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Ada DNA-binding transcriptional dual regulator

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].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
Ada Functional   Apo [IDA] [1]
Ada-Methylated Functional Covalent Holo [BPP], [IPI], [SM] [2], [3]
Evolutionary Family: AraC/XylS
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: ada
  Genome position: 2309341-2310405
  Length: 1065 bp / 354 aa
Operon name: ada-alkB
TU(s) encoding the TF:
Transcription unit        Promoter

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)
repressor (2)
Transcription related (1)
activator (1)
operon (1)
Regulated operon(s) ada-alkB, aidB, alkA
First gene in the operon(s) ada, aidB, alkA
Simple and complex regulons Ada
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

Transcription factor binding sites (TFBSs) arrangements       

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  Ada activator adap Sigma38 -58.5 -80.5 ada, alkB
2310474 2310497 [BPP], [GEA], [HIBSCS], [SM] [1], [4], [5], [6], [7], [8], [9], [10], [11]
  Ada repressor adap Sigma38 -38.5 -60.5 ada, alkB
2310454 2310477 [BPP], [GEA], [HIBSCS], [SM] [1], [6], [7], [9], [11]
  Ada activator aidBp Sigma70 -53.5 -81.5 aidB
4414182 4414205 [BPP], [GEA], [HIBSCS] [4], [5], [12]
  Ada activator alkAp Sigma38 -41.5 -60.5 alkA
2147589 2147612 [BPP], [GEA], [HIBSCS], [SM] [1], [7], [9], [11], [13], [14], [15], [16]

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

PWM logo   


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation


 [IDA] Inferred from direct assay

 [BPP] Binding of purified proteins

 [IPI] Inferred from physical interaction

 [SM] Site mutation

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences


 [1] Saget BM., Walker GC., 1994, The Ada protein acts as both a positive and a negative modulator of Escherichia coli's response to methylating agents., Proc Natl Acad Sci U S A. 91(21):9730-4

 [2] 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

 [3] 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

 [4] 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

 [5] 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

 [6] 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

 [7] 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

 [8] Sakumi K., Igarashi K., Sekiguchi M., Ishihama A., 1993, The Ada protein is a class I transcription factor of Escherichia coli., J Bacteriol. 175(8):2455-7

 [9] 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

 [10] 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

 [11] Teo I., Sedgwick B., Kilpatrick MW., McCarthy TV., Lindahl T., 1986, The intracellular signal for induction of resistance to alkylating agents in E. coli., Cell. 45(2):315-24

 [12] 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

 [13] Furuichi M., Yu CG., Anai M., Sakumi K., Sekiguchi M., 1992, Regulatory elements for expression of the alkA gene in response to alkylating agents., Mol Gen Genet. 236(1):25-32

 [14] 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

 [15] 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

 [16] 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

 [17] Wyatt MD., Pittman DL., 2006, Methylating agents and DNA repair responses: Methylated bases and sources of strand breaks., Chem Res Toxicol. 19(12):1580-94

 [18] 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

 [19] Olsson M., Lindahl T., 1980, Repair of alkylated DNA in Escherichia coli. Methyl group transfer from O6-methylguanine to a protein cysteine residue., J Biol Chem. 255(22):10569-71

 [20] Lindahl T., Demple B., Robins P., 1982, Suicide inactivation of the E. coli O6-methylguanine-DNA methyltransferase., EMBO J. 1(11):1359-63

 [21] 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

 [22] Sedgwick B., 1983, Molecular cloning of a gene which regulates the adaptive response to alkylating agents in Escherichia coli., Mol Gen Genet. 191(3):466-72

 [23] McCarthy JG., Edington BV., Schendel PF., 1983, Inducible repair of phosphotriesters in Escherichia coli., Proc Natl Acad Sci U S A. 80(24):7380-4

 [24] McCarthy TV., Karran P., Lindahl T., 1984, Inducible repair of O-alkylated DNA pyrimidines in Escherichia coli., EMBO J. 3(3):545-50

 [25] 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

 [26] 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

 [27] 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

 [28] Takahashi K., Kawazoe Y., 1987, Methyl iodide, a potent inducer of the adaptive response without appreciable mutagenicity in E. coli., Biochem Biophys Res Commun. 144(1):447-53

 [29] 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

 [30] Vaughan P., Lindahl T., Sedgwick B., 1993, Induction of the adaptive response of Escherichia coli to alkylation damage by the environmental mutagen, methyl chloride., Mutat Res. 293(3):249-57

 [31] Yoshikai T., Nakabeppu Y., Sekiguchi M., 1988, Proteolytic cleavage of Ada protein that carries methyltransferase and transcriptional regulator activities., J Biol Chem. 263(35):19174-80

 [32] 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

 [33] Myers LC., Terranova MP., Nash HM., Markus MA., Verdine GL., 1992, Zinc binding by the methylation signaling domain of the Escherichia coli Ada protein., Biochemistry. 31(19):4541-7

 [34] Myers LC., Verdine GL., Wagner G., 1993, Solution structure of the DNA methyl phosphotriester repair domain of Escherichia coli Ada., Biochemistry. 32(51):14089-94

 [35] Myers LC., Terranova MP., Ferentz AE., Wagner G., Verdine GL., 1993, Repair of DNA methylphosphotriesters through a metalloactivated cysteine nucleophile., Science. 261(5125):1164-7

 [36] 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

 [37] Akimaru H., Sakumi K., Yoshikai T., Anai M., Sekiguchi M., 1990, Positive and negative regulation of transcription by a cleavage product of Ada protein., J Mol Biol. 216(2):261-73

 [38] 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

 [39] Landini P., Hajec LI., Volkert MR., 1994, Structure and transcriptional regulation of the Escherichia coli adaptive response gene aidB., J Bacteriol. 176(21):6583-9

 [40] 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

 [41] Landini P., Volkert MR., 2000, Regulatory responses of the adaptive response to alkylation damage: a simple regulon with complex regulatory features., J Bacteriol. 182(23):6543-9

 [42] 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

 [43] 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

 [44] Defais M., null, The adaptive response in E. coli., Biochimie. 67(3-4):357-60

 [45] Shevell DE., Friedman BM., Walker GC., null, Resistance to alkylation damage in Escherichia coli: role of the Ada protein in induction of the adaptive response., Mutat Res. 233(1-2):53-72

 [46] Volkert MR., 1988, Adaptive response of Escherichia coli to alkylation damage., Environ Mol Mutagen. 11(2):241-55

 [47] Sedgwick B., Lindahl T., 2002, Recent progress on the Ada response for inducible repair of DNA alkylation damage., Oncogene. 21(58):8886-94

 [48] 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

 [49] Mielecki D., Grzesiuk E., 2014, Ada response - a strategy for repair of alkylated DNA in bacteria., FEMS Microbiol Lett. 355(1):1-11

 [50] Daniels DS., Tainer JA., 2000, Conserved structural motifs governing the stoichiometric repair of alkylated DNA by O(6)-alkylguanine-DNA alkyltransferase., Mutat Res. 460(3-4):151-63

 [51] Jones GD., Le Pla RC., Farmer PB., 2010, Phosphotriester adducts (PTEs): DNA's overlooked lesion., Mutagenesis. 25(1):3-16