The Ludwig-Maximilians-Universitaet (LMU) team in Munich has shown that small changes in transfer RNA (tRNA) molecules allow them to self-assemble into a functional unit that can replicate information exponentially. tRNAs are key elements in the evolution of early life forms.
Life as we know it is based on a complex network of interactions that take place on a microscopic scale in biological cells and involve thousands of different molecular species. In our bodies, one fundamental process is repeated countless times each day. In an operation known as replication, proteins duplicate the genetic information encoded in DNA molecules stored in the cell nucleus – before distributing them evenly to two daughter cells during cell division. The data is then selectively copied (‘transcribed’) into what are called RNA molecules (mRNAs), which direct the synthesis of many different proteins needed by the cell type in question. The second type of RNA – RNA transfer (tRNA) – plays a central role in ‘translating’ mRNA into proteins. Transfer RNAs act as mediators between mRNAs and proteins: they ensure that the amino acid subunits that make up each individual protein are assembled in the order specified in the corresponding mRNA.
How could such a complex interaction between DNA replication and mRNA translation into proteins have arisen when living systems first evolved on early Earth? Here we have a classic example of chicken and egg problems: Proteins are needed to transcribe genetic information, but their very synthesis depends on transcription.
LMU physicists led by Professor Dieter Brown have now shown how this puzzle could be solved. They showed that minor changes in the structure of modern tRNA molecules allow them to interact autonomously to create a kind of replication module that is capable of replicating information exponentially. This finding implies that tRNAs – key mediators between transcription and translation in modern cells – may also have been a crucial link between replication and translation in the earliest living systems. So it could provide a neat solution to the question of which came first – genetic information or proteins?
Surprisingly, tRNAs in terms of their sequences and overall structure are highly conserved in all three domains of life, i.e., single-celled Archaea and bacteria (which lack a cell nucleus) and Eukaryotes (organisms whose cells contain a true nucleus). This fact in itself suggests that tRNAs are among the oldest molecules in the biosphere.
Like later steps in the evolution of life, the evolution of replication and translation – and the complex relationship between them – is not the result of a sudden single step. It is better understood as the culmination of an evolutionary journey. “Fundamental phenomena such as self-replication, autocatalysis, self-organization, and compartmentalization probably played an important role in these events,” says Dieter Braun. “And more generally, such physical and chemical processes depend entirely on the availability of environments that provide unbalanced conditions.”
In their experiments, Brown and his colleagues used a set of mutually complementary DNA strands modeled on the characteristic shape of modern tRNAs. Each consisted of two “hairpins” (so-called because each strand could partially pair with itself and form an elongated loop structure), separated by an information string in the middle. Eight such threads can communicate by complementary base pairing to create a complex. Depending on the pairing patterns dictated by the central information areas, this complex was able to encode a four-digit binary code.
Each experiment began with a template – an information structure consisting of two types of central information arrays that define a binary array. This sequence dictated the shape of the complementary molecule with which it can interact in the set of available chains. The researchers went on to demonstrate that a binary structure with a template can be copied multiple times, i.e. amplified, by applying a repetitive sequence of temperature fluctuations between warm and cold. “It is therefore possible that such a replication mechanism could have occurred on a hydrothermal microsystem on early Earth,” Brown says. In particular, aqueous solutions trapped in porous rocks on the seabed would create a favorable environment for such reaction cycles, since in such settings natural temperature oscillations, generated by convection currents, can occur.
During the copying process, complementary threads (extracted from a set of molecules) are paired with the information segment of the template threads. Over time, the adjacent hairpins of these threads also evaporate to form a stable backbone, and temperature oscillations continue to drive the amplification process. If the temperature rises briefly, the template threads are separated from the newly formed replica, and both can then serve as the template threads in the next replication round.
The team was able to show that the system is capable of exponential replication. This is an important finding because it shows that the replication mechanism is particularly resistant to collapse due to the accumulation of errors. The fact that the structure of the replicator complex itself resembles the structure of modern tRNAs suggests that early forms of tRNA may have participated in molecular replication processes, before tRNA molecules assumed their modern role in translating RNA sequences into proteins. “This link between replication and translation in the early evolutionary scenario could provide a solution to the chicken and egg problem,” says Alexandra Kühnlein. It could also explain the characteristic form of proto-tRNAs and elucidate the role of tRNAs before they are co-opted for use in translation.
Laboratory research on the origin of life and the origin of Darwinian evolution at the level of chemical polymers also has implications for the future of biotechnology. “Our research into the early forms of molecular replication and discovering the link between replication and translation brings us one step closer to reconstructing the origin of life,” Brown concludes.