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A sigma factor toolbox for orthogonal gene expression in Escherichia coli

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Abstract
Transfer of multi-gene heterologous pathways into the production host leads to imbalances due to lack of adequate gene expression and regulation. To overcome this problem genetic circuitry is increasingly used, but its performance stays limited by lack of regulatory parts that can used without interference. Therefore there is need for orthogonal expression and regulation systems. In Bacteria, a highly conserved multi subunit core RNA polymerase binds to a sigma factor to form the holoenzyme. This complex is able to recognise a specific promoter and initiate transcription. There are many sigma factors varying in sequence, size and promoter specificity. Most bacteria have several alternative sigma factors that all bind competitively to the core enzyme and target the holoenzyme to different promoters in order to change gene expression in the cell. Some sigma factors recognise each other's promoters and others are very specific. The latter are said to be orthogonal. Here we develop a set of orthogonal expression systems in E. coli based on heterologous sigma factors from Bacillus subtilis with different domain make-ups and that recognise specific promoters. These sigma factors proved to function orthogonally towards each other and the host. Further, we create promoter libraries for three sigma factors. As this set is highly orthogonal and covers a wide range of promoter strengths, it enables fine-tuning of multiple independent channels. As orthogonal on/off switches, anti-sigma factors corresponding to the sigma factors were tested and proved to be orthogonal. TO conclude, this parts toolbox has potential to orthogonally tune multiple outputs to multiple inputs required for the assembly of more complex genetic circuits.

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Please use this url to cite or link to this publication:

MLA
Bervoets, Indra, Maarten Van Brempt, Bob Van Hove, et al. “A Sigma Factor Toolbox for Orthogonal Gene Expression in Escherichia Coli.” Genome Engineering and Synthetic Biology, 3rd Edition, Program Book. 2018. Print.
APA
Bervoets, I., Van Brempt, M., Van Hove, B., Maertens, J., De Mey, M., & Charlier, D. (2018). A sigma factor toolbox for orthogonal gene expression in Escherichia coli. Genome Engineering and Synthetic Biology, 3rd Edition, Program book. Presented at the Genome Engineering and Synthetic Biology (3rd edition).
Chicago author-date
Bervoets, Indra, Maarten Van Brempt, Bob Van Hove, Jo Maertens, Marjan De Mey, and Daniel Charlier. 2018. “A Sigma Factor Toolbox for Orthogonal Gene Expression in Escherichia Coli.” In Genome Engineering and Synthetic Biology, 3rd Edition, Program Book.
Chicago author-date (all authors)
Bervoets, Indra, Maarten Van Brempt, Bob Van Hove, Jo Maertens, Marjan De Mey, and Daniel Charlier. 2018. “A Sigma Factor Toolbox for Orthogonal Gene Expression in Escherichia Coli.” In Genome Engineering and Synthetic Biology, 3rd Edition, Program Book.
Vancouver
1.
Bervoets I, Van Brempt M, Van Hove B, Maertens J, De Mey M, Charlier D. A sigma factor toolbox for orthogonal gene expression in Escherichia coli. Genome Engineering and Synthetic Biology, 3rd Edition, Program book. 2018.
IEEE
[1]
I. Bervoets, M. Van Brempt, B. Van Hove, J. Maertens, M. De Mey, and D. Charlier, “A sigma factor toolbox for orthogonal gene expression in Escherichia coli,” in Genome Engineering and Synthetic Biology, 3rd Edition, Program book, Brugge, Belgium, 2018.
@inproceedings{8545687,
  abstract     = {Transfer of multi-gene heterologous pathways into the production host leads to imbalances due to lack of adequate gene expression and regulation. To overcome this problem genetic circuitry is increasingly used, but its performance stays limited by lack of regulatory parts that can used without interference. Therefore there is need for orthogonal expression and regulation systems. In Bacteria, a highly conserved multi subunit core RNA polymerase binds to a sigma factor to form the holoenzyme. This complex is able to recognise a specific promoter and initiate transcription. There are many sigma factors varying in sequence, size and promoter specificity. Most bacteria have several alternative sigma factors that all bind competitively to the core enzyme and target the holoenzyme to different promoters in order to change gene expression in the cell. Some sigma factors recognise each other's promoters and others are very specific.
The latter are said to be orthogonal. Here we develop a set of orthogonal expression systems in E. coli based on heterologous sigma factors from Bacillus subtilis with different domain make-ups and that recognise specific promoters. These sigma factors proved to function orthogonally towards each other and the host. Further, we create promoter libraries for three sigma factors. As this set is highly orthogonal and covers a wide range of promoter strengths, it enables fine-tuning of multiple independent channels. As orthogonal on/off switches, anti-sigma factors corresponding to the sigma factors were tested and proved to be orthogonal. TO conclude, this parts toolbox has potential to orthogonally tune multiple outputs to multiple inputs required for the assembly of more complex genetic circuits.},
  author       = {Bervoets, Indra and Van Brempt, Maarten and Van Hove, Bob and Maertens, Jo and De Mey, Marjan and Charlier, Daniel},
  booktitle    = {Genome Engineering and Synthetic Biology, 3rd Edition, Program book},
  language     = {eng},
  location     = {Brugge, Belgium},
  title        = {A sigma factor toolbox for orthogonal gene expression in Escherichia coli},
  year         = {2018},
}