Directed evolution and synthetic biology applications to microbial systems

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Highlights

  • •

    Directed evolution allows complex trait engineering at a systems-scale.

  • •

    Synthetic biology accelerates directed evolution with diversity generation tools.

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    Synthetic biology can broaden the spectrum of screenable or selectable traits.

  • •

    Complex trait engineering can allow novel biotechnology applications.

Biotechnology applications require engineering complex multi-genic traits. The lack of knowledge on the genetic basis of complex phenotypes restricts our ability to rationally engineer them. However, complex phenotypes can be engineered at the systems level, utilizing directed evolution strategies that drive whole biological systems toward desired phenotypes without requiring prior knowledge of the genetic basis of the targeted trait. Recent developments in the synthetic biology field accelerates the directed evolution cycle, facilitating engineering of increasingly complex traits in biological systems. In this review, we summarize some of the most recent advances in directed evolution and synthetic biology that allows engineering of complex traits in microbial systems. Then, we discuss applications that can be achieved through engineering at the systems level.

Introduction

Microbes have been successfully employed in a broad range of applications, including in the food, pharmaceutical, petrochemical and bioremediation industries [1]. Increasingly complex applications are demanding more sophisticated designs, that consider optimization of multiple phenotypes such as tolerance, pathway flux, and growth rate, each of which is governed by multiple genes and their interaction with environmental factors. The lack of knowledge on the genetic basis of these complex traits restricts our ability to rationally engineer them. An alternative approach to manipulate these complex phenotypes is to engineer at the systems level [2], driving entire systems toward desired phenotypes without deep a priori knowledge of the underlying mechanisms.

Recent technological developments facilitate engineering of microbes at the systems level. These advances come primarily through the fields of directed evolution, metabolic engineering, and synthetic biology, with successful applications already at the gene, pathway, genome and even multi-organism (consortia) level. This approach sets the stage to explore diverse and complex functions for novel biotechnology applications. In this review, we discuss strategies that can be used to engineer complex traits in microbial systems. Then, we provide examples and applications of biological systems engineering on increasingly complex scales.

Section snippets

Engineering complex traits in microbial systems

Engineering complex traits can be accomplished using directed evolution strategies [3]. Directed evolution mimics natural evolution in more controlled settings to evolve biological systems toward user-defined phenotypes. A common demonstration of this idea is present in adaptive laboratory evolution (ALE) experiments. During ALE, microbial cultures are grown from hundreds of generations in defined selective conditions, which allows evolution of improved phenotypes [4]. As an example, Tenaillon

Applications of synthetic biology on a systems-level

With efficient diversity generation methods (Figure 1) and proper screening or selection strategies (Figure 2), rounds of directed evolution can be successfully employed to engineer complex traits in microbial systems even if the genetic basis are not fully understood. This brings exciting new frontiers on the range of functions and applications that biotechnology will be able to address in the near future. In this section, we describe applications of directed evolution and synthetic biology on

Conclusions and future perspectives

The ability to engineer complex multi-genic phenotypes is fundamental for several biotechnology endeavors and currently restricts the field. The combination of recent synthetic biology tools with directed evolution and metabolic engineering can allow engineering of biological systems as a whole, via manipulation of increasingly complex traits. With these technologies, complex systems and traits are now amenable to engineering, fueling novel biotechnology applications across multiple industrial

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

We would like to thank the Gill lab for discussions on the topic. We also thank the US Department of Energy (Grant DE-SC0008812) and CAPES foundation (Grant No. 0315133) for funding this work.

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