A roadmap towards integrated catalytic systems of the future

Unveiling the spatial rearrangements of exhausted immobilised multi-enzyme systems through cryo-X-ray fluorescence nanoprobe imaging

Enzyme immobilisation is of great importance for the fabrication of heterogeneous biocatalysts, as it allows the stabilisation of proteins using a solid support. Moreover, it permits their reuse in continuous and discontinuous reactors. The behaviour of enzymes at the interface with the materials where they are supported is not well understood during operational conditions. Here, we use X-ray fluorescence (XRF) imaging to study the changes in the overall structure of a heterogeneous biocatalyst formed by two unmodified metalloenzymes (a copper-dependent laccase and a zinc-dependent dehydrogenase) upon incubation, either under drastic (high temperature) or operational conditions. Those two enzymes were co-immobilised reversibly (by electrostatic interactions and His-tag metal coordination) to form a cascade reaction that catalyses the NAD+-dependent oxidation of diols coupled to a laccase-mediator for the in situ regeneration of the redox cofactor. Both the protein scaffolds and the metal cofactors undergo rearrangements during operational use or thermal incubation, but they seem to move as a whole unit within the support. Migration inside the support apparently causes only small alterations to the structure of the protein, yet it leads to the exhaustion of the heterogeneous biocatalyst. As such, we show that the use of advanced X-ray spectroscopy with spatial resolution can help obtain a better understanding of the molecular phenomena that occur during the operation of heterogeneous biocatalysts. Overall, this is fundamental to guide the optimisation for more productive and robust bioprocesses based on immobilised enzyme systems.

Quantitative Online Monitoring of an Immobilized Enzymatic Network by Ion Mobility-Mass Spectrometry

The forward design of in vitro enzymatic reaction networks (ERNs) requires a detailed analysis of network kinetics and potentially hidden interactions between the substrates and enzymes. Although flow chemistry allows for a systematic exploration of how the networks adapt to continuously changing conditions, the analysis of the reaction products is often a bottleneck. Here, we report on the interface between a continuous stirred-tank reactor, in which an immobilized enzymatic network made of 12 enzymes is compartmentalized, and an ion mobility-mass spectrometer. Feeding uniformly 13C-labeled inputs to the enzymatic network generates all isotopically labeled reaction intermediates and products, which are individually detected by ion mobility-mass spectrometry (IMS-MS) based on their mass-to-charge ratios and inverse ion mobilities. The metabolic flux can be continuously and quantitatively monitored by diluting the ERN output with nonlabeled standards of known concentrations. The real-time quantitative data obtained by IMS-MS are then harnessed to train a model of network kinetics, which proves sufficiently predictive to control the ERN output after a single optimally designed experiment. The high resolution of the time-course data provided by this approach is an important stepping stone to design and control sizable and intricate ERNs.

Expanding chemistry through in vitro and in vivo biocatalysis

Living systems contain a vast network of metabolic reactions, providing a wealth of enzymes and cells as potential biocatalysts for chemical processes. The properties of protein and cell biocatalysts-high selectivity, the ability to control reaction sequence and operation in environmentally benign conditions-offer approaches to produce molecules at high efficiency while lowering the cost and environmental impact of industrial chemistry. Furthermore, biocatalysis offers the opportunity to generate chemical structures and functions that may be inaccessible to chemical synthesis. Here we consider developments in enzymes, biosynthetic pathways and cellular engineering that enable their use in catalysis for new chemistry and beyond.

Promoting Photocatalytic Direct C-H Difluoromethylation of Heterocycles using Synergistic Dual-Active-Centered Covalent Organic Frameworks

Difluoromethylation reactions are increasingly important for the creation of fluorine-containing heterocycles, which are core groups in a diverse range of biologically and pharmacologically active ingredients. Ideally, this typically challenging reaction could be performed photocatalytically under mild conditions. To achieve this separation of redox processes would be required for the efficient generation of difluoromethyl radicals and the reduction of oxygen. A covalent organic framework photocatalytic material was, therefore, designed with dual reactive centers. Here, anthracene was used as a reduction site and benzothiadiazole was used as an oxidation site, distributed in a tristyryl triazine framework. Efficient charge separation was ensured by the superior electron-donating and -accepting abilities of the dual centers, creating long-lived photogenerated electron-hole pairs. Photocatalytic difluoromethylation of 16 compounds with high yields and remarkable functional group tolerance was demonstrated; compounds included bioactive molecules such as xanthine and uracil. The structure-function relationship of the dual-active-center photocatalyst was investigated through electron spin resonance, femtosecond transient absorption spectroscopy, and density functional theory calculations.

Iterative design of training data to control intricate enzymatic reaction networks

Kinetic modeling of in vitro enzymatic reaction networks is vital to understand and control the complex behaviors emerging from the nonlinear interactions inside. However, modeling is severely hampered by the lack of training data. Here, we introduce a methodology that combines an active learning-like approach and flow chemistry to efficiently create optimized datasets for a highly interconnected enzymatic reactions network with multiple sub-pathways. The optimal experimental design (OED) algorithm designs a sequence of out-of-equilibrium perturbations to maximize the information about the reaction kinetics, yielding a descriptive model that allows control of the output of the network towards any cost function. We experimentally validate the model by forcing the network to produce different product ratios while maintaining a minimum level of overall conversion efficiency. Our workflow scales with the complexity of the system and enables the optimization of previously unobtainable network outputs.

Pushing the boundaries of phosphorylase cascade reaction for cellobiose production I: Kinetic model development

One-pot cascade reactions of coupled disaccharide phosphorylases enable an efficient transglycosylation via intermediary α-d-glucose 1-phosphate (G1P). Such transformations have promising applications in the production of carbohydrate commodities, including the disaccharide cellobiose for food and feed use. Several studies have shown sucrose and cellobiose phosphorylase for cellobiose synthesis from sucrose, but the boundaries on transformation efficiency that result from kinetic and thermodynamic characteristics of the individual enzyme reactions are not known. Here, we assessed in a step-by-step systematic fashion the practical requirements of a kinetic model to describe cellobiose production at industrially relevant substrate concentrations of up to 600 mM sucrose and glucose each. Mechanistic initial-rate models of the two-substrate reactions of sucrose phosphorylase (sucrose + phosphate → G1P + fructose) and cellobiose phosphorylase (G1P + glucose → cellobiose + phosphate) were needed and additionally required expansion by terms of glucose inhibition, in particular a distinctive two-site glucose substrate inhibition of the cellobiose phosphorylase (from Cellulumonas uda). Combined with mass action terms accounting for the approach to equilibrium, the kinetic model gave an excellent fit and a robust prediction of the full reaction time courses for a wide range of enzyme activities as well as substrate concentrations, including the variable substoichiometric concentration of phosphate. The model thus provides the essential engineering tool to disentangle the highly interrelated factors of conversion efficiency in the coupled enzyme reaction; and it establishes the necessary basis of window of operation calculations for targeted optimizations toward different process tasks.

Enzymatic Oxy- and Amino-Functionalization in Biocatalytic Cascade Synthesis: Recent Advances and Future Perspectives

Biocatalytic cascades are a powerful tool for building complex molecules containing oxygen and nitrogen functionalities. Moreover, the combination of multiple enzymes in one pot offers the possibility to minimize downstream processing and waste production. In this review, we illustrate various recent efforts in the development of multi-step syntheses involving C-O and C-N bond-forming enzymes to produce high value-added compounds, such as pharmaceuticals and polymer precursors. Both in vitro and in vivo examples are discussed, revealing the respective advantages and drawbacks. The use of engineered enzymes to boost the cascades outcome is also addressed and current co-substrate and cofactor recycling strategies are presented, highlighting the importance of atom economy. Finally, tools to overcome current challenges for multi-enzymatic oxy- and amino-functionalization reactions are discussed, including flow systems with immobilized biocatalysts and cascades in confined nanomaterials.

Designing artificial pathways for improving chemical production

Metabolic engineering exploits manipulation of catalytic and regulatory elements to improve a specific function of the host cell, often the synthesis of interesting chemicals. Although naturally occurring pathways are significant resources for metabolic engineering, these pathways are frequently inefficient and suffer from a series of inherent drawbacks. Designing artificial pathways in a rational manner provides a promising alternative for chemicals production. However, the entry barrier of designing artificial pathway is relatively high, which requires researchers a comprehensive and deep understanding of physical, chemical and biological principles. On the other hand, the designed artificial pathways frequently suffer from low efficiencies, which impair their further applications in host cells. Here, we illustrate the concept and basic workflow of retrobiosynthesis in designing artificial pathways, as well as the most currently used methods including the knowledge- and computer-based approaches. Then, we discuss how to obtain desired enzymes for novel biochemistries, and how to trim the initially designed artificial pathways for further improving their functionalities. Finally, we summarize the current applications of artificial pathways from feedstocks utilization to various products synthesis, as well as our future perspectives on designing artificial pathways.

Multiple remote C(sp3)-H functionalizations of aliphatic ketones via bimetallic Cu-Pd catalyzed successive dehydrogenation

The dehydrogenation-triggered multiple C(sp3)-H functionalizations at remote positions γ, δ or ε, ζ to carbonyl groups of aliphatic ketones with aryl/alkenyl carboxylic acids as coupling partners have been achieved using a bimetallic Cu-Pd catalyst system. This reaction allows access to alkenylated isocoumarins and their derivatives in generally good yields with high functional group tolerance. The identification of bimetallic Cu-Pd synergistic catalysis for efficient successive dehydrogenation of aliphatic ketones, which overcomes the long-standing challenge posed by the successive dehydrogenation desaturation of terminally unsubstituted alkyl chains in aliphatic ketones, is essential to achieving this bimetallic Cu-Pd catalyzed dehydrogenation coupling reaction.

Defining Local Chemical Conditions in Magnetosomes of Magnetotactic Bacteria

Defining chemical properties of intracellular organelles is necessary to determine their function(s) as well as understand and mimic the reactions they host. However, the small size of bacterial and archaeal microorganisms often prevents defining local intracellular chemical conditions in a similar way to what has been established for eukaryotic organelles. This work proposes to use magnetite (Fe₃O₄) nanocrystals contained in magnetosome organelles of magnetotactic bacteria as reporters of elemental composition, pH, and redox potential of a hypothetical environment at the site of formation of intracellular magnetite. This methodology requires combining recent single-cell mass spectrometry measurements together with elemental composition of magnetite in trace and minor elements. It enables a quantitative characterization of chemical disequilibria of 30 chemical elements between the intracellular and external media of magnetotactic bacteria, revealing strong transfers of elements with active influx or efflux processes that translate into elemental accumulation (Mo, Se, and Sn) or depletion (Sr and Bi) in the bacterial internal medium of up to seven orders of magnitude relative to the extracellular medium. Using this concept, we show that chemical conditions in magnetosomes are compatible with a pH of 7.5-9.5 and a redox potential of -0.25 to -0.6 V.

A Low-Temperature Annealing Method for Alloy Nanostructures and Metasurfaces: Unlocking a Novel Degree of Freedom

The material and exact shape of a nanostructure determine its optical response, which is especially strong for plasmonic metals. Unfortunately, only a few plasmonic metals are available, which limits the spectral range where these strong optical effects can be utilized. Alloying different plasmonic metals can overcome this limitation, at the expense of using a high-temperature alloying process, which adversely destroys the nanostructure shape. Here, a low-temperature alloying process is developed where the sample is heated at only 300 °C for 8 h followed by 30 min at 450 °C and Au-Ag nanostructures with a broad diversity of shapes, aspect ratios, and stoichiometries are fabricated. Energy-dispersive X-ray spectroscopy and X-ray photoelectron spectroscopy analyses confirm the homogeneous alloying through the entire sample. Varying the alloy stoichiometry tunes the optical response and controls spectral features, such as Fano resonances. Binary metasurfaces that combine nanostructures with different stoichiometries are fabricated using multiple-step electron-beam lithography, and their optical function as a hologram or a Fresnel zone plate is demonstrated at the visible wavelength of λ = 532 nm. This low-temperature annealing technique provides a versatile and cost-effective way of fabricating complex Au-Ag nanostructures with arbitrary stoichiometry.

Recombinant Production of Arginyl Dipeptides by l-Amino Acid Ligase RizA Coupled with ATP Regeneration

Arginyl dipeptides like Arg-Ser, Arg-Ala, and Arg-Gly are salt-taste enhancers and can potentially be used to reduce the salt content of food. The l-amino acid ligase RizA from B. subtilis selectively synthesizes arginyl dipeptides. However, industrial application is prevented by the high cost of the cofactor adenosine triphosphate (ATP). Thus, a coupled reaction system was created consisting of RizA and acetate kinase (AckA) from E. coli providing ATP regeneration from acetyl phosphate. Both enzymes were recombinantly produced in E. coli and purified by affinity chromatography. Biocatalytic reactions were varied and analyzed by RP-HPLC with fluorescence detection. Under optimal conditions the system produced up to 5.9 g/L Arg-Ser corresponding to an ATP efficiency of 23 g Arg-Ser per gram ATP. Using similar conditions with alanine or glycine as second amino acid, 2.6 g/L Arg-Ala or 2.4 g/L Arg Gly were produced. The RizA/AckA system selectively produced substantial amounts of arginyl dipeptides while minimizing the usage of the expensive ATP.

Solid-Phase Assembly of Multienzyme Systems into Artificial Cellulosomes

We herein describe a bioinspired solid-phase assembly of a multienzyme system scaffolded on an artificial cellulosome. An alcohol dehydrogenase and an ω-transaminase were fused to cohesin and dockerin domains to drive their sequential and ordered coimmobilization on agarose porous microbeads. The resulting immobilized scaffolded enzymatic cellulosome was characterized through quartz crystal microbalance with dissipation and confocal laser scanning microscopy to demonstrate that both enzymes interact with each other and physically colocalize within the microbeads. Finally, the assembled multifunctional heterogeneous biocatalyst was tested for the one-pot conversion of alcohols into amines. By using the physically colocalized enzymatic system confined into porous microbeads, the yield of the corresponding amine was 1.3 and 10 times higher than the spatially segregated immobilized system and the free enzymes, respectively. This work establishes the basis of a new concept to organize multienzyme systems at the nanoscale within solid and porous immobilization carriers.

A host-guest semibiological photosynthesis system coupling artificial and natural enzymes for solar alcohol splitting

Development of a versatile, sustainable and efficient photosynthesis system that integrates intricate catalytic networks and energy modules at the same location is of considerable future value to energy transformation. In the present study, we develop a coenzyme-mediated supramolecular host-guest semibiological system that combines artificial and enzymatic catalysis for photocatalytic hydrogen evolution from alcohol dehydrogenation. This approach involves modification of the microenvironment of a dithiolene-embedded metal-organic cage to trap an organic dye and NADH molecule simultaneously, serving as a hydrogenase analogue to induce effective proton reduction inside the artificial host. This abiotic photocatalytic system is further embedded into the pocket of the alcohol dehydrogenase to couple enzymatic alcohol dehydrogenation. This host-guest approach allows in situ regeneration of NAD⁺/NADH couple to transfer protons and electrons between the two catalytic cycles, thereby paving a unique avenue for a synergic combination of abiotic and biotic synthetic sequences for photocatalytic fuel and chemical transformation.

Abiotic–biotic hybrid systems are promising to trap light for fuel and chemical transformation with high efficacy and selectivity. This study reports a coenzyme-mediated supramolecular host-guest semibiological system combining supramolecular catalyst and enzymes for solar alcohol splitting.

Bottom-Up Synthesis of Artificial Cells: Recent Highlights and Future Challenges

The bottom-up approach in synthetic biology aims to create molecular ensembles that reproduce the organization and functions of living organisms and strives to integrate them in a modular and hierarchical fashion toward the basic unit of life-the cell-and beyond. This young field stands on the shoulders of fundamental research in molecular biology and biochemistry, next to synthetic chemistry, and, augmented by an engineering framework, has seen tremendous progress in recent years thanks to multiple technological and scientific advancements. In this timely review of the research over the past decade, we focus on three essential features of living cells: the ability to self-reproduce via recursive cycles of growth and division, the harnessing of energy to drive cellular processes, and the assembly of metabolic pathways. In addition, we cover the increasing efforts to establish multicellular systems via different communication strategies and critically evaluate the potential applications.

An Integrated Cofactor/Co-Product Recycling Cascade for the Biosynthesis of Nylon Monomers from Cycloalkylamines

We report a highly atom-efficient integrated cofactor/co-product recycling cascade employing cycloalkylamines as multifaceted starting materials for the synthesis of nylon building blocks. Reactions using E. coli whole cells as well as purified enzymes produced excellent conversions ranging from >80 and 95 % into desired ω-amino acids, respectively with varying substrate concentrations. The applicability of this tandem biocatalytic cascade was demonstrated to produce the corresponding lactams by employing engineered biocatalysts. For instance, ϵ-caprolactam, a valuable polymer building block was synthesized with 75 % conversion from 10 mM cyclohexylamine by employing whole-cell biocatalysts. This cascade could be an alternative for bio-based production of ω-amino acids and corresponding lactam compounds.

Toward sustainable, cell-free biomanufacturing

Industrial biotechnology is an attractive approach to address the need for low-cost fuels and products from sustainable resources. Unfortunately, cells impose inherent limitations on the effective synthesis and release of target products. One key constraint is that cellular survival objectives often work against the production objectives of biochemical engineers. Additionally, industrial strains release CO₂ and struggle to utilize sustainable, potentially profitable feedstocks. Cell-free biotechnology, which uses biological machinery harvested from cells, can address these challenges with advantages including: (i) shorter development times, (ii) higher volumetric production rates, and (iii) tolerance to otherwise toxic molecules. In this review, we highlight recent advances in cell-free technologies toward the production of non-protein products beyond lab-scale demonstrations and describe guiding principles for designing cell-free systems. Specifically, we discuss carbon and energy sources, reaction homeostasis, and scale-up. Expanding the scope of cell-free biomanufacturing practice could enable innovative approaches for the industrial production of green chemicals.

Nanostructured metal phosphides: from controllable synthesis to sustainable catalysis

Metal phosphides (MPs) with unique and desirable physicochemical properties provide promising potential in practical applications, such as the catalysis, gas/humidity sensor, environmental remediation, and energy storage fields, especially for transition metal phosphides (TMPs) and MPs consisting of group IIIA and IVA metal elements. Most studies, however, on the synthesis of MP nanomaterials still face intractable challenges, encompassing the need for a more thorough understanding of the growth mechanism, strategies for large-scale synthesis of targeted high-quality MPs, and practical achievement of functional applications. This review aims at providing a comprehensive update on the controllable synthetic strategies for MPs from various metal sources. Additionally, different passivation strategies for engineering the structural and electronic properties of MP nanostructures are scrutinized. Then, we showcase the implementable applications of MP-based materials in emerging sustainable catalytic fields including electrocatalysis, photocatalysis, mild thermocatalysis, and related hybrid systems. Finally, we offer a rational perspective on future opportunities and remaining challenges for the development of MPs in the materials science and sustainable catalysis fields.

Synthesis of recoverable thermosensitive Fe3O4 hybrid microgels with controllable catalytic activity

High-efficiency recoverable catalytic magnetite microgel particles, comprising a magnetic Fe₃O₄ nanoparticle (NP) core with a thermo-sensitive poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA) polymer shell, were synthesized through a four-step procedure.