A split ubiquitin system to reveal topology and released peptides of membrane proteins

BACKGROUND: Membrane proteins define biological functions of membranes in cells. Extracellular peptides of transmembrane proteins receive signals from pathogens or environments, and are the major targets of drug developments. Despite of their essential roles, membrane proteins remain elusive in topological studies due to technique difficulties in their expressions and purifications. METHODS: First, the target gene is cloned into a destination vector to fuse with C terminal ubiquitin at the N or C terminus. Then, Cub vector with target gene and Nub(WT) or Nub(G) vectors are transformed into AP4 or AP5 yeast cells, respectively. After mating, the diploid cells are dipped onto selection medium to check the growth. Topology of the target protein is determined according to Table 1. RESULTS: We present a split ubiquitin topology (SUT) analysis system to study the topology and truncation peptide of membrane proteins in a simple yeast experiment. In the SUT system, transcription activator (TA) fused with a nucleo-cytoplasmic protein shows strong auto-activation with both positive and negative control vectors. TA fused with the cytoplasmic end of membrane proteins activates reporter genes only with positive control vector with a wild type N terminal ubiquitin (Nub(WT)). However, TA fused with the extracellular termini of membrane proteins can’t activate reporter genes even with Nub(WT). Interestingly,TA fused with the released peptide of a membrane protein shows autoactivation in the SUT system. CONCLUSION: The SUT system is a simple and fast experimental procedure complementary to computational predictions and large scale proteomic techniques. The preliminary data from SUT are valuable for pathogen recognitions and new drug developments. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12896-017-0391-0) contains supplementary material, which is available to authorized users.