Artificial Beginnings: Understanding the Origin of Life by Recreating It

Thursday 26th July saw the launch of SciLogs.com, a new English language science blog network. SciLogs.com, the brand-new home for Nature Network bloggers, forms part of the SciLogs international collection of blogs which already exist in German, Spanish and Dutch. To celebrate this addition to the NPG science blogging family, some of the NPG blogs are publishing posts focusing on "Beginnings".

Participating in this cross-network blogging festival is nature.com’s Soapbox Science blog, Scitable's Student Voices blog and bloggers from SciLogs.com, SciLogs.de, Scitable and Scientific American’s Blog Network. Join us as we explore the diverse interpretations of beginnings – from scientific examples such as stem cells to first time experiences such as publishing your first paper. You can also follow and contribute to the conversations on social media by using the #BeginScights hashtag.

The Origin of Life on Earth was certainly, in retrospect, and from the human vantage point, the most fateful event in the history of the Universe. On a young, tepid Earth chemistry sprung into biology and set course on a four billion year journey that would eventually lead to us. However, all traces of the first, primitive organisms have vanished. They were outcompeted and devoured by their evolutionary descendents, leaving nothing to form fossils. Though we will never be able to set eyes on the first Earthlings, the first pioneers, we can understand what they must have been like through more subtle, indirect approaches. Comparative biochemistry across the whole of life takes us back quite a ways, though not to the first cells. The most recent common ancestor shared by all living organisms—bacteria, plants, animals, fungi, archaea, and unicellular eukaryotes like amoebae—was born long after the first cell ceased to exist. The only way we can truly understand what life must have been like in its earliest days is to create it ourselves.

Immediately we bump up into the question “What is life?” What are we creating, exactly? Scientists have been asking the question “What is Life?”¹ for generations, and no one has yet come up with a satisfying answer. The common answers usually involve a combination of inheritance, evolution, and metabolism. Ed Regis makes a good case for the latter, but that of course excludes viruses, a judgment that I find unsatisfying³. The Nobel Laureate Jack Szostak, on the other hand, holds that the business of defining life in such terms is pointless and not even useful, and that what we should be focusing on is how chemistry can transition into biology⁴. I’ll leave it at that.

Creating life, whatever we decide it is exactly, will require substantial investment and a coherent toolset. It’s not enough to be really good at making lipid membranes on one day and RNAs on the next; everything must come together for the simple cell—a protocell, as they’re called—to work. I’ll be the first to admit that the field I’m most familiar with, synthetic biology, is largely devoid of the tools for such an undertaking. The unifying tool of synthetic biology is synthetic DNA, whether it’s used to build genetic circuits or entire genomes. Synthetic biology is not concerned with re-creating the Origin of Life. Despite what was claimed by the popular press, Craig Venter’s synthetic cell² was no Second Genesis. Converting the DNA sequence of a bacterial genome in an online database to an actual chemical genome, and using it to bring to life a dead (genome-free) cell was a remarkable accomplishment that will have significant applications yet to come. But building a protocell requires starting from basic materials, not drawing on the genetic repositories of existing organisms.

So what will building a protocell require? The first protocells must have been very simple, with no more than a membrane and replicating molecule trapped inside (or, alternatively, trapped within the membrane⁵). Metabolism had to have been present in some way or another, as the replicating molecule must be fed a source of component parts with which to build copies of itself. The fact that the first protocells must have been very simple is a great gift, metaphorically speaking, to the engineers trying to replicate components of the Origin of Life.

The human-designed protocells will be composed of lipid vesicles, just like our own cells—and probably just like the first protocells, with chemical reactions occurring inside (or on the vesicle membranes themselves)⁶. It turns out that making vesicles with lipid bilayers is quite easy. By extruding lipid solutions through filters of various pore sizes, one can control the typical size of the vesicles that result, and nucleic acids like RNA can easily become encapsulated in the process⁶. The figure at the top of this post shows a miscelle, a clump of lipids like you would find in droplets of oil, next to a linear lipid bilayer. Miscelles can spontaneously form lipid bilayers, which with some frequency circularize to form an enclosed vesicle (for animations of this process, see ref. 7). When the vesicle forms a random sample of the surrounding molecules become trapped inside. Here you see a polymer, say a RNA, with monomers (blue circles) inside, outside, and diffusing through the membrane. Where substrates for replication can’t diffuse through the membrane directly, synthetic membrane-embedded proteins can facilitate the process (of course that is not true to the Origin of Life side of this endeavor, since membrane-bound proteins came later; however it’s worth noting that vesicles—at least some types—are permeable to nucleotides⁸).

We now have a semi-permeable lipid vesicle, but what should we put inside? You might be familiar with the RNA World Hypothesis, which suggests that RNA alone preceded both DNA and protein. It could have even been the very first replicating molecule trapped inside a protocell. The evidence for such a past might be lurking in organisms still alive today, including yourself. RNA is both an information-carrying molecule (messenger RNAs free genetic instructions from their storage in the DNA depository) and a catalytic one. RNAs can regulate gene expression by binding to mRNAs, sometimes even binding a small molecule. Even more impressive, long RNAs sometimes have small sequences within them that spontaneously fold and clip themselves out. But perhaps the most convincing case is that of the ribosome. The ubiquitous molecular machine that produces every protein on Earth is made mostly of RNA, and it’s the ribosomal RNA which coordinates the process of translation (and what’s more, the amino acid ingredients of translation are faithfully brought to the ribosome by none other than RNAs: transfer RNAs). Perhaps it was the ribosome that shepherded in the age of protein dominance in the realm of catalytic activities. The sparse patchwork of protein in today’s ribosomes, like reinforcements keeping an eons-old machine going, seem to me to make the case even more convincing.

The protocell project is dazzling in its plausibility; we know it happened at least once before, so why not in our hands? Plus, the components are common, run-of-the-mill molecules. We have a good handle on membrane structure, but the dream of a self-replicating RNA is yet to be realized. It might even be impossible. However, a RNA molecule has already been created that can copy other RNAs a short way along a template if given a starting point (in the form of a RNA primer)⁸.

The beauty of the protocell idea lies in its adaptability. Even if the single replicating RNA approach fails, there are multitudes of other approaches along a continuum of complexity. The more complex the starting point, the less true we are to modeling the origin of life, but practical utility increases. An intriguing proposal for a protocell microfactory is laid out in the side figure. Protocells have the potential to drastically change our view of manufacturing, especially when it comes to pharmaceuticals. It’s extremely difficult to introduce a new gene pathway into an organism (say, yeast) and have the reasonable level of efficiency required to make the endeavor worthwhile. The cell environment is so complex that we cannot anticipate the emergent behaviors that will crop up when a new system is inserted. However, a protocell is far more complex, and human engineers design every component. The schematic in the figure shows a small protocell factory that produces its own energy from light. Light strikes a protein bound to a small internal vesicle (that is, a vesicle inside the protocell itself), which causes it to pump hydrogen ions inside. The excess of hydrogen ions turns the massive ATPase protein like a water wheel as they escape, forming ATP. This universal energy source can then drive the chemical reactions required to manufacture the desired product. Plus, since the system is so simple it is much easier to tune the levels of expression of the genes in the pathway required to make the product, compared to a yeast or bacterial cell. Anything like this is still years away, but the fact that we can imagine such a system is intriguing.

So are these alive? In theory, protocells could become self-replicating entities, which produce their own energy from light, and use the same genetics that we do (by design, of course). But even the protocell factory, by far more complex than the single replicating RNA protocell, is much simpler than any living bacterium. Yet in the end, it doesn’t matter what we call it; I’ll leave that up to you. It’s the insights into the very earliest stages of life on Earth and the opportunities for manufacturing in ways never before thought possible that will matter most.

Image Credits: Vesicle figures by me. Protocell factory is Figure 4 from ref. 6.

References:

1. Regis, E. What is Life? Investigating the Nature of Life in the Age of Synthetic Biology. New York: Oxford University Press, 2008.

2. Gibson, D. G. et al. Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science 329, 52-56 (2010).

3. Pearson, H. ‘Virophage’ Suggests Viruses are Alive. Nature 454, 677 (2008).

4. Szostak, J. W. Attempts to Define Life Do Not Help to Understand the Origin of Life. Journal of Biomolecular Structure & Dynamics 29, 599-600 (2012).

5. Rasmussen, S. et al. Proto-Organism Kinetics: Evolutionary Dynamics of Lipid Aggregates with Genes and Metabolism. Origins of Life and Evolution of the Biosphere 34, 171–180 (2004).

6. Pohorille, A. & Deamer, D. Artificial Cells: Prospects for Biotechnology. Trends in Biotechnology 20, 123-128 (2002).

7. Szostak Lab Page, Harvard University. Movies.

8. Szostak, J. W., Bartel, D. P., & Luisi, P. L. Synthesizing Life. Nature 409, 387-390 (2001).