CONSTRAINING THE GREAT OXIDATION EVENT WITHIN THE RUBISCO PHYLOGENETIC TREE
Here we use computational models to reconstruct a Rubisco family phylogenetic tree, ancestral amino acid sequences at branching points on the tree, and protein structures for several key ancestors. Analysis of historic substitutions with respect to their structural locations shows that the Rubisco family experienced distinct periods of amino acid substitution enrichment above background levels near and within its active site and subunit interfaces over the interval between Form I and Form III groups in its evolutionary history. One possible interpretation is that these periods of substitution enrichment are coincident with oxidative stresses exerted by the rise of oxygenic photosynthesis in the Precambrian era. This suggests a vast genotype space encoding the carboxylation/oxygenation phenotype, but a relatively small number of mutations are required to tune the biophysical properties of different Rubisco subfamilies.
Our interpretation implies that the periods of Rubisco substitutional enrichment inferred near the transition from anoxic to oxic forms predate the acquisition of Rubisco by fully derived cyanobacterial (i.e., dual photosystem-bearing, oxygen-evolving) clades. The partitioning of extant lineages at high clade levels within our Rubisco phylogeny indicates that horizontal transfer of Rubisco is a relatively infrequent event. Therefore, it is possible that these mutational enrichment periods correspond to the adaptation of key oxygen-sensitive components of Rubisco prior to the Great Oxidation Event.