Methods to study phosphoribosylated ubiquitin ligation and removal

Ubiquitination is a prevalent protein modification catalyzed by E1, E2, and E3 enzymes that activate, conjugate, and ligate, respectively, the ubiquitin protein to substrate protein. In order to establish a mutualistic or parasitic relationship with their eukaryotic hosts, many microorganisms hijack different aspects of the ubiquitination machinery using bacterial proteins that function as E3 ligases or as enzymes that modify E2s or ubiquitin. Recently, the SidE family of effector proteins (SidEs) from the intracellular bacterial pathogen Legionella pneumophila was found to catalyze ubiquitination by a mechanism unrelated to the classical three-enzyme cascade. Instead of utilizing ATP, SidEs-catalyzed ubiquitination reactions are energized by nicotinamide adenine dinucleotide (NAD). Ubiquitin is first activated by ADP-ribosylation at residue Arg42 to form ADP-ribosylated ubiquitin (ADPR-Ub). ADPR-Ub is then cleaved by an activity conferred by a phosphodiesterase (PDE)-related domain also embedded in the SidE family proteins. ADPR-Ub cleavage is coupled to covalent attachment of phosphoribosylated ubiquitin to serine residues of target proteins and the release of AMP. Furthermore, SidE-induced ubiquitination can be reversed by SidJ, another virulence factor from L. pneumophila. Here, we describe the experimental details for SdeA-induced ubiquitination of the small GTPase Rab33b and its reversal by SidJ.