Abstract
Whole cell biosensors (WCBs) have multiple applications for environmental monitoring, detecting a wide range of pollutants. WCBs depend critically on the sensitivity and specificity of the transcription factor (TF) used to detect the analyte. We describe the mechanism of regulation and the structural and biochemical properties of TF families that are used, or could be used, for the development of environmental WCBs. Focusing on the chemical nature of the analyte, we review TFs that respond to aromatic compounds (XylS-AraC, XylR-NtrC, and LysR), metal ions (MerR, ArsR, DtxR, Fur, and NikR) or antibiotics (TetR and MarR). Analyzing the structural domains involved in DNA recognition, we highlight the similitudes in the DNA binding domains (DBDs) of these TF families. Opposite to DBDs, the wide range of analytes detected by TFs results in a diversity of structures at the effector binding domain. The modular architecture of TFs opens the possibility of engineering TFs with hybrid DNA and effector specificities. Yet, the lack of a crisp correlation between structural domains and specific functions makes this a challenging task.
Highlights
Specialty section: This article was submitted to Microbiotechnology, Ecotoxicology and Bioremediation, a section of the journal Frontiers in Microbiology
Focusing on the chemical nature of the analyte, we review transcription factor (TF) that respond to aromatic compounds (XylS-AraC, XylR-NtrC, and LysR), metal ions (MerR, ArsR, DtxR, Fur, and NikR) or antibiotics (TetR and MarR)
Analyzing the structural domains involved in DNA recognition, we highlight the similitudes in the DNA binding domains (DBDs) of these TF families
Summary
Bacteria have evolved a relatively short list of sequence-specific DBDs, commonly displaying one of three basic folds. DBDs contain the helix turn helix (HTH) motif. HTH motif is around 20 amino acids long and comprises two short alpha helices (7–9 amino acids long each). Some HTH motifs contain additional alpha helices to stabilize the motif. Α2 and α3 form the regular HTH motif, α3 being the recognition helix involved in specific interactions with the major groove of the DNA. A less frequent DNA binding motif is the ribbon helix helix (RHH) motif. It consists of a two-stranded anti-parallel β-ribbon followed by two α-helices. DNA recognition is achieved by insertion of the β-ribbon into the major groove, whereas the two helices constitute most of the hydrophobic core and are involved in dimerization (Schreiter and Drennan, 2007). DNA specific contacts involve polar amino acids of their N-terminal β-sheets
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