Broadening the signal specificity of prokaryotic promoters by modifying cis-regulatory elements associated with a single transcription factor

Molecular BioSystems
Rafael Silva-Rocha, Víctor de Lorenzo

Abstract

In this report, we experimentally demonstrate that improving the cis-regulatory region of a target promoter can significantly enhance the response to an otherwise poor inducer. The transcriptional factor (TF) BenR of Pseudomonas putida KT2440 is a member of the AraC/XylS family that activates the Pb promoter in response to benzoate. This TF can also trigger Pb activity in response to 3-methylbenzoate (3MBz), but with lower efficiency. Unlike other family members, BenR appears to recognize one operator partially overlapping the -35 promoter region and which is followed by an upstream DNA sequence that lacks an essential motif for TF binding. By generating a promoter variant composed of two complete operator sequences, we observed an enhancement in the sensitivity of Pb to the two inducers. This effect was more pronounced in the case of 3MBz, for which the transcriptional response was approximately 4-5 times higher with the variant than with the wild type promoter. By comparing the responses of the promoters to different concentrations of the inducers, we observed that the modification of the BenR binding region changes the inherent logic of Pb from an amplifier-like behaviour, in which benzoate acts as the sole input, towards OR...Continue Reading

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Citations

Sep 20, 2012·BMC Systems Biology·Angel Goñi-Moreno, Martyn Amos
Nov 2, 2015·Applied Microbiology and Biotechnology·Regina Mahr, Julia Frunzke
Nov 6, 2012·Current Opinion in Biotechnology·Eduardo DíazJuan Nogales
May 14, 2016·Applied Microbiology and Biotechnology·Regina MahrJulia Frunzke
Jul 1, 2017·Scientific Reports·José Manuel Borrero-de AcuñaIgnacio Poblete-Castro
Mar 28, 2018·Nature Communications·Venkatesh Endalur Gopinarayanan, Nikhil U Nair
Jan 31, 2018·Journal of Industrial Microbiology & Biotechnology·Shuobo ShiHuimin Zhao
Aug 7, 2018·BioMed Research International·Ulysses Amancio de FriasRafael Silva-Rocha
May 12, 2018·International Journal of Genomics·Ananda Sanches-MedeirosRafael Silva-Rocha
Aug 1, 2019·ACS Synthetic Biology·Lummy Maria Oliveira MonteiroRafael Silva-Rocha

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