Pathways

The gcvTHP operon in E. coli contains three genes that encode proteins involved in the glycine cleavage system. This system consists of four proteins, three of which are encoded in this operon, the other being the lipoamide dehydrogenase Lpd protein encoded by the lpd gene. Activation of the system occurs when large concentration of glycine are found in the cell, forming carbon dioxide, ammonia, a reduced pyridine nucleotide that cam be reused, and 5,10-methylenetetrahydrofolate. The operon can be inactivated when the glycine cleavge system transcriptional activator (GcvA) binds to one of four binding sites upstream of the promoter. If glycine levels in the cell are low, GcvA binds successfully, preventing transcription of the operon. However, if there is a high concentration of glycine in the cell, the cleavage system will need to be activated, and glycine can bind to GcvA, preventing its binding upstream of the promoter, and allowing transcription of the operon. The operon can also be inhibited by the transcriptional repressor PurR. Hypoxanthine can bind to PurR, activating it and allowing it to bind to the promoter region of the operon, blocking RNA polymerase and preventing the transcription of the operon. The first gene in the operon, gcvT, encodes an aminomethyltransferase also known as the glycine cleavage system T-protein. This protein transfers the amino group from the intermediate produced by the H-protein, as well as the formation of 5,10-methylenetetrahydrofolate. The second gene, gcvH, encodes the glycine cleavage system H-protein. This protein transfers the methylamine group of glycine between the P and T-proteins of the cleavage system. The final gene in the operon, gcvP, encodes a decarboxylating glycine dehydrogenase, also known as the glycine cleavage system P-protein. This protein binds to and cleaves the amino group of glycine, transferring it to the complex with the H-protein and releasing carbon dioxide.

The high frequency of lyzogenization operon is a polycistronic operon consisting of the genes: hfq, hflX, hflK and hflC. This operon is regulated by CRP-cAMP DNA-binding transcriptional dual regulator being binded to a crp binding site in the -96.5 bp from the promoter

The high frequency of lyzogenization (hfl) operon is a polycistronic operon consisting of the genes: hfq, hflX, hflK and hflC. hfq encodes the RNA-binding protein Hfq which aids in RNA stability , hflX encodes a GTPase involved in ribosomal assembly, hflK encodes a membrane-associated protein and hflC encodes a protease regulatory subunit which regulates protease activity, affecting lysogeny and other cellular processes. This operon is regulated by CRP-cAMP DNA-binding transcriptional dual regulator being binded to a crp binding site in the -96.5 bp from the promoter, thus activating the transcription of the hfl operon. This activation is dependent on the presence of cAMP, which is high when glucose levels are low. The pathway is repressed when cAMP levels decrease when glucose levels are high, thus preventing formation of CRP-cAMP complex. This in turn prevents RNA polymerase from binding efficiently to the promoter thus repressing transcription

The sodB operon in E. coli contains one gene, sodB, that produces the protein superoxide dismutase. Superoxide dismutase takes superoxide radicals found in the cell and adds a hydrogen molecule to them, forming hydrogen peroxide and oxygen, which are less harmful to the cell. This operon is regulated by small regulator RNA molecules, which bind to the complementary mRNA present in the promoter and gene region of the operon. This prevents translation from occurring, so the protein cannot be produced. The operon is also regulated by DNA-binding transcriptional repressors, which instead bind to the DNA and prevents transcription from occurring in various ways.

The leuLABCD operon in E. coli contains five genes that are involved in the synthesis of L-leucine. The HTH-type transcriptional regulator LeuO can activate transcription of the operon. However, if leucine tRNA is present in high amounts in the cell, indicating that levels of leucine are sufficient, it can promote early termination of the transcription after the leuL gene is transcribed. If this does not occur, transcription of the full operon will take place. The first gene in the operon, leuL, encodes the leu operon leader peptide, which may be involved in the attenuation of the transcript depending on the availability of leucine in the cell. The second gene, leuA, encodes for 2-isopropylmalate synthase, an enzyme that adds the acetyl group from acetyl-CoA to 3-methyl-2-oxobutanoate, forming 2-isopropylmalate in the first step of the biosynthesis pathway of leucine. The third gene, leuB, encodes 3-isopropylmalate dehydrogenase, an enzyme that catalyzes the oxidation of 3-isopropylmalate to 3-carboxyl-4-methyl-2-oxopentanoate in the third step of leucine biosynthesis. The fourth and fifth genes, leuC and leuD, encode for the 3-isopropylmalate dehydratase large and small subunits respectively, which combine to form the 3-isopropylmalte dehydratase protein. This is an enzyme that catalzes isomerization of 2-isopropylmalate into 3-isopropylmalate as the second step of leucine biosynthesis.

The lysine carboxylase operon consists of cadB and cadA genes. This operon's transcription activation can be controlled by GadE-RcsB DNA binding transcriptional activator, GadX (GadX DNA-binding transcriptional dual regulator) , CadC (CadC DNA-binding transcriptional activator) or Lrp (Lrp transcriptional dual regulator) in unspecified binding site locations. This operon's transcription inactivation is controlled by H-NS (H-NS DNA-binding transcriptional dual regulator) binding to -32, -129, -175, -260 or -317 bp of the promoter site. This operon's transcription inactivation can also be controlled by ArcA-Phosphorylated DNA-binding transcriptional dual regulator binding to -179 bp of the promoter site.

The lysine carboxylase operon consists of cadB and cadA genes. This operon's transcription activation can be controlled by GadE-RcsB DNA binding transcriptional activator, GadX (GadX DNA-binding transcriptional dual regulator) , CadC (CadC DNA-binding transcriptional activator) or Lrp (Lrp transcriptional dual regulator) in unspecified binding site locations. This operon's transcription inactivation is controlled by H-NS (H-NS DNA-binding transcriptional dual regulator) binding to -32, -129, -175, -260 or -317 bp of the promoter site. This operon's transcription inactivation can also be controlled by ArcA-Phosphorylated DNA-binding transcriptional dual regulator binding to -179 bp of the promoter site.

The lysine carboxylase operon consists of cadB and cadA genes. This operon's transcription activation can be controlled by GadE-RcsB DNA binding transcriptional activator, GadX (GadX DNA-binding transcriptional dual regulator) , CadC (CadC DNA-binding transcriptional activator) or Lrp (Lrp transcriptional dual regulator) in unspecified binding site locations. This operon's transcription inactivation is controlled by H-NS (H-NS DNA-binding transcriptional dual regulator) binding to -32, -129, -175, -260 or -317 bp of the promoter site. This operon's transcription inactivation can also be controlled by ArcA-Phosphorylated DNA-binding transcriptional dual regulator binding to -179 bp of the promoter site.

The lysine carboxylase operon consists of cadB and cadA genes. This operon's transcription activation can be controlled by GadE-RcsB DNA binding transcriptional activator, GadX (GadX DNA-binding transcriptional dual regulator) , CadC (CadC DNA-binding transcriptional activator) or Lrp (Lrp transcriptional dual regulator) in unspecified binding site locations. This operon's transcription inactivation is controlled by H-NS (H-NS DNA-binding transcriptional dual regulator) binding to -32, -129, -175, -260 or -317 bp of the promoter site. This operon's transcription inactivation can also be controlled by ArcA-Phosphorylated DNA-binding transcriptional dual regulator binding to -179 bp of the promoter site under anaerobic conditions

The lysine carboxylase operon consists of cadB and cadA genes. This operon's transcription activation can be controlled by GadE-RcsB DNA binding transcriptional activator, GadX (GadX DNA-binding transcriptional dual regulator) , CadC (CadC DNA-binding transcriptional activator) or Lrp (Lrp transcriptional dual regulator) in unspecified binding site locations. This operon's transcription inactivation is controlled by H-NS (H-NS DNA-binding transcriptional dual regulator) binding to -32, -129, -175, -260 or -317 bp of the promoter site. This operon's transcription inactivation can also be controlled by ArcA-Phosphorylated DNA-binding transcriptional dual regulator binding to -179 bp of the promoter site.