Designing Intracellular Compartments for Efficient Engineered Microbial Cell Factories

Biomolecular Condensate-Based Artificial Organelle for Driving Compartmentalized Flux Control

Microbial cell factories have emerged as versatile bioreactors capable of orchestrating complex metabolic networks to convert renewable feedstocks into high-value biochemicals. Nevertheless, the diffusion-mediated dispersion of metabolic intermediates often compromises biosynthesis efficiency, primarily attributable to the absence of artificial subcellular compartments for spatiotemporal organization of catalytic enzymes. Herein, we established a synthetic biology platform leveraging engineered biomolecular condensates to achieve precise flux control via a modular pathway compartmentalization. First, the fused sarcoma low complexity domain (FUSLCD) was designed to combine the GCN4 to rationally integrate with GCN4 scaffold proteins to create programmable artificial organelles. Second, the protein recruitment and assembly functions of artificial organelles were identified by a short peptide pair or directly fusing with the FUSLCD protein in a spatial organization way. Third, using the 2'-fucosyllactose (2'-FL) de novo biosynthesis pathway as a model system, we demonstrated enhanced pathway efficiency by colocalizing critical enzymes within artificial organelles in engineered E. coli, yielding a significant improvement in 2'-FL titer through flux compartmentalization. This study not only overcome diffusion-limited reactions via engineered spatial organization but also offer a versatile toolkit for optimizing compartmentalized biosynthesis pathways.

Creation of Artificial Subcellular Organelles Using Compartmentalized Escherichia coli Bodies for Artificial Metalloenzyme-Mediated Abiotic Catalysis in Eukaryotic Cells

Artificial metalloenzymes (ArMs) stand out as excellent tools mediating intracellular abiotic transformations due to their multifaceted advantages, including their adaptability through directed evolution and availability as whole-cell catalysts. However, the applications of ArMs as exogenous agents in eukaryotic systems remain challenging due to issues with protein purification and delivery, metalloenzyme stability, and complex catalyst preparation. In this article, we present a method inspired by nature's endosymbiotic process, enabling the direct use of ArMs residing within the bacterial cells that express them as whole-cell-based catalytic platforms in eukaryotic cells. This approach utilizes HaloTag-SNAPTag fusion protein as the ArM scaffold, which undergoes liquid-liquid phase separation to form sanctuaries in Escherichia coli for different ArMs created from the same fusion protein. Such compartmentalized E. coli are then sterilized and granted cell permeability with polymer decoration so that they may enter eukaryotic cells and work as artificial subcellular organelles, mediating abiotic transformations using those well-protected ArMs residing within. We further demonstrate the potential of this strategy in therapeutic applications in proof-of-concept demonstrations, by showing that these encapsulated ArMs can be viable options for intracellular bacterial pathogen elimination and cancer therapy through prodrug activation in live cells and animals. Likely, this strategy will suggest a different pathway for expanding ArM applications in chemical biology and biomedicine.

Compartmentation of multiple metabolic enzymes and their preparation in vitro and in cellulo

Compartmentalization of multiple enzymes in cellulo and in vitro is a means of controlling the cascade reaction of metabolic enzymes. The compartmentation of enzymes through liquid-liquid phase separation may facilitate the reversible control of biocatalytic cascade reactions, thereby reducing the transcriptional and translational burden. This has attracted attention as a potential application in bioproduction. Recent research has demonstrated the existence and regulatory mechanisms of various enzyme compartments within cells. Mounting evidence suggests that enzyme compartmentation allows in vitro and in vivo regulation of cellular metabolism. However, the comprehensive regulatory mechanisms of enzyme condensates in cells and ideal organization of cellular systems remain unknown. This review provides an overview of the recent progress in multiple enzyme compartmentation in cells and summarizes strategies to reconstruct multiple enzyme assemblies in vitro and in cellulo. By examining parallel examples, we have evaluated the consensus and future perspectives of enzyme condensation.

Modular metabolic flux control for kick-starting cascade catalysis through engineering customizable compartment

Microbial compartment provides a promising approach for achieving high-valued chemical biosynthesis from renewable feedstock. However, volatile precursor could be utilized by pathway enzyme, which may hinder and adverse the cascade catalysis within microbial cell factory. Here, a customizable compartment was developed for pathway sequestration using spatially assembled cascade catalysis reaction. Firstly, a phase separation protein was designed to form the intracellular protein condensates, facilitating the construction of a customizable compartment in Escherichia coli. Subsequently, modular assembly and recruitment of customizable compartment were achieved through using a short peptide interaction pair to cluster enzymes or fuse them directly. Finally, the 2'-fucosyllactose (2'-FL) salvage pathway was heterogeneously expressed in microorganisms as a stable targeted chemical and proof-of-concept model, the results showed that anchoring various enzymes required for the 2'-FL cascade catalysis pathway within the customizable compartment created a multiple enzyme condensate system, resulting an improvement of 2'-FL titer compared to both wild type and optimized free enzymes reaction. These findings illustrating an effectively cascade catalysis model that increasing titer and kick-starting metabolic flux control through co-localizing multiple enzymes condensate within microbial cell factories.

Engineering Saccharomyces cerevisiae for Efficient Liquiritigenin Production

Production of liquiritigenin, a plant-derived significant flavonoid traditionally extracted from licorice plants, is constrained by ecological and operational inefficiencies. Despite efforts to achieve heterologous reconstruction of liquiritigenin synthesis pathway in microorganisms, the liquiritigenin titers remain low and the process is still at the proof-of-concept stage, insufficient to replace plant extraction. Herein, to achieve the efficient production of liquiritigenin, the galactose induction system in Saccharomyces cerevisiae was reengineered for better decoupling of production and growth stages, making it more suitable for heterologous pathways, and then applied to a naringenin-producing strain and modified to redirect the pathway for liquiritigenin production. To improve liquiritigenin ratio, a dual NADPH supply system was developed to enhance production capabilities. Subsequently, the concept of using endogenous metabolites to regulate the simplification and optimization of heterologous natural product biosynthetic pathways was proposed, and a general metabolic strategy model for flavonoid compounds, the aromatic ester model, was introduced. The final engineered strain achieved 867.67 mg/L liquiritigenin in the 5 L fermenter. These results demonstrated the innovative use of genetic and metabolic modifications to overcome conventional extraction limitations, providing valuable insights for synthesizing flavonoids and other natural products.

Artificial Compartments Encapsulating Enzymatic Reactions: Towards the Construction of Artificial Organelles

Cells have used compartmentalization to implement complex biological processes involving thousands of enzyme cascade reactions. Enzymes are spatially organized into the cellular compartments to carry out specific and efficient reactions in a spatiotemporally controlled manner. These compartments are divided into membrane-bound and membraneless organelles. Mimicking such cellular compartment systems has been a challenge for years. A variety of artificial scaffolds, including liposomes, polymersomes, proteins, nucleic acids, or hybrid materials have been used to construct artificial membrane-bound or membraneless compartments. These artificial compartments may have great potential for applications in biosynthesis, drug delivery, diagnosis and therapeutics, among others. This review first summarizes the typical examples of cellular compartments. In particular, the recent studies on cellular membraneless organelles (biomolecular condensates) are reviewed. We then summarize the recent advances in the construction of artificial compartments using engineered platforms. Finally, we provide our insights into the construction of biomimetic systems and the applications of these systems. This review article provides a timely summary of the relevant perspectives for the future development of artificial compartments, the building blocks for the construction of artificial organelles or cells.

Intracellular Construction of Organelle-like Compartments Facilitates Metabolic Flux in Escherichia coli

The formation of well-designed synthetic compartments or membraneless organelles for applications in synthetic biology and cellular engineering has aroused enormous interest. However, establishing stable and robust intracellular compartments in bacteria remains a challenge. Here, we use the structured DIX domains derived from Wnt signaling pathway components, more specifically, Dvl2 and Axin1, as building blocks to generate intracellular synthetic compartments in Escherichia coli. Moreover, the aggregation behaviors and physical properties of the DIX-based compartments can be tailored by genetically embedding a specific dimeric domain into the DIX domains. Then, a pair of interacting motifs, consisting of the aforementioned dimeric domain and its corresponding binding ligand, was incorporated to modify the client recruitment pattern of the synthetic compartments. As a proof of concept, the human milk oligosaccharide lacto-N-tetraose (LNT) biosynthesis pathway was selected as a model metabolic pathway. The fermentation results demonstrated that the co-compartmentalization of sequential pathway enzymes into intracellular compartments created by DIX domain, or by the DIX domain in conjunction with interacting motifs, prominently enhanced the metabolic flux and increased LNT production. These synthetic protein compartments may provide a feasible and effective tool to develop versatile organelle-like compartments in bacteria for applications in cellular engineering and synthetic biology.

Metabolic engineering for compartmentalized biosynthesis of the valuable compounds in Saccharomyces cerevisiae

Saccharomyces cerevisiae is commonly used as a microbial cell factory to produce high-value compounds or bulk chemicals due to its genetic operability and suitable intracellular physiological environment. The current biosynthesis pathway for targeted products is primarily rewired in the cytosolic compartment. However, the related precursors, enzymes, and cofactors are frequently distributed in various subcellular compartments, which may limit targeted compounds biosynthesis. To overcome above mentioned limitations, the biosynthesis pathways are localized in different subcellular organelles for product biosynthesis. Subcellular compartmentalization in the production of targeted compounds offers several advantages, mainly relieving competition for precursors from side pathways, improving biosynthesis efficiency in confined spaces, and alleviating the cytotoxicity of certain hydrophobic products. In recent years, subcellular compartmentalization in targeted compound biosynthesis has received extensive attention and has met satisfactory expectations. In this review, we summarize the recent advances in the compartmentalized biosynthesis of the valuable compounds in S. cerevisiae, including terpenoids, sterols, alkaloids, organic acids, and fatty alcohols, etc. Additionally, we describe the characteristics and suitability of different organelles for specific compounds, based on the optimization of pathway reconstruction, cofactor supplementation, and the synthesis of key precursors (metabolites). Finally, we discuss the current challenges and strategies in the field of compartmentalized biosynthesis through subcellular engineering, which will facilitate the production of the complex valuable compounds and offer potential solutions to improve product specificity and productivity in industrial processes.

Compartmentalization of pathway sequential enzymes into synthetic protein compartments for metabolic flux optimization in Escherichia coli

Advancing the formation of artificial membraneless compartments with organizational complexity and diverse functionality remains a challenge. Typically, synthetic compartments or membraneless organelles are made up of intrinsically disordered proteins featuring low-complexity sequences or polypeptides with repeated distinctive short linear motifs. In order to expand the repertoire of tools available for the formation of synthetic membraneless compartments, here, a range of DIshevelled and aXin (DIX) or DIX-like domains undergoing head-to-tail polymerization were demonstrated to self-assemble into aggregates and generate synthetic compartments within E. coli cells. Then, synthetic complex compartments with diverse intracellular morphologies were generated by coexpressing different DIX domains. Further, we genetically incorporated a pair of interacting motifs, comprising a homo-dimeric domain and its anchoring peptide, into the DIX domain and cargo proteins, respectively, resulting in the alteration of both material properties and client recruitment of synthetic compartments. As a proof-of-concept, several human milk oligosaccharide biosynthesis pathways were chosen as model systems. The findings indicated that the recruitment of pathway sequential enzymes into synthetic compartments formed by DIX-DIX heterotypic interactions or by DIX domains embedded with specific interacting motifs efficiently boosted metabolic pathway flux and improved the production of desired chemicals. We propose that these synthetic compartment systems present a potent and adaptable toolkit for controlling metabolic flux and facilitating cellular engineering.

Recent advances in design and application of synthetic membraneless organelles

Membraneless organelles (MLOs) formed by liquid-liquid phase separation (LLPS) have been extensively studied due to their spatiotemporal control of biochemical and cellular processes in living cells. These findings have provided valuable insights into the physicochemical principles underlying the formation and functionalization of biomolecular condensates, which paves the way for the development of versatile phase-separating systems capable of addressing a variety of application scenarios. Here, we highlight the potential of constructing synthetic MLOs with programmable and functional properties. Notably, we organize how these synthetic membraneless compartments have been capitalized to manipulate enzymatic activities and metabolic reactions. The aim of this review is to inspire readerships to deeply comprehend the widespread roles of synthetic MLOs in the regulation enzymatic reactions and control of metabolic processes, and to encourage the rational design of controllable and functional membraneless compartments for a broad range of bioengineering applications.

Bacterial microcompartments as a next-generation metabolic engineering tool: utilizing nature's solution for confining challenging catabolic pathways

Advancements in synthetic biology have facilitated the incorporation of heterologous metabolic pathways into various bacterial chassis, leading to the synthesis of targeted bioproducts. However, total output from heterologous production pathways can suffer from low flux, enzyme promiscuity, formation of toxic intermediates, or intermediate loss to competing reactions, which ultimately hinder their full potential. The self-assembling, easy-to-modify, protein-based bacterial microcompartments (BMCs) offer a sophisticated way to overcome these obstacles by acting as an autonomous catalytic module decoupled from the cell's regulatory and metabolic networks. More than a decade of fundamental research on various types of BMCs, particularly structural studies of shells and their self-assembly, the recruitment of enzymes to BMC shell scaffolds, and the involvement of ancillary proteins such as transporters, regulators, and activating enzymes in the integration of BMCs into the cell's metabolism, has significantly moved the field forward. These advances have enabled bioengineers to design synthetic multi-enzyme BMCs to promote ethanol or hydrogen production, increase cellular polyphosphate levels, and convert glycerol to propanediol or formate to pyruvate. These pioneering efforts demonstrate the enormous potential of synthetic BMCs to encapsulate non-native multi-enzyme biochemical pathways for the synthesis of high-value products.

Designer protein compartments for microbial metabolic engineering

Protein compartments are distinct structures assembled in living cells via self-assembly or phase separation of specific proteins. Significant efforts have been made to discover their molecular structures and formation mechanisms, as well as their fundamental roles in spatiotemporal control of cellular metabolism. Here, we review the design and construction of synthetic protein compartments for spatial organization of target metabolic pathways toward increased efficiency and specificity. In particular, we highlight the compartmentalization strategies and recent examples to speed up desirable metabolic reactions, to reduce the accumulation of toxic metabolic intermediates, and to switch competing metabolic pathways. We also identify the most important challenges that need to be addressed for exploitation of these designer compartments as a versatile toolkit in metabolic reprogramming.

Carotenoid Cleavage Dioxygenase 1 and Its Application for the Production of C13-Apocarotenoids in Microbial Cell Factories: A Review

C13-apocarotenoids are naturally derived from the C9-C10 (C9'-C10') double-bond cleavage of carotenoids by carotenoid cleavage dioxygenases (CCDs). As high-value flavors and fragrances in the food and cosmetic industries, the sustainable production of C13-apocarotenoids is emerging in microbial cell factories by the carotenoid cleavage dioxygenase 1 (CCD1) subfamily. However, the commercialization of microbial-based C13-apocarotenoids is still limited by the poor performance of CCD1, which severely constrains its conversion efficiency from precursor carotenoids. This review focuses on the classification of CCDs and their cleavage modes for carotenoids to generate corresponding apocarotenoids. We then emphatically discuss the advances for C13-apocarotenoid biosynthesis in microbial cell factories with various strategies, including optimization of CCD1 expression, improvement of CCD1's catalytic activity and substrate specificity, strengthening of substrate channeling, and development of oleaginous microbial hosts, which have been verified to increase the conversion rate from carotenoids. Lastly, the current challenges and future directions will be discussed to enhance CCDs' application for C13-apocarotenoids biomanufacturing.