Artificially evolved Synechococcus PCC6301 Rubisco variants exhibit improvements in folding and catalytic efficiency

Abstract

The photosynthetic CO2-fixing enzyme, Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase), is responsible for most of the world's biomass, but is a slow non-specific catalyst. We seek to identify and overcome the chemical and biological constraints that limit the evolutionary potential of Rubisco in Nature. Recently, the horizontal transfer of Calvin cycle genes (rbcL, rbcS and prkA) from cyanobacteria (Synechococcus PCC6301) to gamma-proteobacteria (Escherichia coli) was emulated in the laboratory. Three unique Rubisco variants containing single (M259T) and double (M259T/A8S, M259T/F342S) amino acid substitutions in the L (large) subunit were identified after three rounds of random mutagenesis and selection in E. coli. Here we show that the M259T mutation did not increase steady-state levels of rbcL mRNA or L protein. It instead improved the yield of properly folded L subunit in E. coli 4-9-fold by decreasing its natural propensity to misfold in vivo and/or by enhancing its interaction with the GroES-GroEL chaperonins. The addition of osmolites to the growth media enhanced productive folding of the M259T L subunit relative to the wild-type L subunit, while overexpression of the trigger factor and DnaK/DnaJ/GrpE chaperones impeded Rubisco assembly. The evolved enzymes showed improvement in their kinetic properties with the M259T variant showing a 12% increase in carboxylation turnover rate (k(c)cat), a 15% improvement in its K(M) for CO2 and no change in its K(M) for ribulose-1,5-bisphosphate or its CO2/O2 selectivity. The results of the present study show that the directed evolution of the Synechococcus Rubisco in E. coli can elicit improvements in folding and catalytic efficiency.

Engineering of chimeric eukaryotic/bacterial Rubisco large subunits in <i>Escherichia coli</i>

“…Of the E. coli chaperones, the GroEL-GroES chaperonin system is one of the most intensively studied molecular chaperone systems (Lin and Rye, 2006;RuizGonzález and Fares, 2013). The role of GroEL-GroES chaperonins in enabling Synechococcus Rubisco holoenzyme formation is well-documented (Goloubinoff et al, 1989;Greene et al, 2007;Saschenbrecker et al, 2007;Mueller-Cajar and Whitney, 2008). Overexpression of GroEL-GroES in E. coli increased the amount of catalytically competent cyanobacterial Rubisco (Goloubinoff et al, 1989).…”

Mechanisms of carbon fixation and engineering for increased carbon fixation in cyanobacteria

“…However, no changes either in RuBP affinity or CO 2 /O 2 selectivity were observed [74]. In the same strain, the individual replacement of phenylalanine 342 by valine (F342V), I174V, Q212L, M262T, F345L and F345I increased the affinity for RuBP [75].…”

Advancing Our Understanding and Capacity to Engineer Nature’s CO2-Sequestering Enzyme, Rubisco

“…, and S C/O ) have been selected (Greene et al, 2007;Zhu et al, 2010). In one case, catalytic improvements have been found to be transposable to Rubisco in tobacco (Nicotiana tabacum; Zhu et al, 2010), although how these improvements translate to changes in photosynthesis and plant growth remain unknown.…”