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.

L-Carnitine can stimulate anaerobic growth of E.coli when exogenous electron acceptors (i.e. nitrate, etc.) are absent. During anaerobic growth, E.coli can reduce L-carnitine to γ-butyrobetaine by CoA-linked intermediates when carbon and nitrogen are present in the system. Therefore, L-carnitine may act as external electron acceptor for anaerobic growth as well as generation of an osmoprotectant for cell.

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 biosynthesis of thiamin begins with a PRPP being degraded by reacting with a water molecule and an L-glutamine through a amidophosphoribosyl transferase resulting in the release of an L-glutamate, a diphosphate and a 5-phospho-beta-d-ribosylamine(PRA). The latter compound, PRA, is further degrade through a phosphoribosylamine glycine ligase by reacting with a glycine and an ATP. This reaction results in the release of a hydrogen ion, an ADP, a phosphate and a N1-(5-phospho-beta-d-ribosyl)glycinamide(GAR). GAR can be metabolized by two different phosphoribosylglycinamide formyltransferase. GAR reacts with a N10-formyl tetrahydrofolate, in this case 10-formyl-tetrahydrofolate mono-L-glutamate, through a phosphoribosylglycinamide formyltransferase 1 resulting in the release of a hydroge ion, a tetrahydrofolate and a N2-formyl-N1-(5-phospho-Beta-D-ribosyl)glycinamide(FGAR). On the other hand, GAR can react with a formate and an ATP molecule through a phosphoribosylglycinamide formyltransferase 2 resulting in a release of a ADP, a phosphate, a hydrogen ion and a FGAR. The FGAR compound gets degraded by interacting with a water molecule, an L-glutamine and an ATP molecule thorugh a phosphoribosylformylglycinamide synthase resulting in the release of a L-glutamate, a phosphate, an ADP molecule, a hydrogen ion and a 2-(formamido)-N1-(5-phopho-Beta-D-ribosyl)acetamidine (FGAM). This compound is further degraded by reacting with an ATP molecule through a phosphoribosylformylglycinamide cyclo-ligase resulting in the release of a phosphate, an ADP, a hydrogen ion and a 5-amino-1-(5-phospho-beta-d-ribosyl)imidazole (AIR). The AIR molecule is degraded by reacting with a S-adenosyl-L-methionine through a HMP-P synthase resulting in the release of 3 hydrogen ions, a carbon monoxide, a formate molecule, L-methionine, 5'-deoxyadenosine and 4- amino-2-methyl-5-phophomethylpyrimidine (HMP-P). This resulting compound is phosphorylated thorugh a ATP driven phosphohydroxymethylpyrimidine kinase resulting in the release of an ADP and 4-amino-2-methyl-5-diphosphomethylpyrimidine (HMP-PP). The resulting compound interacts with a thiazole tautomer and 2 hydrogen ion through a Thiamine phosphate synthase resulting in the release of a pyrophosphate, a carbon dioxide molecule and Thiamin phosphate. This compound is phosphorylated through an ATP driven thiamin monophosphate kinase resulting in a release of an ADP and a thiamin diphosphate.

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.

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.

Spermidine is formed from decarboxy-SAM and putrescine by catalyzing spermidine synthase (also knowns as polyamine aminopropyltransferase). The source of putrescine is transported from outside of cell by putrescine/spermidine ABC transporter. Decarboxy-SAM comes from S-Adenosylmethionine with catalyzation of adenosylmethionine decarboxylase and cofactors: pyruvic acid and magnesium. The other product of the aminopropyltransferase reaction is S-methyl-5'-thioadenosine (MTA), which can be recycled back to L-methionine in many organisms, but not in E. coli. Inhibition of E. coli adenosylmethionine decarboxylase by spermidine appears to be the most significant regulator of polyamine biosynthesis, probably limiting it when the intracellular spermidine concentration becomes excessive. In E. coli most intracellular spermidine is bound to nucleic acids and phospholipids. (EcoCyc)

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.

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.

L-Carnitine can stimulate anaerobic growth of E.coli when exogenous electron acceptors (i.e. nitrate, etc.) are absent. During anaerobic growth, E.coli can reduce L-carnitine to γ-butyrobetaine by CoA-linked intermediates when carbon and nitrogen are present in the system. Therefore, L-carnitine may act as external electron acceptor for anaerobic growth as well as generation of an osmoprotectant for cell.