Pathways

Dihydrofolic acid, a product of the folate biosynthesis pathway, can be metabolized by multiple enzymes. Dihydrofolic acid can be reduced by a NADP-driven dihydrofolate reductase resulting in a NADPH, hydrogen ion and folic acid. Dihydrofolic acid can also be reduced by an NADPH-driven dihydrofolate reductase resulting in a NADP and a tetrahydrofolic acid. Folic acid can also produce a tetrahydrofolic acid through a NADPH-driven dihydrofolate reductase. Dihydrofolic acid also interacts with 5-thymidylic acid through a thymidylate synthase resulting in the release of dUMP and 5,10-methylene-THF Tetrahydrofolic acid can be converted into 5,10-methylene-THF through two different reversible reactions. Tetrahydrofolic acid interacts with a S-Aminomethyldihydrolipoylprotein through a aminomethyltransferase resulting in the release of ammonia, a dihydrolipoylprotein and 5,10-Methylene-THF Tetrahydrofolic acid interacts with L-serine through a glycine hydroxymethyltransferase resulting in a glycine, water and 5,10-Methylene-THF. The compound 5,10-methylene-THF reacts with an NADPH dependent methylenetetrahydrofolate reductase [NAD(P)H] resulting in NADP and 5-Methyltetrahydrofolic acid. This compound interacts with homocysteine through a methionine synthase resulting in L-methionine and tetrahydrofolic acid. Tetrahydrofolic acid can be metabolized into 10-formyltetrahydrofolate through 4 different enzymes: 1.- Tetrahydrofolic acid interacts with FAICAR through a phosphoribosylaminoimidazolecarboxamide formyltransferase resulting in a 1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide and a 10-formyltetrahydrofolate 2.-Tetrahydrofolic acid interacts with 5'-Phosphoribosyl-N-formylglycinamide through a phosphoribosylglycinamide formyltransferase 2 resulting in a Glycineamideribotide and a 10-formyltetrahydrofolate 3.-Tetrahydrofolic acid interacts with Formic acid through a formyltetrahydrofolate hydrolase resulting in water and a 10-formyltetrahydrofolate 4.-Tetrahydrofolic acid interacts with N-formylmethionyl-tRNA(fMet) through a 10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase resulting in a L-methionyl-tRNA(Met) and a 10-formyltetrahydrofolate 10-formyltetrahydrofolate can interact with a hydrogen ion through a bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase resulting in water and 5,10-methenyltetrahydrofolic acid. Tetrahydrofolic acid can be metabolized into 5,10-methenyltetrahydrofolic acid by reacting with a 5'-phosphoribosyl-a-N-formylglycineamidine through a phosphoribosylglycinamide formyltransferase 2 resulting in water, glycineamideribotide and 5,10-methenyltetrahydrofolic acid. The latter compound can either interact with water through an aminomethyltransferase resulting in a N5-Formyl-THF, or it can interact with a NADPH driven bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase resulting in a NADP and 5,10-Methylene THF.

The surA-pdxA-rsmA-apaGH operon in E. coli contains five genes that are involved in various functions in the cell. DNA-binding protein Fis can bind to the promoter of this operon, allowing RNAP to bind and transcribe the operon. It can also bind to a promoter upstream of pdxA, and this promoter allows for transcription of the pdxA-rsmA transcription unit. The first gene, surA, encodes a chaperone protein that is involved in the proper folding of outer membrane proteins, and is essential for the formation of the bacteria's pilus. The second gene, pdxA, encodes for 4-hydroxythreonine-4-phosphate dehydrogenase, an envyme involved in the biosynthesis of pyridoxal 5'-phosphate. The third gene, rsmA, encodes ribosomal RNA small subunit methyltransfeerase A, a protein that methylates 16S rRNA, and may be important in the formation of 30S subunits of rRNA. The fourth gene, apaG, produces a protein with currently unknown function. The final gene, apaH, produces diadenosine tetraphosphatase, which hydrolyzes diadenosine tetraphosphatase into two molecules of ADP.

The ilvIH operon in E. coli contains two genes that encode the two subunits of the acetolactate synthase isozyme 3 protein. This protein is used in the biosynthesis of L-isoleucine in the bacteria. The operon is activated by the binding of the leucine-responsive regulatory protein (Lrp) to either of two regions upstream of the promoter. Binding of Lrp to the first upstream region (between -260 and -190) appears to be required for operon transcription, while binding to the downstream region (between -150 and -40) enhances it without being required. The operon can also be negatively regulated by the binding of the DNA-binding protein H-NS, which binds to DNA, altering its structure and preventing RNA polymerase from binding and transcribing the operon. The operon is also negatively regulated by the presence of leucine in the cell, which binds to Lrp, changing its conformation and preventing it from binding to its target sites in the operon. This means that if leucine is present in the cell in high enough concentrations, the operon will be inactivated. The genes in the operon, ilvI and ilvH, encode the acetolactate synthase isozyme 3 large and small subunits respectively. Two large and two small subunits combine to form the final enzyme, which is responsible for the conversion of pyruvate in the cell to (2S)-2-acetolactate, which is then used in future steps to form L-isoleucine.

The arsRBC operon in E. coli contains three genes that are involved in the detoxification of arsenite, arsenate and antimonite in the cell. The operon can be repressed by the arsenical resistance operon repressor, encoded by one of the genes in the operon. It binds to the promoter region of the operon, preventing transcription. The first gene, arsR, encodes the arsenical resistance operon repressor, which inhibits the transcription of the operon. However, in the presence of arsenic, arsenate, antimony and bismuth, its repression of the operon is removed, and the genes can be properly transcribed. The second gene, arsB, encodes an arsenical pump membrane protein which likely forms the channel of an arsenite pump that confers arsenical resistance to the cell. The finalg gene in the operon, arsC, encodes arsenate reductase, an enzyme that reduces arsenate to arsenite, creating a molecule that the arsenical pump can move out of the cell.

The aroF-tyrA operon in E. coli contains two genes that encode proteins involved in chorismate biosynthesis and L-tyrosine biosynthesis respectively. The operon is activated by the redox-sensitive transcriptional activator SoxR, which binds to the promoter region of the operon and when the bacteria is experiencing oxidative stress, it can activate transcription of the operon. The operon can also be repressed by the binding of the transcriptional regulatory protein TyrR. When L-tyrosine levels in the cell are high enough, it can bind to the TyrR protein, forming an active regulatory protein. This can then bind to the promoter region at several different locations, inhibiting transcription of the operon. The first gene in the operon, aroF, encodes a Tyr-sensitive phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthase). This enzyme catalyzes the condensation reaction of D-erythrose 4-phosphate (E4P) and phosphoenolpyruvate (PEP) into 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP). This reaction is the first step in the chorismate biosynthesis pathway, an important compound for bacterial biochemical processes. The second gene, tyrA, encodes the T-protein, an enzyme that catalyzees the formation of prephenate from chorismate. This reaction is a part of the L-tyrosine biosynthesis pathway.

The BioBFCD operon in E. coli contains four genes involved in the biosynthesis of biotin, a molecule important for various metabolic functions in the cell. The operon can be inactivated by the ginding of bifunctional protein BirA when it interacts with the biotin carboxyl carrier protein of acetyl-CoA carboxylase (AccB). This complex forms when AccB is in high concentrations, due to high levels of biotin already in the cell. The first gene in the operon, bioB, encodes biotin synthase, and enzyme that catalyzes conversion of dethiobiotin into biotin. The second gene, bioF, encodes 8-amino-7-oxononanoate synthase. This protein is an enzyme that condenses pimeloyl-[ACP] and L-alanine to form 8-amino-7-oxononanoate. This is later used in biotin biosynthesis. The third gene, bioC, encodes malonyl-[ACP] methyltransferase, a protein that methylates malonyl-thioester to its ester form as a part of biotin biosynthesis. The final gene, bioD, encodes dethiobiotin synthetase. This enzyme forms dethiobiotin, the direct precursor to biotin, by adding a carbon dioxide molecule into 7,8-diaminononanoate, which ends up forming a ring structure. Dethiobiotin is then acted upon by biotin synthase, forming biotin.

The carAB operon in E. coli contains two genes which produce the alpha and beta, or small and large chains of the carbamoyl-phosphate synthase protein. This protein is involved in the L-arginine biosynthesis pathway, and because of this, it can be repressed by the arginine repressor protein. This repressor is preesent when arginine is, preventing the biosynthesis of excess arginine. The first gene in this operon, carA, encodes the alpha or small chain of carbamoyl-phosphate synthase. The second gene, carB, encodes the beta or large chain of the same protein. One of each subunit combines in a heterodimer, which then interact with three other heterodomers to form the final carbamoyl-phosphate synthase protein. This protein is used in the formation of carbamoyl phosphate from glutamine, hydrogen carbonate, ATP and water. This reaction is part of the L-arginine biosynthesis pathway.

The caiTABCDE operon in E. coli contains six genes that produce proteins involved in the anaerobic metabolism of carnitine. This operon can be activated by the aerobic respiration control protein ArcA, which binds to several places upstream of the promoter. This binding activates transcription in the proper conditions, such as the need for fermentative metabolism. The operon can also be repressed by the DNA-binding protein H-NS. This protein binds to and alters the structure of DNA, suppressing the genes until it is removed. Finally, the caiA gene mRNA can specifically be prevented from being translated by small regulatory RNA that binds to the transcript, while the other genes are translated normally. The first gene in the operon, caiT, encodes for the L-carnitine/gamma butyrobetaine antiporter protein, which is responsible for transporting methyl-L-carninte into the cell, while transporting gamma butyrobetaine out of it. The second gene, caiA, encodes crotonobetainyl-CoA reductase, a protein that catalyzes the conversion of crotonobetainyl-CoA into gamma-butyrobetainyl-CoA. This protein is thought to interact with L-carnitine CoA-transferase, the protein encoded by caiB, which transfers the CoA from gamma-butyrobetainyl-CoA to L-carnitine, forming L-carnityl-CoA and gamma-butyrobetaine. It can also transfer between crotonobetainyl-CoA and L-carnitine. The fourth gene in the operon, caiC, encodes a crotonobetaine/carnitine CoA ligase, which like caiB catalyzes the reversible transfer of CoA between carnitine, gamma-butyrobetaine and crotobetaine. The fifth gene, caiD, encodes carnitinyl-CoA dehydratase, which reversibly removes a water molecule from crotonobetainyl-CoA, forming carnitinyl-CoA. The final gene, caiE, encodes a putative transferase whose function is currently unknown. However, when the protein is overexpressed, it functions similarly to caiB and caiD, as a CoA ligase and dehydratase.

The dicB-ydfDE-insD7-intQ operon in E. coli contains five genes, the first of which is part of the inhibition of cell division in E. coli. The other genes may produce proteins of unknown function, and are prophage genes that are present in the E. coli population. This operon can be inactivated by the HTH-type transcriptional regulator DicA, allowing cell division to occur. The first gene in the operon, dicB, encodes the division inhibition protein DicB which prevents cell division from occurring. The second gene, ydfD, encodes an uncharacterized protein YdfD, which may be involved in viral infection of the cell. The third gene, ydfE, encodes a putative uncharacterized protein YdfE, which may be shortened by an insertion element between this gene and intQ. The fourth gene, insD7, which encodes the transpose InsD for insertion element IS2 on F plasmid, a protein involved in transposing the insertion sequence IS2. The final gene, intQ, encodes the putative defective protein IntQ, an integrase used to insert and remove the prophage from the E. coli genome. In this case, the protein may be non-functional due to the presence of the insertion element between the ydfE and intQ genes.

The clpPX operon in E. coli contains two genes that form an ATP-dependent protease that is used in the degradation of improperly folded proteins. It may also be a master protease that can degrade any protein if it contains the right factors for degradation. There are no currently known activators or repressors of this operon. The first gene, clpP, encodes an ATP-dependent Clp protease proteolytic subunit, which combines with identical protein subunits to form two heptameric rings which then assemble back to back to form a disc with a cavity in the middle. The second gene, clpX, encodes an ATP-dependent Clp protease ATP-binding subunit, which forms a hexameric ring that can bind to the ClpP subunits. This protein is responsible for translocation of proteins to the protease, as well as unfolding of the proteins so they can be degraded.