Synthetic biology to access and expand nature's chemical diversity

Michael J. Smanski; Hui Zhou; Jan Claesen; Ben Shen; Michael A. Fischbach; Christopher A. Voigt

doi:10.1038/nrmicro.2015.24

How To Make a Glycopeptide: A Synthetic Biology Approach To Expand Antibiotic Chemical Diversity

ACS Infectious Diseases ◽

10.1021/acsinfecdis.6b00105 ◽

2016 ◽

Vol 2 (9) ◽

pp. 642-650 ◽

Cited By ~ 18

Author(s):

Grace Yim ◽

Wenliang Wang ◽

Maulik N. Thaker ◽

Stephanie Tan ◽

Gerard D. Wright

Keyword(s):

Synthetic Biology ◽

Chemical Diversity ◽

Synthetic Biology Approach

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Cell-free genetic devices confer autonomic and adaptive properties to hydrogels

10.1101/2019.12.12.872622 ◽

2019 ◽

Cited By ~ 1

Author(s):

Colette J. Whitfield ◽

Alice M. Banks ◽

Gema Dura ◽

John Love ◽

Jonathan E. Fieldsend ◽

...

Keyword(s):

Gene Expression ◽

Protein Synthesis ◽

Information Processing ◽

Synthetic Biology ◽

Smart Materials ◽

Living Organism ◽

Chemical Diversity ◽

Biological Information ◽

Self Healing ◽

Wide Range

AbstractSmart materials are able to alter one or more of their properties in response to defined stimuli. Our ability to design and create such materials, however, does not match the diversity and specificity of responses seen within the biological domain. We propose that relocation of molecular phenomena from living cells into hydrogels can be used to confer smart functionality to materials. We establish that cell-free protein synthesis can be conducted in agarose hydrogels, that gene expression occurs throughout the material and that co-expression of genes is possible. We demonstrate that gene expression can be controlled transcriptionally (using in gel gene interactions) and translationally in response to small molecule and nucleic acid triggers. We use this system to design and build a genetic device that can alter the structural property of its chassis material in response to exogenous stimuli. Importantly, we establish that a wide range of hydrogels are appropriate chassis for cell-free synthetic biology, meaning a designer may alter both the genetic and hydrogel components according to the requirements of a given application. We probe the relationship between the physical structure of the gel and in gel protein synthesis and reveal that the material itself may act as a macromolecular crowder enhancing protein synthesis. Given the extensive range of genetically encoded information processing networks in the living kingdom and the structural and chemical diversity of hydrogels, this work establishes a model by which cell-free synthetic biology can be used to create autonomic and adaptive materials.Significance statementSmart materials have the ability to change one or more of their properties (e.g. structure, shape or function) in response to specific triggers. They have applications ranging from light-sensitive sunglasses and drug delivery systems to shape-memory alloys and self-healing coatings. The ability to programme such materials, however, is basic compared to the ability of a living organism to observe, understand and respond to its environment. Here we demonstrate the relocation of biological information processing systems from cells to materials. We achieved this by operating small, programmable genetic devices outside the confines of a living cell and inside hydrogel matrices. These results establish a method for developing materials functionally enhanced with molecular machinery from biological systems.

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GPAHex-A synthetic biology platform for Type IV–V glycopeptide antibiotic production and discovery

Nature Communications ◽

10.1038/s41467-020-19138-5 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Min Xu ◽

Wenliang Wang ◽

Nicholas Waglechner ◽

Elizabeth J. Culp ◽

Allison K. Guitor ◽

...

Keyword(s):

Synthetic Biology ◽

Antibiotic Production ◽

Structural Complexity ◽

Fold Increase ◽

Building Blocks ◽

Chemical Diversity ◽

Glycopeptide Antibiotics ◽

Gram Positive Bacteria ◽

Type Iv

Abstract Glycopeptide antibiotics (GPAs) are essential for the treatment of severe infectious diseases caused by Gram-positive bacteria. The emergence and spread of GPA resistance have propelled the search for more effective GPAs. Given their structural complexity, genetic intractability, and low titer, expansion of GPA chemical diversity using synthetic or medicinal chemistry remains challenging. Here we describe a synthetic biology platform, GPAHex (GPA Heterologous expression), which exploits the genes required for the specialized GPA building blocks, regulation, antibiotic transport, and resistance for the heterologous production of GPAs. Application of the GPAHex platform results in: (1) a 19-fold increase of corbomycin titer compared to the parental strain, (2) the discovery of a teicoplanin-class GPA from an Amycolatopsis isolate, and (3) the overproduction and characterization of a cryptic nonapeptide GPA. GPAHex provides a platform for GPA production and mining of uncharacterized GPAs and provides a blueprint for chassis design for other natural product classes.

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Opportunities for Synthetic Biology in Antibiotics: Expanding Glycopeptide Chemical Diversity

ACS Synthetic Biology ◽

10.1021/sb300092n ◽

2012 ◽

Vol 4 (3) ◽

pp. 195-206 ◽

Cited By ~ 32

Author(s):

Maulik N. Thaker ◽

Gerard D. Wright

Keyword(s):

Synthetic Biology ◽

Chemical Diversity

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RetroPath2.0: a retrosynthesis workflow for metabolic engineers

10.1101/141721 ◽

2017 ◽

Cited By ~ 2

Author(s):

Baudoin Delépine ◽

Thomas Duigou ◽

Pablo Carbonell ◽

Jean-Loup Faulon

Keyword(s):

Synthetic Biology ◽

Open Source ◽

Computer Aided Design ◽

Reaction Network ◽

Ease Of Use ◽

Chemical Diversity ◽

Industrial Biotechnology ◽

List Type ◽

Enzyme Promiscuity ◽

Main Challenge

AbstractSynthetic biology applied to industrial biotechnology is transforming the way we produce chemicals. However, despite advances in the scale and scope of metabolic engineering, the bioproduction process still remains costly. In order to expand the chemical repertoire for the production of next generation compounds, a major engineering biology effort is required in the development of novel design tools that target chemical diversity through rapid and predictable protocols. Addressing that goal involves retrosynthesis approaches that explore the chemical biosynthetic space. However, the complexity associated with the large combinatorial retrosynthesis design space has often been recognized as the main challenge hindering the approach. Here, we provide RetroPath2.0, an automated open source workflow for retrosynthesis based on generalized reaction rules that perform the retrosynthesis search from chassis to target through an efficient and well-controlled protocol. Its easiness of use and the versatility of its applications make of this tool a valuable addition into the biological engineer bench desk. We show through several examples the application of the workflow to biotechnological relevant problems, including the identification of alternative biosynthetic routes through enzyme promiscuity; or the development of biosensors. We demonstrate in that way the ability of the workflow to streamline retrosynthesis pathway design and its major role in reshaping the design, build, test and learn pipeline by driving the process toward the objective of optimizing bioproduction. The RetroPath2.0 workflow is built using tools developed by the bioinformatics and cheminformatics community, because it is open source we anticipate community contributions will likely expand further the features of the workflow.HighlightsState-of-the-art Computer-Aided Design retrosynthesis solutions lack open source and ease of useWe propose RetroPath2.0 a modular and open-source workflow to perform retrosynthesisRetroPath2.0 computes reaction network between Source and Sink sets of compoundsRetroPath2.0 is distributed as a KNIME workflow for desktop computersRetroPath2.0 is ready-for-use and distributed with reaction rulesFundingThis work was supported by the French National Research Agency [ANR-15-CE1-0008], the Biotechnology and Biological Sciences Research Council, Centre for synthetic biology of fine and speciality chemicals [BB/M017702/1]; Synthetic Biology Applications for Protective Materials [EP/N025504/1], and GIP Genopole.

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