Session R36: Physics of Organelles

Is the endoplasmic reticulum an obstacle to intracellular diffusion?

Intracellular spaces are tightly packed and the biggest potential obstacle in the crowded interior of a eukaryotic cell is the endoplasmic reticulum (ER), whose total membrane area can be 20-30 times that of the cell's plasma membrane. Much of this area is in parallel sheets, however the sheet-like ER has also been found to be riddled with spiral dislocations, known as 'Terasaki ramps', in the vicinity of which the sheets’ doubled bilayer membranes can be approximately modeled by helicoids. We analyze diffusion on a surface with locally helicoidal topological dislocations, and use the results to argue that the Terasaki ramps facilitate an efficient transport of water-soluble molecules both within the lumen of the endoplasmic reticulum, and in the adjacent cytoplasmic space. (This is joint work with Michael Wilkinson.)   

Dynamics of and on the endoplasmic reticulum

The interior of eukaryotic cells is highly compartmentalized
by a variety of organelle structures. A particularly prominent
organelle is the endoplasmic reticulum (ER) that feeds virtually
all secretory processes of a cell (amongst other duties). Large
portions of the ER are organized as a vast dynamic network of
membrane tubules that are connected by three-way junctions.
Dispersed on this network are numerous membrane domains, so-called
ER exit sites (ERES), at which nascent proteins leave the ER via
transport vesicles to get transported along the cell's secretory
pathway.
Using time-resolved imaging, we have analyzed the dynamics of ER
junctions and of ERES domains as well as the self-organization of
ERES on the ER network. As a result, we observed that both, ER
junctions and ERES, show a marked subdiffusion with signatures of
an anti-persistent fractional Brownian motion and a strong dependence
on the cytoskeleton's integrity: ER junctions move like monomer units
of (semi)flexible polymers with the overall dynamics of the ER network
being governed by fractons due to the network's self-similar geometry.
Moreover, active cytoskeleton-associated processes endow the subdiffusion
of ER junctions with a distinct nonequilibrium character. In contrast,
ERES rather are mobile domains that perform a quasi-one-dimensional
random walk on the shivering ER backbone. Moreover, ERES show a
self-organization that is reminiscent of two-dimensional droplet
formation where coarsening is hindered by geometric and topological
constraints imposed by ER junctions. In line with this view, a
substantial coarsening of ERES to fewer but larger domains is
observed upon lifting the hindrance via an RNAi-induced reduction
of ER junctions.   

Fundamental limits to organelle biogenesis control in Saccharomyces cerevisiae

Among the most important processes in the self-assembly of the eukaryotic cell is the synthesis of its organelles, specialized biochemical compartments that house processes crucial to cellular physiology. Two critical properties closely linked with organelle function are their copy numbers and sizes. Numerous molecular factors that regulate the numbers and sizes of a diverse array of organelles, including the Golgi, mitochondria, peroxisomes and lipid droplets among others, have been identified. However, our understanding of the quantitative principles governing organelle number and size control remains incomplete. Here, we combine experimental data from the single-celled eukaryote Saccharomyces cerevisiae and mathematical theory to show that cells tolerate substantial fluctuations in organelle number while robustly controlling fluctuations in organelle sizes. In particular, our framework suggests that organelle size increases in random bursts from a limited pool of building blocks, which in turn imposes an asymmetry in optimal organelle number and size control. Burst like growth is a potentially general mechanism by which the cell efficiently assembles subcellular structures from its finite resources.
  

Decoding the variance in intracellular organization of the undifferentiated hiPS cell

The Allen Institute for Cell Science is developing a state space of structural signatures of the undifferentiated human induced pluripotent stem cell (hiPSC) to understand how cells organize and transition between states (cellular morphogenesis). To do this we take advantage of the ~35 endogenous fluorescently tagged hiPSC lines in the Allen Cell Collection (www.allencell.org), each expressing a monoallelic EGFP-tagged protein representing a particular organelle. We develop image-based assays and segmentations for quantitative analyses, taking advantage of thousands of replicate high-resolution 3D images for each structure. We are investigating biological sources of cellular variation in a high-dimensional space that represents integrated intracellular organization. We applied the Allen Cell Structure Segmenter to images of lamin B1-tagged cells to extract nuclear shapes, which we then fit using spherical harmonics. We performed principal component analysis on the fitting coefficients and we found the first five components explain 85% of the total variance. Each of these components was mapped into a mode corresponding to a distinct biological source of variation. The first mode represented nuclear volume, which increases throughout interphase at timescales of hours. The second mode represented how flat (vs. round) a nucleus appeared in the apical-basal axis (Z-direction), which was linked to changes in colony cell packing dynamics consistent with a timescale of several days for cell packing within colonies. The remaining modes represented how elongated a nucleus appeared in the XY plane and how tilted the nucleus appeared along the major and minor axis. We found these modes to be caused by interactions with neighboring cells occurring at timescales of minutes. We are now applying these analyses to develop biophysical models of nuclear shape. Our framework will be extended to cell shape and key intracellular structures in an integrative fashion.   

Modelling membrane-bound cellular organelles with non-equilibrium dynamics

Membrane-bound cellular organelles perform many essential functions, among which the sorting and biochemical maturation of cellular components. Organelles along the secretory and endocytic pathways are strongly out-of-equilibrium structures, which display large stochastic fluctuations of composition and shape resulting from inter-organelle exchange and enzymatic reactions. Understanding how the different molecular mechanisms controlling these processes are orchestrated to yield robust fluxes of matter and to direct particular components to particular locations within the cell is an outstanding problem of great interest for cell biologist, but also for physicists.
In this talk, I will discuss a conceptual model of organelle biogenesis and maintenance that include vesicular exchange (budding, transport, and fusion) and biochemical maturation, i.e. the change of identity of an organelle over time (early to late endosomes, cis to trans Golgi cisternae…). I will show how the non-equilibrium steady-state of an organelle or a network of organelles may be varied in a controlled manner by modifying a limited number of coarse-grained parameters (essentially, the budding, fusion and maturation rates) and discuss the relevance of these results for the structure of the Golgi apparatus.