Genome-Scale Fluxome of Synechococcus elongatus UTEX 2973 Using Transient ¹³C-Labeling Data

Abstract

Synechococcus elongatus UTEX 2973 (Synechococcus 2973) has the shortest reported doubling time (2.1 h) among cyanobacteria, making it a promising platform for the solar-based production of biochemicals. In this meta-analysis, its intracellular flux distribution was recomputed using genome-scale isotopic nonstationary 13 C-metabolic flux analysis given the labeling dynamics of 13 metabolites reported in an earlier study. To achieve this, a genome-scale mapping model, namely imSyu593, was constructed using the imSyn617 mapping model for Synechocystis sp. PCC 6803 (Synechocystis 6803) as the starting point encompassing 593 reactions. The flux elucidation revealed nearly complete conversion (greater than 96%) of the assimilated carbon into biomass in Synechococcus 2973. In contrast, Synechocystis 6803 achieves complete conversion of only 86% of the assimilated carbon. This high biomass yield was enabled by the reincorporation of the fixed carbons lost in anabolic and photorespiratory pathways in conjunction with flux rerouting through a nondecarboxylating reaction such as phosphoketolase. This reincorporation of lost CO 2 sustains a higher flux through the photorespiratory C2 cycle that fully meets the glycine and serine demands for growth. In accordance with the high carbon efficiency drive, acetyl-coenzyme A was entirely produced using the carbon-efficient phosphoketolase pathway. Comparison of the Synechococcus 2973 flux map with that of Synechocystis 6803 revealed differences in the use of Calvin cycle and photorespiratory pathway reactions. The two species used different reactions for the synthesis of metabolites such as fructose-6-phosphate, glycine, sedoheptulose-7-phosphate, and Ser. These findings allude to a highly carbon-efficient metabolism alongside the fast carbon uptake rate in Synechococcus 2973, which explains its faster growth rate.

Pooled CRISPRi screening of the cyanobacterium Synechocystis sp PCC 6803 for enhanced industrial phenotypes

“…This suggests that one route to pyruvate cannot fully substitute for the loss of the other, though interpretation of pyk2 fitness is complicated by its position in an operon (see Discussion). Within the Calvin cycle, two energetically equivalent routes for synthesis of fructose-6-phosphate have been considered: through class-I fructose-bisphosphate aldolase (fda, slr0943) or through transaldolase (talB, slr1793) 19 . Neither of these genes had a low fitness score, though the class-II FBP/ SBP aldolase gene (cbbA, sll0018), which is needed to synthesize sedoheptulose bisphosphate for both proposed routes, did have a low fitness score.…”

Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle

“…Since the term photorespiration is ill-suited to describe the recycling of 2PG in light-independent autotrophs, we suggest using the more general term “Rubisco-related 2-phosphoglycolate salvage” or for short, “phosphoglycolate salvage.” A similar term was used before in a few publications when referring to photorespiration ( 15 – 17 ). Importantly, “salvage” can refer to reassimilation of 2PG to central metabolism, as by the C 2 cycle and the glycerate pathway, or to the complete oxidation of 2PG, as in the oxalate decarboxylation pathway, in which case the term refers to the recycling of reducing power and CO 2 , which can reenter the Calvin cycle.…”

Challenges of cultivated meat production and applications of genome‐scale metabolic modeling

“…A recent review examines the current status and broad applications of GSMs 38 . In addition, the use of stable isotope labels (i.e., 13 C‐metabolic flux analysis [MFA], 13 C‐MFA) has extensively been used in conjunction with GSMs to ascertain internal metabolic fluxes in both microbial 52,53 and eukaryotic 54 systems. These require not only a metabolic model but also atom mapping models that describe the origin and destination of carbons from reactants to products, 55 as indicated in Figure 2b.…”