Dynamic ubiquitin signaling in cell cycle regulation

Abstract

The cell division cycle is driven by a collection of enzymes that coordinate DNA duplication and separation, ensuring that genomic information is faithfully and perpetually maintained. The activity of the effector proteins that perform and coordinate these biological processes oscillates by regulated expression and/or posttranslational modifications. Ubiquitylation is a cardinal cellular modification and is long known for driving cell cycle transitions. In this review, we emphasize emerging concepts of how ubiquitylation brings the necessary dynamicity and plasticity that underlie the processes of DNA replication and mitosis. New studies, often focusing on the regulation of chromosomal proteins like DNA polymerases or kinetochore kinases, are demonstrating that ubiquitylation is a versatile modification that can be used to fine-tune these cell cycle events, frequently through processes that do not involve proteasomal degradation. Understanding how the increasing variety of identified ubiquitin signals are transduced will allow us to develop a deeper mechanistic perception of how the multiple factors come together to faithfully propagate genomic information. Here, we discuss these and additional conceptual challenges that are currently under study toward understanding how ubiquitin governs cell cycle regulation.

Figure 1.

Writing, reading, and editing ubiquitin. (A) Ubiquitin is added to a substrate protein (writing ubiquitin) by E3 ligases, and ubiquitin moieties can be removed (editing ubiquitin) by deubiquitylating enzymes (DUBs). Protein degradation is mostly associated with polyubiquitin chains, in which ubiquitin moieties attach to each other via homotypic lysine-48 (K48) linkages or heterotypic K11/K48 linkages (mixed chain or branched; see Ubiquitin signals produced by CRLs and the APC/C text box). The result of K63-linked polyubiquitylation is distinct and, together with monoubiquitylation (monoUb), it is associated with nonproteolytic outcomes. (B) Ubiquitylation produces a signal that is often dependent on effector proteins or complexes (ubiquitin readers). These include the proteasome, which is a proteolytic machine, or the segregase VCP/p97 (Cdc48 in yeast), which extracts proteins from chromatin, cellular compartments, or protein complexes for recycling or degradation. Other ubiquitin-binding proteins can fulfill a specific function with nonproteolytic outcomes when they are recruited to ubiquitylated substrates (e.g., damage tolerance by error-prone polymerases), potentially altering the localization or activity of the ubiquitylated substrate. By affecting protein interactions or conformations, ubiquitylation may directly alter protein localization or activity. A challenge in present research is to distinguish between a passive effect of ubiquitylation and the action of an unidentified ubiquitin reader.

Figure 2.

The dynamic regulation of unperturbed DNA replication by ubiquitin. Proteolytic and nonproteolytic mechanisms are depicted with light orange and light blue background, respectively, and gray if a determination is incomplete. (A) Overview of the primary events occurring during DNA replication. Activation of the active CMG helicase (CDC45, MCM hexamer, GINS complex) induces the recruitment of the sliding clamp PCNA (depicted in red), which serves as an interaction platform to tether DNA polymerases to chromatin (Moldovan et al., 2007). (B) Polymerase switches occurring in lagging strand synthesis are mediated by ubiquitylation. (C and D) Concomitant with DNA replication, nucleosomes are disassembled and reassembled in a semiconservative manner, incorporating newly synthesized histones, which requires nondegradative ubiquitylation. (E) Termination of chromosomal replication in yeast and Xenopus requires Cdc48/p97 for CMG eviction from the chromatin. Red crosses depict targets of proteasomal degradation, and red circles depict ubiquitin. Ac, acetylation; Sc, Saccharomyces cerevisiae; Xl, Xenopus laevis.

Figure 3.

Ubiquitin in the regulation of protein dynamics and localization in mitosis. Proteolytic and nonproteolytic mechanisms are depicted with light orange and light blue background, respectively. (A) Upon mitotic entry, chromosomes condense and the cell assembles a bipolar mitotic spindle. The kinases Aurora B (AurB) and PLK1 both contribute to the establishment of correct, bioriented, kinetochore–microtubule attachments by destabilizing incorrect attachments and stabilizing correct ones, respectively. (B) Transit to anaphase occurs when the APC/C is no longer inhibited by the MCC and is activated by CDC20. MCC disassembly is promoted by autoubiquitylation of CDC20 within the APC/C-bound MCC and by the ubiquitin reader CUEDC2. The irreversibility of this transition necessitates cyclin B destruction, as otherwise the SAC is reactivated (Clijsters et al., 2014; Rattani et al., 2014; Vázquez-Novelle et al., 2014). (C) Kinetochore recruitment and exclusion of the chromosomal passenger complex (CPC), which includes Aurora B and Survivin, depend on nonproteolytic ubiquitylation. Exclusion of PLK1 from the kinetochore in case of bioriented microtubule attachments also depends on its ubiquitylation. (D and E) Microtubule transport can be promoted by cargo ubiquitylation, as is the case for the spindle assembly factor NuMA and Aurora B. Whether the ubiquitylation of PLK1 promotes its transport to the spindle midzone has not yet been determined. Red crosses depict targets of proteasomal degradation, red circles depict ubiquitin, and purple circles depict Aurora B kinase.