Biotechnological domestication of pseudomonads using synthetic biology

Key Points

  • One of the pillars of contemporary synthetic biology is the use of reliable biological chassis into which users can plug-in and plug-out genetic circuits and new-to-nature properties at will.

  • The microorganisms that are easiest to genetically manipulate in the laboratory are frequently suboptimal for industrial applications owing to physicochemical stress and harsh operation conditions.

  • Hallmark features of pseudomonads as synthetic biology platforms include their pre-endowed metabolic, physiological and stress-endurance traits, which make them adequate for real-life biotechnological needs.

  • The range of molecular tools that are available for the rational manipulation of pseudomonads is continuously increasing in variety and scope. These assets include streamlined plasmid vectors for gene expression and genome editing, as well as a number of in silico tools for the modelling and prediction of metabolic and physiological behaviour of these bacteria.

  • String–weight biological engineering enables the assembly of complex biosystems by combining the physical connectivity of available parts and modules with evolutionary gravitation of input–output transfer functions towards functional optimality.

Abstract

Much of contemporary synthetic biology research relies on the use of bacterial chassis for plugging-in and plugging-out genetic circuits and new-to-nature functionalities. However, the microorganisms that are the easiest to manipulate in the laboratory are often suboptimal for downstream industrial applications, which can involve physicochemical stress and harsh operating conditions. In this Review, we advocate the use of environmental Pseudomonas strains as model organisms that are pre-endowed with the metabolic, physiological and stress-endurance traits that are demanded by current and future synthetic biology and biotechnological needs.

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Figure 1: The quest for an optimal synthetic biology chassis.
Figure 2: Ecological habitats of Pseudomonas spp.
Figure 3: Catabolism of hexoses in Pseudomonas spp: one substrate, different strategies.
Figure 4: Genetic traps to identify biotransformations.
Figure 5: The metabolic heart of Pseudomonas putida KT2440.

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Acknowledgements

This study was supported by the BIO and FEDER CONSOLIDER-INGENIO Program of the Spanish Ministry of Science and Innovation, the ST-FLOW, ARYSIS and EVOPROG Contracts of the EU, the ERANET-IB Program, and the PROMT Project of the CAM. PIN is a researcher from the Consejo Nacional de Investigaciones Científicas y Técnicas (Argentina) and holds a Marie Curie Actions Programme grant obtained from the EU (ALLEGRO, UE-FP7-PEOPLE-2011-IIF-300508).

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Forward-engineering

The rational design of complex objects with properties that can be quantitatively predicted from the attributes of the components.

Biological chassis

An autonomous genetic and/or biochemical scaffold that functions as an dynamic platform for implanting forward-designed biological devices.

Logic gates

Devices that execute binary, Boolean operations in which (typically) one or two inputs with values 1 or 0 are processed into one fixed, digital output (0 or 1 as well). The output of one gate can become the input of another gate, thereby enabling composability and scalability.

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Nikel, P., Martínez-García, E. & de Lorenzo, V. Biotechnological domestication of pseudomonads using synthetic biology. Nat Rev Microbiol 12, 368–379 (2014). https://doi.org/10.1038/nrmicro3253

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