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Ada DNA-binding transcriptional dual regulator

Synonyms: Ada-Methylated, Ada
Summary:
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 [39, 40]. 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 [41, 42, 43, 44, 45, 46, 47, 48].
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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 [APPH], [APPHINH], [IDA], [IMP] [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27]
Ada-Methylated Functional Covalent Holo [BPP], [IPI], [SM] [16], [21]
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
ada-alkB
adap


Regulon       
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
Ada,AidB,Lrp
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[Ada,+](3)
[Ada,-](1)


Transcription factor regulation    


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, Sigma70 -58.5 -80.5 ada, alkB
aaaagcttccTTGTCAGCGAAAAAAATTAAAGCGCaagattgttg
2310474 2310498 [APIORCISFBSCS], [BPP], [GEA], [SM] [15], [20], [23], [28], [29], [30], [31], [32], [33]
  Ada repressor adap Sigma38, Sigma70 -38.5 -60.5 ada, alkB
aaaaaattaaAGCGCAAGATTGTTGGTTTTTGCGTgatggtgacc
2310454 2310478 [APIORCISFBSCS], [BPP], [GEA], [SM] [15], [23], [30], [31], [33]
  Ada activator aidBp Sigma70, Sigma38 -53.5 -81.5 aidB
cgcattacatTGCTGGATAAGAATGTTTTAGCAATctctttctgt
4414182 4414206 [APIORCISFBSCS], [BPP], [GEA] [28], [29], [34]
  Ada activator alkAp Sigma38, Sigma70 -41.5 -60.5 alkA
gccgtcgcgaCAACCGGAATATGAAAGCAAAGCGCagcgtctgaa
2147589 2147613 [APIORCISFBSCS], [BPP], [GEA], [SM] [15], [23], [31], [33], [35], [36], [37], [38]


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


Evidence    

 [APPH] Assay of protein purified to homogeneity

 [APPHINH] Assay of protein purified to homogeneity from its native host

 [IDA] Inferred from direct assay

 [IMP] Inferred from mutant phenotype

 [BPP] Binding of purified proteins

 [IPI] Inferred from physical interaction

 [SM] Site mutation

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [GEA] Gene expression analysis



Reference(s)    

 [1] Demple B., 1986, Mutant Escherichia coli Ada proteins simultaneously defective in the repair of O6-methylguanine and in gene activation., Nucleic Acids Res 14(14):5575-89

 [2] Habazettl J., Myers LC., Yuan F., Verdine GL., Wagner G., 1996, Backbone dynamics, amide hydrogen exchange, and resonance assignments of the DNA methylphosphotriester repair domain of Escherichia coli Ada using NMR., Biochemistry 35(29):9335-48

 [3] Karran P., Lindahl T., Griffin B., 1979, Adaptive response to alkylating agents involves alteration in situ of O6-methylguanine residues in DNA., Nature 280(5717):76-7

 [4] 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

 [5] Lemotte PK., Walker GC., 1985, Induction and autoregulation of ada, a positively acting element regulating the response of Escherichia coli K-12 to methylating agents., J Bacteriol 161(3):888-95

 [6] Lin Y., Dotsch V., Wintner T., Peariso K., Myers LC., Penner-Hahn JE., Verdine GL., Wagner G., 2001, Structural basis for the functional switch of the E. coli Ada protein., Biochemistry 40(14):4261-71

 [7] Mackay WJ., Han S., Samson LD., 1994, DNA alkylation repair limits spontaneous base substitution mutations in Escherichia coli., J Bacteriol 176(11):3224-30

 [8] Margison GP., Cooper DP., Brennand J., 1985, Cloning of the E. coli O6-methylguanine and methylphosphotriester methyltransferase gene using a functional DNA repair assay., Nucleic Acids Res 13(6):1939-52

 [9] Myers LC., Cushing TD., Wagner G., Verdine GL., 1994, Metal-coordination sphere in the methylated Ada protein-DNA co-complex., Chem Biol 1(2):91-7

 [10] Myers LC., Jackow F., Verdine GL., 1995, Metal dependence of transcriptional switching in Escherichia coli Ada., J Biol Chem 270(12):6664-70

 [11] 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

 [12] 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

 [13] Rebeck GW., Samson L., 1991, Increased spontaneous mutation and alkylation sensitivity of Escherichia coli strains lacking the ogt O6-methylguanine DNA repair methyltransferase., J Bacteriol 173(6):2068-76

 [14] Robins P., Cairns J., 1979, Quantitation of the adaptive response to alkylating agents., Nature 280(5717):74-6

 [15] 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

 [16] 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

 [17] Schendel PF., Robins PE., 1978, Repair of O6-methylguanine in adapted Escherichia coli., Proc Natl Acad Sci U S A 75(12):6017-20

 [18] Shevell DE., LeMotte PK., Walker GC., 1988, Alteration of the carboxyl-terminal domain of Ada protein influences its inducibility, specificity, and strength as a transcriptional activator., J Bacteriol 170(11):5263-71

 [19] Takano K., Nakabeppu Y., Sekiguchi M., 1988, Functional sites of the Ada regulatory protein of Escherichia coli. Analysis by amino acid substitutions., J Mol Biol 201(2):261-71

 [20] 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

 [21] 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

 [22] Taverna P., Sedgwick B., 1996, Generation of an endogenous DNA-methylating agent by nitrosation in Escherichia coli., J Bacteriol 178(17):5105-11

 [23] 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

 [24] Uphoff S., 2018, Real-time dynamics of mutagenesis reveal the chronology of DNA repair and damage tolerance responses in single cells., Proc Natl Acad Sci U S A 115(28):E6516-E6525

 [25] Vaughan P., Sedgwick B., Hall J., Gannon J., Lindahl T., 1991, Environmental mutagens that induce the adaptive response to alkylating agents in Escherichia coli., Carcinogenesis 12(2):263-8

 [26] Vericat JA., Guerrero R., Barbe J., 1988, Inhibition of the SOS response of Escherichia coli by the Ada protein., J Bacteriol 170(3):1354-9

 [27] Volkert MR., 1989, Altered induction of the adaptive response to alkylation damage in Escherichia coli recF mutants., J Bacteriol 171(1):99-103

 [28] 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

 [29] 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

 [30] 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

 [31] 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

 [32] 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

 [33] 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

 [34] 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

 [35] 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

 [36] 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

 [37] 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

 [38] 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

 [39] Wyatt MD, Pittman DL, 2006, Methylating agents and DNA repair responses: Methylated bases and sources of strand breaks., Chem Res Toxicol, 2006 Dec

 [40] 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, 2007

 [41] 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, 1980 Nov 25

 [42] Lindahl T, Demple B, Robins P, 1982, Suicide inactivation of the E. coli O6-methylguanine-DNA methyltransferase., EMBO J, 1982

 [43] 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, 1982 Nov 25

 [44] Sedgwick B, 1983, Molecular cloning of a gene which regulates the adaptive response to alkylating agents in Escherichia coli., Mol Gen Genet, 1983

 [45] McCarthy JG, Edington BV, Schendel PF, 1983, Inducible repair of phosphotriesters in Escherichia coli., Proc Natl Acad Sci U S A, 1983 Dec

 [46] McCarthy TV, Karran P, Lindahl T, 1984, Inducible repair of O-alkylated DNA pyrimidines in Escherichia coli., EMBO J, 1984 Mar

 [47] 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, 1984 Sep

 [48] 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, 1985 May

 [49] Takahashi K, Kawazoe Y, 1987, Methyl iodide, a potent inducer of the adaptive response without appreciable mutagenicity in E. coli., Biochem Biophys Res Commun, 1987 Apr 14

 [50] 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, 1988 Sep 25

 [51] 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, 1993 Mar

 [52] Yoshikai T, Nakabeppu Y, Sekiguchi M, 1988, Proteolytic cleavage of Ada protein that carries methyltransferase and transcriptional regulator activities., J Biol Chem, 1988 Dec 15

 [53] 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, 1994 Apr 1

 [54] 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, 1992 May 19

 [55] Myers LC, Verdine GL, Wagner G, 1993, Solution structure of the DNA methyl phosphotriester repair domain of Escherichia coli Ada., Biochemistry, 1993 Dec 28

 [56] Myers LC, Terranova MP, Ferentz AE, Wagner G, Verdine GL, 1993, Repair of DNA methylphosphotriesters through a metalloactivated cysteine nucleophile., Science, 1993 Aug 27

 [57] 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, 1990 Nov 20

 [58] 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, 1991 Oct 15

 [59] 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

 [60] Landini P, Volkert MR, 2000, Regulatory responses of the adaptive response to alkylation damage: a simple regulon with complex regulatory features., J Bacteriol, 2000 Dec

 [61] He C, Hus JC, Sun LJ, Zhou P, Norman DP, Dötsch 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, 2005 Oct 7

 [62] 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, 2016 Mar 4

 [63] Defais M, 1985, The adaptive response in E. coli., Biochimie, 1985 Mar-Apr

 [64] Shevell DE, Friedman BM, Walker GC, 1990, Resistance to alkylation damage in Escherichia coli: role of the Ada protein in induction of the adaptive response., Mutat Res, 1990 Nov-Dec

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

 [66] Sedgwick B, Lindahl T, 2002, Recent progress on the Ada response for inducible repair of DNA alkylation damage., Oncogene, 2002 Dec 16

 [67] 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, 2002 Sep

 [68] Mielecki D, Grzesiuk E, 2014, Ada response - a strategy for repair of alkylated DNA in bacteria., FEMS Microbiol Lett, 2014 Jun

 [69] Daniels DS, Tainer JA, 2000, Conserved structural motifs governing the stoichiometric repair of alkylated DNA by O(6)-alkylguanine-DNA alkyltransferase., Mutat Res, 2000 Aug 30

 [70] Jones GD, Le Pla RC, Farmer PB, 2010, Phosphotriester adducts (PTEs): DNA's overlooked lesion., Mutagenesis, 2010 Jan



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