The emerging family of CULLIN3-RING ubiquitin ligases (CRL3s): cellular functions and disease implications

Abstract

Protein ubiquitylation is a post-translational modification that controls all aspects of eukaryotic cell functionality, and its defective regulation is manifested in various human diseases. The ubiquitylation process requires a set of enzymes, of which the ubiquitin ligases (E3s) are the substrate recognition components. Modular CULLIN-RING ubiquitin ligases (CRLs) are the most prevalent class of E3s, comprising hundreds of distinct CRL complexes with the potential to recruit as many and even more protein substrates. Best understood at both structural and functional levels are CRL1 or SCF (SKP1/CUL1/F-box protein) complexes, representing the founding member of this class of multimeric E3s. Another CRL subfamily, called CRL3, is composed of the molecular scaffold CULLIN3 and the RING protein RBX1, in combination with one of numerous BTB domain proteins acting as substrate adaptors. Recent work has firmly established CRL3s as major regulators of different cellular and developmental processes as well as stress responses in both metazoans and higher plants. In humans, functional alterations of CRL3s have been associated with various pathologies, including metabolic disorders, muscle, and nerve degeneration, as well as cancer. In this review, we summarize recent discoveries on the function of CRL3s in both metazoans and plants, and discuss their mode of regulation and specificities.

Figure 1

Structural organization of SCF/CRL1 and the CRL3 complexes. (A) The SCF/CRL1 and the CRL3 complexes share a similar catalytic core module composed of the scaffold proteins CUL1 and CUL3, respectively, and the RING finger protein RBX1 (also known as Hrt1 or ROC1). Single-subunit BTB domain proteins bridge CUL3-RBX1 to substrates, while this function requires an SKP1/FBP heterodimer in SCF/CRL1. Substrate recognition is governed by an independent protein–protein interaction domain (PID) found in most of the FBPs and CUL3-interacting BTB domain proteins. (B) Non-exhaustive list of protein domains is commonly found associated with the BTB domain in CRL3 adaptors. MATH and Ankyrin domains occur in both metazoans and higher plants, while other domains are specific to either kingdom. BTB-KELCH; BTB-WD40; BTB-T1-Kv (voltage-gated potassium channel T1); BTB-Rho (Ras homology); BTB-bZip (basic leucine Zipper); BTB-MATH (Meprin and TRAF homology); BTB-ANKYRIN repeat; BTB-NPH3 (non-phototropic hypocotyl 3); BTB-TPR (Tetratrico Peptide Repeat); BTB-ARM (Armadillo); BTB-TAZ (Transcriptional Adaptor Zinc finger); BTB-PENT (Pentapeptide).

Figure 2

Mode of regulation of CRL3 activity and substrate recognition. (A) Nrf2 is constitutively targeted for Keap1-dependent degradation under normal conditions. In response to oxidative stress, oxidative modifications (denoted as (e), electrophile) on Keap1 impair its activity and result in Nrf2 stabilization. (B) In plant immunity, the transcription coactivator NPR1 is regulated at several levels. In unchallenged cells, NPR1 is predominantly sequestered in the cytoplasm in an oligomeric form through redox-sensitive intermolecular disulphide bonds. Upon pathogen infection, salicylic acid (SA) signals lead to alterations in reduction potential and partially relieves NPR1 to enter the nucleus. High SA concentrations immediately at sites of infection promote its binding to the BTB protein NPR3 and enhance NPR3–NPR1 interaction and subsequent NPR1 degradation, thereby favouring programmed cell death. Lower SA levels in neighbouring cells are insufficient to trigger NPR3-mediated NPR1 ubiquitylation, enabling NPR1 to accumulate and establish systemic acquired resistance (SAR). See text for details.

Figure 3

Speculative models on substrate accommodation by BTB protein dimerization. The model in (A) corresponds to the well-described binding of the Nrf2 transcription factor via two different binding sites to the Kelch domains of the Keap1 homodimer (McMahon et al, 2006). Models (B–D) represent speculative variations involving substrate recognition by BTB protein heterodimers (B) or cases considering both BTB protein and substrate homo- and hetero-dimerization (C, D).