Structural analysis of Spi-B DNA-binding Ets domain recognizing 5′-AGAA-3′ and 5′-GGAA-3′ sequences

Plasmacytoid dendritic cells produce large amounts of type-I interferon (IFN–I) upon sensing nucleic acid components of pathogens by Toll-like receptors (TLR7 and TLR9). The transcription factor Spi-B has the DNA-binding Ets domain, and transactivates the Ifna4 promoter co-operatively with IFN regulatory factor-7 (IRF-7) for TLR7/TLR9-induced IFN-I production. Spi-B associates with IRF-7, and activates transcription by binding to the 5′-AGAA-3′ sequence, being different from 5′-GGAA-3′, known as the Ets domain recognition sequence. To understand the molecular mechanism for the co-operative transactivation of the Ifna4 promoter by Spi-B and IRF-7, we performed X-ray structural determination of the Spi-B Ets domain in complex with target DNAs, including 5′-AGAA-3′ and 5′-GGAA-3′ sequences. Furthermore, we conducted a modeling study of the complex of the Spi-B and IRF-7 with Ifna4 promoter DNA. X-ray structures showed that the binding of the Spi-B Ets domain induces a kink in DNA at the recognition sequence, and a more kinked DNA structure was observed in 5′-AGAA-3′ than 5′-GGAA-3’. A modeling study showed that the Spi-B-induced kinked DNA structure in 5′-AGAA-3′ is favorable for Spi-B and IRF-7 to approach each other for association on DNA.