Structural insights into the functional divergence of WhiB-like proteins in Mycobacterium tuberculosis

WhiB7 represents a distinct subclass of transcription factors in the WhiB-Like (Wbl) family, a unique group of iron-sulfur (4Fe-4S] cluster-containing proteins exclusive to the phylum of Actinobacteria. In Mycobacterium tuberculosis (Mtb), WhiB7 interacts with domain 4 of the primary sigma factor (σA4) in the RNA polymerase holoenzyme and activates genes involved in multiple drug resistance and redox homeostasis. Here, we report crystal structures of the WhiB7:σA4 complex alone and bound to its target promoter DNA at 1.55-Å and 2.6-Å resolution, respectively. These structures show how WhiB7 regulates gene expression by interacting with both σA4 and the AT-rich sequence upstream of the −35 promoter DNA via its C-terminal DNA-binding motif, the AT-hook. By combining comparative structural analysis of the two high-resolution σA4-bound Wbl structures with molecular and biochemical approaches, we identify the structural basis of the functional divergence between the two distinct subclasses of Wbl proteins in Mtb. [Display omitted] •WhiB7 binds to the same site of the primary sigma factor σA as WhiB1•Fe-S cluster of WhiB7 is stable to O2 upon binding to σA in the RNAP holoenzyme•AT-hook of WhiB7 enhances DNA binding and induces DNA conformational changes•Structural arrangements of WhiB7 are optimal for AT-hook binding to DNA WhiB7 is an Fe-S cluster-bound transcription factor in mycobacteria that is activated by multiple antibiotics. Wan et al. provide an atomic view of how WhiB7 activates transcription by binding to σA and AT-rich promoter DNA, and they identify the structural motifs that enable WhiB7 to function differently from its paralog WhiB1.