Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes
Fig 5
Central carbon metabolism and the pentose phosphate pathway represent a hotspot for Calvin cycle adaptations.
Color indicates the consensus rank of enzymes on a logarithmic scale. Points above the color scale bar represent the consensus rank of individual enzymes. Line thickness indicates whether the enzyme-encoding genes were enriched or depleted in CBB-positive genomes. Dashed lines indicate that the enzyme was not detected or that it was removed because it was Prk or Rubisco (see Materials and methods). Co-factors and small molecules such as CO2 have been omitted from most reactions. Arrows are used where enzymes that mainly catalyze specific directions rank differently. Special characters indicate pyrophosphate-dependent phosphofructo-1-kinase (*) and 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (†). The map is based on relevant subsystems of KEGG’s central carbon metabolism map (map01200) and related maps. The logarithm of consensus ranks for Enzyme Commission (EC) numbers were normalized to the range 0 to 1 and encoded as color. We also encoded significant EC enrichment or depletion in CBB-positive genomes as different colors. The EC-to-color tables were submitted to KEGG’s pathway mapping tool (https://www.genome.jp/kegg/tool/map_pathway2.html) to yield annotated maps that were then used as templates for drawing the figure. Note that the reaction SBP to S7P is represented by EC 3.1.3.11, rather than the eukaryotic SBPase EC 3.1.3.37, assuming that EC 3.1.3.11 represents bifunctional F/SBPase (Fbp). Also note that when multiple ECs mapped to the same reaction, only the best ranking EC color was used, unless special patterns of interest were present, e.g. 3PG to 2PG (†). Abbreviations: 2OG, 2-oxoglutarate; 2PG, 2-phosphoglycerate; 3HP, 3-hydroxypropionate; 3PG, 3-phosphoglycerate; AC, acetate; ACAH, acetaldehyde; AC-CoA, acetyl-CoA; ACP, acetyl phosphate; Ald, fructose-bisphosphate aldolase; BPG, 1,3-bisphosphoglycerate; CIT, citrate; CM-CoA, citramalyl-CoA; Cyt c, cytochrome c; DCHB, dicarboxylate-hydroxybutyrate; DD-Gn6P, 2-dehydro-3-deoxy-gluconate-6-phosphate; DHAP, dihydroxyacetone phosphate; DHFUM, dihydroxyfumarate; E4P, erythrose-4-phosphate; Eda, 2-dehydro-3-deoxy-phosphogluconate aldolase; Edd, 6-phosphogluconate dehydratase; EtOH, ethanol; F6P, fructose-6-phosphate; FBP, fructose-1,6-bisphosphate; Fbp, fructose 1,6-bisphosphate phosphatase; FUM, fumarate; G1P, glucose-1-phosphate; G6P, glucose-6-phosphate; G, glycerate; GAP, glyceraldehyde-3-phosphate; GLX, glyoxylate; Gly, glycine; GLYC, glycolate; Gnd, 6-phosphogluconate dehydrogenase; Gn6P, gluconate-6-phosphate; GnL6P, glucono-1,5-lactone 6-phosphate; HPHB, hydroxypropionate-hydroxybutyrate; HPYR, hydroxypyruvate; Hu6P, arabino-3-hexulose-6-phosphate; ICIT, isocitrate; LAC, lactate; MAL, malate; MAL-CoA, malyl-CoA; MM-CoA, methylmalonyl-CoA; m-TAR, meso-tartrate; OA, oxaloacetate; OGLYC, oxaloglycolate; PEP, phosphoenolpyruvate; PEPC, phosphoenolpyruvate carboxylase; PEPK, phosphoenolpyruvate carboxykinase; Pgl, 6-phosphogluconolactonase; PGLYC, phosphoglycolate; PRPP, 5-phosphoribosyl 1-pyrophosphate; PYR, pyruvate; R1P, ribose-1-phosphate; R5P, ribose-5-phosphate; Ru5P, ribulose-5-phosphate; RuBP, ribulose-1,5-bisphosphate; S7P, sedoheptulose-7-phosphate; SBP, sedoheptulose-1,7-bisphosphate; Ser, serine; SSA, succinate semialdehyde; SUCC, succinate; SUCC-CoA, succinyl-CoA; TAR, tartrate; TARS, tartronate semialdehyde; TCA, tri-carboxylic acid; Tkt, transketolase; Xfpk, phosphoketolase; Xu5P, xylulose-5-phosphate; Zwf, glucose-6-phosphate dehydrogenase.