Endoplasmic Reticulum Structure Determines Optimal Ribosome Density

TL;DR

A model that explains a physical reason for why the cell creates different structures of the ER is presented and is pushed to predict that depending on the future life of the translated protein and overall demand for protein expression, the cell will utilize one structure of the ER over another.

Abstract

Recent work has shown an increasing interest in understanding the structure of the endoplasmic reticulum (ER) and how ribosomes are displayed on it. Here we present a model that explains a physical reason for why the cell creates different structures of the ER. Due to the diffusion of biomolecules, we find that flat sheets and a matrix of tubules have different regimes of optimized capture efficiency. We extend the model to explain the observed difference in density of ribosomes on the structures of the ER. Due to the capture efficiency of tubules, less ribosomes are needed on those structures. For flat sheets, more ribosome coverage at biological separation distance is needed to match the same fraction of relative flux. We then push the model to predict that depending on the future life of the translated protein and overall demand for protein expression, the cell will utilize one structure of the ER over another. Predictions are compared with experimental data.

Figures (3)

• Figure 1: (a) Plot showing the dependence of fractional capacitance for the single sheet geometry on fractional area covered by ribosomes. As expected, a small fraction of area covered leads to near saturation. (b) Same plot as in (a) except with $\log_{10}$ scaling. (c) Heatmap of the fractional capacitance for the double sheet geometry as a function of both separation and fractional area covered. Red contour shows where fractional capacitance is half saturated.
• Figure 2: Heatmap of the fractional capacitance difference between the double and single sheet geometries. There is a critical distance and filling such that the double sheet becomes more efficient. Red contour shows where fractional capacitance difference is zero.
• Figure 3: (a) Heatmap of the fractional capacitance difference for a double sheet and fixed tube. Red contour shows where fractional capacitance difference is zero. (b) Fractional capacitance comparison between the double sheet and tubular geometries with known parameters.