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Ratchets and clocks: the cell cycle, ubiquitylation and protein turnover

Nature Reviews Molecular Cell Biology volume 4, pages 855–864 (2003)Cite this article

Key Points

  • Many important cell-cycle regulatory proteins are regulated post-translationally by ubiquitin-mediated proteolysis. These include both positive and negative regulators of the cell cycle.

  • One central role of regulated proteolysis in the context of cell-cycle control is to enforce irreversible cell-cycle phase transitions. This is often accomplished by the rapid and concerted turnover of a negative regulatory protein that impedes a cell-cycle phase transition.

  • Another important role of regulated proteolysis is to restrict the window of accumulation of a cell-cycle regulatory protein to the specific time when the function of that protein is required. Such a strategy prevents significant cell-cycle events occurring out of context.

  • There are two general classes of protein ubiquitin ligase that target cell-cycle regulatory proteins for destruction: APC/C and SCF. Whereas cell-cycle regulation of APC/C activity is intrinsic to the ligase itself, cell-cycle regulation of SCF activity is usually mediated by substrate phosphorylation.

  • SCF protein ubiquitin ligases consist of three core invariant subunits plus one of several variable specificity factors known as F-box proteins. SCFCdc4, which is conserved from yeast to humans, is the SCF protein ubiquitin ligase designated by the F-box-protein Cdc4.

  • In yeast, SCFCdc4 targets a cyclin-dependent-kinase inhibitor Sic1, thereby promoting a timely and irreversible transition from G1 to S-phase. In mammalian cells, the homologous protein ubiquitin ligase targets the positive cell-cycle-regulator cyclin E. Mutations in the human CDC4 gene are linked to cancer, presumably because they lead to deregulation of cyclin E through the cell cycle.

Abstract

Both the cell-cycle and ubiquitin-mediated-proteolysis fields have come of age over the past ten years. One byproduct of the impressive progress in these areas of investigation is the realization that they are intricately related: cell-cycle control is crucially dependent on the ubiquitin-mediated degradation of key regulatory proteins. Very recent advances have allowed an understanding of protein degradation and cell-cycle control at greatly enhanced levels of resolution. Consolidating these advances is likely to provide new insights into the regulatory biology of cell-cycle transitions.

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Figure 1: Key cell-cycle regulatory proteins targeted by ubiquitin-mediated proteolysis.
Figure 2: Creating an irreversible cell-cycle transition.
Figure 3: Limiting the interval of expression to the interval of required function.
Figure 4: Architecture and subunit composition of the APC/C and SCF complexes.
Figure 5: Sic1 phosphorylation sets a threshold for the G1–S transition in yeast.

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Authors and Affiliations

  1. Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, California, USA

    Steven I. Reed

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  1. Steven I. Reed
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DATABASES

FlyBase

Archipelago

LocusLink

Cullin

F-box

Saccharomyces genome database

Cdc4

CDH1

Cdk1

Esp1

Grr1

Met30

Pds1

Sic1

Swe1

SwissProt

APC/C2

APC/C11

CDC4

Cdc20

Cdk2

CKS1

Cul-1

cyclin E

EMI1

p21cip1

p27Kip1

Roc1

Securin

Skp1

β-TrCP

ubiquitin

Glossary

CYCLIN

The positive regulatory subunits of cyclin-dependent kinases, usually regulated by ubiquitin-mediated proteolysis.

UBIQUITIN

A 76-amino-acid polypeptide that is conjugated through an isopeptide linkage to other proteins. Most commonly, such conjugates are targeted for degradation by the proteasome.

HETEROCHRONIC EXPRESSION

Expression of a protein at an inappropriate or abnormal time.

PROTEIN-UBIQUITIN LIGASE

An enzyme, or enzyme complex, responsible for transferring ubiquitin to a target protein.

SCF

A class of protein-ubiquitin ligase containing three core subunits (Cul1/Cdc53, Skp1 and Roc1/Rbx1) and a variable substrate-recognition subunit, which is known as an F-box protein.

ANEUPLOIDY

The ploidy of a cell refers to the number of sets of chromosomes that it contains. Aneuploid karyotypes are those whose chromosome complements are not a simple multiple of the haploid set.

CLB

Yeast cyclins with structural homology to metazoan cyclin B.

CLN

Yeast G1 cyclins that lack strong structural homology to any metazoan cyclins.

p130

A member of the pocket protein family of cell-cycle inhibitors. p130 has two modes of action: establishing transcriptional repression complexes with E2F transcription factors and inhibiting cyclin-E–Cdk2 complexes.

PROTEASOME

A large intracellular protease assembly that targets ubiquitylated proteins.

SPINDLE

A highly dynamic, bipolar array of microtubules that forms during mitosis or meiosis and serves to move the duplicated chromosomes apart.

DEGRON

A sequence required for destabilization of a protein, usually by functioning as a recognition signal for a protein-ubiquitin ligase.

D-BOX

One of two degron sequences recognized by the APC/C.

KEN-BOX

One of two degron sequences recognized by the APC/C.

CRYO-ELECTRON MICROSCOPY

A technique by which, using a special cryoholder, cryofixed biological samples are directly imaged in the transmission-electron microscope under low-dose conditions and at low temperature (at least −170 °C). The sample can be either a frozen layer or a suspension.

RING-FINGER PROTEINS

A family of proteins structurally defined by the presence of the zinc-binding ring-finger motif. The ring consensus sequence is: CX2CX(9–39)CX(1–3)HX(2–3)C/HX2CX(4–48)CX2C. The cysteines and histidines represent metal-binding sites. The first, second, fifth and sixth of these bind one zinc ion and the third, fourth, seventh and eighth bind the second zinc ion.

PHOSPHODEGRON

The phosphorylated sequence on a protein recognized by an SCF ligase.

WD40 β-PROPELLER

A protein-interaction domain consisting of 40 amino-acid repeats that form a propeller-like structure, in which each repeat contributes a blade.

DOMINANT-NEGATIVE

A defective protein that retains interaction capabilities and so distorts or competes with normal proteins.

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Reed, S. Ratchets and clocks: the cell cycle, ubiquitylation and protein turnover. Nat Rev Mol Cell Biol 4, 855–864 (2003). https://doi.org/10.1038/nrm1246

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