Single-molecule study reveals the frenetic lives of proteins in gradients

Single-molecule study reveals the frenetic lives of proteins in gradients

Protein concentration gradients are a common strategy to compartmentalize activities within cells and tissues.

Gradients position the division plane of bacterial cells, regulate the size of yeast cells, and pattern embryos (1⇓–3).

Among the most studied gradients is the Bicoid gradient of Drosophila.

Bicoid protein is synthesized from a localized source of bcd mRNA at the anterior-most pole of the embryo (4, 5).

In one model, newly synthesized Bicoid is proposed to diffuse away from this point source and to turn over at a constant rate throughout the cytoplasm, thus generating an anterior-rich protein concentration gradient (6) (Fig. 1A).

Drosophila embryos, however, are unusually large (>400 μm) syncytial cells.

Smaller cells are unlikely to support Bicoid-like gradients, since the rate of protein diffusion in the cytoplasm is typically too fast (10 μm²⋅s⁻¹) to prevent proteins from sampling the entire cytoplasm within seconds (2, 7).

If so, how do most cells generate protein gradients?

In 2008, Lipkow and Odde (8) offered a simple solution to this dilemma.

Using theoretical modeling, they demonstrated that protein gradients can be sustained in cells of any size by coupling regulation of protein diffusivity to a spatially segregated protein modification system.

The reversible protein modification (e.g., phosphorylation) toggles the protein between two states with different diffusion coefficients (one fast and one slow).

Imposing a spatial bias in the distribution of one of the protein modification enzymes (e.g., the kinase) locally increases the concentration of one diffusive state, thus generating a protein concentration gradient whose steepness is proportional to the amplitude of the difference in protein diffusion coefficients (8).

In PNAS, Wu et al. (9) provide remarkable experimental evidence that such a mechanism drives the formation of cytoplasmic gradients

local differences in the rate of FD-to-SD switching is what drives gradient formation.

kinetic switching could be used to generate stable gradients over a wide range of diffusion constants.

These studies highlight the importance of balancing the on/off rates of the protein modifications that mediate the kinetic switch.

Interestingly, regulation of membrane binding by a spatially segregated phosphorylation / dephosphorylation cycle has already been suggested to promote the formation of another intracellular gradient.

In principle, variations in the rate of kinetic switching and in the distributions of the kinase, phosphatase, and anchor could generate gradients with different steepness, shape, and location.

Connecting the formation of one gradient to that of another, as in the case of MEX-5 and PIE-1, expands gradient possibilities even further.

The versatility and rapidity of gradient formation by kinetic switching suggest that this mechanism may be a common strategy to pattern cells in a wide range of developmental contexts.

what determines the location of the source 

what determines the spatiotemporal coupling regulation of protein diffusivity to a spatially segregated protein modification system

what determines spatiotemporally this reversible protein modification?

what determines spatiotemporally the toggling of the protein between two states (SD/FD) with different diffusion coefficients (one fast and one slow)?

what determines spatiotemporally the imposition of a spatial bias in the distribution?