The nucleoid of rapidly growing Escherichia coli localizes close to the inner membrane and is organized by transcription, translation, and cell geometry

Christoph Spahn (), Stuart Middlemiss, Estibaliz Gómez- de-Mariscal, Ricardo Henriques, Helge B. Bode, Séamus Holden and Mike Heilemann ()
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Christoph Spahn: Goethe University Frankfurt
Stuart Middlemiss: Newcastle University Biosciences Institute, Faculty of Medical Sciences
Estibaliz Gómez- de-Mariscal: Instituto Gulbenkian de Ciência
Ricardo Henriques: Instituto Gulbenkian de Ciência
Helge B. Bode: Max Planck Institute for Terrestrial Microbiology
Séamus Holden: Newcastle University Biosciences Institute, Faculty of Medical Sciences
Mike Heilemann: Goethe University Frankfurt

Nature Communications, 2025, vol. 16, issue 1, 1-18

Abstract: Abstract Bacterial chromosomes are spatiotemporally organized and sensitive to environmental changes. However, the mechanisms underlying chromosome configuration and reorganization are not fully understood. Here, we use single-molecule localization microscopy and live-cell imaging to show that the Escherichia coli nucleoid adopts a condensed, membrane-proximal configuration during rapid growth. Drug treatment induces a rapid collapse of the nucleoid from an apparently membrane-bound state within 10 min of halting transcription and translation. This hints toward an active role of transertion (coupled transcription, translation, and membrane insertion) in nucleoid organization, while cell wall synthesis inhibitors only affect nucleoid organization during morphological changes. Further, we provide evidence that the nucleoid spatially correlates with elongasomes in unperturbed cells, suggesting that large membrane-bound complexes might be hotspots for transertion. The observed correlation diminishes in cells with changed cell geometry or upon inhibition of protein biosynthesis. Replication inhibition experiments, as well as multi-drug treatments highlight the role of entropic effects and transcription in nucleoid condensation and positioning. Thus, our results indicate that transcription and translation, possibly in the context of transertion, act as a principal organizer of the bacterial nucleoid, and show that an altered metabolic state and antibiotic treatment lead to major changes in the spatial organization of the nucleoid.

Date: 2025
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DOI: 10.1038/s41467-025-58723-4

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