A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence

Reliza J. McGinnis, Chad A. Brambley, Brandon Stamey, William C. Green, Kimberly N. Gragg, Erin R. Cafferty, Thomas C. Terwilliger, Michal Hammel, Thomas J. Hollis, Justin M. Miller, Maria D. Gainey () and Jamie R. Wallen ()
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Reliza J. McGinnis: Western Carolina University, Department of Chemistry and Physics
Chad A. Brambley: Middle Tennessee State University, Department of Chemistry
Brandon Stamey: Western Carolina University, Department of Chemistry and Physics
William C. Green: Western Carolina University, Department of Chemistry and Physics
Kimberly N. Gragg: Western Carolina University, Department of Chemistry and Physics
Erin R. Cafferty: Western Carolina University, Department of Chemistry and Physics
Thomas C. Terwilliger: New Mexico Consortium
Michal Hammel: Lawrence Berkeley National Laboratory
Thomas J. Hollis: Wake Forest University School of Medicine, Medical Center Boulevard
Justin M. Miller: Middle Tennessee State University, Department of Chemistry
Maria D. Gainey: Western Carolina University, Department of Chemistry and Physics
Jamie R. Wallen: Western Carolina University, Department of Chemistry and Physics

Nature Communications, 2022, vol. 13, issue 1, 1-15

Abstract: Abstract Regulation of bacteriophage gene expression involves repressor proteins that bind and downregulate early lytic promoters. A large group of mycobacteriophages code for repressors that are unusual in also terminating transcription elongation at numerous binding sites (stoperators) distributed across the phage genome. Here we provide the X-ray crystal structure of a mycobacteriophage immunity repressor bound to DNA, which reveals the binding of a monomer to an asymmetric DNA sequence using two independent DNA binding domains. The structure is supported by small-angle X-ray scattering, DNA binding, molecular dynamics, and in vivo immunity assays. We propose a model for how dual DNA binding domains facilitate regulation of both transcription initiation and elongation, while enabling evolution of other superinfection immune specificities.

Date: 2022
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DOI: 10.1038/s41467-022-31678-6

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