The chaperone mediated assembly of Rubisco and its SynBio potential

Abstract

Rubisco is the CO2-fixing enzyme in photosynthesis. As the rate limiting step in the carbon fixing reactions of photosynthesis, increasing the carboxylation properties of Rubisco presents a longstanding target for improving plant growth. The enzyme is found across photosynthetic life in a range of forms - these forms differ in structure and in the accessory proteins required for folding, holoenzyme assembly and metabolic repair. By and large the structural complementarity requirements of the accessory proteins with their cognate Rubiscos are species specific, but more generally eukaryotic Rubiscos are unable to fold in prokaryotic assembly systems, and occasionally vice versa. This specificity imposes limits on research opportunities; for instance tools, such as directed evolution systems, developed in the model prokaryotic expression system Escherichia coli, cannot be used on higher plant Rubiscos. The co-expression of Rubisco with its required accessory proteins is an approach to overcome limitations of expression incompatibilities, here we exploit that approach in both plant and E. coli systems. This thesis aimed to facilitate the expression of tobacco Rubisco in E. coli through the co-expression of its chloroplast protein assembly machinery. Among multiple approaches trialed, a golden gate based, modular and reliable system for plant Rubisco expression in E. coli was developed and was particularly valuable for future research applications. The modularity of the E. coli expression system allowed investigation of the degree to which this system mimicked the natural protein folding capabilities of tobacco chloroplasts. Chloroplast transformed tobacco lines expressing chimeric Rubisco containing the small subunit (S) from tobacco, and the large subunit (L) from a diverse selection of non-tobacco plants were found to show extensive divergence in their capability to assemble L8S8 holoenzyme complexes. Curiously this expression profile did not strictly link with L-subunit phylogeny or sequence similarity. Production of the same hybrid plant L8S8 Rubiscos in the E. coli expression system mimicked that of the tobacco lines however the E. coli exhibited dichotomous expression. That is, the hybrid Rubiscos were produced either in high abundance or not at all in E. coli - in contrast to the broad gradient of expression observed in tobacco chloroplasts. In both systems, the chimeric Rubiscos were found to possess different kinetic properties when compared to the relevant Rubisco large subunit's native enzyme. This provides more evidence that the small does influence Rubisco kinetics. Kinetics, however, were not the same between the expression systems, highlighting another difference between the chloroplast and E. coli expression. The underlying mechanisms behind this were unclear. The robust plant Rubisco E. coli expression system facilitated the purification of recombinant, epitope tag free homogenous Rubiscos, providing a unique opportunity to investigate the role of the small subunit in governing Rubisco interactions with is metabolic repair protein Rubisco activase. While no equivocal role for the S-subunit was evident in the L8S8-Rca interactions, the versatility of the recombinant expression system for the rapid study of plant Rubisco structure and function was demonstrated. The inability to express eukaryotic Rubiscos in prokaryotes is mirrored by the inability of most non-plant Rubiscos to be effectively expressed in plant chloroplasts, if at all. To address this expression bottle-neck the prokaryotic protein folding GroE chaperonin components (GroEL/ES) were transformed into the tobacco chloroplast genome. The selectable marker gene in the GroE expressing lines was excised via homologous recombination marker excision. This provides a new tobacco plastome transformation genotype chassis for synthetic biology applications seeking to express a broader range of non-cognate proteins in plants.