PNNL

Abstract

In Rhodbacter sphaeroides, transcriptional response to singlet oxygen is controlled by the ECF (extracytoplasmic function) transcription factor, ??. ECF ?’s comprise the largest and most divergent group of the ?70-family members and are negatively regulated by their cognate anti-? factor. Here, we determine the crystal structure of the Rhodobacter sphaeroides ECF ? factor, ?E, in an inhibitory complex with its anti-?, ChrR. The structure reveals that ChrR is composed of two structural domains separated by a flexible linker. The N-terminal domain sterically occludes the two primary binding determinants on ?E for core RNA polymerase and is thus referred to as the ASD (anti-? domain). Genetic and biochemical characterization of the two domains show that the ASD is sufficient to inhibit ?E dependant transcription and the C-terminal domain is required for response to singlet oxygen and the release of ?E from the ASD. In addition, structural and sequence analyses of the ASD of ChrR and other ECF anti-?’s, reveal that the N-terminal domain of different groups of ECF anti-?’s share a common structural fold with some sequence similarity. Bioinformatics studies show that the ASD occurs in as many as one third of ECF anti-?’s, many of which have diverse C-terminal domains. The conserved ASD are sometimes fused to diverse C-terminal domains. These studies reveal that the ASD class of anti-?’s are extraordinarily diverse, based on the type of ??factors they are associated with and the C-terminal domains to which they are linked.