Protein Ubiquitination in IR-Induced DNA Damage Response

Abstract

Ionizing radiation is a major source of double-strand DNA breaks, the most detrimental form of DNA damage that, if left unrepaired, leads to genomic instability and cancer. Eukaryotic cells have evolved a DNA damage response (DDR), an intricate network that can be rapidly activated to response to such challenge. Mutations in genes that encode DDR proteins are associated with many genetic diseases, suggesting the importance of DDR in maintaining genomic integrity (1-5). DDR is a sophisticated signal transduction network comprised of proteins that are capable of sensing DNA damage, amplifying the signals and executing various cellular functions that have direct impact on cell fate. Of great importance for the understanding of DDR are series of studies that aim to identify proteome-wide substrates of checkpoint kinase ATM/ATR. These unbiased screens greatly expanded the DDR landscape and revealed the involvement of a broad spectrum of pathways that were not previously known (6, 7). One of the most intriguing observations made in these studies is the over-representation of proteins involved in ubiquitin proteasome system (UPS) pathways. Ubiquitin (Ub) is a 76 amino acid protein that can be post-translationally covalently attached to the lysine residues of target proteins(8). Ubiquitin can influence the function of its target proteins by altering their enzymatic activity, abundance or localization (9-14). In this chapter, we will focus mainly on the role of ubiquitination in DDR signaling and cell cycle regulation. Following a brief introduction to principles of ubiquitination and ubiquitin-like modification, we will present an overview of enzymes and substrates that have been identified over the last two decades of intensive research. Finally, we will introduce recent advances in application of affinity purification and mass spectrometric-based identification of ubiquitinated proteins.