Complex Diffusion in Bacteria

Bohrer, Christopher H.; Xiao, Jie

doi:10.1007/978-3-030-46886-6_2

Cited by 17 publications

(11 citation statements)

References 118 publications

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“…Diffusion restrictions in murine myocytes are much greater than described for molecular crowding in bacteria (McGuffee and Elcock, 2010), as well as in non-muscle mammalian cells (Verkman, 2002; Rivas and Minton, 2016). Particularly for bacteria, diffusion restrictions are characterized in much detail (McGuffee and Elcock, 2010; Gallet et al, 2017; Bohrer and Xiao, 2020), and molecular simulations are quite advanced (Trovato and Tozzini, 2014; Bohrer and Xiao, 2020). In those models, only a two to three fold reduction of diffusion coefficients occurs as hydrated radii increase from 1 to 4 nm (i.e.…”

Section: Discussionmentioning

confidence: 99%

Pore-like diffusion barriers in murine cardiac myocytes

Deisl

Chung

Hilgemann

2023

Preprint

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Using both optical and electrical methods, we document that solute diffusion in the cytoplasm of BL6 murine cardiac myocytes becomes restricted >30-fold as molecular weight increases from 30 to 2000, roughly as expected for pores with dimensions of cardiac porin channels. The Bodipy-FL ATP analogue diffuses ~50-fold slower in BL6 cardiac cytoplasm than in free water. From several fluorophores analyzed, our estimates of bound fluorophore fractions range from 0.1 for a 2 kD FITC-labeled polyethylene glycol to 0.93 for sulforhodamine. We estimate that diffusion coefficients of unbound fluorophores range from 0.5 to 8 x 10-7 cm2/s. Analysis of Na/K pump and veratridine-modified Na channel currents confirms that Na diffusion is nearly unrestricted (time constant for equilibration with the pipette tip, ~20 s). Using three different approaches, we estimate that ATP diffuses 8 to 10-times slower in the cytoplasm of BL6 myocytes than in free water. To address whether restrictions are caused more by cytoplasmic protein or membrane networks, we verified first that a protein gel, 10 gram% gelatin, restricts solute diffusion with strong dependence on molecular weight. Solute diffusion in membrane-extracted cardiac myofilaments, confined laterally by suction into large-diameter pipette tips, is however less restricted than in intact myocytes. Notably, myofilaments from equivalently extracted skeletal (diaphragm) myocytes restrict diffusion less than cardiac myofilaments. Solute diffusion in myocytes with sarcolemma permeabilized by beta-escin (70 micromolar) is similarly restricted as in intact myocytes. Diffusion restriction in cardiac myocytes is strain-dependent, being about two-fold greater in BL6 myocytes than in myocytes with a CD1/J6/129svJ background. Furthermore, diffusion is 2.5-fold more restricted in CD1/J6/129svJ myocytes lacking the mitochondrial porin, Vdac1, than in WT CD1/J6/129svJ myocytes. We conclude that both myofilaments and mitochondria networks restrict diffusion in cardiac myocytes. As a result, long-range solute diffusion may preferentially occur via passage through porin channels and intramembrane mitochondrial spaces, where diffusion is less restricted than in myofilament spaces.

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Section: Discussionmentioning

confidence: 99%

Pore-like diffusion barriers in murine cardiac myocytes

Deisl

Chung

Hilgemann

2023

Preprint

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“…Diffusion measured near the cell boundary and in the cell pole regions of rod-shaped bacteria appears slower than in the cell center due to confinement effects 16,38,[56][57][58] . We recently showed 16 that the ra'o between the diffusion coefficient at the cell poles and cell center is lower for SMdM data than for simulated data, where par0cles are treated as mathema0cal points moving of random mo0on.…”

Section: Sbrd Versus Smdm Analysis Of the Diffusion Coefficient At Th...mentioning

confidence: 98%

Simulation-based Reconstructed Diffusion unveils the effect of aging on protein diffusion in Escherichia coli

Mantovanelli

Linnik

Punter

et al. 2023

Preprint

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We have developed Simulation-based Reconstructed Diffusion (SbRD) to determine diffusion coefficients corrected for confinement effects and for the bias introduced by two-dimensional models describing a three-dimensional motion. We validate the method on simulated diffusion data in three-dimensional cell-shaped compartments. We use SbRD, combined with a new cell detection method, to infer the diffusion coefficients of a set of native proteins in Escherichia coli. We observe slower diffusion at the cell poles than in the nucleoid region of exponentially growing cells. We find that this observation is independent of the presence of polysomes. Furthermore, we show that the newly formed pole of dividing cells exhibits a faster diffusion than the old one. We hypothesize that the observed slowdown at the cell poles is caused by the accumulation of aggregated or damaged proteins, and that the effect is asymmetric due to cell aging.

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“…Cells are generally not spheres, and taking into account the real time‐dependent distribution of their metabolites is far from straightforward. Furthermore, compartmentalization is a critical feature of the development of metabolism (de Lorenzo et al ., 2015; Bohrer and Xiao, 2020) and this implies that realistic models must make the most of representations that consider the cells’ shape and the way they divide. Exactly as illustrated previously with the case of populations of cells moving on plates, many phenomenological models try to fit with 3D observations to represent the cell’s geometry.…”

Section: Synthetic Biology In Silicomentioning

confidence: 99%

In vivo, in vitro and in silico: an open space for the development of microbe‐based applications of synthetic biology

Danchin

2021

Microbial Biotechnology

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Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computeraided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.

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Complex Diffusion in Bacteria

Cited by 17 publications

References 118 publications

Pore-like diffusion barriers in murine cardiac myocytes

Pore-like diffusion barriers in murine cardiac myocytes

Simulation-based Reconstructed Diffusion unveils the effect of aging on protein diffusion in Escherichia coli

In vivo, in vitro and in silico: an open space for the development of microbe‐based applications of synthetic biology

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