Cytoplasmic organization promotes protein diffusion in Xenopus extracts

William Y. C. Huang, Xianrui Cheng () and James E. Ferrell ()
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William Y. C. Huang: Stanford University School of Medicine
Xianrui Cheng: Stanford University School of Medicine
James E. Ferrell: Stanford University School of Medicine

Nature Communications, 2022, vol. 13, issue 1, 1-10

Abstract: Abstract The cytoplasm is highly organized. However, the extent to which this organization influences the dynamics of cytoplasmic proteins is not well understood. Here, we use Xenopus laevis egg extracts as a model system to study diffusion dynamics in organized versus disorganized cytoplasm. Such extracts are initially homogenized and disorganized, and self-organize into cell-like units over the course of tens of minutes. Using fluorescence correlation spectroscopy, we observe that as the cytoplasm organizes, protein diffusion speeds up by about a factor of two over a length scale of a few hundred nanometers, eventually approaching the diffusion time measured in organelle-depleted cytosol. Even though the ordered cytoplasm contained organelles and cytoskeletal elements that might interfere with diffusion, the convergence of protein diffusion in the cytoplasm toward that in organelle-depleted cytosol suggests that subcellular organization maximizes protein diffusivity. The effect of organization on diffusion varies with molecular size, with the effects being largest for protein-sized molecules, and with the time scale of the measurement. These results show that cytoplasmic organization promotes the efficient diffusion of protein molecules in a densely packed environment.

Date: 2022
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DOI: 10.1038/s41467-022-33339-0

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