Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803

Abstract

Cyanobacteria are an important group of photoautotrophic organisms that can synthesize valuable bio-products by harnessing solar energy. They are endowed with high photosynthetic efficiencies and diverse metabolic capabilities that confer the ability to convert solar energy into a variety of biofuels and their precursors. However, less well studied are the similarities and differences in metabolism of different species of cyanobacteria as they pertain to their suitability as microbial production chassis. Here we assemble, update and compare genome-scale models (iCyt773 and iSyn731) for two phylogenetically related cyanobacterial species, namely Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. All reactions are elementally and charge balanced and localized into four different intracellular compartments (i.e., periplasm, cytosol, carboxysome and thylakoid lumen) and biomass descriptions are derived based on experimental measurements. Newly added reactions absent in earlier models (266 and 322, respectively) span most metabolic pathways with an emphasis on lipid biosynthesis. All thermodynamically infeasible loops are identified and eliminated from both models. Comparisons of model predictions against gene essentiality data reveal a specificity of 0.94 (94/100) and a sensitivity of 1 (19/19) for the Synechocystis iSyn731 model. The diurnal rhythm of Cyanothece 51142 metabolism is modeled by constructing separate (light/dark) biomass equations and introducing regulatory restrictions over light and dark phases. Specific metabolic pathway differences between the two cyanobacteria alluding to different bio-production potentials are reflected in both models.

Figure 1. Comparison of model derived and experimentally measured flux ranges for Synechocystis 6803 under the maximum biomass condition.

Basis is 100 millimole of CO₂ plus H₂CO₃.

Figure 2. Comparison of gene essentiality/viability data with predictions by a number of Synechocystis 6803 models.

(A) Tabulated growth (i.e., G) or non-growth (i.e., NG) predictions and experimental data. The first number denotes the number of GG, GNG, NGG and NGNG combinations whereas the second number signifies the number of experimentally observed lethal (or viable) mutants, and (B) Definition and comparison of specificity and sensitivity of all three models. Note that GG denotes both in silico and in vivo growth, NGG represents no growth in silico but in vivo growth. NGNG implies no growth for either in silico or in vivo, whereas GNG marks growth in silico but no growth in vivo.

Figure 3. Venn diagram depicting (common and unique) reactions and metabolites between (A) iJN678 and iSyn731, (B) iCce806 and iCyt773, and (C) iSyn731 and iCyt773 models.

Figure 4. Schematics that illustrate the thermodynamically infeasible cycles and subsequent resolution strategies.

(A) Cycles present in iJN678 , and (B) Cycles present in iCce805 . Blue colored lines represent the original reaction directionality whereas green ones denote modified directionality to eliminate cycle.

Figure 5. List of added reactions across pathways.

(A) iSyn731 compared to iJN678 , and (B) iCyt773 compared to iCce806 .

Figure 6. Examples of pathways that differ between the two cyanobacteria.

(A) Nonfermentative alcohol production pathway highlighting the present and absent enzymes in Cyanothece 51142 and Synechocystis 6803, and (B) Alkane biosynthesis pathways in Cyanothece 51142 and Synechocystis 6803.