Thermodynamic and structural analysis of the interactions between Epstein-Barr virus transcription factors and the host targeting factor RBP-Jkappa

Epstein-Barr virus (EBV) asymptomatically infects >90% of the world population but is also associated with multiple malignancies. The EBV latent nuclear proteins EBNA2, 3A, 3B and 3C orchestrate changes in host gene transcription to drive B-cell immortalisation by hijacking cellular DNA-binding transcription factors. This project set out to obtain thermodynamic and structural information on host transcription factor RBP-Jkappa, the DNA-binding mediator of the Notch pathway, and its interactions with the EBNAs. EBNA2 activates transcription by binding RBP-Jkappa through the same WFP motif found in Notch proteins. EBNA3 proteins bind RBP-Jkappa through a distinct motif (TFGC) and compete with EBNA2 for binding, inhibiting EBNA2-mediated gene activation, but can also use RBP-Jkappa to bind DNA independently. Interestingly, EBNA3C also contains an adjacent WFP motif (WTP) that can bind RBP-Jkappa in vitro. We used Isothermal Titration Calorimetry (ITC) to measure binding affinities of EBNA2 and EBNA3C peptides containing these motifs to RBP-Jkappa. We found that EBNA2 peptides bound RBPJ-kappa via its WWP motif with an affinity 10-fold less than the WLP motif of Notch 2. Surprisingly, we found that EBNA3 peptides containing TFGC motifs did not bind to RBP-Jkappa in vitro. Phosphorylation of the threonine in this motif did not lead to any detectable binding. However, EBNA3C peptides containing both the TFGC and WTP motifs bound RBP-Jkappa with a similar affinity to EBNA2 peptides, but this interaction was entirely mediated by the WTP motif. We also demonstrated that the EBNA3C TFGC peptide could not compete with EBNA2 for RBP-Jkappa binding using a fluorescent polarisation binding assay. Interestingly, we found that an EBNA3A peptide bound weakly to RBP-Jkappa via a motif with similar physiochemistry to the Notch WTP motif (FKL) and not its TLFC motif. These data indicate that TFGC motifs in EBNA3 proteins may only direct RBPJ-kappa binding in the context of other EBNA3C residues in a properly folded full-length protein or may mediate indirect binding.