Pathways

The codBA operon in E. coli contains two genes which encode proteins involved in cytosine entry into the cell, as well as its deamination. The operon can be activated by the bining of nitrogen assimilation regulatory protein Nac, which activates transcription at the promoter in the case of low nitrogen levels in the cell. With this operon activated, cytosine can be broken down into the nitrogen source, and can even be the sole nitrogen source if necessary. The operon can also be deactivated by the binding of the PurR transcriptional repressor to the promoter. This repressor is activated by a purine such as guanine, or its derivatives such as hypoxanthine. The first gene in the operon, codB, encodes cytosine permease, an enzyme that is necessary for cytosine to be able to enter the cell. The second gene, codA, encodes cytosine deaminase, an enzyme that catalyzes the deamination of cytosine into uracil, with the addition of a water molecule.

The mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC operon in E. coli contains a total of 16 genes that are also known as the division cell wall (dcw) gene cluster. These genes are involved in cell division, as well as peptidoglycan synthesis. The only terminator in the operon occurs at the end, so all 16 genes can be transcribed at one time. The operon can be repressed by the transcriptional regulator protein MraZ, which is encoded by the first gene in the operon. The operon excluding the first two proteins can also be repressed by the LexA repressor protein, which inhibits the promoter upstream of ftsL. LexA binds to the promoter region, preventing RNA polymerase from binding in response to something that would cause DNA replication to be halted. The genes after this promoter do not have additional promoters until the ftsQAZ-lpxC genes, which are further regulated. Firstly, regulatory protein SdiA can bind to the promoter upstream of ftsQ and repress the transcription of the four downstream genes. The promoter upstream of the ftsA gene can be activated by the transcriptional regulatory protein RcsB, which is involved in regulation of cell division genes and membrane protein synthesis among other functions. Finally, the compound guanosine 3'-diphosphate 5'-triphosphate (ppGpp) can bind to the promoter upstream of the ftsZ gene, activating transcription. The first gene, mraZ, encodes the transcriptional regulator protein MraZ that regulates the operon. The second gene, rsmH, encodes ribosomal RNA small subunit methyltransferase H, a protein that methylates 16S rRNA. The third gene, ftsL, encodes cell division protein FtsL, a protein that is essential for cell division and may link together cytoplasmic and periplasmic cell division proteins. The fourth gene, ftsI, encodes the peptidoglycan synthase ftsI, another protein essential for cell division that catalyzes cross-linking of the peptidoglycan in the cell wall as the cell divides. The fifth gene, murE, encodes UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) 2,6-diaminopimelate ligase. This protein is an enzyme that adds meso-diaminopimelic acid to UMAG, as part of the biosynthesis of peptidoglycan used in the bacteria's cell wall. The sixth gene, murF, encodes UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase. This protein is an enzyme that catalyzes the formation of UDP-N-acetylmuramoyl-pentapeptide, which is a precursor to murein, another name for peptidoglycan. The seventh gene, mraY, encodes phospho-N-acetylmuramoyl-pentapeptide-transferase. This protein is an enzyme that catalyzes the first step of lipid reactions in peptidoglycan biosynthesis. The eigth gene, murD, encodes UDP-N-acetylmuramoylalanine--D-glutamate ligase, an enzyme that catalyzes the addition of glutamate to UDP-N-acetylmuramoyl-L-alanine (UMA) as part of peptidoglycan biosynthesis. The ninth gene, ftsW, encodes a probable peptidoglycan glycosyltransferase protein that functions as a peptidoglycan polymerase. It was previously thought to be a lipid flippase, but there is evidence to suggest that MurJ is instead the flippase. The tenth gene, murG, encodes UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase. This protein is involved in cell wall formation, catalyzing the formation of undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)GlcNAc. The eleventh gene, MurC, encoes UDP-N-acetylmuramate--L-alanine ligase, a protein that is involved in peptidoglycan biosynthesis and cell wall formation. The twelfth gene, ddlB, encodes D-alanine--D-alanine ligase B, a protein that catalyzes the addition of two D-alanine molecules together to form D-alanyl-D-alanine, which is involved in peptidoglycan biosynthesis. The thirteenth gene, ftsQ, encodes cell divison protein FtsQ, an essential cell division protein. It may, along with ftsI, link cytoplasmic and periplasmic cell divions proteins, as well as potentially help formation of the divisome. The divisome is a protein comple that controls cell division. The fourteenth gene, ftsA, encodes cell division protein FtsA, a protein essential for cell division that helps with the formation and possible anchoring of the Z-ring. The Z-ring is formed from FtsZ protein filaments that form a ring around the centre of the cell and triggers splitting of the cell in two. The fifteenth gene, ftsZ, encodes cell division protein FtsZ, which is responsible for forming the Z-ring or contractile ring where the cell will divide. The final gene in the operon, lpxC, encodes UDP-3-O-acyl-N-acetylglucosamine deacetylase. This protein is involved in the biosynthesis of lipid A, a lipid compound found on the outer membrane of gram negative bacteria. Lipid A is considered an endotoxin, and is partially responsible for the activation of an immune response to gram negative bacterial infection.

The cvpA-purF-ubiX operon in E. coli contains three genes that encode various proteins. The operon can be inhibited by the PurR transcriptional repressor, which binds to the promoter region and represses transcription. Hypoxanthine can also bind to PurR, which induces a conformational change in the protein, allowing it to bind more strongly to DNA, and increasing its repressive properties. The first gene in the operon, cvpA, encodes the colicin V producrtion protein, which is required for colicin V to be produced via a plasmid. Colicins are toxins produced by bacteria that can be used to kill other bacterial strains than the one releasing them. The second gene, purF, encodes amidophosphoribosyltransferase, a protein that forms a homotetramer along with magnesium as a cofactor, and catalyzes the formation of phosphoribosylamine from glutamine or ammonia and phosphoribosylpyrophosphate. Phosphoribosylamine is then used to form inosinic acid, which can then be used to form AMP and GMP. The final gene, ubiX, encodes 3-octaprenyl-4-hydroxybenzoate carboxy-lyase, a protein that catalyzes the synthesis of prenyl-FMNH2 and a phosphate group from FMNH2 and dimethylallyl phosphate. It can also work with the UbiD protein in the biosynthesis of coenzyme Q.

The dnaKJ operon in E. coli contains two genes which produce two chaperone and heat shock proteins. Heat shock proteins are induced when cellular stress is present. In addition to heat shock, this stress can also be caused by toxins such as heavy metals in the cell's environment. In this case, the operon is activated by RNA polymerase sigma factor RpoH, also know as sigma 32 or sigma H. This protein is produced when the bacteria is exposed to heat or other stress, and allows other heat shock proteins to be expressed. The first gene in the operon, dnaK, encodes the protein chaperone DnaK, also known as the 70 kilodalton heat shock protein (Hsp70). This chaperone binds to partially synthesized proteins and prevents them from aggregating before folding can occur. It can also bind to proteins that are transported across the cell membrane, as they remain unfolded until they are in place and are at risk for aggregation. When the cell is stressed, proteins can become damaged, leading to unfolding and aggregation. Hsp70 can bind to these proteins, preventing aggregation and allowing proper refolding. The second gene, dnaJ, encodes the protein chaperone DnaJ, which is also known as the 40 kilodalton heat shock protein (Hsp40). This protein also interacts with unfolded protein chains to prevent their aggregation

The DNA replication (dnaTC) operon is a bicistronic operon consisting of dnaC and dnaT. This operon is regulated by a rho-independent terminator. The product of dnaC and dnaT are respectively primosomal protein 1 and DNA replication protein DnaC. DnaT is also responsible for inducting replication of stable DNA during SOS response.

The rpoZ-spoT-trmH-recG operon in E. coli contais four genes that encode proteins involved in DNA and RNA processing. The operon can be repressed by the RNA polymerase-binding transcription factor DksA - ppGpp complex. This complex forms when levels of ppGpp are increased in the cell, typically in conditions where there is a shortage of amino acids, and it inhibits binding of RNA polymerase to the promoter. This helps to slow bacterial translation, preserving the amino acids that are present. The first gene in the operon, rpoZ, encodes DNA-directed RNA polymerase subunit omega, one of the three different proteins in the DNA-directed RNA polymerase complex. It is used in the cell to promote the assembly of RNA polymerase and the initiation of transcription. The second gene, spoT, encodes the bifunctional (p)ppGpp synthase and hydrolase SpoT, an enzyme that can either produce or degrade ppGpp, depending on the current conditions in the cell. The third gene, trmH, encodes tRNA guanosine-2'-O-methyltransferase, an enzyme that catalyzes the methylation of some tRNAs. The final gene, recG, encodes the ATP-dependent DNA helicase recG, a helicase that is important for both DNA repair and recombination.

The dnaAN-recF operon in E. coli contains three genes that encode proteins involved in DNA repair and replication. The operon can be activated by the binding of HTH-type transcriptional regulator ArgP, which can bind upstream or downstream of the promoter, allowing for transcription activation. The operon can also be controlled to the binding of the chromosomal replication indicator protein DnaA complexed with ATP, which can either inhibit or activate transcription of the operon depending on the number of DnaA-ATP complexes bound. When cells have grown, DnaA is produced and can accumulate, leading to more availability in the cell to bind to the operon binding sites. When enough is bound, it unwinds the DNA, allowing helicases to bind, promoting transcription of the operon. The first gene, dnaA, encodes the chromosomal replication initiator protein DnaA, which acts on this operon, as well as several others involved in DNA replication within the cell. The second gene, dnaN, encodes the DNA polymerase III subunit beta, also known as the beta sliding clamp. This protein clamps DNA polymerase III onto the DNA, allowing it to act along the length of the DNA. The final gene in the operon, recF, encodes the DNA replication and repair protein RecF, a protein required for DNA replication, as well as recombination.

The tRNA-tufB operon in E. coli contains a total of five genes. Four of these encode tRNA molecules, while the final one encodes an elongation factor used in bacterial translation. The operon is regulated in two ways. It can be activated by the DNA-binding protein Fis, which binds upstream of the operon promoter and it increases gene transcription by altering the chromatin structure, making it easier for RNA polymerase to bind. The operon can also be negatively regulated by guanosine 3'-diphosphate 5-'triphosphate (ppgpp), a compound that is produced in E. coli in response to stress. ppgpp binds to the promoter region of the operon and inhibits transcription from occurring. The first four genes, thrU, tyrU, glyT and thrT are all transcribed into tRNA molecules. thrU and thrT are both threonine tRNAs with different anticodons (UGU and GGU), while tyrU is a tyrosine tRNA with the anticodin GUA, and glyT is a glycine tRNA with the anticodin UCC. The fifth gene in the operon, tufB, encodes the elongation factor Tu 2 protein. This protein binds the activated tRNAs in the ribosome, allowing for transcription to take place, and as such it is necessary for cell growth and function.

The folC-dedD operon in E. coli contains two genes that are involved in various processes in the cell. There are currently no known activators or inhibitors of the operon. The first gene, folC, encodes a bifunctional dihydrofolate synthase and folylpolyglutamate synthase protein. This catalyzes the conversion of 7,8-dihydrofolate fro glutamate and d7,8-dihydropteroate, as well as the formation of folylpolyglutamates. These are further used in cofactor biosynthesis by the cell. The second gene, dedD, encodes a cell division protein. It is non-essential for the cell, and may be used during cell constriction during division, making the process more efficient.

The gspCDEFGHIJKLMO operon in E. coli contains a total of twelve genes, which encode for the proteins that make up the type II secretion system (T2SS) protein. The T2SS is responsible for moving proteins such as toxins and enzymes that cause symptoms associated with bacterial infection across the two cell membranes of the bacteria. This operon is regulated by DNA-binding protein H-NS, which binds to the DNA of the promoter, changing its conformation and preventing the RNA polymerase from binding to the promoter and transcribing the genes in the operon. The first gene, gspC, encodes for the putative T2SS protein C, which makes up part of the inner membrane complex of the secretion system, along with the proteins produced by gspF, gspL and gspM. After these, gspD encodes for the putative T2SS protein for export D, which forms a homo-pentadecamer pore in the outer membrane of the bacteria, which allows the exported substances to exit the cell. gspE encodes protein subunit E, which is the secretion ATPase. This protein binds to ATP and hydrolyzes it, and the energy produced by this is used to construct and deconstruct the pseudopillus, which is involved in the movement of substances across the periplasm and out of the cell. Another complex that is formed is the pseudopilus, which is made from pseudopilin proteins encoded by gspG, gspH, gspI, gspJ and gspK. These proteins are all activated by the leader peptidase integral membrane protein encoded by gspO, which is found in the inner membrane and allows for the formation of mature pseudopilin proteins.