Pathways

Camellia nitidissima is common traditional ethnic medicine in Guangxi, which takes effect by clearing away heat and toxic materials and diuretic detumescence.

Camellia nitidissima is common traditional ethnic medicine in Guangxi, which takes effect by clearing away heat and toxic materials and diuretic detumescence.

Camalexin is a compound produced by Arabadopsis thaliana, used in plant defense. Its accumulation is induced by contact with parasites, and it inhibits the growth of those parasites. Synthesis of camalexin starts with L-tryptophan, which reacts using tryptophan N-monooxygenases 1 and 2 to form N-hydroxy-L-tryptophan. This then reacts using the same enzyme to form N,N-dihydroxy-L-tryptophan, which spontaneously forms (E)-indol-3-ylacetaldoxime. (E)-indol-3-ylacetaldoxime reversibly reacts with a indoleacetaldoxime dehydratase enzyme to form (Z)-indol-3-ylacetaldoxime, its isomer. The isomer then loses a water molecule via indoleacetaldoxime dehydratase again, forming 3-indoleacetonitrile. Another reaction with indoleacetaldoxime dehydratase forms 2-hydroxy-2-(1H-indol-3-yl0acetonitrile, which then reacts one final time with the indoleacetaldoxime dehydratase enzyme to lose a water molecule and form dehydro(indole-3-yl)acetonitrile. At this point, a glutatione molecule is added using glutatione S-transferase F6 to form (glutation-S-yl)(1H-indol-3-yl)acetonitrile. A water molecule is added by gamma-glutamyl peptidases 1 and 3, as well as glutathione hydrolase 3, forming L-glutamic acid as a side product, as well as (L-cysteinylglycin-S-yl)(1H-indol-3-yl)acetonitrile. An unknown enzyme then catalyzes a reaction that adds a water molecule and removes a glycine, forming 2-(cystein-S-yl)-2-(1H-indol-3-yl)-acetonitrile. Then, in a reaction using bifunctional dihydrocamalexate synthase/camalexin synthase, an oxygen molecule is added, a hydrogen ion, hydrogen cyanide molecule and water molecule are removed, and (R)-dihydrocamalexate is formed. Finally, the same enzyme catalyzes the formation of camalexin, the final product of this pathway.

Crassulacean Acid Metabolism (CAM) is a specialized photosynthetic pathway predominantly observed in plants, but certain cyanobacteria exhibit similar metabolic adaptations to optimize carbon fixation under fluctuating environmental conditions. CAM operates in two phases: the dark phase and the light phase, allowing organisms to conserve water and improve carbon efficiency. During the dark phase, CO₂ is taken up and fixed into organic acids, such as malate, which are stored in vacuole-like structures or cytoplasmic pools. This is facilitated by the enzyme phosphoenolpyruvate carboxylase (PEPC). In the light phase, the stored organic acids are decarboxylated to release CO₂, which is then refixed by the Calvin-Benson cycle in the presence of light-driven ATP and NADPH generation via photosynthesis. This temporal separation of CO₂ uptake and utilization allows CAM-adapted cyanobacteria to thrive in environments with limited water availability or high salinity, where daytime stomatal opening (or equivalent carbon uptake processes) would lead to excessive water loss. While CAM-like pathways in bacteria are less well understood compared to plants, they represent an important ecological adaptation for survival in extreme habitats.

The cbb operon is crucial for carbon dioxide fixation through the Calvin-Benson-Bassham (CBB) cycle. This operon is encoded in duplicate within the genome, consisting of several genes that work together to facilitate CO2 uptake and conversion into organic compounds. CbbL encodes for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the key enzyme in the CBB cycle that catalyzes CO2 fixation. CbbS encodes for the small subunit of RuBisCO, which pairs with the large subunit to form the functional enzyme. cbbX is believed to be involved in the regulation of the CBB cycle and plays a role in the assembly and stability of the RuBisCO complex. CbbR encodes the transcription regulator CbbR,which activates or represses the cbb operon in response to phosphoenolpyruvate (PEP) levels, by binding to specific sites near the cbb promoter. When PEP levels are high, CbbR represses cbb operon transcription and activates its transcription when PEP levels are low. The operon’s expression is additionally influenced by RegA which forms part of the RegA/RegB global transcription regulation system, which enhances the cbb operon’s promoter activity.

The Calvin cycle is the primary carbon dioxide fixation pathway found in all green plants, including Solanum lycopersicum. This important cycle of chemical reactions can be divided into three stages: fixation, reduction, and regeneration. In the fixation stage, D-ribulose-1, 5-bisphosphate (RuBP) is reduced into two molecules of 3-phospho-D-glycerate by the enzyme RubisCO (ribulose biphosphate carboxylase). In the reduction stage the two molecules of 3-phospho-D-glycerate are phosphorylated and then reductively dephosphorylated to D-glyceraldehyde 3-phosphate. Three iterations of this cycle result in 3 molecules of carbon dioxide fixed, thus forming 6 molecules of D-glyceraldehyde 3-phosphate. The final stage (regeneration) is a highly complex series of rearrangement reactions that result in the regeneration of RuBP, the key carbon dioxide acceptor.

Photosynthesis involves the transfer and harvesting of energy from sunlight and the fixation of carbon dioxide into carbohydrates. This process occurs in higher plants, including Arabidopsis thaliana. Oxygenic photosynthesis requires water, which acts as an electron donor molecule. The reactions which involve the trapping of sunlight are known as "light reactions", and result in the production of NADPH, adenosine triphosphate, and molecular oxygen. The "dark reactions" are known as the Calvin cycle, and involve the use of the products of the light reactions to fix carbon dioxide and produce carbohydrates. The light-independent Calvin-Benson cycle consist of nine reactions that take place in the chloroplast stroma. Beginning with the enzyme RuBisCO, D-ribulose-1,5-bisphosphate is converted into 3-phosphoglyceric acid. It requires magnesium ion as a cofactor. Next, chloroplastic glyceraldehyde 3-phosphate dehydrogenase catalyzes the conversion of glyceric acid 1,3-biphosphate into D-glyceraldehyde 3-phosphate. Then triose-phosphate isomerase catalyzes the conversion of D-glyceraldehyde 3-phosphate into dihydroxyacetone phosphate. Next, the enzyme fructose-bisphosphate aldolase catalyzes the conversion of dihydroxyacetone phosphate into fructose 1,6-bisphosphate. Then fructose-1,6-bisphosphatase catalyzes the conversion of fructose 1,6-bisphosphate into fructose-6-phosphate. It requires magnesium ion as a cofactor. Next, transketolase catalyzes the conversion of fructose-6-phosphate into xylulose 5-phosphate. It requires a divalent metal cation and thiamine diphosphate as cofactors. Then the enzyme ribulose-phosphate 3-epimerase is catalyzes the interconverson of xylulose 5-phosphate and D-ribulose 5-phosphate. Lastly, phosphoribulokinase catalyzes the conversion of D-ribulose 5-phosphate to regenerate D-ribulose-1,5-bisphosphate. An alternative pathway intersects the Calvin-Benson cycle providing another route to synthesize D-ribulose 5-phosphate and D-xylulose 5-phosphate, which both feed back into the main cycle, from dihydroxyacetone phosphate. This subpathway begins with the predicted enzyme sedoheptulose-1,7-bisphosphate aldolase theorized to catalyze the converson of glycerone phosphate and D-erythrose 4-phosphate into sedoheptulose-1,7-bisphosphate. Next, sedoheptulose-1,7-bisphosphatase catalyzes the conversion of sedoheptulose-1,7-bisphosphate into D-sedoheptulose 7-phosphate. Next, transketolase catalyzes the converson of D-sedoheptulose 7-phosphate into D-ribose 5-phosphate and D-xylulose 5-phosphate (which feeds back into the main cycle). Lastly, ribose-5-phosphate isomerase is the probable enzyme that catalyzes the interconverson of D-ribose 5-phosphate and D-ribulose 5-phosphate. D-ribulose 5-phosphate feeds back into the main cycle.

The Calvin-Benson cycle, also known as the reductive pentose phosphate cycle, is a central pathway for carbon fixation in bacteria, particularly in photoautotrophs and chemoautotrophs. This cycle enables bacteria to convert inorganic carbon dioxide (CO₂) into organic molecules, primarily glyceraldehyde-3-phosphate (G3P), which serves as a precursor for glucose and other essential cellular components. The cycle begins with the carboxylation of ribulose-1,5-bisphosphate (RuBP) by the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), producing two molecules of 3-phosphoglycerate (3-PGA). These molecules are then phosphorylated and reduced using ATP and NADPH, respectively, to generate G3P. Part of the G3P is used to regenerate RuBP through a series of reactions involving sugar phosphate intermediates, while the remainder can be directed toward biosynthesis pathways. The Calvin-Benson cycle is energetically demanding, requiring significant input of ATP and NADPH, often supplied by photosynthesis in phototrophic bacteria or oxidation of inorganic compounds in chemolithoautotrophs. This pathway is essential for autotrophic bacterial growth and plays a key role in global carbon cycling by converting atmospheric CO₂ into biomass, contributing to primary productivity in diverse ecosystems.