< Back to Article

Redox poise in R. rubrum phototrophic growth drives large-scale changes in macromolecular pathways

Fig 2

Overview of cyclic photophosphorylation by the branched-cyclic Q cycle, hydrogen uptake, and primary and secondary biosynthetic pathways of Rhodospirillum rubrum included in the thermo-kinetic model.

Red dashed arrows indicate the flow of single electrons in the Q cycle unless otherwise noted, and each cytochrome C (Cyt_C) carries each, so two (2) Cyt−C proteins are required. For hydrogen uptake, note the specific redox carrier that interacts with the HupSLM [Ni-Fe] hydrogenase is not known and thus indicated by X/H₂X for a general thermodynamically acceptable redox carrier, e.g., NAD(P)+/NAD(P)H. Both the oxidative and reductive versions of the TCA cycle were tested in the modeling. The reductive TCA cycle was used in the final model. The main pathways for CO₂ uptake or release are highlighted in orange blocks. Metabolites (alphabetical order): 2PG - 2-phospho-glycerate, 3PG - 3-phospho-glycerate (2 indicates the formation of 2 molecules from RuBP), Ac-CoA - acetyl-CoA, KG - 2-keto-glutarate, BPG - 1,3-bisphospho-glycerate, Cit - citrate, CCA - citryl-CoA (intermediate of Citrate Synthase), CoA-SH - Coenzyme A, DHAP - dihydroxyacetone phosphate, E4P - erythrose-4-phosphate, F6P - fructose-6-phosphate, Fum - fumarate, G3P - glyceraldehyde-3-phosphate, G6P - glucose-6-phosphate, H4THF – Tetrahydrofolate, Hcy – homocysteine, Isc - isocitrate, LPS - lipopolysaccharide, Mal - malate, MCA - malyl-CoA, MmCA - methylmalyl-CoA, Oxa - oxaloacetate, PCA - propanoyl-CoA, PEP - phosphoenol-pyruvate, PHB - polyhydroxybutyrate, Pyr - pyruvate, R-CH3 - methylated methyl acceptor (R), Q/QH₂ - oxidized and - reduced quinone, R5P - ribose-5-phosphate, Ru5P - ribulose-5-phosphate, RuBP - ribulose-1,5-bisphosphate, SAM – S-adenosyl-methionine, SAH – S-adenosyl-homocysteine, S7P - sedoheptulose-7-phosphate, SBP - sedoheptulose-1,7-bisphosphate, SCA - succinyl-CoA, Suc - succinate, Xu5P - xylulose-5-phosphate, - a redox carrier. All amino acids are indicated by standard 3-letter code. Enzymes (alphabetical order): ACL - acetate:CoA ligase (AMP-forming), ACON – aconitase, CLY – ATP-independent citrate lyase, CS - Citrate Synthase (with CCA intermediate) Cyt_bc1-ISP - complex of cytchrome b (heme b560 and b566 containing) cytochrome c1 (heme c containing) and Rieske iron sulfur protein (ISP, yellow), Cyt_C - bacterial cytochrome C2 (heme c containing), Eno – enolase, F₀F₁ - ATP synthasae, FBPA – fructose-1,6-bisphosphate aldolase, FBPase – fructose-1,6-bisphosphotase, FRD – fumarate reductase, FUM – fumarase, GAPDH – glyceraldehyde-3-phosphate dehydrogenase, GPI – glucose-6-phosphate isomerase, HupSLM - Uptake hydrogenase complex of small, large, and medium subunits, IDH – isocitrate dehydrogenase, KGOR – 2-keto-glutarate:ferredoxin oxidoreductase (-KG synthase), MDH – malate dehydrogenase, NAD-ME – NAD-dependent malic enzyme, ODC – oxaloacetate decarboxylase, PEP-CK – phosphoenol-pyruvate carboxykinase, PFK – phosphofructokinase, PFOR – pyruvate-ferredoxin oxidoreductase (pyruvate synthase), PGK – 3-phosphoglycerate kinase, PGM – 3-phosphoglycerate mutase, PK – pyruvate kinase, PRK – phosphoribulokinase, RC(P870) - Type II photosynthetic reaction center with characteristic P870 pigment for photo-oxidation of , RPE – ribulose-5-phosphate epimerase, RPI – ribose-5-phosphate isomerase, RubisCO – ribulose-1,5-bisphosphate oxygenase/carboxylase, SBPase – sedoheptulose-1,7-bisphosphate phosphatase, SCS – succinyl-CoA synthetase, TKT – transketolase, TPI – triose-phosphate isomerase.

doi: https://doi.org/10.1371/journal.pcbi.1013015.g002