>Published data about mutations
>5|P06134|ADA regulatory protein (Regulatory protein of adaptative response) [Contains: Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) (O-6-methylguanine-DNA alkyltransferase)]|Escherichia coli|AraC
The C321A mutation of  Ada protein results in the constitutive activation of the ada promoter.
>9|Q9ZN78|A-factor receptor protein (A-factor binding protein)|Streptomyces griseus|TetR
The change of the proline 115 to serine in ArpA (out side the hypothetical DNA recognition domain) abolish DNA-binding ability but not ligand binding ability.
The replacement of valine 41 to alanine, in the hypothetical HTH domain of ArpA abolished DNA-binding activity but not A-factor binding activity.
The replacement of tryptophan 119 to alanine generated a mutant ArpA that was unable to bind A-factor, thus resulting in an A-factor insensitive mutant that bound normally to its target DNA.
>15|P03021|Arabinose operon regulatory protein|Escherichia coli O157:H7|AraC
N-terminal deletions extending beyond the sixth aminoacid of AraC generates constitutive regulatory behaviour of the promoter ParaBAD. Mutagenesis of the DNA coding the first 20 aminoacids of AraC yields constitutive mutants and even in presence of arabinose all induce ParaBAD.
N-terminal arm is not essential for transcription activation but plays an important role in holding the system in a non-activating state.
The mutation, N16D, is of particular interest. N16 is not seen in the crystal structure of the AraC dimerization domain determined in the absence of arabinose because the N-terminal arm 18 residues are disordered, but in the presence of arabinose, residues 7-18 fold over the arabinose and make many interactions with it. The introduction of the negatively charged aspartic residue at position 16 appears to create a charge-charge interaction network among D16, K43, and R99 that holds the arm to the dimerization domain even in the absence of arabinose. This frees the DNA-binding domains and allows them to bind cis to I1-I2 half-sites and activate transcription.
Mutating the two positively charged residues to alanines individually and collectively decreased or eliminated the constitutivity created by the N16D mutation.
>35|P43506|HTH-type transcriptional repressor Bm3R1|Bacillus megaterium|TetR
The strain G39E has a single base change that resulted in a glycine to glutamate substitution in the beta-turn region of the DNA binding motif. This mutant can not bind to DNA and constitutively expresses P450BM-3.
>60|P41782|Transcriptional regulator hilD|Salmonella typhimurium|AraC
A mutation in hilD significantly reduces the ability of Salmonella typhimurium to to enter tissue culture cells.
>82|P39897|HTH-type transcriptional regulator mtrR|Neisseria gonorrhoeae|TetR
There are several mutations in the mtrR region that reduce or abrogate the MtrR function. These mutations belongs to two main types according to its location:.
mutations into the coding region of mtrR.
and mutations into the promoter region of mtrR.
There are two types of mutations into the coding region: within the hypothetical helix-turn-helix DNA-binding motif Gly-45 to Asp and Ala-40 to Thr. Outside the HTH domain the substitution His-105 to Tyr resulted in an inactive mutant. It is thought that these mutations reduce the DNA-binding of MtrR protein or their stability.
In the promoter region of mtrR have been observed two mutantions that affect to the 13 bp inverted repeat.
One is a single bp deletion in the 13 bp sequence, that leads high level of hydrophobic agents resistance.
The other is a dinucleotide insertion (TT) in the 13 bp sequence, that enhances bacterial resistance only to macrolide antibiotics azytrhomycin and erythromycin, but not to other hydrophobic antimicrobial agents such as the no-ionic detergent Triton X-100.
Examples of mutations that confers HA resistance phenotype:.
Strain BR87 contain the substitution Gly45 to Asp45.
Strain 3035 contains the substitution His105 to Tyr105.
Strain KH11, which expresses an intermediate level of HA resistance, contains a deletion in the mtrR gene that leaves only 60 nucleotides at the 5’ end of the coding sequence, but this does not include the DNA sequence that encodes the helix-turn-helix domain.
Strains CH95 and KH15, highly HA resistants, have the single bp deletion in the 13 bp inverted repeat.
The strain CL1 had enhanced resistance to HAs (erythromycin and Triton X-100), and contains the transition A(-26) to G, that reduces the binding affinity of MtrR protein (the numbering refer to the transcription start point of mtrCDE).
The strain 9604 contains a double TT insertion within the 13 bo inverted repeat, resulting in a enhanced resistance to azithromycin and erythromycin without changing susceptibility to other HAs.
>110|P09377|L-rhamnose operon regulatory protein rhaS|Escherichia coli|AraC
Random mutation studies and a genetic loss-of-contact approach was used to identify which residues of the two HTH contact with DNA. It was found that Arg202 and Arg206 in HTH-1 made specific contacts with nucleotides at -65 and -67 in rhaI1 and -48 in rhaI2. Asp250 and Asp252 in the other HTH motif, both contact bp -79 in rhaI1.
>114|P16114|Regulatory protein rns|Escherichia coli|AraC
Mutations at the DNA of site I, T-106-C, reduced Rns-dependent expression from Pcoo by 24% compared to that from the wild-type promoter. Mutations at site II, T-45-C, had a more dramatic effect: expression was reduced by 43%. Thus, while the two binding sites are not equivalent in their contributions to activation, they are both required for full expression from Pcoo.
>122|P39885|HTH-type transcriptional regulator tcmR (Tetracenomycin C transcriptional repressor)|Streptomyces glaucescens|TetR
The Streptomyces glaucescens WMH1068 mutant is a TCM C-resistant nonproducing strain that has a deletion in the tcmL polyketide synthase gene being incapable of producing any of the TCM metabolites.
A mutant derived from the WMH1068 strain, which has a 439 bp deletion (between nucleotides 163 and 656) that includes the greater part of the coding sequence of tcmR gene, exhibits constitutive expression of the tcmA gene.
>126|P04483|Tetracycline repressor protein class B from transposon Tn10|Escherichia coli|TetR
Each of 22 amino acids in the proposed HTH operator binding motif of TetR(B) was replaced by alanine and one by valine to determine their role in tet operator recognition by a loss of contact analysis with 16 operator variants. One class of amino acids consisting of T27 and R28 in the first alpha-helix and L41, Y42, W43 and H44 in the recognition alpha-helix, are quantitatively most important for wild-type operator binding. These residues are probably involved in the structural architecture of the motif. A second class of residues is  quantitatively less important for binding, but determines specifity by forming base pair specific contacts to three positions in tet operator. These residues are Q38, P39 and T40 at the N-terminus of the recognition alpha-helix.
The W43 is important for the tet operator recognition.
>166|P07859|XylDLEGF operon transcriptional activator|Pseudomonas putida|AraC
Mutations within the alpha-helix-turn-alpha-helix motif  228-251 of XylS result in different phenotypes. Mutant XylSS229I stimulates high basal transcription levels from Pm in the absence of effectors.
Mutations within the third alpha-helix (residues 256-274 in XylS) decreases the transcriptional activity from Pm.
Mutations in proline 309, which is a very well conserved residue in the XylS/AraC family, results in mutants unable to stimulate transcription from Pm.
Mutations in residues 37, 41, 45, 88, 92, 137, 151, 153, 155, 256 and 288 influence the capacity to recognize substituted benzoate effectors. Arginine 41 seems to be a critical residue for interaction with effectors. Residues 137 and 153 influence affinity for effectors.
Point mutations inside the proposed XylS binding motifs of Pm decrease the activity.
>258|O52834|AlcR (Alcaligin siderophore system regulator)|Bordetella bronchiseptica|AraC
Mutations in alcR result in defects in both alcaligin biosynthesis and transport.
>269|O70020|IcaR|Staphylococcus epidermidis|TetR
A 5-nucleotide deletion (TATTT) in the ica promoter region enhaces  transcription of the ica locus and induces constitutive hyperproduction of PNAG in the mutant strain of Staphyloccus aureus MN8m, independently from IcaR effect.
The equivalent regions in S. aureus SE5 and RP62A strains show a TATTA motif in the same position.
>291|Q8KLP4|Repressor|Stenotrophomonas maltophilia|TetR
The mutant smeDEF overproducing strain D457R constins and A/T mutation at position 498, wich results in a Leu166Gln change. It seems that this point mutation is responsible for the inactivation of smeT nad futher overexpression od smeDEF.
>388|Q47074|BfpT protein|Escherichia coli|AraC
Insertional inactivation of bfpT supresses bfpA transcription, BfpA protein production and the localized adherence (LA) phenotype. The bfpT null mutation is complemented by the introduction of the bfpTVW gene cluster or two plasmids carrying bfpT and bfpW, respectively. However, introduction of bfpT + bfpV, bfpV alone, bfpW alone, or bfpV + bfpW did not enable the recovery of the wild-type phenotype.
>409|Q56831|Hrp protein (Fragment)|Xanthomonas oryzae|AraC
A mutation in hrpXo results in the loss of pathogenicity on rice and in the loss of hypersensitivity on non hosts such as Datura stramonium and radishes.
>416|Q60011|Virginiae butanolide receptor|Streptomyces virginiae|TetR
The Streptomyces virginae mutant strain NH1 was created by homologous recombination. This mutant strain has an internal 99 bp deletion, resulting in an frame deletion of 33 amino acids residues, including the second helix of the putative HTH DNA-binding domain motif.
The Streptomyces virginae mutant strain NH2 was created by homologous recombination. This strain contains a deletion in the barA gene, that results in the C-terminally truncated BarA retaining the intact HTH DNA-binding motif.
>840|Q9AIQ9|IcaR|Staphylococcus caprae|TetR
A 5-nucleotide deletion (TATTT) in the ica promoter region enhaces  transcription of the ica locus and induces constitutive hyperproduction of PNAG in the mutant strain MN8m, independiently from IcaR effect.
The equivalent regions in S. caprae 96007 show a TATTA motif in the same position.
>963|Q9R9T9|Efflux pump regulator SrpR|Pseudomonas putida|TetR
It seems that Pseudomonas putida S12 employs the insertion element ISS12 as a mutator element to generate diverse mutations to swiftly adapt when confronted with severe adverse conditions.
>966|Q9RAJ1|Inactive regulatory protein|Mycobacterium sp. GP1|TetR
The product of the gene dhaR is a repressor of the expression of the gene dhaA in other organisms such as Rhodococcus rhodochrous NCIMB13064. In contrast in Mycobacterium sp. strain GP1 the gene dhaR possesses a 12 nucleotides deletion that inactivates to the regulatory protein DhaR, leading to constitutive expression of the gene dhaA.
>1386|O52066|AlcR (Transcriptional regulator)|Bordetella pertussis|AraC
Mutations in alcR resulted in defects in both alcaligin biosynthesis and transport.
>2162|Q56951|AraC-like regulator YbtA (Transcriptional regulator YbtA)|Yersinia pestis|AraC
Mutations within a putative siderophore biosynthetic gene (irp2) decrease Psn expression.
>5460|15928251|ica operon transcriptional regulator IcaR|Staphylococcus aureus subsp. aureus N315|TetR
A 5-nucleotide deletion (TATTT) in the ica promoter region augments transcription of the ica locus and induces constitutive hyperproduction of PNAG in the mutant strain MN8m, independiently from IcaR effect.