A missing link in Earth's chemistry timeline may have been discovered

Lina Portman4 weeks ago

1 4 minutes read

A missing piece of the Earth's evolutionary timeline may have been found. Using computer modeling, a team of scientists explored how working backwards from modern biochemistry could help determine how simple, non-living chemicals are present in early life. Earth gave rise to complex molecules that led to the emergence of life as we know it.

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

Previous modeling studies have provided valuable information, but have always run into a problem: Their models of the evolution of metabolism have consistently failed to produce many of the complex molecules used by modern life – and the reason is not clear. not clear.

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Notably, there is uncertainty about the continuity of this metabolic timeline, particularly the extent to which ancient biochemical processes that may have disappeared over time. time shaped the metabolic processes we know today.

“In particular, chemical reactions unrelated to biochemistry have been discussed as missing steps in early biosynthetic pathways, suggesting that records of these chemical transformations were lost throughout evolutionary history “, said the researchers from the Tokyo Institute of Technology and the California Institute of Technology. Institute of Technology wrote in an article describing the new missing link. “It remains unclear to what extent 'extinct' biochemistry is necessary to enable the generation of modern metabolism from early terrestrial environments.”

To solve this conundrum, scientists sought to model possible evolutionary pathways that could have brought modern metabolism from its earliest terrestrial predecessors to the present day. They therefore explored biochemical evolution at the level of the biosphere, that is to say on the scale of an entire ecosystem, and integrated influences and factors such as geochemical and atmospheric environments, as well as the how organisms might interact.

“It has long been hypothesized 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, which was not involved in the study, told Space.com. “The suggestion that remnants of ancient metabolic pathways may be hidden in the modern biosphere and yet undetected 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 taken place and evolved. during the chronology studied. The researchers then simulated the expansion of a network of chemical reactions from a set of initial compounds believed to have been found on early Earth. These included 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 the beginnings of geochemistry to complex metabolic networks appears to be a robust, iterative approach to this question,” Jordan said.

However, as with other modeling experiments, the researchers' model failed to reproduce even a fraction of the molecules used in modern biochemical processes, leaving the vast majority inaccessible from the starting compounds. . Assuming that these results were limited because the dataset included only known cataloged biochemical reactions, the researchers expanded the Kyoto database to also include a set of hypothetical biochemical reactions, adding 20,183 new pathways.

To build a model of the evolutionary history of metabolism on a biosphere scale, the research team compiled a database of 12,262 biochemical reactions from the Encyclopedia of Genes and Genomes database of Kyoto (KEGG). (Image credit: Goldford, JE, Nat Ecol Evol (2024))

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

The authors noted that a key 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 expansion scope. of the model. In fact, a rapid test in which adenine, a common derivative of purine, was added to the pool of seed compounds resulted in an approximately 50% increase in the number of modern biomolecules the model was able to predict.

Further experimentation confirmed what the authors called a “purine bottleneck,” which appears to prevent the emergence of geochemical precursor metabolism in the model. The problem appears to be related to the body of evidence for modern biochemical reactions, in which the production of purines, such as adenosine triphosphate (ATP), is autocatalytic. This means that several steps in the ATP synthesis pathway require ATP itself – without ATP, new ATP cannot be created. This self-cycling caused the model to stop.

To resolve this bottleneck, scientists hypothesized that this self-catalyzing dependence may have been more “relaxed” in primitive metabolic pathways, because the role that ATP currently plays could have been provided by inorganic molecules called polyphosphates. By replacing ATP in the reactions in the database (only eight in total required this change), almost all of contemporary central metabolism could be achieved.

“We may never know exactly, but our research has provided important evidence that only eight new reactions, all reminiscent of common biochemical reactions, are needed to connect geochemistry and biochemistry,” said Harrison Smith, the one of the authors of the study. Press release. “This does not prove that the space of missing biochemistry is small, but it shows that even reactions that have disappeared can be rediscovered from clues left by modern biochemistry.”

“The big question that remains unanswered is whether we can show experimentally that the steps from geochemistry to biochemistry are possible following a trajectory such as this.” [this]”, Jordan added. “These results should encourage others in the field to continue examining this transition. This shows us that the blueprint for chemistry that led to the emergence of life can be found in existing biochemistry. »

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