A recent study demonstrates that a few "forgotten" biochemical reactions can transform simple geochemical compounds into complex molecules essential for life.
The origin of life on Earth remains a scientific enigma. A key question is how much of the history of life has been lost over time. A species may stop using a biochemical reaction, and if this happens across multiple species, these reactions can be "forgotten."
Researchers from the
Earth-Life Science Institute (ELSI) at Tokyo Institute of Technology and the
California Institute of Technology (CalTech) have explored this question. They hypothesized that forgotten chemistry would appear as discontinuities in the path from simple geochemical molecules to complex biological molecules.
Primitive Earth contained simple compounds such as hydrogen sulfide, ammonia, and carbon dioxide. Billions of years ago, primitive life used these molecules as raw materials. Over time, biochemical processes transformed these precursors into compounds still present today, representing the earliest metabolic pathways.
To model the history of biochemistry, researchers from ELSI and CalTech used the
Kyoto Encyclopedia of Genes and Genomes database, which catalogs over 12,000 biochemical reactions. They began modeling the progressive development of metabolism.
Previous attempts to model the evolution of metabolism had failed to produce the most common complex molecules of current life. The researchers found that only a few molecules could be produced. To bypass this problem, they determined the number of missing reactions. Their research led them to adenosine triphosphate (ATP), a crucial molecule in biochemistry.
ATP is the energy currency of cells. However, the reactions that form ATP require ATP itself, creating a cyclical dependence. To solve this problem, the researchers allowed ATP-generating reactions to use polyphosphate instead of ATP, modifying only eight reactions in total. This enabled them to achieve nearly all contemporary central metabolism.
The researchers were thus able to estimate the relative age of common metabolites and pose precise questions about the history of metabolic pathways. They discovered that biological pathways can form linearly or in a mosaic pattern.
This research shows that even vanished biochemical reactions can be rediscovered from the clues left by modern biochemistry.