Evolutionary Engineering for Industrial Microbiology
Superficially, evolutionary engineering is a paradoxical field that balances competing interests. In natural settings, evolution iteratively selects and enriches subpopulations that are best adapted to a particular ecological niche using random processes
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Evolutionary Engineering for Industrial Microbiology Niti Vanee*, Adam B. Fisher*, and Stephen S. Fong
Abstract Superficially, evolutionary engineering is a paradoxical field that balances competing interests. In natural settings, evolution iteratively selects and enriches subpopulations that are best adapted to a particular ecological niche using random processes such as genetic mutation. In engineering desired approaches utilize rational prospective design to address targeted problems. When considering details of evolutionary and engineering processes, more commonality can be found. Engineering relies on detailed knowledge of the problem parameters and design properties in order to predict design outcomes that would be an optimized solution. When detailed knowledge of a system is lacking, engineers often employ algorithmic search strategies to identify empirical solutions. Evolution epitomizes this iterative optimization by continuously diversifying design options from a parental design, and then selecting the progeny designs that represent satisfactory solutions. In this chapter, the technique of applying the natural principles of evolution to engineer microbes for industrial applications is discussed to highlight the challenges and principles of evolutionary engineering. Keywords Cellular objectives • Directed evolution • Diversity • Engineering objectives • Evolutionary engineering • Fitness landscapes • Industrial microbiology • Screening and selection
*The authors Niti Vanee and Adam B. Fisher are contributed equally. N. Vanee • A.B. Fisher • S.S. Fong (*) Department of Chemical and Life Science Engineering, Virginia Commonwealth University, 601 W. Main Street, Room 422, 843028, Richmond, VA 23284-3028, USA e-mail: [email protected] X. Wang et al. (eds.), Reprogramming Microbial Metabolic Pathways, Subcellular Biochemistry 64, DOI 10.1007/978-94-007-5055-5_3, © Springer Science+Business Media Dordrecht 2012
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Abbreviations ADAM array-based discovery of adaptive mutations CO cellular objectives EMS ethyl methane sulfonate EO engineering objectives EvoEng evolutionary engineering MAGE multiplex automated genome engineering NTG nitroso-methyl guanidine Oligo(s) oligonucleotide(s) RNAseq RNA sequencing SELEX selectable evolution of ligands by exponential enrichment SS solution space StEP staggered extension process TRMR trackable multiplex recombineering
3.1
Introduction
The interaction of humans and microorganisms has a long history including the domestication of microbes as early as the fifth century BC for a variety of fermentation processes such as baking and viticulture. With the progression of time and scientific knowledge, microbiology has been applied to many industrial sectors including food, waste treatment, health and medicine, and more recently, energy. The microbes used in these processes have all been advantageous over other production methodologies due to the unique properties of life: a self-replicating system, capable of organizing highly complex, chaotic chemistry in
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