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Comprehensive study on Escherichia coli genomic expression : does position really matter?

(2020) METABOLIC ENGINEERING. 62. p.10-19
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Abstract
As a biorefinery platform host, Escherichia coli has been used extensively to produce metabolites of commercial interest. Integration of foreign DNA onto the bacterial genome allows for stable expression overcoming the need for plasmid expression and its associated instability. Despite the development of numerous tools and genome editing technologies, the question of where to incorporate a synthetic pathway remains unanswered. To address this issue, we studied the genomic expression in E. coli and linked it not only to 26 rationally selected genomic locations, but also to the gene direction in relation to the DNA replication fork, to the carbon and nitrogen source, to DNA folding and supercoiling, and to metabolic burden. To enable these experiments, we have designed a fluorescent expression cassette to eliminate specific local effects on gene expression. Overall it can be concluded that although the expression range obtained by changing the genomic location of a pathway is small compared to the range typically seen in promoter-RBS libraries, the effect of culture medium, environmental stress and metabolic burden can be substantial. The characterization of multiple effects on genomic expression, and the associated libraries of well-characterized strains, will only stimulate and improve the creation of stable production hosts fit for industrial settings.
Keywords
Biotechnology, Applied Microbiology and Biotechnology, Bioengineering, Escherichia coli, Metabolic burden, Genomic expression, Position effect, Industrial biotechnology, GENE-EXPRESSION, FLUORESCENT PROTEINS, TRANSCRIPTION, INTEGRATION, CHROMOSOME, MOLECULES, SEQUENCE, PRECISE, SYSTEMS, DESIGN

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MLA
Goormans, Anke, et al. “Comprehensive Study on Escherichia Coli Genomic Expression : Does Position Really Matter?” METABOLIC ENGINEERING, vol. 62, 2020, pp. 10–19, doi:10.1016/j.ymben.2020.07.007.
APA
Goormans, A., Snoeck, N., Decadt, H., Vermeulen, K., Peters, G., Coussement, P., … Soetaert, W. (2020). Comprehensive study on Escherichia coli genomic expression : does position really matter? METABOLIC ENGINEERING, 62, 10–19. https://doi.org/10.1016/j.ymben.2020.07.007
Chicago author-date
Goormans, Anke, Nico Snoeck, Hannes Decadt, Karel Vermeulen, Gert Peters, Pieter Coussement, Dries Van Herpe, Joeri J. Beauprez, Sofie De Maeseneire, and Wim Soetaert. 2020. “Comprehensive Study on Escherichia Coli Genomic Expression : Does Position Really Matter?” METABOLIC ENGINEERING 62: 10–19. https://doi.org/10.1016/j.ymben.2020.07.007.
Chicago author-date (all authors)
Goormans, Anke, Nico Snoeck, Hannes Decadt, Karel Vermeulen, Gert Peters, Pieter Coussement, Dries Van Herpe, Joeri J. Beauprez, Sofie De Maeseneire, and Wim Soetaert. 2020. “Comprehensive Study on Escherichia Coli Genomic Expression : Does Position Really Matter?” METABOLIC ENGINEERING 62: 10–19. doi:10.1016/j.ymben.2020.07.007.
Vancouver
1.
Goormans A, Snoeck N, Decadt H, Vermeulen K, Peters G, Coussement P, et al. Comprehensive study on Escherichia coli genomic expression : does position really matter? METABOLIC ENGINEERING. 2020;62:10–9.
IEEE
[1]
A. Goormans et al., “Comprehensive study on Escherichia coli genomic expression : does position really matter?,” METABOLIC ENGINEERING, vol. 62, pp. 10–19, 2020.
@article{8673924,
  abstract     = {{As a biorefinery platform host, Escherichia coli has been used extensively to produce metabolites of commercial interest. Integration of foreign DNA onto the bacterial genome allows for stable expression overcoming the need for plasmid expression and its associated instability. Despite the development of numerous tools and genome editing technologies, the question of where to incorporate a synthetic pathway remains unanswered. To address this issue, we studied the genomic expression in E. coli and linked it not only to 26 rationally selected genomic locations, but also to the gene direction in relation to the DNA replication fork, to the carbon and nitrogen source, to DNA folding and supercoiling, and to metabolic burden. To enable these experiments, we have designed a fluorescent expression cassette to eliminate specific local effects on gene expression. Overall it can be concluded that although the expression range obtained by changing the genomic location of a pathway is small compared to the range typically seen in promoter-RBS libraries, the effect of culture medium, environmental stress and metabolic burden can be substantial. The characterization of multiple effects on genomic expression, and the associated libraries of well-characterized strains, will only stimulate and improve the creation of stable production hosts fit for industrial settings.}},
  author       = {{Goormans, Anke and Snoeck, Nico and Decadt, Hannes and Vermeulen, Karel and Peters, Gert and Coussement, Pieter and Van Herpe, Dries and Beauprez, Joeri J. and De Maeseneire, Sofie and Soetaert, Wim}},
  issn         = {{1096-7176}},
  journal      = {{METABOLIC ENGINEERING}},
  keywords     = {{Biotechnology,Applied Microbiology and Biotechnology,Bioengineering,Escherichia coli,Metabolic burden,Genomic expression,Position effect,Industrial biotechnology,GENE-EXPRESSION,FLUORESCENT PROTEINS,TRANSCRIPTION,INTEGRATION,CHROMOSOME,MOLECULES,SEQUENCE,PRECISE,SYSTEMS,DESIGN}},
  language     = {{eng}},
  pages        = {{10--19}},
  title        = {{Comprehensive study on Escherichia coli genomic expression : does position really matter?}},
  url          = {{http://dx.doi.org/10.1016/j.ymben.2020.07.007}},
  volume       = {{62}},
  year         = {{2020}},
}

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