Interfacing non-enzymatic catalysis with living microorganisms

Single-cell phenotyping of extracellular electron transfer via microdroplet encapsulation

Electroactive organisms contribute to metal cycling, pollutant removal, and other redox-driven environmental processes via extracellular electron transfer (EET). Unfortunately, developing genotype-phenotype relationships for electroactive organisms is challenging because EET is necessarily removed from the cell of origin. Microdroplet emulsions, which encapsulate individual cells in aqueous droplets, have been used to study a variety of extracellular phenotypes but have not been applied to investigate EET. Here, we describe the development of a microdroplet emulsion system to sort and enrich EET-capable organisms from complex populations. We validated our system using the model electrogen Shewanella oneidensis and described the tooling of a benchtop microfluidic system for oxygen-limited conditions. We demonstrated the enrichment of strains exhibiting electroactive phenotypes from mixed wild-type and EET-deficient populations. As a proof-of-concept application, we collected samples from iron sedimentation in Town Lake (Austin, TX) and subjected them to microdroplet enrichment. We measured an increase in electroactive organisms in the sorted population that was distinct compared to a population growing in bulk culture with Fe(III) as the sole electron acceptor. Finally, two bacterial species not previously shown to be EET-capable, Cronobacter sakazakii and Vagococcus fessus, were further cultured and characterized for electroactivity. Our results demonstrate the utility of microdroplet emulsions for isolating and identifying EET-capable bacteria.IMPORTANCEThis work outlines a new high-throughput method for identifying electroactive bacteria from mixed populations. Electroactive bacteria play key roles in iron trafficking, soil remediation, and pollutant degradation. Many existing methods for identifying electroactive bacteria are coupled to microbial growth and fitness-as a result, the contributions from weak or poor-growing electrogens are often muted. However, extracellular electron transfer (EET) has historically been difficult to study in high-throughput in a mixed population since extracellular reduction is challenging to trace back to the parent cell and there are no suitable fluorescent readouts for EET. Our method circumvents these challenges by utilizing an aqueous microdroplet emulsion wherein a single cell is statistically isolated in a pico- to nano-liter-sized droplet. Then, via fluorescence obtained from copper reduction, the mixed population can be fluorescently sorted and gated by performance. Utilizing our technique, we characterize two previously unrecognized weak electrogens Vagococcus fessus and Cronobacter sakazakii.

Concatenating Microbial, Enzymatic, and Organometallic Catalysis for Integrated Conversion of Renewable Carbon Sources

The chemical industry can now seize the opportunity to improve the sustainability of its processes by replacing fossil carbon sources with renewable alternatives such as CO2, biomass, and plastics, thereby thinking ahead and having a look into the future. For their conversion to intermediate and final products, different types of catalysts-microbial, enzymatic, and organometallic-can be applied. The first part of this review shows how these catalysts can work separately in parallel, each route with unique requirements and advantages. While the different types of catalysts are often seen as competitive approaches, an increasing number of examples highlight, how combinations and concatenations of catalysts of the complete spectrum can open new roads to new products. Therefore, the second part focuses on the different catalysts either in one-step, one-pot transformations or in reaction cascades. In the former, the reaction conditions must be conflated but purification steps are minimized. In the latter, each catalyst can work under optimal conditions and the "hand-over points" should be chosen according to defined criteria like minimal energy usage during separation procedures. The examples are discussed in the context of the contributions of catalysis to the envisaged (bio)economy.

Utilizing microbial metabolite in catalytic cascade synthesis of conjugated oligomers for In-Situ regulation of biological activity

Despite the advances of multistep enzymatic cascade reactions, their incorporation with abiotic reactions in living organisms remains challenging in synthetic biology. Herein, we combined microbial metabolic pathways and Pd-catalyzed processes for in-situ generation of bioactive conjugated oligomers. Our biocompatible one-pot coupling reaction utilized the fermentation process of engineered E. coli that converted glucose to styrene, which participated in the Pd-catalyzed Heck reaction for in-situ synthesis of conjugated oligomers. This process serves a great interest in understanding resistance evolution by utilizing the inhibitory activity of the synthesized conjugated oligomers. The approach allows for the in-situ combination of biological metabolism and CC coupling reactions, opening up new possibilities for the biosynthesis of unnatural molecules and enabling the in-situ regulation of the bioactivity of the obtained products.

Interfacing Whole Cell Biocatalysis with a Biocompatible Pictet-Spengler Reaction for One-Pot Syntheses of Tetrahydroisoquinolines and Tryptolines

Biocatalytic processes are highly selective and specific. However, their utility is limited by the comparatively narrow scope of enzyme-catalysed transformations. To expand product scope, we are developing biocompatible processes that combine biocatalytic reactions with chemo-catalysis in single-flask processes. Here, we show that a chemocatalysed Pictet-Spengler annulation can be interfaced with biocatalysed alcohol oxidation. This two-step, one-pot cascade reaction converts tyramine and aliphatic alcohols to tetrahydroisoquinoline alkaloids in aqueous buffer at mild pH. Tryptamine derivatives are also efficiently converted to tryptolines. Optimization of stoichiometry, pH, reaction time, and whole-cell catalyst deliver the tetrahydroisouinolines and tryptolines in >90 % and >40 % isolated yield, respectively, with excellent regioselectivity.

Nanoconstruction on Living Cell Surfaces with Cucurbit[7]uril-Based Supramolecular Polymer Chemistry: Toward Cell-Based Delivery of Bio-Orthogonal Catalytic Systems

Employing living cells as carriers to transport transition metal-based catalysts for target-specific bio-orthogonal catalysis represents a cutting-edge approach in advancing precision biomedical applications. One of the initial hurdles in this endeavor involves effectively attaching the catalysts to the carrier cells while preserving the cells' innate ability to interact with biological systems and maintaining the unaltered catalytic activity. In this study, we have developed an innovative layer-by-layer method that leverages a noncovalent interaction between cucurbit[7]uril and adamantane as the primary driving force for crafting polymeric nanostructures on the surfaces of these carrier cells. The strong binding affinity between the host-guest pair ensures the creation of a durable polymer coating on the cell surfaces. Meanwhile, the layer-by-layer process offers high adaptability, facilitating the efficient loading of bio-orthogonal catalysts onto cell surfaces. Importantly, the polymeric coating shows no discernible impact on the cells' physiological characteristics, including their tropism, migration, and differentiation, while preserving the effectiveness of the bio-orthogonal catalysts.

Biocompatible α-Methylenation of Metabolic Butyraldehyde in Living Bacteria

Small molecule organocatalysts are abundant in all living organisms. However, their use as organocatalysts in cells has been underexplored. Herein, we report that organocatalytic aldol chemistry can be interfaced with living Escherichia coli to enable the α-methylenation of cellular aldehydes using biogenic amines such as L-Pro or phosphate. The biocompatible reaction is mild and can be interfaced with butyraldehyde generated from D-glucose via engineered metabolism to enable the production of 2-methylenebutanal (2-MB) and 2-methylbutanal (2-MBA) by anaerobic fermentation, and 2-methylbutanol (2-MBO) by whole-cell catalysis. Overall, this study demonstrates the combination of non-enzymatic organocatalytic and metabolic reactions in vivo for the sustainable synthesis of valuable non-natural chemicals that cannot be accessed using enzymatic chemistry alone.

Tyramine Derivatives Catalyze the Aldol Dimerization of Butyraldehyde in the Presence of Escherichia coli

Biogenic amine organocatalysts have transformed the field of synthetic organic chemistry. Yet despite their use in synthesis and to label biomolecules in vitro, amine organocatalysis in vivo has received comparatively little attention - despite the potential of such reactions to be interfaced with living cells and to modify cellular metabolites. Herein we report that biogenic amines derived from L-tyrosine catalyze the self-aldol condensation of butanal to 2-ethylhexenal - a key intermediate in the production of the bulk chemical 2-ethylhexanol - in the presence of living Escherichia coli and outperform many amine organocatalysts currently used in synthetic organic chemistry. Furthermore, we demonstrate that cell lysate from E. coli and the prolific amine overproducer Corynebacterium glutamicum ATCC 13032 catalyze this reaction in vitro, demonstrating the potential for microbial metabolism to be used as a source of organocatalysts for biocompatible reactions in cells.

Hydrodechlorination of Aryl Chlorides Under Biocompatible Conditions

Developing nonenzymatic chemistry that is nontoxic to microbial organisms creates the potential to integrate synthetic chemistry with metabolism and offers new remediation strategies. Chlorinated organic compounds known to bioaccumulate and cause harmful environmental impact can be converted into less damaging derivatives through hydrodehalogenation. The hydrodechlorination of substituted aryl chlorides using Pd/C and ammonium formate in biological media under physiological conditions (neutral pH, moderate temperature, and ambient pressure) is reported. The reaction conditions were successful for a range of aryl chlorides with electron-donating and -withdrawing groups, limited by the solubility of substrates in aqueous media. Soluble substrates gave good yields (60-98%) of the reduction product within 48 h. The relative toxicities of each reaction component were tested separately and together against bacteria, and the reaction proceeded in bacterial cultures containing an aryl chloride with robust cell growth. This work offers an initial step toward the removal of aryl chlorides from waste streams that currently use bacterial degradation to remove pollutants.

Extracellular Electron Transfer Enables Cellular Control of Cu(I)-Catalyzed Alkyne-Azide Cycloaddition

Extracellular electron transfer (EET) is an anaerobic respiration process that couples carbon oxidation to the reduction of metal species. In the presence of a suitable metal catalyst, EET allows for cellular metabolism to control a variety of synthetic transformations. Here, we report the use of EET from the electroactive bacterium Shewanella oneidensis for metabolic and genetic control over Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC). CuAAC conversion under anaerobic and aerobic conditions was dependent on live, actively respiring S. oneidensis cells. The reaction progress and kinetics were manipulated by tailoring the central carbon metabolism. Similarly, EET-CuAAC activity was dependent on specific EET pathways that could be regulated via inducible expression of EET-relevant proteins: MtrC, MtrA, and CymA. EET-driven CuAAC exhibited modularity and robustness in the ligand and substrate scope. Furthermore, the living nature of this system could be exploited to perform multiple reaction cycles without regeneration, something inaccessible to traditional chemical reductants. Finally, S. oneidensis enabled bioorthogonal CuAAC membrane labeling on live mammalian cells without affecting cell viability, suggesting that S. oneidensis can act as a dynamically tunable biocatalyst in complex environments. In summary, our results demonstrate how EET can expand the reaction scope available to living systems by enabling cellular control of CuAAC.

Improved polyhydroxybutyrate production by Cupriavidus necator and the photocatalyst graphitic carbon nitride from fructose under low light intensity

The photocatalyst graphitic carbon nitride (g-C₃N₄) is known to photostimulate the production of the bioplastic polyhydroxybutyrate (PHB) by Cupriavidus necator. In previous studies, the combination of C. necator and g-C₃N₄ increased PHB yield from either an organic or inorganic carbon substrate under a light intensity of 4200 lx. Here, different parameters including light intensity, pH, temperature, nitrogen and carbon concentrations, aeration, and inoculum size were explored to maximize PHB production by hybrid photosynthesis from fructose and visible light. A g-C₃N₄/C. necator culture grown with a lower light intensity of 2100 lx, an inoculum size of 128.30 × 10⁶ CFU ml^-1, and constant aeration produced 7.16 g l^-1 d^-1 PHB with a product yield from fructose of 60.94%. Furthermore, the ratio of incident photons harvested by g-C₃N₄ converted into NADPH+H⁺ by C. necator for PHB production was improved to 19.74% after the process optimization. In comparison, the PHB production rate of a non-optimized g-C₃N₄/C. necator system exposed to 4200 lx was only 2.94 g l^-1 d^-1 with a product yield from fructose of 33.29%. These results demonstrate that hybrid photosynthesis productivity can be significantly augmented by decreasing light intensity and adjusting other parameters, which is promising for future bioproduction applications.

Azaphilone alkaloids: prospective source of natural food pigments

Azaphilone, biosynthesized by polyketide synthase, is a class of fungal metabolites. In this review, after brief introduction of the natural azaphilone diversity, we in detail discussed azaphilic addition reaction involving conversion of natural azaphilone into the corresponding azaphilone alkaloid. Then, setting red Monascus pigments (a traditional food colorant in China) as example, we presented a new strategy, i.e., interfacing azaphilic addition reaction with living microbial metabolism in a one-pot process, to produce azaphilone alkaloid with a specified amine residue (red Monascus pigments) during submerged culture. Benefit from the red Monascus pigments with a specified amine residue, the influence of primary amine on characteristics of the food colorant was highlighted. Finally, the progress for screening of alternative azaphilone alkaloids (production from interfacing azaphilic addition reaction with submerged culture of Talaromyces sp. or Penicillium sp.) as natural food colorant was reviewed. KEY POINTS: • Azaphilic addition reaction of natural azaphilone is biocompatible • Red Monascus pigment is a classic example of azaphilone alkaloids • Azaphilone alkaloids are alterative natural food colorant.