Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973

Abstract

The photosynthetic capabilities of cyanobacteria make them interesting candidates for industrial bioproduction. One obstacle to large-scale implementation of cyanobacteria is their limited growth rates as compared to industrial mainstays. Synechococcus UTEX 2973, a strain closely related to Synechococcus PCC 7942, was recently identified as having the fastest measured growth rate among cyanobacteria. To facilitate the development of 2973 as a model organism we developed in this study the genome-scale metabolic model iSyu683. Experimental data were used to define CO₂ uptake rates as well as the biomass compositions for each strain. The inclusion of constraints based on experimental measurements of CO₂ uptake resulted in a ratio of the growth rates of Synechococcus 2973 to Synechococcus 7942 of 2.03, which nearly recapitulates the in vivo growth rate ratio of 2.13. This identified the difference in carbon uptake rate as the main factor contributing to the divergent growth rates. Additionally four SNPs were identified as possible contributors to modified kinetic parameters of metabolic enzymes and candidates for further study. Comparisons against more established cyanobacterial strains identified a number of differences between the strains along with a correlation between the number of cytochrome c oxidase operons and heterotrophic or diazotrophic capabilities.

Figure 1. Categorization of in silico gene knockout predictions in Synechococcus 7942 as compared to in vivo data.

Figure 2. Mass fractions of the main constituents of biomass for the two Synechococcus strains.

(a) Mass fractions for Synechococcus 7942 (b) Mass fractions for Synechococcus 2973. Color-Category relationship: orange – glycogen, red – lipids, green – amino acids, purple – nucleic acids, blue – other.

Figure 3. Fraction of select pathways with non-overlapping flux ranges between the two Synechococcus strains.

Pathway annotations from iSyn731 and SEED were used. All flux ranges were standardized by the amount of carbon taken up. Grey represented the percentage of reactions with that pathway annotation whose flux ranges overlapped. Blue and green represent the percentage of reactions with non-overlapping ranges where Synechococcus 7942 and Synechococcus 2973 had higher flux respectively.