Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria \u3ci\u3eCyanothece\u3c/i\u3e sp. ATCC 51142 and \u3ci\u3eSynechocystis\u3c/i\u3e sp. PCC 6803

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 byconstructing 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

Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria <em>Cyanothece</em> sp. ATCC 51142 and <em>Synechocystis</em> sp. PCC 6803

<div><p>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 (<em>i</em>Cyt773 and <em>i</em>Syn731) for two phylogenetically related cyanobacterial species, namely <em>Cyanothece</em> sp. ATCC 51142 and <em>Synechocystis</em> 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 <em>Synechocystis i</em>Syn731 model. The diurnal rhythm of <em>Cyanothece</em> 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.</p> </div

Comparison of ¹³C MFA flux measurements [35] vs. model-predicted flux ranges.

<p>Comparison of ¹³C MFA flux measurements <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048285#pone.0048285-Young1" target="_blank">[35]</a> vs. model-predicted flux ranges.</p

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

<p>(A) Cycles present in <i>i</i>JN678 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048285#pone.0048285-Nogales1" target="_blank">[32]</a>, and (B) Cycles present in <i>i</i>Cce805 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048285#pone.0048285-Vu1" target="_blank">[25]</a>. Blue colored lines represent the original reaction directionality whereas green ones denote modified directionality to eliminate cycle.</p

List of added reactions across pathways.

<p>(A) <i>i</i>Syn731 compared to <i>i</i>JN678 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048285#pone.0048285-Nogales1" target="_blank">[32]</a>, and (B) <i>i</i>Cyt773 compared to <i>i</i>Cce806 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048285#pone.0048285-Vu1" target="_blank">[25]</a>.</p

Summary of connectivity restoration in <i>Synechocystis</i> 6803 <i>i</i>Syn731 and <i>Cyanothece</i> 51142 <i>i</i>Cyt773 models.

<p>Summary of connectivity restoration in <i>Synechocystis</i> 6803 <i>i</i>Syn731 and <i>Cyanothece</i> 51142 <i>i</i>Cyt773 models.</p

<i>Synechocystis</i> 6803 <i>i</i>Syn731 and <i>Cyanothece</i> 51142 <i>i</i>Cyt773 model statistics.

a<p>Others include proteins involve in complex relationships, e.g. multiple proteins act as protein complex which is one of the isozymes for any specific reaction.</p>b<p>Spontaneous reactions are those without any enzyme as well as gene association.</p>c<p>Metabolites represent total number of metabolites with considering their compartmental specificity.</p

Examples of pathways that differ between the two cyanobacteria.

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

Venn diagram depicting (common and unique) reactions and metabolites between (A) <i>i</i>JN678 [<b>32</b>] and <i>i</i>Syn731, (B) <i>i</i>Cce806 [<b>25</b>] and <i>i</i>Cyt773, and (C) <i>i</i>Syn731 and <i>i</i>Cyt773 models.

<p>Venn diagram depicting (common and unique) reactions and metabolites between (A) <i>i</i>JN678 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048285#pone.0048285-Nogales1" target="_blank">[<b>32</b>]</a> and <i>i</i>Syn731, (B) <i>i</i>Cce806 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048285#pone.0048285-Vu1" target="_blank">[<b>25</b>]</a> and <i>i</i>Cyt773, and (C) <i>i</i>Syn731 and <i>i</i>Cyt773 models.</p

Comparison of gene essentiality/viability data with predictions by a number of <i>Synechocystis</i> 6803 models.

<p>(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 <i>in silico</i> and <i>in vivo</i> growth, NGG represents no growth <i>in silico</i> but <i>in vivo</i> growth. NGNG implies no growth for either <i>in silico</i> or <i>in vivo</i>, whereas GNG marks growth <i>in silico</i> but no growth <i>in vivo</i>.</p