Diffusion of Exit Sites on the Endoplasmic Reticulum: A Random Walk on a Shivering Backbone

Abstract

Major parts of the endoplasmic reticulum (ER) in eukaryotic cells are organized as a dynamic network of membrane tubules connected by three-way junctions. On this network, self-assembled membrane domains, called ER exit sites (ERES), provide platforms at which nascent cargo proteins are packaged into vesicular carriers for subsequent transport along the secretory pathway. Although ERES appear stationary and spatially confined on long timescales, we show here via singleparticle tracking that they exhibit a microtubule-dependent and heterogeneous anomalous diffusion behavior on short and intermediate timescales. By quantifying key parameters of their random walk, we show that the subdiffusive motion of ERES is distinct from that of ER junctions, i.e., ERES are not tied to junctions but rather are mobile on ER tubules. We complement and corroborate our experimental findings with model simulations that also indicate that ERES are not actively moved by microtubules. Altogether, our study shows that ERES perform a random walk on the shivering ER backbone, indirectly powered by microtubular activity. Similar phenomena can be expected for other domains on subcellular structures, setting a caveat for the interpretation of domain-tracking data.

Single-Particle Tracking Reveals Anti-Persistent Subdiffusion in Cell Extracts

“…Let us briefly insert here an intuitive explanation of why a lognormal-like shape of is seen here and has also been reported frequently in the literature for other experiments (see [ 18 , 22 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 ] for examples). For the simplicity of the argument, we restrict ourselves to standard Brownian motion with Gaussian increment statistics and no memory kernel.…”

“…Scaling exponents α < 1 are commonly referred to as 'subdiffusion', whereas values 1 < α < 2 are termed 'superdiffusion'. Subdiffusion with scaling exponents 0.3 < α < 0.9 has been observed very frequently, at least on short and intermediate time scales, for tracer particles in complex media, e.g., in equilibrated biomimetic crowded fluids [6][7][8][9][10], in the cytoplasm [6,[11][12][13][14][15] and in the nucleoplasm [11,[16][17][18] of living cells, as well as on biomembranes [19][20][21][22]; see also [23,24] for extensive reviews. Cell extracts, which are basically only the cytosol of an ensemble of cells without larger organelle compartments, constitute an intermediate between artificial equilibrated media and nonequilibrium fluids inside living cells.…”

“…Scaling exponents are commonly referred to as ‘subdiffusion’, whereas values are termed ‘superdiffusion’. Subdiffusion with scaling exponents has been observed very frequently, at least on short and intermediate time scales, for tracer particles in complex media, e.g., in equilibrated biomimetic crowded fluids [ 6 , 7 , 8 , 9 , 10 ], in the cytoplasm [ 6 , 11 , 12 , 13 , 14 , 15 ] and in the nucleoplasm [ 11 , 16 , 17 , 18 ] of living cells, as well as on biomembranes [ 19 , 20 , 21 , 22 ]; see also [ 23 , 24 ] for extensive reviews.…”

Diffusive search and trajectories on tubular networks: a propagator approach

“…Proteins destined for secretion are co-translationally inserted into the ER membrane or lumen, undergo folding and quality control [ 45 , 46 ], and must leave the ER through punctate ER exit sites (ERES). These ERES are largely immobile sites scattered throughout the network [ 47 ] (Fig. 2 b) and proteins are assumed to diffuse to one of these sites for capture and packaging into vesicles that enable them to leave the ER and proceed to further steps of secretory processing [ 48 , 49 ].…”

Intertwined and Finely Balanced: Endoplasmic Reticulum Morphology, Dynamics, Function, and Diseases

“…ER dynamics in mammalian cells can be categorised into three types: oscillation of established network elements; the dynamics of particles within the ER lumen or membrane; and generation of new network elements (see Figure 3 ). The purpose of ER dynamics is still unclear, but the predominant theory is that oscillations accelerate the processes carried out in the ER by facilitating the movement of lumenal and transmembrane particles [ 25 , 180 , 181 ].…”