Role of p97/VCP (Cdc48) in genome stability

Abstract

Ubiquitin-dependent molecular chaperone p97, also known as valosin-containing protein (VCP) or Cdc48, is an AAA ATPase involved in protein turnover and degradation. p97 converts its own ATPase hydrolysis into remodeling activity on a myriad of ubiquitinated substrates from different cellular locations and pathways. In this way, p97 mediates extraction of targeted protein from cellular compartments or protein complexes. p97-dependent protein extraction from various cellular environments maintains cellular protein homeostasis. In recent years, p97-dependent protein extraction from chromatin has emerged as an essential evolutionarily conserved process for maintaining genome stability. Inactivation of p97 segregase activity leads to accumulation of ubiquitinated substrates on chromatin, consequently leading to protein-induced chromatin stress (PICHROS). PICHROS directly and negatively affects multiple DNA metabolic processes, including replication, damage responses, mitosis, and transcription, leading to genotoxic stress and genome instability. By summarizing and critically evaluating recent data on p97 function in various chromatin-associated protein degradation processes, we propose establishing p97 as a genome caretaker.

Keywords: Cdc48; DNA damage response; DNA repair; DNA replication; chromatin-associated protein degradation; genome stability; p97/VCP; protein-induced chromatin stress.

FIGURE 1

p97 and its three core adaptors regulate diverse cellular functions. (A) Domain structure of p97 monomer: N-terminal region (yellow), L1 and L2 linker regions (gray), two ATPase cassettes D1 and D2 (green), and the C-terminal tail (blue). (B) p97 homohexamer forms a barrel-like structure that mutually binds one of three core adaptor complexes, Npl4–Ufd1 heterodimer, UBXD1 or p47, and regulates diverse cellular functions as indicated in white boxes. ERAD, endoplasmic reticulum-associated degradation; RAD, ribosomal-associated degradation; CAD, chromatin-associated degradation.

FIGURE 2

Chromatin-associated protein degradation (CAD) regulated by p97^{–Ufd1–Npl4}. Chromatin-bound proteins (S represents any known p97 substrate on chromatin) are polyubiquitinated and sumoylated by specific E3 ubiquitin and SUMO ligases. p97^{–Ufd1–Npl4} complex is recruited to polyubiquitinated substrates by a ubiquitin-binding domain in Npl4 or Ufd1. ATP hydrolysis, located in the D2 ATPase cassette, induces conformational changes in the p97 molecule to remodel and release chromatin-bound substrates. Extracted substrates are either degraded by proteasomes or recycled. The p97^{–Ufd1–Npl4} complex maintains CAD and prevents PICHROS.

FIGURE 3

Protein-induced chromatin stress (PICHROS). As indicated in Figure 2, chromatin-bound substrates are polyubiquitinated, but cannot be removed due to inactivation of p97. Accumulation of polyubiquitinated substrates on chromatin causes PICHROS that severely disturbs, mostly inhibits, essential DNA metabolic processes, such as DNA replication, transcription, or DNA repair, and leads to genome instability.

FIGURE 4

Role of p97 in genome stability. The circle represents a summary of p97 functions in diverse cellular processes, from yeast to human, essential for maintenance of genome stability. Key players from different species are abbreviated with human homologous (e.g., yeast Cdc48 and Ubx5 is equivalent to human p97 and UBXD7). The p97 homohexamer is centrally located. The first ring (blue) represents two core adaptor complexes, Ufd1–Npl4 and p47. The second ring (orange) represents the next tier of p97 adaptors that direct the function of p97 core complexes. DVC1 directs p97^{–Ufd1–Npl4} function toward TLS, and UBXD7 and UBXD9 direct p97^{–Ufd1–Npl4} toward stalled transcription and TC-NER. The third ring (gray) represents E3 ubiquitin ligases that ubiquitinate p97-substrates. The fourth ring (green) represents p97-substrates that must be remodeled (extracted) by p97 to avoid PICHROS and prevent genome instability. The fifth ring (white) represents different cellular processes in which p97 plays an essential role for maintenance of genome stability. PP1, protein phosphates 1/Glc7 in yeast; CDK inhibitor, cyclin-dependent kinase inhibitor Far1p in yeast; L3MBTL1, polycomb protein that contains malignant brain tumor (MBT) domain; CDT1, chromatin licensing and DNA replication factor 1; SET8, histone methyltransferase; XMAP215, processive microtubule polymerase; TPX2, microtubule associated protein; PLX1, polo-like kinase; DNA pol δ and η DNA polymerases delta and eta.