Abstract
Microbial cell factories have proven to be an economical means of production for many bulk, specialty, and fine chemical products. However, we still lack both a holistic understanding of organism physiology and the ability to predictively tune enzyme activities in vivo, thus slowing down rational engineering of industrially relevant strains. An alternative concept to rational engineering is to use evolution as the driving force to select for desired changes, an approach often described as evolutionary engineering. In evolutionary engineering, in vivo selections for a desired phenotype are combined with either generation of spontaneous mutations or some form of targeted or random mutagenesis. Evolutionary engineering has been used to successfully engineer easily selectable phenotypes, such as utilization of a suboptimal nutrient source or tolerance to inhibitory substrates or products. In this review, we focus primarily on a more challenging problem—the use of evolutionary engineering for improving the production of chemicals in microbes directly. We describe recent developments in evolutionary engineering strategies, in general, and discuss, in detail, case studies where production of a chemical has been successfully achieved through evolutionary engineering by coupling production to cellular growth.
Highlights
The idea of using microbes as cell factories for chemicals has a long history and is well established as an industrial activity [1]
We describe the full workflow of the evolutionary engineering approach, including in design of growth-coupling strategies, approaches to speed up evolution by creating genetic diversity, silico design of growth-coupling strategies, approaches to speed up evolution by creating genetic practical implementation of laboratory evolution in vivo, and the use of resequencing and other omics diversity, practical implementation of laboratory evolution in vivo, and the use of resequencing and approaches to understand the genetic changes that occur in the evolutionary process
The growth-coupled adaptive laboratory evolution (ALE) strategies that this review focuses on are not the only approach to perform evolutionary engineering for chemical production
Summary
The idea of using microbes as cell factories for chemicals has a long history and is well established as an industrial activity [1]. Cells exposed a suboptimal environment, such as the presence a toxic for than is intended for.are Examples of these to types of evolutionary engineering studies includeofevolution compound, and is quitetounlikely cells can escape such hydrolysis selection and optimize for ability a thermotolerance [18],itability toleratethat ionic liquids used in biomass [19], or for the different phenotype than is intended for. Examples of these types of evolutionary engineering studies to utilize efficiently suboptimal carbon sources, such as glycerol [20].
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