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Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in live Escherichia coli cells.
Valverde-Mendez, Diana; Sunol, Alp M; Bratton, Benjamin P; Delarue, Morgan; Hofmann, Jennifer L; Sheehan, Joseph P; Gitai, Zemer; Holt, Liam J; Shaevitz, Joshua W; Zia, Roseanna N.
Afiliación
  • Valverde-Mendez D; Department of Physics, Princeton University, Princeton, NJ 08540, USA.
  • Sunol AM; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA.
  • Bratton BP; Department of Chemical Engineering, Stanford University, , Stanford, CA 94305, USA.
  • Delarue M; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA.
  • Hofmann JL; Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA.
  • Sheehan JP; Department of Pathology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37235, USA.
  • Gitai Z; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA.
  • Holt LJ; Vanderbilt Institute for Infection, Inflammation and Immunology, Vanderbilt University, Nashville, TN 37235, USA.
  • Shaevitz JW; LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France.
  • Zia RN; Department of Chemical Engineering, Stanford University, , Stanford, CA 94305, USA.
bioRxiv ; 2024 Mar 28.
Article en En | MEDLINE | ID: mdl-38585850
ABSTRACT
The crowded bacterial cytoplasm is comprised of biomolecules that span several orders of magnitude in size and electrical charge. This complexity has been proposed as the source of the rich spatial organization and apparent anomalous diffusion of intracellular components, although this has not been tested directly. Here, we use biplane microscopy to track the 3D motion of self-assembled bacterial Genetically Encoded Multimeric nanoparticles (bGEMs) with tunable size (20 to 50 nm) and charge (-2160 to +1800 e) in live Escherichia coli cells. To probe intermolecular details at spatial and temporal resolutions beyond experimental limits, we also developed a colloidal whole-cell model that explicitly represents the size and charge of cytoplasmic macromolecules and the porous structure of the bacterial nucleoid. Combining these techniques, we show that bGEMs spatially segregate by size, with small 20-nm particles enriched inside the nucleoid, and larger and/or positively charged particles excluded from this region. Localization is driven by entropic and electrostatic forces arising from cytoplasmic polydispersity, nucleoid structure, geometrical confinement, and interactions with other biomolecules including ribosomes and DNA. We observe that at the timescales of traditional single molecule tracking experiments, motion appears sub-diffusive for all particle sizes and charges. However, using computer simulations with higher temporal resolution, we find that the apparent anomalous exponents are governed by the region of the cell in which bGEMs are located. Molecular motion does not display anomalous diffusion on short time scales and the apparent sub-diffusion arises from geometrical confinement within the nucleoid and by the cell boundary.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: BioRxiv Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: BioRxiv Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos