General Microbiology - Schlegel, H. 1987

Utilization of inorganic hydrogen donors: aerobic chemolithotrophic bacteria
CO2 fixation

Most organisms capable of growing under conditions where carbon dioxide serves as the sole carbon source fix it via the ribulose bisphosphate cycle (the Calvin-Bassham cycle). These organisms include aerobic chemolithoautotrophic Bacteria, almost all phototrophic bacteria, cyanobacteria, and green plants. The Calvin-Bassham cycle is definitely not involved in $ ext{CO}_2$ assimilation in methanogenic and acetogenic bacteria, although they are also chemolithoautotrophs.

The ribulose bisphosphate cycle is characterized by two Enzymes not found in other metabolic pathways: phosphoribulokinase and ribulose bisphosphate carboxylase. The latter enzyme is the most abundant protein on our planet in terms of sheer quantity. The ribulose bisphosphate cycle is a reductive process in which $ ext{CO}_2$ is reduced to the carbohydrate level. Three distinct phases can be distinguished within the cycle: 1) the carboxylation reaction, 2) reduction, and 3) the regeneration of molecules acting as $ ext{CO}_2$ acceptors.

Carboxylation reaction. Catalyzed by ribulose bisphosphate carboxylase, $ ext{CO}_2$ is added to ribulose-1,5-bisphosphate, yielding two molecules of 3-phosphoglyceric acid:

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This same enzyme can also catalyze another reaction. In the absence of $ ext{CO}_2$ and in the presence of $ ext{O}_2$, it exhibits oxygenase activity, oxidizing ribulose bisphosphate to phosphoglycolate and 3-phosphoglycerate. This reaction is involved in The formation of glycolic acid in autotrophic bacteria and green plants, and consequently, in Photorespiration.

Reduction reaction. The carboxylation reaction is followed by the reduction of the carboxyl group of 3-phosphoglycerate to an aldehyde group. This stage involves reactions already familiar from the fructose bisphosphate pathway (Section 7.2.1), namely, phosphorylation driven by 3-phosphoglycerate kinase at the expense of ATP, and reduction mediated by glyceraldehyde-3-phosphate dehydrogenase utilizing $ ext{NAD(P)H}_2$. In bacteria, this reaction is NAD-dependent, whereas in plants it depends on $ ext{NADP}^1$.

Fig. 11.2. Schematic of two possible pathways for pentose phosphate regeneration from triose phosphates and fructose-6-phosphate. Left: steps in the synthesis of nucleic acid pentoses (ribose, deoxyribose) operating via transaldolase. Right: steps in the regeneration of the $ ext{CO}_2$ acceptor during $ ext{CO}_2$ fixation (ribulose-1,5-bisphosphate), involving sedoheptulose-1,7-bisphosphate and aldolase, but omitting transaldolase. F-6-P = fructose-6-phosphate; GA-3-P = glyceraldehyde-3-phosphate; DHA-P = dihydroxyacetone phosphate; E-4-P = erythrose-4-phosphate; SG-7-P = sedoheptulose-7-phosphate; SG-bP = sedoheptulose-1,7-bisphosphate; Xu-5-P = xylulose-5-phosphate; R-5-P = ribose-5-phosphate. Enzymes (circled numbers): 1 - transaldolase; 2 - transketolase; 3 - fructose bisphosphate aldolase; 4 - fructose bisphosphatase.

The reduction of 3-phosphoglycerate represents the precise step in $ ext{CO}_2$ assimilation that requires an investment of energy and reducing power. Subsequent stages proceed at approximately the same energy level.

Regeneration of $ ext{CO}_2$ acceptors. Glyceraldehyde-3-phosphate exists in equilibrium with dihydroxyacetone phosphate (the triose phosphate isomerase reaction), and both triose phosphates are in equilibrium with fructose-1,6-bisphosphate (the aldolase reaction).

Fructose bisphosphate is dephosphorylated by fructose bisphosphatase to yield fructose-6-phosphate. Subsequently, one molecule of fructose-6-phosphate and three molecules of triose phosphate react to form three molecules of ribose-5-phosphate. Some of the enzymes catalyzing these conversions also participate in the oxidative pentose phosphate cycle. The first of these conversions is the transketolase reaction (Fig. 11.2, right). Transketolase catalyzes The transfer of a glycolyl group from a ketose monophosphate to an aldose phosphate. In the process, glycolaldehyde is temporarily bound to Thiamine diphosphate (thiamine pyrophosphate), which acts as a coenzyme, yielding an "active glycolaldehyde." The tetrose phosphate (erythrose-4-phosphate) generated during the transketolase reaction is converted via an aldolase reaction with dihydroxyacetone phosphate into sedoheptulose-1,7-bisphosphate. The latter undergoes C-1 dephosphorylation mediated by fructose bisphosphatase, producing sedoheptulose-7-phosphate. This sugar phosphate Hydrolysis is irreversible, providing a key point for Metabolic Regulation.

¹ In cyanobacteria, this reduction reaction also utilizes NADPH. Ed. note.

It has been definitively established for higher plants that during Photosynthesis, the regeneration of ribulose-5-phosphate proceeds via sedoheptulose-1,7-bisphosphate (Fig. 11.2, right); however, in the dark, pentose phosphate synthesis proceeds directly to sedoheptulose-7-phosphate via the transaldolase reaction (Fig. 11.2, left).

The glycolyl group of sedoheptulose-7-phosphate is transferred to glyceraldehyde-3-phosphate with the help of transketolase, leading to the formation of two pentose phosphates. These pentose phosphates (ribulose-5-phosphate and xylulose-5-phosphate) are in equilibrium with ribulose-5-phosphate. The final reaction of the ribulose bisphosphate cycle is the ATP-dependent phosphorylation of ribulose-5-phosphate by phosphoribulokinase to form ribulose-1,5-bisphosphate.

Stoichiometry of the ribulose bisphosphate cycle. The synthesis of 1 mole of hexose from 6 moles of $ ext{CO}_2$ requires six complete turns. The overall stoichiometry of $ ext{CO}_2$ fixation in the ribulose bisphosphate cycle can be represented by the following equation:

Although the cycle is depicted as closed, many of its intermediates serve as essential precursors for the synthesis of cellular components: 3-phosphoglycerate gives rise to Pyruvate and acetyl-CoA, erythrose-4-phosphate to aromatic Amino Acids, ribulose-5-phosphate is utilized for nucleotide synthesis, and hexose phosphates are used to build polymers. The regulation of several enzymes participating in the cycle presumably serves two purposes: on the one hand, excessive amounts of ATP should not be squandered on $ ext{CO}_2$ fixation (which carries a high energy cost); on the other hand, the cycle must not be interrupted—a fate that could befall it if its intermediates were excessively drained away (pp. 496–497).

Other pathways of autotrophic $ ext{CO}_2$ fixation. Although currently the most vital for the biosphere, $ ext{CO}_2$ fixation via the ribulose bisphosphate cycle is by no means the only reaction sequence leading to the synthesis of organic matter. Anaerobic autotrophic bacteria possess two alternative mechanisms for $ ext{CO}_2$ assimilation. Methanogenic, acetogenic, and sulfate-reducing (sulfidogenic) bacteria capable of using $ ext{H}_2$ or $ ext{CO}$ as an electron donor reduce $ ext{CO}_2$ via the anaerobic acetyl-CoA pathway to acetyl-CoA and pyruvate (Section 9.4). The latter then enters central biosynthetic pathways through well-known reactions.

Green sulfur bacteria (*Chlorobium limicola* f. *thiosulfatophilum*) fix $ ext{CO}_2$ exclusively via the Reactions of the reductive Tricarboxylic Acid Cycle, where $ ext{CO}_2$ fixation is driven by the reductive carboxylation of succinyl-CoA.

A comparison of all Three types of autotrophic $ ext{CO}_2$ fixation leads to the Conclusion that anaerobic processes are more energy-efficient than aerobic ones. The synthesis of 1 mole of triose phosphate from 3 moles of $ ext{CO}_2$ via the anaerobic acetyl-CoA pathway requires an expenditure of only 3 moles of ATP, compared to 5 moles of ATP in the reductive tricarboxylic acid cycle and 9 moles of ATP in the ribulose bisphosphate cycle. General $ ext{CO}_2$ fixation reactions. We have repeatedly noted that heterotrophic organisms also require carbon dioxide and incorporate it into their METABOLISM. The roles of pyruvate and phosphoenolpyruvate carboxylation in the functioning of The Tricarboxylic Acid Cycle have been highlighted. The metabolic intermediates into which $ ext{CO}_2$ can be incorporated are illustrated in Fig. 11.3.

Fig. 11.3. Incorporation of $ ext{CO}_2$ into various metabolic intermediates.

The aforementioned $ ext{CO}_2$ fixation reactions play diverse roles across different organisms. Some serve to activate metabolites or to replenish central biochemical pathways with intermediates. Ferredoxin-dependent reductive carboxylation reactions occur exclusively in certain anaerobic and phototrophic bacteria.