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Ada DNA-binding transcriptional dual regulator

Synonyms: Ada, Ada-Methylated
Summary:
The transcription factor Ada, for Adaptive response to alkylation damage, is positively autoregulated [1, 6]and controls the transcription of the genes involved in the process of reparation of alkylated DNA [1, 1, 4, 5, 12, 14, 17] also called the adaptive response [18, 19, 20] O6-methylguanine and O4-methylthymine are the major mutagenic lesions resulting from exposure of DNA to simple alkylating agents such as N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), N-methyl-N-nitrosourea (MNU) and, to a lesser degree, methane methanesulfonate (MMS) [1, 17, 18, 19] The O6-methylguanine and O4-methylthymine alkylation products constitute potentially mutagenic lesions due to their tendency to mispair with thymine and with guanine, respectively, forming transition mutations. In Escherichia coli there are two separate direct repair mechanisms for the reversal of these types of alkylating lesions through the involvement of two methyltransferases, Ada and Ogt [19]
This regulator contains two functional domains: an N-terminal domain, which contains a motif for DNA binding, and the C-terminal domain, which is involved in the interaction with the RNA polymerase [8, 20, 21, 22, 23, 24, 25] This regulator removes methyl groups (as well as larger groups) from the guanine and thymine substrates and transfers them to its own cysteine residue (Cys-321) in the C-terminal domain.
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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
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 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
aaagcttcctTGTCAGCGAAAAAAATTAAAGCGCaagattgttg
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
aaaaattaaaGCGCAAGATTGTTGGTTTTTGCGTgatggtgacc
2310454 2310477 [BPP], [GEA], [HIBSCS], [SM] [1], [6], [7], [9], [11]
  Ada activator aidBp Sigma70 -53.5 -81.5 aidB
cgcattacatTGCTGGATAAGAATGTTTTAGCAAtctctttctg
4414182 4414205 [BPP], [GEA], [HIBSCS] [4], [5], [12]
  Ada activator alkAp Sigma38 -41.5 -60.5 alkA
ccgtcgcgacAACCGGAATATGAAAGCAAAGCGCagcgtctgaa
2147589 2147612 [BPP], [GEA], [HIBSCS], [SM] [1], [7], [9], [11], [13], [14], [15], [16]


Alignment and PSSM for Ada TFBSs    

Aligned TFBS of Ada   
  Sequence
 

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    

 [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



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] 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

 [18] 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

 [19] 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

 [20] 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

 [21] 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

 [22] 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

 [23] 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

 [24] 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

 [25] 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

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

 [27] 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

 [28] 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

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



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