Characteristic Behavior of Crowding Macromolecules Confined in Cell-Sized Droplets

Yanagisawa, Miho; Sakaue, Takahiro; Yoshikawa, Kenichi

doi:10.1016/b978-0-12-800046-5.00007-2

Cited by 25 publications

(28 citation statements)

References 66 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Microdroplets covered with a lipid layer were prepared as reported previously (1,19). Briefly, dry lipid films with Rh-PE (0.1 mol% of total lipid amount) were prepared on the bottom of a glass tube.…”

Section: Methodsmentioning

confidence: 99%

“…cytoskeleton | self-assembly | DNA gel | lipid droplet | liposome L iposomes have been used as artificial cell models to understand cell shape, membrane protein function, and lipid− protein interaction, among other biological functions (1)(2)(3). In addition, liposomes have been used as a platform for biosensing and as drug delivery systems (DDS) because of their excellent biocompatibility and biodegradability (4).…”

mentioning

confidence: 99%

See 1 more Smart Citation

DNA cytoskeleton for stabilizing artificial cells

Kurokawa

Fujiwara

Morita

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

127

123

View full text Add to dashboard Cite

Cell-sized liposomes and droplets coated with lipid layers have been used as platforms for understanding live cells, constructing artificial cells, and implementing functional biomedical tools such as biosensing platforms and drug delivery systems. However, these systems are very fragile, which results from the absence of cytoskeletons in these systems. Here, we construct an artificial cytoskeleton using DNA nanostructures. The designed DNA oligomers form a Y-shaped nanostructure and connect to each other with their complementary sticky ends to form networks. To undercoat lipid membranes with this DNA network, we used cationic lipids that attract negatively charged DNA. By encapsulating the DNA into the droplets, we successfully created a DNA shell underneath the membrane. The DNA shells increased interfacial tension, elastic modulus, and shear modulus of the droplet surface, consequently stabilizing the lipid droplets. Such drastic changes in stability were detected only when the DNA shell was in the gel phase. Furthermore, we demonstrate that liposomes with the DNA gel shell are substantially tolerant against outer osmotic shock. These results clearly show the DNA gel shell is a stabilizer of the lipid membrane akin to the cytoskeleton in live cells.iposomes have been used as artificial cell models to understand cell shape, membrane protein function, and lipid− protein interaction, among other biological functions (1-3). In addition, liposomes have been used as a platform for biosensing and as drug delivery systems (DDS) because of their excellent biocompatibility and biodegradability (4). However, liposomes collapse easily against environmental shifts and mechanical forces because of their low bending modulus. The fragility of liposomes causes uncontrolled leakage of the entrapped compounds and thus inhibits their use in biomedical applications and artificial cells experiments.In contrast, cell membranes are tolerant against environmental shifts and mechanical forces. The stability of cell membrane arises from the cytoskeleton underneath the membrane. The major component of cytoskeletons is actin (5). Actin gels show high elasticity (6), which ensures the stability of cell membranes against various forces. For liposomes, the use of actin filaments as a cytoskeleton is not an optimal strategy for the following three reasons: First, although actin bundles and actomyosin rings have been reconstituted in artificial cells (7,8), formation of an actin cortex underneath artificial membranes has been still challenging. Second, actin is hard to modify by chemical and genetic means because of its essentiality for cell growth. Third, the physicochemical properties of actin gels are still unclear (9, 10). Hence, the cytoskeleton of liposomes should be constructed with defined and designable materials. To accomplish this aim, DNA nanotechnology, which uses limited components with high designability in a nanometer scale (11), is a feasible candidate to construct cytoskeleton structures in artificial cells.DNA nanostructure...

show abstract

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

DNA cytoskeleton for stabilizing artificial cells

Kurokawa

Fujiwara

Morita

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

127

123

View full text Add to dashboard Cite

show abstract

“…Recent studies have unveiled that confinement inside cell-sized space alters both the behaviors of biochemical reactions and molecular diffusion (Yanagisawa et al, 2014b; Küchler et al, 2016; Watanabe and Yanagisawa, 2018). Because RD waves appear only in limited parameter ranges (Zhabotinsky et al, 1995; Epstein and Showalter, 1996), encapsulation inside a cell-sized space should shift the conditions that are suitable for Min wave emergence, such as the diffusion and interaction of the wave's elements.…”

Section: Introductionmentioning

confidence: 99%

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

Kohyama

Yoshinaga

Yanagisawa

et al. 2019

eLife

Self Cite

View full text Add to dashboard Cite

The Min system, a system that determines the bacterial cell division plane, uses changes in the localization of proteins (a Min wave) that emerges by reaction-diffusion coupling. Although previous studies have shown that space sizes and boundaries modulate the shape and speed of Min waves, their effects on wave emergence were still elusive. Here, by using a microsized fully confined space to mimic live cells, we revealed that confinement changes the conditions for the emergence of Min waves. In the microsized space, an increased surface-to-volume ratio changed the localization efficiency of proteins on membranes, and therefore, suppression of the localization change was necessary for the stable generation of Min waves. Furthermore, we showed that the cell-sized space strictly limits parameters for wave emergence because confinement inhibits both the instability and excitability of the system. These results show that confinement of reaction-diffusion systems has the potential to control spatiotemporal patterns in live cells.

show abstract

“…Internal polymer confinement in vivo is due to macromolecular crowding, which enforces DNA condensation in bacterial cells [17,18] where the volume fraction occupied by crowding macromolecules such as RNA, ribosomes, or other biomacromolecules reaches ϕ = 30 ... 35% [19][20][21][22]. The abundance of crowding agents effects a viscoelastic environment [23][24][25] that severely alters the diffusional dynamics of submicron endogenous cytoplasmic granules and of tracers inside living cells [26][27][28][29][30][31].…”

Section: Introductionmentioning

confidence: 99%

Mixing and segregation of ring polymers: spatial confinement and molecular crowding effects

2014

View full text Add to dashboard Cite

During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the dynamics and statistical behavior of two flexible ring polymers in the presence of cylindrical confinement and crowding molecules. From extensive computer simulations we determine the degree of ring-ring overlap and the number of inter-monomer contacts for varying volume fractions ϕ of crowders. We also examine the entropic demixing of polymer rings in the presence of mobile crowders and determine the characteristic times of the internal polymer dynamics. Effects of the ring length on ring-ring overlap are also analyzed. In particular, on systematic variation of the fraction of crowding molecules, a ϕ − ( ) 1 -scaling is found for the ring-ring overlap length along the cylinder axis, and a non-monotonic dependence of the 3D ring-ring contact number with a maximum at ϕ ≈ 0.2 is obtained. Our results demonstrate that polymer rings are demixed and separated by particular entropy-favourable partitioning of crowders along the axis of the cylindrical simulation box. These findings help to rationalize the implications of macromolecular crowding for circular DNA molecules in confined spaces inside bacteria as well as in localized cellular compartments inside eukaryotic cells. 2 0 . 5 9 in terms of the ring New J. Phys. 16 (2014) 053047 J Shin et al New J. Phys. 16 (2014) 053047 J Shin et al R 2 0.9 was predicted [44, 77]. New J. Phys. 16 (2014) 053047 J Shin et al 6 From the corresponding probability density Δ ( ) p z AB CM along the cylinder axis we compute the free energy of the overlap of the two rings in terms of New J. Phys. 16 (2014) 053047 J Shin et al 7 New J. Phys. 16 (2014) 053047 J Shin et al 8 New J. Phys. 16 (2014) 053047 J Shin et al AB and N n AB . These results are illustrated in figure 13, which is New J. Phys. 16 (2014) 053047 J Shin et al 15 New J. Phys. 16 (2014) 053047 J Shin et al 16 4 Recent experiments show that in E. coli active protein oscillations guide the demixing of the chromosomes and thus assist entropic effects, see [83].

show abstract

Characteristic Behavior of Crowding Macromolecules Confined in Cell-Sized Droplets

Cited by 25 publications

References 66 publications

DNA cytoskeleton for stabilizing artificial cells

DNA cytoskeleton for stabilizing artificial cells

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

Mixing and segregation of ring polymers: spatial confinement and molecular crowding effects

Contact Info

Product

Resources

About