Uncovering Ubiquitin and Ubiquitin-like Signaling Networks

1. INTRODUCTION Proteomes are significantly more complex than genomes and transcriptomes due to protein processing and extensive post-translational modification (PTM) of proteins. Hundreds of different modifications exist. Release 66 of the RESID database 1ferent modifications, including small chemical modifications such as phosphorylation, acetylation, and methylation and modification by small proteins, including ubiquitin and ubiquitin-like (UBL) proteins that are covalently coupled to proteins to regulate their activity. A wide variety of cellular processes are regulated by these reversible modifications, including transcription , replication, cell-cycle progression, and responses to DNA damage. Protein modifications have been studied for many years at the level of single target proteins, but currently available technologies enable proteome-wide studies of these modifications by mass spectrometry (MS). 2,3 Powerful proteomics tools are available to study phosphorylation and acetylation at a systems-wide level in a site-specific manner. It is more challenging to study ubiquitin targets and targets for ubiquitin-like proteins at a proteome-wide level in a site-specific manner due to the relatively large size of these modifications, but hundreds of potential target proteins have been uncovered over the past eight years, mainly in a non-site-specific manner. This review is focused on uncovering signaling networks for ubiquitin and ubiquitin-like proteins by mass spectro-metry and highlights the site-specific studies published in 2010 and 2011. Site-specific methodologies will likely have a major impact on the ubiquitin field in the near future. The methodology, results, challenges, pitfalls, crosstalk with other PTMs, and future directions are discussed in this review.