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

The resulting artificial cells (sometimes called protocells) might be quite different from any extant or extinct form of life, perhaps orders of magnitude smaller than the smallest bacterium, and their synthesis need not recapitulate life’s actual origins. A number of complementary studies have been steadily progressing toward the chemical construction of artificial cells (2–8). The two back-to-back workshops (1)—one held jointly at Los Alamos National Laboratory (LANL) and the Santa Fe Institute (SFI), and the other in Dortmund, Germany, at the seventh European Conference on Artificial Life—strived to encompass the full spectrum of this research.

There are two approaches to synthesizing artificial cells. The top-down approach aims to create them by simplifying and genetically reprogramming existing cells with simple genomes. Although the two workshops included a notable top-down exemplar, they focused primarily on the more general and more challenging bottom- up approach that aims to assemble artificial cells from scratch using nonliving organic and inorganic materials.

Although the definition of life is notoriously controversial, there is general agreement that a localized molecular assemblage should be considered alive if it continually regenerates itself, replicates itself, and is capable of evolving. Regeneration and replication involve transforming molecules and energy from the environment into cellular aggregations, and evolution requires heritable variation in cellular processes. The current consensus is that the simplest way to achieve these characteristics is to house informational polymers (such as DNA and RNA) and a metabolic system that chemically regulates and regenerates cellular components within a physical container (such as a lipid vesicle).

The workshops reviewed the state of the art in artificial cell research, much of which focuses on self-replicating lipid vesicles. David Deamer (Univ. of California, Santa Cruz) and Pier Luigi Luisi (ETH Zurich) each described the production of lipids using light energy, and the templatedirected self-replication of RNA within a lipid vesicle. In addition, Luisi demonstrated the polymerization of amino acids into proteins on the vesicle surface, which acts as a catalyst for the polymerization process. The principal hurdle remains the synthesis of efficient RNA replicases and related enzymes entirely within an artificial cell. Martin Hanczyc (Harvard Univ.) showed how the formation of lipid vesicles can be catalyzed by encapsulated clay particles with RNA adsorbed on their surfaces (see the figure) (9). This suggests that encapsulated clay could catalyze both the formation of lipid vesicles and the polymerization of RNA.

Successfully integrating different chemical systems is a key challenge in artificial cell research. Steen Rasmussen (LANL) and Liaohai Chen (Argonne National Laboratory) presented a minimal protocell design in which a small lipid aggregate (for example, a micelle) acts as a container by anchoring a lipophilic peptide nucleic acid (PNA, an analog of DNA with a pseudopeptide backbone) on its exterior (see the figure) (7). Peter Nielsen (Univ. of Copenhagen) amplified the benefits of using PNA as the informational polymer in such a system, and Kim Rasmussen (LANL) described experimentally and theoretically the hybridization instabilities and charge transfer in DNA-like doublehelix systems. In the Chen-Rasmussen protocell, light-driven metabolic processes synthesize lipids and PNA, with the PNA acting as both an information molecule and as an electron-relay chain. This is the first explicit proposal that integrates genetics, metabolism, and containment in one chemical system. Metabolism in this system has been shown to produce lipids, but experimental realization of the rest of the integrated system has not yet been achieved.

The workshops also included experiments that use the top-down approach to artificial cell construction. Hamilton Smith (Institute for Biological Energy Alternatives, Rockville, Maryland) described an ongoing project to first simplify the genome of Mycoplasma genitalium (the organism with the simplest known genome), and then augment it with genes that encode proteins with desired functions. This topdown approach will probably produce the first impressive results because it can adopt wholesale the proven capacity of nature’s biochemistry to integrate the complex reaction pathways crucial to cellular life, and because it relies on mature laboratory technology for DNA sequencing, synthesis, and manipulation. However, in the long run, the bottom-up approach might provide access to biochemical systems that are incompatible with or inaccessible using existing cellular cellular chemistry, thus yielding a more diverse set of artificial cells with a wider range of useful properties.

An emerging frontier in the development of artificial cells is the use of combinatorial chemistry to aid in the search for suitable chemical systems. John McCaskill (Fraunhofer-Gesellschaft, Germany) described technology that could integrate different chemical systems by developing chemical reactions across multiple spatially separated micrometer-sized channels, which act as computer-controlled microreactors. This technology could also provide “life-support” for artificial cells and their precursors, creating stepping stones toward autonomous artificial cells and enabling them to be programmed to perform useful functions. Statistics that enable open-ended evolution to be identified in data from evolving systems were described by Norman Packard (ProtoLife Srl) and Mark Bedau (Reed College, Portland, Oregon). Open-ended evolution is characterized by a continued ability to invent new properties —so far only the evolution of life on Earth (data partly from the fossil record) and human technology (data from patents) have been shown to generate adaptive novelty in an open-ended manner. Packard explained how statistics could be coupled with McCaskill’s technology to automate the search for chemical systems that might be useful for artificial cells. Gunter von Kiedrowski (Ruhr-Univ. Bochum, Germany) described a new set of chemical reactions that use molecular elements he called “tetrabots.” Such tetrabots could provide an important step toward replicating more general, spatially extended, DNA-like nanoarchitectures.

Several presentations described broader issues underpinning artificial cell theory, simulation, and experiment. Stirling Colgate (LANL), David Krakauer (SFI), Harold Morowitz (George Mason Univ., Virginia), and Eric Smith (SFI) attempted to clarify the distinction between nonliving and living matter. They described how nonliving chemical reactions, driven by thermodynamics, explore the state of space in an ergodical fashion, and thus tend to conduct a random exhaustive search of all possibilities; in contrast, living systems explore a combinatorially large space of possibilities through an evolutionary process. This echoed a central workshop theme: how and when information becomes a dominant factor in the evolution of life, that is, how and when selection plays a greater role than thermodynamics in the observed distribution of phenotypes. Peter Stadler (Univ. Leipzig) reviewed selection using replicator network dynamics, a theoretical framework describing population growth produced by different kinetic conditions. Smith and Morowitz further described how the citric acid cycle of living cells might be a thermodynamic attractor for all possible metabolic networks, thus explaining its appearance at the core of all living systems. Universal scaling in biological systems was discussed by Geoff West (SFI) and Woody Woodruff (LANL), who explained why regular patterns can be found, for example, between an organism’s weight and metabolic rate, regardless of whether the organism is a bacterium or an elephant. Shelly Copley (Univ. of Colorado, Boulder) explained how catalysts operate in living systems today and how these were likely to have evolved from less efficient precursors. Andrew Shreve (LANL) presented a rich variety of self-assembled nanomaterials that display specific emergent properties of a mechanical, photonic, or fluidic nature.

Computational methods are now powerful enough to suggest new experiments. Yi Jiang (LANL) reviewed the state of the art for molecular multiscale simulations in which the challenge is to connect realistic but slow molecular dynamic simulations with less accurate but fast higher level simulations. Andy Pohorille (NASA Ames Research Center, California) used simulations to argue that nongenomic early organisms could undergo evolution before the origin of organisms with genes. Takashi Ikegami (Univ. of Tokyo) presented simulations of a simple and abstract model of metabolic chemistry that demonstrates the spontaneous formation and reproduction of cell-like structures.

The workshops started with some tension tension between the origin of life perspective and the more general concern with synthesizing the simplest possible artificial cells. However, the participants eventually agreed that different artificial cell proposals might suggest different prebiotic niches. The workshop ended with a road-mapping exercise on four interrelated issues: (i) What is the boundary between physical and biological phenomena? (ii) What are key hurdles to integrating genes and energetics within a container? (iii) How can theory and simulation better inform artificial cell experiment? (iv) What are the most likely early technological applications of artificial cell research?

In time, research on these forms of artificial life will illuminate the perennial questions “What is life?” and “Where do we come from?” It will also eventually produce dramatic new technologies, such as self-repairing and self-replicating nanomachines. With metabolisms and genetics unlike those of existing organisms, such machines would literally form the basis of a living technology possessing powerful capabilities and raising important social and ethical implications. These issues were elaborated by Bedau, who suggested that the pursuit of these new technologies should be guided by what he called a “cautious courage” perspective. All workshop participants agreed that useful artificial cells will eventually be created, but there was no consensus about when.

References

1. www.ees.lanl.gov/protocells
2. C. Hutchinson et al., Science286, 2165 (1999).
3. M. Bedau et al., Artif. Life6, 363 (2000).
4. J. Szostak et al., Nature409, 387 (2001).
5. A. Pohorille, D. Deamer, Trends Biotechnol. 20, 123 (2002).
6. L. Eckardt et al., Nature420, 286 (2002).
7 S. Rasmussen et al., Artif. Life9, 269 (2003).
8. P. L. Luisi, Origins Life Evol. Biosph. 34, 1 (2004).
9. M. M Hanczyc et al., Science302, 618 (2003).
10. Fraunhofer

Via: ProtoLife
Bron: Science Magazine, 13 februari 2004