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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 [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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
Ada Functional   Apo [EXP-IDA] W [1]
Ada-Methylated Functional Covalent Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION], [EXP-IPI] S [2], [3]
Evolutionary Family: AraC/XylS
TFBs length: 24
TFBs symmetry: inverted-repeat
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
ada-alkB
adap2


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,+](6)
[Ada,-](2)


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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  Ada activator adap Sigma70 -58.5 -80.5 ada, alkB
aaaagcttccTTGTCAGCGAAAAAAATTAAAGCGCaagattgttg
 2310474 2310498 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [4], [4], [5], [5], [6], [6], [7], [8], [9], [9], [10], [11], [11]
  Ada repressor adap Sigma70 -38.5 -60.5 ada, alkB
aaaaaattaaAGCGCAAGATTGTTGGTTTTTGCGTgatggtgacc
 2310454 2310478 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [6], [6], [7], [9], [9], [11]
  Ada activator adap2 Sigma38 -58.5 -80.5 ada, alkB
aaaagcttccTTGTCAGCGAAAAAAATTAAAGCGCaagattgttg
 2310474 2310498 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [4], [4], [5], [5], [6], [6], [7], [8], [9], [9], [10], [11], [11]
  Ada repressor adap2 Sigma38 -38.5 -60.5 ada, alkB
aaaaaattaaAGCGCAAGATTGTTGGTTTTTGCGTgatggtgacc
 2310454 2310478 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [6], [6], [7], [9], [9], [11]
  Ada activator aidBp1 Sigma70 -53.5 -81.5 aidB
cgcattacatTGCTGGATAAGAATGTTTTAGCAATctctttctgt
 4414182 4414206 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [4], [4], [5], [5], [12], [12]
  Ada activator aidBp2 Sigma38 -53.5 -81.5 aidB
cgcattacatTGCTGGATAAGAATGTTTTAGCAATctctttctgt
 4414182 4414206 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [4], [4], [5], [5], [12], [12]
  Ada activator alkAp Sigma70 -41.5 -60.5 alkA
gccgtcgcgaCAACCGGAATATGAAAGCAAAGCGCagcgtctgaa
 2147589 2147613 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [7], [9], [11], [11], [13], [13], [14], [14], [15], [16], [16]
  Ada activator alkAp2 Sigma38 -41.5 -60.5 alkA
gccgtcgcgaCAACCGGAATATGAAAGCAAAGCGCagcgtctgaa
 2147589 2147613 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [7], [9], [11], [11], [13], [13], [14], [14], [15], [16], [16]


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    

 [EXP-IDA] Inferred from direct assay

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IPI] Inferred from physical interaction

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.


Reference(s)    

 [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 10.1021/tx060164e

 [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 None

 [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 None

 [20] Lindahl T, Demple B, Robins P, 1982, Suicide inactivation of the E. coli O6-methylguanine-DNA methyltransferase., EMBO J, 1(11):1359 10.1002/j.1460-2075.1982.tb01323.x

 [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 None

 [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 10.1007/BF00425764

 [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 10.1073/pnas.80.24.7380

 [24] McCarthy TV, Karran P, Lindahl T, 1984, Inducible repair of O-alkylated DNA pyrimidines in Escherichia coli., EMBO J, 3(3):545 10.1002/j.1460-2075.1984.tb01844.x

 [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 10.1002/j.1460-2075.1984.tb02105.x

 [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 10.1073/pnas.82.9.2688

 [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 10.1016/s0006-291x(87)80530-2

 [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 None

 [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 10.1016/0921-8777(93)90076-s

 [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 None

 [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 10.1002/j.1460-2075.1994.tb06410.x

 [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 10.1021/bi00134a002

 [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 10.1021/bi00214a003

 [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 10.1126/science.8395079

 [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 10.1016/S0022-2836(05)80318-3

 [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 10.1073/pnas.88.20.9001

 [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 10.1128/JB.182.23.6543-6549.2000

 [42] 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, 20(1):117 10.1016/j.molcel.2005.08.013

 [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 10.1126/science.aac9786

 [44] Uphoff S, 2019, A Quantitative Model Explains Single-Cell Dynamics of the Adaptive Response in Escherichia coli., Biophys J, 117(6):1156 10.1016/j.bpj.2019.08.009

 [45] Defais M, 1985, The adaptive response in E. coli., Biochimie, 67(3-4):357 10.1016/s0300-9084(85)80080-8

 [46] 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, 233(1-2):53 10.1016/0027-5107(90)90151-s

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

 [48] Sedgwick B, Lindahl T, 2002, Recent progress on the Ada response for inducible repair of DNA alkylation damage., Oncogene, 21(58):8886 10.1038/sj.onc.1205998

 [49] 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 10.1016/s1383-5742(02)00025-x

 [50] Mielecki D, Grzesiuk E, 2014, Ada response - a strategy for repair of alkylated DNA in bacteria., FEMS Microbiol Lett, 355(1):1 10.1111/1574-6968.12462

 [51] 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 10.1016/s0921-8777(00)00024-0

 [52] Jones GD, Le Pla RC, Farmer PB, 2010, Phosphotriester adducts (PTEs): DNA's overlooked lesion., Mutagenesis, 25(1):3 10.1093/mutage/gep038


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