Slow molecular evolution of rubisco limits adaptive improvement of CO₂ assimilation

Abstract

Rubisco assimilates CO₂ to form the sugars that fuel life on Earth. Although rubisco is the source of most carbon in the biosphere, it is a surprisingly inefficient catalyst with a modest carboxylase turnover rate and a competing oxygenase activity which results in the loss of fixed CO₂. These apparent shortcomings of rubisco present a puzzling evolutionary paradox: why does the enzyme appear well suited to the high CO₂ low O₂ conditions of its origin, rather than the low CO₂ high O₂ conditions of the present day? To help answer this question, we perform a phylogenetically resolved analysis of the molecular and kinetic evolution of Form I rubisco. We discover that rubisco is among the slowest evolving genes on Earth. Specifically, we find that the rubisco catalytic large subunit evolves substantially slower than its cognate small subunit, and is slower than >98% of all other genes and enzymes across the tree of life. Next, through simultaneous analysis of rubisco molecular and kinetic evolution in C₃ angiosperms, we demonstrate that despite its slow molecular evolution, rubisco kinetics have evolved, and are continuing to evolve, to improve CO₂/O₂ specificity, carboxylase turnover and overall carboxylation efficiency. Thus, slow molecular evolution has severely limited rubisco kinetic optimisation, resulting in the present enzyme that is poorly adapted for current conditions.