DHAP-dependent aldolases from (hyper)thermophiles: biochemistry and applications

Multienzyme Cascade Synthesis of Rare Sugars From Glycerol in Bacillus subtilis

BACKGROUND

Rare sugars are valuable and unique monosaccharides extensively utilized in the food, cosmetics, and pharmaceutical industries. Considering the high purification costs and the complex processes of enzymatic synthesis, whole-cell conversion has emerged as a significantly important alternative. The Escherichia coli strain was initially used in whole-cell synthesis of rare sugars. However, its pathogenic nature poses limitations to its widespread applications. Consequently, there is an urgent need to explore biologically safe strains for the efficient production of rare sugars.

RESULTS

In this study, the generally regarded as safe (GRAS) strain Bacillus subtilis was employed as the chassis cells to produce rare sugars via whole-cell conversion. Three genes encoding alditol oxidase (AldO), L-rhamnulose-1-phosphate aldolase (RhaD), and fructose-1-phosphatase (YqaB) involved in rare sugars biosynthesis were heterogeneously expressed in B. subtilis to convert the only substrate glycerol into rare sugars. To enhance the expression levels of the relevant enzymes in B. subtilis, different promoters for aldO, rhaD, and yqaB were investigated and optimized in this system. Under the optimized reaction conditions, the maximum total production titer was 16.96 g/L of D-allulose and D-sorbose with a conversion yield of 33.9% from glycerol. Furthermore, the engineered strain produced 26.68 g/L of D-allulose and D-sorbose through fed-batch for the whole-cell conversion, representing the highest titer from glycerol reported to date.

CONCLUSION

This study demonstrated an efficient and cost-effective method for the synthesis of rare sugars, providing a food-grade platform with the potential to meet the growing demand for rare sugars in industries.

Recent advances in enzymatic carbon-carbon bond formation

Enzymatic carbon-carbon (C-C) bond formation reactions have become an effective and invaluable tool for designing new biological and medicinal molecules, often with asymmetric features. This review provides a systematic overview of key C-C bond formation reactions and enzymes, with the focus of reaction mechanisms and recent advances. These reactions include the aldol reaction, Henry reaction, Knoevenagel condensation, Michael addition, Friedel-Crafts alkylation and acylation, Mannich reaction, Morita-Baylis-Hillman (MBH) reaction, Diels-Alder reaction, acyloin condensations via Thiamine Diphosphate (ThDP)-dependent enzymes, oxidative and reductive C-C bond formation, C-C bond formation through C1 resource utilization, radical enzymes for C-C bond formation, and other C-C bond formation reactions.

Multifunctional Fructose 1,6-Bisphosphate Aldolase as a Therapeutic Target

Fructose 1,6-bisphosphate aldolase is a ubiquitous cytosolic enzyme that catalyzes the fourth step of glycolysis. Aldolases are classified into three groups: Class-I, Class-IA, and Class-II; all classes share similar structural features but low amino acid identity. Apart from their conserved role in carbohydrate metabolism, aldolases have been reported to perform numerous non-enzymatic functions. Here we review the myriad "moonlighting" functions of this classical enzyme, many of which are centered on its ability to bind to an array of partner proteins that impact cellular scaffolding, signaling, transcription, and motility. In addition to the cytosolic location, aldolase has been found the extracellular surface of several pathogenic bacteria, fungi, protozoans, and metazoans. In the extracellular space, the enzyme has been reported to perform virulence-enhancing moonlighting functions e.g., plasminogen binding, host cell adhesion, and immunomodulation. Aldolase's importance has made it both a drug target and vaccine candidate. In this review, we note the several inhibitors that have been synthesized with high specificity for the aldolases of pathogens and cancer cells and have been shown to inhibit classical enzyme activity and moonlighting functions. We also review the many trials in which recombinant aldolases have been used as vaccine targets against a wide variety of pathogenic organisms including bacteria, fungi, and metazoan parasites. Most of such trials generated significant protection from challenge infection, correlated with antigen-specific cellular and humoral immune responses. We argue that refinement of aldolase antigen preparations and expansion of immunization trials should be encouraged to promote the advancement of promising, protective aldolase vaccines.

Progress in Stereoselective Construction of C-C Bonds Enabled by Aldolases and Hydroxynitrile Lyases

The creation of C-C bonds is an effective strategy for constructing complex compounds from simple synthetic blocks. Although many methods have been developed for C-C bond construction, the stereoselective creation of new C-C bonds remains a challenge. The selectivities (enantioselectivity, regioselectivity, and chemoselectivity) of biocatalysts are higher than those of chemical catalysts, therefore biocatalysts are excellent candidates for use in stereoselective C-C bond formation. Here, we summarize progress made in the past 10 years in stereoselective C-C bond formation enabled by two classic types of enzyme, aldolases and hydroxynitrile lyases. The information in this review will enable the development of new routes to the stereoselective construction of C-C bonds.

Current Advances on Structure-Function Relationships of Pyridoxal 5'-Phosphate-Dependent Enzymes

Pyridoxal 5′-phosphate (PLP) functions as a coenzyme in many enzymatic processes, including decarboxylation, deamination, transamination, racemization, and others. Enzymes, requiring PLP, are commonly termed PLP-dependent enzymes, and they are widely involved in crucial cellular metabolic pathways in most of (if not all) living organisms. The chemical mechanisms for PLP-mediated reactions have been well elaborated and accepted with an emphasis on the pure chemical steps, but how the chemical steps are processed by enzymes, especially by functions of active site residues, are not fully elucidated. Furthermore, the specific mechanism of an enzyme in relation to the one for a similar class of enzymes seems scarcely described or discussed. This discussion aims to link the specific mechanism described for the individual enzyme to the same types of enzymes from different species with aminotransferases, decarboxylases, racemase, aldolase, cystathionine β-synthase, aromatic phenylacetaldehyde synthase, et al. as models. The structural factors that contribute to the reaction mechanisms, particularly active site residues critical for dictating the reaction specificity, are summarized in this review.

Multidisciplinary involvement and potential of thermophiles

The full biotechnological exploitation of thermostable enzymes in industrial processes is necessary for their commercial interest and industrious value. The heat-tolerant and heat-resistant enzymes are a key for efficient and cost-effective translation of substrates into useful products for commercial applications. The thermophilic, hyperthermophilic, and microorganisms adapted to extreme temperatures (i.e., low-temperature lovers or psychrophiles) are a rich source of thermostable enzymes with broad-ranging thermal properties, which have structural and functional stability to underpin a variety of technologies. These enzymes are under scrutiny for their great biotechnological potential. Temperature is one of the most critical parameters that shape microorganisms and their biomolecules for stability under harsh environmental conditions. This review describes in detail the sources of thermophiles and thermostable enzymes from prokaryotes and eukaryotes (microbial cell factories). Furthermore, the review critically examines perspectives to improve modern biocatalysts, its production and performance aiming to increase their value for biotechnology through higher standards, specificity, resistance, lowing costs, etc. These thermostable and thermally adapted extremophilic enzymes have been used in a wide range of industries that span all six enzyme classes. Thus, in particular, target of this review paper is to show the possibility of both high-value-low-volume (e.g., fine-chemical synthesis) and low-value-high-volume by-products (e.g., fuels) by minimizing changes to current industrial processes.

Biosynthesis of dendroketose from different carbon sources using in vitro and in vivo metabolic engineering strategies

BACKGROUND

Asymmetric aldol-type C-C bond formation with ketones used as electrophilic receptor remains a challenging reaction for aldolases as biocatalysts. To date, only one kind of dihydroxyacetone phosphate (DHAP)-dependent aldolases has been discovered and applied to synthesize branched-chain sugars directly using DHAP and dihydroxyacetone (DHA) as substrate. However, the unstable and high-cost properties of DHAP limit large-scale application. Therefore, biosynthesis of branched-chain sugar from low-cost and abundant carbon sources is essential.

RESULTS

The detailed catalytic property of l-rhamnulose-1-phosphate aldolase (RhaD) and l-fuculose-1-phosphate aldolase (FucA) from Escherichia coli in catalyzing the aldol reactions with DHA as electrophilic receptors was characterized. Furthermore, we calculated the Bürgi-Dunitz trajectory using molecular dynamics simulations, thereby revealing the original sources of the catalytic efficiency of RhaD and FucA. A multi-enzyme reaction system composed of formolase, DHA kinase, RhaD, fructose-1-phosphatase, and polyphosphate kinase was constructed to in vitro produce dendroketose, a branched-chain sugar, from one-carbon formaldehyde. The conversion rate reached 86% through employing a one-pot, two-stage reaction process. Moreover, we constructed two artificial pathways in Corynebacterium glutamicum to obtain this product in vivo starting from glucose or glycerol. Fermentation with glycerol as feedstock produced 6.4 g/L dendroketose with a yield of 0.45 mol/mol glycerol, representing 90% of the maximum theoretical value. Additionally, the dendroketose production reached 36.3 g/L with a yield of 0.46 mol/mol glucose when glucose served as the sole carbon resource.

CONCLUSIONS

The detailed enzyme kinetics data of the two DHAP-dependent aldolases with DHA as electrophilic receptors were presented in this study. In addition, insights into this catalytic property were given via in silico simulations. Moreover, the cost-effective synthesis of dendroketose starting from one-, three-, and six-carbon resources was achieved through in vivo and in vitro metabolic engineering strategies. This rare branched-chain ketohexose may serve as precursor to prepare 4-hydroxymethylfurfural and branched-chain alkanes using chemical method.

Recent advances in the synthesis of rare sugars using DHAP-dependent aldolases

The occurrence rates of non-communicable diseases like obesity, diabetes and hyperlipidemia have increased remarkably due to excessive consumption of a high-energy diet. Rare sugars therefore have become increasingly attractive owing to their unique nutritional properties. In the past two decades, various rare sugars have been successfully prepared guided by the "Izumoring strategy". As a valuable complement to the Izumoring approach, the controllable dihydroxyacetone phosphate (DHAP)-dependent aldolases have generally predictable regio- and stereoselectivity, which makes them powerful tools in C-C bond construction and rare sugar production. However, the main disadvantage for this group of aldolases is their strict substrate specificity toward the donor molecule DHAP, a very expensive and relatively unstable compound. Among the current methods involving DHAP, the one that couples DHAP production from inexpensive starting materials (for instance, glycerol, DL-glycerol 3-phosphate, dihydroxyacetone, and glucose) with aldol condensation appears to be the most promising. This review thus focuses on recent advances in the application of L-rhamnulose-1-phosphate aldolase (RhaD), L-fuculose-1-phosphate aldolase (FucA), and D-fructose-1,6-bisphosphate aldolase (FruA) for rare sugar synthesis in vitro and in vivo, while illustrating strategies for supplying DHAP in efficient and economical ways.

Thermophiles in the genomic era: Biodiversity, science, and applications

Thermophiles and hyperthermophiles are present in various regions of the Earth, including volcanic environments, hot springs, mud pots, fumaroles, geysers, coastal thermal springs, and even deep-sea hydrothermal vents. They are also found in man-made environments, such as heated compost facilities, reactors, and spray dryers. Thermophiles, hyperthermophiles, and their bioproducts facilitate various industrial, agricultural, and medicinal applications and offer potential solutions to environmental damages and the demand for biofuels. Intensified efforts to sequence the entire genome of hyperthermophiles and thermophiles are increasing rapidly, as evidenced by the fact that over 120 complete genome sequences of the hyperthermophiles Aquificae, Thermotogae, Crenarchaeota, and Euryarchaeota are now available. In this review, we summarise the major current applications of thermophiles and thermozymes. In addition, emphasis is placed on recent progress in understanding the biodiversity, genomes, transcriptomes, metagenomes, and single-cell sequencing of thermophiles in the genomic era.