DNA binding mechanism of WhiB4 from Mycobacterium tuberculosis

Abstract Mycobacterium tuberculosis (Mtb), the pathogen of tuberculosis, has latently infected about one-third of the world’s population and may lead to severe clinical symptoms and death. The WhiB4 protein, a transcription factor, plays a crucial role in the survival and pathology of Mtb. WhiB4 leads to the condensation of mycobacterial nucleoids and regulates the expression of genes involved in central metabolism, respiration, and maintaining redox homeostasis. Here, we report the solution structure of reduced apo-WhiB4 monomer, which consists of an unstructured N-terminal domain with four cysteine residues and a helix-turn-helix C-terminal domain that plays a major role in DNA binding. The C-terminal domain of WhiB4 binds DNA at the minor groove, with five positively charged lysine/arginine residues contacting DNA sugar-phosphate backbones through electrostatic interactions. AT-rich DNA sequences with narrower minor grooves are more preferred by WhiB4. The binding affinity of a single C-terminal domain of WhiB4 is weak. When oxidized, WhiB4 can form dimers and oligomers in different forms through disulfide bonds, which should significantly enhance its DNA binding ability through multivalent effect and change the local structure of target genes and influence their transcription. These structural features form the basis for WhiB4 to function as a redox-sensitive transcription factor in Mtb.