title: Isolation of a non-genomic origin fluoroquinolone responsive regulatory element using a combinatorial bioengineering approach.
abstract: Advances in chemical biology have led to selection of synthetic functional nucleic acids for in vivo applications. Discovery of synthetic nucleic acid regulatory elements has been a long-standing goal of chemical biologists. Availability of vast genome level genetic resources has motivated efforts for discovery and understanding of inducible synthetic genetic regulatory elements. Such elements can lead to custom-design of switches and sensors, oscillators, digital logic evaluators and cell-cell communicators. Here, we describe a simple, robust and universally applicable module for discovery of inducible gene regulatory elements. The distinguishing feature is the use of a toxic peptide as a reporter to suppress the background of unwanted bacterial recombinants. Using this strategy, we show that it is possible to isolate genetic elements of non-genomic origin which specifically get activated in the presence of DNA gyrase A inhibitors belonging to fluoroquinolone (FQ) group of chemicals. Further, using a system level genetic resource, we prove that the genetic regulation is exerted through histone-like nucleoid structuring (H-NS) repressor protein. Till date, there are no reports of in vivo selection of non-genomic origin inducible regulatory promoter like elements. Our strategy opens an uncharted route to discover inducible synthetic regulatory elements from biologically-inspired nucleic acid sequences.
authors.affiliation: Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247 667, India.
authors.forename: Santosh Kumar
authors.initials: SK
authors.lastname: Srivastava
authors.affiliation: Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247 667, India.
authors.forename: V Rajesh
authors.initials: VR
authors.lastname: Iyer
authors.affiliation: Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247 667, India.
authors.forename: Tamoghna
authors.initials: T
authors.lastname: Ghosh
authors.affiliation: Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247 667, India.
authors.forename: Paramesh Ramulu
authors.initials: PR
authors.lastname: Lambadi
authors.affiliation: Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247 667, India.
authors.forename: Ranjana
authors.initials: R
authors.lastname: Pathania
authors.affiliation: Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247 667, India naveenbiochem@gmail.com.
authors.forename: Naveen Kumar
authors.initials: NK
authors.lastname: Navani
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry* / Q000494:pharmacology; D001483:Base Sequence; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism; D036781:Fimbriae Proteins / Q000235:genetics* / Q000378:metabolism; D024841:Fluoroquinolones / Q000737:chemistry* / Q000494:pharmacology; D015870:Gene Expression; D015723:Gene Library; D017930:Genes, Reporter; D005818:Genetic Engineering; D049452:Green Fluorescent Proteins / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000235:genetics; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D020218:Response Elements
chemical_list: D000900:Anti-Bacterial Agents; D029968:Escherichia coli Proteins; C529458:FimG protein, E coli; D024841:Fluoroquinolones; D009841:Oligonucleotides; D049452:Green Fluorescent Proteins; D036781:Fimbriae Proteins
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