Creating Flavin Reductase Variants with Thermostable and Solvent-Tolerant Properties by Rational-Design Engineering

Exploring the role of flavin-dependent monooxygenases in the biosynthesis of aromatic compounds

Hydroxylated aromatic compounds exhibit exceptional biological activities. In the biosynthesis of these compounds, three types of hydroxylases are commonly employed: cytochrome P450 (CYP450), pterin-dependent monooxygenase (PDM), and flavin-dependent monooxygenase (FDM). Among these, FDM is a preferred choice due to its small molecular weight, stable expression in both prokaryotic and eukaryotic fermentation systems, and a relatively high concentration of necessary cofactors. However, the catalytic efficiency of many FDMs falls short of meeting the demands of large-scale production. Additionally, challenges arise from the limited availability of cofactors and compatibility issues among enzyme components. Recently, significant progress has been achieved in improving its catalytic efficiency, but have not yet detailed and informative viewed so far. Therefore, this review emphasizes the advancements in FDMs for the biosynthesis of hydroxylated aromatic compounds and presents a summary of three strategies aimed at enhancing their catalytic efficiency: (a) Developing efficient enzyme mutants through protein engineering; (b) enhancing the supply and rapid circulation of critical cofactors; (c) facilitating cofactors delivery for enhancing FDMs catalytic efficiency. Furthermore, the current challenges and further perspectives on improving catalytic efficiency of FDMs are also discussed.

4-Hydroxyphenylacetate 3-Hydroxylase (4HPA3H): A Vigorous Monooxygenase for Versatile O-Hydroxylation Applications in the Biosynthesis of Phenolic Derivatives

4-Hydroxyphenylacetate 3-hydroxylase (4HPA3H) is a long-known class of two-component flavin-dependent monooxygenases from bacteria, including an oxygenase component (EC 1.14.14.9) and a reductase component (EC 1.5.1.36), with the latter being accountable for delivering the cofactor (reduced flavin) essential for o-hydroxylation. 4HPA3H has a broad substrate spectrum involved in key biological processes, including cellular catabolism, detoxification, and the biosynthesis of bioactive molecules. Additionally, it specifically hydroxylates the o-position of the C4 position of the benzene ring in phenolic compounds, generating high-value polyhydroxyphenols. As a non-P450 o-hydroxylase, 4HPA3H offers a viable alternative for the de novo synthesis of valuable natural products. The enzyme holds the potential to replace plant-derived P450s in the o-hydroxylation of plant polyphenols, addressing the current significant challenge in engineering specific microbial strains with P450s. This review summarizes the source distribution, structural properties, and mechanism of 4HPA3Hs and their application in the biosynthesis of natural products in recent years. The potential industrial applications and prospects of 4HPA3H biocatalysts are also presented.

A high catalytic efficiency and chemotolerant formate dehydrogenase from Bacillus simplex

NAD+ -dependent formate dehydrogenase (FDH) catalyzes the conversion of formate and NAD+ to produce carbon dioxide and NADH. The reaction is biotechnologically important because FDH is widely used for NADH regeneration in various enzymatic syntheses. However, major drawbacks of this versatile enzyme in industrial applications are its low activity, requiring its utilization in large amounts to achieve optimal process conditions. Here, FDH from Bacillus simplex (BsFDH) was characterized for its biochemical and catalytic properties in comparison to FDH from Pseudomonas sp. 101 (PsFDH), a commonly used FDH in various biocatalytic reactions. The data revealed that BsFDH possesses high formate oxidizing activity with a kcat value of 15.3 ± 1.9 s-1 at 25°C compared to 7.7 ± 1.0 s-1 for PsFDH. At the optimum temperature (60°C), BsFDH exhibited 6-fold greater activity than PsFDH. The BsFDH displayed higher pH stability and a superior tolerance toward sodium azide and H2 O2 inactivation, showing a 200-fold higher Ki value for azide inhibition and remaining stable in the presence of 0.5% H2 O2 compared to PsFDH. The application of BsFDH as a cofactor regeneration system for the detoxification of 4-nitrophenol by the reaction of HadA, which produced a H2 O2 byproduct was demonstrated. The biocatalytic cascades using BsFDH demonstrated a distinct superior conversion activity because the system tolerated H2 O2 well. Altogether, the data showed that BsFDH is a robust enzyme suitable for future application in industrial biotechnology.

Structure and biochemical characterization of an extradiol 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Acinetobacter baumannii

3,4-Dihydroxyphenylacetate (DHPA) 2,3-dioxygenase (EC 1.13.11.15) from Acinetobacter baumannii (AbDHPAO) is an enzyme that catalyzes the 2,3-extradiol ring-cleavage of DHPA in the p-hydroxyphenylacetate (HPA) degradation pathway. While the biochemical reactions of various DHPAOs have been reported, only structures of DHPAO from Brevibacterium fuscum and their homologs are available. Here, we report the X-ray structure and biochemical characterization of an Fe2+-specific AbDHPAO that shares 12% sequence identity to the enzyme from B. fuscum. The 1.8 Å X-ray structure of apo-AbDHPAO was determined with four subunits per asymmetric unit, consistent with a homotetrameric structure. Interestingly, the αβ-sandwiched fold of the AbDHPAO subunit is different from the dual β-barrel-like motif of the well-characterized B. fuscum DHPAO structures; instead, it is similar to the structures of non-DHPA extradiol dioxygenases from Comamonas sp. and Sphingomonas paucimobilis. Similarly, these extradiol dioxygenases share the same chemistry owing to a conserved 2-His-1-carboxylate catalytic motif. Structure analysis and molecular docking suggested that the Fe2+ cofactor and substrate binding sites consist of the conserved residues His12, His57, and Glu238 forming a 2-His-1-carboxylate motif ligating to Fe2+ and DHPA bound with Fe2+ in an octahedral coordination. In addition to DHPA, AbDHPAO can also use other 3,4-dihydroxyphenylacetate derivatives with different aliphatic carboxylic acid substituents as substrates, albeit with low reactivity. Altogether, this report provides a better understanding of the structure and biochemical properties of AbDHPAO and its homologs, which is advancing further modification of DHPAO in future applications.

Analyzing Current Trends and Possible Strategies to Improve Sucrose Isomerases' Thermostability

Due to their ability to produce isomaltulose, sucrose isomerases are enzymes that have caught the attention of researchers and entrepreneurs since the 1950s. However, their low activity and stability at temperatures above 40 °C have been a bottleneck for their industrial application. Specifically, the instability of these enzymes has been a challenge when it comes to their use for the synthesis and manufacturing of chemicals on a practical scale. This is because industrial processes often require biocatalysts that can withstand harsh reaction conditions, like high temperatures. Since the 1980s, there have been significant advancements in the thermal stabilization engineering of enzymes. Based on the literature from the past few decades and the latest achievements in protein engineering, this article systematically describes the strategies used to enhance the thermal stability of sucrose isomerases. Additionally, from a theoretical perspective, we discuss other potential mechanisms that could be used for this purpose.

Enzymatic cofactor regeneration systems: A new perspective on efficiency assessment

Nowadays, the specificity of enzymatic processes makes them more and more important every year, and their usage on an industrial scale seems to be necessary. Enzymatic cofactors, however, play a crucial part in the prospective applications of enzymes, because they are indispensable for conducting highly effective biocatalytic activities. Due to the relatively high cost of these compounds and their consumption during the processes carried out, it has become crucial to develop systems for cofactor regeneration. Therefore, in this review, an attempt was made to summarize current knowledge on enzymatic regeneration methods, which are characterized by high specificity, non-toxicity and reported to be highly efficient. The regeneration of cofactors, such as nicotinamide dinucleotides, coenzyme A, adenosine 5'-triphosphate and flavin nucleotides, which are necessary for the proper functioning of a large number of enzymes, is discussed, as well as potential directions for further development of these systems are highlighted. This review discusses a range of highly effective cofactor regeneration systems along with the productive synthesis of many useful chemicals, including the simultaneous renewal of several cofactors at the same time. Additionally, the impact of the enzyme immobilization process on improving the stability and the potential for multiple uses of the developed cofactor regeneration systems was also presented. Moreover, an attempt was made to emphasize the importance of the presented research, as well as the identification of research gaps, which mainly result from the lack of available literature on this topic.

Luciferin Synthesis and Pesticide Detection by Luminescence Enzymatic Cascades

D-Luciferin (D-LH₂ ), a substrate of firefly luciferase (Fluc), is important for a wide range of bioluminescence applications. This work reports a new and green method using enzymatic reactions (HELP, HadA Enzyme for Luciferin Preparation) to convert 19 phenolic derivatives to 8 D-LH₂ analogues with ≈51 % yield. The method can synthesize the novel 5'-methyl-D-LH₂ and 4',5'-dimethyl-D-LH₂ , which have never been synthesized or found in nature. 5'-Methyl-D-LH₂ emits brighter and longer wavelength light than the D-LH₂ . Using HELP, we further developed LUMOS (Luminescence Measurement of Organophosphate and Derivatives) technology for in situ detection of organophosphate pesticides (OPs) including parathion, methyl parathion, EPN, profenofos, and fenitrothion by coupling the reactions of OPs hydrolase and Fluc. The LUMOS technology can detect these OPs at parts per trillion (ppt) levels. The method can directly detect OPs in food and biological samples without requiring sample pretreatment.

Rational-Design Engineering to Improve Enzyme Thermostability

The fundamentals of thermostability engineering need to be carried out for proteins with low thermal stability to expand their utilization. Thus, comprehension of the thermal stability regulating factors of proteins is needful for the engineering of their thermostability. Protein engineering aims to overcome their natural limitations in tough conditions by refining protein stability and activity. Rational-design approach requires a crystal structure dataset along with the biophysical information, protein function, and sequence-based data, especially consensus sequence that is favorable for the protein folding during natural evolution. It can be attained by either single- or multiple-point mutation, by which amino acids are changed. In fact, these mutation approaches show several benefits. For example, the offered mutations are produced after an evaluation and design, which raise the chance to acquire favorable mutations. The rational-design engineering can improve the biochemical properties of enzymes, including the kinetic behaviors, substrate specificity, thermostability, and organic solvent tolerance. Moreover, this approach considerably reduces the library size, so less effort and time can be employed. Here, we apply the computational algorithms and programs with experiments to create thermostable enzymes that will be beneficial for future applications.

Enzymes, In Vivo Biocatalysis, and Metabolic Engineering for Enabling a Circular Economy and Sustainability

Since the industrial revolution, the rapid growth and development of global industries have depended largely upon the utilization of coal-derived chemicals, and more recently, the utilization of petroleum-based chemicals. These developments have followed a linear economy model (produce, consume, and dispose). As the world is facing a serious threat from the climate change crisis, a more sustainable solution for manufacturing, i.e., circular economy in which waste from the same or different industries can be used as feedstocks or resources for production offers an attractive industrial/business model. In nature, biological systems, i.e., microorganisms routinely use their enzymes and metabolic pathways to convert organic and inorganic wastes to synthesize biochemicals and energy required for their growth. Therefore, an understanding of how selected enzymes convert biobased feedstocks into special (bio)chemicals serves as an important basis from which to build on for applications in biocatalysis, metabolic engineering, and synthetic biology to enable biobased processes that are greener and cleaner for the environment. This review article highlights the current state of knowledge regarding the enzymatic reactions used in converting biobased wastes (lignocellulosic biomass, sugar, phenolic acid, triglyceride, fatty acid, and glycerol) and greenhouse gases (CO₂ and CH₄) into value-added products and discusses the current progress made in their metabolic engineering. The commercial aspects and life cycle assessment of products from enzymatic and metabolic engineering are also discussed. Continued development in the field of metabolic engineering would offer diversified solutions which are sustainable and renewable for manufacturing valuable chemicals.

Use of Bacterial Luciferase as a Reporter Gene in Eukaryotic Systems

Reporter gene assays are powerful tools for monitoring dynamic molecular changes and for evaluating the responses that occur at the genetic elements within cells in response to exogenous molecules. In general, various protein systems can be used as reporter genes, including luciferases. Here, the present protocol introduces a unique reporter gene system for monitoring molecular events in cells using bacterial luciferase (lux), which can generate blue-green light suitable for gene reporter applications with the highest cost performance. The protocol also guides the assay conditions and necessary components for using of lux gene (lux) as a eukaryotic reporter system. The lux system can be applied to monitor variety of molecular events inside mammalian cellular systems.

Phenolic hydroxylases

Many flavin-dependent phenolic hydroxylases (monooxygenases) have been extensively investigated. Their crystal structures and reaction mechanisms are well understood. These enzymes belong to groups A and D of the flavin-dependent monooxygenases and can be classified as single-component and two-component flavin-dependent monooxygenases. The insertion of molecular oxygen into the substrates catalyzed by these enzymes is beneficial for modifying the biological properties of phenolic compounds and their derivatives. This chapter provides an in-depth discussion of the structural features of single-component and two-component flavin-dependent phenolic hydroxylases. The reaction mechanisms of selected enzymes, including 3-hydroxy-benzoate 4-hydroxylase (PHBH) and 3-hydroxy-benzoate 6-hydroxylase as representatives of single-component enzymes and 3-hydroxyphenylacetate 4-hydroxylase (HPAH) as a representative of two-component enzymes, are discussed in detail. This chapter comprises the following four main parts: general reaction, structures, reaction mechanisms, and enzyme engineering for biocatalytic applications. Enzymes belonging to the same group catalyze similar reactions but have different unique structural features to control their reactivity to substrates and the formation and stabilization of C4a-hydroperoxyflavin. Protein engineering has been employed to improve the ability to use these enzymes to synthesize valuable compounds. A thorough understanding of the structural and mechanistic features controlling enzyme reactivity is useful for enzyme redesign and enzyme engineering for future biocatalytic applications.