Metabolic Engineering Mevalonate Pathway Mediated by RNA Scaffolds for Mevalonate and Isoprene Production in Escherichia coli

Engineering Escherichia coli for Perillyl Alcohol Production with Reduced Endogenous Dehydrogenation

Perillyl alcohol is a widely utilized antitumor agent in cancer therapy. Due to the limitations associated with chemical synthesis and plant extraction methods, bioengineering microorganisms for the production of perillyl alcohol and its precursor limonene offers a more scalable and industrially compatible approach. In this study, we present the design of an Escherichia coli cell factory capable of de novo synthesis of limonene and perillyl alcohol from glucose. A comprehensive systems engineering approach was employed to increase precursor availability, enhance electron transfer efficiency, and reduce byproduct formation, resulting in efficient perillyl alcohol production. Specifically, ribosome-binding site optimization and increased enzyme expression improved limonene production to 417.04 mg/L. Additionally, the overexpression of cytochrome P450 electron transport proteins, knockdown of endogenous ethanol dehydrogenase to prevent product loss, and implementation of two-phase fermentation led to the production of 309.1 mg/L perillyl alcohol in shake flask cultures, which marks the highest titer reported for shake flask systems. This illustrates the critical role of reducing perillyl aldehyde byproduct formation in enhancing the feasibility of Escherichia coli-based perillyl alcohol production, providing a foundation for its economical large-scale production via microbial bioprocessing.

Review of Recent Advances in Microbial Production and Applications of Nerolidol

Nerolidol, an oxygenated sesquiterpene (C15H26O) that occurs in plants, exhibits significant bioactivities such as antioxidant, anti-inflammatory, antimicrobial, and neuroprotective activities. It is a U.S. Food and Drug Administration-approved flavoring agent and a common ingredient in several commercial products such as toiletries and detergents. In addition, the potential applications of nerolidol that may prove beneficial for human health, agriculture, and the food industry have garnered increasing attention from researchers in these fields. Recent years have witnessed the application of metabolic engineering and synthetic biology strategies for constructing microbial cell factories that can produce nerolidol, which is considered a sustainable and economical approach. This review summarizes recent research on the biological activities and applications of nerolidol as well as nerolidol production using microbial cell factories. In addition, the synthesis of bioactive derivatives of nerolidol is addressed. In summary, this review provides readers with an updated understanding of the potential applications and green production prospects of nerolidol.

Engineering microbial cell factories by multiplexed spatiotemporal control of cellular metabolism: Advances, challenges, and future perspectives

Generally, the metabolism in microbial organism is an intricate, spatiotemporal process that emerges from gene regulatory networks, which affects the efficiency of product biosynthesis. With the coming age of synthetic biology, spatiotemporal control systems have been explored as versatile strategies to promote product biosynthesis at both spatial and temporal levels. Meanwhile, the designer synthetic compartments provide new and promising approaches to engineerable spatiotemporal control systems to construct high-performance microbial cell factories. In this article, we comprehensively summarize recent developments in spatiotemporal control systems for tailoring advanced cell factories, and illustrate how to apply spatiotemporal control systems in different microbial species with desired applications. Future challenges of spatiotemporal control systems and perspectives are also discussed.

Shaping up a Mevalonate Pathway in the E. coli-E. coli Coculture System for the Production of Sesquiterpenes

Sesquiterpenoids are one of the most diverse families of natural compounds with various bioactivities and functions. The introduction of an exogenous mevalonate pathway was recognized to be the proficient approach in Escherichia coli for sesquiterpene biosynthesis. It is challenging from the coordination of the pathway constituents to forge an active mevalonate pathway, especially the balance of mevalonate generation and consumption by the top and bottom portions of the mevalonate pathway. In this study, the pathway constituents were categorized to hierarchically assemble an active mevalonate pathway, which was optimized in a Kronecker product fashion and evaluated with host adaptation. Finally, the E. coli-E. coli coculture system was created to minimize the mevalonate accumulation. As a result, these engineering processes significantly maximized pathway efficiency and improved sesquiterpene biosynthesis, which suggests an easy-to-use approach to erect E. coli cell factories for sesquiterpene production.

Advances in multi-enzyme co-localization strategies for the construction of microbial cell factory

Biomanufacturing, driven by technologies such as synthetic biology, offers significant potential to advance the bioeconomy and promote sustainable development. It is anticipated to transform traditional manufacturing and become a key industry in future strategies. Cell factories are the core of biomanufacturing. The advancement of synthetic biology and growing market demand have led to the production of a greater variety of natural products and increasingly complex metabolic pathways. However, this progress also presents challenges, notably the conflict between natural product production and chassis cell growth. This conflict results in low productivity and yield, adverse side effects, metabolic imbalances, and growth retardation. Enzyme co-localization strategies have emerged as a promising solution. This article reviews recent progress and applications of these strategies in constructing cell factories for efficient natural product production. It comprehensively describes the applications of enzyme-based compartmentalization, metabolic pathway-based compartmentalization, and synthetic organelle-based compartmentalization in improving product titers. The article also explores future research directions and the prospects of combining multiple strategies with advanced technologies.

Application of Acetate as a Substrate for the Production of Value-Added Chemicals in Escherichia coli

At present, the production of the majority of valuable chemicals is dependent on the microbial fermentation of carbohydrate substrates. However, direct competition is a potential problem for microbial feedstocks that are also used within the food/feed industries. The use of alternative carbon sources, such as acetate, has therefore become a research focus. As a common organic acid, acetate can be generated from lignocellulosic biomass and C1 gases, as well as being a major byproduct in microbial fermentation, especially in the presence of an excess carbon source. As a model microorganism, Escherichia coli has been widely applied in the production of valuable chemicals using different carbon sources. Recently, several valuable chemicals (e.g., succinic acid, itaconic acid, isobutanol, and mevalonic acid) have been investigated for synthesis in E. coli using acetate as the sole carbon source. In this review, we summarize the acetate metabolic pathway in E. coli and recent research into the microbial production of chemical compounds in E. coli using acetate as the carbon source. Although microbial synthetic pathways for different compounds have been developed in E. coli, the production titer and yield are insufficient for commercial applications. Finally, we discuss the development prospects and challenges of using acetate for microbial fermentation.

Optimization of IspSib stability through directed evolution to improve isoprene production

Enzyme stability is often a limiting factor in the microbial production of high-value-added chemicals and commercial enzymes. A previous study by our research group revealed that the unstable isoprene synthase from Ipomoea batatas (IspSib) critically limits isoprene production in engineered Escherichia coli. Directed evolution was, therefore, performed in the present study to improve the thermostability of IspSib. First, a tripartite protein folding system designated as lac'-IspSib-'lac, which could couple the stability of IspSib to antibiotic ampicillin resistance, was successfully constructed for the high-throughput screening of variants. Directed evolution of IspSib was then performed through two rounds of random mutation and site-saturation mutation, which produced three variants with higher stability: IspSibN397V A476V, IspSibN397V A476T, and IspSibN397V A476C. The subsequent in vitro thermostability test confirmed the increased protein stability. The melting temperatures of the screened variants IspSibN397V A476V, IspSibN397V A476T, and IspSibN397V A476C were 45.1 ± 0.9°C, 46.1 ± 0.7°C, and 47.2 ± 0.3°C, respectively, each of which was higher than the melting temperature of wild-type IspSib (41.5 ± 0.4°C). The production of isoprene at the shake-flask fermentation level was increased by 1.94-folds, to 1,335 mg/L, when using IspSibN397V A476T. These findings provide insights into the optimization of the thermostability of terpene synthases, which are key enzymes for isoprenoid production in engineered microorganisms. In addition, the present study would serve as a successful example of improving enzyme stability without requiring detailed structural information or catalytic reaction mechanisms.IMPORTANCEThe poor thermostability of IspSib critically limits isoprene production in engineered Escherichia coli. A tripartite protein folding system designated as lac'-IspSib-'lac, which could couple the stability of IspSib to antibiotic ampicillin resistance, was successfully constructed for the first time. In order to improve the enzyme stability of IspSib, the directed evolution of IspSib was performed through error-PCR, and high-throughput screening was realized using the lac'-IspSib-'lac system. Three positive variants with increased thermostability were obtained. The thermostability test and the melting temperature analysis confirmed the increased stability of the enzyme. The production of isoprene was increased by 1.94-folds, to 1,335 mg/L, using IspSibN397V A476T. The directed evolution process reported here is also applicable to other terpene synthases key to isoprenoid production.

Advances in the optimization of central carbon metabolism in metabolic engineering

Central carbon metabolism (CCM), including glycolysis, tricarboxylic acid cycle and the pentose phosphate pathway, is the most fundamental metabolic process in the activities of living organisms that maintains normal cellular growth. CCM has been widely used in microbial metabolic engineering in recent years due to its unique regulatory role in cellular metabolism. Using yeast and Escherichia coli as the representative organisms, we summarized the metabolic engineering strategies on the optimization of CCM in eukaryotic and prokaryotic microbial chassis, such as the introduction of heterologous CCM metabolic pathways and the optimization of key enzymes or regulatory factors, to lay the groundwork for the future use of CCM optimization in metabolic engineering. Furthermore, the bottlenecks in the application of CCM optimization in metabolic engineering and future application prospects are summarized.