Isomerases and epimerases for biotransformation of pentoses

Characterization of a novel recombinant D-mannose isomerase from Bifidobacterium bifidum and its catalytic mechanism

Due to the increasing demand for health-conscious and environmentally friendly products, D-mannose has gained significant attention as a natural, low-calorie sweetener. The use of D-mannose isomerases (D-MIases) for D-mannose production has emerged as a prominent area of research, offering superior advantages compared with conventional methods such as plant extraction and chemical synthesis. In this study, a gene encoding D-MIase was cloned from Bifidobacterium and expressed in E. coli BL21 (DE3). The heterologously expressed enzyme, Bifi-mannose, formed a trimer with a molecular weight of 146.3 kDa and a melting temperature (Tm) of 63.39 ± 1.3 °C. Bifi-mannose exhibited optimal catalytic activity at pH 7.5 and 55 °C, and retained more than 80% of its activity after a 3-hour incubation at 55 °C, demonstrating excellent thermal stability. The Km, Vmax, and kcat/Km values of Bifi-mannose for D-fructose isomerization were determined as 538.7 ± 62.5 mM, 11.7 ± 0.9 μmol·mg1·s1, and 1.02 ± 0.3 mM1·s1, respectively. Notably, under optimized conditions, catalytic yields of 29.4, 87.1, and 148.5 mg·mL1 were achieved when using 100, 300, and 500 mg·mL1 of D-fructose as substrates, resulting in a high conversion rate (29%). Furthermore, kinetic parameters and molecular docking studies revealed that His387 residue primarily participates in the opening of the pyranose ring, while His253 acts as a basic catalyst in the isomerization process.

Application of circular dichroism-based assays to racemases and epimerases: Recognition and catalysis of reactions of chiral substrates by mandelate racemase

Racemases and epimerases have attracted much interest because of their astonishing ability to catalyze the rapid α-deprotonation of carbon acid substrates with high pK_a values (∼13-30) leading to the formation of d-amino acids or various carbohydrate diastereomers that serve important roles in both normal physiology and pathology. Enzymatic assays to measure the initial rates of reactions catalyzed by these enzymes are discussed using mandelate racemase (MR) as an example. For MR, a convenient, rapid, and versatile circular dichroism (CD)-based assay has been used to determine the kinetic parameters accompanying the MR-catalyzed racemization of mandelate and alternative substrates. This direct, continuous assay permits real time monitoring of reaction progress, the rapid determination of initial velocities, and immediate recognition of anomalous behaviors. MR recognizes chiral substrates primarily through interactions of the phenyl ring of (R)- or (S)-mandelate with the hydrophobic R- or S-pocket at the active site, respectively. During catalysis, the carboxylate and α-hydroxyl groups of the substrate remain fixed in place through interactions with the Mg²⁺ ion and multiple H-bonding interactions, while the phenyl ring moves between the R- and S-pockets. The minimal requirements for the substrate appear to be the presence of a glycolate or glycolamide moiety, and a hydrophobic group of limited size that can stabilize the carbanionic intermediate through resonance or strong inductive effects. Similar CD-based assays may be applied to determine the activity of other racemases or epimerases with proper consideration of the molar ellipticity, wavelength, overall absorbance of the sample, and the light pathlength.

The Mastigamoeba balamuthi Genome and the Nature of the Free-Living Ancestor of Entamoeba

The transition of free-living organisms to parasitic organisms is a mysterious process that occurs in all major eukaryotic lineages. Parasites display seemingly unique features associated with their pathogenicity; however, it is important to distinguish ancestral preconditions to parasitism from truly new parasite-specific functions. Here, we sequenced the genome and transcriptome of anaerobic free-living Mastigamoeba balamuthi and performed phylogenomic analysis of four related members of the Archamoebae, including Entamoeba histolytica, an important intestinal pathogen of humans. We aimed to trace gene histories throughout the adaptation of the aerobic ancestor of Archamoebae to anaerobiosis and throughout the transition from a free-living to a parasitic lifestyle. These events were associated with massive gene losses that, in parasitic lineages, resulted in a reduction in structural features, complete losses of some metabolic pathways, and a reduction in metabolic complexity. By reconstructing the features of the common ancestor of Archamoebae, we estimated preconditions for the evolution of parasitism in this lineage. The ancestor could apparently form chitinous cysts, possessed proteolytic enzyme machinery, compartmentalized the sulfate activation pathway in mitochondrion-related organelles, and possessed the components for anaerobic energy metabolism. After the split of Entamoebidae, this lineage gained genes encoding surface membrane proteins that are involved in host–parasite interactions. In contrast, gene gains identified in the M. balamuthi lineage were predominantly associated with polysaccharide catabolic processes. A phylogenetic analysis of acquired genes suggested an essential role of lateral gene transfer in parasite evolution (Entamoeba) and in adaptation to anaerobic aquatic sediments (Mastigamoeba).

Expanding the Enzyme Repertoire for Sugar Nucleotide Epimerization: The CDP-Tyvelose 2-Epimerase from Thermodesulfatator atlanticus for Glucose/Mannose Interconversion

Epimerization of sugar nucleotides is central to the structural diversification of monosaccharide building blocks for cellular biosynthesis. Epimerase applicability to carbohydrate synthesis can be limited, however, by the high degree of substrate specificity exhibited by most sugar nucleotide epimerases. Here, we discovered a promiscuous type of CDP-tyvelose 2-epimerase (TyvE)-like enzyme that promotes C2-epimerization in all nucleotide (CDP, UDP, GDP, ADP, TDP)-activated forms of d-glucose. This new epimerase, originating from Thermodesulfatator atlanticus, is a functional homodimer that contains one tightly bound NAD⁺/subunit and shows optimum activity at 70°C and pH 9.5. The enzyme exhibits a k _cat with CDP-dglucose of ∼1.0 min^-1 (pH 7.5, 60°C). To characterize the epimerase kinetically and probe its substrate specificity, we developed chemo-enzymatic syntheses for CDP-dmannose, CDP-6-deoxy-dglucose, CDP-3-deoxy-dglucose and CDP-6-deoxy-dxylo-hexopyranos-4-ulose. Attempts to obtain CDP-dparatose and CDP-dtyvelose were not successful. Using high-resolution carbohydrate analytics and in situ NMR to monitor the enzymatic conversions (60°C, pH 7.5), we show that the CDP-dmannose/CDP-dglucose ratio at equilibrium is 0.67 (± 0.1), determined from the kinetic Haldane relationship and directly from the reaction. We further show that deoxygenation at sugar C6 enhances the enzyme activity 5-fold compared to CDP-dglucose whereas deoxygenation at C3 renders the substrate inactive. Phylogenetic analysis places the T. atlanticus epimerase into a distinct subgroup within the sugar nucleotide epimerase family of SDR (short-chain dehydrogenases/reductases), for which the current study now provides the functional context. Collectively, our results expand an emerging toolbox of epimerase-catalyzed reactions for sugar nucleotide synthesis.IMPORTANCE Epimerases of the sugar nucleotide-modifying class of enzymes have attracted considerable interest in carbohydrate (bio)chemistry, for the mechanistic challenges and the opportunities for synthesis involved in the reactions catalyzed. Discovery of new epimerases with expanded scope of sugar nucleotide substrates used is important to promote the mechanistic inquiry and can facilitate the development of new enzyme applications. Here, a CDP-tyvelose 2-epimerase-like enzyme from Thermodesulfatator atlanticus is shown to catalyze sugar C2 epimerization in CDP-glucose and other nucleotide-activated forms of dglucose. The reactions are new to nature in the context of enzymatic sugar nucleotide modification. The current study explores the substrate scope of the discovered C2-epimerase and, based on modeling, suggests structure-function relationships that may be important for specificity and catalysis.

Engineering ribose-5-phosphate isomerase B from a central carbon metabolic enzyme to a promising sugar biocatalyst

Ribose-5-phosphate isomerase B (RpiB) was first identified in the pentose phosphate pathway responsible for the inter-conversion of ribose-5-phosphate and ribulose-5-phosphate. Though there are seldom key enzymes in central carbon metabolic system developed as useful biocatalysts, RpiB with the advantages of wide substrate scope and high stereoselectivity has become a potential biotechnological tool to fulfill the demand of rare sugars currently. In this review, the pivotal roles of RpiB in carbon metabolism are summarized, and their sequence identity and structural similarity are discussed. Substrate binding and catalytic mechanisms are illustrated to provide solid foundations for enzyme engineering. Interesting differences in origin, physiological function, structure, and catalytic mechanism between RpiB and ribose-5-phosphate isomerase A are introduced. Moreover, enzyme engineering efforts for rare sugar production are stressed, and prospects of future development are concluded briefly in the viewpoint of biocatalysis. Aided by the progresses of structural and computational biology, the application of RpiB will be promoted greatly in the preparation of valuable molecules. KEY POINTS: • Detailed illustration of RpiB's vital function in central carbon metabolism. • Potential of RpiB in sequence, substrate scope, and mechanism for application. • Enzyme engineering efforts to promote RpiB in the preparation of rare sugars.

Biochemical and structural insights into an Ochrobactrum sp. CSL1 ribose-5-phosphate isomerase A and its roles in isomerization of rare sugars

Rare sugars have received increasing attention due to their important applications as sweeteners and building blocks. The substrate specificity and catalytic properties of ribose-5-phosphate isomerase A (RpiA) in isomerization of rare sugars have not been extensively explored. In this study, an RpiA from Ochrobactrum sp. CSL1 was cloned and expressed in Escherichia coli. The biochemical and reaction features were explored and its broad substrate specificity was identified. A higher reaction rate in isomerizing l-rhamnose to l-rhamnulose by OsRpiA, compared with OsRpiB found in the same strain indicated higher efficiency in preparing rare sugars, which was verified by kinetics study. The 2.8 Å resolution structure of OsRpiA was then solved and used in subsequent molecular dynamics experiments, providing a possible explanation for its distinct substrate specificity. The present study highlighted the unique role of microbial RpiA in preparing rare sugars, and its structural information provided a reliable reference for further reaction mechanism research and enzyme engineering work.

Recent advances in properties, production, and applications of L-ribulose

Currently, due to the special functions and potential application values, rare sugars become the hot topic in carbohydrate fields. L-Ribulose, an isomer of L-ribose, is an expensive rare ketopentose. As an important precursor for other rare sugars and L-nucleoside analogue synthesis, L-ribulose attracts more and more attention in recent days. Compared with complicated chemical synthesis, the bioconversion method becomes a good alternative approach to L-ribulose production. Generally, the bioconversion of L-ribulose was linked with ribitol, L-arabinose, L-ribose, L-xylulose, and L-arabitol. Herein, an overview of recent advances in the metabolic pathway, chemical synthesis, bioproduction of L-ribulose, and the potential application of L-ribulose is reviewed in detail in this paper. KEY POINTS: 1. L-Ribulose is a rare sugar and the key precursor for L-ribose production. 2. L-Ribulose is the starting material for L-nucleoside derivative synthesis. 3. Chemical synthesis, bioproduction, and applications of L-ribulose are reviewed.

Cobalamin-Dependent Apparent Intramolecular Methyl Transfer for Biocatalytic Constitutional Isomerization of Catechol Monomethyl Ethers

Isomerization is a fundamental reaction in chemistry. However, isomerization of phenyl methyl ethers has not been described yet. Using a cobalamin-dependent methyl transferase, a reversible shuttle concept was investigated for isomerization of catechol monomethyl ethers. The methyl ether of substituted catechol derivatives was successfully transferred onto the adjacent hydroxy moiety. For instance, the cobalamin-dependent biocatalyst transformed isovanillin to its regioisomer vanillin with significant regioisomeric excess (68% vanillin). To the best of our knowledge, isomerization by methyl transfer employing a methyl transferase has not been reported before.