Origin of life: The chicken-and-egg problem

RNA abstract concept illustration 

A Ludwig-Maximilians-Universitaet (LMU) in Munich team has shown that slight alterations in transfer-RNA molecules (tRNAs) 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, which take place at microscopic scales in biological cells, and involve thousands of distinct molecular species. In our bodies, one fundamental process is repeated countless times every day. In an operation known as replication, proteins duplicate the genetic information encoded in the DNA molecules stored in the cell nucleus -- before distributing them equally to the two daughter cells during cell division. The information is then selectively copied ('transcribed') into what are called messenger RNA molecules (mRNAs), which direct the synthesis of the many different proteins required by the cell type concerned. A second type of RNA -- transfer RNA (tRNA) -- plays a central role in the 'translation' of mRNAs into proteins. Transfer RNAs act as intermediaries between mRNAs and proteins: they ensure that the amino-acid subunits of which each particular protein consists are put together in the sequence specified by the corresponding mRNA.

How could such a complex interplay between DNA replication and the translation of mRNAs into proteins have arisen when living systems first evolved on the early Earth? We have here a classical example of the chicken-and-the-egg problem: Proteins are required for transcription of the genetic information, but their synthesis itself depends on transcription.

LMU physicists led by Professor Dieter Braun have now demonstrated how this conundrum could have been resolved. They have shown that minor modifications in the structures of modern tRNA molecules permit them to autonomously interact to form a kind of replication module, which is capable of exponentially replicating information. This finding implies that tRNAs -- the key intermediaries between transcription and translation in modern cells -- could also have been the crucial link between replication and translation in the earliest living systems. It could therefore provide a neat solution to the question of which came first -- genetic information or proteins?

Strikingly, in terms of their sequences and overall structure, tRNAs are highly conserved in all three domains of life, i.e. the unicellular Archaea and Bacteria (which lack a cell nucleus) and the Eukaryota (organisms whose cells contain a true nucleus). This fact in itself suggests that tRNAs are among the most ancient molecules in the biosphere.

Like the later steps in the evolution of life, the evolution of replication and translation -- and the complex relationship between them -- was 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 are likely to have played important roles in these developments," says Dieter Braun. "And on a more general note, such physical and chemical processes are wholly dependent on the availability of environments that provide non-equilibrium conditions."

In their experiments, Braun and his colleagues used a set of reciprocally complementary DNA strands modeled on the characteristic form of modern tRNAs. Each was made up of two 'hairpins' (so called because each strand could partially pair with itself and form an elongated loop structure), separated by an informational sequence in the middle. Eight such strands can interact via complementary base-pairing to form a complex. Depending on the pairing patterns dictated by the central informational regions, this complex was able to encode a 4-digit binary code.

Each experiment began with a template -- an informational structure made up of two types of the central informational sequences that define a binary sequence. This sequence dictated the form of the complementary molecule with which it can interact in the pool of available strands. The researchers went on to demonstrate that the templated binary structure can be repeatedly copied, i.e. amplified, by applying a repeating sequence of temperature fluctuations between warm and cold. "It is therefore conceivable that such a replication mechanism could have taken place on a hydrothermal microsystem on the early Earth," says Braun. In particular, aqueous solutions trapped in porous rocks on the seafloor would have provided a favorable environment for such reaction cycles, since natural temperature oscillations, generated by convection currents, are known to occur in such settings.

During the copying process, complementary strands (drawn from the pool of molecules) pair up with the informational segment of the template strands. In the course of time, the adjacent hairpins of these strands also pair up to form a stable backbone, and temperature oscillations continue to drive the amplification process. If the temperature is increased for a brief period, the template strands are separated from the newly formed replicate, and both can then serve as template strands in the next round of replication.

The team was able to show that the system is capable of exponential replication. This is an important finding, as it shows that the replication mechanism is particularly resistant to collapse owing to the accumulation of errors. The fact that the structure of the replicator complex itself resembles that of modern tRNAs suggests that early forms of tRNA could have participated in molecular replication processes, before tRNA molecules assumed their modern role in the translation of messenger RNA sequences into proteins. "This link between replication and translation in an early evolutionary scenario could provide a solution to the chicken-and-the-egg problem," says Alexandra Kühnlein. It could also account for the characteristic form of proto-tRNAs, and elucidate the role of tRNAs before they were co-opted for use in translation.

 

How a single gene alteration may have separated modern humans from predecessors

 

DNA illustration

As a professor of pediatrics and cellular and molecular medicine at University of California San Diego School of Medicine, Alysson R. Muotri, PhD, has long studied how the brain develops and what goes wrong in neurological disorders. For almost as long, he has also been curious about the evolution of the human brain -- what changed that makes us so different from preceding Neanderthals and Denisovans, our closest evolutionary relatives, now extinct?

Evolutionary studies rely heavily on two tools -- genetics and fossil analysis -- to explore how a species changes over time. But neither approach can reveal much about brain development and function because brains do not fossilize, Muotri said. There is no physical record to study.

So Muotri decided to try stem cells, a tool not often applied in evolutionary reconstructions. Stem cells, the self-renewing precursors of other cell types, can be used to build brain organoids -- "mini brains" in a laboratory dish. Muotri and colleagues have pioneered the use of stem cells to compare humans to other primates, such as chimpanzees and bonobos, but until now a comparison with extinct species was not thought possible.

In a study published February 11, 2021 in Science, Muotri's team catalogued the differences between the genomes of diverse modern human populations and the Neanderthals and Denisovans, who lived during the Pleistocene Epoch, approximately 2.6 million to 11,700 years ago. Mimicking an alteration they found in one gene, the researchers used stem cells to engineer "Neanderthal-ized" brain organoids.

"It's fascinating to see that a single base-pair alteration in human DNA can change how the brain is wired," said Muotri, senior author of the study and director of the UC San Diego Stem Cell Program and a member of the Sanford Consortium for Regenerative Medicine. "We don't know exactly how and when in our evolutionary history that change occurred. But it seems to be significant, and could help explain some of our modern capabilities in social behavior, language, adaptation, creativity and use of technology."

The team initially found 61 genes that differed between modern humans and our extinct relatives. One of these altered genes -- NOVA1 -- caught Muotri's attention because it's a master gene regulator, influencing many other genes during early brain development. The researchers used CRISPR gene editing to engineer modern human stem cells with the Neanderthal-like mutation in NOVA1. Then they coaxed the stem cells into forming brain cells and ultimately Neanderthal-ized brain organoids.

Brain organoids are little clusters of brain cells formed by stem cells, but they aren't exactly brains (for one, they lack connections to other organ systems, such as blood vessels). Yet organoids are useful models for studying genetics, disease development and responses to infections and therapeutic drugs. Muotri's team has even optimized the brain organoid-building process to achieve organized electrical oscillatory waves similar to those produced by the human brain.

The Neanderthal-ized brain organoids looked very different than modern human brain organoids, even to the naked eye. They had a distinctly different shape. Peering deeper, the team found that modern and Neanderthal-ized brain organoids also differ in the way their cells proliferate and how their synapses -- the connections between neurons -- form. Even the proteins involved in synapses differed. And electrical impulses displayed higher activity at earlier stages, but didn't synchronize in networks in Neanderthal-ized brain organoids.