Rubisco is evolving for improved catalytic efficiency and CO₂assimilation in plants

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.

Evolution of increased complexity and specificity at the dawn of form I Rubiscos

“…However, it also enabled the accumulation of substitutions that created a dependence on the interaction. Rubisco is a slow-evolving ( 35 ), notoriously constrained enzyme ( 36 , 37 ), and the recruitment of an epistatic modifier like the SSU may have been the only way for it to access high specificity.…”

The evolutionary constraints on angiosperm chloroplast adaptation

“…It means that factors other than the function of the encoded protein have been important in constraining the evolvability of plastid genes. In this context, it is noteworthy that the constraints identified here may help provide a mechanistic explanation for the strong phylogenetic constraints that have limited the adaptation of rubisco enzyme kinetics (Bouvier, et al 2021) and why rubisco is one of the slowest evolving enzymes on earth (Bouvier, et al 2022). Specifically, evolutionary constraints intrinsic to the location, mRNA abundance and amino acid composition of rubisco (in addition to functional constrains on the protein) may help to explain why it has been so slow to adapt to changing atmospheric conditions, and consequently why it is poorly suited to the O 2 -rich, CO 2 -poor atmosphere of the present day.…”

Response to Tcherkez and Farquhar: Rubisco adaptation is more limited by phylogenetic constraint than by catalytic trade-off

“…In summary, therefore, although rubisco catalytic trade-offs exist as determined by chemistry, these represent a less serious constraint on rubisco kinetic adaptation compared to previous assumptions. Instead, phylogenetic constraints, likely caused by slow molecular evolution in rubisco (Bouvier et al, 2022) and more general constraints on the molecular evolution of chloroplast encoded genes (Robbins and Kelly, 2022), have presented a more significant barrier to improved rubisco catalytic efficiency.…”

“…In actual fact, phylogenetic constraints have limited rubisco kinetic adaptation to a greater extent than the combined action of catalytic tradeoffs. These phylogenetic constraints are caused by multiple evolutionary factors act to limit rubisco molecular sequence evolution (Bouvier et al, 2022) and combined, help to explain why the enzyme is poorly efficient under present-day conditions but better adapted to the former high CO 2 , low O 2 atmosphere in which it evolved. These conclusions agree with recent studies which have also emphasized that kinetic trait correlations are generally too weak to support the rubisco tradeoff model (Cummins et al, 2019(Cummins et al, , 2018Flamholz et al, 2019;Galmés et al, 2014) as well as experimental results from rubisco engineering efforts which have been able to successfully produce enzyme variants that deviate from proposed catalytic trade-offs (Wilson et al, 2018;Zhou and Whitney, 2019).…”