Revisiting Trade-offs between Rubisco Kinetic Parameters

Abstract

Rubisco is the primary carboxylase of the Calvin cycle, the most abundant enzyme in the biosphere, and one of the best-characterized enzymes. On the basis of correlations between Rubisco kinetic parameters, it is widely posited that constraints embedded in the catalytic mechanism enforce trade-offs between CO2 specificity, S C/O, and maximum carboxylation rate, k cat,C. However, the reasoning that established this view was based on data from ≈20 organisms. Here, we re-examine models of trade-offs in Rubisco catalysis using a data set from ≈300 organisms. Correlations between kinetic parameters are substantially attenuated in this larger data set, with the inverse relationship between k cat,C and S C/O being a key example. Nonetheless, measured kinetic parameters display extremely limited variation, consistent with a view of Rubisco as a highly constrained enzyme. More than 95% of k cat,C values are between 1 and 10 s–1, and no measured k cat,C exceeds 15 s–1. Similarly, S C/O varies by only 30% among Form I Rubiscos and <10% among C3 plant enzymes. Limited variation in S C/O forces a strong positive correlation between the catalytic efficiencies (k cat/K M) for carboxylation and oxygenation, consistent with a model of Rubisco catalysis in which increasing the rate of addition of CO2 to the enzyme–substrate complex requires an equal increase in the O2 addition rate. Altogether, these data suggest that Rubisco evolution is tightly constrained by the physicochemical limits of CO2/O2 discrimination.

Photorespiration in the context of Rubisco biochemistry, CO2 diffusion and metabolism

“…From an evolutionary perspective, S c/o is fairly constrained within C 3 plants ( c. 85–110 mol mol −1 at 25°C) (Hermida‐Carrera et al , ; Orr et al , ), but varies substantially when other organisms such as green and non‐green algae or photosynthetic bacteria are included in the comparison, due in part to their different forms of Rubisco ( c. 10 mol mol −1 in photosynthetic bacteria, up to c. 240 mol mol −1 in red algae) (Savir et al , ; Young et al , ; Flamholz et al , ). This variation in specificity is negatively correlated with a variation in , which has led to the conclusion that there is an unavoidable trade‐off between S c/o and , meaning that Rubisco is well optimized to its environmental conditions (Tcherkez et al , ; Savir et al , ).…”

“…This variation in specificity is negatively correlated with a variation in , which has led to the conclusion that there is an unavoidable trade‐off between S c/o and , meaning that Rubisco is well optimized to its environmental conditions (Tcherkez et al , ; Savir et al , ). However, more recent analyses based on data obtained from many more species weaken the apparent inverse relationship between S c/o and (Galmés et al , ; Flamholz et al , ), suggesting that photosynthetic organisms have some capacity to adjust V o relative to V c without compromising the catalytic rate too much.…”

Awakening a latent carbon fixation cycle inEscherichia coli

“…Indeed, the GED cycle itself was previously ignored as Gnd was considered to be an irreversible decarboxylating enzyme. As we have shown here, however, Gnd can catalyze the carboxylation reaction quite efficiently, with a kcat almost double that of a typical plant Rubisco 35 . This finding is similar to a recent study that found that citrate synthasewhich is usually thought to be irreversiblecan catalyze citrate cleavage, thus enabling carbon fixation via a unique variant of the reductive TCA cycle 50,51 .…”

“…We found Gnd to have a rather high kcat in the reductive carboxylation direction, approaching 6 s -1 (5.9 ± 0.2 s -1 with Ru5P as substrate, Table 1 and Supplementary Fig. S2), about twice as high as the kcat of most plant Rubisco variants 35 . The affinity of Gnd towards CO2 is high enough to enable saturation under elevated CO2 concentrations: KM = 0.9 ± 0.1 mM ( Table 1 and Supplementary Fig.…”

Photorespiration pathways in a chemolithoautotroph

“…In this study, we explore metabolic routes involved in photorespiration of Cupriavidus necator H16 (formerly known as Ralstonia eutropha or Alcaligenes eutrophus), the best-studied chemolithoautotrophic microorganism that fixes CO 2 fixation via the Calvin cycle (12)(13)(14). Unlike cyanobacteria, C. necator does not harbor a CO 2 concentrating mechanism (i.e., a carboxysome with appropriate inorganic carbon transporters), as evident from the relatively high CO 2 specificity of its Rubisco, which falls within the range reported for plants but is much higher than that found in cyanobacteria (15)(16)(17). Very little is known about photorespiration in C. necator.…”