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

Engineered interaction elements enable enhanced multi-enzyme assembly and cascade biocatalysis for indigo synthesis

Efficient interacting peptides or protein scaffolds can be used to achieve multi-enzymatic cascade reactions to trigger substrate channeling effect, prevent intermediate diffusion, and control the flux of metabolites. However, the limited availability of existing interactive elements hinders the broad application of the multi-enzyme assembly strategy. Here, a peptide-peptide pair (PB1C/PB2N) and a protein-peptide pair (importin/PB2C) were fused to the target protein to induce protein assembly for the first time. The newly developed interactive elements, when combined with the existing RIDD/RIAD pair, can more efficiently achieve multi-enzymatic cascade reactions. The indigo synthesis pathway was optimized through cascade biocatalysis based on these interactive elements. As a result, compared with the co-expression of multiple enzymes, the interaction element-based cascade biocatalysis increased the yield of indigo by twofold. Our results demonstrate the potential of PB1C/PB2N and importin/PB2C scaffold systems as tools for enzyme assembly to control metabolic flux and increase the efficiency of biosynthetic pathways.

An Intelligent Electrochemical Multi-Enzyme Molecular Machine for Chiral Chemical

In vitro multi-enzyme synthesis pathways harness the core elements of cellular synthesis while simplifying the complexities of cellular processes, facilitating the production of high-value chemicals. However, these in vitro synthesis processes often operate like a "black box" with limited monitoring of each reaction step, leading to a low substrate conversion efficiency. In this study, we present an intelligent multi-enzyme molecular machine(iMEMM) as a model system for achieving the deracemization of D, L-phosphinothricin (D, L-PPT). The entire system leverages electrochemical power and enzyme-catalyzed (cascade) reactions to establish substrate channel and enhance efficiency. By modularizing each reaction step and using electrochemical real-time monitoring of the reaction process, a single-step electrobiotransformation efficiency of up to 98 % and a chiral target L-PPT synthesis efficiency exceeding 99 % have been achieved. This iMEMM eliminates the need for intermediate separation, enabling a "substrate in, product out" process. Our research paves the way for future green, intelligent, and automated biological manufacturing.

Engineering metabolic flux for the microbial synthesis of aromatic compounds

Microbial cell factories have emerged as a sustainable alternative to traditional chemical synthesis and plant extraction methods for producing aromatic compounds. However, achieving economically viable production of these compounds in microbial systems remains a significant challenge. This review summarizes the latest advancements in metabolic flux regulation during the microbial production of aromatic compounds, providing an overview of its applications and practical outcomes. Various strategies aimed at improving the utilization of extracellular substrates, enhancing the efficiency of synthetic pathways for target products, and rewiring intracellular metabolic networks to boost the titer, yield, and productivity of aromatic compounds are discussed. Additionally, the persistent challenges in this field and potential solutions are highlighted.

Semirational Design of SenC to Enhance Organic Selenium Biosynthesis

Organic selenium, a bioavailable form of the essential trace element selenium, holds significant potential for improving human health through dietary supplements and functional foods. However, low bioconversion efficiency has primarily limited the biosynthesis of organic selenium compounds. Here, we focused on enhancing the biosynthesis of organic selenium by optimising the expression and activity of two key enzymes, SenB and SenC, involved in the conversion process. We compared several expression systems, including fusion expression and dual-promoter approaches, and optimised reaction conditions such as temperature, pH and incubation time. Our results showed that mutations of SenC more than doubled enzyme activity, resulting in a corresponding rise in the intermediate SeP. Notably, the fusion expression of SenB and SenC exhibited the highest conversion rate of organic selenium, achieving over 95% under optimal conditions. Our findings provide a basis for organic selenium production through microbial biotechnology.

Immobilized Multi-Enzyme/Nanozyme Biomimetic Cascade Catalysis for Biosensing Applications

Multiple enzyme-induced cascade catalysis has an indispensable role in the process of complex life activities, and is widely used to construct robust biosensors for analyzing various targets. The immobilized multi-enzyme cascade catalysis system is a novel biomimetic catalysis strategy that immobilizes various enzymes with different functions in stable carriers to simulate the synergistic catalysis of multiple enzymes in biological systems, which enables high stability of enzymes and efficiency enzymatic cascade catalysis. Nanozymes, a type of nanomaterial with intrinsic enzyme-like characteristics and excellent stabilities, are also widely applied instead of enzymes to construct immobilized cascade systems, achieving better catalytic performance and reaction stability. Due to good stability, reusability, and remarkably high efficiency, the immobilized multi-enzyme/nanozyme biomimetic cascade catalysis systems show distinct advantages in promoting signal transduction and amplification, thereby attracting vast research interest in biosensing applications. This review focuses on the research progress of the immobilized multi-enzyme/nanozyme biomimetic cascade catalysis systems in recent years. The construction approaches, factors affecting the efficiency, and applications for sensitive biosensing are discussed in detail. Further, their challenges and outlooks for future study are also provided.

Converting Bacillus subtilis 168 to a Synthetic Methylotroph by Combinatorial Metabolic Regulation Strategies

Methanol, which can come from methane or carbon dioxide, is a valuable renewable one-carbon (C1) feedstock for the production of biofuels and food chemicals. A new method was developed to create a multienzyme complex by combining methanol dehydrogenase (Mdh), 3-hexulose-6-phosphate synthase (Hps), and 6-phospho-3-hexuloseisomerase (Phi) in equal parts using SpyTag/Catcher and DogTag/Catcher systems. This self-assembly of multiple enzymes improves the conversion of methanol to fructose-6-phosphate (F6P) and was used to engineer a synthetic methylotroph from B. subtilis 168 that could efficiently utilize methanol. Various metabolic regulations related to key carbon pathways were tested and integrated to boost methanol consumption in this engineered strain. The final strain, B. subtilis SM6, could consume 3.87 g/L of methanol, marking the highest level of coutilization with xylose to date. The strategies employed in this research optimized the distribution of metabolic flow for formaldehyde and xylose, offering valuable insights for future studies on synthetic methylotrophs.

Local structural flexibility drives oligomorphism in computationally designed protein assemblies

Many naturally occurring protein assemblies have dynamic structures that allow them to perform specialized functions. Although computational methods for designing novel self-assembling proteins have advanced substantially over the past decade, they primarily focus on designing static structures. Here we characterize three distinct computationally designed protein assemblies that exhibit unanticipated structural diversity arising from flexibility in their subunits. Cryo-EM single-particle reconstructions and native mass spectrometry reveal two distinct architectures for two assemblies, while six cryo-EM reconstructions for the third likely represent a subset of its solution-phase structures. Structural modeling and molecular dynamics simulations indicate that constrained flexibility within the subunits of each assembly promotes a defined range of architectures rather than nonspecific aggregation. Redesigning the flexible region in one building block rescues the intended monomorphic assembly. These findings highlight structural flexibility as a powerful design principle, enabling exploration of new structural and functional spaces in protein assembly design.

Combining Protein Phase Separation and Bio-orthogonal Linking to Coimmobilize Enzymes for Cascade Biocatalysis

The designed and ordered co-immobilization of multiple enzymes for vectorial biocatalysis is challenging. Here, a combination of protein phase separation and bioorthogonal linking is used to generate a zeolitic imidazole framework (ZIF-8) containing co-immobilized enzymes. Zn2+ ions induce the clustering of minimal protein modules, such as 6-His tag, proline-rich motif (PRM) and SRC homology 3 (SH3) domains, and allow for phase separation of the coupled aldoketoreductase (AKR) and alcohol dehydrogenase (ADH) at low concentrations. This is achieved by fusing SpyCatcher and PRM-SH3-6His peptide fragments to the C and N termini of AKR, respectively, and the SpyTag to ADH. Addition of 2-methylimidazole results in droplet formation and enables in situ spatial embedding the recombinant AKR and ADH to generate the cascade biocalysis system encapsulated in ZIF-8 (AAE@ZIF). In synthesizing (S)-1-(2-chlorophenyl) ethanol, ater 6 cycles, the yield can still reach 91%, with 99.99% enantiomeric excess (ee) value for each cycle. However, the yield could only reach 72.9% when traditionally encapsulated AKR and ADH in ZIF-8 are used. Thus, this work demonstrates that a combination of protein phase separation and bio-orthogonal linking enables the in situ creation of a stable and spatially organized bi-enzyme system with enhanced channeling effects in ZIF-8.

Localized Cas12a-based cascade amplification for sensitive and robust detection of APE1

APE1, an essential enzyme for DNA repair, is overexpressed in various cancers and has been identified as a potential biomarker for cancer diagnosis. However, detecting APE1 at low expression levels in the early stage of cancer presents a significant obstacle. Here, we introduced a novel localized Cas12a-based cascade amplification (LCas12a-CA) method. This method confined both the terminal deoxynucleotidyl transferase and the crRNA/Cas12a complex onto the surfaces of gold nanoparticles (AuNPs). This confinement not only boosts the stability of the multiple enzymes but also induces a substrate channeling effect. As a result, it significantly accelerates the reaction rate and enhances the sensitivity of APE1 detection. Upon the addition of APE1, the AP sites within the APE1 primer can be recognized and cleaved by APE1, exposing the 3'-OH ends. In the presence of LCas12a-CA, polyA sequences are generated at 3'-OH ends with the help of TdT and dATP. The sequences directly enter the Cas12a system, activating the trans-cleavage activity of Cas12a, thereby cutting the reporters on the surface of AuNPs and releasing fluorescence. Our platform demonstrates a detection limit (LOD) as low as 2.51 × 10-6 U/mL, which is more than 60 times lower than that of free Cas12a-CA. Furthermore, the LCas12a-CA exhibits enhanced resistance ability in extreme environments and has been proven effective for the detection of APE1 in clinical samples. Overall, this work offers a promising platform for robust biosensing in cancer diagnosis and prognosis.

Design of a Genetically Programmable and Customizable Protein Scaffolding System for the Hierarchical Assembly of Robust, Functional Macroscale Materials

Inspired by the properties of natural protein-based biomaterials, protein nanomaterials are increasingly designed with natural or engineered peptides or with protein building blocks. Few examples describe the design of functional protein-based materials for biotechnological applications that can be readily manufactured, are amenable to functionalization, and exhibit robust assembly properties for macroscale material formation. Here, we designed a protein-scaffolding system that self-assembles into robust, macroscale materials suitable for in vitro cell-free applications. By controlling the coexpression in Escherichia coli of self-assembling scaffold building blocks with and without modifications for covalent attachment of cross-linking cargo proteins, hybrid scaffolds with spatially organized conjugation sites are overproduced that can be readily isolated. Cargo proteins, including enzymes, are rapidly cross-linked onto scaffolds for the formation of functional materials. We show that these materials can be used for the in vitro operation of a coimmobilized two-enzyme reaction and that the protein material can be recovered and reused. We believe that this work will provide a versatile platform for the design and scalable production of functional materials with customizable properties and the robustness required for biotechnological applications.

A carbon-based bifunctional heterogeneous enzyme: toward sustainable pollution control

We present a study on an immobilized functional enzyme (IFE), a novel biomaterial with exceptional sustainability in enzyme utility, widely employed across various fields worldwide. However, conventional carriers are prone to eroding the active functional domain of the IFE, thereby weakening its intrinsic enzyme activity. Consequently, there is a burgeoning interest in developing next-generation IFEs. In this study, we engineered a carbon-based bifunctional heterogeneous enzyme (MIP-AMWCNTs@lipase) for the intelligent recognition of di(2-ethylhexyl)phthalate (DEHP), a common plasticizer. The heterogeneous enzyme contains a bifunctional structural domain that both enriches and degrades DEHP. We investigated its dual-response performance for the enrichment and specific removal of DEHP. The imprinting factor of the carrier for DEHP was 3.4, demonstrating selectivity for DEHP. The removal rate reached up to 94.2% over a short period. The heterogeneous enzyme exhibited robust activity, catalytic efficiency, and excellent stability under harsh environmental conditions, retaining 77.7% of its initial lipase activity after 7 cycles. Furthermore, we proposed a stepwise heterogeneous enzyme reaction kinetic model based on the Michaelis-Menten equation to enhance our understanding of enzyme reaction kinetics. Our study employs a dual-effect recognition strategy of molecular blotting and enzyme immobilization to establish a method for the removal of organic pollutants. These findings hold significant implications for the fields of biomaterials and environmental science.

Carrier-free immobilized enzymatic reactor based on CipA-fused carbonyl reductase for efficient synthesis of chiral alcohol with cofactor self-sufficiency

In this study, based on the self-assembly strategy, we fused CipA with carbonyl reductase LXCARS154Y derived from Leifsonia xyli by gene coding, and successfully performed the carrier-free immobilization of LXCARS154Y. The immobilized enzyme was then characterized using scanning electron microscope (SEM), dynamic light scattering (DLS) and fourier transform infrared spectroscopy (FTIR). Compared with the free enzyme, the immobilized LXCARS154Y exhibited a 2.3-fold improvement in the catalytic efficiency kcat/km for the synthesis of a chiral pharmaceutical intermediate (R)-3,5-bis(trifluoromethyl)phenyl ethanol ((R)-BTPE) by reducing 3,5-bis(trifluoromethyl)acetophenone (BTAP). Moreover, the immobilized enzyme showed the enhanced stability while maintaining over 61 % relative activity after 18 cycles of batch reaction. Further, when CipA-fused carbonyl reductase was employed for (R)-BTPE production in a continuous flow reaction, almost complete yield (97.0 %) was achieved within 7 h at 2 M (512.3 g/L) of BTAP concentration, with a space-time yield of 1717.1 g·L-1·d-1. Notably, we observed the retention of cofactor NADH by CipA-based enzyme aggregates, resulting in a higher total turnover number (TTN) of 4815 to facilitate this bioreductive process. This research developed a concise strategy for efficient preparation of chiral intermediate with cofactor self-sufficiency via continuous flow biocatalysis, and the relevant mechanism was also explored.

Microtiter Plate Immobilization Screening for Prototyping Heterogeneous Enzyme Cascades

Immobilization is a key enabling technology in applied biocatalysis that facilitates the separation, recovery, and reuse of heterogeneous biocatalysts. However, finding a consensus immobilization protocol for several enzymes forming a multi-enzyme system is extremely difficult and relies on a combinatorial trial-and-error approach. Herein, we describe a protocol in which 17 different carriers functionalized with different reactive groups are tested in a 96-well microtiter plate to screen up to 21 immobilization protocols for up to 18 enzymes. This screening includes an activity and stability assay to select the optimal immobilization chemistry to achieve the most active and stable heterogeneous biocatalysts. The information retrieved from the screening can be rationalized using a Python-based application CapiPy. Finally, through scoring the screening results, we find the consensus immobilization protocol to assemble an immobilized four-enzyme system to transform vinyl acetate into (S)-3-hydroxybutyric acid. This methodology opens a path to speed up the prototyping of immobilized multi-enzyme pathways for chemical manufacturing.

Substrate-induced assembly of cascade enzymes and catalytic surfactants: nanoarchitectonics at the oil-in-water droplet interface

The heterogeneous distribution of lipids and lipid-bound proteins in a plasma membrane has functional advantages. Herein, in a synthetic system, we demonstrate the assembly of three enzymes involved in cascade reactions, in response to the substrate of the first enzyme at the oil-water interface being stabilized by a Zn(II)-metallosurfactant. Then we show substrate-mediated catalytically-active cluster formation of the metallosurfactant in a binary mixture with another non-catalytic surfactant at the interface. The catalytic ability can be tuned by controlling clustering through the addition of phosphate ions. Overall this work demonstrates functionally diverse supramolecular nanoarchitectonics at the oil-water interface.

An In Vitro Hybrid Biocatalytic System Enabled by a Combination of Surface-Displayed, Purified, and Cell-Free Expressed Enzymes

Enzymatic cascades have become a green and sustainable approach for the synthesis of valuable chemicals and pharmaceuticals. Using sequential enzymes to construct a multienzyme complex is an effective way to enhance the overall performance of biosynthetic routes. Here we report the design of an efficient in vitro hybrid biocatalytic system by assembling three enzymes that can convert styrene to (S)-1-phenyl-1,2-ethanediol. Specifically, we prepared the three enzymes in different ways, which were cell surface-displayed, purified, and cell-free expressed. To assemble them, we fused two orthogonal peptide-protein pairs (i.e., SpyTag/SpyCatcher and SnoopTag/SnoopCatcher) to the three enzymes, allowing their spatial organization by covalent assembly. By doing this, we constructed a multienzyme complex, which could enhance the production of (S)-1-phenyl-1,2-ethanediol by 3 times compared to the free-floating enzyme system without assembly. After optimization of the reaction system, the final product yield reached 234.6 μM with a substrate conversion rate of 46.9% (based on 0.5 mM styrene). Taken together, our strategy integrates the merits of advanced biochemical engineering techniques, including cellular surface display, spatial enzyme organization, and cell-free expression, which offers a new solution for chemical biosynthesis by enzymatic cascade biotransformation. We, therefore, anticipate that our approach will hold great potential for designing and constructing highly efficient systems to synthesize chemicals of agricultural, industrial, and pharmaceutical significance.

Engineering bio-brick protein scaffolds for organizing enzyme assemblies

Enzyme scaffolding is an emerging approach for enhancing the catalytic efficiency of multi-enzymatic cascades by controlling their spatial organization and stoichiometry. This study introduces a novel family of engineered SCAffolding Bricks, named SCABs, utilizing the consensus tetratricopeptide repeat (CTPR) domain for organized multi-enzyme systems. Two SCAB systems are developed, one employing head-to-tail interactions with reversible covalent disulfide bonds, the other relying on non-covalent metal-driven assembly via engineered metal coordinating interfaces. Enzymes are directly fused to SCAB modules, triggering assembly in a non-reducing environment or by metal presence. A proof-of-concept with formate dehydrogenase (FDH) and L-alanine dehydrogenase (AlaDH) shows enhanced specific productivity by 3.6-fold compared to free enzymes, with the covalent stapling outperforming the metal-driven assembly. This enhancement likely stems from higher-order supramolecular assembly and improved NADH cofactor regeneration, resulting in more efficient cascades. This study underscores the potential of protein engineering to tailor scaffolds, leveraging supramolecular spatial-organizing tools, for more efficient enzymatic cascade reactions.

DNA Framework-Programmed Nanoscale Enzyme Assemblies

Multienzyme assemblies mediated by multivalent interaction play a crucial role in cellular processes. However, the three-dimensional (3D) programming of an enzyme complex with defined enzyme activity in vitro remains unexplored, primarily owing to limitations in precisely controlling the spatial topological configuration. Herein, we introduce a nanoscale 3D enzyme assembly using a tetrahedral DNA framework (TDF), enabling the replication of spatial topological configuration and maintenance of an identical edge-to-edge distance akin to natural enzymes. Our results demonstrate that 3D nanoscale enzyme assemblies in both two-enzyme systems (glucose oxidase (GOx)/horseradish peroxidase (HRP)) and three-enzyme systems (amylglucosidase (AGO)/GOx/HRP) lead to enhanced cascade catalytic activity compared to the low-dimensional structure, resulting in ∼5.9- and ∼7.7-fold enhancements over homogeneous diffusional mixtures of free enzymes, respectively. Furthermore, we demonstrate the enzyme assemblies for the detection of the metabolism biomarkers creatinine and creatine, achieving a low limit of detection, high sensitivity, and broad detection range.

Constructing Protein-Scaffolded Multienzyme Assembly Enhances the Coupling Efficiency of the P450 System for Efficient Daidzein Biosynthesis from (2S)-Naringenin

Daidzein is a major isoflavone compound with an immense pharmaceutical value. This study applied a novel P450 CYP82D26 which can biosynthesize daidzein from (2S)-naringenin. However, the recombinant P450 systems often suffer from low coupling efficiency, leading to an electron transfer efficiency decrease and harmful reactive oxygen species release, thereby compromising their stability and catalytic efficiency. To address these challenges, the SH3-GBD-PDZ (SGP) protein scaffold was applied to assemble a multienzyme system comprising CYP82D26, P450 reductase, and NADP+-dependent aldehyde reductase in desired stoichiometric ratios. Results showed that the coupling efficiency of the P450 system was significantly increased, primarily attributed to the channeling effect of NADPH resulting from the proximity of tethered enzymes and the electrostatic interactions between NADPH and SGP. Assembling this SGP-scaffolded assembly system in Escherichia coli yielded a titer of 240.5 mg/L daidzein with an 86% (2S)-naringenin conversion rate, which showed a 9-fold increase over the free enzymes of the P450 system. These results underscore the potential application of the SGP-scaffolded multienzyme system in enhancing the coupling and catalytic efficiency of the P450 system.

Programming interchangeable and reversible heterooligomeric protein self-assembly using a bifunctional ligand

Protein design for self-assembly allows us to explore the emergence of protein-protein interfaces through various chemical interactions. Heterooligomers, unlike homooligomers, inherently offer a comprehensive range of structural and functional variations. Besides, the macromolecular repertoire and their applications would significantly expand if protein components could be easily interchangeable. This study demonstrates that a rationally designed bifunctional linker containing an enzyme inhibitor and maleimide can guide the formation of diverse protein heterooligomers in an easily applicable and exchangeable manner without extensive sequence optimizations. As proof of concept, we selected four structurally and functionally unrelated proteins, carbonic anhydrase, aldolase, acetyltransferase, and encapsulin, as building block proteins. The combinations of two proteins with the bifunctional linker yielded four two-component heterooligomers with discrete sizes, shapes, and enzyme activities. Besides, the overall size and formation kinetics of the heterooligomers alter upon adding metal chelators, acidic buffer components, and reducing agents, showing the reversibility and tunability in the protein self-assembly. Given that the functional groups of both the linker and protein components are readily interchangeable, our work broadens the scope of protein-assembled architectures and their potential applications as functional biomaterials.

Local structural flexibility drives oligomorphism in computationally designed protein assemblies

Many naturally occurring protein assemblies have dynamic structures that allow them to perform specialized functions. For example, clathrin coats adopt a wide variety of architectures to adapt to vesicular cargos of various sizes. Although computational methods for designing novel self-assembling proteins have advanced substantially over the past decade, most existing methods focus on designing static structures with high accuracy. Here we characterize the structures of three distinct computationally designed protein assemblies that each form multiple unanticipated architectures, and identify flexibility in specific regions of the subunits of each assembly as the source of structural diversity. Cryo-EM single-particle reconstructions and native mass spectrometry showed that only two distinct architectures were observed in two of the three cases, while we obtained six cryo-EM reconstructions that likely represent a subset of the architectures present in solution in the third case. Structural modeling and molecular dynamics simulations indicated that the surprising observation of a defined range of architectures, instead of non-specific aggregation, can be explained by constrained flexibility within the building blocks. Our results suggest that deliberate use of structural flexibility as a design principle will allow exploration of previously inaccessible structural and functional space in designed protein assemblies.

Temperature-Controlled Expression of a Recombinant Human-like Collagen I Peptide in Escherichia coli

Collagen is the functional protein of the skin, tendons, ligaments, cartilage, bone, and connective tissue. Due to its extraordinary properties, collagen has a wide range of applications in biomedicine, tissue engineering, food, and cosmetics. In this study, we designed a functional fragment of human type I collagen (rhLCOL-I) and expressed it in Escherichia coli (E. coli) BL21(DE3) PlysS containing a thermal-induced plasmid, pBV-rhLCOL-I. The results indicated that the optimal expression level of the rhLCOL-I reached 36.3% of the total protein at 42 °C, and expressed in soluble form. In a 7 L fermentation, the yield of purified rhLCOL-I was 1.88 g/L. Interestingly, the plasmid, pBV220-rhLCOL-I, was excellently stable during the fermentation process, even in the absence of antibiotics. Functional analyses indicated that rhLCOL-I had the capacity to promote skin cell migration and adhesion in vitro and in vivo. Taken together, we developed a high-level and low-cost approach to produce collagen fragments suitable for medical applications in E. coli.