Dynamic Photosynthetic Labeling and Carbon-Positional Mass Spectrometry Monitor in Vivo RUBISCO Carbon Assimilation Rates.

RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (RUBISCO) is the most abundant enzyme and CO2 bio-sequestration system on Earth. Its in vivo activity is usually determined by 14CO2 incorporation into 3-phosphoglycerate (3PGA). However, the radiometric analysis of 3PGA does not distinguish carbon positions. Hence, RUBISCO activity that fixes carbon into the 1-C position of 3PGA and Calvin-Benson-Bassham (CBB) cycle activities that redistribute carbon into its 2-C and 3-C positions are not resolved. This study aims to develop technology that differentiates between these activities. In source fragmentation of gas chromatography-mass spectrometry (GC-MS) enables paired isotopologue distribution analyses of fragmented substructures and the complete metabolite structure. GC-MS measurements after dynamic photosynthetic 13CO2 labeling allowed quantification of the 13C fractional enrichment (E13C) and molar carbon assimilation rates (A13C) at carbon position 1-C of 3PGA by combining E13C from carbon positions 2,3-C2 and 1,2,3-C3 with quantification of 3PGA concentrations. We validated the procedure using two GC-time of flight-MS instruments, operated at nominal or high mass resolution, and tested the expected 3PGA positional labeling by in vivo glycolysis of positional labeled glucose isotopomers. Mutant analysis of the highly divergent GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASEs (GAPDH1 and 2) from Synechocystis sp. PCC 6803 revealed full inactivation of the CBB cycle with maintained RUBISCO activity in Delta gapdh2 and a CBB cycle modulating role of GAPDH1 under fluctuating CO2 supply. RUBISCO activity in the CBB-deficient Delta gapdh2 can re-assimilate CO2 released by catabolic pathways. We suggest that RUBISCO activity in Synechocystis can scavenge carbon lost through the pentose phosphate pathway or other cellular decarboxylation reactions. An integrative approach enables the analysis of RUBISCO-mediated carbon assimilation and reveals continued RUBISCO activity in cyanobacteria following inactivation of the Calvin-Benson-Bassham cycle.