Synthetic biology’s quest towards biochemical self-replicators
From synthetic building blocks to engineered life
What is life?
The short answer is that there is no universally accepted definition. The deeper scientists inquire, the more complex the question becomes, because nature is ripe with self-replicating systems, living grey zones from autocatalytic chemistry to elusive megaviruses to early microorganisms. There are however some characteristics which are shared among all known terrestrial living systems.
Life is a self-contained, self-regulating, self-organizing, self-reproducing, inter-connected, open thermodynamic network of component parts which performs work, existing in a complex regime which combines stability and adaptability in the phase transition between order and chaos, as a plant, animal, fungus, or microbe. -Macklem PT. and Seely A.
Notably, most scientific definitions of life are quite descriptive, giving a sense that “life” as a concept is more an arbitrary destinction we humans make rather than a self-evident construct of natural laws. Where these fine destinctive lines run is, like many things in science, up for further investigation and philosophy. Nitpicking aside, most can agree that at a certain stage of complexity, for example a bacterial cell, a system entirely composed of “dead” molecules, charged atoms and kinetic energy suddenly becomes alive. (Some even after millions of years being practically dead)
In that sense, ‘living’ is an emergent property out of the interplay of countless ‘dead’ parts, together achieving what none by itself is capable of.
Despite the poetic beauty, emergence is a common phenomenon in our universe, which brings us to the main question of this article. Can we engineer life?
The science of engineering living systems
Synthetic biology (SynBio) is the broad scientific domain in charge of engineering biological systems. And similar to life itself, definitions are mushy. SynBio employs methodology from biological, chemical, mathematical, engineering and computer-science, often works with molecular building blocks rather than living systems, and SynBio engineers regularily display the familiar ‘can-do’ attitude of a silicon valley start-up. The dominant view: Biology is just nanotechnology which can ultimately be hacked and bend to human will. These ‘hacks’ start from simple optimizations of biological systems to re-writing or replacing existing biological mechanims or even adding de novo capabilities. For these reasons, SynBio will play an essential role in targeting many global problems of the 21st century, from food security to climate change. The holy grail however lies in the creation of synthetic life itself. A feat we are far of. But how far exactly?
A model of a biochemical constructor
Biochemical constructors are systems which use exisiting sets of biological nanotechnology, for example protein machinery or DNA molecules from bacteria, and use them in artificial environments like chemostats or bioreactors. The rough idea is to achieve some kind of system homeostasis (read: system survival) for a prolonged time that exceeds the individual half-lifes of the system’s constituent components. In order to achieve that, the system has to constantly re-construct itself, while only being provided with energy and basic building blocks (e.g. amino acids). Not that dissimilar to a biological cell, which maintains its constitutent components and biological function through nutrients and energy. Another way to look at biochemical constructors is indeed to imagine them as the smallest, most reductionist version of a biological cell.
Biochemical constructors are of inherent interest to researchers who not only want to create artificial life-like systems, but also learn what design principles life follows.
The latest attempt at building biochemical constructors was recently published from a team at EPFL in Switzerland. ( Lavickova B. et al, Nature, 2020). They used a microfluidic reactor cell to have absolute control of nutrient and energy flows to and from their nucleic acid/protein-based self-regenerating system.
As a core constructor, they used the PURE (protein synthesis using recombinant elements) system, which was developed in 2005 by Japanese reseachers (Shimizu et al.) and is often used by synbio researchers as a viable starting point for achieving self-regeneration. Although clear capability to self-regenerate has not been shown for the PURE system previously. This is where Lavickova B and colleagues come in. By using the combination of PURE system, microfluidic chemostats, and a fluorescent protein readout, the researcher could assess activity and performance of self-regeneration in real-time. They then implemented a ‘kick-start’ method to ‘boot-up’ regeneration of essential PURE proteins from DNA templates. Within that setup, they could probe which parameters (varying nutrient/protein/DNA concentrations) had the strongest impact on component self-regeneration, thereby learning about wider principles self-replicating systems.
We demonstrate the concept and feasibility of this approach by regenerating different aminoacyl-tRNA synthetases (aaRSs). We also regenerated T7 RNA polymerase (RNAP) and mapped system optimality by varying T7 RNAP DNA concentration and were able to explain the observed genotype-phenotype landscape with a biophysical resource limitation model.
From that, the researcher were able to build a simple resource-limitation model, which can be described by both yield (the systems capacity to produce non-essential fluorescent protein) and robustness (the systems capacity to survive). With that model, they could then formaly describe how changes in protein expression, or DNA concentration, impacts on yield or robustness of their system. For example, if an essential constructor protein is not present, than yield (=fluorescent signal of GFP) will be zero. Once the systems starts producing the missing constructor protein, yield rapidly increases. However, if a critical value of constructor protein production is exceeded, yield drops again, because of resource competition and so-called loading effects.
Given that behavior, the researchers concluded that for each component part there exists a pareto optimality with all other components and resources in the system.
This makes sustainable self-regeneration a balancing act of the highest order.
No one is more aware of the engineering troubles ahead than the authors:
We demonstrate how a biochemical constructor could be created by implementing a transcriptiontranslation system running at steady-state on a micro-chemostat that supplies the reaction with resources and energy. […]
[…] a number of considerable challenges remain. It will be critical to develop a transcription-translation system with a high enough synthesis rate to self-regenerate all of its components. The PURE system is currently orders of magnitude away from this target
[…] A second major challenge lies in achieving functional in vitro ribosome biogenesis.
[…] Many [other] challenges remain, but pieces to the puzzle are being added at an increasing rate. It is thus not far-fetched to consider that synthetic life, engineered by humans from basic building blocks, may be a possibility.
— Lavickova et al.
Conclusion
Creating a partially self-regenerating biochemical constructor is a considerable achievement, yet what the study of Lavickova and colleagues truly shows us is how much further we have to go in matching nature’s ingenuity and craft when it comes to living systems.
Life, a force that seemed almost like magic for most of humanity’s existence, has finally entered the realm of science and engineering.
While today we are nowhere close to create living systems, scientists all around the world have already begun chipping away secrets from the design principles of “living” machines. All of our discoveries reaffirm the awesome and humbling complexity in the finetuning mechanics of even the most simple biological life forms. Life might not be magical, but it is the most harmonic balancing act we will ever know.
I don’t know about you, but for me, there is some poetic beauty in that.
