Synthetic protein scaffolds for the colocalisation of co-acting enzymes

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.

Insights into the regulation of mRNA translation by scaffolding proteins

Regionalisation of molecular mechanisms allows cells to fine-tune their responses to dynamic environments. In this context, scaffolds are well-known mediators of localised protein activity. These phenomenal proteins act as docking sites where pathway components are brought together to ensure efficient and reliable flow of information within the cell. Although scaffolds are mostly understood as hubs for signalling communication, some have also been studied as regulators of mRNA translation. Here, we provide a brief overview of the work unravelling how scaffolding proteins facilitate the cross-talk between the two processes. Firstly, we examine the activity of AKAP1 and AKAP12, two signalling proteins that not only have the capacity to anchor mRNAs to membranes but can also regulate protein synthesis. Next, we review the studies that uncovered how the ribosome-associated protein RACK1 orchestrates translation initiation. We also discuss the evidence pointing to the scaffolds Ezrin and LASP1 as regulators of early translation stages. In the end, we conclude with some open questions and propose future directions that will bring new insights into the regulation of mRNA translation by scaffolding proteins.

Design of pseudosymmetric protein hetero-oligomers

Pseudosymmetric hetero-oligomers with three or more unique subunits with overall structural (but not sequence) symmetry play key roles in biology, and systematic approaches for generating such proteins de novo would provide new routes to controlling cell signaling and designing complex protein materials. However, the de novo design of protein hetero-oligomers with three or more distinct chains with nearly identical structures is a challenging unsolved problem because it requires the accurate design of multiple protein-protein interfaces simultaneously. Here, we describe a divide-and-conquer approach that breaks the multiple-interface design challenge into a set of more tractable symmetric single-interface redesign tasks, followed by structural recombination of the validated homo-oligomers into pseudosymmetric hetero-oligomers. Starting from de novo designed circular homo-oligomers composed of 9 or 24 tandemly repeated units, we redesigned the inter-subunit interfaces to generate 19 new homo-oligomers and structurally recombined them to make 24 new hetero-oligomers, including ABC heterotrimers, A2B2 heterotetramers, and A3B3 and A2B2C2 heterohexamers which assemble with high structural specificity. The symmetric homo-oligomers and pseudosymmetric hetero-oligomers generated for each system have identical or nearly identical backbones, and hence are ideal building blocks for generating and functionalizing larger symmetric and pseudosymmetric assemblies.

Epigallocatechin Gallate Combine with Ice Glazing: A Promising Way to Preserve the Quality of Frozen Eriocheir sinensis

The quality of frozen Eriocheir sinensis plays an important role in influencing consumer preference. Polyphenol oxidase (PPO) activity changes are commonly used to evaluate melanosis in aquatic products. In this study, we examined the interactions between epigallocatechin gallate (EGCG) and PPO. Further, we investigated whether treatment with EGCG in combination with ice glazing could restrict melanosis in E. sinensis during frozen storage and maintain its quality. The results demonstrated that EGCG inhibited PPO activity in a dose-dependent manner and firmly binds to the active pocket of PPO, thereby altering its tertiary structure. The melanosis and oxidation of E. sinensis in frozen storage were significantly reduced by adding 0.1 g/L EGCG combined with ice-glazing treatment (EGCG + IG). EGCG + IG improved the melanosis score of E. sinensis after six-week storage by 77.17%, and reduced protein and lipid oxidation by 10.80% and 62.46%, respectively, compared with untreated specimens. Moreover, the umami and sweet amino acids were better retained. Among the combined treatments, ice glazing effectively inhibited oxidation, whereas EGCG significantly inhibited melanosis. In summary, EGCG combine with ice glazing, is an effective way to maintain the quality of frozen E. sinensis and could also be studied to store other aquatic products.

A Closer Look at Type I Left-Handed β-Helices Provides a Better Understanding in Their Sequence-Structure Relationship: Toward Their Rational Design

Understanding the sequence-structure relationship in protein is of fundamental interest, but has practical applications such as the rational design of peptides and proteins. This relationship in the Type I left-handed β-helix containing proteins is updated and revisited in this study. Analyzing the available experimental structures in the Protein Data Bank, we could describe, further in detail, the structural features that are important for the stability of this fold, as well as its nucleation and termination. This study is meant to complete previous work, as it provides a separate analysis of the N-terminal and C-terminal rungs of the helix. Particular sequence motifs of these rungs are described along with the structural element they form.

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.

Metabolic engineering and fermentation of microorganisms for carotenoids production

Carotenoids are natural pigments that exhibit a wide range of red, orange, and yellow colors and are extensively used in the food, nutraceuticals, cosmetics, and aquaculture industries. While advances in systems metabolic engineering have established a foundation for constructing carotenoid-producing microbial cell factories at a laboratory scale, translating these technologies to industrial scales remains a big challenge. Moreover, there is a need to devise cost-effective methods for downstream processing and purification of carotenoids. In this review, we discuss recent strategies in metabolic engineering, such as metabolic flux optimization, enzyme assembly, and storage capacity engineering, aimed at constructing high-performance carotenoid-producing microbial strains. We also review recent approaches for cost-effective downstream processing and purification of carotenoids.

Engineering highly productive cyanobacteria towards carbon negative emissions technologies

Cyanobacteria are a diverse and ecologically important group of photosynthetic prokaryotes that contribute significantly to the global carbon cycle through the capture of CO2 as biomass. Cyanobacterial biotechnology could play a key role in a sustainable bioeconomy through negative emissions technologies (NETs), such as carbon sequestration or bioproduction. However, the primary issues of low productivities and high infrastructure costs currently limit the commercialisation of such applications. The isolation of several fast-growing strains and recent advancements in molecular biology tools now offer promising new avenues for improving yields, including metabolic engineering approaches guided by high-throughput screening and metabolic models. Furthermore, emerging research on engineering coculture communities could help to develop more robust culturing systems to support broader NET applications.

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.

Self-Assembly of Nanofilaments in Cyanobacteria for Protein Co-localization

Cyanobacteria offer great potential as alternative biotechnological hosts due to their photoautotrophic capacities. However, in comparison to established heterotrophic hosts, several key aspects, such as product titers, are still lagging behind. Nanobiotechnology is an emerging field with great potential to improve existing hosts, but so far, it has barely been explored in microbial photosynthetic systems. Here, we report the establishment of large proteinaceous nanofilaments in the unicellular model cyanobacterium Synechocystis sp. PCC 6803 and the fast-growing cyanobacterial strain Synechococcus elongatus UTEX 2973. Transmission electron microscopy and electron tomography demonstrated that expression of pduA*, encoding a modified bacterial microcompartment shell protein, led to the generation of bundles of longitudinally aligned nanofilaments in S. elongatus UTEX 2973 and shorter filamentous structures in Synechocystis sp. PCC 6803. Comparative proteomics showed that PduA* was at least 50 times more abundant than the second most abundant protein in the cell and that nanofilament assembly had only a minor impact on cellular metabolism. Finally, as a proof-of-concept for co-localization with the filaments, we targeted a fluorescent reporter protein, mCitrine, to PduA* by fusion with an encapsulation peptide that natively interacts with PduA. The establishment of nanofilaments in cyanobacterial cells is an important step toward cellular organization of heterologous pathways and the establishment of cyanobacteria as next-generation hosts.

Research progress of multi-enzyme complexes based on the design of scaffold protein

Multi-enzyme complexes designed based on scaffold proteins are a current topic in molecular enzyme engineering. They have been gradually applied to increase the production of enzyme cascades, thereby achieving effective biosynthetic pathways. This paper reviews the recent progress in the design strategy and application of multi-enzyme complexes. First, the metabolic channels in the multi-enzyme complex have been introduced, and the construction strategies of the multi-enzyme complex emerging in recent years have been summarized. Then, the discovered enzyme cascades related to scaffold proteins are discussed, emphasizing on the influence of the linker on the fusion enzyme (fusion protein) and its possible mechanism. This review is expected to provide a more theoretical basis for the modification of multi-enzyme complexes and broaden their applications in synthetic biology.

Stepwise design of pseudosymmetric protein hetero-oligomers

Pseudosymmetric hetero-oligomers with three or more unique subunits with overall structural (but not sequence) symmetry play key roles in biology, and systematic approaches for generating such proteins de novo would provide new routes to controlling cell signaling and designing complex protein materials. However, the de novo design of protein hetero-oligomers with three or more distinct chains with nearly identical structures is a challenging problem because it requires the accurate design of multiple protein-protein interfaces simultaneously. Here, we describe a divide-and-conquer approach that breaks the multiple-interface design challenge into a set of more tractable symmetric single-interface redesign problems, followed by structural recombination of the validated homo-oligomers into pseudosymmetric hetero-oligomers. Starting from de novo designed circular homo-oligomers composed of 9 or 24 tandemly repeated units, we redesigned the inter-subunit interfaces to generate 15 new homo-oligomers and recombined them to make 17 new hetero-oligomers, including ABC heterotrimers, A2B2 heterotetramers, and A3B3 and A2B2C2 heterohexamers which assemble with high structural specificity. The symmetric homo-oligomers and pseudosymmetric hetero-oligomers generated for each system share a common backbone, and hence are ideal building blocks for generating and functionalizing larger symmetric assemblies.

Engineered Artificial Membraneless Organelles in Saccharomyces cerevisiae To Enhance Chemical Production

Microbial cell factories provide a green and sustainable opportunity to produce value-added products from renewable feedstock. However, the leakage of toxic or volatile intermediates decreases the efficiency of microbial cell factories. In this study, membraneless organelles (MLOs) were reconstructed in Saccharomyces cerevisiae by the disordered protein sequence A-IDPs. A regulation system was designed to spatiotemporally regulate the size and rigidity of MLOs. Manipulating the MLO size of strain ZP03-FM, the amounts of assimilated methanol and malate were increased by 162 % and 61 %, respectively. Furthermore, manipulating the MLO rigidity in strain ZP04-RB made acetyl-coA synthesis from oxidative glycolysis change to non-oxidative glycolysis; consequently, CO₂ release decreased by 35 % and the n-butanol yield increased by 20 %. This artificial MLO provides a strategy for the co-localization of enzymes to channel C₁ starting materials into value-added chemicals.

Current challenges in designer cellulosome engineering

Designer cellulosomes (DCs) are engineered multi-enzyme complexes, comprising carbohydrate-active enzymes attached to a common backbone, the scaffoldin, via high-affinity cohesin-dockerin interactions. The use of DCs in the degradation of renewable biomass polymers is a promising approach for biorefineries. Indeed, DCs have shown significant hydrolytic activities due to the enhanced enzyme-substrate proximity and inter-enzyme synergies, but technical hurdles in DC engineering have hindered further progress towards industrial application. The challenge in DC engineering lies in the large diversity of possible building blocks and architectures, resulting in a multivariate and immense design space. Simultaneously, the precise DC composition affects many relevant parameters such as activity, stability, and manufacturability. Since protein engineers face a lack of high-throughput approaches to explore this vast design space, DC engineering may result in an unsatisfying outcome. This review provides a roadmap to guide researchers through the process of DC engineering. Each step, starting from concept to evaluation, is described and provided with its challenges, along with possible solutions, both for DCs that are assembled in vitro or are displayed on the yeast cell surface. KEY POINTS: • Construction of designer cellulosomes is a multi-step process. • Designer cellulosome research deals with multivariate construction challenges. • Boosting designer cellulosome efficiency requires exploring a vast design space.

Metabolic pathway assembly using docking domains from type I cis-AT polyketide synthases

Engineered metabolic pathways in microbial cell factories often have no natural organization and have challenging flux imbalances, leading to low biocatalytic efficiency. Modular polyketide synthases (PKSs) are multienzyme complexes that synthesize polyketide products via an assembly line thiotemplate mechanism. Here, we develop a strategy named mimic PKS enzyme assembly line (mPKSeal) that assembles key cascade enzymes to enhance biocatalytic efficiency and increase target production by recruiting cascade enzymes tagged with docking domains from type I cis-AT PKS. We apply this strategy to the astaxanthin biosynthetic pathway in engineered Escherichia coli for multienzyme assembly to increase astaxanthin production by 2.4-fold. The docking pairs, from the same PKSs or those from different cis-AT PKSs evidently belonging to distinct classes, are effective enzyme assembly tools for increasing astaxanthin production. This study addresses the challenge of cascade catalytic efficiency and highlights the potential for engineering enzyme assembly.

Assembly artificial pathway in design connecting media can increase biosynthetic efficiency, but the choice of connecting media is limited. Here, the authors develop a new protein assembly strategy using a pool of docking peptides from polyketide synthase and show its application in astaxanthin biosynthesis in E. coli.

Phase-Separated Multienzyme Compartmentalization for Terpene Biosynthesis in a Prokaryote

Liquid-liquid phase separation (LLPS) forms biomolecular condensates or coacervates in cells. Metabolic enzymes can form phase-separated subcellular compartments that enrich enzymes, cofactors, and substrates. Herein, we report the construction of synthetic multienzyme condensates that catalyze the biosynthesis of a terpene, α-farnesene, in the prokaryote E. coli. RGGRGG derived from LAF-1 was used as the scaffold protein to form the condensates by LLPS. Multienzyme condensates were then formed by assembling two enzymes Idi and IspA through an RIAD/RIDD interaction. Multienzyme condensates constructed inside E. coli cells compartmentalized the cytosolic space into regions of high and low enzyme density and led to a significant enhancement of α-farnesene production. This work demonstrates LLPS-driven compartmentalization of the cytosolic space of prokaryotic cells, condensation of a biosynthetic pathway, and enhancement of the biosynthesis of α-farnesene.

Combinatorial assembly and optimisation of designer cellulosomes: a galactomannan case study

BACKGROUND

Designer cellulosomes are self-assembled chimeric enzyme complexes that can be used to improve lignocellulosic biomass degradation. They are composed of a synthetic multimodular backbone protein, termed the scaffoldin, and a range of different chimeric docking enzymes that degrade polysaccharides. Over the years, several functional designer cellulosomes have been constructed. Since many parameters influence the efficiency of these multi-enzyme complexes, there is a need to optimise designer cellulosome architecture by testing combinatorial arrangements of docking enzyme and scaffoldin variants. However, the modular cloning procedures are tedious and cumbersome.

RESULTS

VersaTile is a combinatorial DNA assembly method, allowing the rapid construction and thus comparison of a range of modular proteins. Here, we present the extension of the VersaTile platform to facilitate the construction of designer cellulosomes. We have constructed a tile repository, composed of dockerins, cohesins, linkers, tags and enzymatically active modules. The developed toolbox allows us to efficiently create and optimise designer cellulosomes at an unprecedented speed. As a proof of concept, a trivalent designer cellulosome able to degrade the specific hemicellulose substrate, galactomannan, was constructed and optimised. The main factors influencing cellulosome efficiency were found to be the selected dockerins and linkers and the docking enzyme ratio on the scaffoldin. The optimised designer cellulosome was able to hydrolyse the galactomannan polysaccharide and release mannose and galactose monomers.

CONCLUSION

We have eliminated one of the main technical hurdles in the designer cellulosome field and anticipate the VersaTile platform to be a starting point in the development of more elaborate multi-enzyme complexes.

Programming an Orthogonal Self-Assembling Protein Cascade Based on Reactive Peptide-Protein Pairs for In Vitro Enzymatic Trehalose Production

Trehalose is an important rare sugar that protects biomolecules against environmental stress. We herein introduce a dual enzyme cascade strategy that regulates the proportion of cargos and scaffolds, to maximize the benefits of enzyme immobilization. Based upon the self-assembling properties of the shell protein (EutM) from the ethanolamine utilization (Eut) bacterial microcompartment, we implemented the catalytic synthesis of trehalose from soluble starch with the coimmobilization of α-amylase and trehalose synthase. This strategy improved enzymatic cascade activity and operational stability. The cascade system enabled the efficient production of trehalose with a yield of ∼3.44 g/(L U), 1.5 times that of the free system. Moreover, its activity was maintained over 12 h, while the free system was almost completely inactivated after 4 h, demonstrating significantly enhanced thermostability. In conclusion, an attractive self-assembly coimmobilization platform was developed, which provides an effective biological process for the enzymatic synthesis of trehalose in vitro.

Self-assembled recombinant camel serum albumin nanoparticles-encapsulated hemin with peroxidase-like activity for colorimetric detection of hydrogen peroxide and glucose

The construction of enzyme mimics using protein protection layers possesses advantages of high biocompatibility and superior catalytic activity, which is desirable for biomedical applications including diseases diagnosis. Here, from E. coli expression system, recombinant protein of camel serum albumin (rCSA) from Camelus bactrianus was successfully obtained to encapsulate hemin via the self-assemble method without additional toxic organic reagents. As compared with that of horseradish peroxidase, the produced rCSA-hemin nanoparticles exhibited enhanced enzyme-mimicking activity and stability under harsh experimental conditions. Additionally, the steady-state kinetic analysis of rCSA-hemin in the solution revealed its higher affinity to the substrates. Therefore, a colorimetric detection method of H₂O₂ and glucose was constructed with a linear range of 2.5-500 μM with an LOD of 2.39 and 2.42 μM, respectively, which was also applied for the determination of glucose in the serum samples with satisfying recovery ratio ranging from 101.1% to 112.1%. The constructed camel protein-derived nanozyme system of remarkable stability holds promising potentials for the versatile biomedical uses.

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.