The Solution Structures and Interaction of SinR and SinI: Elucidating the Mechanism of Action of the Master Regulator Switch for Biofilm Formation in Bacillus subtilis.

Abstract

Bacteria have developed numerous protection strategies to ensure survival in harsh environments, with perhaps the most robust method being the formation of a protective biofilm. In biofilms, bacterial cells are embedded within a matrix that is composed of a complex mixture of polysaccharides, proteins, and DNA. The gram-positive bacterium Bacillus subtilis has become a model organism for studying regulatory networks directing biofilm formation. The phenotypic transition from a planktonic to biofilm state is regulated by the activity of the transcriptional repressor, SinR, and its inactivation by its primary antagonist, SinI. In this work, we present the first full-length structural model of tetrameric SinR using a hybrid approach combining high-resolution solution nuclear magnetic resonance (NMR), chemical cross-linking, mass spectrometry, and molecular docking. We also present the solution NMR structure of the antagonist SinI dimer and probe the mechanism behind the SinR-SinI interaction using a combination of biochemical and biophysical techniques. As a result of these findings, we propose that SinI utilizes a residue replacement mechanism to block SinR multimerization, resulting in diminished DNA binding and concomitant decreased repressor activity. Finally, we provide an evidence-based mechanism that confirms how disruption of the SinR tetramer by SinI regulates gene expression.

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Published Version (Please cite this version)

10.1016/j.jmb.2019.08.019

Publication Info

Milton, Morgan E, G Logan Draughn, Benjamin G Bobay, Sean D Stowe, Andrew L Olson, Erik A Feldmann, Richele J Thompson, Katherine H Myers, et al. (2020). The Solution Structures and Interaction of SinR and SinI: Elucidating the Mechanism of Action of the Master Regulator Switch for Biofilm Formation in Bacillus subtilis. Journal of molecular biology, 432(2). pp. 343–357. 10.1016/j.jmb.2019.08.019 Retrieved from https://hdl.handle.net/10161/28914.

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Scholars@Duke

Bobay

Benjamin Bobay

Assistant Professor in Radiology

I am the Assistant Director of the Duke University NMR Center and an Assistant Professor in the Duke Radiology Department. I was originally trained as a structural biochemist with an emphasis on utilizing NMR and continue to use this technique daily helping collaborators characterize protein structures and small molecules through a diverse set of NMR experiments. Through the structural characterization of various proteins, from both planta and eukaryotes, I have developed a robust protocol of utilizing computational biology for describing binding events, mutations, post-translations modifications (PTMs), and/or general behavior within in silico solution scenarios. I have utilized these techniques in collaborations ranging from plant pathologists at the Swammerdam Institute for Life Sciences department at the University of Amsterdam to biomedical engineers at North Carolina State University to professors in the Pediatrics department at Duke University. These studies have centered around the structural and functional consequences of PTMs (such as phosphorylation), mutation events, truncation of multi-domain proteins, dimer pulling experiments, to screening of large databases of ligands for potential binding events. Through this combination of NMR and computational biology I have amassed 50 peer-reviewed published articles and countless roles on scientific projects, as well as the development of several tutorials concerning the creation of ligand databases and high-throughput screening of large databases utilizing several different molecular dynamic and computational docking programs.


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