Trends in Biotechnology
Volume 29, Issue 8, August 2011, Pages 370-378
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Review
Systems metabolic engineering for chemicals and materials

https://doi.org/10.1016/j.tibtech.2011.04.001Get rights and content

Metabolic engineering has contributed significantly to the enhanced production of various value-added and commodity chemicals and materials from renewable resources in the past two decades. Recently, metabolic engineering has been upgraded to the systems level (thus, systems metabolic engineering) by the integrated use of global technologies of systems biology, fine design capabilities of synthetic biology, and rational–random mutagenesis through evolutionary engineering. By systems metabolic engineering, production of natural and unnatural chemicals and materials can be better optimized in a multiplexed way on a genome scale, with reduced time and effort. Here, we review the recent trends in systems metabolic engineering for the production of chemicals and materials by presenting general strategies and showcasing representative examples.

Introduction

Global demand for the development of sustainable processes for the production of chemicals and materials from renewable biomass rather than from fossil fuel resources has been increasing. In this context, microorganisms have been employed for the production of various chemicals and materials, but their efficiencies are rather low when they are isolated from nature. During the past few decades, successful examples that have overcome this obstacle have combined traditionally employed methods of random mutation and selection with metabolic engineering to produce high-value chemicals in good yield 1, 2, 3, 4, 5.

In addition, recent advances in three emerging fields, systems biology, synthetic biology, and evolutionary engineering have allowed us to perform metabolic engineering more systematically and globally. Systems biology aims at unraveling the underlying principles of biological systems through profiling the whole cellular characteristics using high-throughput technologies together with computational methods (Box 1) 6, 7, 8, 9, 10. Thus, systems biology continues to provide genome-wide information that facilitates metabolic engineering at various phases by predicting gene targets to be manipulated throughout the whole cellular network, which characterizes functional behavior of the biological system from a holistic perspective, and identifies novel biological entities that contribute to the enhanced production of chemicals and materials 3, 5.

Synthetic biology aims at creating novel biologically functional parts, modules and systems by employing various molecular biology and synthetic DNA tools together with mathematical methodologies, and has been successfully applied in various metabolic engineering experiments (Box 2) 11, 12, 13. Several synthetic functions and modules have been developed to redirect metabolic pathways to produce novel metabolites [14]; compute Boolean operations according to input signals [15]; regulate metabolic fluxes in response to environmental changes [16]; perform a specific biological behavior such as on/off switch and oscillation 17, 18; and allow communication among cells [19].

As a result of the complex nature of cellular regulation and its association with metabolic networks, it is often difficult to achieve the desired cellular phenotype with metabolic engineering strategy alone. Hence, evolutionary engineering (Box 3), in which the expression levels of multiple genes are tuned and adapted simultaneously and autonomously by following the rules of natural selection for the desired cellular properties, can be used as a complementary technique in metabolic engineering. In addition, the genotypic changes achieved by evolutionary engineering that lead to a new cellular phenotype can be examined at the systems level, to reveal the target changes required for obtaining such a phenotype.

Here, we review recent advances in systems metabolic engineering for producer strain improvement by integrating the strategies of metabolic engineering with systems biology, synthetic biology, and evolutionary engineering (Figure 1, Figure 2). Recent milestones in combining two of these approaches, such as systems and synthetic biology, systems biology and evolutionary engineering, and synthetic biology and evolutionary engineering are also described, together with representative examples (Figure 1, Figure 2). Based on these examples, we propose how these technologies can be further combined in a synergistic manner. Systems metabolic engineering will become an essential strategy for the efficient production of chemicals and materials from renewable biomass.

Section snippets

Systems biology for metabolic engineering

For the holistic understanding of cellular and metabolic characteristics of microorganisms, systems biological analyses are performed to combine genome, transcriptome, proteome, metabolome, and fluxome, together with gene regulatory and signaling information (Box 1). Through such analyses, much detailed understanding of cellular and metabolic characteristics can be obtained, which can consequently result in identification of target genes to be manipulated 20, 21. Recently, we have employed this

Synthetic biology for metabolic engineering

Use of synthetic biology in metabolic engineering has mainly focused on constructing synthetic pathways for producing non-native or unnatural chemicals in cells and modulating genetic expression and circuits (Box 2). For producing non-native or unnatural products in a preferred host strain, the heterologous genes that encode enzymes that convert an existing cellular metabolite to a desired product can be cloned, synthesized or assembled from various sources and introduced into the host strain

Evolutionary engineering for metabolic engineering

Evolutionary engineering is a process that improves performance of the host strain by adaptive or random evolution of cells under a specified environmental or genetic condition (Box 3). This strategy has often been combined with metabolic engineering and is referred to as metabolic evolution 44, 45, 46, 47; the evolved strains by evolutionary engineering can be further optimized by metabolic engineering and vice versa. This approach has been employed for the improved production of succinate by

Integration of systems biology, synthetic biology, and evolutionary engineering for metabolic engineering

Recent recruitment of systems biology, synthetic biology and evolutionary engineering to metabolic engineering is exerting a positive impact on strain development for the improved production of chemicals and materials. However, there remain challenges that include: difficulties in suggesting multiple target genes to be manipulated; creating novel enzymes and pathways to achieve new desired functions; predicting and monitoring metabolic characteristics before and after pathway modifications;

Conclusion

Systems biology, synthetic biology, and evolutionary engineering have already been changing the way in which metabolic engineering is performed, which has given rise to systems metabolic engineering 3, 14, 20. Importantly, increased understanding of a cell by systems biology, creation of a cell by synthetic biology, and adaptation of a cell by evolutionary engineering synergistically have extended the spectrum of metabolic engineering for efficient production of various chemicals and materials;

Acknowledgments

We would like to thank Dr. Hyun Uk Kim for editing the manuscript. This work was supported by the Advanced Biomass R&D Center of Korea (ABC-2010-0029799) through the Global Frontier Research Program of the Ministry of Education, Science and Technology (MEST). Further support by World Class University program (R32-2008-000-10142-0) of MEST and GS Caltex is appreciated.

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