Wednesday, 3 March 2021

Abiogenesis News - That God-Shaped Gap is Getting Smaller!

A replicator made of tRNA-like sequences
© Kudella / LMU
Origin of life: The chicken-and-the-egg problem | News - LMU München

Another shovel-full of science just got thrown into Creationism's favourite God-shaped gap, abiogenesis.

A Team of German scientists led by Professor Dieter Braun of the Ludwig Maximilians Universität (LMU), München, have shown how to resolve the classic 'chicken and egg' conundrum when explaining the origins of living systems, that proteins are required for transcription of the genetic information, but their synthesis itself depends on transcription.

It involved Darwinian evolution at a molecular level! As always when science solves a problem, magic was found not to be required!

The LMU press release explains the problem:

Abstract

Can replication and translation emerge in a single mechanism via self-assembly? The key molecule, transfer RNA (tRNA), is one of the most ancient molecules and contains the genetic code. Our experiments show how a pool of oligonucleotides, adapted with minor mutations from tRNA, spontaneously formed molecular assemblies and replicated information autonomously using only reversible hybridization under thermal oscillations. The pool of cross-complementary hairpins self-selected by agglomeration and sedimentation. The metastable DNA hairpins bound to a template and then interconnected by hybridization. Thermal oscillations separated replicates from their templates and drove an exponential, cross-catalytic replication. The molecular assembly could encode and replicate binary sequences with a replication fidelity corresponding to 85–90 % per nucleotide. The replication by a self-assembly of tRNA-like sequences suggests that early forms of tRNA could have been involved in molecular replication. This would link the evolution of translation to a mechanism of molecular replication.

Kühnlein, Alexandra; Lanzmich, Simon A; Braun, Dieter
tRNA sequences can assemble into a replicator
eLife
2021;10:e63431 DOI: 10.7554/eLife.63431

Copyright: © 2021 The authors. Published by elife
Open access. Reprinted under a Creative Commons Attribution 4.0 International License (CC BY 4.0)



eLife digest

The genetic code stored within DNA contains the instructions for manufacturing all the proteins organisms need to develop, grow and survive. This requires molecular machines that ‘transcribe’ regions of the genetic code into RNA molecules which are then ‘translated’ into the string of amino acids that form the final protein. However, these molecular machines and other proteins are also needed to replicate and synthesize the sequences stored in DNA. This presents evolutionary biologists with a ‘chicken-and-egg’ situation: which came first, the DNA sequences needed to manufacture proteins or the proteins needed to transcribe and translate DNA?

Understanding the order in which DNA replication and protein translation evolved is challenging as these processes are tightly intertwined in modern-day species. One theory, known as the ‘RNA world hypothesis’, suggests that all life on Earth began with a single RNA molecule that was able to make copies of itself, as DNA does today. To investigate this hypothesis, Kühnlein, Lanzmich and Braun studied a molecule called transfer RNA (or tRNA for short) which is responsible for translating RNA into proteins. tRNA is assumed to be one of the earliest evolved molecules in biology. Yet, why it was present in early life forms before it was needed for translation still remained somewhat of a mystery.

To gain a better understanding of tRNA’s role early in evolution, Kühnlein, Lanzmich and Braun made small changes to its genetic code and then carried out tests on these tRNA-like sequences. The experiments showed these ‘early’ forms of tRNA can actually self-assemble into a molecule which is capable of replicating the information stored in its sequence. It suggests early forms of tRNA could have been involved in replication before modern tRNA developed its role in protein translation.

With these experiments, Kühnlein, Lanzmich and Braun have identified a possible evolutionary link between DNA replication and protein translation, suggesting the two processes emerged through one shared pathway: tRNA. This deepens our understanding about the origins of early life, while taking biochemists one step closer to their distant goal of recreating self-replicating molecular machines in the laboratory.
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...

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?

Complex relationship

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.

A step closer to the reconstruction of the origin of life

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.

Laboratory research on the origin of life and the emergence of Darwinian evolution at the level of chemical polymers also has implications for the future of biotechnology. “Our investigations of early forms of molecular replication and our discovery of a link between replication and translation brings us a step closer to the reconstruction of the origin of life,” Braun concludes.
The team's research is published open access today in eLife|

This piece of research highlights the difference between science and creationism and why Creationist 'science' has never progressed beyond the Bronze Age when people who knew no better thought the Universe ran on magic. Creationists look for a difficult problem and declare it to be evidence for Creationism - "this is too difficult for science therefore the magic deity my mummy and daddy believed in must have done it! No further investigation is needed!".

Science, on the other hand, looks for real solutions - and eventually finds them. In other words, science is a tool for closing those gaps in our knowledge and understanding that religion makes people satisfied with having, so their ever-shrinking god has somewhere to expand into.

Gods expand so as to fill the ignorance available to them.










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