Synthetic Scaffold Systems for Increasing the Efficiency of Metabolic Pathways in Microorganisms

SIMPLE SUMMARY: Biotechnology involves the use of living organisms to create high-value products. Bacteria and yeast, in particular, are widely applied for such processes, but they may not naturally produce certain products, such as amino acids, organic acids, and alcohols in large amounts, if at all. Hence, the field of metabolic engineering has emerged for “tweaking” the biosynthetic pathways of these cells to encourage the high production of desired products. However, the complexity of the many metabolic pathways in natural cells makes it difficult to ensure that only the molecular components and pathways related to the desired product are enhanced. Very often, competing metabolic pathways and toxic intermediates will lower the production efficiency. Biological scaffolds have thus emerged as one strategy for anchoring the correct enzymes and substrates in place, and in the right orientation, to improve the production process in the cells. This review introduces the different categories of molecular scaffolds (i.e., protein, RNA, and DNA scaffolds) that have been developed, and compares their pros and cons and enhancement of production yields. It is emphasized that the design of these scaffolds is still a trial-and-error process, and further studies are needed to shed light on their underlying mechanisms so that better scaffolds can be developed. ABSTRACT: Microbes have been the preferred hosts for producing high-value chemicals from cheap raw materials. However, metabolic flux imbalance, the presence of competing pathways, and toxic intermediates often lead to low production efficiency. The spatial organization of the substrates, intermediates, and enzymes is critical to ensuring efficient metabolic activity by microorganisms. One of the most common approaches for bringing the key components of biosynthetic pathways together is through molecular scaffolds, which involves the clustering of pathway enzymes on engineered molecules via different interacting mechanisms. In particular, synthetic scaffold systems have been applied to improve the efficiency of various heterologous and synthetic pathways in Escherichia coli and Saccharomyces cerevisiae, with varying degrees of success. Herein, we review the recent developments and applications of protein-based and nucleic acid-based scaffold systems and discuss current challenges and future directions in the use of such approaches.