Transitions from Nonliving to Living Matter

Rasmussen, Steen; Chen, Liaohai; Deamer, David W.; Krakauer, David C.; Packard, Norman H.; Stadler, Peter F.; Bedau, Mark A.

doi:10.1126/science.1093669

Cited by 355 publications

(204 citation statements)

References 8 publications

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“…The game is popular among children and adults to decide on trivial disputes that have no obvious winner, but it is also the basis for the explanation of fascinating evolutionary processes that describe the essence of predator-prey interactions and evolutionary games [1][2][3][4]. Foremost, games of cyclic dominance play a prominent role in explaining the intriguing diversity in nature [5][6][7][8][9][10][11], but they are also able to provide insights into Darwinian selection [12] as well as structural complexity [13] and prebiotic evolution [14].…”

Section: Introductionmentioning

confidence: 99%

From pairwise to group interactions in games of cyclic dominance

2014

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We study the rock-paper-scissors game in structured populations, where the invasion rates determine individual payoffs that govern the process of strategy change. The traditional version of the game is recovered if the payoffs for each potential invasion stem from a single pairwise interaction. However, the transformation of invasion rates to payoffs also allows the usage of larger interaction ranges. In addition to the traditional pairwise interaction, we therefore consider simultaneous interactions with all nearest neighbors, as well as with all nearest and next-nearest neighbors, thus effectively going from single pair to group interactions in games of cyclic dominance. We show that differences in the interaction range affect not only the stationary fractions of strategies but also their relations of dominance. The transition from pairwise to group interactions can thus decelerate and even revert the direction of the invasion between the competing strategies. Like in evolutionary social dilemmas, in games of cyclic dominance, too, the indirect multipoint interactions that are due to group interactions hence play a pivotal role. Our results indicate that, in addition to the invasion rates, the interaction range is at least as important for the maintenance of biodiversity among cyclically competing strategies.

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Section: Introductionmentioning

confidence: 99%

From pairwise to group interactions in games of cyclic dominance

2014

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“…microdroplets | macromolecular crowding P rotocells are minimal compartmentalized systems exhibiting key characteristics of cellular function, including metabolism and replication (1,2). Lipid vesicles are considered the prototypical protocell as they can form functional microscopic spherical assemblies suited for in vitro gene expression (3,4).…”

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confidence: 99%

Enhanced transcription rates in membrane-free protocells formed by coacervation of cell lysate

Соколова

Spruijt

Hansen

et al. 2013

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

318

322

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Liquid-liquid phase transitions in complex mixtures of proteins and other molecules produce crowded compartments supporting in vitro transcription and translation. We developed a method based on picoliter water-in-oil droplets to induce coacervation in Escherichia coli cell lysate and follow gene expression under crowded and noncrowded conditions. Coacervation creates an artificial cell-like environment in which the rate of mRNA production is increased significantly. Fits to the measured transcription rates show a two orders of magnitude larger binding constant between DNA and T7 RNA polymerase, and five to six times larger rate constant for transcription in crowded environments, strikingly similar to in vivo rates. The effect of crowding on interactions and kinetics of the fundamental machinery of gene expression has a direct impact on our understanding of biochemical networks in vivo. Moreover, our results show the intrinsic potential of cellular components to facilitate macromolecular organization into membranefree compartments by phase separation.microdroplets | macromolecular crowding P rotocells are minimal compartmentalized systems exhibiting key characteristics of cellular function, including metabolism and replication (1, 2). Lipid vesicles are considered the prototypical protocell as they can form functional microscopic spherical assemblies suited for in vitro gene expression (3, 4). Compartmentalization via lipid bilayers is considered essential for the emergence of cells (4), but there are alternative models based on liquid-liquid phase transitions that lead to the emergence of compartments (5, 6). Compartmentalization is but one characteristic, as protocells ideally also mimic the highly crowded interior of living cells, which have total macromolecule concentrations in excess of 300 g/L (7). Examples in which compartmentalization and high local concentrations are obtained concurrently, include DNA brushes (8), aqueous two-phase systems (9), and liquid coacervates (10). Phase separation or coacervation occurs in a wide range of polymer and protein solutions, often triggered by changes in temperature or salt concentration, or by the addition of coacervating agents (11). The (complex) coacervate droplets that are formed in such systems present macromolecularly crowded, aqueous, physical compartments, 1-100 μm in diameter (12). Recent work has identified similar liquid phase transitions in vivo in the formation of intracellular non-membrane-bound compartments exhibiting liquid-like properties, slowed down diffusion, and strongly interacting macromolecular components (13,14). Well-studied examples are the intracellular localization of DNA or RNA and proteins in Cajal bodies, P granules, and nucleoli (15-17), which can contain over 100 components. Such complexity has not been achieved in two-phase systems in vitro (18,19). Although the physics of coacervates is well understood, progress in their development as protocell models has stalled, because of the lack of demonstrations of complex biochemical proce...

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“…Current cells are very complex, as a result of a long evolutionary process, and have sophisticated mechanisms for cellular division regulation. However, the analysis of minimal cellular structures can contribute to a better understanding of possible prebiotic scenarios in which cellular life could have originated (Maynard Smith and Szathma´ry, 2001) as well as in the design and synthesis of new artificial protocells (Rasmussen et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Protocell self-reproduction in a spatially extended metabolism–vesicle system

Macía

Solé

2007

Journal of Theoretical Biology

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Cellular life requires the presence of a set of biochemical mechanisms in order to maintain a predictable process of growth and division. Several attempts have been made towards the building of minimal protocells from a top-down approach, i.e. by using available biomolecules. This type of synthetic approach has so far been only partially successful, and appropriate models of the synthetic protocell cycle might be needed to guide future experiments. In this paper, we present a simple biochemically and physically feasible model of cell replication involving a discrete semi-permeable vesicle with an internal minimal metabolism involving two reactive centers. It is shown that such a system can effectively undergo a whole cell replication cycle. The model can be used as a basic framework to model whole protocell dynamics including more complex sets of reactions. The possible implementation of our design in future synthetic protocells is outlined. r

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Transitions from Nonliving to Living Matter

Cited by 355 publications

References 8 publications

From pairwise to group interactions in games of cyclic dominance

From pairwise to group interactions in games of cyclic dominance

Enhanced transcription rates in membrane-free protocells formed by coacervation of cell lysate

Protocell self-reproduction in a spatially extended metabolism–vesicle system

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