|Synonyms: Ada-Methylated, Ada|
ada encodes a bifunctional methyltransferase and transcriptional regulator which is a key component of the adaptive response - the mechanism of adaption induced after exposure to small amounts of DNA alkylating agents.
O6-methylguanine (O6--meG) and O4-methylthymine (O4-meT) are two of a number of nucleobase modifications that result from exposure of DNA to alkylating agents - both chemical [eg. N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), N-methyl-N-nitrosourea (MNU), methane methanesulfonate (MMS)] and endogenous; O6-meG and O4-meT modifications constitute potentially mutagenic lesions due to their tendency to mispair with thymine and with guanine, respectively, inducing transition mutations (reviewed in [17, 18].
The Ada protein contains two major domains: an N-terminal domain (N-Ada), which demethylates Sp-diastereoisomers of DNA methylphosphotriesters by irreversible methyl transfer to its Cys-38 residue (initially thought to be Cys69) and converts Ada into a transcription regulator, and a C-terminal domain (C-Ada) which demethylates the mutagenic bases, O6-meG and O4-meT, by irreversible methyl transfer to Cys-321. Early characterization of Ada and the inducible response to DNA alkylation was done in E. coli B (see [19, 20, 21, 22, 23, 24, 25, 26].
The proteins from E. coli K-12 and E. coli B differ by 6 amino acid alterations . Ada can be also be activated as a transcriptional regulator through a direct methylation by MMS and methyl iodide [28, 29, 30].Read more >
Purified Ada is cleaved by cellular proteinases into two smaller polypeptides derived from the N-terminal and C-terminal halves of the protein . The C-terminal 178 amino acid domain of Ada (from E. coli B) has been purified and crystallised; in this structure Cys-321 is buried suggesting that conformational change is required for contact with the methyl group of a DNA molecule . N-Ada (purifed from E. coli B) binds a zinc molecule which is tetrahedrally coordinated to 4 cysteine residues (Cys38, Cys42, Cys69 and Cys72); zinc is required for correct protein folding [33, 34, 35].
Ada is autoregulated and regulates transcription of the genes encoding |FRAME: EG11222-MONOMER AlkA |, |FRAME: EG10037-MONOMER AlkB | and |FRAME: CPLX0-7691 AidB | proteins [1, 6, 8, 29, 36, 37, 38, 39] The mechanism of transcription regulation by Ada varies depending on the target promoter [4, 7, 14, 40] (and see review by . Transcription activation by Ada is controlled by a methylation dependent electrostatic switch whereby methylation of Cys38 enhances DNA binding by reducing the electrostatic repulsion between N-Ada and the sugar-phosphate backbone of DNA [3, 42].
Undamaged cells produce, on average, one Ada molecule per generation; some cells have no Ada molecules and thus cannot trigger the adaptive response. The stochastic activation of Ada results in subpopulations that do not efficiently repair alkylation damage and accumulate mutations .
We have modified the reported length of the binding site of this protein to 13 bp, according to the proposal by Teo et al . Other authors have proposed different lengths and consensus sequences for Ada [5, 9], but Nakamura et al showed that deletions in this consensus sequence (AAANNAAAGCGCA) decrease the activity of β-galactosidase .
ada: adaptive response to alkylation damage
Reviews: [44, 45, 46, 47, 48, 49].
Related reviews: [50, 51]
|Sensing class:||Using internal synthesized signals|
|Connectivity class:||Local Regulator|
|Length:||1065 bp / 354 aa|
|TU(s) encoding the TF:||
|Regulated gene(s)||ada, aidB, alkA, alkB|
|Multifun term(s) of regulated gene(s)||
MultiFun Term (List of genes associated to the multifun term)
DNA repair (3)
ada, alkA, alkB
Transcription related (1)
|Regulated operon(s)||ada-alkB, aidB, alkA|
|First gene in the operon(s)||ada, aidB, alkA|
|Simple and complex regulons|
|Simple and complex regulatory phrases||
Regulatory phrase (List of promoters regulated by the phrase)
|Functional conformation||Function||Promoter||Sigma factor||Central Rel-Pos||Distance to first Gene||Genes||Sequence||LeftPos||RightPos||Evidence (Confirmed, Strong, Weak)||References|
|2310474||2310497||[BPP], [GEA], [HIBSCS], [SM]||, , , , , , , , |
|2310454||2310477||[BPP], [GEA], [HIBSCS], [SM]||, , , , |
|4414182||4414205||[BPP], [GEA], [HIBSCS]||, , |
|2147589||2147612||[BPP], [GEA], [HIBSCS], [SM]||, , , , , , , |
|Alignment and PSSM for Ada TFBSs|
|Aligned TFBS of Ada|
|Position weight matrix (PWM).|
A 3 3 2 3 3 3 0 0 3 3 3 2 1 0 0 4 2 0 3 C 1 0 0 1 1 1 0 2 1 0 0 0 2 2 4 0 0 3 0 G 0 0 1 0 0 0 2 0 0 0 0 2 0 2 0 0 2 1 1 T 0 1 1 0 0 0 2 2 0 1 1 0 1 0 0 0 0 0 0
|Evolutionary conservation of regulatory elements|
 Sakashita H., Sakuma T., Akitomo Y., Ohkubo T., Kainosho M., Sekiguchi M., Morikawa K., 1995, Sequence-specific DNA recognition of the Escherichia coli Ada protein associated with the methylation-dependent functional switch for transcriptional regulation., J Biochem. 118(6):1184-91
 Takinowaki H., Matsuda Y., Yoshida T., Kobayashi Y., Ohkubo T., 2006, The solution structure of the methylated form of the N-terminal 16-kDa domain of Escherichia coli Ada protein., Protein Sci. 15(3):487-97
 Landini P., Volkert MR., 1995, RNA polymerase alpha subunit binding site in positively controlled promoters: a new model for RNA polymerase-promoter interaction and transcriptional activation in the Escherichia coli ada and aidB genes., EMBO J. 14(17):4329-35
 Landini P., Volkert MR., 1995, Transcriptional activation of the Escherichia coli adaptive response gene aidB is mediated by binding of methylated Ada protein. Evidence for a new consensus sequence for Ada-binding sites., J Biol Chem. 270(14):8285-9
 Nakamura T., Tokumoto Y., Sakumi K., Koike G., Nakabeppu Y., Sekiguchi M., 1988, Expression of the ada gene of Escherichia coli in response to alkylating agents. Identification of transcriptional regulatory elements., J Mol Biol. 202(3):483-94
 Saget BM., Shevell DE., Walker GC., 1995, Alteration of lysine 178 in the hinge region of the Escherichia coli ada protein interferes with activation of ada, but not alkA, transcription., J Bacteriol. 177(5):1268-74
 Sakumi K., Sekiguchi M., 1989, Regulation of expression of the ada gene controlling the adaptive response. Interactions with the ada promoter of the Ada protein and RNA polymerase., J Mol Biol. 205(2):373-85
 Taketomi A., Nakabeppu Y., Ihara K., Hart DJ., Furuichi M., Sekiguchi M., 1996, Requirement for two conserved cysteine residues in the Ada protein of Escherichia coli for transactivation of the ada promoter., Mol Gen Genet. 250(5):523-32
 Volkert MR., Hajec LI., Matijasevic Z., Fang FC., Prince R., 1994, Induction of the Escherichia coli aidB gene under oxygen-limiting conditions requires a functional rpoS (katF) gene., J Bacteriol. 176(24):7638-45
 Landini P., Busby SJ., 1999, The Escherichia coli Ada protein can interact with two distinct determinants in the sigma70 subunit of RNA polymerase according to promoter architecture: identification of the target of Ada activation at the alkA promoter., J Bacteriol. 181(5):1524-9
 Landini P., Busby SJ., 1999, Expression of the Escherichia coli ada regulon in stationary phase: evidence for rpoS-dependent negative regulation of alkA transcription., J Bacteriol. 181(21):6836-9
 Landini P., Gaal T., Ross W., Volkert MR., 1997, The RNA polymerase alpha subunit carboxyl-terminal domain is required for both basal and activated transcription from the alkA promoter., J Biol Chem. 272(25):15914-9
 Nieminuszczy J., Grzesiuk E., 2007, Bacterial DNA repair genes and their eukaryotic homologues: 3. AlkB dioxygenase and Ada methyltransferase in the direct repair of alkylated DNA., Acta Biochim Pol. 54(3):459-68
 Demple B., Jacobsson A., Olsson M., Robins P., Lindahl T., 1982, Repair of alkylated DNA in Escherichia coli. Physical properties of O6-methylguanine-DNA methyltransferase., J Biol Chem. 257(22):13776-80
 Teo I., Sedgwick B., Demple B., Li B., Lindahl T., 1984, Induction of resistance to alkylating agents in E. coli: the ada+ gene product serves both as a regulatory protein and as an enzyme for repair of mutagenic damage., EMBO J. 3(9):2151-7
 Demple B., Sedgwick B., Robins P., Totty N., Waterfield MD., Lindahl T., 1985, Active site and complete sequence of the suicidal methyltransferase that counters alkylation mutagenesis., Proc Natl Acad Sci U S A. 82(9):2688-92
 Nakabeppu Y., Kondo H., Kawabata S., Iwanaga S., Sekiguchi M., 1985, Purification and structure of the intact Ada regulatory protein of Escherichia coli K12, O6-methylguanine-DNA methyltransferase., J Biol Chem. 260(12):7281-8
 Takahashi K., Kawazoe Y., Sakumi K., Nakabeppu Y., Sekiguchi M., 1988, Activation of Ada protein as a transcriptional regulator by direct alkylation with methylating agents., J Biol Chem. 263(27):13490-2
 Moore MH., Gulbis JM., Dodson EJ., Demple B., Moody PC., 1994, Crystal structure of a suicidal DNA repair protein: the Ada O6-methylguanine-DNA methyltransferase from E. coli., EMBO J. 13(7):1495-501
 Nakabeppu Y., Sekiguchi M., 1986, Regulatory mechanisms for induction of synthesis of repair enzymes in response to alkylating agents: ada protein acts as a transcriptional regulator., Proc Natl Acad Sci U S A. 83(17):6297-301
 Shevell DE., Walker GC., 1991, A region of the Ada DNA-repair protein required for the activation of ada transcription is not necessary for activation of alkA., Proc Natl Acad Sci U S A. 88(20):9001-5
 Landini P., Bown JA., Volkert MR., Busby SJ., 1998, Ada protein-RNA polymerase sigma subunit interaction and alpha subunit-promoter DNA interaction are necessary at different steps in transcription initiation at the Escherichia coli Ada and aidB promoters., J Biol Chem. 273(21):13307-12
 He C., Hus JC., Sun LJ., Zhou P., Norman DP., Dotsch V., Wei H., Gross JD., Lane WS., Wagner G., Verdine GL., 2005, A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli ada., Mol Cell. 20(1):117-29
 Uphoff S., Lord ND., Okumus B., Potvin-Trottier L., Sherratt DJ., Paulsson J., 2016, Stochastic activation of a DNA damage response causes cell-to-cell mutation rate variation., Science. 351(6277):1094-7
 Kleibl K., 2002, Molecular mechanisms of adaptive response to alkylating agents in Escherichia coli and some remarks on O(6)-methylguanine DNA-methyltransferase in other organisms., Mutat Res. 512(1):67-84