Geologic evidence for the rise of oxygen at ~2.0 by and the existence of fossils of oxygenic photosynthetic bacteria at least 500 million years prior have yet to be explained. One way of assessing this phenomenon is to look for metabolic inventions or discoveries that may have precipitated a wholesale change in the way oceanic cyanobacterial communities may have done business. These inventions can leave signatures in extant nucleic acid sequence data. We considered i) nitrogen fixation, ii) nitrogenase protection systems, or iii) sufficient genetic sophistication to allow host/symbiont intracellular transport (eukarygenesis) as candidates, either alone or in combination, to explain the lag time. The goal was to find a suitable molecule or metabolic pathway that encompasses the three candidate events listed, as well as photosynthesis.

Ferreodoxins are proteins containing iron-sulfur clusters as a prosthetic group. They are ancient, small, and reside in the cytosol. They function in a variety of oxidation- reduction systems, but most notably in nitrogen fixation and photosynthesis. They can be divided into two broad groups: i)bacterial ferredoxins which contain 2[4Fe-4S] clusters and are ubiquitous in bacteria and archaea and ii) the plant ferredoxins which contain [2Fe-2S] clusters and are found primarily in cyanobacteria, plastids, and vertebrates. Using sequence data from over 300 organisms within both groups of ferredoxins, we have reconstructed the phylogeny of both molecules. We subsequently mapped on to these phylogenies the abilility to fix nitrogen and the ability to do oxygenic/anoxygenic photosynthesis. An intercomparison of the two separate phylogenies allows for a relative timeline of the events described above.

Our initial analysis indicate that with regards to ferredoxin evolution, non photosynthetic purple bacteria are the most ancient lineage, followed by the cyanobacteria and nitrogen fixation appears to have been in place prior to photosynthesis.