Browsing Pathways

This pathway demonstrate the biosynthesis of thiazole moiety in E.coli K-12 strain and Salmonella enterica serovar Typhimurium. L-Tyrosine is generated from tyrosine biosynthesis. With S-Adenosylmethionine and NADPH, L-Tyrosine can be catalyzed into four different small molecules: 4-methylcatechol, dehydroglycine, 5'-deoxyadenosine and L-methionine as well as NADP by dehydroglycine synthase (encoded by thiH gene). Meanwhile, 1-deoxyxylulose-5-phosphate synthase (encoded by dxs gene) catalyzes pyruvic acid and D-Glyceraldehyde 3-phosphate into 1-Deoxy-D-xylulose 5-phosphate. The final reaction of the pathway is facilitated by thiazole synthase (encoded by thiG and thiH), which require a thiocarboxy-[ThiS-Protein], 1-deoxy-D-xylulose 5-phosphate and 2-iminoacetate to form 2-((2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate for Thiamin Diphosphate Biosynthesis, as well as a ThiS sulfur-carrier protein and water.

Aminopropylcadaverine, a polyamine, is the final product of aminopropylcadaverine biosynthesis pathway. Polyamines are involved in protein synthesis, DNA and RNA related processes, as well as the facilitation of cell stress resistance and membrane integrity; therefore polyamines are essential for cell growth. In this pathway, L-lysine is produced by lysine biosynthesis, then lysine decarboxylase will convert L-lysine into cadaverine. In the final step, spermidine synthase will catalyze cadaverine and decarboxy-SAM to aminopropylcadaverine as well as 5'-Methylthioadenosine.

Uracil is a pyrimidine nucleobase found in RNA, and can be used as a source of nitrogen for E. coli. There are at least three pathways through which uracil is degraded. This one begins with uracil, which originates from purine degradation. The putative monooxygenase enzyme rutA catalyzes the breakdown of uracil into peroxyaminoacrylate, using FMNH2 as a cofactor. Peroxyaminoacrylate is then broken down into both carbamic acid and 3-aminoacrylate following the addition of a water molecule by the putative isochorismatase family protein rutB. Carbamic acid can then spontaneously, with the addition of a hydrogen ion, split into an ammonium ion and a molecule of carbon dioxide. 3-aminoacrylate, on the other hand, is catalyzed by the UPF0076 protein rutC to form 2-aminoacrylic acid. This compound enters into a reaction catalyzed by protein rutD, which adds a water molecule and hydrogen ion and forms malonic semialdehyde with ammonium being a byproduct. Finally, the putative NADH dehydrogenase/NAD(P)H nitroreductase rutE complex converts malonic semialdehyde into hydroxypropionic acid, which is then used to form other necessary chemicals. The ammonium ions produced will be the important source of nitrogen for the bacteria.

Diacetylchitobiose (also known as N,N'-diacetylchitobiose and chitobiose) is a sole source of carbon for E.coli. PTS system mannitol-specific EIICBA component facilitates the imports of diacetylchitobiose as well as the phosphorylation to diacetylchitobiose 6'-phosphate. Later on, diacetylchitobiose 6'-phosphate is hydrolyzed to N-monoacetylchitobiose 6'-phosphate, which also produce acetic acid. N-monoacetylchitobiose 6'-phosphate undergoes further hydrolyzation to form N-Acetyl-D-Glucosamine 6-Phosphate and glucosamine by monoacetylchitobiose-6-phosphate hydrolase.

The pathway starts with trans-cinnamate interacting with a hydrogen ion, an oxygen molecule, and a NADH through a cinnamate dioxygenase resulting in a NAD and a cis-3-(3-Carboxyethenyl)-3,5-cyclohexadiene-1,2-diol which then interact together through a 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase resulting in the release of a hydrogen ion, an NADH molecule and a 2,3 dihydroxy-trans-cinnamate. The second way by which the 2,3 dihydroxy-trans-cinnamate is acquired is through a 3-hydroxy-trans-cinnamate interacting with a hydrogen ion, a NADH and an oxygen molecule through a 3-(3-hydroxyphenyl)propionate 2-hydroxylase resulting in the release of a NAD molecule, a water molecule and a 2,3-dihydroxy-trans-cinnamate. The compound 2,3 dihydroxy-trans-cinnamate then interacts with an oxygen molecule through a 2,3-dihydroxyphenylpropionate 1,2-dioxygenase resulting in a hydrogen ion and a 2-hydroxy-6-oxonona-2,4,7-triene-1,9-dioate. The latter compound then interacts with a water molecule through a 2-hydroxy-6-oxononatrienedioate hydrolase resulting in a release of a hydrogen ion, a fumarate molecule and (2Z)-2-hydroxypenta-2,4-dienoate. The latter compound reacts spontaneously to isomerize into a 2-oxopent-4-enoate. This compound is then hydrated through a 2-oxopent-4-enoate hydratase resulting in a 4-hydroxy-2-oxopentanoate. This compound then interacts with a 4-hydroxy-2-ketovalerate aldolase resulting in the release of a pyruvate, and an acetaldehyde. The acetaldehyde then interacts with a coenzyme A and a NAD molecule through a acetaldehyde dehydrogenase resulting in a hydrogen ion, a NADH and an acetyl-coa which can be incorporated into the TCA cycle

The pathway can start in various spots. First step in this case starts with NADH interacting with a menaquinone oxidoreductase resulting in the release of a NADH and a hydrogen Ion, at the same time in the inner membrane a menaquinone interacts with 2 electrons and 2 hydrogen ions thus releasing a menaquinol. This allows for 4 hydrogen ions to be transferred from the cytosol to the periplasmic space. The menaquinol then interacts with a dimethyl sulfoxide reductase resulting in the release of 2 hydrogen ion and 2 electrons. At the same time dimethyl sulfoxide and 2 hydrogen ions interact with the enzyme resulting in the release of a dimethyl sulfide and a water molecule, this reaction happening in the periplasmic space. The second set of reactions starts with a hydrogen interacting with a menaquinone oxidoreductase resulting in the release of two electrons being released into the inner membrane which then react with with 2 hydrogen ion and a menaquinone to produce a menaquinol. This menaquinol then reacts with a trimethylamine N-oxide reductase following the same steps as mentioned before. The third set of reactions starts with with formate interacting with a formate dehydrogenase-O resulting in a release of carbon dioxide and a hydrogen ion, this releases 2 electrons that interact with a menaquinone and two hydrogen ions. This releases a menaquinol which then reacts with a trimethylamine N-oxide reductase following the same steps as mentioned before

PreQ0 or 7-cyano-7-carbaguanine is biosynthesized by degrading GTP. GTP first interacts with water through a GTP cyclohydrolase resulting in the release of a formate, a hydrogen ion and a 7,8-dihydroneopterin 3'-triphosphate. The latter compound then interacts with water through a 6-carboxy-5,6,7,8-tetrahydropterin synthase resulting in a acetaldehyde, triphosphate, 2 hydrogen ion and 6-carboxy-5,6,7,8-tetrahydropterin. The latter compound then reacts spontaneously with a hydrogen ion resulting in the release of a ammonium molecule and a 7-carboxy-7-deazaguanine. This compound then interacts with ATP and ammonium through 7-cyano-7-deazaguanine synthase resulting in the release of water, phosphate, ADP, hydrogen ion and a 7-cyano-7-carbaguanine. The degradation of 7-cyano-7-deazaguanine can lead to produce a preQ1 or a queuine by reacting with 3 hydrogen ions and 2 NADPH through a 7-cyano-7-deazaguanine reductase. PreQ1 then interacts with a guanine 34 in tRNA through a tRNA-guanine transglycosylase resulting in a release of a guanine and a 7-aminomethyl-7-deazaguanosine 34 in tRNA. This nucleic acid then interacts with SAM through a S-adenosylmethionine tRNA ribosyltransferase-isomerase resulting in a release of a hydrogen ion, L-methionine, adenine and an epoxyqueuosine

The pathway can start in various spots. First step in this case starts with NADH interacting with a menaquinone oxidoreductase resulting in the release of a NADH and a hydrogen Ion, at the same time in the inner membrane a menaquinone interacts with 2 electrons and 2 hydrogen ions thus releasing a menaquinol. This allows for 4 hydrogen ions to be transferred from the cytosol to the periplasmic space. The menaquinol then interacts with a trimethylamine N-oxide reductase resulting in the release of 2 hydrogen ion and 2 electrons. At the same time trimethylamine N-oxide and 3 hydrogen ions interact with the enzyme trimethylamine N-oxide reductase resulting in the release of a trimethylamine and a water molecule, this reaction happening in the periplasmic space. The second set of reactions starts with a hydrogen interacting with a menaquinone oxidoreductase resulting in the release of two electrons being released into the inner membrane which then react with with 2 hydrogen ion and a menaquinone to produce a menaquinol. This menaquinol then reacts with a trimethylamine N-oxide reductase following the same steps as mentioned before. The third set of reactions starts with with formate interacting with a formate dehydrogenase-O resulting in a release of carbon dioxide and a hydrogen ion, this releases 2 electrons that interact with a menaquinone and two hydrogen ions. This releases a menaquinol which then reacts with a trimethylamine N-oxide reductase following the same steps as mentioned before

This pathway demonstrates the biosynthesis of tetrahydromonapterin in E.coli. However, it is still unclear about biological role of tetrahydromonapterin. GTP cyclohydrolase 1 generates formic acid and 7,8-dihydroneopterin 3'-triphosphate with cofactor GTP and water. 7,8-dihydroneopterin 3'-triphosphate is converted to dihydromonapterin-triphosphate by d-erythro-7,8-dihydroneopterin triphosphate epimerase (folX). Later, dihydromonapterin-triphosphate is hydroxylated to dihydromethysticin, and eventually form tetrahydromonapterin via dihydromonapterin reductase (folM) with cofactor NADPH.

The process of oleic acid B-oxidation starts with a 2-trans,5-cis-tetradecadienoyl-CoA that can be either be processed by an enoyl-CoA hydratase by interacting with a water molecules resulting in a 3-hydroxy-5-cis-tetradecenoyl-CoA, which can be oxidized in the fatty acid beta-oxidation. On the other hand 2-trans,5-cis-tetradecadienoyl-CoA can become a 3-trans,5-cis-tetradecadienoyl-CoA through a isomerase. This results interact with a water molecule through a acyl-CoA thioesterase resulting in a hydrogen ion, a coenzyme A and a 3,5-tetradecadienoate