Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis

Wan, Tao; Horová, Magdaléna; Khetrapal, Vimmy; Li, Shanren; Jones, Camden; Schacht, Andrew; Sun, Xinghui; Zhang, LiMei

doi:10.1016/j.jbc.2023.104777

Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis

Journal Article · Tue May 30 00:00:00 EDT 2023 · Journal of Biological Chemistry

DOI:https://doi.org/10.1016/j.jbc.2023.104777· OSTI ID:2423935

Wan, Tao ^[1]; Horová, Magdaléna ^[1]; Khetrapal, Vimmy ^[1]; Li, Shanren ^[1]; Jones, Camden ^[1]; Schacht, Andrew ^[1]; Sun, Xinghui ^[1]; ^[1]

Univ. of Nebraska, Lincoln, NE (United States)

Mycobacterium tuberculosis (Mtb) WhiB3 is an iron–sulfur cluster-containing transcription factor belonging to a subclass of the WhiB-Like (Wbl) family that is widely distributed in the phylum Actinobacteria. WhiB3 plays a crucial role in the survival and pathogenesis of Mtb. It binds to the conserved region 4 of the principal sigma factor (σ^A₄) in the RNA polymerase holoenzyme to regulate gene expression like other known Wbl proteins in Mtb. However, the structural basis of how WhiB3 coordinates with σ^A₄ to bind DNA and regulate transcription is unclear. Here we determined crystal structures of the WhiB3:σ^A₄ complex without and with DNA at 1.5 Å and 2.45 Å, respectively, to elucidate how WhiB3 interacts with DNA to regulate gene expression. These structures reveal that the WhiB3:σ^A₄ complex shares a molecular interface similar to other structurally characterized Wbl proteins and also possesses a subclass-specific Arg-rich DNA-binding motif. We demonstrate that this newly defined Arg-rich motif is required for WhiB3 binding to DNA in vitro and transcriptional regulation in Mycobacterium smegmatis. Together, our study provides empirical evidence of how WhiB3 regulates gene expression in Mtb by partnering with σ^A₄ and engaging with DNA via the subclass-specific structural motif, distinct from the modes of DNA interaction by WhiB1 and WhiB7.

View Accepted Manuscript (DOE)

Research Organization:: SLAC National Accelerator Laboratory, Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Science Foundation (NSF)

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 2423935

Journal Information:: Journal of Biological Chemistry, Journal Name: Journal of Biological Chemistry Journal Issue: 6 Vol. 299; ISSN 0021-9258

Publisher:: American Society for Biochemistry and Molecular BiologyCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
Wbl family
WhiB3
X-ray crystallography
iron-sulfur cluster
transcription factor

Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis

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References (52)

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