Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools

Wannemaeker, Lien De; Bervoets, Indra; Mey, Marjan De

doi:10.1016/j.biotechadv.2022.108028

Cited by 8 publications

(6 citation statements)

References 157 publications

(296 reference statements)

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“…Furthermore, the standardization protocol presented here is a promising starting point for the development of calibration protocols for different microbial hosts. This is especially interesting since several researchers in synthetic biology are exploring nonstandard hosts for a wide variety of applications . By selecting the appropriate size of the spheres, this method could be converted into a standardization protocol for a range of different interesting microbial hosts.…”

Section: Discussionmentioning

confidence: 99%

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Standardization of Fluorescent Reporter Assays in Synthetic Biology across the Visible Light Spectrum

De Wannemaeker,

Mey,

Bervoets

et al. 2023

ACS Synth. Biol.

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In synthetic biology, Fluorescent reporters are frequently used to characterize the expression levels obtained from both genetic parts such as promoters and ribosome binding sites as well as from complex genetic circuits. To this end, plate readers offer an easy and high-throughput way of characterizing both the growth and fluorescence expression levels of cell cultures. However, despite the similar mode of action used in different devices, their output is not comparable due to intrinsic differences in their setup. Additionally, the generated output is expressed using arbitrary units, limiting reliable comparison of results to measurements taken within one single experiment using one specific plate reader, hampering the transferability of data across different plate readers and laboratories. This article presents an easy and accessible calibration method for transforming the device-specific output into a standardized output expressing the amount of fluorescence per well as a known equivalent fluorophore concentration per cell for fluorescent reporters spanning the visible light spectrum. This calibration method follows a 2-fold approach determining both the estimated number of cells and the equivalent chemical fluorophore concentration per well. It will contribute to the comparison of plate reader experiments between different laboratories across the world and will therefore greatly improve the reliability and exchange of both results and genetic parts between research groups.

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Section: Discussionmentioning

confidence: 99%

“…This is especially interesting since several researchers in synthetic biology are exploring nonstandard hosts for a wide variety of applications. 17 By selecting the appropriate size of the spheres, this method could be converted into a standardization protocol for a range of different interesting microbial hosts.…”

Section: ■ Conclusionmentioning

confidence: 99%

Standardization of Fluorescent Reporter Assays in Synthetic Biology across the Visible Light Spectrum

De Wannemaeker,

Mey,

Bervoets

et al. 2023

ACS Synth. Biol.

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“…the host range of the activities encoded in the constructs. This involves not just the replication origins but also expression signals for enabling genes to be expressed in a large variety of hosts ( 64 ). Also, there is considerable room for standardizing mini-transposon delivery vectors (and other integrative tools) beyond the prototypes currently listed in the SEVAsib Table.…”

Section: Discussionmentioning

confidence: 99%

SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes

Martínez‐García

Fraile

Algar

et al. 2022

Nucleic Acids Research

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The SEVA platform (https://seva-plasmids.com) was launched one decade ago, both as a database (DB) and as a physical repository of plasmid vectors for genetic analysis and engineering of Gram-negative bacteria with a structure and nomenclature that follows a strict, fixed architecture of functional DNA segments. While the current update keeps the basic features of earlier versions, the platform has been upgraded not only with many more ready-to-use plasmids but also with features that expand the range of target species, harmonize DNA assembly methods and enable new applications. In particular, SEVA 4.0 includes (i) a sub-collection of plasmids for easing the composition of multiple DNA segments with MoClo/Golden Gate technology, (ii) vectors for Gram-positive bacteria and yeast and [iii] off-the-shelf constructs with built-in functionalities. A growing collection of plasmids that capture part of the standard—but not its entirety—has been compiled also into the DB and repository as a separate corpus (SEVAsib) because of its value as a resource for constructing and deploying phenotypes of interest. Maintenance and curation of the DB were accompanied by dedicated diffusion and communication channels that make the SEVA platform a popular resource for genetic analyses, genome editing and bioengineering of a large number of microorganisms.

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“…However, the scope of these remarkable achievements has been confined to a few model organisms, such as Escherichia coli and Saccharomyces cerevisiae , which have served as the primary platforms for demonstrating novel regulatory modalities and enabling tools. While these organisms have indeed showcased their potential for real‐world applications (e.g., E. coli Nissle 1917‐based bacterial therapeutics against cancer and metabolic disorder [6]), other non‐model organisms, with unique metabolisms (e.g., precursor turnover, product secretion, and tolerance to extreme conditions) and adaptations for specific environments (e.g., human organs, tumors, soil, and ocean), harbor immense potential for a myriad of unexplored applications [7]. Therefore, transferring the genetic parts and tools to non‐model organisms presents a thrilling opportunity to transform genetic circuits from laboratory to field and extend their applications far beyond the traditional boundaries.…”

Section: Figurementioning

confidence: 99%

Toward predictable universal genetic circuit design

Gao,

Wang

2024

Quant. Biol.

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Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools

Cited by 8 publications

References 157 publications

Standardization of Fluorescent Reporter Assays in Synthetic Biology across the Visible Light Spectrum

Standardization of Fluorescent Reporter Assays in Synthetic Biology across the Visible Light Spectrum

SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes

Toward predictable universal genetic circuit design

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