Metabolic Engineering of Escherichia coli for Natural Product Biosynthesis

E. coli has emerged as a prominent host for natural product biosynthesis. Improved enzymes with higher activity, altered substrate specificity, and product selectivity can be obtained by structure-based or computer simulation-based protein engineering. Balancing the expression levels of genes or pathway modules is effective in increasing the metabolic flux towards target compounds. System-wide analysis of metabolic networks, omics analysis, adaptive laboratory evolution, and biosensor-based screening can further increase the production of target compounds. Systems metabolic engineering allows the development of engineered E. coli strains that are capable of more efficiently producing diverse natural products. Natural products are widely employed in our daily lives as food additives, pharmaceuticals, nutraceuticals, and cosmetic ingredients, among others. However, their supply has often been limited because of low-yield extraction from natural resources such as plants. To overcome this problem, metabolically engineered Escherichia coli has emerged as a cell factory for natural product biosynthesis because of many advantages including the availability of well-established tools and strategies for metabolic engineering and high cell density culture, in addition to its high growth rate. We review state-of-the-art metabolic engineering strategies for enhanced production of natural products in E. coli, together with representative examples. Future challenges and prospects of natural product biosynthesis by engineered E. coli are also discussed. Natural products are widely employed in our daily lives as food additives, pharmaceuticals, nutraceuticals, and cosmetic ingredients, among others. However, their supply has often been limited because of low-yield extraction from natural resources such as plants. To overcome this problem, metabolically engineered Escherichia coli has emerged as a cell factory for natural product biosynthesis because of many advantages including the availability of well-established tools and strategies for metabolic engineering and high cell density culture, in addition to its high growth rate. We review state-of-the-art metabolic engineering strategies for enhanced production of natural products in E. coli, together with representative examples. Future challenges and prospects of natural product biosynthesis by engineered E. coli are also discussed. a process for the rapid isolation of strains with desirable phenotypes by multiple rounds of cultivation and selection. a tool for quantifying metabolic fluxes through isotopomer analysis using stable 13C-labeled tracers. The propagation of 13C-labeled compounds over time can be tracked using mass spectrometry to record and analyze labeling patterns in metabolic intermediates or final products. an RNA-guided target gene knockdown technology which involves the action of a catalytically dead Cas9 (dCas9) protein to inhibit target gene transcription through engineered guide RNAs. a ubiquitous enzyme belonging to the hemoprotein family which primarily functions as monooxygenase; requires a partner reductase for electron donation. a process for the rapid isolation of superior enzymes by multiple rounds of mutation and selection. a phenomenon when the activity of an enzyme is suppressed by the end product or intermediates of the pathway; an inhibitor interacts with the target enzyme by binding to an allosteric site, which is followed by conformational changes of the enzyme. a set of genome-wide metabolic reaction models containing gene–protein–reaction association information that describes the entire cellular metabolism of a specific organism. a broad set of algorithms that are used to perform calculations and tasks based on patterns and inferences using training data. a genetic construct that converts the abundance of a target molecule into an observable signal in a proportional manner. a multidomain enzyme or a complex of enzymes that catalyze polyketide biosynthesis; these can be classified into three major types (types I, II, and III) according to their mechanism of carbon chain elongation. an enzyme which can catalyze multiple side reactions or can utilize multiple substrates beyond its main substrate. a strategy that spatially recruits multiple enzymes using synthetic scaffolds to efficiently deliver and convert metabolic intermediates. a trans-acting target-specific knockdown tool comprising a noncoding RNA (harboring a target-specific antisense sequence, a scaffold, and a terminator) and Hfq protein; it inhibits translation by binding to the translation initiation region of the target mRNA. an interdisciplinary field of study which integrates traditional metabolic engineering with systems biology, synthetic biology, and evolutionary engineering to provide a holistic approach to microbial metabolism for enhanced production of target chemicals while considering upstream to downstream bioprocesses. a designable intergenic region harboring two hairpin loops flanking an RNase E site; the stability of the target gene mRNA is determined by the secondary structure of the intergenic region.