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Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering

Marjan De Mey (UGent) , Jo Maertens (UGent) , Gaspard Lequeux (UGent) , Wim Soetaert (UGent) and Erick Vandamme (UGent)
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Abstract
Background: Nowadays, the focus in metabolic engineering research is shifting from massive overexpression and inactivation of genes towards the model-based fine tuning of gene expression. In this context, the construction of a library of synthetic promoters of Escherichia coli as a useful tool for fine tuning gene expression is discussed here. Results: A degenerated oligonucleotide sequence that encodes consensus sequences for E. coli promoters separated by spacers of random sequences has been designed and synthesized. This 57 bp long sequence contains 24 conserved, 13 semi-conserved (W, R and D) and 20 random nucleotides. This mixture of DNA fragments was cloned into a promoter probing vector (pVIK165). The ligation mixtures were transformed into competent E. coli MA8 and the resulting clones were screened for GFP activity by measuring the relative fluorescence units; some clones produced high fluorescence intensity, others weak fluorescence intensity. The clones cover a range of promoter activities from 21.79 RFU/OD600 ml to 7606.83 RFU/OD600 ml. 57 promoters were sequenced and used for promoter analysis. The present results conclusively show that the postulates, which link promoter strength to anomalies in the -10 box and/ or -35 box, and to the length of the spacer, are not generally valid. However, by applying Partial Least Squares regression, a model describing the promoter strength was built and validated. Conclusion: For Escherichia coli, the promoter strength can not been linked to anomalies in the 10 box and/or -35 box, and to the length of the spacer. Also a probabilistic approach to relate the promoter sequence to its strength has some drawbacks. However, by applying Partial Least Squares regression, a good correlation was found between promoter sequence and promoter strength. This PLS model can be a useful tool to rationally design a suitable promoter in order to fine tune gene expression.
Keywords
PROKARYOTIC PROMOTERS, TUNING GENETIC-CONTROL, BACTERIAL PROMOTERS, SEQUENCE, EXPRESSION, DNA, IDENTIFICATION, COMPILATION, REGRESSION, STRENGTH

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Chicago
De Mey, Marjan, Jo Maertens, Gaspard Lequeux, Wim Soetaert, and Erick Vandamme. 2007. “Construction and Model-based Analysis of a Promoter Library for E. Coli: An Indispensable Tool for Metabolic Engineering.” Bmc Biotechnology 7.
APA
De Mey, Marjan, Maertens, J., Lequeux, G., Soetaert, W., & Vandamme, E. (2007). Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering. BMC BIOTECHNOLOGY, 7.
Vancouver
1.
De Mey M, Maertens J, Lequeux G, Soetaert W, Vandamme E. Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering. BMC BIOTECHNOLOGY. 2007;7.
MLA
De Mey, Marjan, Jo Maertens, Gaspard Lequeux, et al. “Construction and Model-based Analysis of a Promoter Library for E. Coli: An Indispensable Tool for Metabolic Engineering.” BMC BIOTECHNOLOGY 7 (2007): n. pag. Print.
@article{387815,
  abstract     = {Background: Nowadays, the focus in metabolic engineering research is shifting from massive overexpression and inactivation of genes towards the model-based fine tuning of gene expression. In this context, the construction of a library of synthetic promoters of Escherichia coli as a useful tool for fine tuning gene expression is discussed here.
Results: A degenerated oligonucleotide sequence that encodes consensus sequences for E. coli promoters separated by spacers of random sequences has been designed and synthesized. This 57 bp long sequence contains 24 conserved, 13 semi-conserved (W, R and D) and 20 random nucleotides. This mixture of DNA fragments was cloned into a promoter probing vector (pVIK165). The ligation mixtures were transformed into competent E. coli MA8 and the resulting clones were screened for GFP activity by measuring the relative fluorescence units; some clones produced high fluorescence intensity, others weak fluorescence intensity. The clones cover a range of promoter activities from 21.79 RFU/OD600 ml to 7606.83 RFU/OD600 ml. 57 promoters were sequenced and used for promoter analysis. The present results conclusively show that the postulates, which link promoter strength to anomalies in the -10 box and/ or -35 box, and to the length of the spacer, are not generally valid. However, by applying Partial Least Squares regression, a model describing the promoter strength was built and validated.
Conclusion: For Escherichia coli, the promoter strength can not been linked to anomalies in the 10 box and/or -35 box, and to the length of the spacer. Also a probabilistic approach to relate the promoter sequence to its strength has some drawbacks. However, by applying Partial Least Squares regression, a good correlation was found between promoter sequence and promoter strength. This PLS model can be a useful tool to rationally design a suitable promoter in order to fine tune gene expression.},
  author       = {De Mey, Marjan and Maertens, Jo and Lequeux, Gaspard and Soetaert, Wim and Vandamme, Erick},
  issn         = {1472-6750},
  journal      = {BMC BIOTECHNOLOGY},
  language     = {eng},
  title        = {Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering},
  url          = {http://dx.doi.org/10.1186/1472-6750-7-34},
  volume       = {7},
  year         = {2007},
}

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