Proteins are composed of the elements C, H, O, N and S.  Amino acid sequence changes can affect organisms’ overall demand for these elements, especially in highly-expressed proteins, such as the enzyme ribulose bisphosphate carboxylase (Rubisco) in plants.  Environmental nutrient limitation can leave signatures in protein sequences by favoring amino acids with low proportions of the limiting element. Particularly, enzymes dealing with nutrient uptake are predicted to contain low proportions of the nutrient they assimilate.  Hence the sequence of Rubisco, which fixes atmospheric C, might be expected to have evolved to be proportionately C-poor in plants for which C is relatively limiting.

Although plant growth is mainly N limited, C limitation can occur.  In arid environments, plants with Crassulacean Acid Metabolism (CAM) avoid desiccation by accumulating CO₂ at night and closing their stomata in the day.  Daytime CO₂ stores become extremely depleted, limiting efficiency and potentially selecting for C conservation in Rubisco.  By contrast, C4 plants use light-driven pumps to concentrate CO₂ spatially around Rubisco; the enzyme therefore never suffers CO₂ shortage.

We analyzed the C, O, N and S composition of GenBank Rubisco large-subunit sequences from C3 (n=13,364), C4 (n=112), and CAM (n=215) plant species, corrected for phylogeny using taxonomic relationships.  We predicted that, owing to C limitation, Rubisco in CAM plants would be C-poor relative to C3 and C4 plants.  We also predicted that, in CAM plants, being C rather than N limited, N conservation in Rubisco sequences would be relaxed relative to other plants.  Other constituent elements should not change relative to each other. 

Results/Conclusions

Consistent with predictions, Rubisco from CAM plants was proportionately much lower in C than from C3 plants, and showed lower variance.  CAM Rubisco was also higher in N than C3 Rubisco, and similar in S composition, but lower in O.  C4 Rubisco sequences were similar in C, N and S to those of C3 plants, but higher in O.

Although a functional explanation cannot be excluded without manipulative studies, one interpretation of these findings is that CAM plants are under selective pressure to conserve C in the highly expressed Rubisco sequence because their growth is limited by CO₂ storage capacity rather than by N availability, and that, freed from N limitation, N conservation in CAM Rubisco is concomitantly relaxed. If so, this is a rare comparative demonstration of large-scale proteomic consequences of shifts in environmental nutrient limitation.