Improving medium chain fatty acid production in Escherichia coli by multiple transporter engineering

Rhodotorula sp. as a promising host for microbial cell factories

Rhodotorula sp. is a red yeast that has emerged as a promising host for microbial cell factories. Under specific conditions, Rhodotorula sp. can accumulate lipids that constitute over 70% of its dry cell weight, underscoring its potential in lipid compound production. Additionally, it can utilize a variety of carbon sources, including glucose, xylose, and volatile fatty acids, and exhibits high tolerance to low-cost carbon sources and industrial by-products, showcasing its excellent performance in industrial processes. Furthermore, the native mevalonate pathway of Rhodotorula sp. enables its efficient synthesis of antioxidant carotenoids and other terpenoids, which are widely applied in the food, pharmaceutical, and cosmetic industries. Due to its excellent accumulation ability of lipophilic compounds, metabolic diversity, and environmental adaptability, this review summarizes recent advances in genetic elements and metabolic engineering technologies for Rhodotorula sp., emphasizing its potential as a chassis cell factory for the production of lipids, carotenoids, and other chemicals. It also highlights key factors influencing commercial fermentation processes and concludes with challenges and solutions for further developing Rhodotorula sp. as microbial chassis.

Just passing through: Deploying aquaporins in microbial cell factories

As microbial membranes are naturally impermeable to even the smallest biomolecules, transporter proteins are physiologically essential for normal cell functioning. This makes transporters a key target area for engineering enhanced cell factories. As part of the wider cellular transportome, aquaporins (AQPs) are responsible for transporting small polar solutes, encompassing many compounds which are of great interest for industrial biotechnology, including cell feedstocks, numerous commercially relevant polyols and even weak organic acids. In this review, examples of cell factory engineering by targeting AQPs are presented. These AQP modifications aid in redirecting carbon fluxes and boosting bioconversions either by enhanced feedstock uptake, improved intermediate retention, increasing product export into the media or superior cell viability against stressors with applications in both bacterial and yeast production platforms. Additionally, the future potential for AQP deployment and targeting is discussed, showcasing hurdles and considerations of this strategy as well as recent advances and future directions in the field. By leveraging the natural diversity of AQPs and breakthroughs in channel protein engineering, these transporters are poised to be promising tools capable of enhancing a wide variety of biotechnological processes.

Highly flexible cell membranes are the key to efficient production of lipophilic compounds

Lipophilic compounds have a variety of positive effects on human physiological functions and exhibit good effects in the prevention and treatment of clinical diseases. This has led to significant interest in the technical applications of synthetic biology for the production of lipophilic compounds. However, the strict selective permeability of the cell membrane and the hydrophobic nature of lipophilic compounds pose significant challenges to their production. During fermentation, lipophilic compounds tend to accumulate within cell membrane compartments rather than being secreted extracellularly. The toxic effects of excessive lipophilic compound accumulation can threaten cell viability, while the limited space within the cell membrane restricts further increases in production yield. Consequently, to achieve efficient production of lipophilic compounds, research is increasingly focused on constructing robust and multifunctional microbial cell factories. Utilizing membrane engineering techniques to construct highly flexible cell membranes is considered an effective strategy to break through the upper limit of lipophilic compound production. Currently, there are two main approaches to cell membrane modification: constructing artificial storage compartments for lipophilic compounds and engineering the cell membrane structure to facilitate product outflow. This review summarizes recent cell membrane engineering strategies applied in microbial cell factories for the production of liposoluble compounds, discussing the challenges and future prospects. These strategies enhance membrane flexibility and effectively promote the production of liposoluble compounds.

Application of synthetic biology strategies to promote biosynthesis of fatty acids and their derivatives

Fatty acids and their derivatives are indispensable biomolecules in all organisms, and can be used as intermediates in the synthesis of pharmaceuticals, biofuels and pesticides, and thus their demand has increased dramatically in recent years. In addition to serving as structural components of cell membranes and metabolic energy, fatty acids and their derivatives can also be used as signal transduction and regulatory bioactive molecules to regulate cell functions. Biosynthesis of fatty acids and their derivatives through microbial catalysis provides green and alternative options to meet the goal. However, the low biosynthetic titer of fatty acids and their derivatives limits their industrial production and application. In this review, we first summarize the metabolic pathways and related enzymes of fatty acids and their derivatives biosynthesis. Then, the strategies and research progress of biosynthesis of fatty acids and derivatives through metabolic and enzyme engineering were reviewed. The biosynthesis of saturated fatty acids (medium chain fatty acids and long chain fatty acids), bioactive fatty acids (PUFAs, oxylipins, ether lipids), and their derivatives with microbial and enzymatic catalysis were respectively summarized. Finally, synthetic biology strategies to improve fatty acids and their derivatives production through enzyme rational design, carbon metabolism flux, cofactors balance, and metabolic pathways design were discussed. The review provides references and prospects for fatty acids and their derivatives biosynthesis and industrial production.

Recent advances in microbial production of medium chain fatty acid from renewable carbon resources: a comprehensive review

Microbial production of medium chain length fatty acids (MCFAs) from renewable resources is becoming increasingly important in establishing a sustainable and clean chemical industry. This review comprehensively summarizes current advances in microbial MCFA production from renewable resources. Detailed information is provided on two major MCFA production pathways using various renewable resources and other auxiliary pathways supporting MCFA production to help understand the fundamentals of bio-based MCFA production. In addition, conventional and well-studied MCFA producers are classified into two categories, natural and synthetic producers, and their characteristics on MCFA production are outlined. Moreover, various engineering strategies employed to achieve the highest MCFAs production up to date are showcased together with key enzymes suggested for MCFA overproduction. Finally, future challenges and perspectives are discussed towards more efficient production of bio-based MCFA production.

Metabolic Engineering: Methodologies and Applications

Metabolic engineering aims to improve the production of economically valuable molecules through the genetic manipulation of microbial metabolism. While the discipline is a little over 30 years old, advancements in metabolic engineering have given way to industrial-level molecule production benefitting multiple industries such as chemical, agriculture, food, pharmaceutical, and energy industries. This review describes the design, build, test, and learn steps necessary for leading a successful metabolic engineering campaign. Moreover, we highlight major applications of metabolic engineering, including synthesizing chemicals and fuels, broadening substrate utilization, and improving host robustness with a focus on specific case studies. Finally, we conclude with a discussion on perspectives and future challenges related to metabolic engineering.

Transporter Engineering in Microbial Cell Factory Boosts Biomanufacturing Capacity

Microbial cell factories (MCFs) are typical and widely used platforms in biomanufacturing for designing and constructing synthesis pathways of target compounds in microorganisms. In MCFs, transporter engineering is especially significant for improving the biomanufacturing efficiency and capacity through enhancing substrate absorption, promoting intracellular mass transfer of intermediate metabolites, and improving transmembrane export of target products. This review discusses the current methods and strategies of mining and characterizing suitable transporters and presents the cases of transporter engineering in the production of various chemicals in MCFs.

Efficient Biosynthesis of 10-Hydroxy-2-decenoic Acid Using a NAD(P)H Regeneration P450 System and Whole-Cell Catalytic Biosynthesis

10-Hydroxy-2-decenoic acid (10-HDA) is an α,β-unsaturated medium-chain carboxylic acid containing a terminal hydroxyl group. It has various unique properties and great economic value. We improved the two-step biosynthesis method of 10-HDA. The conversion rate of the intermediate product trans-2-decenoic acid in the first step of 10-HDA synthesis could reach 93.1 ± 1.3% by combining transporter overexpression and permeation technology strategies. Moreover, the extracellular trans-2-decenoic acid content was five times greater than the intracellular content when 2.0% (v/v) triton X-100 and 1.2% (v/v) tween-80 were each used. In the second step of 10-HDA synthesis, we regenerated NAD(P)H by overexpressing a glucose dehydrogenase with the P450 enzyme (CYP153A33/M228L-CPRBM3) in Escherichia coli, improving the catalytic performance of the trans-2-decenoic acid terminal hydroxylation. Finally, the yield of 10-HDA was 486.5 mg/L using decanoic acid as the substrate with two-step continuous biosynthesis. Our research provides a simplified production strategy to promote the two-step continuous whole-cell catalytic biosynthesis of 10-HDA and other α,β-unsaturated carboxylic acid derivatives.

Force in numbers: high-throughput screening approaches to unlock microbial transport

Biological membranes are inherently complex, making transport processes in microbial cell factories a significant bottleneck. Lack of knowledge on transport proteins' characteristics and the need for advanced technical equipment often hamper transporter identification and optimization. For these reasons, moving away from individual characterization and towards high-throughput mining, engineering, and screening of transporters is an increasingly attractive approach. Superior transporters can be selected from large libraries by coupling their activity to growth, for substrates that function as feedstocks or toxic compounds. Other compounds can be screened thanks to recent advances in the design and deployment of synthetic genetic circuits (biosensors). Furthermore, novel strategies are rapidly increasing the repertoire of biomolecule transporters susceptible to high-throughput selection methods.

Overview of the Cellular Stress Responses Involved in Fatty Acid Overproduction in E. coli

Research on microbial fatty acid metabolism started in the late 1960s, and till date, various developments have aided in elucidating the fatty acid metabolism in great depth. Over the years, synthesis of microbial fatty acid has drawn industrial attention due to its diverse applications. However, fatty acid overproduction imparts various stresses on its metabolic pathways causing a bottleneck to further increase the fatty acid yields. Numerous strategies to increase fatty acid titres in Escherichia coli by pathway modulation have already been published, but the stress generated during fatty acid overproduction is relatively less studied. Stresses like pH, osmolarity and oxidative stress, not only lower fatty acid titres, but also alter the cell membrane composition, protein expression and membrane fluidity. This review discusses an overview of fatty acid synthesis pathway and presents a panoramic view of various stresses caused due to fatty acid overproduction in E. coli. It also addresses how certain stresses like high temperature and nitrogen limitation can boost fatty acid production. This review paper also highlights the interconnections that exist between these stresses.

Analytical methods in fatty acid analysis for microbial applications: the recent trends

Fatty acids are among the most important components of many biological systems and have been highlighted in many research fields in recent decades. In the food industry, it is important to check the amount and types of fatty acids in edible oils, beverages and other foods products, and checking the fatty acids parameters are among the quality control parameters for those products. In medical applications, investigation of fatty acids in biological samples and comparing imbalances in them can help to diagnose some diseases. On the other hand, the development of cell factories for the production of biofuels and other valuable chemicals requires the accurate analysis of fatty acids, which serve as precursors in development of those products. As a result, given all these different applications of fatty acids, rapid and accurate methods for characterization and quantification of fatty acids are essential. In recent years, various methods for the analysis of fatty acids have been proposed, which according to the specific purpose of the analysis, some of them can be used with consideration of speed, accuracy and cost. In this article, the available methods for the analysis of fatty acids are reviewed with a special emphasis on the analysis of microbial samples to pave the way for more widespread metabolic engineering research.

Efflux Transporters' Engineering and Their Application in Microbial Production of Heterologous Metabolites

Metabolic engineering of microbial hosts for the production of heterologous metabolites and biochemicals is an enabling technology to generate meaningful quantities of desired products that may be otherwise difficult to produce by traditional means. Heterologous metabolite production can be restricted by the accumulation of toxic products within the cell. Efflux transport proteins (transporters) provide a potential solution to facilitate the export of these products, mitigate toxic effects, and enhance production. Recent investigations using knockout lines, heterologous expression, and expression profiling of transporters have revealed candidates that can enhance the export of heterologous metabolites from microbial cell systems. Transporter engineering efforts have revealed that some exhibit flexible substrate specificity and may have broader application potentials. In this Review, the major superfamilies of efflux transporters, their mechanistic modes of action, selection of appropriate efflux transporters for desired compounds, and potential transporter engineering strategies are described for potential applications in enhancing engineered microbial metabolite production. Future studies in substrate recognition, heterologous expression, and combinatorial engineering of efflux transporters will assist efforts to enhance heterologous metabolite production in microbial hosts.

Microbial fatty acid transport proteins and their biotechnological potential

Fatty acid metabolism has been widely studied in various organisms. However, fatty acid transport has received less attention, even though it plays vital physiological roles, such as export of toxic free fatty acids or uptake of exogenous fatty acids. Hence, there are important knowledge gaps in how fatty acids cross biological membranes, and many mechanisms and proteins involved in these processes still need to be determined. The lack of information is more predominant in microorganisms, even though the identification of fatty acids transporters in these cells could lead to establishing new drug targets or improvements in microbial cell factories. This review provides a thorough analysis of the current information on fatty acid transporters in microorganisms, including bacteria, yeasts and microalgae species. Most available information relates to the model organisms Escherichia coli and Saccharomyces cerevisiae, but transport systems of other species are also discussed. Intracellular trafficking of fatty acids and their transport through organelle membranes in eukaryotic organisms is described as well. Finally, applied studies and engineering efforts using fatty acids transporters are presented to show the applied potential of these transporters and to stress the need for further identification of new transporters and their engineering.

Microbial physiological engineering increases the efficiency of microbial cell factories

Microbial cell factories provide vital platforms for the production of chemicals. Advanced biotechnological toolboxes have been developed to enhance their efficiency. However, these tools have limitations in improving physiological functions, and therefore boosting the efficiency (e.g. titer, rate, and yield) of microbial cell factories remains a challenge. In this review, we propose a strategy of microbial physiological engineering (MPE) to improve the efficiency of microbial cell factories. This strategy integrates tools from synthetic and systems biology to characterize and regulate physiological functions during chemical synthesis. MPE strategies mainly focus on the efficiency of substrate utilization, growth performance, stress tolerance, and the product export capacity of cell factories. In short, this review provides a new framework for resolving the bottlenecks that currently exist in low-efficiency cell factories.

Transporter engineering in microbial cell factories: the ins, the outs, and the in-betweens

Engineering the transport of small molecules is an effective approach to improve the performance of microbial cell factories. Transporter engineering can improve the utilization of low-cost alternative substrates, reduce the loss of pathway intermediates, and increase the titer and production rate of the target product. However, transporters are not commonly engineered in strain development programs because the functions of most of the transport proteins are not known. In the recent years, a variety of methods have been developed for identification of transporters for specific substrates and for characterizing transport mechanisms. This review presents recent examples of successful transport engineering for cell factories and discusses the methods for transporter identification and characterization.

Developing a pathway-independent and full-autonomous global resource allocation strategy to dynamically switching phenotypic states

A grand challenge of biological chemical production is the competition between synthetic circuits and host genes for limited cellular resources. Quorum sensing (QS)-based dynamic pathway regulations provide a pathway-independent way to rebalance metabolic flux over the course of the fermentation. Most cases, however, these pathway-independent strategies only have capacity for a single QS circuit functional in one cell. Furthermore, current dynamic regulations mainly provide localized control of metabolic flux. Here, with the aid of engineering synthetic orthogonal quorum-related circuits and global mRNA decay, we report a pathway-independent dynamic resource allocation strategy, which allows us to independently controlling two different phenotypic states to globally redistribute cellular resources toward synthetic circuits. The strategy which could pathway-independently and globally self-regulate two desired cell phenotypes including growth and production phenotypes could totally eliminate the need for human supervision of the entire fermentation.

A challenge for biological chemical production is the completion between synthetic circuits and host resources. Here the authors the authors use quorum sensing circuits and global mRNA decay to independently control two phenotypic states.

Engineering microbial cell morphology and membrane homeostasis toward industrial applications

Microbial cell factory performance is significantly affected by the cell morphology and membrane homeostasis. It is important to ensure that cell factories are able to regulate cell morphology and maintain membrane homeostasis. Cell morphology can be controlled by regulating the formation of elongasomes and divisomes, which change the shapes of cells from rods to fibers, large spheres, or mini-cells. Membrane homeostasis can also be controlled by regulating the homeostasis of membrane lipids and proteins, thereby improving the robustness of microbes in toxic environments. In the present review, we discuss promising developments in cell morphology and membrane homeostasis engineering that have improved microbial cell factory performance.

Transporter Engineering for Microbial Manufacturing

Microbes play an important role in biotransformation and biosynthesis of biofuels, natural products, and polymers. Therefore, microbial manufacturing has been widely used in medicine, industry, and agriculture. However, common strategies including enzyme engineering, pathway optimization, and host engineering are generally inadequate to obtain an efficient microbial production system. Transporter engineering provides an alternative strategy to promote the transmembrane transfer of substrates, intermediates, and final products in microbial cells and thus enhances production by alleviating feedback inhibition and cytotoxicity caused by final products. According to the current studies in transport engineering, native transporters usually have low expression and poor transportation ability, resulting in inefficient transport processes and microbial production. In this review, current approaches for transporter mining, characterization, and verification are comprehensively summarized. Practical approaches to enhance the transport system in engineered cells, such as balancing transporter overexpression and cell growth, and evolution of native transporters are discussed. Furthermore, the applications of transporter engineering in microbial manufacturing, including enhancement of substrate utilization, concentration of metabolic flux to the target pathway, and acceleration of efflux and recovery of products, demonstrate its outstanding advantages and promising prospects.

Engineering transport systems for microbial production

The rapid development in the field of metabolic engineering has enabled complex modifications of metabolic pathways to generate a diverse product portfolio. Manipulating substrate uptake and product export is an important research area in metabolic engineering. Optimization of transport systems has the potential to enhance microbial production of renewable fuels and chemicals. This chapter comprehensively reviews the transport systems critical for microbial production as well as current genetic engineering strategies to improve transport functions and thus production metrics. In addition, this chapter highlights recent advancements in engineering microbial efflux systems to enhance cellular tolerance to industrially relevant chemical stress. Lastly, future directions to address current technological gaps are discussed.

Biosynthesis of Medium-Chain ω-Hydroxy Fatty Acids by AlkBGT of Pseudomonas putida GPo1 With Native FadL in Engineered Escherichia coli

Hydroxy fatty acids (HFAs) are valuable compounds that are widely used in medical, cosmetic and food fields. Production of ω-HFAs via bioconversion by engineered Escherichia coli has received a lot of attention because this process is environmentally friendly. In this study, a whole-cell bio-catalysis strategy was established to synthesize medium-chain ω-HFAs based on the AlkBGT hydroxylation system from Pseudomonas putida GPo1. The effects of blocking the β-oxidation of fatty acids (FAs) and enhancing the transportation of FAs on ω-HFAs bio-production were also investigated. When fadE and fadD were deleted, the consumption of decanoic acid decreased, and the yield of ω-hydroxydecanoic acid was enhanced remarkably. Additionally, the co-expression of the FA transporter protein, FadL, played an important role in increasing the conversion rate of ω-hydroxydecanoic acid. As a result, the concentration and yield of ω-hydroxydecanoic acid in NH03(pBGT-fadL) increased to 309 mg/L and 0.86 mol/mol, respectively. This whole-cell bio-catalysis system was further applied to the biosynthesis of ω-hydroxyoctanoic acid and ω-hydroxydodecanoic acid using octanoic acid and dodecanoic acid as substrates, respectively. The concentrations of ω-hydroxyoctanoic acid and ω-hydroxydodecanoic acid reached 275.48 and 249.03 mg/L, with yields of 0.63 and 0.56 mol/mol, respectively. This study demonstrated that the overexpression of AlkBGT coupled with native FadL is an efficient strategy to synthesize medium-chain ω-HFAs from medium-chain FAs in fadE and fadD mutant E. coli strains.