A missing link in the timeline of Earth’s chemistry may have been found

A missing piece of Earth’s evolutionary timeline may have been found. Using computational models, a team of scientists explored how working back into modern biochemistry could help map out how simple, non-living chemicals were present on early Soil gave rise to complex molecules that led to the origin of life as we know it.

Researchers believe that modern metabolism – the life-sustaining biochemical processes that occur in living things – evolved from the primitive geochemical environment of ancient Earth, using available materials and energy sources. Although it is an interesting idea, evidence for the transition from primitive geochemistry to modern biochemistry is still lacking.

Previous modeling studies have provided valuable insights, but have always encountered a problem: their models of metabolism evolution have consistently failed to produce many of the complex molecules used by modern life – and the reason why is not clearly.

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In particular, there is uncertainty about the continuity in this metabolic timeline, particularly the extent to which ancient biochemical processes that may have disappeared over time time formed the metabolic processes we know today.

“In particular, chemical reactions unrelated to biochemistry have been cited as missing steps in early biosynthetic pathways, indicating that data on these chemical transformations have been lost throughout evolutionary history,” says the research team from the Tokyo Institute of Technology and the California Institute of Technology. Institute of Technology wrote in a paper describing the new missing link. “It remains unclear to what extent ‘extinct’ biochemistry is necessary to enable the generation of modern metabolism from early Earth environments.”

A metabolic mystery

To unravel this puzzle, the scientists attempted to model possible evolutionary pathways that could have brought modern metabolism from its early Earth predecessors to the present day. Therefore, they investigated biochemical evolution at the biosphere level, that is, at the scale of an entire ecosystem, and integrated influences and factors such as geochemical and atmospheric environments, as well as how organisms can interact with each other.

“It has long been believed that the roots of biochemistry lie in the geochemistry of the early Earth,” said Seán Jordan, associate professor of biogeochemistry and astrobiology at Dublin City University, who was not involved in the research, told Space.com. “The suggestion that remnants of ancient metabolic pathways may be hidden in the modern biosphere and yet undiscovered is fascinating and exciting.”

The team used the Kyoto Encyclopedia of Genes and Genomes database, which has cataloged just over 12,000 biochemical reactions, as the model’s repository for all possible biochemical reactions that could have occurred and evolved during the timeline studied. Researchers then simulated the expansion of a chemical reaction network, starting with a series of initial compounds that would have been found on the early Earth. These include various metals and inorganic molecules, such as iron, hydrogen sulfide, carbon dioxide and ammonia, as well as organic substrates that could have been formed by ancient carbon fixation reactions.

“Using a network expansion algorithm to trace a path from early geochemistry to complex metabolic networks seems like a solid, iterative approach to this question,” Jordan said.

But like other modeling experiments, the researchers’ model initially failed to reproduce even a fraction of the molecules used in modern biochemical processes, leaving the vast majority inaccessible from the seed compounds. Hypothesizing that these results were limited because the dataset included only known cataloged biochemical reactions, the researchers expanded the Kyoto database with a set of hypothetical biochemical reactions, adding 20,183 new pathways.

A pie chart on the left and a gray bar chart on the right.

A pie chart on the left and a gray bar chart on the right.

Repetition of the experiment with this extended reaction set resulted in only a slight increase in scope, “suggesting that neither currently cataloged nor predicted biochemistry contains transformations necessary to achieve the vast majority of known metabolites.”

The authors noted that an important precursor to a class of compounds called purines, which are important building blocks for biological molecules such as DNA and RNA, was not found in the model’s expansion options. In fact, a quick test adding adenine, a common purine derivative, to the pool of seed compounds resulted in an approximately 50% increase in the number of modern biomolecules the model could predict.

Further experiments confirmed what the authors termed a ‘purine bottleneck’, which apparently prevents the emergence of metabolism from geochemical precursors in the model. The problem seemed related to the data set of modern biochemical reactions, where the production of purines, such as adenosine triphosphate (ATP), is autocatalytic. This means that multiple steps in the ATP synthetic pathway require ATP itself – without ATP, new ATP cannot be created. This self-driving caused the model to come to a standstill.

To solve the bottleneck, the scientists hypothesized that this self-catalyzing dependency might be more “relaxed” in primitive metabolic pathways, since the role ATP currently plays could be carried out by inorganic molecules known as polyphosphates. By replacing ATP in the database reactions (only eight in total required this change), almost all of contemporary nuclear metabolism could be achieved.

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“We may never know exactly, but our research has provided an important piece of evidence: Only eight new reactions, all reminiscent of common biochemical reactions, are needed to bridge geochemistry and biochemistry,” says Harrison Smith, one of the study’s authors. press release. “This doesn’t prove that the space of missing biochemistry is small, but it does show that even extinct reactions can be rediscovered based on clues left behind in modern biochemistry.”

“The big question that remains unanswered is whether we can experimentally demonstrate that the steps from geochemistry to biochemistry are possible following a trajectory like [this]Jordan added. ‘These findings should encourage others in the field to continue investigating this transition. It shows us that the blueprint for the chemistry that led to the origin of life can be found in existing biochemistry.”

The study was published in March in the journal Nature Ecology & Evolution.

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