Regulation of cell cycle drivers by Cullin-RING ubiquitin ligases

Abstract

The last decade has revealed new roles for Cullin-RING ubiquitin ligases (CRLs) in a myriad of cellular processes, including cell cycle progression. In addition to CRL1, also named SCF (SKP1-Cullin 1-F box protein), which has been known for decades as an important factor in the regulation of the cell cycle, it is now evident that all eight CRL family members are involved in the intricate cellular pathways driving cell cycle progression. In this review, we summarize the structure of CRLs and their functions in driving the cell cycle. We focus on how CRLs target key proteins for degradation or otherwise alter their functions to control the progression over the various cell cycle phases leading to cell division. We also summarize how CRLs and the anaphase-promoting complex/cyclosome (APC/C) ligase complex closely cooperate to govern efficient cell cycle progression.

Fig. 1

a Schematic representation of human cullin structural domains. Cullins are displayed by size with the smallest cullin (CUL2) on top and aligned based on their neddylation site (asterisk). CRL domain information was retrieved from InterPro (https://www.ebi.ac.uk/interpro/). CH Cullin homology domain; CR cullin repeats. CR are very flexible and may account for CRL conformation change after the activation of target substrates; CPH, CUL7, PARC, and HERC2-containing domain; APC10, a domain homologous to a sequence element termed the DOC domain and found in proteins that mediate ubiquitination reactions. b Each CRL protein complex is formed from a scaffold protein or Cullin (Cullin 1, 2, 3, 4A, 4B, 5, 7 or 9), a RING finger protein (RBX1 or RBX2), an adaptor protein (SKP1 for CRL1 and CRL7 or EloC/EloB for CRL2 and CRL5, BTB for CRL3, DDB1 for CRL4s and FBXW8 or SMU1 for CRL7) and a receptor-substrate recognition protein (F-box family for CRL1 and CRL7, VHL family member for CRL2, BTB for CRL3, DCAF family for CRL4s and SOCS family for CRL5). Approximate number of known CRL receptors for each indicated CRL. c CRL complex dynamics. Deneddylated and inactive free cullins can bind to CAND1. Cullin neddylation, which is catalyzed by a NEDD8-activating enzyme and ligase and ubiquitin-conjugating enzyme, allows cullins to interact with other CRLs when released from CAND1. Neddylation is believed to induce conformational changes in CRLs (blue arrow), which leads to their interaction with the E2-ubiquitin complex and substrate ubiquitination. Ubiquitination often leads to proteolytic degradation or substrate inactivation. Cullin neddylation is reversed by the COP9/CSN signalosome, which triggers CRL disassembly.

Fig. 2. Depiction of key proteins targeted by CRLs during cell cycle progression.

CDK complexes drive cell cycle progression. CDK levels remain stable throughout the cell cycle phases, whereas fluctuations in the levels of CDK activators (CDC25A/B and cyclins) and inhibitors (p21, p27, and p57) cause changes in CDK activities. Thus, CRL-mediated destruction of CDK-regulating proteins allows the disassembly and assembly of different cyclin-CDK complexes in the cell cycle phases (transfer from the CDK2-Cyclin E complex in S phase to CDK2-Cyclin A in G2 phase and from CDK1-Cyclin in G2 phase to CDK1-Cyclin B in M phase). CRLs also control cell cycle progression by the degradation of pocket proteins such as RB and p130, in turn promoting the activation of E2F transcription factors and the expression of genes needed for subsequent phases of the cell cycle, including EMI1, Cyclin A, and Cyclin E. In late S, E2Fs are targeted for destruction by CRL1, promoting cell cycle progression to G2 while preventing premature S-phase entry. Substrates targeted by CRLs are symbolized with green inhibition symbols. CRLs with superscripts denote the specific CRL-receptor complexes involved is a particular pathway. The “+” sign denotes CDK activation by CDC24A/B (by dephosphorylation).

Fig. 3. CRLs and cell cycle progression through G2/M.

a Diagram depicting how CRLs promote timely substrate ubiquitination during G2/M. Substrates are categorized into five groups (transcription, CDK activities, chromosomes, modulators of other E3 ligases and others) and color coded to match their CRLs. b Schematic summary of CRLs, substrate receptors and substrates involved in the regulation of cell cycle progression through G2/M. Substrates are categorized into three groups (regulation of transcription, regulation of CDKs and mitotic factors and regulation of other E3 ligases). CRL complexes, substrate receptors, phosphorylation and ubiquitination are color coded as indicated.

Fig. 4. Examples of cross talk between CRLs and APC/C complex ligases for efficient cell cycle progression.

CRL1^SKP2 activity is suppressed by APC/C^CDH1 in G1, but during the G1/S transition, Cyclin E/CDK2 inactivates APC/C^CDH1, leading to the accumulation of SKP2. CRL1^SKP2 and Cyclin-CDK activation of E2Fs promotes EMI1 expression, leading to APC/C inhibition throughout the S phase. The capacity of CRL1^FBXW7 to target Cyclin E for destruction can affect APC/C activity. APC/C and CRL1^{Cyclin F} form a reciprocal feedback loop controlling cell cycle progression, with Cyclin F and CDH1 antagonizing each other. Cyclin F is targeted for ubiquitination and degradation by APC/C^CDH1 in the G1 phase, while CDH1 itself is a substrate of CRL1^{Cyclin F} in the S phase. BUB3 prevents premature chromosome segregation by blocking APC/C from associating with its coactivator CDC20. Prior to entry into metaphase, CRL4^RBBP7 targets BUB3 for degradation, allowing APC/C activation. WEE1, a negative regulator of APC/C^CDC20, is targeted for degradation by CRL1^β-TrCP in a Cyclin B1/CDK1-dependent manner. Substrates targeted by CRLs are symbolized with green inhibition symbols (see text for details).