Cells depend on the proper functioning of an ensemble of networked, molecular machines to control diverse processes from cell proliferation to cell death to differentiation. The ubiquitin system can rapidly degrade the modular regulatory components of these molecular machines, contributing to the precise operation and synchronization of complex cellular processes (Figure 1). Given this critical role, the ubiquitin system is often deregulated in disease.

The ubiquitin-mediated proteolysis of many cellular regulators is controlled by the SCF ubiquitin ligases (Figure 2), which are composed of four subunits (Skp1, Cul1, Rbx1, and a variable F-box protein). In our initial studies, we used a yeast two-hybrid screen and bioinformatics to identify Skp1 binding proteins, resulting in the annotation of a family of 69 human F-box proteins (see list). Subsequently, we have focused on elucidating the biological function of the individual SCF complexes and SCF-like ubiquitin ligase complexes, such as other CRLs (cullin-RING ligases) and the Anaphase Promoting Complex/Cyclosome (APC/C).

Regulated proteolysis by SCF ubiquitin ligases provides many advantages for regulatory systems: 

1.Sixty-nine different F-box proteins provide highly specific substrate selection (see list).

2.Ubiquitin-mediated proteolysis unidirectional (There is no way to reverse degradation.)  (Figure 3) See also NEW animation

3.The abundance of proteins can be controlled both temporally and spatially  (Figure 4).

4.SCF-mediated ubiquitylation rapidly responds to different stimuli (Figure 5).


   

Notably, only a handful of the 69 human F-box proteins have well-established substrates (Figure 6).  Therefore, one of the goals of our lab is to study the functions of orphan F-box proteins and systematically identify their biologically significant substrates. Most SCF substrates require phosphorylation for recognition by their specific F-box proteins, so we are also interested in identifying the kinases that facilitate substrate recognition. The requirement for substrate phosphorylation indicates that SCF ligases contribute to cellular processes in part by “sensing” the activity of kinases, and, in many cases, this “sensing” can be combinatorial, requiring the cooperative phosphorylation of a substrate by kinases from two distinct pathways. Therefore, elucidation of both the F-box protein and kinase(s) for each substrate is required to fully understand substrate targeting and degradation.

Our laboratory has successfully utilized proteomic approaches for substrate identification, revealing the role of SCF ubiquitin ligases in many biological functions.  These unbiased methods have broadened our research interests to a more far-reaching vision that links together many (at first glance) disparate cellular pathways controlling cell proliferation, DNA-damage checkpoints, centrosome duplication, transcription, protein synthesis, ribosome biogenesis, apoptosis, and circadian clock oscillations. Major examples are detailed below:

Fun

  - Cyclin F-mediated degradation of SLBP limits H2A.X accumulation and apoptosis upon DNA damage in G2 (See Figure)


  -  βTrCP- and Plk1-mediated degradation of Cep68 and Separase-mediated cleavage of PCNT promote Cep215 removal

from the PCM to allow centriole separation and disengagement/licensing (See Figure)


   - FBXL2-mediated degradation of p85β controls the PI3K signaling cascade  (See Figure)


   - FBX011-mediated degradation of CDT2 controls the timing of cell cycle exit  (See Figure)


   - Cyclin F controls genome stability and DNA repair via RRM2 degradation (See Figure)


    - FBXO11 targets BCL6 for degradation and is mutated in DLBCLs, leading to BCL6 stabilization  (See Figure)


    - FBXW7 mediates the degradation of p100 to allow efficient NF-kB activation (See Figure)


    - Cyclin F controls centrosome homeostasis and mitotic fidelity via CP110 degradation (See Figure)


    - βTrCP and CK1α control mTOR by targeting DEPTOR for degradation (See Figure)


    - βTrCP and RSK control cell survival by targeting BimEL for degradation (See Figure)


    - βTrCP controls the spindle checkpoint and chromosome stability by targeting REST for degradation (See Figure)

    - FBXL3 controls the oscillation of the circadian clock by targeting Cryptochrome proteins for degradation (See Figure)


    - FBXL10 epigenetically controls the transcription of ribosomal genes (See Figure)

    - βTrCP and S6K control protein translation by targeting PDCD4 for degradation (See Figure)


    - βTrCP and Plk1 control the recovery from genotoxic stress by targeting Claspin for degradation (See Figure)

   

    - Cdc14B and Cdh1 inactivate the βTrCP-Plk1 axis to allow Claspin accumulation in response to DNA damage (See Figure)


    - Skp2 positively controls CDK1 and CDK2 activity by targeting p27 for degradation (See Figure)