Browsing Pathways

Purine nucleotides are eventually degraded to ammonia and carbon dioxide. This pathway follows the degradation of AMP to a urate intermediate in the cytosol via xanthine conversion from hypoxanthine. First, AMP deaminase catalyzes the conversion of AMP is into IMP. Second, the predicted enzyme 5′-nucleotidase (coloured orange in the image) is theorized to convert IMP into inosine. Third, ribonucleoside hydrolase converts inosine into hypoxanthine. Fourth, xanthine dehydrogenase is an enzyme that requires [2Fe-2S] cluster, FAD, and Moco as cofactors for catalyzing two subsequent reaction in the AMP degradation pathway: the conversion of hypoxanthine into xanthine and the conversion of xanthine into urate.

CMP-3-deoxy-D-manno-octulosonate (CMP-Kdo) biosynthesis is a pathway that occurs in the cytosol by which D-ribulose 5-phosphate becomes CMP-3-deoxy-D-manno-octulosonate (CMP-Kdo). Kdo is a component in the plant cell wall, specifically of pectic polysaccharide rhamnogalacturonan II. First, arabinose-5-phosphate isomerase catalyzes the conversion of D-ribulose 5-phosphate to D-arabinose 5-phosphate. Second, D-arabinose 5-phosphate is spontaneously converted into D-arabinofuranose 5-phosphate. Third, 3-deoxy-8-phosphooctulonate synthase converts D-arabinofuranose 5-phosphate into 3-deoxy-D-manno-octulosonate 8-phosphate (KDO-8P). This enzme is a homotetramer. Fourth, the predicted enzyme 3-deoxy-manno-octulosonate-8-phosphatase (coloured orange in the image) is theorized to catalyze the conversion of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO-8P) into 3-deoxy-D-manno-2-octulosonate (Kdo). The last reaction is localized to the mitochondria outer membrane whereby 3-deoxy-manno-octulosonate cytidylyltransferase (coloured dark green in the image) catalyzes the conversion of 3-deoxy-D-manno-2-octulosonate (Kdo) into CMP-3-deoxy-D-manno-octulosonate (CMP-Kdo). This enzyme requires a magnesium ion as a cofactor.

The Leloir pathway is a metabolic pathway for the catabolism of D-galactose into D-glucopyranose 6-phosphate named after Luis Federico Leloir . Since galactose cannot be directly used for glycolysis, it needs to be converted into a different form. This pathway starts in the cytosol and finishes in the chloroplast. First, aldose 1-epimerase is a predicted enzyme (coloured orange in the image) that is theorized to catalyze the conversion of beta-D-galactose into alpha-D-galactose. This enzyme has not yet been elucidated for Arabidopsis thaliana. Second, galactokinase catalyzes the conversion of alpha-D-galactose into alpha-D-galactose 1-phosphate. Third, D-galactose-1-phosphate uridylyltransferase is a predicted enzyme theorized to catalyze the reaction whereby alpha-D-galactose 1-phosphate and UDP-glucose is converted into alpha-D-glucopyranose 1-phosphate and UDP-galactose. This enzyme has not yet been elucidated in Arabidopsis thaliana. UDP-glucose and UDP-galactose can be interconverted by the enzyme UDP-glucose 4-epimerase which requires NAD as a cofactor. Alpha-D-glucopyranose 1-phosphate must then be imported into the chloroplast, by a yet not discovered alpha-D-glucopyranose 1-phosphate transporter. Last, phosphoglucomutase uses magnesium ion as a cofactor to convert alpha-D-glucopyranose 1-phosphate into D-glucopyranose 6-phosphate.

In higher plants, the primary seed storage reserve is triacylglycerol rather than carbohydrates. Thus, triacylglycerol degradation is an important pathway from which plants obtain energy for growth. First, triacylglycerol lipase, an enzyme localized to the oil body (storage vacuole) membrane, catalyzes the conversion of a triglyceride into a 1,2-diglyceride. Second, the predicted enzyme diglyceride lipase (coloured orange in the image) is theorized to catalyze the conversion of a 1,2-diglyceride iinto a 2-acylglycerol. Third, a 2-acylglycerol is spontaneously converted into a 1-monoglyceride. Fourth, acylhydrolase catalyzes the conversion of a 1-monoglyceride into glycerol. Fifth, glycerol kinase catalyzes the conversion of glycerol into glycerol 3-phosphate. Sixth, glycerol-3-phosphate dehydrogenase (coloured dark green in the image), localized to the mitochondrial inner membrane, catalyzes the conversion of glycerol 3-phosphate into glycerone phosphate.

Gibberellins (GAs) are a large class of tetracyclic diterpenoid plant hormones that regulate numerous growth and developmental processes, such as seed germination, organ elongation, and flowering induction. All known gibberellins share an ent-gibberellane skeleton and follow the same synthesis pathway. Biosynthesis begins in the plasmids via the terpenoid pathway and finishes in the endoplasmic reticulum and cytosol where they undergo modification until a biologically-active form is reached (GA1, GA3, GA4, or GA7). Gibberellins are named in the order that they are discovered (GA1 through GAn). Gibberellin biosynthesis via non C-3, non C-13 hydroxylation occurs in the cytosol and converts the inactive GA12 to the active GA4, and inactive GA36 and GA13. The first two reactions are catalyzed by gibberellin 20-oxidase, requiring Fe2+ and L-ascorbate as cofactors. It first converts gibberellin A12 into gibberellin A15 and then into gibberellin A24. Gibberellin A24 has three different fates. The first route involves the conversion of gibberellin A24 into gibberellin A9 by gibberellin 20-oxidase and then the subsequent conversion of gibberellin A9 into the active gibberellin A4 by gibberellin 3-oxidase. It requires Fe2+ and L-ascorbate as cofactors. The second route involves the conversion of gibberellin A24 into gibberellin A36 by gibberellin 3-oxidase. The third route involves the conversion of gibberellin A24 into gibberellin A25 by gibberellin 20-oxidase and then the subsequent conversion of gibberellin A25 into gibberellin A13 by a not yet elucidated gibberellin oxidase (coloured orange in the image).

Naphthols, harmful phenolic foreign compounds encountered by plants in the soil, must be modified to lower their toxicity. A yet unelucidated phenol beta-glucosyltransferase (coloured orange in the image) in Arabidopsis thaliana glucosylates napthtols (e.g. 2-naphthol into 2-naphthol glucoside, 1-naphthol into 1-naphthol glucoside). Glucosylation may then be followed by malonylation catalyzed by phenolic glucoside malonyltransferase ( e.g. 4-methylumbelliferyl glucoside into 4-methylumbelliferone 6'-O-malonylglucoside, 2-naphthol glucoside into 2-naphthol 6'-O-malonylglucoside, and 1-naphthol glucoside into 1-naphthol 6'-O-malonylglucoside). Unlike the excreted glucosides, the malonylated compounds are retained within vacuoles.

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. Photosynthesis begins with photosystem II, located in the thylakoid membrane within chloroplasts, which captures light energy to transfer electrons from water to plastoquinone. This process generates oxygen as well as a proton gradient used to synthesize ATP. The D1/D2 (psbA/psbD) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors. Next, the cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI). Plastoquinol shuttles electrons from PSII to cytochrome b6-f complex. Plastocyanin shuttles electrons from cytochrome b6-f complex to PSI. Photosystem I is a plastocyanin-ferredoxin oxidoreductase which uses light energy to transfer an electron from the donor P700 chlorophyll pair to the electron acceptors A0, A1, FX, FA and FB in turn. The function of PSI is to produce the NADPH necessary for the reduction of CO2 in the Calvin-Benson cycle. Finally, the proton gradient allows ATPase to synthesize ATP from ADP. 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.

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.

Vitamin C (ascorbate) is a vitamin found in food and used as a dietary supplement. The vast majority of animals and plants are able to synthesize vitamin C, through a sequence of enzyme-driven steps, which convert monosaccharides to vitamin C. In plants, this is accomplished through the conversion of mannose or galactose to ascorbic acid starting in the cytosol and ending in the mitochondrial matrix . First, GDP-mannose 3,5-epimerase catalyzes the reversible epimerization of GDP-D-mannose into either GDP-L-gulose or GDP-L-galactose. It also can reversibly epimerize GDP-L-gulose into GDP-L-galactose and vice versa. It requires NAD as a cofactor. Second, GDP-L-galactose phosphorylase catalyzes the conversion of GDP-L-galactose into L-galactose 1-phosphate. Third, L-galactose 1-phosphate phosphatase catalyzes the conversion of L-galactose 1-phosphate into L-galactose. It requires magnesium ion as a cofactor. Fourth, L-galactose dehydrogenase catalyzes the conversion of L-galactose into L-galactono-1,4-lactone. L-galactono-1,4-lactone must then be imported into the mitochondrial matrix by a predicted innermitochondrial membrane transporter to complete ascorbate synthesis. L-galactono-1,4-lactone dehydrogenase, localized to the innermitochondrial membrane (coloured dark green in the image), catalyzes two reactions in ascorbate metabolism: the conversion of L-galactono-1,4-lactone into L-ascorbate and the subsequent conversion of L-ascorbate into L-dehydroascorbate. It requires FAD as a cofactor. Ascorbate can then be converted into monodehydroascorbate radical by the mitochondrial L-ascorbate peroxidase S (this plays a key role in hydrogen peroxide removal). Monodehydroascorbate reductase 5 then can convert monodehydroascorbate radical back into L-ascorbate.

Butanoate or butyrate is the traditional name for the conjugate base of butanoic acid (also known as butyric acid). Butanoate metabolism includes L-glutamate degradation into the signal molecule GABA followed by subsequent reactions to make further products. Glutamate decarboxylase is an enzyme in the cytosol that catalyzes the conversion of L-glutamate into 4-aminobutanoate (GABA). It requires pyridoxal 5'-phosphate as a cofactor. This is followed by GABA permease, belonging to the APC Family of transport proteins, transporting GABA from the cytosol into the mitochondria matrix. Next, gamma-aminobutyrate transaminase degrades gamma-amino butyric acid (GABA) into succinate semialdehyde and uses either pyruvate or glyoxylate as an amino-group acceptor. The pyruvate-dependent activity is reversible while the glyoxylate-dependent activity is irreversible. Afterwards, succinate-semialdehyde dehydrogenase oxidizes succinate semialdehyde into succinate. A predicted succinate semialdehyde transporter in the mitochondria inner membrane is theorized to export succinate semialdehyde from the mitochondrial matrix into the cytosol. There, glyoxylate/succinic semialdehyde reductase catalyzes the reversible conversion of succinate semialdehyde into 4-hydroxybutanoate. Butanoate metabolism in Arabidopsis thaliana also includes reactions involving acetyl-CoA and acetoacetyl-CoA. 3-hydroxybutyryl-CoA dehydrogenase is a predicted enzyme (coloured orange in the image) in the cytosol that is theorized to catalyze the reversible conversion of 3-hydroxybutanoyl-CoA into acetoacetyl-CoA. Acetyl-CoA acetyltransferase then catalyzes the reversible conversion of acetoacetyl-CoA into acetyl-CoA. Then, hydroxymethylglutaryl-CoA synthase condenses acetyl-CoA with acetoacetyl-CoA to form 3-hydroxy-3-methylglutaryl-CoA. This is followed by a predicted 3-hydroxy-3-methylglutaryl-CoA transporter localized to the mitochondria inner membrane that is theorized to import 3-hydroxy-3-methylglutaryl-CoA into the mitochondrial matrix from the cytosol. Once there, hydroxymethylglutaryl-CoA lyase catalyzes the synthesis of acetoacetate and acetyl-CoA from 3-hydroxy-3-methylglutaryl-CoA.