Synthetic Protein Scaffolds for Biosynthetic Pathway Colocalization on Lipid Droplet Membranes

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.

Hyperproduction of 7-dehydrocholesterol by rewiring the post-squalene module in lipid droplets of Saccharomyces cerevisiae

Lipid droplets (LDs) are specialized organelles that store neutral lipids to reduce the negative effects of lipotoxicity on cells. However, many neutral lipids are precursors for the synthesis of sterols and complex terpenoids, and this sequestration often greatly limits the efficient biosynthesis of sterols and complex terpenoids. In this study, taking 7-dehydrocholesterol (7-DHC) synthesis in Saccharomyces cerevisiae as an example, we revealed the blocking mechanism of LD sequestration on the efficient synthesis of metabolic products and found that LDs can sequester a significant amount of squalene, the precursor of 7-DHC, effectively preventing it from being directed toward the post-squalene pathway. Based on this, a post-squalene pathway was reconstructed on LDs, which resulted in a 28.7% increase in the 7-DHC titer, reaching 684.1 mg/L, whereas the squalene titer was reduced by approximately 97%. Subsequently, the triacylglycerol degradation pathway was weakened to release the storage space in LDs, and the esterification pathway was concurrently strengthened to guide 7-DHC storage within LDs, which further increased 7-DHC production, reaching 792.9 mg/L. Finally, by reducing the NADH/NAD + ratio to alleviate the redox imbalance, the 7-DHC titer reached 867.6 mg/L in shake flask and 5.1 g/L in a 3-L bioreactor, which is the highest reported titer to date. In summary, this study provides new insights into the important role of LDs in sterol synthesis and offers a novel strategy for constructing cell factories for the efficient synthesis of sterol compounds.

Molecular mechanics studies of factors affecting overall rate in cascade reactions: Multi-enzyme colocalization and environment

Millions of years of evolution have optimized many biosynthetic pathways by use of multi-step catalysis. In addition, multi-step metabolic pathways are commonly found in and on membrane-bound organelles in eukaryotic biochemistry. The fundamental mechanisms that facilitate these reaction processes provide strategies to bioengineer metabolic pathways in synthetic chemistry. Using Brownian dynamics simulations, here we modeled intermediate substrate transportation of colocalized yeast-ester biosynthesis enzymes on the membrane. The substrate acetate ion traveled from the pocket of aldehyde dehydrogenase to its target enzyme acetyl-CoA synthetase, then the substrate acetyl CoA diffused from Acs1 to the active site of the next enzyme, alcohol-O-acetyltransferase. Arranging two enzymes with the smallest inter-enzyme distance of 60 Å had the fastest average substrate association time as compared with anchoring enzymes with larger inter-enzyme distances. When the off-target side reactions were turned on, most substrates were lost, which suggests that native localization is necessary for efficient final product synthesis. We also evaluated the effects of intermolecular interactions, local substrate concentrations, and membrane environment to bring mechanistic insights into the colocalization pathways. The computation work demonstrates that creating spatially organized multi-enzymes on membranes can be an effective strategy to increase final product synthesis in bioengineering systems.

Functionalizing Yeast Lipid Droplets as Versatile Biomaterials

Lipid droplets (LD) are dynamic cellular organelles of ≈1 µm diameter in yeast where a neutral lipid core is surrounded by a phospholipid monolayer and attendant proteins. Beyond the storage of lipids, opportunities for LD engineering remain underdeveloped but they show excellent potential as new biomaterials. In this research, LD from yeast Saccharomyces cerevisiae is engineered to display mCherry fluorescent protein, Halotag ligand binding protein, plasma membrane binding v-SNARE protein, and carbonic anhydrase enzyme via linkage to oleosin, an LD anchoring protein. Each protein-oleosin fusion is coded via a single gene construct. The expressed fusion proteins are specifically displayed on LD and their functions can be assessed within cells by fluorescence confocal microscopy, TEM, and as isolated materials via AFM, flow cytometry, spectrophotometry, and by enzyme activity assay. LD isolated from the cell are shown to be robust and stabilize proteins anchored into them. These engineered LD function as reporters, bind specific ligands, guide LD and their attendant proteins into union with the plasma membrane, and catalyze reactions. Here, engineered LD functions are extended well beyond traditional lipid storage toward new material applications aided by a versatile oleosin platform anchored into LD and displaying linked proteins.

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.

Engineering sub-organelles of a diploid Saccharomyces cerevisiae to enhance the production of 7-dehydrocholesterol

7-Dehydrocholesterol (7-DHC) is widely present in various organisms and is an important precursor of vitamin D3. Despite significant improvements in the biosynthesis of 7-DHC, it remains insufficient to meet the industrial demands. In this study, we reported high-level production of 7-DHC in an industrial Saccharomyces cerevisiae leveraging subcellular organelles. Initially, the copy numbers of DHCR24 were increased in combination with sterol transcriptional factor engineering and rebalanced the redox power of the strain. Subsequently, the effects of compartmentalizing the post-squalene pathway in peroxisomes were validated by assembling various pathway modules in this organelle. Furthermore, several peroxisomes engineering was conducted to enhance the production of 7-DHC. Utilizing the peroxisome as a vessel for partial post-squalene pathways, the potential of yeast for 7-dehydrocholesterol production was demonstrated by achieving a 26-fold increase over the initial production level. 7-DHC titer reached 640.77 mg/L in shake flasks and 4.28 g/L in a 10 L bench-top fermentor, the highest titer ever reported. The present work lays solid foundation for large-scale and cost-effective production of 7-DHC for practical applications.

Transcending membrane barriers: advances in membrane engineering to enhance the production capacity of microbial cell factories

Microbial cell factories serve as pivotal platforms for the production of high-value natural products, which tend to accumulate on the cell membrane due to their hydrophobic properties. However, the limited space of the cell membrane presents a bottleneck for the accumulation of these products. To enhance the production of intracellular natural products and alleviate the burden on the cell membrane caused by product accumulation, researchers have implemented various membrane engineering strategies. These strategies involve modifying the membrane components and structures of microbial cell factories to achieve efficient accumulation of target products. This review summarizes recent advances in the application of membrane engineering technologies in microbial cell factories, providing case studies involving Escherichia coli and yeast. Through these strategies, researchers have not only improved the tolerance of cells but also optimized intracellular storage space, significantly enhancing the production efficiency of natural products. This article aims to provide scientific evidence and references for further enhancing the efficiency of similar cell factories.

E and M SARS-CoV-2 membrane protein expression and enrichment with plant lipid droplets

Plants are gaining traction as a cost-effective and scalable platform for producing recombinant proteins. However, expressing integral membrane proteins in plants is challenging due to their hydrophobic nature. In our study, we used transient and stable expression systems in Nicotiana benthamiana and Camelina sativa respectively to express SARS-CoV-2 E and M integral proteins, and target them to lipid droplets (LDs). LDs offer an ideal environment for folding hydrophobic proteins and aid in their purification through flotation. We tested various protein fusions with different linkers and tags and used three dimensional structure predictions to assess their effects. E and M mostly localized in the ER in N. benthamiana leaves but E could be targeted to LDs in oil accumulating tobacco when fused with oleosin, a LD integral protein. In Camelina sativa seeds, E and M were however found associated with purified LDs. By enhancing the accumulation of E and M within LDs through oleosin, we enriched these proteins in the purified floating fraction. This strategy provides an alternative approach for efficiently producing and purifying hydrophobic pharmaceuticals and vaccines using plant systems.

Engineering status of protein for improving microbial cell factories

With the development of metabolic engineering and synthetic biology, microbial cell factories (MCFs) have provided an efficient and sustainable method to synthesize a series of chemicals from renewable feedstocks. However, the efficiency of MCFs is usually limited by the inappropriate status of protein. Thus, engineering status of protein is essential to achieve efficient bioproduction with high titer, yield and productivity. In this review, we summarize the engineering strategies for metabolic protein status, including protein engineering for boosting microbial catalytic efficiency, protein modification for regulating microbial metabolic capacity, and protein assembly for enhancing microbial synthetic capacity. Finally, we highlight future challenges and prospects of improving microbial cell factories by engineering status of protein.

Application of artificial scaffold systems in microbial metabolic engineering

In nature, metabolic pathways are often organized into complex structures such as multienzyme complexes, enzyme molecular scaffolds, or reaction microcompartments. These structures help facilitate multi-step metabolic reactions. However, engineered metabolic pathways in microbial cell factories do not possess inherent metabolic regulatory mechanisms, which can result in metabolic imbalance. Taking inspiration from nature, scientists have successfully developed synthetic scaffolds to enhance the performance of engineered metabolic pathways in microbial cell factories. By recruiting enzymes, synthetic scaffolds facilitate the formation of multi-enzyme complexes, leading to the modulation of enzyme spatial distribution, increased enzyme activity, and a reduction in the loss of intermediate products and the toxicity associated with harmful intermediates within cells. In recent years, scaffolds based on proteins, nucleic acids, and various organelles have been developed and employed to facilitate multiple metabolic pathways. Despite varying degrees of success, synthetic scaffolds still encounter numerous challenges. The objective of this review is to provide a comprehensive introduction to these synthetic scaffolds and discuss their latest research advancements and challenges.

Metabolic Engineering of Model Microorganisms for the Production of Xanthophyll

Xanthophyll is an oxidated version of carotenoid. It presents significant value to the pharmaceutical, food, and cosmetic industries due to its specific antioxidant activity and variety of colors. Chemical processing and conventional extraction from natural organisms are still the main sources of xanthophyll. However, the current industrial production model can no longer meet the demand for human health care, reducing petrochemical energy consumption and green sustainable development. With the swift development of genetic metabolic engineering, xanthophyll synthesis by the metabolic engineering of model microorganisms shows great application potential. At present, compared to carotenes such as lycopene and β-carotene, xanthophyll has a relatively low production in engineering microorganisms due to its stronger inherent antioxidation, relatively high polarity, and longer metabolic pathway. This review comprehensively summarized the progress in xanthophyll synthesis by the metabolic engineering of model microorganisms, described strategies to improve xanthophyll production in detail, and proposed the current challenges and future efforts needed to build commercialized xanthophyll-producing microorganisms.

Engineered repeat proteins as scaffolds to assemble multi-enzyme systems for efficient cell-free biosynthesis

Multi-enzymatic cascades with enzymes arranged in close-proximity through a protein scaffold can trigger a substrate channeling effect, allowing for efficient cofactor reuse with industrial potential. However, precise nanometric organization of enzymes challenges the design of scaffolds. In this study, we create a nanometrically organized multi-enzymatic system exploiting engineered Tetrapeptide Repeat Affinity Proteins (TRAPs) as scaffolding for biocatalysis. We genetically fuse TRAP domains and program them to selectively and orthogonally recognize peptide-tags fused to enzymes, which upon binding form spatially organized metabolomes. In addition, the scaffold encodes binding sites to selectively and reversibly sequester reaction intermediates like cofactors via electrostatic interactions, increasing their local concentration and, consequently, the catalytic efficiency. This concept is demonstrated for the biosynthesis of amino acids and amines using up to three enzymes. Scaffolded multi-enzyme systems present up to 5-fold higher specific productivity than the non-scaffolded ones. In-depth analysis suggests that channeling of NADH cofactor between the assembled enzymes enhances the overall cascade throughput and the product yield. Moreover, we immobilize this biomolecular scaffold on solid supports, creating reusable heterogeneous multi-functional biocatalysts for consecutive operational batch cycles. Our results demonstrate the potential of TRAP-scaffolding systems as spatial-organizing tools to increase the efficiency of cell-free biosynthetic pathways.

Engineering membrane architecture for biotechnological applications

Cellular membranes, predominantly described as a dynamic bilayer, are composed of different lipids, transmembrane proteins, and carbohydrates. Most research on biological membranes focuses on the identification, characterization, and mechanistic aspects of their different components. These studies provide a fundamental understanding of membrane structure, function, and dynamics, establishing a basis for the development of membrane engineering strategies. To date, approaches in this field concentrate on membrane adaptation to harsh conditions during industrial fermentation, which can be caused by temperature, osmotic, or organic solvent stress. With advances in the field of metabolic engineering and synthetic biology, recent breakthroughs include proof of concept microbial production of essential medicines, such as cannabinoids and vinblastine. However, long pathways, low yields, and host adaptation continue to pose challenges to the efficient scale up production of many important compounds. The lipid bilayer is profoundly linked to the activity of heterologous membrane-bound enzymes and transport of metabolites. Therefore, strategies for improving enzyme performance, facilitating pathway reconstruction, and enabling storage of products to increase the yields directly involve cellular membranes. At the forefront of membrane engineering research are re-emerging approaches in lipid research and synthetic biology that manipulate membrane size and composition and target lipid profiles across species. This review summarizes engineering strategies applied to cellular membranes and discusses the challenges and future perspectives, particularly with regards to their applications in host engineering and bioproduction.

Designing Intracellular Compartments for Efficient Engineered Microbial Cell Factories

With the rapid development of synthetic biology, various kinds of microbial cell factories (MCFs) have been successfully constructed to produce high-value-added compounds. However, the complexity of metabolic regulation and pathway crosstalk always cause issues such as intermediate metabolite accumulation, byproduct generation, and metabolic burden in MCFs, resulting in low efficiencies and low yields of industrial biomanufacturing. Such issues could be solved by spatially rearranging the pathways using intracellular compartments. In this review, design strategies are summarized and discussed based on the types and characteristics of natural and artificial subcellular compartments. This review systematically presents information for the construction of efficient MCFs with intracellular compartments in terms of four aspects of design strategy goals: (1) improving local reactant concentration; (2) intercepting and isolating competing pathways; (3) providing specific reaction substances and environments; and (4) storing and accumulating products.

Assembly of Metabolons in Yeast Using Cas6-Mediated RNA Scaffolding

Cells often localize pathway enzymes in close proximity to reduce substrate loss via diffusion and to ensure that carbon flux is directed toward the desired product. To emulate this strategy for the biosynthesis of heterologous products in yeast, we have taken advantage of the highly specific Cas6-RNA interaction and the predictability of RNA hybridizations to demonstrate Cas6-mediated RNA-guided protein assembly within the yeast cytosol. The feasibility of this synthetic scaffolding technique for protein localization was first demonstrated using a split luciferase reporter system with each part fused to a different Cas6 protein. In Saccharomyces cerevisiae, the luminescence signal increased 3.6- to 20-fold when the functional RNA scaffold was also expressed. Expression of a trigger RNA, designed to prevent the formation of a functional scaffold by strand displacement, decreased the luminescence signal by nearly 2.3-fold. Temporal control was also possible, with induction of scaffold expression resulting in an up to 11.6-fold increase in luminescence after 23 h. Cas6-mediated assembly was applied to create a two-enzyme metabolon to redirect a branch of the violacein biosynthesis pathway. Localizing VioC and VioE together increased the amount of deoxyviolacein (desired) relative to prodeoxyviolacein (undesired) by 2-fold. To assess the generality of this colocalization method in other yeast systems, the split luciferase reporter system was evaluated in Kluyveromyces marxianus; RNA scaffold expression resulted in an increase in the luminescence signal of up to 1.9-fold. The simplicity and flexibility of the design suggest that this strategy can be used to create metabolons in a wide range of recombinant hosts of interest.

Synthetic Multienzyme Assemblies for Natural Product Biosynthesis

In nature, enzymes that catalyze sequential reactions are often assembled as clusters or complexes. The formation of multienzyme complexes, or metabolons, brings the enzyme active sites into proximity to promote intermediate transfer, decrease intermediate leakage, and streamline the metabolic flux towards the desired products. We and others have developed synthetic versions of metabolons through various strategies to enhance the catalytic rates for synthesizing valuable chemicals inside microbes. Synthetic multienzyme complexes range from static enzyme nanostructures to dynamic enzyme coacervates. Enzyme complexation optimizes the metabolic fluxes inside microbes, increases the product titer, and supplies the field with high-yield microbe strains that are amenable to large-scale fermentation. Enzyme complexes constructed inside microbial cells can be separated as independent entities and catalyze biosynthetic reactions ex vivo; such a feature gains these complexes another name, "synthetic organelles" - new subcellular entities with independent structures and functions. Still, the field is seeking new strategies to better balance dynamicity and confinement and to achieve finer control of local compartmentalization in the cells, as the natural multienzyme complexes do. Industrial applications of synthetic multienzyme complexes for the large-scale production of valuable chemicals are yet to be realized. This review focuses on synthetic multienzyme complexes that are constructed and function inside microbial cells.

Strengthening microbial cell factories for efficient production of bioactive molecules

High demand of bioactive molecules (food additives, antibiotics, plant growth enhancers, cosmetics, pigments and other commercial products) is the prime need for the betterment of human life where the applicability of the synthetic chemical product is on the saturation due to associated toxicity and ornamentations. It has been noticed that the discovery and productivity of such molecules in natural scenarios are limited due to low cellular yields as well as less optimized conventional methods. In this respect, microbial cell factories timely fulfilling the requirement of synthesizing bioactive molecules by improving production yield and screening more promising structural homologues of the native molecule. Where the robustness of the microbial host can be potentially achieved by taking advantage of cell engineering approaches such as tuning functional and adjustable factors, metabolic balancing, adapting cellular transcription machinery, applying high throughput OMICs tools, stability of genotype/phenotype, organelle optimizations, genome editing (CRISPER/Cas mediated system) and also by developing accurate model systems via machine-learning tools. In this article, we provide an overview from traditional to recent trends and the application of newly developed technologies, for strengthening the systemic approaches and providing future directions for enhancing the robustness of microbial cell factories to speed up the production of biomolecules for commercial purposes.

Interaction between the Anchoring Domain of A-Kinase Anchoring Proteins and the Dimerization and Docking Domain of Protein Kinase A: A Potent Tool for Synthetic Biology

Nature is enriched with specific interactions between receptor proteins and their cognate ligands. These interacting pairs can be exploited and applied for the construction of well-ordered multicomponent assemblies with multivalency and multifunctionality. One of the research hotspots of this area is the formation of multienzyme complexes with stable and tunable architectures, which may bear the potential to facilitate cascade biocatalysis and/or strengthen metabolic fluxes. Here we focus on a special interacting pair, the anchoring domain (AD) derived from A-kinase anchoring protein and its interacting dimerization and docking domain (DDD) derived from cyclic AMP-dependent protein kinase, which has potential to be an effective and powerful synthetic biology tool for the construction of multienzyme assemblies. We review the origin and interaction mechanism of AD-DDD, followed by the application of this so-called dock-and-lock pair to form various bioconjugates with multivalency and multispecificity. Then several recent studies related to the construction of multienzyme complexes using AD-DDD, and more specifically, the RIAD-RIDD interacting pair, are presented. Finally, we also discuss the great biotechnology potential and perspectives of AD-DDD as a potent synthetic biology tool for post-translational modifications.

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

Co-localizing biochemical processes is a great strategy when expressing the heterologous metabolic pathway for product biosynthesis. The RNA scaffold is a flexible and efficient synthetic compartmentalization method to co-localize the enzymes involved in the metabolic pathway by binding to the specific RNA, binding domains fused with the engineered enzymes. Herein, we designed two artificial RNA scaffold structures─0D RNA scaffolds and 2D RNA scaffolds─using the reported aptamers PP7 and BIV-Tat and the corresponding RNA-binding domains (RBDs). We verified the interaction of the RBD and RNA aptamer in vitro and in vivo. Then, we determined the efficiencies of these RNA scaffolds by co-localizing fluorescent proteins. We employed the RNA scaffolds combined with the enzyme fusion strategies to increase the metabolic flux involved in the enzymes of the mevalonate pathway for mevalonate and isoprene production. Compared with the no RNA scaffold strain, the mevalonate levels of the 0D RNA scaffolds and 2D RNA scaffolds increased by 84.1% (3.13 ± 0.03 g/L) and 76.5% (3.00 ± 0.09 g/L), respectively. We applied the 0D RNA scaffolds for increasing the isoprene production by localizing the enzymes involved in a heterologous multi-enzyme pathway. When applying the RNA scaffolds for co-localizing the enzymes mvaE and mvaS, the isoprene production reached to 609.3 ± 57.9 mg/L, increasing by 142% compared with the no RNA scaffold strain. Our results indicate that the RNA scaffold is a powerful tool for improving the efficiencies of the reaction process in the metabolic pathway.

Recent progress in strategies for steroid production in yeasts

As essential structural molecules of fungal cell membrane, ergosterol is not only an important component of fungal growth and stress-resistance but also a key precursor for manufacturing steroid drugs of pharmaceutical or agricultural significance. So far, ergosterol biosynthesis in yeast has been elucidated elaborately, and efforts have been made to increase ergosterol production through regulation of ergosterol metabolism and storage. Furthermore, the same intermediates shared by yeasts and animals or plants make the construction of heterologous sterol pathways in yeast a promising approach to synthesize valuable steroids, such as phytosteroids and animal steroid hormones. During these challenging processes, several obstacles have arisen and been combated with great endeavors. This paper reviews recent research progress of yeast metabolic engineering for improving the production of ergosterol and heterologous steroids. The remaining tactics are also discussed.

Quantitative Structure-Activity Relationship Enables the Rational Design of Lipid Droplet-Targeting Carbon Dots for Visualizing Bisphenol A-Induced Nonalcoholic Fatty Liver Disease-like Changes

Lipid droplets (LDs) play indispensable roles in numerous physiological processes; hence, the visualization of the dynamic behavior of LDs in living cells is of great importance in physiological and pathological research. In this article, the quantitative structure-activity relationship (QSAR) theory was employed as an effective design strategy for the development of organelle-targeting carbon dots (CDs). The lipid-water partition coefficient (Log P) of the QSAR was adopted as a key parameter to predict the cellular uptake and subcellular localization of CDs in live cells. By carefully adjusting the molecular structure and lipophilicity of the precursors, p-phenylenediamine-derivatized nucleolus-targeting hydrophilic CDs were converted to lipophilic CDs [4-piperidinoaniline (PA) CDs] with inherent LD-targeting performance. The PA CDs were able to indicate the dynamic behavior of LDs and visualize the changes of bisphenol A-induced nonalcoholic fatty liver disease-like changes in a cellular model. The QSAR strategy of CDs demonstrated here is expected to be increasingly exploited as a powerful design tool for developing various organelle-targeting CDs.

Engineering yeast subcellular compartments for increased production of the lipophilic natural products ginsenosides

Eukaryotic yeasts have a variety of subcellular compartments and are ideal platform strains for the construction of complex heterologous natural product biosynthesis pathways. Improving the synthesis efficiency of microbial cell factories through the utilization and modification of subcellular compartments by synthetic biology has good application prospects. Here, we used the yeast PLN1 protein to target the normally endoplasmic reticulum (ER)-localized cytochrome P450 enzyme protopanaxadiol (PPD) synthase (PPDS) to lipid droplets (LDs), which are the storage organelles of the PPDS substrate dammarenediol-II (DD). The efficiency of converting DD to PPD was significantly increased by 394%, and the conversion rate of DD increased from 17.4% to 86.0%. Furthermore, increasing the volume of LDs can significantly enhance the production of DD and its derivatives, but the change in the ratio of the volume and surface area of LDs decreased the conversion efficiency of DD to PPD. Additionally, the biosynthetic pathways of the PPD-type saponin ginsenoside compound K (CK) was reconstituted in a PPD-producing chassis strain, and CK production reached 21.8 mg/L/OD, 4.4-fold higher compared to the native ER-expression strategy. Next, we enhanced the expression of the Pn3-29 gene module to further reduce the accumulation of PPD and increase the production of CK to 41.3 mg/L/OD. Finally, the CK titer of the resulting strain reached 5 g/L in 5 L fed-batch fermentations. This study provides a new strategy for engineering yeast to produce complex natural products.

Infrequent metadynamics study of rare-event electrostatic channeling

The efficiency of cascade reactions, which consist of multiple chemical transformations that occur in a single pot without purification steps, is limited by the transport efficiency of intermediates between adjacent steps. Electrostatic channeling is a proven strategy for intermediate transfer in natural chemical cascades, but implementation into artificial cascades remains a challenge. Here, we combine infrequent metadynamics (InMetaD), umbrella sampling (US), and kinetic Monte Carlo (KMC) models to computationally study the transfer mechanism of glucose-6-phosphate (G6P) on a poly-arginine peptide bridging hexokinase (HK) and glucose-6-dehydrogenase (G6PDH). Transport of G6P by hopping in the presence of poly-arginine peptides is shown to be a rare event, and InMetaD is used to compute the hopping activation energy. US simulations capture the configurational change in the desorption process and enable the determination of the desorption energy. Parameterized by these results, a KMC model is used to estimate transport efficiency for the bridged enzyme complex. Results are compared to a similar complex using a poly-lysine bridge, using kinetic lag time as a metric. Even at a high ionic strength of 120 mM, poly-arginine peptides may be capable of more efficient transport as compared to poly-lysine, with a predicted lag time of 6 seconds for poly-arginine, compared to a previously reported lag time of 59 seconds for poly-lysine. This work indicates that poly-arginine peptides may be an improved bridge structure for electrostatic channeling of anionic intermediates.

Compartmentalized Reconstitution of Post-squalene Pathway for 7-Dehydrocholesterol Overproduction in Saccharomyces cerevisiae

7-Dehydrocholesterol (7-DHC) is the direct precursor to manufacture vitamin D₃. Our previous study has achieved 7-DHC synthesis in Saccharomyces cerevisiae based on the endogenous post-squalene pathway. However, the distribution of post-squalene enzymes between the endoplasmic reticulum (ER) and lipid bodies (LD) might raise difficulties for ERG proteins to catalyze and deliver sterol intermediates, resulting in unbalanced metabolic flow and low product yield. Herein, we intended to rearrange the subcellular location of post-squalene enzymes to alleviate metabolic bottleneck and boost 7-DHC production. After identifying the location of DHCR24 (C-24 reductase, the only heterologous protein for 7-DHC biosynthesis) on ER, all the ER-located enzymes were grouped into four modules: ERG1/11/24, ERG25/26/27, ERG2/3, and DHCR24. These modules attempted to be overexpressed either on ER or on LDs. As a result, expression of LD-targeted DHCR24 and ER-located ERG1/11/24 could promote the conversion efficiency among the sterol intermediates to 7-DHC, while locating module ERG2/3 into LDs improved the whole metabolic flux of the post-squalene pathway. Coexpressing LD-targeted ERG2/3 and DHCR24 (generating strain SyBE_Sc01250035) improved 7-DHC production from 187.7 to 308.2 mg/L at shake-flask level. Further expressing ER-targeted module ERG1/11/24 in strain SyBE_Sc01250035 dramatically reduced squalene accumulation from 620.2 mg/L to the lowest level (by 93.8%) as well as improved 7-DHC production to the highest level (to 342.2 mg/L). Then targeting module ERG25/26/27 to LDs further increased 7-DHC titer to 360.6 mg/L, which is the highest shake-flask level production for 7-DHC ever reported. Our study not only proposes and further proves the concept of pathway compartmentalized reconstitution to regulate metabolic flux but also provides a promising chassis to produce other steroidal compounds through the post-squalene pathway.

Synthetic Protein Scaffolds for Improving R-(-)-Linalool Production in Escherichia coli

R-(-)-Linalool is widely used in the pharmaceutical, agrochemical, and fragrance industries; however, its applications are limited owing to low yield and high cost of production. To improve the production efficiency of R-(-)-linalool in Escherichia coli, three enzymes [E. coli-derived isopentenyl diphosphate isomerase, Abies grandis-derived geranyl diphosphate synthase, and Streptomyces clavuligerus-derived (3R)-linalool synthases] were physically colocalized to synthetic complexes using synthetic protein scaffolds of GTPase-binding domain, Src homology 3, and PSD95/DlgA/Zo-1. R-(-)-Linalool was produced at the highest concentration in the strain IGL114 containing a scaffold ratio of 1:1:4. By further optimizing the inducer, temperature, and glycerol concentration, the production titer of R-(-)-linalool in the shake flask was increased by approximately 10 times compared with that of the scaffold-free control and was 2.78 times the previously reported yield. The production in the fermenter was about 1.5 times the previous highest production. In general, the final strain accumulated 277.8 and 1523.2 mg/L R-(-)-linalool under the conditions of shake-flask and fed-batch fermentation, respectively. This study provides a foundation for the assembly of bacterial intracellular protein scaffolds.

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

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.

Successful Enzyme Colocalization Strategies in Yeast for Increased Synthesis of Non-native Products

Yeast cell factories, particularly Saccharomyces cerevisiae, have proven valuable for the synthesis of non-native compounds, ranging from commodity chemicals to complex natural products. One significant challenge has been ensuring sufficient carbon flux to the desired product. Traditionally, this has been addressed by strategies involving "pushing" and "pulling" the carbon flux toward the products by overexpression while "blocking" competing pathways via downregulation or gene deletion. Colocalization of enzymes is an alternate and complementary metabolic engineering strategy to control flux and increase pathway efficiency toward the synthesis of non-native products. Spatially controlling the pathway enzymes of interest, and thus positioning them in close proximity, increases the likelihood of reaction along that pathway. This mini-review focuses on the recent developments and applications of colocalization strategies, including enzyme scaffolding, construction of synthetic organelles, and organelle targeting, in both S. cerevisiae and non-conventional yeast hosts. Challenges with these techniques and future directions will also be discussed.

Engineering bioscaffolds for enzyme assembly

With the demand for green, safe, and continuous biocatalysis, bioscaffolds, compared with synthetic scaffolds, have become a desirable candidate for constructing enzyme assemblages because of their biocompatibility and regenerability. Biocompatibility makes bioscaffolds more suitable for safe and green production, especially in food processing, production of bioactive agents, and diagnosis. The regenerability can enable the engineered biocatalysts regenerate through simple self-proliferation without complex re-modification, which is attractive for continuous biocatalytic processes. In view of the unique biocompatibility and regenerability of bioscaffolds, they can be classified into non-living (polysaccharide, nucleic acid, and protein) and living (virus, bacteria, fungi, spore, and biofilm) bioscaffolds, which can fully satisfy these two unique properties, respectively. Enzymes assembled onto non-living bioscaffolds are based on single or complex components, while enzymes assembled onto living bioscaffolds are based on living bodies. In terms of their unique biocompatibility and regenerability, this review mainly covers the current advances in the research and application of non-living and living bioscaffolds with focus on engineering strategies for enzyme assembly. Finally, the future development of bioscaffolds for enzyme assembly is also discussed. Hopefully, this review will attract the interest of researchers in various fields and empower the development of biocatalysis, biomedicine, environmental remediation, therapy, and diagnosis.

Nature Inspired Multienzyme Immobilization: Strategies and Concepts

In a biological system, the spatiotemporal arrangement of enzymes in a dense cellular milieu, subcellular compartments, membrane-associated enzyme complexes on cell surfaces, scaffold-organized proteins, protein clusters, and modular enzymes have presented many paradigms for possible multienzyme immobilization designs that were adapted artificially. In metabolic channeling, the catalytic sites of participating enzymes are close enough to channelize the transient compound, creating a high local concentration of the metabolite and minimizing the interference of a competing pathway for the same precursor. Over the years, these phenomena had motivated researchers to make their immobilization approach naturally realistic by generating multienzyme fusion, cluster formation via affinity domain-ligand binding, cross-linking, conjugation on/in the biomolecular scaffold of the protein and nucleic acids, and self-assembly of amphiphilic molecules. This review begins with the discussion of substrate channeling strategies and recent empirical efforts to build it synthetically. After that, an elaborate discussion covering prevalent concepts related to the enhancement of immobilized enzymes' catalytic performance is presented. Further, the central part of the review summarizes the progress in nature motivated multienzyme assembly over the past decade. In this section, special attention has been rendered by classifying the nature-inspired strategies into three main categories: (i) multienzyme/domain complex mimic (scaffold-free), (ii) immobilization on the biomolecular scaffold, and (iii) compartmentalization. In particular, a detailed overview is correlated to the natural counterpart with advances made in the field. We have then discussed the beneficial account of coassembly of multienzymes and provided a synopsis of the essential parameters in the rational coimmobilization design.

Multi-Enzyme Systems in Flow Chemistry

Recent years have witnessed a growing interest in the use of biocatalysts in flow reactors. This merging combines the high selectivity and mild operation conditions typical of biocatalysis with enhanced mass transfer and resource efficiency associated to flow chemistry. Additionally, it provides a sound environment to emulate Nature by mimicking metabolic pathways in living cells and to produce goods through the systematic organization of enzymes towards efficient cascade reactions. Moreover, by enabling the combination of enzymes from different hosts, this approach paves the way for novel pathways. The present review aims to present recent developments within the scope of flow chemistry involving multi-enzymatic cascade reactions. The types of reactors used are briefly addressed. Immobilization methodologies and strategies for the application of the immobilized biocatalysts are presented and discussed. Key aspects related to the use of whole cells in flow chemistry are presented. The combination of chemocatalysis and biocatalysis is also addressed and relevant aspects are highlighted. Challenges faced in the transition from microscale to industrial scale are presented and discussed.

Metabolons, enzyme-enzyme assemblies that mediate substrate channeling, and their roles in plant metabolism

Metabolons are transient multi-protein complexes of sequential enzymes that mediate substrate channeling. They differ from multi-enzyme complexes in that they are dynamic, rather than permanent, and as such have considerably lower dissociation constants. Despite the fact that a huge number of metabolons have been suggested to exist in plants, most of these claims are erroneous as only a handful of these have been proven to channel metabolites. We believe that physical protein-protein interactions between consecutive enzymes of a pathway should rather be called enzyme-enzyme assemblies. In this review, we describe how metabolons are generally assembled by transient interactions and held together by both structural elements and non-covalent interactions. Experimental evidence for their existence comes from protein-protein interaction studies, which indicate that the enzymes physically interact, and direct substrate channeling measurements, which indicate that they functionally interact. Unfortunately, advances in cell biology and proteomics have far outstripped those in classical enzymology and flux measurements, rendering most reports reliant purely on interactome studies. Recent developments in co-fractionation mass spectrometry will likely further exacerbate this bias. Given this, only dynamic enzyme-enzyme assemblies in which both physical and functional interactions have been demonstrated should be termed metabolons. We discuss the level of evidence for the manifold plant pathways that have been postulated to contain metabolons and then list examples in both primary and secondary metabolism for which strong evidence has been provided to support these claims. In doing so, we pay particular attention to experimental and mathematical approaches to study metabolons as well as complexities that arise in attempting to follow them. Finally, we discuss perspectives for improving our understanding of these fascinating but enigmatic interactions.

CRISPR/Cas-directed programmable assembly of multi-enzyme complexes

We describe a versatile CRISPR/Cas-based strategy to construct multi-enzyme complexes scaffolded on a DNA template in programmable patterns. Catalytically inactive dCas9 nuclease was used in combination with SpyCatcher-SpyTag chemistry to assemble enzymes in a highly modular fashion. Five enzymes comprising the violacein biosynthesis pathway were precisely organized in nanometer proximity; a notable increase in violacein production demonstrated the benefits of scaffolding.

Microbial Cell Factory for Efficiently Synthesizing Plant Natural Products via Optimizing the Location and Adaptation of Pathway on Genome Scale

Plant natural products (PNPs) possess important pharmacological activities and are widely used in cosmetics, health care products, and as food additives. Currently, most PNPs are mainly extracted from cultivated plants, and the yield is limited by the long growth cycle, climate change and complex processing steps, which makes the process unsustainable. However, the complex structure of PNPs significantly reduces the efficiency of chemical synthesis. With the development of metabolic engineering and synthetic biology, heterologous biosynthesis of PNPs in microbial cell factories offers an attractive alternative. Based on the in-depth mining and analysis of genome and transcriptome data, the biosynthetic pathways of a number of natural products have been successfully elucidated, which lays the crucial foundation for heterologous production. However, there are several problems in the microbial synthesis of PNPs, including toxicity of intermediates, low enzyme activity, multiple auxotrophic dependence, and uncontrollable metabolic network. Although various metabolic engineering strategies have been developed to solve these problems, optimizing the location and adaptation of pathways on the whole-genome scale is an important strategy in microorganisms. From this perspective, this review introduces the application of CRISPR/Cas9 in editing PNPs biosynthesis pathways in model microorganisms, the influences of pathway location, and the approaches for optimizing the adaptation between metabolic pathways and chassis hosts for facilitating PNPs biosynthesis.

Conjugated Protein Domains as Engineered Scaffold Proteins

Assembly of proteins into higher-order complexes generates specificity and selectivity in cellular signaling. Signaling complex formation is facilitated by scaffold proteins that use modular scaffolding domains, which recruit specific pathway enzymes. Multimerization and recombination of these conjugated native domains allows the generation of libraries of engineered multidomain scaffold proteins. Analysis of these engineered proteins has provided molecular insight into the regulatory mechanism of the native scaffold proteins and the applicability of these synthetic variants. This topical review highlights the use of engineered, conjugated multidomain scaffold proteins on different length scales in the context of synthetic signaling pathways, metabolic engineering, liquid-liquid phase separation, and hydrogel formation.

Enzyme Assembly for Compartmentalized Metabolic Flux Control

Enzyme assembly by ligand binding or physically sequestrating enzymes, substrates, or metabolites into isolated compartments can bring key molecules closer to enhance the flux of a metabolic pathway. The emergence of enzyme assembly has provided both opportunities and challenges for metabolic engineering. At present, with the development of synthetic biology and systems biology, a variety of enzyme assembly strategies have been proposed, from the initial direct enzyme fusion to scaffold-free assembly, as well as artificial scaffolds, such as nucleic acid/protein scaffolds, and even some more complex physical compartments. These assembly strategies have been explored and applied to the synthesis of various important bio-based products, and have achieved different degrees of success. Despite some achievements, enzyme assembly, especially in vivo, still has many problems that have attracted significant attention from researchers. Here, we focus on some selected examples to review recent research on scaffold-free strategies, synthetic artificial scaffolds, and physical compartments for enzyme assembly or pathway sequestration, and we discuss their notable advances. In addition, the potential applications and challenges in the applications are highlighted.

Construction of artificial membrane transport metabolons – an emerging strategy in metabolic engineering

The term ‘membrane transport metabolon’ refers to the physical association of membrane transporters with enzymes that metabolize the transported substrates. In naturally evolved systems, physiological relevance of coupling transport with sequential enzymatic reactions resides, for instance, in faster turnover rates, protection of substrates from competing pathways or shielding the cellular environment from toxic compounds. Such underlying principles offer attractive possibilities for metabolic engineering approaches and concepts for constructing artificial transporter-enzyme complexes are recently being developed. In this minireview, the modes of substrate channeling across biological membranes and design principles for artificial transport metabolons are discussed.

Synthetic Protein Scaffolding at Biological Membranes

Protein scaffolding is a natural phenomenon whereby proteins colocalize into macromolecular complexes via specific protein-protein interactions. In the case of metabolic enzymes, protein scaffolding drives metabolic flux through specific pathways by colocalizing enzyme active sites. Synthetic protein scaffolding is increasingly used as a mechanism to improve product specificity and yields in metabolic engineering projects. To date, synthetic scaffolding has focused primarily on soluble enzyme systems, but many metabolic pathways for high-value secondary metabolites depend on membrane-bound enzymes. The compositional diversity of biological membranes and general challenges associated with modifying membrane proteins complicate scaffolding with membrane-requiring enzymes. Several recent studies have introduced new approaches to protein scaffolding at membrane surfaces, with notable success in improving product yields from specific metabolic pathways.

Nature's recyclers: anaerobic microbial communities drive crude biomass deconstruction

Microbial communities within anaerobic ecosystems have evolved to degrade and recycle carbon throughout the earth. A number of strains have been isolated from anaerobic microbial communities, which are rich in carbohydrate active enzymes (CAZymes) to liberate fermentable sugars from crude plant biomass (lignocellulose). However, natural anaerobic communities host a wealth of microbial diversity that has yet to be harnessed for biotechnological applications to hydrolyze crude biomass into sugars and value-added products. This review highlights recent advances in 'omics' techniques to sequence anaerobic microbial genomes, decipher microbial membership, and characterize CAZyme diversity in anaerobic microbiomes. With a focus on the herbivore rumen, we further discuss methods to discover new CAZymes, including those found within multi-enzyme fungal cellulosomes. Emerging techniques to characterize the interwoven metabolism and spatial interactions between anaerobes are also reviewed, which will prove critical to developing a predictive understanding of anaerobic communities to guide in microbiome engineering.

Proteomics Analysis of Lipid Droplets from the Oleaginous Alga Chromochloris zofingiensis Reveals Novel Proteins for Lipid Metabolism

Chromochloris zofingiensis represents an industrially relevant and unique green alga, given its capability of synthesizing triacylglycerol (TAG) and astaxanthin simultaneously for storage in lipid droplets (LDs). To further decipher lipid metabolism, the nitrogen deprivation (ND)-induced LDs from C. zofingiensis were isolated, purified, and subjected to proteomic analysis. Intriguingly, many C. zofingiensis LD proteins had no orthologs present in LD proteome of the model alga Chlamydomonas reinhardtii. Seven novel LD proteins (i.e., two functionally unknown proteins, two caleosins, two lipases, and one l-gulonolactone oxidase) and the major LD protein (MLDP), which were all transcriptionally up-regulated by ND, were selected for further investigation. Heterologous expression in yeast demonstrated that all tested LD proteins were localized to LDs and all except the two functionally unknown proteins enabled yeast to produce more TAG. MLDP could restore the phenotype of mldp mutant strain and enhance TAG synthesis in wild-type strain of C. reinhardtii. Although MLDP and caleosins had a comparable abundance in LDs, they responded distinctly to ND at the transcriptional level. The two lipases, instead of functioning as TAG lipases, likely recycled polar lipids to support TAG synthesis. For the first time, we reported that l-gulonolactone oxidase was abundant in LDs and facilitated TAG accumulation. Moreover, we also proposed a novel working model for C. zofingiensis LDs. Taken together, our work unravels the unique characteristics of C. zofingiensis LDs and provides insights into algal LD biogenesis and TAG synthesis, which would facilitate genetic engineering of this alga for TAG improvement.