title: An effective strategy for a whole-cell biosensor based on putative effector interaction site of the regulatory DmpR protein.
abstract: OBJECTIVE
  The detection of bioavailable phenol is a very important issue in environmental and human hazard assessment. Despite modest developments recently, there is a stern need for development of novel biosensors with high sensitivity for priority phenol pollutants. DmpR (Dimethyl phenol regulatory protein), an NtrC-like regulatory protein for the phenol degradation of Pseudomonas sp. strain CF600, represents an attractive biosensor regimen. Thus, we sought to design a novel biosensor by modifying the phenol detection capacity of DmpR by using mutagenic PCR.
  
  
  METHODS
  Binding sites of 'A' domain of DmpR were predicted by LIGSITE, and molecular docking was performed by using GOLD to identify the regions where phenol may interact with DmpR. Total five point mutations, one single at position 42 (Phe-to-Leu), two double at 140 (Asp-to-Glu) and 143 (Gln-to-Leu), and two double at L113M (Leu-to- Met) and D116A (Asp-to- Ala) were created in DmpR by site-directed mutagenesis to construct the reporter plasmids pRLuc42R, pRLuc140p143R, and pRLuc113p116R, respectively. Luciferase assays were performed to measure the activity of luc gene in the presence of phenol and its derivatives, while RT-PCR was used to check the expression of luc gene in the presence of phenol.
  
  
  RESULTS
  Only pRLuc42R and pRLuc113p116R showed positive responses to phenolic effectors. The lowest detectable concentration of phenol was 0.5 µM (0.047 mg/L), 0.1 µM for 2, 4-dimethylphenol and 2-nitrophenol, 10 µM for 2, 4, 6-trichlorophenol and 2-chlorophenol, 100 µM for 2, 4-dichlorophenol, 0.01 µM for 4-nitrophenol, and 1 µM for o-cresol. These concentrations were measured by modified luciferase assay within 3 hrs compared to 6-7 hrs in previous studies. Importantly, increased expression of luciferase gene of pRLuc42R was observed by RT-PCR.
  
  
  CONCLUSIONS
  The present study offers an effective strategy to design a quick and sensitive biosensor for phenol by constructing recombinant bacteria having DmpR gene.
authors.affiliation: Institute of Genomics and Integrative Biology, Mall Road, Delhi, India.
authors.forename: Saurabh
authors.initials: S
authors.lastname: Gupta
authors.forename: Mritunjay
authors.initials: M
authors.lastname: Saxena
authors.forename: Neeru
authors.initials: N
authors.lastname: Saini
authors.lastname: Mahmooduzzafar
authors.forename: Rita
authors.initials: R
authors.lastname: Kumar
authors.forename: Anil
authors.initials: A
authors.lastname: Kumar
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D015374:Biosensing Techniques / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015534:Trans-Activators / Q000737:chemistry / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; C080133:DmpR protein, Pseudomonas; D015534:Trans-Activators