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Ada DNA-binding transcriptional dual regulator

Synonyms: Ada, Ada-Methylated
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 []. 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 [38, 39].
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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]
Ada-Methylated Functional Covalent Holo [BPP] [16]
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,-](1)
[Ada,+](3)


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 -81.0 ada, alkB
caacaatcttGCGCTTTAATTTTTTTCGCTGACAaggaagcttt
2310474 2310498 [BPP], [GEA], [HIBSCS], [SM] [15], [20], [23], [27], [28], [29], [30], [31], [32]
  Ada repressor adap Sigma38, Sigma70 -38.5 -61.0 ada, alkB
ggtcaccatcACGCAAAAACCAACAATCTTGCGCtttaattttt
2310454 2310478 [BPP], [GEA], [HIBSCS], [SM] [15], [23], [29], [30], [32]
  Ada activator aidBp Sigma70, Sigma38 -53.5 -81.0 aidB
cgcattacatTGCTGGATAAGAATGTTTTAGCAAtctctttctg
4414182 4414206 [BPP], [GEA], [HIBSCS] [27], [28], [33]
  Ada activator alkAp Sigma38, Sigma70 -41.5 -61.0 alkA
ttcagacgctGCGCTTTGCTTTCATATTCCGGTTgtcgcgacgg
2147589 2147613 [BPP], [GEA], [HIBSCS], [SM] [15], [23], [30], [32], [34], [35], [36], [37]


Alignment and PSSM for Ada TFBSs    

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


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

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation



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] 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

 [25] 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

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

 [27] 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

 [28] 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

 [29] 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

 [30] 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

 [31] 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

 [32] 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

 [33] 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

 [34] 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

 [35] 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

 [36] 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

 [37] 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

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

 [39] 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

 [40] 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

 [41] 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

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

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



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