Computational analysis into the potential of azo dyes as a feedstock for actinorhodin biosynthesis in Pseudomonas putida.

Fermentation-based biosynthesis in synthetic biology relies heavily on sugar-derived feedstocks, a limited and carbon-intensive commodity. Unconventional feedstocks from less-noble sources such as waste are being utilized to produce high-value chemical products. Azo dyes, a major pollutant commonly discharged by food, textile, and pharmaceutical industries, present significant health and environmental risks. We explore the potential of engineering Pseudomonas putida KT2440 to utilize azo dyes as a substrate to produce a polyketide, actinorhodin (ACT). Using the constrained minimal cut sets (cMCS) approach, we identified metabolic interventions that optimize ACT biosynthesis and compare the growth-coupling solutions attainable on an azo dye compared to glucose. Our results predicted that azo dyes could perform better as a feedstock for ACT biosynthesis than glucose as it allowed growth-coupling regimes that are unfeasible with glucose and generated an 18.28% higher maximum ACT flux. By examining the flux distributions enabled in different carbon sources, we observed that carbon fluxes from aromatic compounds like azo dyes have a unique capability to leverage gluconeogenesis to support both growth and production of secondary metabolites that produce excess NADH. Carbon sources are commonly chosen based on the host organism, availability, cost, and environmental implications. We demonstrated that careful selection of carbon sources is also crucial to ensure that the resulting flux distribution is suitable for further metabolic engineering of microbial cell factories.

Conversion and synthesis of chemicals catalyzed by fungal cytochrome P450 monooxygenases: A review.

Cytochrome P450s (also called CYPs or P450s) are a superfamily of heme-containing monooxygenases. They are distributed in all biological kingdoms. Most fungi have at least two P450-encoding genes, CYP51 and CYP61, which are housekeeping genes that play important roles in the synthesis of sterols. However, the kingdom fungi is an interesting source of numerous P450s. Here, we review reports on fungal P450s and their applications in the bioconversion and biosynthesis of chemicals. We highlight their history, availability, and versatility. We describe their involvement in hydroxylation, dealkylation, oxygenation, C═C epoxidation, C-C cleavage, C-C ring formation and expansion, C-C ring contraction, and uncommon reactions in bioconversion and/or biosynthesis pathways. The ability of P450s to catalyze these reactions makes them promising enzymes for many applications. Thus, we also discuss future prospects in this field. We hope that this review will stimulate further study and exploitation of fungal P450s for specific reactions and applications.

Latent Functions and Applications of Cytochrome P450 Monooxygenases from Thamnidium elegans: A Novel Biocatalyst for 14α-Hydroxylation of Testosterone.

Cytochrome P450 monooxygenases (P450s) are ubiquitous enzymes with high availability and diversity in nature. Fungi provide a diverse and complex array of P450s, and these enzymes play essential roles in various secondary metabolic processes. Besides the physiological impacts of P450s on fungal life, their versatile functions are attractive for use in advanced applications of the biotechnology sector. Herein, we report gene identification and functional characterization of P450s from the zygomycetous fungus Thamnidium elegans (TeCYPs). We identified 48 TeCYP genes, including two putative pseudogenes, from the whole-genome sequence of T. elegans. Furthermore, we constructed a functional library of TeCYPs and heterologously expressed 46 TeCYPs in Saccharomyces cerevisiae. Recombinants of S. cerevisiae were then used as whole-cell biocatalysts for bioconversion of various compounds. Catalytic potentials of various TeCYPs were demonstrated through a functionomic survey to convert a series of compounds, including steroidal substrates. Notably, CYP5312A4 was found to be highly active against testosterone. Based on nuclear magnetic resonance analysis, enzymatic conversion of testosterone to 14α-hydroxytestosterone by CYP5312A4 was demonstrated. This is the first report to identify a novel fungal P450 that catalyzes the 14α-hydroxylation of testosterone. In addition, we explored the latent potentials of TeCYPs using various substrates. This study provides a platform to further study the potential use of TeCYPs as catalysts in pharmaceutical and agricultural industries and biotechnology.

Designed protein multimerization and polymerization for functionalization of proteins.

Multimeric and polymeric proteins are large biomacromolecules consisting of multiple protein molecules as their monomeric units, connected through covalent or non-covalent bonds. Genetic modification and post-translational modifications (PTMs) of proteins offer alternative strategies for designing and creating multimeric and polymeric proteins. Multimeric proteins are commonly prepared by genetic modification, whereas polymeric proteins are usually created through PTMs. There are two methods that can be applied to create polymeric proteins: self-assembly and crosslinking. Self-assembly offers a spontaneous reaction without a catalyst, while the crosslinking reaction offers some catalyst options, such as chemicals and enzymes. In addition, enzymes are excellent catalysts because they provide site-specificity, rapid reaction, mild reaction conditions, and activity and functionality maintenance of protein polymers. However, only a few enzymes are applicable for the preparation of protein polymers. Most of the other enzymes are effective only for protein conjugation or labeling. Here, we review novel and applicable strategies for the preparation of multimeric proteins through genetic modification and self-assembly. We then describe the formation of protein polymers through site-selective crosslinking reactions catalyzed by enzymes, crosslinking reactions of non-natural amino acids, and protein-peptide (SpyCatcher/SpyTag) interactions. Finally, we discuss the potential applications of these protein polymers.

Strategies for Making Multimeric and Polymeric Bifunctional Protein Conjugates and Their Applications as Bioanalytical Tools.

Enzymes play a central role in the detection of target molecules in biotechnological fields. Most probes used in detection are bifunctional proteins comprising enzymes and binding proteins conjugated by chemical reactions. To create a highly sensitive detection probe, it is essential to increase the enzyme-to-binding protein ratio in the probe. However, if the chemical reactions required to prepare the probe are insufficiently site-specific, the detection probe may lose functionality. Genetic modifications and enzyme-mediated post-translational modifications (PTMs) can ensure the site-specific conjugation of proteins. They are therefore promising strategies for the production of detection probes with high enzyme contents, i.e., polymeric bifunctional proteins. Herein, we review recent advances in the preparation of bifunctional protein conjugates and polymeric bifunctional protein conjugates for detection. We have summarized research on genetically fused proteins and enzymatically prepared polymeric bifunctional proteins, and will discuss the potential use of protein polymers in various detection applications.

Linear Polymerization of Protein by Sterically Controlled Enzymatic Cross-Linking with a Tyrosine-Containing Peptide Loop.

The structure of a protein complex needs to be controlled appropriately to maximize its functions. Herein, we report the linear polymerization of bacterial alkaline phosphatase (BAP) through the site-specific cross-linking reaction catalyzed by Trametes sp. laccase (TL). We introduced a peptide loop containing a tyrosine (Y-Loop) to BAP, and the Y-Looped BAP was treated with TL. The Y-Looped BAP formed linear polymers, whereas BAP fused with a C-terminal peptide containing a tyrosine (Y-tag) showed an irregular shape after TL treatment. The sterically confined structure of the Y-Loop could be responsible for the formation of linear BAP polymers. TL-catalyzed copolymerization of Y-Looped BAP and a Y-tagged chimeric antibody-binding protein, pG2pA-Y, resulted in the formation of linear bifunctional protein copolymers that could be employed as protein probes in an enzyme-linked immunosorbent assay (ELISA). Copolymers comprising Y-Looped BAP and pG2pA-Y at a molar ratio of 100:1 exhibited the highest signal in the ELISA with 26- and 20-fold higher than a genetically fused chimeric protein, BAP-pG2pA-Y, and its polymeric form, respectively. This result revealed that the morphology of the copolymers was the most critical feature to improve the functionality of the protein polymers as detection probes, not only for immunoassays but also for other diagnostic applications.

Polymerization of Horseradish Peroxidase by a Laccase-Catalyzed Tyrosine Coupling Reaction.

The polymerization of proteins can create newly active and large bio-macromolecular assemblies that exhibit unique functionalities depending on the properties of the building block proteins and the protein units in polymers. Herein, the first enzymatic polymerization of horseradish peroxidase (HRP) is reported. Recombinant HRPs fused with a tyrosine-tag (Y-tag) through a flexible linker at the N- and/or C-termini are expressed in silkworm, Bombyx mori. Trametes sp. laccase (TL) is used to activate the tyrosine of Y-tagged HRPs with molecular O2 to form a tyrosyl-free radical, which initiates the tyrosine coupling reaction between the HRP units. A covalent dityrosine linkage is also formed through a HRP-catalyzed self-crosslinking reaction in the presence of H2 O2 . The addition of H2 O2 in the self-polymerization of Y-tagged HRPs results in lower activity of the HRP polymers, whereas TL provides site-selectivity, mild reaction conditions and maintains the activity of the polymeric products. The cocrosslinking of Y-tagged HRPs and HRP-protein G (Y-HRP-pG) units catalyzed by TL shows a higher signal in enzyme-linked immunosorbent assay (ELISA) than the genetically pG-fused HRP, Y-HRP-pG, and its polymers. This new enzymatic polymerization of HRP promises to provide highly active and functionalized polymers for biomedical applications and diagnostics probes.

Laccase-catalyzed bioconjugation of tyrosine-tagged functional proteins.

The site-specific cross-linking of functional proteins creates macromolecular assemblies that exhibit unique biochemical and/or physicochemical properties. Herein, we explored the potential of laccase as a biocatalyst for the site-specific cross-linking of tyrosine-tagged proteins. Trametes sp. laccase (TL) was selected as the cross-linking catalyst, and Escherichia coli alkaline phosphatase (BAP) and antibody-binding proteins (pG2pAs) were employed as model proteins. The protein models were genetically fused to a peptide tag containing a tyrosine residue (Y-tag) at the N- and/or C-termini. Proteins without Y-tags were used as controls. The Y-tagged proteins could be recognized by TL as macromolecular substrates, leading to the oxidative formation of protein polymers, whereas no polymerization was observed with intact BAP or pG2pA. The TL-catalyzed cross-linking of Y-tagged proteins proceeded at a relatively high pH in comparison with that of small phenolic substrates. Co-polymers of BAP and pG2pA were able to be prepared by mixing the aqueous solution of each component in the presence of TL. A combination of bis-Y-tagged pG2pA (Y-pG2pA-Y) and Y-tagged BAP (BAP-Y) yielded functional co-polymers compatible with enzyme-linked immunosorbent assay (ELISA). The detection limit of the ELISA of ovalbumin with anti-OVA IgG depended on the molar ratio of BAP-Y and Y-pG2pA-Y in the TL-catalyzed cross-linking reaction. A high molar ratio of BAP-Y to Y-pG2pA-Y (75:1) resulted in the highest absorbance in the ELISA. The results suggested that the formation of a bifunctional protein polymer with a high molar ratio of signaling unit to antibody-binding unit gave better performance in antigen detection than using lower ratios.