Rubisco Adaptation Is More Limited by Phylogenetic Constraint Than by Catalytic Trade-off

Abstract

Rubisco assimilates CO2 to form the sugars that fuel life on earth. Correlations between rubisco kinetic traits across species have led to the proposition that rubisco adaptation is highly constrained by catalytic trade-offs. However, these analyses did not consider the phylogenetic context of the enzymes that were analyzed. Thus, it is possible that the correlations observed were an artefact of the presence of phylogenetic signal in rubisco kinetics and the phylogenetic relationship between the species that were sampled. Here, we conducted a phylogenetically resolved analysis of rubisco kinetics and show that there is a significant phylogenetic signal in rubisco kinetic traits. We re-evaluated the extent of catalytic trade-offs accounting for this phylogenetic signal and found that all were attenuated. Following phylogenetic correction, the largest catalytic trade-offs were observed between the Michaelis constant for CO2 and carboxylase turnover (∼21-37%), and between the Michaelis constants for CO2 and O2 (∼9-19%), respectively. All other catalytic trade-offs were substantially attenuated such that they were marginal (<9%) or non-significant. This phylogenetically resolved analysis of rubisco kinetic evolution also identified kinetic changes that occur concomitant with the evolution of C4 photosynthesis. Finally, we show that phylogenetic constraints have played a larger role than catalytic trade-offs in limiting the evolution of rubisco kinetics. Thus, although there is strong evidence for some catalytic trade-offs, rubisco adaptation has been more limited by phylogenetic constraint than by the combined action of all catalytic trade-offs.

Keywords: C4 photosynthesis; catalytic constraint; evolution; phylogenetic constraint; rubisco.

Fig. 1.

The evolution of rubisco kinetic traits in angiosperms. Phylogenetic tree of angiosperms showing the kinetic trait values in the rubiscos used in this data set and the inferred ancestral kinetic traits for internal branches on the tree. Scale bars for color schemes are presented next to each tree. Species names have been abbreviated for legibility and are provided in full in supplementary file 1, table S4, Supplementary Material online. S_C/O: specificity. k_catC: carboxylase turnover per site. K_C: the Michaelis constant for CO₂. K_C^air the inferred Michaelis constant for CO₂ in 20.95% O₂ air_.K_O: the Michaelis constant for O₂.

Fig. 2.

The distributions of values for rubisco kinetic traits in angiosperms. Species are grouped by their photosynthetic type (rows). S_C/O: specificity. k_catC: carboxylase turnover per site. K_C: the Michaelis constant for CO₂. K_C^air the inferred Michaelis constant for CO₂ in 20.95% O₂ air_.K_O: the Michaelis constant for O₂. K_RuBP: the Michaelis constant for ribulose 1,5-bisphosphate. Plants have been classified as those which perform C₃ photosynthesis (C₃; n = 107), C₄ photosynthesis (C₄; n = 21), C₃–C₄ intermediates (C₃–C₄; n = 6), C₄-like (C₄-like; n = 3). The X axis for all plots is on a log scale, where respective units are shown in column labels. The raw data set used can be found in supplementary file 2, Supplementary Material online.

Fig. 3.

The correlations between rubisco kinetic traits in angiosperms. (A) Heatmap depicting the variation in kinetic traits across the species used in this study (± SD away from each respective kinetic trait mean). Species labels on the tree are color coded by photosynthetic type (C₃: black, C₃–C₄ intermediates: red, C₄-like: blue, and C₄: green), and have been abbreviated for legibility (for full names refer to supplementary file 1, table S4, Supplementary Material online). (B) The relationships between all pairwise combinations of log transformed rubisco kinetic traits. (C) Pairwise correlation coefficients (percent variance explained) and associated P-values between rubisco kinetic traits assessed using non-phylogenetic least squares regression models or phylogenetic least squares regression models. Phylogenetic and non-phylogenetic least squares regressions were fit to both the complete set of angiosperms in the data set and the subset which perform C₃ photosynthesis. Significance values are represented as α levels, where; α = 0.001 if P < 0.001, α = 0.01 if 0.001 < P < 0.01, α = 0.05 if 0.01 < P < 0.05, and α = ns if P > 0.05.

Fig. 4.

The constraints on rubisco kinetic adaptation in angiosperms. (A) The variation (%) in rubisco kinetic traits across angiosperms that can be explained by phylogenetic constraint and each catalytic trade-off. (B) As in (A) but for C₃ angiosperms only. (C) Boxplot of all variation explained in each kinetic trait by kinetic trait correlations in comparison to variation explained by phylogeny in angiosperms. The phylogenetic constraints on the carboxylase-related traits Phy_CX (includes Phy_Sc/o, Phy_Kcatc, and Phy_Kc) and phylogenetic constraints on the oxygenase-related trait Phy_ox (includes Phy_Ko only) are presented separately. (D) As in (C) but for C₃ angiosperms only.

Fig. 5.

Kinetic and phylogenetic constraints on rubisco adaptation across all photosynthetic organisms. (A) Pairwise correlation coefficients (percent variance explained) and associated P-values between different rubisco kinetic traits assessed using non-phylogenetic least squares regression models or phylogenetic least squares regression models. Significance values are represented as α levels, where α  =  0.001 if P < 0.001, α  =  0.01 if 0.001 < P < 0.01, α  =  0.05 if 0.01 < p < 0.05, and α = ns if P > 0.05. (B) The variation (%) in rubisco kinetic traits across all photosynthetic organisms that can be explained by phylogenetic constraint and each catalytic trade-off. (C) Boxplot of all variation explained in each kinetic trait by kinetic trait correlations in comparison to variation explained by phylogeny in all photosynthetic organisms. The phylogenetic constraints on the carboxylase-related traits Phy_CX (includes Phy_Sc/o, Phy_Kcatc, and Phy_Kc) and phylogenetic constraints on the oxygenase-related trait Phy_ox (includes Phy_Ko only) are presented separately.