.2.7 (ref.). Two runs of four chains were run for 15 million generations using the parameters aamodelpr = mixed, nst = 6 and rates = invgamma. Posterior probabilities of >0.5 are shown for corresponding nodes. The subfamilies identified from the phylogenetic analysis and their corresponding domains are marked on the right. BTB/POZ proteins that have been functionally identified as substrate adaptors of CRL3s are marked with red asterisks. Those that have been studied but not experimentally shown to bind CUL3 are marked with red triangles. red circles indicate subfamilies that only exist in plants. The BTB–nPH3 proteins that have an additional coiled-coil domain in their structures are marked with a green letter ‘C’.

Fig. 3 |. Examples for CRL3 regulation.

a, Control of subcellular partitioning of CRL3 components. While BPM2 constitutively localizes to the nucleus and mediates DREB2A ubiquitylation, BPM4 translocates from the cytoplasm to the nucleus upon heat stress, where it interacts with DREB2A and promotes its degradation. By mediating DREB2A degradation, BPMs negatively modulate the heat stress response to avoid the effects on plant growth of excess DREB2A. b, Salicylic acid (SA) regulates CUL3^NPR1/3/4 substrate function. NPR1 is a master regulator of SAR in salicylic acid-regulated plant immunity. In an uninfected cell, basal levels of salicylic acid lead to CUL3^NPR4-mediated degradation of most of the NPR1 to prevent spurious activation of resistance. Pathogen infection increases salicylic acid levels, which inhibits CUL3^NPR4 but promotes CUL3^NPR3-mediated degradation of NPR1 to allow EDS1 and WRKY transcription and establish ETI. In neighbouring cells, where salicylic acid levels are lower, CUL3^NPR3-mediated degradation of NPR1 is reduced, enabling the accumulation of NPR1 and transcription of SAR genes; in the cytoplasm, salicylic acid also induces the formation of NPR1 condensates (SINCs), which mediate CUL3^NPR1 degradation of cytoplasmic proteins, such as EDS1 and WRKY transcription factors^–.