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.

Phosphatidylcholines (PC) are a class of phospholipids that incorporate a phosphocholine headgroup into a diacylglycerol backbone. They are the most abundant phospholipid in eukaryotic cell membranes and has both structural and signalling roles. In eukaryotes, there exist two phosphatidylcholine biosynthesis pathways: the Kennedy pathway and the methylation pathway. The Kennedy pathway begins with the direct phosphorylation of free choline into phosphocholine followed by conversion into CDP-choline and subsequently phosphatidylcholine. It is the major synthesis route in animals. The methylation pathway involves the 3 successive methylations of phosphoethanolamine to form phosphocholine which is then funnelled into the Kennedy pathway to make phosphatidylcholine. In plants, phosphatidylcholine biosynthesis is implemented using a mix between the two pathways. An alternative of the methylation pathway uses phosphatidylethanolamine as a starting compound, but no enzyme has been found in Arabidopsis to catalyze the first methylation to form phosphatidyl-N-methylethanolamine. Many enzymes involved in this pathway are localized to the cell membrane but are not drawn as such for clarity. Instead, they are indicated with a dark green colour and appear to be free floating in the cytosol. The first reaction of the Kennedy pathway involves the membrane-localized enzyme choline/ethanolamine kinase catalyzing the conversion of choline into phosphocholine. Second, choline-phosphate cytidylyltransferase catalyzes the conversion of phosphocholine to CDP-choline. Last, choline/ethanolaminephosphotransferase, localized to the cell membrane, catalyzes phosphatidylcholine biosynthesis from CDP-choline. It requires either magnesium or manganese ions as cofactors. Note that phosphatidylcholine can be converted to either phosphocholine by a non-specific phospholipase or converted to choline by phospholipase D. Phosphocholine can also be converted to choline via phosphoethanolamine/phosphocholine phosphatase. The methylation pathway begins with serine decarboxylase catalyzing the biosynthesis of ethanolamine from serine. It requires pyridoxal 5'-phosphate as a cofactor. Next, choline/ethanolamine kinase, localized to the cell membrane, catalyzes the conversion of ethanolamine to phosphoethanolamine. Phosphoethanolamine N-methyltransferase (PEAMT), located in the cytosol, then catalyzes three sequential N-methylation steps to convert phosphoethanolamine to phosphocholine. PEAMT uses S-adenosyl-L-methionine as a methyl donor. Phosphocholine then enters the Kennedy pathway. Alternatively, in a subpathway parallel to the Kennedy pathway, phosphoethanolamine can be converted into phosphatidylethanolamine. Phosphatidylethanolamine is also synthesized from phosphatidylserine in the endoplasmic reticulum by phosphatidylserine decarboxylase. Note that phosphatidylethanolamine can be converted to either phosphoethanolamine by a non-specific phospholipase or converted to ethanolamine by phospholipase D. The two methylated intermediates N-methylethanolamine phosphate and N-dimethylethanolamine phosphate can also undergo reactions parallel to the Kennedy pathway to form the methylated intermediates of phosphatidylethanolamine (otherwise catalyzed by phosphatidyl-N-methylethanolamine N-methyltransferase, localized to the endoplasmic reticulum membrane, to form phosphatidylcholine).

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.

Fatty acids constitute a large energy source for the body. The cellular membrane is also made up of fatty acids. During starvation times, fatty acids can provide energy to humans for numerous days. Fatty acid metabolism is also known as beta-oxidation. During metabolism, acetyl CoA is produced that can then enter the citric acid cycle. When ATP is needed, ATP may be generated by increasing fatty acid metabolism. Fatty acid metabolism is essentially the reverse reaction of fatty acid synthesis.

Ammonia can be rerouted from the urine and recycled into the body for use in nitrogen metabolism. Glutamate and glutamine play an important role in this process. There are many other processes that act to recycle ammonia. asparaginase recycles ammonia from asparagine. Glycine cleavage system generates ammonia from glycine. Histidine ammonia lyase forms ammonia from histidine. Serine dehydratase also produces ammonia by cleaving serine.

Glutathione (GSH) is an low-molecular-weight thiol and antioxidant in various species such as plants, mammals and microbes. Glutathione plays important roles in nutrient metabolism, gene expression, etc. and sufficient protein nutrition is important for maintenance of GSH homeostasis. Glutathione is synthesized from glutamate, cysteine, and glycine sequentially by gamma-glutamylcysteine synthetase and GSH synthetase. L-Glutamic acid and cysteine are synthesized to form gamma-glutamylcysteine by glutamate-cysteine ligase that is powered by ATP. Gamma-glutamylcysteine and glycine can be synthesized to form glutathione by enzyme glutathione synthetase that is powered by ATP, too. Glutathione exists oxidized (GSSG) states and in reduced (GSH) state. Oxidation of glutathione happens due to relatively high concentration of glutathione within cells.

Amylase enzymes secreted in saliva by the parotid gland and in the small intestine play an important role in initiating starch digestion. The products of starch digestion are but not limited to maltotriose, maltose, limit dextrin, and glucose. The action of enterocytes of the small intestine microvilli further break down limit dextrins and disaccharides into monosaccharides: glucose, galactose, and fructose. Once released from starch or once ingested, sucrose can be degraded into beta-D-fructose and alpha-D-glucose via lysosomal alpha-glucosidase or sucrose-isomaltase. Beta-D-fructose can be converted to beta-D-fructose-6-phosphate by glucokinase and then to alpha-D-glucose-6-phosphate by the action of glucose phosphate isomerase. Phosphoglucomutase 1 can then act on alpha-D-glucose-6-phosphate (G6P) to generate alpha-D-glucose-1-phosphate. Alpha-D-glucose-1-phosphate (G6P) has several possible fates. It can enter into gluconeogenesis, glycolysis or the nucleotide sugar metabolism pathway. UDP-glucose pyrophosphorylase 2 can convert alpha-D-glucose-1-phosphate into UDP-glucose, which can then be converted to UDP-xylose or UDP-glucuronate and, eventually to glucuronate. UDP-glucose can also serve as a precursor to the synthesis of glycogen via glycogen synthase. Glycogen is an analogue of amylopectin (“plant starch”) and acts as a secondary short-term energy storage for animal cells. It’s formed primarily in liver and muscle tissues, but is also formed at secondary sites such as the central nervous system and the stomach. In both cases it exists as free granules in the cytosol. Glycogen is a crucial element of the glucose cycle as another enzyme, glycogen phosphorylase, cleaves off glycogen from the nonreducing ends of a chain to producer glucose-1-phosphate monomers. From there, the glucose-1-phosphate monomers have three possible fates: (1) enter the glycolysis pathway as glucose-6—phosphate (G6P) to generate energy, (2) enter the pentose phosphate pathway to produce NADPH and pentose sugar, or (3) enter the gluconeogenesis pathway by being dephosphorylated into glucose in liver or kidney tissues. To initiate the process of glycogen chain-lengthening, glycogenin is required because glycogen synthase can only add to existing chains. This action is subsequently followed by the action of glycogen synthase which catalyzes the formation of polymers of UDP-glucose connected by (α1→4) glycosidic bonds to form a glycogen chain. Importantly, amylo (α1→4) to (α1→6) transglycosylase catalyzes glycogen branch formation via the transfer of 6-7 glucose residues from a nonreducing end with greater than 11 residues to the C-6 OH- group in the interior of a glycogen molecule.

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).

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.

Androstenedione is an endogenous weak androgen steroid hormone that is a precursor of testosterone and other androgens, as well as of estrogens like estrone . Its metabolism occurs primarily in the endoplasmic reticulum (membrane-associated enzymes are coloured dark green in the image). Conversion of androstenedione to testosterone requires the enzyme testosterone 17-beta-dehydrogenase 3. Conversion of androstenedione to estrone involves three successive reactions catalyzed by the enzyme aromatase (cytochrome P450 19A1). Androstenedione can also be converted into etiocholanolone glucuronide, androsterone glucuronide, and adrenosterone. The three-reaction subpathway to synthesize etiocholanolone glucuronide begins with the enzyme 3-oxo-5-beta-steroid 4-dehydrogenase catalyzing the conversion of androstenedione to etiocholanedione. This is followed by the conversion of etiocholanedione to etiocholanolone which is catalyzed by aldo-keto reductase family 1 member C4. Lastly, the large membrane-associated multimer UDP-glucuronosyltransferase 1-1 catalyzes the conversion of etiocholanolone to etiocholanolone glucuronide. The three-reaction subpathway to synthesize androsterone glucuronide begins with the conversion of androstenedione to androstanedione via 3-oxo-5-alpha-steroid 4-dehydrogenase 1. Anstrostanedione is then converted into androsterone via aldo-keto reductase family 1 member C4. The last reaction to form androsterone glucuronide is catalyzed by the large multimer UDP-glucuronosyltransferase 1-1. The two-reaction subpathway to synthesize adrenosterone begins in the mitochondrial inner membrane where androstenedione is first converted into 11beta-hydroxyandrost-4-ene-3,17-dione by the enzyme cytochrome P450 11B1. Following transport to the endoplasmic reticulum, 11beta-hydroxyandrost-4-ene-3,17-dione is converted into adrenosterone via corticosteroid 11-beta-dehydrogenase isozyme 1.