Mechanisms and function of substrate recruitment by F-box proteins

Abstract

S phase kinase-associated protein 1 (SKP1)-cullin 1 (CUL1)-F-box protein (SCF) ubiquitin ligase complexes use a family of F-box proteins as substrate adaptors to mediate the degradation of a large number of regulatory proteins involved in diverse processes. The dysregulation of SCF complexes and their substrates contributes to multiple pathologies. In the 14 years since the identification and annotation of the F-box protein family, the continued identification and characterization of novel substrates has greatly expanded our knowledge of the regulation of substrate targeting and the roles of F-box proteins in biological processes. Here, we focus on the evolution of our understanding of substrate recruitment by F-box proteins, the dysregulation of substrate recruitment in disease and potential avenues for F-box protein-directed disease therapies.

Figure 1. The cullin–RING ligase family

Cullin (CUL) proteins form the backbones of ubiquitin ligase complexes. CUL7 and CUL9 are atypical cullins owing to their large size and the incorporation of additional homology domains. APC2, the core of the APC/C (anaphase promoting complex; also known as the cyclosome), is distantly related to cullins. Each cullin–RING ligase (CRL) complex is modular, with variable substrate adaptors. CRL1 (better known as S phase kinase-associated protein 1 (SKP1)–CUL1–F-box protein (SCF) complex) uses SKP1 and F-box proteins as substrate adaptors, and CRL2 and CRL5 ligases use elongin B, elongin C and SOCS (suppressor of cytokine signalling) box proteins. The substrate adaptors for CRL3 are BTB (bric-a-brac-tramtrack-broad complex) proteins. CRL4A and CRL4B use DDB1 (DNA damage-binding protein 1) and DCAF (DDB1- and CUL4-associated factor) proteins. CRL7 uses SKP1 and a single F-box protein (F-box and WD40 domain 8 (FBXW8)). The substrate adaptors for CRL9 are not known. The full molecular architecture of the APC/C remains unclear, in part because it contains many more proteins (shown in blue) than the CRL complexes. APC/C uses either CDC20 or CDH1 (CDC20 homologue 1) as a substrate adaptor. The substrate for each complex is shown in yellow. RBX1, RING-box protein 1.

Figure 2. Recognition of substrates by F-box proteins

F-box proteins recognize their substrates in multiple ways. Often, various recognition mechanisms are combined to impart precise regulation of substrate degradation. Eight different modes of recognition and regulation are shown, as discussed in the main text. These simple concepts of regulation and recognition are often combined in substrates. For example, phosphodegron recognition can be combined with priming phosphorylations, or the recognition of non-modified degrons can be paired with restricted degron access.

Figure 3. Dysregulation of F-box protein-mediated degradation in disease

Dysregulation of F-box protein-mediated degradation can occur by the overexpression of an F-box protein, deletion of an F-box protein, point mutation of an F-box protein or mutation of substrate degrons. In addition, the expression of microbial proteins can increase or decrease substrate degradation, or lead to the degradation of alternative substrates. Ub, ubiquitylation.

Figure 4. Generalized and context-dependent functions of F-box proteins

Studies of S phase kinase-associated protein 2 (SKP2), F-box and WD40 domain 7 (FBXW7) and β-transducin repeat-containing protein (βTrCP) show that F-box proteins can have generalized and/or context-dependent functions. As shown in mouse models, SKP2 functions as an oncoprotein that ubiquitylates and hence degrades growth suppressive substrates. Moreover, in mouse models, FBXW7 functions as a tumour suppressor by ubiquitylating growth-promoting substrates, but this role is cell type specific. In B cell lineages, FBXW7 actually has a pro-survival role by mediating the degradation of p100, an inhibitor of nuclear factor-κB (NF-κB) signalling. βTrCP function is highly stimulus and cell type specific, and it has a role in many disparate pathways, including pathways beyond cell growth and proliferation. BORA, aurora borealis; BIMEL, BCL-2-interacting mediator of cell death extra long; EMI1, early mitotic inhibitor 1; IκB, inhibitor of κB; PDCD4, programmed cell death 4; PER, period; PFKFB3, 6-phosphofructo-2-kinase/ fructose-2,6-biphosphatase 3; REST, RE1-silencing transcription factor.