Modular assembling process of an in-silico protocell

Schneider, Eugenia; Mangold, Michael

doi:10.1016/j.biosystems.2017.12.004

Cited by 6 publications

(6 citation statements)

References 42 publications

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“…Here we show that a model‐based approach with validated models and corresponding isolated experimental parts allows exploring new concepts to solve these kinds of problems . On the one hand the identification and validation of biosynthetic submodules generates the necessary mechanistic understanding.…”

Section: Discussion and Outlookmentioning

confidence: 99%

“…In the considered example, the identified control tasks are (i) to prevent the depletion of enzymes, (ii) to keep the concentrations of positioner molecules on a certain level, and (iii) to synchronize the growth of the tube‐shaped membrane and the growth of the contractile ring. These suggestions have been successfully reevaluated and implemented in silico by a hypothetical link between the membrane growth and enzyme formation rate, inspired by the analysis of a modularized whole‐cell model …”

Section: Conceptmentioning

confidence: 99%

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Towards Design of Self‐Organizing Biomimetic Systems

2019

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The ability of designing biosynthetic systems with well‐defined functional biomodules from scratch is an ambitious and revolutionary goal to deliver innovative, engineered solutions to future challenges in biotechnology and process systems engineering. In this work, several key challenges including modularization, functional biomodule identification, and assembly are discussed. In addition, an in silico protocell modeling approach is presented as a foundation for a computational model‐based toolkit for rational analysis and modular design of biomimetic systems.

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Section: Discussion and Outlookmentioning

confidence: 99%

Section: Conceptmentioning

confidence: 99%

Towards Design of Self‐Organizing Biomimetic Systems

2019

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“…[303] Similar models incorporating basic metabolism into protocell compartments have been established. [304][305][306]…”

Section: Protocells In Silicomentioning

confidence: 99%

Protocells: Milestones and Recent Advances

Gözen

Köksal

Põldsalu

et al. 2022

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to assemble astonishing pieces of a complicated puzzle, and realized that further advancement requires input from multiple branches of science, not just biology as the primary life science. Detailed hypotheses have been established about the different scenarios of the emergence of life, including the "RNA world," [1] the "lipid world," [2] "replicator first," [3] "metabolism first," [4][5][6] and others. Although the origin of life is still surrounded by many open questions, our understanding of chemical, physicochemical, and biochemical processes possibly involved in the ancient events preceding Darwinian evolution has seen much progress. We have come a long way from Leduc's physicochemical, inorganic matter-centered view on the beginning of the evolution, yet the matter of the transition from nonliving to living matter still remains largely unsolved, and one of the great scientific problems of our time.The phylogenetic tree of different living domains reflects that life has evolved from simple to more complex structures, i.e., from single-to multicellular organisms. The oldest fossil evidence dating back 3.5 Gy (billion years) comes from stromatolites, [7][8][9][10] microorganismal residues in sedimentary rocks. [11] There appears to be a gap of knowledge regarding the period of evolution between the first primitive hypothetical cells and the fossilized ancient bacteria, which can be considered as an already advanced form of life. [12] It is highly likely that intermediate primitive cell precursors preceded the single-cell organisms. The hypothetical prebiotic structures that were the stepping stone to first self-sustaining living cells are commonly termed "protocells." The possibility of a strong link between the formation of protocells and the origin of life can today be reasonably assumed.One cannot easily proceed in the context of the evolution of cell-based organisms without briefly illuminating the concept of life as we know it on our planet. Over time, different requirements have been proposed for an entity to be considered alive. According to Tibor Ganti's chemoton model, [13] a protocell contains three autocatalytic subsystems: a membrane subsystem that keeps the components together and intact, a metabolic subsystem that captures energy and material resources, and an information subsystem that processes and transfers heritable information to progeny. To be considered alive, these subsystems must be unified and function co-operatively for the survival and evolution of the supersystem. Pohorille and Deamer suggested a modified set of 7 criteria related to the chemoton. [14] At about the same time, Oro defined the requirements by 10 characteristic features. [15] Despite their differences, these descriptions align well with NASA's broader definition of life: "a self-sustaining chemical system capable of Darwinian evolution."The origin of life is still one of humankind's great mysteries. At the transition between nonliving and living matter, protocells, initially featureless aggregates of abiotic matter, ga...

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“…These include the biochemistry effects in a confined environment ( Sakamoto et al, 2018 ), the communication behaviors triggered by signal molecules ( Rampioni et al, 2014 ), or the design of membrane proteins on lipids ( Alford et al, 2020 ). Recently, the module assembling process was successfully established through the computer-aided design, which consisted of a membrane proliferating module, a membrane contraction module, and a positioning module ( Schneider and Mangold, 2018 ). This result has greatly revealed the advance of computer-aided technology.…”

Section: Unitymentioning

confidence: 99%

Modularize and Unite: Toward Creating a Functional Artificial Cell

Wang

Yang

2021

Front. Mol. Biosci.

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An artificial cell is a simplified model of a living system, bringing breakthroughs into both basic life science and applied research. The bottom-up strategy instructs the construction of an artificial cell from nonliving materials, which could be complicated and interdisciplinary considering the inherent complexity of living cells. Although significant progress has been achieved in the past 2 decades, the area is still facing some problems, such as poor compatibility with complex bio-systems, instability, and low standardization of the construction method. In this review, we propose creating artificial cells through the integration of different functional modules. Furthermore, we divide the function requirements of an artificial cell into four essential parts (metabolism, energy supplement, proliferation, and communication) and discuss the present researches. Then we propose that the compartment and the reestablishment of the communication system would be essential for the reasonable integration of functional modules. Although enormous challenges remain, the modular construction would facilitate the simplification and standardization of an artificial cell toward a natural living system. This function-based strategy would also broaden the application of artificial cells and represent the steps of imitating and surpassing nature.

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Modular assembling process of an in-silico protocell

Cited by 6 publications

References 42 publications

Towards Design of Self‐Organizing Biomimetic Systems

Towards Design of Self‐Organizing Biomimetic Systems

Protocells: Milestones and Recent Advances

Modularize and Unite: Toward Creating a Functional Artificial Cell

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