Literature DB >> 27837353

Tailor-made transcriptional biosensors for optimizing microbial cell factories.

Brecht De Paepe1, Gert Peters1, Pieter Coussement1, Jo Maertens1, Marjan De Mey2.   

Abstract

Monitoring cellular behavior and eventually properly adapting cellular processes is key to handle the enormous complexity of today's metabolic engineering questions. Hence, transcriptional biosensors bear the potential to augment and accelerate current metabolic engineering strategies, catalyzing vital advances in industrial biotechnology. The development of such transcriptional biosensors typically starts with exploring nature's richness. Hence, in a first part, the transcriptional biosensor architecture and the various modi operandi are briefly discussed, as well as experimental and computational methods and relevant ontologies to search for natural transcription factors and their corresponding binding sites. In the second part of this review, various engineering approaches are reviewed to tune the main characteristics of these (natural) transcriptional biosensors, i.e., the response curve and ligand specificity, in view of specific industrial biotechnology applications, which is illustrated using success stories of transcriptional biosensor engineering.

Keywords:  Ligand specificity engineering; Prokaryotes; Response curve engineering; Transcriptional biosensor; Transcriptional regulation

Mesh:

Substances:

Year:  2016        PMID: 27837353     DOI: 10.1007/s10295-016-1862-3

Source DB:  PubMed          Journal:  J Ind Microbiol Biotechnol        ISSN: 1367-5435            Impact factor:   3.346


  175 in total

1.  DNA looping and physical constraints on transcription regulation.

Authors:  José M G Vilar; Stanislas Leibler
Journal:  J Mol Biol       Date:  2003-08-29       Impact factor: 5.469

2.  A biophysical approach to transcription factor binding site discovery.

Authors:  Marko Djordjevic; Anirvan M Sengupta; Boris I Shraiman
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

3.  Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea.

Authors:  Ernesto Pérez-Rueda; Julio Collado-Vides; Lorenzo Segovia
Journal:  Comput Biol Chem       Date:  2004-12       Impact factor: 2.877

4.  Mining ChIP-chip data for transcription factor and cofactor binding sites.

Authors:  Andrew D Smith; Pavel Sumazin; Debopriya Das; Michael Q Zhang
Journal:  Bioinformatics       Date:  2005-06       Impact factor: 6.937

5.  Design, construction, and characterization of a set of biosensors for aromatic compounds.

Authors:  Haoran Xue; Hailing Shi; Zhou Yu; Shuaixin He; Shiyu Liu; Yuhang Hou; Xingjie Pan; Huan Wang; Pu Zheng; Can Cui; Helena Viets; Jing Liang; Yihao Zhang; Shuobing Chen; Haoqian M Zhang; Qi Ouyang
Journal:  ACS Synth Biol       Date:  2014-12-19       Impact factor: 5.110

6.  A Parts Database with Consensus Parameter Estimation for Synthetic Circuit Design.

Authors:  Linh Huynh; Ilias Tagkopoulos
Journal:  ACS Synth Biol       Date:  2016-07-25       Impact factor: 5.110

7.  Screening of an Escherichia coli promoter library for a phenylalanine biosensor.

Authors:  Regina Mahr; Raphael Freiherr von Boeselager; Johanna Wiechert; Julia Frunzke
Journal:  Appl Microbiol Biotechnol       Date:  2016-05-12       Impact factor: 4.813

8.  AraC regulatory protein mutants with altered effector specificity.

Authors:  Shuang-Yan Tang; Hossein Fazelinia; Patrick C Cirino
Journal:  J Am Chem Soc       Date:  2008-03-21       Impact factor: 15.419

9.  Engineering an allosteric transcription factor to respond to new ligands.

Authors:  Noah D Taylor; Alexander S Garruss; Rocco Moretti; Sum Chan; Mark A Arbing; Duilio Cascio; Jameson K Rogers; Farren J Isaacs; Sriram Kosuri; David Baker; Stanley Fields; George M Church; Srivatsan Raman
Journal:  Nat Methods       Date:  2015-12-21       Impact factor: 28.547

10.  Design, construction and characterization of a set of insulated bacterial promoters.

Authors:  Joseph H Davis; Adam J Rubin; Robert T Sauer
Journal:  Nucleic Acids Res       Date:  2010-09-15       Impact factor: 16.971

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  21 in total

Review 1.  Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology.

Authors:  Indra Bervoets; Daniel Charlier
Journal:  FEMS Microbiol Rev       Date:  2019-05-01       Impact factor: 16.408

2.  Directed Evolution of Transcription Factor-Based Biosensors for Altered Effector Specificity.

Authors:  Leopoldo Ferreira Marques Machado; Neil Dixon
Journal:  Methods Mol Biol       Date:  2022

3.  Fluorescence-Activated Cell Sorting as a Tool for Recombinant Strain Screening.

Authors:  Christos Skrekas; Raphael Ferreira; Florian David
Journal:  Methods Mol Biol       Date:  2022

4.  A Versatile Transcription Factor Biosensor System Responsive to Multiple Aromatic and Indole Inducers.

Authors:  Mohamed A Nasr; Logan R Timmins; Vincent J J Martin; David H Kwan
Journal:  ACS Synth Biol       Date:  2022-03-22       Impact factor: 5.249

5.  A Förster Resonance Energy Transfer-Based Ratiometric Sensor with the Allosteric Transcription Factor TetR.

Authors:  Thuy T Nguyen; Margaret Chern; R C Baer; James Galagan; Allison M Dennis
Journal:  Small       Date:  2020-04-06       Impact factor: 13.281

Review 6.  Biosensing in Smart Engineered Probiotics.

Authors:  Austin G Rottinghaus; Matthew B Amrofell; Tae Seok Moon
Journal:  Biotechnol J       Date:  2020-01-07       Impact factor: 4.677

7.  Robust and flexible platform for directed evolution of yeast genetic switches.

Authors:  Masahiro Tominaga; Kenta Nozaki; Daisuke Umeno; Jun Ishii; Akihiko Kondo
Journal:  Nat Commun       Date:  2021-03-23       Impact factor: 14.919

Review 8.  Transcription factor-based biosensors: a molecular-guided approach for natural product engineering.

Authors:  Melissa M Mitchler; Jessie M Garcia; Nichole E Montero; Gavin J Williams
Journal:  Curr Opin Biotechnol       Date:  2021-01-23       Impact factor: 10.279

Review 9.  Recent trends in biocatalysis.

Authors:  Dong Yi; Thomas Bayer; Christoffel P S Badenhorst; Shuke Wu; Mark Doerr; Matthias Höhne; Uwe T Bornscheuer
Journal:  Chem Soc Rev       Date:  2021-06-18       Impact factor: 60.615

10.  Lighting up yeast cell factories by transcription factor-based biosensors.

Authors:  Vasil D'Ambrosio; Michael K Jensen
Journal:  FEMS Yeast Res       Date:  2017-11-01       Impact factor: 2.796

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