Predicting the Effects of Coevolution on Rubisco: A Study on Carbon Dioxide Fixation by Bryophytes

Bryophytes, among the first branching terrestrial plants, has the ability to alleviate the greenhouse effect by lowering atmospheric CO2 concentrations. In bryophytes, carbon fixation is facilitated by the enzyme Rubisco within the photosynthetic Calvin–Benson–Bassham cycle. Under conditions of low CO2 concentration relative to O2, the regulation of Rubisco activity can be achieved by incorporating alternative substrates that resemble RuBP, such as 2-CABP, to mitigate unproductive oxygenation reactions and enhance both photosynthetic rates and carbon fixation. This work examines the Rubisco sequences in three bryophyte taxa: liverworts, hornworts, and mosses, to identify coevolving groups implicated in the process of resistance to 2-CABP, which eventually influences carbon fixation by activating photorespiration. ClustalOmega was employed to produce a MSA methodology of filtered protein sequences utilising default settings. Furthermore, PhyML generated the phylogenetic tree using the obtained alignment. CoMap v1.5.2, utilising a compensation and grouping methodology, was utilised to identify coevolving residues. The whole structure of Rubisco proteins was not located in the PDB. The AlphaFold Protein Structure Database supplied the structure of the Rubisco protein. Furthermore, four distinct tools—I-TASSER, PyMOL V2.2.3, PSIPRED, and DSSP—forecasted the secondary structural state of residues. The pooled forecasts of a minimum of three instruments were considered. Coevolving residues are in binding, active, and secondary structures. With the DynaMut online service, point mutations' effects on protein dynamics and stability were examined in the Rubisco structure. One coevolving amino acid was a point mutation. The 2-CABP-Rubisco complex can significantly contribute to the reduction of greenhouse gases in the environment.Aspartic acid (acidic), Asparagine (non-charged polar), Histidine, and Tyrosine coevolve in bryophytes. Mutant hornworts have considerably fewer conserved residues than wild kinds, suggesting that mutation disrupts target protein function.