Genome-Scale Reconstruction and Analysis of the Metabolic Network in the Hyperthermophilic Archaeon Sulfolobus Solfataricus

<div><p>We describe the reconstruction of a genome-scale metabolic model of the crenarchaeon <em>Sulfolobus solfataricus</em>, a hyperthermoacidophilic microorganism. It grows in terrestrial volcanic hot springs with growth occurring at pH 2–4 (optimum 3.5) and a temperature of 75–80°C (optimum 80°C). The genome of <em>Sulfolobus solfataricus P2</em> contains 2,992,245 bp on a single circular chromosome and encodes 2,977 proteins and a number of RNAs. The network comprises 718 metabolic and 58 transport/exchange reactions and 705 unique metabolites, based on the annotated genome and available biochemical data. Using the model in conjunction with constraint-based methods, we simulated the metabolic fluxes induced by different environmental and genetic conditions. The predictions were compared to experimental measurements and phenotypes of <em>S. solfataricus</em>. Furthermore, the performance of the network for 35 different carbon sources known for <em>S. solfataricus</em> from the literature was simulated. Comparing the growth on different carbon sources revealed that glycerol is the carbon source with the highest biomass flux per imported carbon atom (75% higher than glucose). Experimental data was also used to fit the model to phenotypic observations. In addition to the commonly known heterotrophic growth of <em>S. solfataricus</em>, the crenarchaeon is also able to grow autotrophically using the hydroxypropionate-hydroxybutyrate cycle for bicarbonate fixation. We integrated this pathway into our model and compared bicarbonate fixation with growth on glucose as sole carbon source. Finally, we tested the robustness of the metabolism with respect to gene deletions using the method of Minimization of Metabolic Adjustment (MOMA), which predicted that 18% of all possible single gene deletions would be lethal for the organism.</p> </div

Central carbon metabolism in <i>S. solfataricus</i> with flux distribution for growth on HCO₃⁻.

<p>Solid arrows show the used pathways and their directions. Dashed arrows show available but not used pathways. Arrow size represents predicted flux though the pathways. Enzymes in this pathway: (1) glucose 1-dehydrogenase, (2) gluconolactonase, (3) gluconate dehydratase (4) 2-dehydro-3-deoxygluconokinase, (5) 2-dehydro-3-deoxy-phosphogluconate aldolase, (6) glyceraldehyde-3-phosphate dehydrogenase, (7) phosphoglycerate mutase, (8) phosphopyruvate hydratase, (9) pyruvate kinase, (10) pyruvate synthase, (11) citrate (Si)-synthase, (12) aconitate hydratase, (13) isocitrate dehydrogenase, (14) 2-oxoglutarate synthase, (15) succinate-CoA ligase, (16) succinate dehydrogenase, (17) fumarate hydratase, (18) malate dehydrogenase, (19) glucose 1-dehydrogenase, (20) galactonate dehydratase, (21) 2-keto-3-deoxygluconate aldolase, (22) aldehyde dehydrogenase, (23) glycerate kinase, (24) malate dehydrogenase, (25) phosphoenolpyruvate carboxykinase (GTP), (26) phosphoenolpyruvate carboxylase, ((27) pyruvate carboxylase, (28) triose-phosphate isomerase, (29) fructose-bisphosphate aldolase, (30) fructose-bisphosphatase, (31) glucose-6-phosphate isomerase, (32) beta-phosphoglucomutase, (33) glucose-1-phosphate adenylyltransferase, (34) starch synthase, (35) glucan 1,4-alpha-glucosidase, (36) 6-phospho-3-hexuloisomerase, (37) 3-hexulose-6-phosphate synthase, (38) ribose-5-phosphate isomerase, (39) ribose-phosphate diphosphokinase, (40) transketolase, (41) transketolase, (42) sulfite reductase, (43) phosphoadenylyl-sulfate reductase, (44) sulfate adenylyltransferase, (45) adenylyl-sulfate kinase, (46) 3′(2′),5′-bisphosphate nucleotidase, (47) phosphoglycerate kinase, (48) glyceraldehyde-3-phosphate dehydrogenase.</p

Central carbon metabolism in <i>S. solfataricus</i> with flux distribution for growth on phenol.

<p>Solid arrows show the used pathways and their directions. Dashed arrows show available but not used pathways. Arrow size represents predicted flux though the pathways. Enzymes in this pathway: (1) glucose 1-dehydrogenase, (2) gluconolactonase, (3) gluconate dehydratase (4) 2-dehydro-3-deoxygluconokinase, (5) 2-dehydro-3-deoxy-phosphogluconate aldolase, (6) glyceraldehyde-3-phosphate dehydrogenase, (7) phosphoglycerate mutase, (8) phosphopyruvate hydratase, (9) pyruvate kinase, (10) pyruvate synthase, (11) citrate (Si)-synthase, (12) aconitate hydratase, (13) isocitrate dehydrogenase, (14) 2-oxoglutarate synthase, (15) succinate-CoA ligase, (16) succinate dehydrogenase, (17) fumarate hydratase, (18) malate dehydrogenase, (19) glucose 1-dehydrogenase, (20) galactonate dehydratase, (21) 2-keto-3-deoxygluconate aldolase, (22) aldehyde dehydrogenase, (23) glycerate kinase, (24) malate dehydrogenase, (25) phosphoenolpyruvate carboxykinase (GTP), (26) phosphoenolpyruvate carboxylase, ((27) pyruvate carboxylase, (28) triose-phosphate isomerase, (29) fructose-bisphosphate aldolase, (30) fructose-bisphosphatase, (31) glucose-6-phosphate isomerase, (32) beta-phosphoglucomutase, (33) glucose-1-phosphate adenylyltransferase, (34) starch synthase, (35) glucan 1,4-alpha-glucosidase, (36) 6-phospho-3-hexuloisomerase, (37) 3-hexulose-6-phosphate synthase, (38) ribose-5-phosphate isomerase, (39) ribose-phosphate diphosphokinase, (40) transketolase, (41) transketolase, (42) sulfite reductase, (43) phosphoadenylyl-sulfate reductase, (44) sulfate adenylyltransferase, (45) adenylyl-sulfate kinase, (46) 3′(2′),5′-bisphosphate nucleotidase, (47) phosphoglycerate kinase, (48) glyceraldehyde-3-phosphate dehydrogenase, (49) phenol 2-monooxygenase, (50) catechol 2,3-dioxygenase, (51) 2-hydroxymuconate-semialdehyde hydrolase, (52) 2-oxopent-4-enoate hydratase, (53) 4-hydroxy-2-ketovalerate aldolase, (54) aldehyde dehydrogenase, (55) acetate-CoA ligase.</p

Hydroxypropionate-hydroxybutyrate cycle and tricarboxylic acid cycle in <i>S. solfataricus</i> with flux distribution for growth on HCO₃⁻.

<p>Solid arrows show the used pathways and their directions. Dashed arrows show available but not used pathways. Arrow size represents predicted flux though the pathways. Enzymes in the hydroxypropionate-hydroxybutyrate cycle are: (1) acetyl-CoA C-acetyltransferase, (2) acetyl-CoA carboxylase, (3) malonyl-CoA reductase (NADPH), (4) malonic semialdehyde reductase (NADPH), (5) 3-hydroxypropionate-CoA ligase, (6) 3-hydroxypropionyl-CoA dehydratase, (7) acryloyl-CoA reductase (NADPH), (8) propionyl-CoA carboxylase, (9) methylmalonyl-CoA epimerase, (10) methylmalonyl-CoA mutase, (11) succinyl-CoA reductase, (12) succinic semialdehyde reductase (NADPH), (13) 4-hydroxybutyrate-CoA ligase, (14) 4-hydroxybutyryl-CoA dehydratase, (15) enoyl-CoA hydratase, (16) (S)-3-hydroxybutyryl-CoA dehydrogenase (NAD⁺).</p

Diagram of the influence of non-growth-associated maintenance (NGAM) energy on the biomass flux and the respiration in <i>S. solfataricus</i>.

<p>Diagram of the influence of non-growth-associated maintenance (NGAM) energy on the biomass flux and the respiration in <i>S. solfataricus</i>.</p

Scatter plot of the flux distributions during growth on glucose and the carbon fixation scenario.

<p>Red dots show significant differences, and blue dots show not significant differences between both scenarios. Blue labels describe not significant differences. The numbers indicate the number of involved reactions.</p

Comparison of the properties of the metabolic reconstructions of <i>S. solfataricus</i>, <i>M. barkeri</i>, <i>C. salexigens</i>, <i>M. tuberculosis</i>, and <i>E. coli</i>.

<p>Comparison of the properties of the metabolic reconstructions of <i>S. solfataricus</i>, <i>M. barkeri</i>, <i>C. salexigens</i>, <i>M. tuberculosis</i>, and <i>E. coli</i>.</p

Scatter plot of the flux distributions during growth on glucose and the phenol-utilizing scenario.

<p>Red dots show significant differences and blue dots show not significant differences between both scenarios. Blue labels describe not significant differences. The numbers indicate the number of involved reactions.</p

Central carbon metabolism in <i>S. solfataricus</i> with flux distribution for growth on glucose.

<p>Solid arrows show the used pathways and their directions. Dashed arrows show available but not used pathways. Arrow size represents predicted flux though the pathways. Enzymes in this pathway: (1) glucose 1-dehydrogenase, (2) gluconolactonase, (3) gluconate dehydratase (4) 2-dehydro-3-deoxygluconokinase, (5) 2-dehydro-3-deoxy-phosphogluconate aldolase, (6) glyceraldehyde-3-phosphate dehydrogenase, (7) phosphoglycerate mutase, (8) phosphopyruvate hydratase, (9) pyruvate kinase, (10) pyruvate synthase, (11) citrate (Si)-synthase, (12) aconitate hydratase, (13) isocitrate dehydrogenase, (14) 2-oxoglutarate synthase, (15) succinate-CoA ligase, (16) succinate dehydrogenase, (17) fumarate hydratase, (18) malate dehydrogenase, (19) glucose 1-dehydrogenase, (20) galactonate dehydratase, (21) 2-keto-3-deoxygluconate aldolase, (22) aldehyde dehydrogenase, (23) glycerate kinase, (24) malate dehydrogenase, (25) phosphoenolpyruvate carboxykinase (GTP), (26) phosphoenolpyruvate carboxylase, (27) pyruvate carboxylase, (28) triose-phosphate isomerase, (29) fructose-bisphosphate aldolase, (30) fructose-bisphosphatase, (31) glucose-6-phosphate isomerase, (32) beta-phosphoglucomutase, (33) glucose-1-phosphate adenylyltransferase, (34) starch synthase, (35) glucan 1,4-alpha-glucosidase, (36) 6-phospho-3-hexuloisomerase, (37) 3-hexulose-6-phosphate synthase, (38) ribose-5-phosphate isomerase, (39) ribose-phosphate diphosphokinase, (40) transketolase, (41) transketolase, (42) sulfite reductase, (43) phosphoadenylyl-sulfate reductase, (44) sulfate adenylyltransferase, (45) adenylyl-sulfate kinase, (46) 3′(2′),5′-bisphosphate nucleotidase, (47) phosphoglycerate kinase, (48) glyceraldehyde-3-phosphate dehydrogenase.</p

Additional file 16: of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

Venn diagram of differentially expressed genes (CONV-R versus GF) that also contain DMPs within a 5-kb window. (PDF 377 kb