Control of protein-based pattern formation via guiding cues

Abstract

Proteins control many vital functions in living cells, such as cell growth and cell division. Reliable coordination of these functions requires the spatial and temporal organizaton of proteins inside cells, which encodes information about the cell's geometry and the cell-cycle stage. Such protein patterns arise from protein transport and reaction kinetics, and they can be controlled by various guiding cues within the cell. Here, we review how protein patterns are guided by cell size and shape, by other protein patterns that act as templates, and by the mechanical properties of the cell. The basic mechanisms of guided pattern formation are elucidated with reference to recent observations in various biological model organisms. We posit that understanding the controlled formation of protein patterns in cells will be an essential part of understanding information processing in living systems.

Coarsening and wavelength selection far from equilibrium: a unifying framework based on singular perturbation theory

“…Intriguingly, these systems can form spatially heterogeneous patterns, for example, via a coupling of reactions and particle diffusion, or by phase separation. Both processes are known to play an important role in the spatial self-organization of the cell [7,26,106,107]. Phase separation, and biomolecular condensation in general, as well as intracellular protein-pattern formation are processes that (approximately) conserve the total number of molecules of each species.…”

“…Another aspect of domain geometry is bulk-surface coupling. Owing to the cycling of proteins between membrane-bound and cytosolic states, this is a fundamental property of many protein-based, pattern-forming systems, and has a profound impact on the patterns that emerge [5,26,109,[127][128][129]. However, the impact of bulk-surface coupling on wavelength selection remains largely unexplored and is an important open problem for future research.…”

“…Relating back to the biological context, pattern formation does not (always) start out from a homogeneous steady state but for example via nucleation, boundary effects, or initial, spatial templates such that the pattern is part of a whole pattern cascade [20,26,131,132]. Allowing for a transient coarsening process which interrupts at a scale separated from the scale of the initial instability may give a robust mechanism to select a pattern.…”

“…Originally, Alan Turing proposed such systems to explain the patterning during morphogenesis, i.e., the development of organisms [1]. By now, reactiondiffusion systems are found to describe diverse biological processes as for example intracellular protein pattern formation [7,8,[24][25][26] or signaling via trigger waves [27]. In the intracellular context, the timescale of protein production and degradation is long compared to the timescale of pattern formation, and the total number of proteins can be assumed to be (approximately) constant.…”

The intertwined physics of active chemical reactions and phase separation

“…Such spatial control over reactions can determine resulting patterns [126,127] and localize droplets [128,129]. Finally, the interplay between bulk and surface dynamics implies a prominent role of geometry, which was described in detail for traditional reaction-diffusion systems, like the Min oscillations [130,131], but could also control droplets, e.g., at the origin-of-life [132]. Spatially patterned catalysts could provide detailed control over the kinetics of chemical reactions, which in turn affect where droplets form.…”