Special Issue "Protocells - Designs for Life"

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A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Life Sciences".

Deadline for manuscript submissions: closed (31 July 2014)

Special Issue Editors

Guest Editor
Prof. Dr. Fabio Mavelli (Website)

Chemistry Department, University of Bari, Via Orabona 4, 70124 Bari
Interests: origins of life; emergence of life, synthetic cells; confined reactions; stochastic simulations; random fluctuation effects
Guest Editor
Dr. Pasquale Stano (Website)

Science Department, University Roma Tre, Viale G. Marconi 446, 00146 Rome
Interests: origins of life; synthetic biology; artificial life; synthetic cells; drug delivery; bio-chem-ICTs

Special Issue Information

Dear Colleagues,

Over the last few decades, the study of liposome-based minimal cell models has gained prominence in an interdisciplinary field concerning the origins of life and synthetic biology. These models have stimulated, and continue to stimulate, a large number of scientists, whose contributions are complementary.
From an experimental point of view, several approaches are currently under scrutiny, from the semi-synthetic cell model, to one that is strictly prebiotic, to the fully synthetic one. Despite the apparent diversity in this research field, recent efforts and discoveries have collectively contributed to increasing our knowledge of the physico-chemical conditions that promoted the transition from non-living to living matter; this knowledge sheds light on the origin of early cells on earth and at the same time, enables novel advancements in synthetic cell technology that might be useful for applicative research.
On the other hand, the structure of these cell model systems, whose complexity is sufficient for displaying emergent properties (but at the same time is “minimal”), can also be studied via detailed in silico models with both deterministic and stochastic approaches. These computational studies, especially when based on realistic hypotheses or on parameters inferred by experimental data, allow for the exploration of dynamical behaviors that can be difficult to investigate experimentally. The studies can also be useful for elucidating the effects of reaction compartmentalization and the rule of random fluctuations on protocell population dynamics.
Altogether, in silico and in vitro investigations are paving the way to a novel research arena that appears to be both very rich (thanks to its intrinsic interdisciplinary character) and promising (because only via synthetic/constructive approaches is it possible to enquire about the features of simple, early cells). This approach also stimulates more theoretical considerations with respect to intriguing questions, such as “what is life?” and further supports abiogenesis as the best theoretical framework, from a scientific viewpoint, for understanding the emergence of living systems on Earth.
Therefore, the study of minimal cell models is now an exciting multidisciplinary area of research mainly aimed at identifying the physico-chemical constraints (or unexpected and helpful emerging features) that are pertinent to the organization of dynamic chemical networks inside micro-compartments. This Special Issue covers all aspects of minimal cell models(i.e., experimental and computational models). The submission of scientific perspectives, comprehensive reviews or research articles is most welcome.

Prof. Dr. Fabio Mavelli
Dr. Pasquale Stano
Guest Editors

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 600 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Keywords

  • artificial cells
  • autopoiesis
  • cell-free systems
  • emergence of life
  • minimal cells
  • origin of life
  • protocells
  • random fluctuations effect
  • stochastic simulations

Published Papers (18 papers)

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Editorial

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Open AccessEditorial Protocells Models in Origin of Life and Synthetic Biology
Life 2015, 5(4), 1700-1702; doi:10.3390/life5041700
Received: 24 November 2015 / Revised: 1 December 2015 / Accepted: 2 December 2015 / Published: 8 December 2015
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(This article belongs to the Special Issue Protocells - Designs for Life)

Research

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Open AccessArticle Physical Routes to Primitive Cells: An Experimental Model Based on the Spontaneous Entrapment of Enzymes inside Micrometer-Sized Liposomes
Life 2015, 5(1), 969-996; doi:10.3390/life5010969
Received: 13 February 2015 / Revised: 8 March 2015 / Accepted: 10 March 2015 / Published: 18 March 2015
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Abstract
How did primitive living cells originate? The formation of early cells, which were probably solute-filled vesicles capable of performing a rudimentary metabolism (and possibly self-reproduction), is still one of the big unsolved questions in origin of life. We have recently used lipid [...] Read more.
How did primitive living cells originate? The formation of early cells, which were probably solute-filled vesicles capable of performing a rudimentary metabolism (and possibly self-reproduction), is still one of the big unsolved questions in origin of life. We have recently used lipid vesicles (liposomes) as primitive cell models, aiming at the study of the physical mechanisms for macromolecules encapsulation. We have reported that proteins and ribosomes can be encapsulated very efficiently, against statistical expectations, inside a small number of liposomes. Moreover the transcription-translation mixture, which realistically mimics a sort of minimal metabolic network, can be functionally reconstituted in liposomes owing to a self-concentration mechanism. Here we firstly summarize the recent advancements in this research line, highlighting how these results open a new vista on the phenomena that could have been important for the formation of functional primitive cells. Then, we present new evidences on the non-random entrapment of macromolecules (proteins, dextrans) in phospholipid vesicle, and in particular we show how enzymatic reactions can be accelerated because of the enhancement of their concentration inside liposomes. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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Open AccessArticle Coupled Phases and Combinatorial Selection in Fluctuating Hydrothermal Pools: A Scenario to Guide Experimental Approaches to the Origin of Cellular Life
Life 2015, 5(1), 872-887; doi:10.3390/life5010872
Received: 12 October 2014 / Revised: 17 February 2015 / Accepted: 6 March 2015 / Published: 13 March 2015
Cited by 17 | PDF Full-text (1643 KB) | HTML Full-text | XML Full-text
Abstract
Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution in dehydrated films on mineral surfaces followed by encapsulation and [...] Read more.
Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution in dehydrated films on mineral surfaces followed by encapsulation and combinatorial selection in a hydrated bulk phase. The dehydrated phase can consist of concentrated eutectic mixtures or multilamellar liquid crystalline matrices. Both conditions organize and concentrate potential monomers and thereby promote polymerization reactions that are driven by reduced water activity in the dehydrated phase. In the case of multilamellar lipid matrices, polymers that have been synthesized are captured in lipid vesicles upon rehydration to produce a variety of molecular systems. Each vesicle represents a protocell, an “experiment” in a natural version of combinatorial chemistry. Two kinds of selective processes can then occur. The first is a physical process in which relatively stable molecular systems will be preferentially selected. The second is a chemical process in which rare combinations of encapsulated polymers form systems capable of capturing energy and nutrients to undergo growth by catalyzed polymerization. Given continued cycling over extended time spans, such combinatorial processes will give rise to molecular systems having the fundamental properties of life. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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Open AccessArticle Emergent Chemical Behavior in Variable-Volume Protocells
Life 2015, 5(1), 181-211; doi:10.3390/life5010181
Received: 14 October 2014 / Accepted: 4 January 2015 / Published: 13 January 2015
Cited by 2 | PDF Full-text (1444 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Artificial protocellular compartments and lipid vesicles have been used as model systems to understand the origins and requirements for early cells, as well as to design encapsulated reactors for biotechnology. One prominent feature of vesicles is the semi-permeable nature of their membranes, [...] Read more.
Artificial protocellular compartments and lipid vesicles have been used as model systems to understand the origins and requirements for early cells, as well as to design encapsulated reactors for biotechnology. One prominent feature of vesicles is the semi-permeable nature of their membranes, able to support passive diffusion of individual solute species into/out of the compartment, in addition to an osmotic water flow in the opposite direction to the net solute concentration gradient. Crucially, this water flow affects the internal aqueous volume of the vesicle in response to osmotic imbalances, in particular those created by ongoing reactions within the system. In this theoretical study, we pay attention to this often overlooked aspect and show, via the use of a simple semi-spatial vesicle reactor model, that a changing solvent volume introduces interesting non-linearities into an encapsulated chemistry. Focusing on bistability, we demonstrate how a changing volume compartment can degenerate existing bistable reactions, but also promote emergent bistability from very simple reactions, which are not bistable in bulk conditions. One particularly remarkable effect is that two or more chemically-independent reactions, with mutually exclusive reaction kinetics, are able to couple their dynamics through the variation of solvent volume inside the vesicle. Our results suggest that other chemical innovations should be expected when more realistic and active properties of protocellular compartments are taken into account. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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Open AccessArticle Reconciling Ligase Ribozyme Activity with Fatty Acid Vesicle Stability
Life 2014, 4(4), 929-943; doi:10.3390/life4040929
Received: 7 October 2014 / Revised: 21 November 2014 / Accepted: 3 December 2014 / Published: 11 December 2014
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Abstract
The “RNA world” and the “Lipid world” theories for the origin of cellular life are often considered incompatible due to the differences in the environmental conditions at which they can emerge. One obstacle resides in the conflicting requirements for divalent metal ions, [...] Read more.
The “RNA world” and the “Lipid world” theories for the origin of cellular life are often considered incompatible due to the differences in the environmental conditions at which they can emerge. One obstacle resides in the conflicting requirements for divalent metal ions, in particular Mg2+, with respect to optimal ribozyme activity, fatty acid vesicle stability and protection against RNA strand cleavage. Here, we report on the activity of a short L1 ligase ribozyme in the presence of myristoleic acid (MA) vesicles at varying concentrations of Mg2+. The ligation rate is significantly lower at low-Mg2+ conditions. However, the loss of activity is overcompensated by the increased stability of RNA leading to a larger amount of intact ligated substrate after long reaction periods. Combining RNA ligation assays with fatty acid vesicles we found that MA vesicles made of 5 mM amphiphile are stable and do not impair ligase ribozyme activity in the presence of approximately 2 mM Mg2+. These results provide a scenario in which catalytic RNA and primordial membrane assembly can coexist in the same environment. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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Open AccessArticle Growth and Division in a Dynamic Protocell Model
Life 2014, 4(4), 837-864; doi:10.3390/life4040837
Received: 30 August 2014 / Revised: 25 October 2014 / Accepted: 10 November 2014 / Published: 3 December 2014
Cited by 4 | PDF Full-text (683 KB) | HTML Full-text | XML Full-text
Abstract
In this paper a new model of growing and dividing protocells is described, whose main features are (i) a lipid container that grows according to the composition of the molecular milieu (ii) a set of “genetic memory molecules” (GMMs) that undergo catalytic [...] Read more.
In this paper a new model of growing and dividing protocells is described, whose main features are (i) a lipid container that grows according to the composition of the molecular milieu (ii) a set of “genetic memory molecules” (GMMs) that undergo catalytic reactions in the internal aqueous phase and (iii) a set of stochastic kinetic equations for the GMMs. The mass exchange between the external environment and the internal phase is described by simulating a semipermeable membrane and a flow driven by the differences in chemical potentials, thereby avoiding to resort to sometimes misleading simplifications, e.g., that of a flow reactor. Under simple assumptions, it is shown that synchronization takes place between the rate of replication of the GMMs and that of the container, provided that the set of reactions hosts a so-called RAF (Reflexive Autocatalytic, Food-generated) set whose influence on synchronization is hereafter discussed. It is also shown that a slight modification of the basic model that takes into account a rate-limiting term, makes possible the growth of novelties, allowing in such a way suitable evolution: so the model represents an effective basis for understanding the main abstract properties of populations of protocells. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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Open AccessArticle Compartmentalization and Cell Division through Molecular Discreteness and Crowding in a Catalytic Reaction Network
Life 2014, 4(4), 586-597; doi:10.3390/life4040586
Received: 23 September 2014 / Revised: 17 October 2014 / Accepted: 22 October 2014 / Published: 29 October 2014
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Abstract
Explanation of the emergence of primitive cellular structures from a set of chemical reactions is necessary to unveil the origin of life and to experimentally synthesize protocells. By simulating a cellular automaton model with a two-species hypercycle, we demonstrate the reproduction of [...] Read more.
Explanation of the emergence of primitive cellular structures from a set of chemical reactions is necessary to unveil the origin of life and to experimentally synthesize protocells. By simulating a cellular automaton model with a two-species hypercycle, we demonstrate the reproduction of a localized cluster; that is, a protocell with a growth-division process emerges when the replication and degradation speeds of one species are respectively slower than those of the other species, because of overcrowding of molecules as a natural outcome of the replication. The protocell exhibits synchrony between its division process and replication of the minority molecule. We discuss the effects of the crowding molecule on the formation of primitive structures. The generality of this result is demonstrated through the extension of our model to a hypercycle with three molecular species, where a localized layered structure of molecules continues to divide, triggered by the replication of a minority molecule at the center. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
Open AccessArticle Designing with Protocells: Applications of a Novel Technical Platform
Life 2014, 4(3), 457-490; doi:10.3390/life4030457
Received: 2 August 2014 / Accepted: 25 August 2014 / Published: 5 September 2014
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Abstract
The paper offers a design perspective on protocell applications and presents original research that characterizes the life-like qualities of the Bütschli dynamic droplet system, as a particular “species” of protocell. Specific focus is given to the possibility of protocell species becoming a [...] Read more.
The paper offers a design perspective on protocell applications and presents original research that characterizes the life-like qualities of the Bütschli dynamic droplet system, as a particular “species” of protocell. Specific focus is given to the possibility of protocell species becoming a technical platform for designing and engineering life-like solutions to address design challenges. An alternative framing of the protocell, based on process philosophy, sheds light on its capabilities as a technology that can deal with probability and whose ontology is consistent with complexity, nonlinear dynamics and the flow of energy and matter. However, the proposed technical systems do not yet formally exist as products or mature technologies. Their potential applications are therefore experimentally examined within a design context as architectural “projects”—an established way of considering proposals that have not yet been realized, like an extended hypothesis. Exemplary design-led projects are introduced, such as The Hylozoic Ground and Future Venice, which aim to “discover”, rather than “solve”, challenges to examine a set of possibilities that have not yet been resolved. The value of such exploration in design practice is in opening up a set of potential directions for further assessment before complex challenges are procedurally implemented. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)

Review

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Open AccessReview Current Ideas about Prebiological Compartmentalization
Life 2015, 5(2), 1239-1263; doi:10.3390/life5021239
Received: 3 March 2015 / Revised: 1 April 2015 / Accepted: 2 April 2015 / Published: 10 April 2015
Cited by 7 | PDF Full-text (328 KB) | HTML Full-text | XML Full-text
Abstract
Contemporary biological cells are highly sophisticated dynamic compartment systems which separate an internal volume from the external medium through a boundary, which controls, in complex ways, the exchange of matter and energy between the cell’s interior and the environment. Since such compartmentalization [...] Read more.
Contemporary biological cells are highly sophisticated dynamic compartment systems which separate an internal volume from the external medium through a boundary, which controls, in complex ways, the exchange of matter and energy between the cell’s interior and the environment. Since such compartmentalization is a fundamental principle of all forms of life, scenarios have been elaborated about the emergence of prebiological compartments on early Earth, in particular about their likely structural characteristics and dynamic features. Chemical systems that consist of potentially prebiological compartments and chemical reaction networks have been designed to model pre-cellular systems. These systems are often referred to as “protocells”. Past and current protocell model systems are presented and compared. Since the prebiotic formation of cell-like compartments is directly linked to the prebiotic availability of compartment building blocks, a few aspects on the likely chemical inventory on the early Earth are also summarized. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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Open AccessReview Engineering Protocells: Prospects for Self-Assembly and Nanoscale Production-Lines
Life 2015, 5(2), 1019-1053; doi:10.3390/life5021019
Received: 1 January 2015 / Revised: 9 March 2015 / Accepted: 16 March 2015 / Published: 25 March 2015
Cited by 5 | PDF Full-text (1156 KB) | HTML Full-text | XML Full-text
Abstract
The increasing ease of producing nucleic acids and proteins to specification offers potential for design and fabrication of artificial synthetic “organisms” with a myriad of possible capabilities. The prospects for these synthetic organisms are significant, with potential applications in diverse fields including [...] Read more.
The increasing ease of producing nucleic acids and proteins to specification offers potential for design and fabrication of artificial synthetic “organisms” with a myriad of possible capabilities. The prospects for these synthetic organisms are significant, with potential applications in diverse fields including synthesis of pharmaceuticals, sources of renewable fuel and environmental cleanup. Until now, artificial cell technology has been largely restricted to the modification and metabolic engineering of living unicellular organisms. This review discusses emerging possibilities for developing synthetic protocell “machines” assembled entirely from individual biological components. We describe a host of recent technological advances that could potentially be harnessed in design and construction of synthetic protocells, some of which have already been utilized toward these ends. More elaborate designs include options for building self-assembling machines by incorporating cellular transport and assembly machinery. We also discuss production in miniature, using microfluidic production lines. While there are still many unknowns in the design, engineering and optimization of protocells, current technologies are now tantalizingly close to the capabilities required to build the first prototype protocells with potential real-world applications. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
Open AccessReview From Vesicles to Protocells: The Roles of Amphiphilic Molecules
Life 2015, 5(1), 651-675; doi:10.3390/life5010651
Received: 11 October 2014 / Revised: 11 February 2015 / Accepted: 24 February 2015 / Published: 2 March 2015
Cited by 1 | PDF Full-text (6411 KB) | HTML Full-text | XML Full-text
Abstract
It is very challenging to construct protocells from molecular assemblies. An important step in this challenge is the achievement of vesicle dynamics that are relevant to cellular functions, such as membrane trafficking and self-reproduction, using amphiphilic molecules. Soft matter physics will play [...] Read more.
It is very challenging to construct protocells from molecular assemblies. An important step in this challenge is the achievement of vesicle dynamics that are relevant to cellular functions, such as membrane trafficking and self-reproduction, using amphiphilic molecules. Soft matter physics will play an important role in the development of vesicles that have these functions. Here, we show that simple binary phospholipid vesicles have the potential to reproduce the relevant functions of adhesion, pore formation and self-reproduction of vesicles, by coupling the lipid geometries (spontaneous curvatures) and the phase separation. This achievement will elucidate the pathway from molecular assembly to cellular life. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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Open AccessReview Nanoporous Silica-Based Protocells at Multiple Scales for Designs of Life and Nanomedicine
Life 2015, 5(1), 214-229; doi:10.3390/life5010214
Received: 30 October 2014 / Revised: 29 December 2014 / Accepted: 6 January 2015 / Published: 19 January 2015
Cited by 3 | PDF Full-text (1455 KB) | HTML Full-text | XML Full-text
Abstract
Various protocell models have been constructed de novo with the bottom-up approach. Here we describe a silica-based protocell composed of a nanoporous amorphous silica core encapsulated within a lipid bilayer built by self-assembly that provides for independent definition of cell interior and [...] Read more.
Various protocell models have been constructed de novo with the bottom-up approach. Here we describe a silica-based protocell composed of a nanoporous amorphous silica core encapsulated within a lipid bilayer built by self-assembly that provides for independent definition of cell interior and the surface membrane. In this review, we will first describe the essential features of this architecture and then summarize the current development of silica-based protocells at both micro- and nanoscale with diverse functionalities. As the structure of the silica is relatively static, silica-core protocells do not have the ability to change shape, but their interior structure provides a highly crowded and, in some cases, authentic scaffold upon which biomolecular components and systems could be reconstituted. In basic research, the larger protocells based on precise silica replicas of cells could be developed into geometrically realistic bioreactor platforms to enable cellular functions like coupled biochemical reactions, while in translational research smaller protocells based on mesoporous silica nanoparticles are being developed for targeted nanomedicine. Ultimately we see two different motivations for protocell research and development: (1) to emulate life in order to understand it; and (2) to use biomimicry to engineer desired cellular interactions. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
Open AccessReview Synthetic Biology: A Bridge between Artificial and Natural Cells
Life 2014, 4(4), 1092-1116; doi:10.3390/life4041092
Received: 1 October 2014 / Revised: 2 December 2014 / Accepted: 11 December 2014 / Published: 19 December 2014
Cited by 3 | PDF Full-text (3162 KB) | HTML Full-text | XML Full-text
Abstract
Artificial cells are simple cell-like entities that possess certain properties of natural cells. In general, artificial cells are constructed using three parts: (1) biological membranes that serve as protective barriers, while allowing communication between the cells and the environment; (2) transcription and [...] Read more.
Artificial cells are simple cell-like entities that possess certain properties of natural cells. In general, artificial cells are constructed using three parts: (1) biological membranes that serve as protective barriers, while allowing communication between the cells and the environment; (2) transcription and translation machinery that synthesize proteins based on genetic sequences; and (3) genetic modules that control the dynamics of the whole cell. Artificial cells are minimal and well-defined systems that can be more easily engineered and controlled when compared to natural cells. Artificial cells can be used as biomimetic systems to study and understand natural dynamics of cells with minimal interference from cellular complexity. However, there remain significant gaps between artificial and natural cells. How much information can we encode into artificial cells? What is the minimal number of factors that are necessary to achieve robust functioning of artificial cells? Can artificial cells communicate with their environments efficiently? Can artificial cells replicate, divide or even evolve? Here, we review synthetic biological methods that could shrink the gaps between artificial and natural cells. The closure of these gaps will lead to advancement in synthetic biology, cellular biology and biomedical applications. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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Open AccessReview Droplets: Unconventional Protocell Model with Life-Like Dynamics and Room to Grow
Life 2014, 4(4), 1038-1049; doi:10.3390/life4041038
Received: 31 October 2014 / Revised: 8 December 2014 / Accepted: 11 December 2014 / Published: 17 December 2014
Cited by 5 | PDF Full-text (539 KB) | HTML Full-text | XML Full-text
Abstract
Over the past few decades, several protocell models have been developed that mimic certain essential characteristics of living cells. These protocells tend to be highly reductionist simplifications of living cells with prominent bilayer membrane boundaries, encapsulated metabolisms and/or encapsulated biologically-derived polymers as [...] Read more.
Over the past few decades, several protocell models have been developed that mimic certain essential characteristics of living cells. These protocells tend to be highly reductionist simplifications of living cells with prominent bilayer membrane boundaries, encapsulated metabolisms and/or encapsulated biologically-derived polymers as potential sources of information coding. In parallel with this conventional work, a novel protocell model based on droplets is also being developed. Such water-in-oil and oil-in-water droplet systems can possess chemical and biochemical transformations and biomolecule production, self-movement, self-division, individuality, group dynamics, and perhaps the fundamentals of intelligent systems and evolution. Given the diverse functionality possible with droplets as mimics of living cells, this system has the potential to be the first true embodiment of artificial life that is an orthologous departure from the one familiar type of biological life. This paper will synthesize the recent activity to develop droplets as protocell models. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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Open AccessReview Toward Spatially Regulated Division of Protocells: Insights into the E. coli Min System from in Vitro Studies
Life 2014, 4(4), 915-928; doi:10.3390/life4040915
Received: 24 October 2014 / Revised: 25 November 2014 / Accepted: 3 December 2014 / Published: 11 December 2014
Cited by 3 | PDF Full-text (536 KB) | HTML Full-text | XML Full-text
Abstract
For reconstruction of controlled cell division in a minimal cell model, or protocell, a positioning mechanism that spatially regulates division is indispensable. In Escherichia coli, the Min proteins oscillate from pole to pole to determine the division site by inhibition of [...] Read more.
For reconstruction of controlled cell division in a minimal cell model, or protocell, a positioning mechanism that spatially regulates division is indispensable. In Escherichia coli, the Min proteins oscillate from pole to pole to determine the division site by inhibition of the primary divisome protein FtsZ anywhere but in the cell middle. Remarkably, when reconstituted under defined conditions in vitro, the Min proteins self-organize into spatiotemporal patterns in the presence of a lipid membrane and ATP. We review recent progress made in studying the Min system in vitro, particularly focusing on the effects of various physicochemical parameters and boundary conditions on pattern formation. Furthermore, we discuss implications and challenges for utilizing the Min system for division site placement in protocells. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
Open AccessReview Synergism and Mutualism in Non-Enzymatic RNA Polymerization
Life 2014, 4(4), 598-620; doi:10.3390/life4040598
Received: 18 September 2014 / Revised: 15 October 2014 / Accepted: 17 October 2014 / Published: 3 November 2014
Cited by 3 | PDF Full-text (2220 KB) | HTML Full-text | XML Full-text
Abstract
The link between non-enzymatic RNA polymerization and RNA self-replication is a key step towards the “RNA world” and still far from being solved, despite extensive research. Clay minerals, lipids and, more recently, peptides were found to catalyze the non-enzymatic synthesis of RNA [...] Read more.
The link between non-enzymatic RNA polymerization and RNA self-replication is a key step towards the “RNA world” and still far from being solved, despite extensive research. Clay minerals, lipids and, more recently, peptides were found to catalyze the non-enzymatic synthesis of RNA oligomers. Herein, a review of the main models for the formation of the first RNA polymers is presented in such a way as to emphasize the cooperation between life’s building blocks in their emergence and evolution. A logical outcome of the previous results is a combination of these models, in which RNA polymerization might have been catalyzed cooperatively by clays, lipids and peptides in one multi-component prebiotic soup. The resulting RNAs and oligopeptides might have mutualistically evolved towards functional RNAs and catalytic peptides, preceding the first RNA replication, thus supporting an RNA-peptide world. The investigation of such a system is a formidable challenge, given its complexity deriving from a tremendously large number of reactants and innumerable products. A rudimentary experimental design is outlined, which could be used in an initial attempt to study a quaternary component system. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)

Other

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Open AccessConcept Paper Protocells: At the Interface of Life and Non-Life
Life 2015, 5(1), 447-458; doi:10.3390/life5010447
Received: 25 October 2014 / Accepted: 2 February 2015 / Published: 9 February 2015
PDF Full-text (455 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The cellular form, manifesting as a membrane-bounded system (comprising various functional molecules), is essential to life. The ultimate reason for this is that, typically, one functional molecule can only adopt one “correct” structure to perform one special function (e.g., an enzyme), and [...] Read more.
The cellular form, manifesting as a membrane-bounded system (comprising various functional molecules), is essential to life. The ultimate reason for this is that, typically, one functional molecule can only adopt one “correct” structure to perform one special function (e.g., an enzyme), and thus molecular cooperation is inevitable. While this is particularly true for advanced life with complex functions, it should have already been true for life at its outset with only limited functions, which entailed some sort of primitive cellular form—“protocells”. At the very beginning, the protocells may have even been unable to intervene in the growth of their own membrane, which can be called “pseudo-protocells”. Then, the ability to synthesize membrane components (amphiphiles) may have emerged under selective pressure, leading to “true-protocells”. The emergence of a “chromosome” (with genes linked together)—thus avoiding “gene-loss” during the protocell division, was another key event in the evolution of protocells. Such “unitary-protocells”, containing a central genetic molecule, may have appeared as a milestone—in principle, since then life could evolve endlessly, “gaining” more and more functions by introducing new genes. To synthesize in laboratory these different types of protocells, which stand at the interface between life and non-life, would greatly enhance our understanding on the essence of life. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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Open AccessShort Note Does DNA Exert an Active Role in Generating Cell-Sized Spheres in an Aqueous Solution with a Crowding Binary Polymer?
Life 2015, 5(1), 459-466; doi:10.3390/life5010459
Received: 5 November 2014 / Accepted: 2 February 2015 / Published: 9 February 2015
PDF Full-text (768 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
We report the spontaneous generation of a cell-like morphology in an environment crowded with the polymers dextran and polyethylene glycol (PEG) in the presence of DNA. DNA molecules were selectively located in the interior of dextran-rich micro-droplets, when the composition of an [...] Read more.
We report the spontaneous generation of a cell-like morphology in an environment crowded with the polymers dextran and polyethylene glycol (PEG) in the presence of DNA. DNA molecules were selectively located in the interior of dextran-rich micro-droplets, when the composition of an aqueous two-phase system (ATPS) was near the critical condition of phase-segregation. The resulting micro-droplets could be controlled by the use of optical tweezers. As an example of laser manipulation, the dynamic fusion of two droplets is reported, which resembles the process of cell division in time-reverse. A hypothetical scenario for the emergence of a primitive cell with DNA is briefly discussed. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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