SDSC+ Folks are at it again: Ancient Life and Metals Sims

Researchers in computational biology and marine science have combined their diverse expertise and found that trace-metal usage by present-day organisms probably derives from major changes in ocean chemistry occurring over geological time scales.

Using protein structures for the first time in such a study, the research establishes one of the influences that geochemistry has had upon life.

The study, published in this week’s edition of the Proceedings of the National Academy of Sciences, sought to verify the theory that the rise in atmospheric oxygen some 2.3 billion years ago, and attendant shifts in ocean chemistry, led to changes in types of metals used with protein structures. Such changes are hypothesized to have led to the diversification and increased complexity of the life we see today.

Scientists Chris Dupont, Song Yang, Brian Palenik and Philip Bourne from the San Diego Supercomputer Center (SDSC), Scripps Institution of Oceanography, and the departments of chemistry and biochemistry and pharmacology at the University of California, San Diego (UCSD) analyzed the metal-binding characteristics of all known protein structures found in all kingdoms of life.

"Protein structures are ideal for this study," Bourne said, "since they are much more conserved than protein sequences, traditionally used in such studies and, furthermore, metal binding can be inferred directly."

Using data generated by Dupont and Yang, the group established that the three superkingdoms of life - Archaea, Bacteria and Eukarya -- all use metals differently. The differences reflect the availability of such metals in the ocean as the respective superkingdoms evolved.

The authors conclude that, "these conserved trends are proteomic imprints of changes in trace-metal bioavailability in the ancient ocean that highlight a major evolutionary shift in biological trace-metal usage."