Engineered β-Lactoglobulin Produced in E. coli: Purification, Biophysical and Structural Characterisation

T7 RNA polymerase-guided base editor for accelerated continuous evolution in Bacillus subtilis

Targeted in vivo hypermutation mediated by base deaminase-T7 RNA polymerase (T7 RNAP) fusions promotes genetic diversification and accelerates continuous directed evolution. Due to the lack of a T7RNAP expression regulation system and functionally compatible linker for fusion protein expression, T7RNAP-guided continuous evolution has not been established in Bacillus subtilis, which limited long gene fragment continuous evolution targeted on genome. Here, we developed BS-MutaT7 system, which introduced mutations into specific genomic regions by leveraging chimeric fusions of base deaminases with T7RNAP in B. subtilis. We selected seven different sources of adenosine and cytosine deaminases, 14 fusion protein linkers to be fused with T7RNAP, constructing four libraries with the size of 5000, where deaminases were fused at either the N- or C-terminus of T7RNAP. Based on the efficiency of binding to T7 promoter and high mutagenesis activity, two optimal chimeric mutators, BS-MutaT7A (TadA8e-Linker0-T7RNAP) and BS-MutaT7C (PmCDA1-(GGGGS)3-T7RNAP co-expressed with UGI) were identified. The target mutation rates reached 1.2 × 10-5 per base per generation (s.p.b.) and 5.8 × 10-5 s.p.b., representing 7000-fold and 37,000-fold increases over the genomic mutation rate, respectively. Both exhibited high processivity, maintaining mutation rates of 5.8 × 10-6 s.p.b. and 2.9 × 10-5 s.p.b. within a 5 kb DNA region. Notably, BS-MutaT7C exhibited superior mutagenic activity, making it well-suited for applications requiring intensive and sustained genomic diversification. Application of BS-MutaT7 enabled a 16-fold increase in tigecycline resistance and enhanced β-lactoglobulin (β-Lg) expression by evolving the global transcriptional regulator codY, achieving a β-Lg titer of 3.92 g/L. These results highlight BS-MutaT7 as a powerful and versatile tool for genome-scale continuous evolution in B. subtilis.

Binding a C12-appended rhenium-(Bispyridine) carbonyl complex to β-Lactoglobulin: Effects of pH & cysteine modification on calyx affinity

Due to its commercial availability and well-defined structure, the interaction between bovine protein β-lactoglobulin (βLG) and a wide variety of non-native ligands - including transition metal complexes - has been explored, but its application as an artificial metalloenzyme scaffold is limited. This protein is hypothesized to transport fatty acids and other nutrients during juvenile development, and it binds hydrophobic ligands inside a binding pocket constructed upon an 8-stranded β-barrel, called the 'calyx'. Herein, we compare the binding behavior of two rhenium(anthracene-bispyridine) ('Anth-py2') tricarbonyl complexes, one with a 12‑carbon chain appended to the ligand scaffold ('C12Anth-py2') to βLG. We investigate (i) how calyx-binding specificity is affected by pH (which controls βLG structure at the entrance to the calyx) and (ii) modification of a free cysteine residue located in a putative second binding site of βLG (SMe-βLG). The binding affinities of [Re(C12Anth-py2)(CO)3(solv)]+ (ReC12) and [Re(Anth-py2)(CO)3(solv)]+ (ReCH) for βLG at pH 7.3 were similar at 36 ± 2 μM and 43 ± 1 μM, respectively. The KD of ReC12 decreased by ∼13 μM at pH 6.1 due to a well-known conformational change (Tanford transition) at the entrance to the calyx; the KD value was not significantly affected by Cys121 modification, indicating β-barrel calyx binding specificity. In contrast, ReCH experienced a decrease in KD in response to blocking the second binding (SMe-βLG), but was also unaffected by pH. The results show an increase in binding affinity and specificity as a result of targeted ligand design and utilization of native protein characteristics. The findings will inform and improve the design of future βLG-derived ArMs.

β-Lactoglobulin Enhances Clay and Activated Carbon Binding and Protection Properties for Cadmium and Lead

The removal of heavy metals from wastewater remains a challenge due to the limitations of current remediation methods. This study aims to develop multicomponent composites as inexpensive and environmentally friendly sorbents with enhanced capture of cadmium (Cd) and lead (Pb). The composites are based on calcium montmorillonite (CM) and activated carbon (AC) because of their proven effectiveness as sorbents for diverse toxins in environmental settings. In this study, we used a combination of computational and experimental methods to delineate that β-lactoglobulin enhances CM and AC binding and protection properties for Cd and Pb. Modeling and molecular dynamics simulations investigated the formation of material systems formed by CM and AC in complex with β-lactoglobulin and predicted their capacity to bind heavy metal ions at neutral pH conditions. Our simulations suggest that the enhanced binding properties of the material systems are attributed to the presence of several binding pockets formed by β-lactoglobulin for the two heavy metal ions. At neutral pH conditions, divalent Cd and Pb shared comparable binding propensities in all material systems, with the former being consistently higher than the latter. To validate the interactions depicted in simulations, two ecotoxicological models (L. minor and H. vulgaris) were exposed to Cd, Pb, and a mixture of the two. The inclusion of CM-lactoglobulin (β-lactoglobulin amended CM) and AC-lactoglobulin (β-lactoglobulin amended AC) at 0.05-0.2% efficiently and dose-dependently reduced the severe toxicity of metals and increased the growth parameters. This high efficacy of protection shown in the ecotoxicological models may result from the numerous possible interaction pockets of the β-lactoglobulin-amended materials depicted in simulations. The ecotoxicological models support the agreement with computations. This study serves as a proof of concept on how computations in tandem with experiments can be used in the design of multicomponent clay- and carbon-based sorbent amended systems with augmented functionalities for particular toxins.

Identification of additional mechanistically important residues in the multidrug transporter styMdtM of Salmonella Typhi

Multidrug efflux is a well-established mechanism of drug resistance in bacterial pathogens like Salmonella Typhi. styMdtM (locus name; STY4874) is a multidrug efflux transporter of the major facilitator superfamily expressed in S. Typhi. Functional assays identified several residues important for its transport activity. Here, we used an AlphaFold model to identify additional residues for analysis by mutagenesis. Mutation of peripheral residue Cys185 had no effect on the structure or function of the transporter. However, substitution of channel-lining residues Tyr29 and Tyr231 completely abolished transport function. Finally, mutation of Gln294, which faces peripheral helices of the transporter, resulted in the loss of transport of some substrates. Crystallization studies yielded diffraction data for the wild-type protein at 4.5 Å resolution and allowed the unit cell parameters to be established as a = b = 64.3 Å, c = 245.4 Å, α = β = γ = 90°, in space group P4. Our studies represent a further stepping stone towards a mechanistic understanding of the clinically important multidrug transporter styMdtM.Communicated by Ramaswamy H. Sarma.

Cell factory-based milk protein biomanufacturing: Advances and perspectives

The increasing global population and protein demand cause global challenges for food supply. Fueled by significant developments in synthetic biology, microbial cell factories are constructed for the bioproduction of milk proteins, providing a promising approach for scalable and cost-effective production of alternative proteins. This review focused on the synthetic biology-based microbial cell factory construction for milk protein bioproduction. The composition, content, and functions of major milk proteins were first summarized, especially for caseins, α-lactalbumin, and β-lactoglobulin. An economic analysis was performed to determine whether cell factory-based milk protein production is economically viable for industrial production. Cell factory-based milk protein production is proved to be economically viable for industrial production. However, there still exist some challenges for cell factory-based milk protein biomanufacturing and application, including the inefficient production of milk proteins, insufficient investigation of protein functional property, and insufficient food safety evaluation. Constructing new high-efficiency genetic regulatory elements and genome editing tools, coexpression/overexpression of chaperone genes, and engineering protein secretion pathways and establishing a cost-effective protein purification method are possible ways to improve the production efficiency. Milk protein biomanufacturing is one of the promising approaches to acquiring alternative proteins in the future, which is of great importance for supporting cellular agriculture.

Amyloid-like aggregation of recombinant β-lactoglobulin at pH 3.5 and 7.0: Is disulfide bond removal the key to fibrillation?

Functional nanofibrils from globular proteins are usually formed by heating for several hours at pH 2.0, which induces acidic hydrolysis and consecutive self-association. The functional properties of these micro-metre-long anisotropic structures are promising for biodegradable biomaterials and food applications, but their stability at pH > 2.0 is low. The results presented here show that modified β-lactoglobulin can also form nanofibrils by heating at neutral pH without prior acidic hydrolysis; the key is removing covalent disulfide bonds. The aggregation behaviour of various recombinant β-lactoglobulin variants was systemically studied at pH 3.5 and 7.0. The suppression of intra- and intermolecular disulfide bonds by eliminating one to three out of the five cysteines makes the non-covalent interactions more prevalent and allow for structural rearrangement. This stimulated the linear growth of worm-like aggregates. Full elimination of all five cysteines led to the transformation of worm-like aggregates into actual fibril structures (several hundreds of nanometres long) at pH 7.0. This understanding of the role of cysteine in protein-protein interactions will help to identify proteins and protein modifications to form functional aggregates at neutral pH.

New ligand-binding sites identified in the crystal structures of β-lactoglobulin complexes with desipramine

The homodimeric β-lactoglobulin belongs to the lipocalin family of proteins that transport a wide range of hydrophobic molecules and can be modified by mutagenesis to develop specificity for novel groups of ligands. In this work, new lactoglobulin variants, FAF (I56F/L39A/M107F) and FAW (I56F/L39A/M107W), were produced and their interactions with the tricyclic drug desipramine (DSM) were studied using X-ray crystallography, calorimetry (ITC) and circular dichroism (CD). The ITC and CD data showed micromolar affinity of the mutants for DSM and interactions according to the classical one-site binding model. However, the crystal structures unambiguously showed that the FAF and FAW dimers are capable of binding DSM not only inside the β-barrel as expected, but also at the dimer interface and at the entrance to the binding pocket. The presented high-resolution crystal structures therefore provide important evidence of the existence of alternative ligand-binding sites in the β-lactoglobulin molecule. Analysis of the crystal structures highlighted the importance of shape complementarity for ligand recognition and selectivity. The binding sites identified in the crystal structures of the FAF-DSM and FAW-DSM complexes together with data from the existing literature are used to establish a systematic classification of the ligand-binding sites in the β-lactoglobulin molecule.

Can recombinant milk proteins replace those produced by animals?

The consumption of animal proteins in general, and dairy proteins in particular, is associated with sustainability and animal welfare issues. Recombinant synthesis of milk proteins is therefore receiving increasing interest, with several studies showing synthesis of milk proteins using a wide range of expression systems. Achieving a high yield and purity is essential for economic production. Besides the synthesis, also the construction of the specific structure in which milk proteins are present in animal milks, casein micelles, is needed. Looking at the current state-of-the-art, the steps to produce recombinant dairy products are technically feasible, but whether it can be implemented at low cost, with the process being environmentally friendly, remains to be seen in the coming years.

Alternatives to Meat and Dairy

The increasing size and affluence of the global population have led to a rising demand for high-protein foods such as dairy and meat. Because it will be impossible to supply sufficient protein to everyone solely with dairy and meat, we need to transition at least part of our diets toward protein foods that are more sustainable to produce. The best way to convince consumers to make this transition is to offer products that easily fit into their current habits and diets by mimicking the original foods. This review focuses on methods of creating an internal microstructure close to that of the animal-based originals. One can directly employ plant products, use intermediates such as cell factories, or grow cultured meat by using nutrients of plant origin. We discuss methods of creating high-quality alternatives to meat and dairy foods, describe their relative merits, and provide an outlook toward the future.

Comparative study of concatemer efficiency as an isotope-labelled internal standard for allergen quantification

Mass spectrometry-based methods coupled with stable isotope dilution have become effective and widely used methods for the detection and quantification of food allergens. Current methods target signature peptides resulting from proteolytic digestion of proteins of the allergenic ingredient. The choice of appropriate stable isotope-labelled internal standard is crucial, given the diversity of encountered food matrices which can affect sample preparation and analysis. We propose the use of concatemer, an artificial and stable isotope-labelled protein composed of several concatenated signature peptides as internal standard. With a comparative analysis of three matrices contaminated with four allergens (egg, milk, peanut, and hazelnut), the concatemer approach was found to offer advantages associated with the use of labelled proteins, ideal but unaffordable, and circumvent certain limitations of traditionally used synthetic peptides as internal standards. Although used in the proteomic field for more than a decade, concatemer strategy has not yet been applied for food analysis.

Methyl-selective isotope labeling using α-ketoisovalerate for the yeast Pichia pastoris recombinant protein expression system

Methyl-detected NMR spectroscopy is a useful tool for investigating the structures and interactions of large macromolecules such as membrane proteins. The procedures for preparation of methyl-specific isotopically-labeled proteins were established for the Escherichia coli (E. coli) expression system, but typically it is not feasible to express eukaryotic proteins using E. coli. The Pichia pastoris (P. pastoris) expression system is the most common yeast expression system, and is known to be superior to the E. coli system for the expression of mammalian proteins, including secretory and membrane proteins. However, this system has not yet been optimized for methyl-specific isotope labeling, especially for Val/Leu-methyl specific isotope incorporation. To overcome this difficulty, we explored various culture conditions for the yeast cells to efficiently uptake Val/Leu precursors. Among the searched conditions, we found that the cultivation pH has a critical effect on Val/Leu precursor uptake. At an acidic cultivation pH, the uptake of the Val/Leu precursor was increased, and methyl groups of Val and Leu in the synthesized recombinant protein yielded intense ¹H-¹³C correlation signals. Based on these results, we present optimized protocols for the Val/Leu-methyl-selective ¹³C incorporation by the P. pastoris expression system.