Abstract
RuBisCO is the most abundant enzyme on earth; it regulates the organic carbon cycle in the biosphere. Studying its structural evolution will help to develop new strategies of genetic improvement in order to increase food production and mitigate CO2 emissions. In the present work, we evaluate how the evolution of sequence and structure among isoforms I, II and III of RuBisCO defines their intrinsic flexibility and residue-residue interactions. To do this, we used a multilevel approach based on phylogenetic inferences, multiple sequence alignment, normal mode analysis, and molecular dynamics. Our results show that the three isoforms exhibit greater fluctuation in the loop between αB and βC, and also present a positive correlation with loop 6, an important region for enzymatic activity because it regulates RuBisCO conformational states. Likewise, an increase in the flexibility of the loop structure between αB and βC, as well as Lys330 (form II) and Lys322 (form III) of loop 6, is important to increase photosynthetic efficiency. Thus, the cross-correlation dynamics analysis showed changes in the direction of movement of the secondary structures in the three isoforms. Finally, key amino acid residues related to the flexibility of the RuBisCO structure were indicated, providing important information for its enzymatic engineering.
Highlights
Principal component analysis (PCA) was carried out. 73% of the total variance of the atomic fluctuations was captured along the first principal component (PC), while the second and third dimensions were necessary to capture 83.2 and 88.2, respectively (Figure 1)
Our PCA showed a wide range of the conformational space of the RuBisCO crystal structures, allowing the identification of different isoforms
Phylogenetic analysis supports the idea that RuBisCO evolved from the same ancestral enzyme, conserving the residues involved in substrate binding and catalytic activity
Summary
RuBisCO (ribulose-1,5-bisphosphate carboxylase oxygenase) is the most abundant enzyme in nature and plays essential functions in the entry of carbon into the biosphere and in photorespiration processes [1]. It is found in most autotrophic organisms such as bacteria, archaea and eukarya (algae, higher plants) [2]. Isoform I is the predominant enzyme in nature and is found in cyanobacteria, green algae and in higher and lower plants It is a holoenzyme consisting of eight large (RbcL) and eight small (RbcS) subunits [5]. Isoform II has a distinct physiological role, and it is used primarily to allow the Calvin–Benson–Bassham pathway to balance the cell redox potential [7,8]
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