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Towards a rational approach to promoter engineering : understanding the complexity of transcription initiation in prokaryotes

Cara Deal (UGent) , Lien De Wannemaeker (UGent) and Marjan De Mey (UGent)
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Abstract
Promoter sequences are important genetic control elements. Through their interaction with RNA polymerase they determine transcription strength and specificity, thereby regulating the first step in gene expression. Consequently, they can be targeted as elements to control predictability and tuneability of a genetic circuit, which is essential in applications such as the development of robust microbial cell factories. This review considers the promoter elements implicated in the three stages of transcription initiation, detailing the complex interplay of sequence-specific interactions that are involved, and highlighting that DNA sequence features beyond the core promoter elements work in a combinatorial manner to determine transcriptional strength. In particular, we emphasize that, aside from promoter recognition, transcription initiation is also defined by the kinetics of open complex formation and promoter escape, which are also known to be highly sequence specific. Significantly, we focus on how insights into these interactions can be manipulated to lay the foundation for a more rational approach to promoter engineering. Unravelling the intricate and sequence-specific regulation of transcription initiation by promoter sequences is crucial, as an in-depth understanding of promoter-RNA polymerase interactions can pave the way to a more rational approach to promoter engineering.
Keywords
COLI RNA-POLYMERASE, ESCHERICHIA-COLI, STRUCTURAL BASIS, RECOGNITION ELEMENT, ABORTIVE INITIATION, ALPHA-SUBUNIT, SIGMA(70) SUBUNIT, BACILLUS-SUBTILIS, SIGMA-70 SUBUNIT, GENE-EXPRESSION, transcription initiation, promoter sequence, promoter engineering, sigma factors, synthetic biology

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MLA
Deal, Cara, et al. “Towards a Rational Approach to Promoter Engineering : Understanding the Complexity of Transcription Initiation in Prokaryotes.” FEMS MICROBIOLOGY REVIEWS, vol. 48, no. 2, 2024, doi:10.1093/femsre/fuae004.
APA
Deal, C., De Wannemaeker, L., & De Mey, M. (2024). Towards a rational approach to promoter engineering : understanding the complexity of transcription initiation in prokaryotes. FEMS MICROBIOLOGY REVIEWS, 48(2). https://doi.org/10.1093/femsre/fuae004
Chicago author-date
Deal, Cara, Lien De Wannemaeker, and Marjan De Mey. 2024. “Towards a Rational Approach to Promoter Engineering : Understanding the Complexity of Transcription Initiation in Prokaryotes.” FEMS MICROBIOLOGY REVIEWS 48 (2). https://doi.org/10.1093/femsre/fuae004.
Chicago author-date (all authors)
Deal, Cara, Lien De Wannemaeker, and Marjan De Mey. 2024. “Towards a Rational Approach to Promoter Engineering : Understanding the Complexity of Transcription Initiation in Prokaryotes.” FEMS MICROBIOLOGY REVIEWS 48 (2). doi:10.1093/femsre/fuae004.
Vancouver
1.
Deal C, De Wannemaeker L, De Mey M. Towards a rational approach to promoter engineering : understanding the complexity of transcription initiation in prokaryotes. FEMS MICROBIOLOGY REVIEWS. 2024;48(2).
IEEE
[1]
C. Deal, L. De Wannemaeker, and M. De Mey, “Towards a rational approach to promoter engineering : understanding the complexity of transcription initiation in prokaryotes,” FEMS MICROBIOLOGY REVIEWS, vol. 48, no. 2, 2024.
@article{01HVGXYPB2ZMA3WSQ1GG6BGF91,
  abstract     = {{Promoter sequences are important genetic control elements. Through their interaction with RNA polymerase they determine transcription strength and specificity, thereby regulating the first step in gene expression. Consequently, they can be targeted as elements to control predictability and tuneability of a genetic circuit, which is essential in applications such as the development of robust microbial cell factories. This review considers the promoter elements implicated in the three stages of transcription initiation, detailing the complex interplay of sequence-specific interactions that are involved, and highlighting that DNA sequence features beyond the core promoter elements work in a combinatorial manner to determine transcriptional strength. In particular, we emphasize that, aside from promoter recognition, transcription initiation is also defined by the kinetics of open complex formation and promoter escape, which are also known to be highly sequence specific. Significantly, we focus on how insights into these interactions can be manipulated to lay the foundation for a more rational approach to promoter engineering.

 Unravelling the intricate and sequence-specific regulation of transcription initiation by promoter sequences is crucial, as an in-depth understanding of promoter-RNA polymerase interactions can pave the way to a more rational approach to promoter engineering.}},
  articleno    = {{fuae004}},
  author       = {{Deal, Cara and De Wannemaeker, Lien and De Mey, Marjan}},
  issn         = {{0168-6445}},
  journal      = {{FEMS MICROBIOLOGY REVIEWS}},
  keywords     = {{COLI RNA-POLYMERASE,ESCHERICHIA-COLI,STRUCTURAL BASIS,RECOGNITION ELEMENT,ABORTIVE INITIATION,ALPHA-SUBUNIT,SIGMA(70) SUBUNIT,BACILLUS-SUBTILIS,SIGMA-70 SUBUNIT,GENE-EXPRESSION,transcription initiation,promoter sequence,promoter engineering,sigma factors,synthetic biology}},
  language     = {{eng}},
  number       = {{2}},
  pages        = {{15}},
  title        = {{Towards a rational approach to promoter engineering : understanding the complexity of transcription initiation in prokaryotes}},
  url          = {{http://doi.org/10.1093/femsre/fuae004}},
  volume       = {{48}},
  year         = {{2024}},
}

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