The objectives of this research program are to develop an understanding of the plausible reactions that could occur on the peribiotic Earth. We, thus, wish to: i) constrain the problem to simplify and focus the task of other scientists who are interested in making the structurally complex molecules that are essential in current life; ii) attack some of the problems of concentration, catalysis, and network formation that are essential to the formation of spontaneously evolving, dissipative systems; iii) assemble plausible lists of elementary reactants and processes leading toward those commonly found in current metabolism; iv) develop rationales for the existence of “chemical fossils”: that is, molecules, reactions, and processes that seem to be common to all life (so far as we know), and thus seem to offer hints about the very earliest, common, stages the formation of proto-cells.
The Chemical Origin of Networks
Several theories of the origins of life propose that life emerged spontaneously from the self-assembly of organic reactions, (im)probably occurring chaotically in complex mixtures of molecules.1 The chemistry that permit the assembly of simple organic reactions into networks with complex emergent behaviors, however, remain incompletely understood.
The ability to rationally design networks of molecular reactions could provide important insights into research on the origins of life. We recently designed a reaction network that could oscillate under continuous flow conditions, using a microreactor (a continuously stirred tank reactor, CSTR), to provide an elemental model for a protocell (Figure 1a).2 The oscillations are a result of three logical steps in the network (i-iii, highlighted in grey), which can be described by a set of reactions and their corresponding time traces (Figure 1b): (i) a “triggering step”, that produces the activator (ethanethiol) but that is immediately being inhibited by a strong inhibitor (maleimide). The inhibitor concentration thus creates a critical threshold that needs to be overcome, providing a lag phase. (ii) “Auto-amplification”, during which each ethanethiol is converted into two new thiols (i.e. cysteamine, and alanine mercaptoethyl amide) facilitated by sulfide-disulfide exchange and Kent ligation. This reaction (or set of reactions) is autocatalytic and abruptly converts cysteamine into an amide. (iii) “Termination”, when the majority of produced thiols have been inhibited, or depleted. The system, then recharges refilling with reactants (indicated by the decrease followed by an increase in 3b). Under appropriate conditions (e.g., pH, temperature, space velocity), thiols are sequentially produced and consumed, and depleted, creating oscillations in their concentration over time. This system does not directly mimic the reactions involved in metabolism (and is not intended to), but it is similar in its complexity to simple metabolic cycles, it is easy to study (by examining its oscillations), and it does not involve enzymatic catalysis (which could not have been present at the origins of metabolism).
We demonstrated that molecular networks could display fundamental properties of dynamic systems such as bistability and oscillations (Figure 2A). The thiol network is the first experimental example using organic molecules that might have existed on the early Earth.3 This “network approach” allows us use chemistry to tune the intrinsic network processes (such as the trigger-amplification modules depicted in Figure 2B), and utilize the ability of a reaction network to sustain oscillations (a collective property of the network) as an observable behavior to further examine how networks of reactions organize, adapt, and evolve in order to better understand the emerging principles of life from simple reactions.
|Figure 1. Thiol reaction network. (A) Network components of the designed reaction network composed of an alanine thioester (1), cystamine (2), and inhibitors maleimide (3a) and acrylaminde (3b). When fed into a continuous stirred tank reactor (CSTR), the components together create an oscillating behavior. (B) Detailed reaction scheme of network based on three logical steps: (i) triggering, (ii) auto-amplification, (iii) termination. The corresponding time traces are simulated using a mathematical model described in our recent work.2|
|Figure 2: Rationally designed network capable of bistability and stable oscillations.2 (B) Experimental data, showing bistability that is controlled by the space velocity (i.e., the parameter that determines the rate of the exchange of the components, or the products of the reactions, of the network with the environment) and examples of oscillations in time of the autocatalytic thiol network under continuous flow conditions. (A) Simplified “network motif” depicting the reactions designed network, with thiols (RSH, in red) being the key node connecting the network components.|
1. Whitesides, G.M., The Improbability of Life, Fitness of the Cosmos for Life: Biochemistry and Fine Tuning, Barrows, J.D., Morris, S.C., Freeland, S.J., and Harper, C.L., Jr., Eds., Cambridge University Press, 2008.
2. Semenov, S. N.; Kraft, L. J.; Ainla, A.; Zhao, M.; Baghbanzadeh, M.; Campbell, V. E.; Kang, K.; Fox, J. M.; Whitesides, G. M., Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions. Nature 537 (7622), 656-60, 2016.
3. Bracher, P. J., Snyder, P. W., Bohall, B. R. & Whitesides, G. M. The relative rates of thiol-thioester exchange and hydrolysis for alkyl and aryl thioalkanoates in water. Orig. Life Evol. Biosph. 41, 399–412, 2011.