Nanoparticle Fabrication on Bacterial Microcompartment Surface for the Development of Hybrid Enzyme-Inorganic Catalyst

Progress and Obstacles in Employing Carbon Quantum Dots for Sustainable Wastewater Treatment

We explored the potential of carbon quantum dots (CQDs) as novel materials for wastewater treatment and their role towards environmental sustainability. The advantages of CQDs over other carbon-based materials, when synthesized using the same precursor material and for the same contaminant, are discussed, enabling future researchers to choose the appropriate material. CQDs have demonstrated exceptional adaptability in various wastewater treatment, acting as efficient adsorbents for contaminants, exhibiting excellent photocatalytic properties for degradation of organic pollutants, and functioning as highly sensitive sensors for water quality monitoring. We found that bottom-up approach has better control over particle size (resulting CQDs: 1-4 nm), whereas top-down synthesis approach (resulting CQDs: 2-10 nm) have more potential for large scale applications and tunability. Transmission electron microscopy (TEM) remains the most expensive characterization technique, which provides the best resolution of the CQD's surface. The study emphasizes on the environmental impact and safety considerations pertaining to CQDs by emphasizing the need for thorough toxicity evaluation, and necessary environmental precautions. The study identifies the lacunae pertaining to critical challenges in practical implementation of CQDs, such as scalability, competition of co-existing contaminants, and stability. Finally, future research directions are proposed, advocating green synthesis approaches, tailored surface functionalization, and, lowering the overall cost for analysis, synthesis and application of CQDs.

Chemodiversity of soil organic matters determines biodegradation of polychlorinated biphenyls by a graphene oxide-assisted bacterial agent

A promising strategy for degrading persistent organic pollutants (POPs) in soil is amendment with nanomaterial-assisted functional bacteria. However, the influence of soil organic matter chemodiversity on the performance of nanomaterial-assisted bacterial agents remains unclear. Herein, different types of soil (Mollisol soil, MS; Ultisol soil, US; and Inceptisol soil, IS) were inoculated with a graphene oxide (GO)-assisted bacterial agent (Bradyrhizobium diazoefficiens USDA 110, B. diazoefficiens USDA 110) to investigate the association between soil organic matter chemodiversity and stimulation of polychlorinated biphenyl (PCB) degradation. Results indicated that the high-aromatic solid organic matter (SOM) inhibited PCB bioavailability, and lignin-dominant dissolved organic matter (DOM) with high biotransformation potential was a favored substrate for all PCB degraders, which led to no stimulation of PCB degradation in MS. Differently, high-aliphatic SOM in US and IS promoted PCB bioavailability. The high/low biotransformation potential of multiple DOM components (e.g., lignin, condensed hydrocarbon, unsaturated hydrocarbon, etc.) in US/IS further resulted to the enhanced PCB degradation by B. diazoefficiens USDA 110 (up to 30.34%) /all PCB degraders (up to 17.65%), respectively. Overall, the category and biotransformation potential of DOM components and the aromaticity of SOM collaboratively determine the stimulation of GO-assisted bacterial agent on PCB degradation.

Hollow Mesoporous Carbon-Based Enzyme Nanoreactor for the Confined and Interfacial Biocatalytic Synthesis of Phytosterol Esters

Rationally designing carriers to obtain efficient and stable immobilized enzymes for the production of food raw materials is always a challenge. In this work, hollow cube carbon (HMC) as a carrier of Candida rugosa lipase (CRL) was prepared to construct a Pickering interfacial biocatalysis system, which was applied to biphasic biocatalysis. For comparison, the nonporous carbon (HC) and porous MoS₂ (HMoS₂) were also designed. On these grounds, p-NPP and linolenic acid were selected as the representative substrates for hydrolysis and esterification reactions. Under the optimal conditions, the protein loading amount, specific activity, and expressed activity of CRL immobilized on HMC (HMC@CRL) were 167.2 mg g^-1, 5.41 U mg^-1, and 32.34 U/mg protein, respectively. In the "oil-water" biphase, the relative hydrolytic activity of HMC@CRL was higher than that of HC@CRL, HMoS₂@CRL, and CRL by 50, 68, and 80%, respectively, as well as itself in one phase. Compared to other reports (1.13%), HMC@CRL demonstrated a satisfactory hydrolysis rate (3.02%) and was the fastest among all other biocatalysts in the biphase. Moreover, compared with the free CRL in one-phase system, the Pickering interfacial biphasic biocatalyst, HMC@CRL, exhibited a higher esterification rate (85%, 2.7-fold enhancement). Therefore, the HMC@CRL nanoreactors had more optimal performance in the field of biomanufacturing and food industry.

Caffeic Acid Modified Nanomicelles Inhibit Articular Cartilage Deterioration and Reduce Disease Severity in Experimental Inflammatory Arthritis

Inflammation plays an important role in the development of rheumatoid arthritis (RA). NR4A1 is an anti-inflammatory orphan nuclear receptor involved in protection from inflammatory stimuli in RA. In this study we have explored the anti-inflammatory potential of the FDA-approved drug 9-aminoacridine (9AA) and the natural compound caffeic acid (CA) conjugated to nanomicelles for the treatment of RA. We have synthesized methoxy polyethylene glycol polycaprolactone block copolymer (mPEG-b-PCL) by ring opening polymerization of ε-caprolactone. Then, we conjugated the hydrophilic caffeic acid (CA) with mPEG-b-PCL micelles via Steglich esterification and incorporated the 9AA drug. These nanomicelles were formulated by the solvent evaporation method with a size distribution around 190 nm and showed maximum drug loading capacity along with sustained drug release behavior. Furthermore, we tested the therapeutic potential of the formulated 9AA-encapsulated CA-conjugated nanomicelles (9AA-NMs) against an experimental RA model. We observed promising results which showed alleviation of arthritic symptoms by reducing inflammation, joint damage, bone erosion, and swelling. Further, collagen destruction was significantly reduced in articular cartilage, as shown by safranin-O and toluidine blue staining. The protective mechanism might be due to the simultaneous inhibition of NF-κB by 9AA and CA, whereas the activation of NR4A1 by 9AA leads to the suppression of HIF-1α. This combined therapeutic effect of 9AA and CA has enhanced the therapeutic efficacy of 9AA-NM and markedly reduced the severity of inflammatory arthritis. Unlike existing drugs for pain management and with limited efficacy, 9AA-NM exerted a disease-relevant activation/blockade that alleviated inflammation and exhibited marked therapeutic efficacy against RA.

Barrier-free liquid condensates of nanocatalysts as effective concentrators of catalysis

Traditional methods of molecular confinement have physicochemical barriers that restrict the free passage of substrates/products. Here, we explored liquid-liquid phase separation as a method to restrain protein-metal nanocomposites within barrier-free condensates. Confinement within liquid droplets was independent of the protein's native conformation and amplified the catalytic efficiency of metal nanocatalysts by one order of magnitude.

A major shell protein of 1,2-propanediol utilization microcompartment conserves the activity of its signature enzyme at higher temperatures

A classic example of an all-protein natural nano-bioreactor, the bacterial microcompartment is a special kind of prokaryotic organelle that confine enzymes within a small volume enveloped by an outer protein shell. These protein compartments metabolize specific organic molecules, allowing bacteria to survive in restricted nutrient environments. In this work, 1,2-propanediol utilization microcompartment (PduMCP)  is used as a model to study the effect of molecular confinement on the stability and catalytic activity of native enzymes in microcompartment. A combination of enzyme assays, spectroscopic techniques, binding assays, and computational analysis are used to evaluate the impact of the major shell protein PduBB' on the stability and activity of PduMCP's signature enzyme, diol dehydratase PduCDE. While free PduCDE shows ~45% reduction in its optimum activity (activity at 37 o C) when exposed to a temperature of 45°C, it retains similar activity up to 50°C when encapsulated within PduMCP. PduBB', a major component of the outer shell of PduMCP, preserves the catalytic efficiency of PduCDE under thermal stress and prevents temperature-induced unfolding and aggregation of PduCDE in vitro . We observe that while both PduB and PduB' interact with the enzyme with micromolar affinity, only the PduBB' combination influences its activity and stability, highlighting the importance of the unique PduBB' combination in the functioning of PduMCP.

Varying protein architectures in 3-dimensions for scaffolding and modulating properties of catalytic gold nanoparticles

Fabrication and development of nanoscale materials with tunable structural and functional properties require a dynamic arrangement of nanoparticles on architectural templates. The function of nanoparticles not only depends on the property of the nanoparticles but also on their spatial orientations. Proteins with self-assembling properties which can be genetically engineered to varying architectural designs for scaffolds can be used to develop different orientations of nanoparticles in three dimensions. Here, we report the use of naturally self-assembling bacterial micro-compartment shell protein (PduA) assemblies in 2D and its single-point mutant variant (PduA[K26A]) in 3D architectures for the reduction and fabrication of gold nanoparticles. Interestingly, the different spatial organization of gold nanoparticles resulted in a smaller size in the 3D architect scaffold. Here, we observed a two-fold increase in catalytic activity and six-fold higher affinity toward TMB (3,3',5,5'-tetramethylbenzidine) substrate as a measure of higher peroxidase activity (nanozymatic) in the case of PduA[K26A] 3D scaffold. This approach demonstrates that the hierarchical organization of scaffold enables the fine-tuning of nanoparticle properties, thus paving the way toward the design of new nanoscale materials.

Biophysical approaches to understand and re-purpose bacterial microcompartments

Bacterial microcompartments represent a modular class of prokaryotic organelles associated with metabolic processes. They harbor a congregation of enzymes that work in cascade within a small, confined volume. These sophisticated nano-engineered crafts of nature offer a tempting paradigm for the fabrication of biosynthetic nanoreactors. Repurposing bacterial microcompartments to develop nanostructures with desired functions requires a careful manipulation in their structural makeup and composition. This calls for a comprehensive understanding of all the interactions of the physical components which frame such molecular architectures. Over recent years, several biophysical techniques have been essential in illuminating the role played by bacterial microcompartments within cells, and have revealed crucial details regarding the morphology, physical properties and functions of their constituent proteins. This has promoted contemplation of ideas for engineering microcompartments inspired biomaterials with novel features and functions.

Protein morphology drives the structure and catalytic activity of bio-inorganic hybrids

Bio-hybrid materials have received a lot of attention in view of their bio-mimicking nature. One such biomimetic material with catalytic activity are the protein derived floral nanohybrid. Copper phosphate coordinated flakes can be curated to distinct floral morphology using proteins. Structurally two different proteins with similar size and with no known enzymatic activity are used to evaluate the role of protein structure and morphology, on the structure-activity relationship of the developed hybrid nanoflowers. Globular protein BSA and bacterial microcompartment domain protein PduBB' are selected. PduBB' because of self-assembling nature forms extended sheets, whereas BSA lacks specific assembly. The developed hybrid NFs differ in their morphology and also in their mimicry as a biological catalyst. The present investigation highlights the importance of the quaternary structure of proteins in tailoring the structure and function of the h-NFs. The results in this manuscript will motivate and guide designing, engineering and selection of glue material for fabricating biomacromolecule derived biohybrid material to mimic natural enzymes of potential industrial application.

Advances in the World of Bacterial Microcompartments

Bacterial microcompartments (MCPs) are extremely large (100-400 nm) and diverse proteinaceous organelles that compartmentalize multistep metabolic pathways, increasing their efficiency and sequestering toxic and/or volatile intermediates. This review highlights recent studies that have expanded our understanding of the diversity, structure, function, and potential biotechnological uses of MCPs. Several new types of MCPs have been identified and characterized revealing new functions and potential new associations with human disease. Recent structural studies of MCP proteins and recombinant MCP shells have provided new insights into MCP assembly and mechanisms and raised new questions about MCP structure. We also discuss recent work on biotechnology applications that use MCP principles to develop nanobioreactors, nanocontainers, and molecular scaffolds.

Prokaryotic Organelles: Bacterial Microcompartments in E. coli and Salmonella

Bacterial microcompartments (MCPs) are proteinaceous organelles consisting of a metabolic pathway encapsulated within a selectively permeable protein shell. Hundreds of species of bacteria produce MCPs of at least nine different types, and MCP metabolism is associated with enteric pathogenesis, cancer, and heart disease. This review focuses chiefly on the four types of catabolic MCPs (metabolosomes) found in Escherichia coli and Salmonella: the propanediol utilization (pdu), ethanolamine utilization (eut), choline utilization (cut), and glycyl radical propanediol (grp) MCPs. Although the great majority of work done on catabolic MCPs has been carried out with Salmonella and E. coli, research outside the group is mentioned where necessary for a comprehensive understanding. Salient characteristics found across MCPs are discussed, including enzymatic reactions and shell composition, with particular attention paid to key differences between classes of MCPs. We also highlight relevant research on the dynamic processes of MCP assembly, protein targeting, and the mechanisms that underlie selective permeability. Lastly, we discuss emerging biotechnology applications based on MCP principles and point out challenges, unanswered questions, and future directions.

Visualizing in Vivo Dynamics of Designer Nanoscaffolds

Enzymes of natural biochemical pathways are routinely subcellularly organized in space and time in order to improve pathway efficacy and control. Designer scaffolding platforms are under development to confer similar benefits upon engineered pathways. Herein, we evaluate bacterial microcompartment shell (pfam0936-domain) proteins as modules for constructing well-defined nanometer scale scaffolds in vivo. We use a suite of visualization techniques to evaluate scaffold assembly and dynamics. We demonstrate recruitment of target cargo molecules onto assembled scaffolds by appending reciprocally interacting adaptor domains. These interactions can be refined by fine-tuning the scaffold expression level. Real-time observation of this system reveals a nucleation-limited step where multiple scaffolds initially form within a cell. Over time, nucleated scaffolds reorganize into a single intracellular assembly, likely due to interscaffold competition for protein subunits. Our results suggest design considerations for using self-assembling proteins as building blocks to construct nanoscaffolds, while also providing a platform to visualize scaffold-cargo dynamics in vivo.

Functional protein shells fabricated from the self-assembling protein sheets of prokaryotic organelles

Fabricating single component protein compartments from the shells proteins of bacterial microcompartments.

A Combined Mechanochemical and Calcination Route to Mixed Cobalt Oxides for the Selective Catalytic Reduction of Nitrophenols

Para-, or 4-nitrophenol, and related nitroaromatics are broadly used compounds in industrial processes and as a result are among the most common anthropogenic pollutants in aqueous industrial effluent; this requires development of practical remediation strategies. Their catalytic reduction to the less toxic and synthetically desirable aminophenols is one strategy. However, to date, the majority of work focuses on catalysts based on precisely tailored, and often noble metal-based nanoparticles. The cost of such systems hampers practical, larger scale application. We report a facile route to bulk cobalt oxide-based materials, via a combined mechanochemical and calcination approach. Vibratory ball milling of CoCl2(H2O)6 with KOH, and subsequent calcination afforded three cobalt oxide-based materials with different combinations of CoO(OH), Co(OH)2, and Co3O4 with different crystallite domains/sizes and surface areas; Co@100, Co@350 and Co@600 (Co@###; # = calcination temp). All three prove active for the catalytic reduction of 4-nitrophenol and related aminonitrophenols. In the case of 4-nitrophenol, Co@350 proved to be the most active catalyst, therein its retention of activity over prolonged exposure to air, moisture, and reducing environments, and applicability in flow processes is demonstrated.

Graphene oxide quantum dots stimulate indigenous bacteria to remove oil contamination

Oil spills occur frequently worldwide, resulting in severe damage to water and to human health. Polycyclic aromatic hydrocarbons (PAHs) are the primary toxic components in oil contamination. PAH-degrading microbes have attracted significant attention, but difficulty in their selection and proliferation limits their applications. Graphene oxide quantum dots (GOQDs) improve the proliferation of an indigenous PAH-degrading strain, Bacillus cereus, more effectively than large graphene oxide flakes. Bacillus cereus can metabolize a variety of xenobiotic aromatic compounds as carbon sources and is used in bioremediation. GOQDs contain a variety of aromatic hydrocarbon structures, explaining why the bacteria achieve strong tolerance to PAHs. GOQD-activated cytokinesis increases the secretion of substances important for biofilm formation (extracellular polymeric substances), which further accelerates PAH removal. Proteomic analysis reveals the molecular mechanisms underlying GOQD-induced microbial proliferation. GOQDs induce the overexpression of microbial divisomal proteins associated with division initiation, DNA replication and peptidoglycan hydrolysis/synthesis. Importantly, PAH removal mediated by GOQD-treated Bacillus cereus does not require the addition of GOQDs. The effects of GOQDs on a strain persist for at least 20 generations, suggesting their possible use in low-cost applications. This work proposes a strategy to remove oil contamination using an indigenous bacterial system enhanced by nanomaterials.

Stereoselective Double Reduction of 3-Methyl-2-cyclohexenone, by Use of Palladium and Platinum Nanoparticles, in Tandem with Alcohol Dehydrogenase

The combination of metal nanoparticles (Pd or Pt NPs) with NAD-dependent thermostable alcohol dehydrogenase (TADH) resulted in the one-flask catalytic double reduction of 3-methyl-2-cyclohexenone to 3-(1S,3S)-methylcyclohexanol. In this article, some assumptions about the interactions between a chemocatalyst and a biocatalyst have been proposed. It was demonstrated that the size of the NPs was the critical parameter for the mutual inhibition: the bigger the NPs, the more harmful for the enzyme they were, even if the NPs themselves were only moderately inactivated. Conversely, the smaller the NPs, the more minimal the TADH denaturation, although they were dramatically inhibited. Resuming, the chemocatalysts were very sensitive to deactivation, which was not related to the amount of enzyme used, while the inhibition of the biocatalyst can be strongly reduced by minimizing the NPs/TADH ratio used to catalyze the reaction. Among some methods to avoid direct binding of NPs with TADH, we found that using large Pd NPs and protecting their surfaces with a silica shell, the overall yield of 3-(1S,3S)-methylcyclohexanol was maximized (36%).