DNA deformability in sequence-dependent capture of E. coli gyrase

To understand how gyrase interacts with DNA and selects a site of action, we created an ad hoc shape-based recognition methodology to ascertain the DNA sequence from cryoEM density maps as a string of purines and pyrimidines, which matched to the DNA minicircle sequence in our two previous cryoEM structures of negatively supercoiled DNA bound to E. coli gyrase. For one structure, the Gate- or G-segment sequence contains base-pair steps that are among the most flexible in the minicircle, facilitating the bend. The sequence flanking this G-segment is highly inflexible, preventing wrapping the β-pinwheel of gyrase. In the other structure, a flexible DNA minicircle sequence wraps a β-pinwheel of gyrase and the G-segment contains base-pair steps of average deformability. This work highlights how DNA sequence and deformability impact gyrase. It also demonstrates the utility of both identifying DNA sequences from cryoEM structures and assessing base-pair step deformability.

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Publication Details

Journal
Nature Communications
Published
2026-04-20
DOI
https://doi.org/10.1038/s41467-026-71884-0
Primary Topic
Bacterial Genetics and Biotechnology
Type
article
Field-Weighted Citation Impact
0.00

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article

DNA deformability in sequence-dependent capture of E. coli gyrase

Valérie Lamour, Lynn Zechiedrich, Jonathan M. Fogg, Matthew L. Baker et al.
Nature Communications
Bacterial Genetics and Biotechnology
article

DNA deformability in sequence-dependent capture of E. coli gyrase

Valérie Lamour, Lynn Zechiedrich, Jonathan M. Fogg, Matthew L. Baker, N. Marechal, Wilma K. Olson, Ryan Eckerty, Silvia Summers, Haley R. Johnson, Marlène Vayssières
article en

Abstract

To understand how gyrase interacts with DNA and selects a site of action, we created an ad hoc shape-based recognition methodology to ascertain the DNA sequence from cryoEM density maps as a string of purines and pyrimidines, which matched to the DNA minicircle sequence in our two previous cryoEM structures of negatively supercoiled DNA bound to E. coli gyrase. For one structure, the Gate- or G-segment sequence contains base-pair steps that are among the most flexible in the minicircle, facilitating the bend. The sequence flanking this G-segment is highly inflexible, preventing wrapping the β-pinwheel of gyrase. In the other structure, a flexible DNA minicircle sequence wraps a β-pinwheel of gyrase and the G-segment contains base-pair steps of average deformability. This work highlights how DNA sequence and deformability impact gyrase. It also demonstrates the utility of both identifying DNA sequences from cryoEM structures and assessing base-pair step deformability.

Nature Communications
Rutgers, The State University of New Jersey (US), Centre National de la Recherche Scientifique (FR), Georgia Institute of Technology (US), Inserm (FR), Baylor College of Medicine (US), Institut de génétique et de biologie moléculaire et cellulaire (FR), Quantitative BioSciences (US), Hôpitaux Universitaires de Strasbourg (FR), Integrated Structural Biology Grenoble (FR), The University of Texas Health Science Center at Houston (US)
Welch Foundation, National Institutes of Health
Openalex Percentile: Top 19%
Bacterial Genetics and Biotechnology
DOIOpen Access PDFOpenAlex
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