Search bioRxiv⌕ Search

Biology subjects

Kohyama, S.

Publications and source records attributed to Kohyama, S..

3 recordsLinked to original sources

Mutual dependence between membrane phase separation and bacterial division protein dynamics in synthetic cell models

Cell membranes in bacteria are laterally polarized to produce specific environments for membrane proteins, e.g., proteins involved in cell division which accumulate at mid-cell or the cell poles. An interesting result of such membrane-lipid interplay is the reorganization of lipid domains together with membrane-bound proteins at the onset of cell division, suggesting a functional significance of membrane compartments in the cell cycle. Here, by adopting the key bacterial division proteins MinCDE and FtsZ as an archetypal spatial patterning system, we present a simple vesicle-based in vitro model to explore the mutual dependence of protein pattern formation and membrane heterogeneity. Like many other peripheral membrane proteins, MinDE exhibit preferential binding and macro-scale pattern formation at Ld domains, which leads to altered oscillation mode selection in phase-separated membrane compartments (GUVs). Moreover, incorporating bacterial division proteins within phase-separated GUVs leads to blebbing-like membrane deformations followed by the reorganization of Lo domains aligning at the neck region of the bleb, which agrees well with the domain rearrangement in bacterial membranes immediately preceding the radial constriction process. Overall, the presented in vitro model system showcases a basic framework to better comprehend the cellular division mechanism in consideration of complex cellular lipid environments.

synthetic biology↗

Designing a protein with emergent function by combined in silico, in vitro and in vivo screening

Recently, utilization of machine learning (ML) based methods has led to astonishing progress in protein design and, thus, the design of new biological functionality. However, emergent functions that require higher-order molecular interactions, such as the ability to self-organize, are still extremely challenging to implement. Here, we describe a comprehensive in silico, in vitro, and in vitro screening pipeline (i3-screening) to develop and validate ML-designed artificial homologs of a bacterial protein that confers its role in cell division through the emergent function of spatiotemporal pattern formation. Moreover, we present complete substitution of a wildtype gene by an ML-designed artificial homolog in Escherichia coli. These results raise great hopes for the next level of synthetic biology, where ML-designed synthetic proteins will be used to engineer cellular functions.

synthetic biology↗

Cell-sized confinement controls generation and stability of a protein wave for spatiotemporal regulation in cells

Min system, which determines the cell division plane of bacteria, uses the localization change of protein (Min wave) emerged by a reaction-diffusion coupling. Although previous studies have shown that cell-sized space and boundaries modulate shape and speed of Min waves, its effects on Min wave emergence was still elusive. Here, by using a fully confined microsized space as a mimic of live cells, we revealed that confinement changes conditions for Min wave emergence. In the microsized space, an increase of surface-to-volume ratio changed the localization efficiency of proteins on membranes, and therefore, suppression of the localization change was necessary to produce stable Min wave generations. Furthermore, we showed that the cell-sized space more strictly limits parameters for wave emergence because confinement inhibits instability and excitability of the system. These results illuminate that confinement of reaction-diffusion systems works as a controller of spatiotemporal patterns in live cells.

biophysics↗