Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria

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Abstract

Non-model bacteria like Pseudomonas putida, Lactococcus lactis and other species have unique and versatile metabolisms, offering unique opportunities for Synthetic Biology (SynBio). However, key genome editing and recombineering tools require optimization and large-scale multiplexing to unlock the full SynBio potential of these bacteria. In addition, the limited availability of a set of characterized, species-specific biological parts hampers the construction of reliable genetic circuitry. Mining of currently available, diverse bacteriophages could complete the SynBio toolbox, as they constitute an unexplored treasure trove for fully adapted metabolic modulators and orthogonally-functioning parts, driven by the longstanding co-evolution between phage and host.

Abstract

Non-model bacteria offer unique and versatile metabolisms for synthetic biology. In this Perspective, the authors explore the limited availability of well-characterised biological parts in these species and argue that bacteriophages represent a diverse trove of orthogonal parts.

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Double-slit photoelectron interference in strong-field ionization of the neon dimer

Maksim Kunitski, Nicolas Eicke, Pia Huber … (2019)

Wave-particle duality is an inherent peculiarity of the quantum world. The double-slit experiment has been frequently used for understanding different aspects of this fundamental concept. The occurrence of interference rests on the lack of which-way information and on the absence of decoherence mechanisms, which could scramble the wave fronts. Here, we report on the observation of two-center interference in the molecular-frame photoelectron momentum distribution upon ionization of the neon dimer by a strong laser field. Postselection of ions, which are measured in coincidence with electrons, allows choosing the symmetry of the residual ion, leading to observation of both, gerade and ungerade, types of interference.

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Structural absorption by barbule microstructures of super black bird of paradise feathers

Dakota E. McCoy, Teresa J. Feo, Todd Alan Harvey … (2018)

Many studies have shown how pigments and internal nanostructures generate color in nature. External surface structures can also influence appearance, such as by causing multiple scattering of light (structural absorption) to produce a velvety, super black appearance. Here we show that feathers from five species of birds of paradise (Aves: Paradisaeidae) structurally absorb incident light to produce extremely low-reflectance, super black plumages. Directional reflectance of these feathers (0.05–0.31%) approaches that of man-made ultra-absorbent materials. SEM, nano-CT, and ray-tracing simulations show that super black feathers have titled arrays of highly modified barbules, which cause more multiple scattering, resulting in more structural absorption, than normal black feathers. Super black feathers have an extreme directional reflectance bias and appear darkest when viewed from the distal direction. We hypothesize that structurally absorbing, super black plumage evolved through sensory bias to enhance the perceived brilliance of adjacent color patches during courtship display.

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Programming cells by multiplex genome engineering and accelerated evolution.

Harris Wang, Farren J. Isaacs, Peter A Carr … (2009)

The breadth of genomic diversity found among organisms in nature allows populations to adapt to diverse environments. However, genomic diversity is difficult to generate in the laboratory and new phenotypes do not easily arise on practical timescales. Although in vitro and directed evolution methods have created genetic variants with usefully altered phenotypes, these methods are limited to laborious and serial manipulation of single genes and are not used for parallel and continuous directed evolution of gene networks or genomes. Here, we describe multiplex automated genome engineering (MAGE) for large-scale programming and evolution of cells. MAGE simultaneously targets many locations on the chromosome for modification in a single cell or across a population of cells, thus producing combinatorial genomic diversity. Because the process is cyclical and scalable, we constructed prototype devices that automate the MAGE technology to facilitate rapid and continuous generation of a diverse set of genetic changes (mismatches, insertions, deletions). We applied MAGE to optimize the 1-deoxy-D-xylulose-5-phosphate (DXP) biosynthesis pathway in Escherichia coli to overproduce the industrially important isoprenoid lycopene. Twenty-four genetic components in the DXP pathway were modified simultaneously using a complex pool of synthetic DNA, creating over 4.3 billion combinatorial genomic variants per day. We isolated variants with more than fivefold increase in lycopene production within 3 days, a significant improvement over existing metabolic engineering techniques. Our multiplex approach embraces engineering in the context of evolution by expediting the design and evolution of organisms with new and improved properties.

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Author and article information

Contributors

Rob Lavigne:

ORCID: http://orcid.org/0000-0001-7377-1314

rob.lavigne@kuleuven.be

Journal

Journal ID (nlm-ta): Nat Commun

Journal ID (iso-abbrev): Nat Commun

Title: Nature Communications

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2041-1723

Publication date (Electronic): 20 October 2020

Publication date PMC-release: 20 October 2020

Publication date Collection: 2020

Volume: 11

Electronic Location Identifier: 5294

Affiliations

[1 ]GRID grid.5596.f, ISNI 0000 0001 0668 7884, Department of Biosystems, Laboratory of Gene Technology, , KU Leuven, ; Kasteelpark Arenberg 21 box 2462, 3001 Leuven, BE Belgium

[2 ]GRID grid.5170.3, ISNI 0000 0001 2181 8870, The Novo Nordisk Foundation Center for Biosustainability, , Technical University of Denmark, ; Kemitorvet, Building 220, 2800 Kgs Lyngby, DK Denmark

Author information

Eveline-Marie Lammens http://orcid.org/0000-0002-4946-4469

Pablo Ivan Nikel http://orcid.org/0000-0002-9313-7481

Rob Lavigne http://orcid.org/0000-0001-7377-1314

Article

Publisher ID: 19124

DOI: 10.1038/s41467-020-19124-x

PMC ID: 7576135

PubMed ID: 33082347

SO-VID: 4020dc94-418d-4839-8722-846779e3df0a

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 17 April 2020

Date accepted : 25 September 2020

Funding

Funded by: FundRef https://doi.org/10.13039/100010661, EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020);

Award ID: 819800

Award ID: 814418

Award ID: 819800

Award Recipient : Eveline-Marie Lammens Pablo Ivan Nikel Rob Lavigne

Funded by: FundRef https://doi.org/10.13039/501100009708, Novo Nordisk Fonden (Novo Nordisk Foundation);

Award ID: NNF10CC1016517

Award ID: NNF18OC0034818

Award Recipient : Pablo Ivan Nikel

Funded by: FundRef https://doi.org/10.13039/501100004836, Det Frie Forskningsråd (Danish Council for Independent Research);

Award ID: 8021-00039B

Award Recipient : Pablo Ivan Nikel

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ScienceOpen disciplines: Uncategorized

Keywords: bacteriophages,genetic circuit engineering,synthetic biology

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ScienceOpen disciplines: Uncategorized

Keywords: bacteriophages, genetic circuit engineering, synthetic biology

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Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria

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Most cited references 168

Double-slit photoelectron interference in strong-field ionization of the neon dimer

Structural absorption by barbule microstructures of super black bird of paradise feathers

Programming cells by multiplex genome engineering and accelerated evolution.

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