Insights into the biosynthesis of septacidin l-heptosamine moiety unveils a VOC family sugar epimerase

l-Heptopyranoses are important components of bacterial polysaccharides and biological active secondary metabolites like septacidin (SEP), which represents a group of nucleoside antibiotics with antitumor, antifungal, and pain-relief activities. However, little is known about the formation mechanisms of those l-heptose moieties. In this study, we deciphered the biosynthetic pathway of the l,l-gluco-heptosamine moiety in SEPs by functional characterizing four genes and proposed that SepI initiates the process by oxidizing the 4'-hydroxyl of l-glycero-α-d-manno-heptose moiety of SEP-328 ( 2) to a keto group. Subsequently, SepJ (C5 epimerase) and SepA (C3 epimerase) shape the 4'-keto-l-heptopyranose moiety by sequential epimerization reactions. At the last step, an aminotransferase SepG installs the 4'-amino group of the l,l-gluco-heptosamine moiety to generate SEP-327 ( 3). An interesting phenomenon is that the SEP intermediates with 4'-keto-l-heptopyranose moieties exist as special bicyclic sugars with hemiacetal-hemiketal structures. Notably, l-pyranose is usually converted from d-pyranose by bifunctional C3/C5 epimerase. SepA is an unprecedented monofunctional l-pyranose C3 epimerase. Further in silico and experimental studies revealed that it represents an overlooked metal dependent-sugar epimerase family bearing vicinal oxygen chelate (VOC) architecture.

Characterization of a UDP-glucose 4-epimerase from Acinetobacter Baumannii / 中国药科大学学报

@#The purpose of this article is to express the UDP-glucose 4-epimerase from Acinetobacter baumannii AB0057, characterize its enzymatic properties and analyze its structure and function.The epimerase gene was constructed into pET-28a expression vector and heterologously expressed in BL21(DE3).Enzyme activity was assayed using high performance liquid chromatography.The structure and key residues were analyzed by phylogenetic analysis, sequence alignment, homology modeling and molecular docking.Results indicated that the recombinant enzyme Gne1 was expressed at a molecular weight of 38.9 kD, with an optimum temperature of 44 °C and an optimum pH of 6.0 .Michaelis-Menten parameters KM and kcat were (1.227 ± 0.082 4) mmol/L and (82.64 ± 3.562) × 10-3?min-1, respectively.This enzyme belongs to NADB_Rossmann superfamily and UDP_G4E_1_SDR_e subgroup with typical GXGXXG and YXXXK sequence motifs.The N-terminal structural domain bound to NAD, while the C-terminal structural domain bound to substrate, and the catalytic key sites were S125 and Y150.The current work verified the epimerase activity of Gne1, explained its sequence and structural features, revealed its binding mode with substrates and cofactors, and analyzed the key residues, which provides a basis for protein engineering to improve the epimerase activity and then use biological enzymatic method to synthesize rare functional sugars.

Construction and immobilization of recombinant Bacillus subtilis with D-allulose 3-epimerase / 生物工程学报

D-allulose-3-epimerase (DPEase) is the key enzyme for isomerization of D-fructose to D-allulose. In order to improve its thermal stability, short amphiphilic peptides (SAP) were fused to the N-terminal of DPEase. SDS-PAGE analysis showed that the heterologously expressed DPEase folded correctly in Bacillus subtilis, and the protein size was 33 kDa. After incubation at 40 °C for 48 h, the residual enzyme activity of SAP1-DSDPEase was 58%. To make the recombinant B. subtilis strain reusable, cells were immobilized with a composite carrier of sodium alginate (SA) and titanium dioxide (TiO2). The results showed that 2% SA, 2% CaCl2, 0.03% glutaraldehyde solution and a ratio of TiO2 to SA of 1:4 were optimal for immobilization. Under these conditions, up to 82% of the activity of immobilized cells could be retained. Compared with free cells, the optimal reaction temperature of immobilized cells remained unchanged at 80 °C but the thermal stability improved. After 10 consecutive cycles, the mechanical strength remained unchanged, while 58% of the enzyme activity could be retained, with a conversion rate of 28.8% achieved. This study demonstrated a simple approach for using SAPs to improve the thermal stability of recombinant enzymes. Moreover, addition of TiO2 into SA during immobilization was demonstrated to increase the mechanical strength and reduce cell leakage.

Molecular Cloning and Sequence Analysis of GgUGE Gene in Glycyrrhiza glabra / 中国实验方剂学杂志

Objective::To clone the cDNA sequence of UDP-glucose 4-epimerase (UGE) in Glycyrrhiza glabra and analyze its sequence, so as to explore the potential relationship between the UGE gene and the molecular regulatory mechanisms of glycyrrhizic acid biosynthesis. Method::The cDNA sequence of UGE was cloned from the root of G. glabra by reverse transcription polymerase chain reaction (RT-PCR), then sequenced and analyzed by bioinformatics software. Results::A GgUGE cDNA sequence with the full length of 1 121 bp was obtained. The open reading fame (ORF) of GgUGE was 1 053 bp, encoding 350 amino acid residues. The GgUGE cDNA sequence was submitted to GenBank, and the accession No. was MK638908. Sequence analysis showed that GgUGE was an unstable hydrophilic protein, its average relative molecular weight was 39.02 kDa, and isoelectric point was 6.13. It contained no signal peptides or transmembrane domains. Its secondary structure mainly constituted of α-helix and had a conversed domain of UDP-glucose 4-epimerase superfamily. The homologoue analysis showed that the cDNA and amino acid sequences of GgUGE had the closest evolutionary relationship to Leguminosae and relatively distant evolutionary relationship to Salicaceae. Conclusion::In this study, GgUGE cDNA sequence is successfully cloned from G. glabra for the very first time, which will provide reference for studying the function of GgUGE and explaining the molecular regulatory mechanisms of glycyrrhizic acid biosynthesis in G. glabra.

Expression optimization and molecular modification of heparin C5 epimerase / 生物工程学报

Heparin and heparan sulfate are a class of glycosaminoglycans for clinical anticoagulation. Heparosan N-sulfate-glucuronate 5-epimerase (C5, EC 5.1.3.17) is a critical modifying enzyme in the synthesis of heparin and heparan sulfate, and catalyzes the inversion of carboxyl group at position 5 on D-glucuronic acid (D-GlcA) of N-sulfoheparosan to form L-iduronic acid (L-IdoA). In this study, the heparin C5 epimerase gene Glce from zebrafish was expressed and molecularly modified in Escherichia coli. After comparing three expression vectors of pET-20b (+), pET-28a (+) and pCold Ⅲ, C5 activity reached the highest ((1 873.61±5.42) U/L) with the vector pCold Ⅲ. Then we fused the solution-promoting label SET2 at the N-terminal for increasing the soluble expression of C5. As a result, the soluble protein expression was increased by 50% compared with the control, and the enzyme activity reached (2 409±6.43) U/L. Based on this, site-directed mutations near the substrate binding pocket were performed through rational design, the optimal mutant (V153R) enzyme activity and specific enzyme activity were (5 804±5.63) U/L and (145.1±2.33) U/mg, respectively 2.41-fold and 2.28-fold of the original enzyme. Modification and expression optimization of heparin C5 epimerase has laid the foundation for heparin enzymatic catalytic biosynthesis.

Research progress of D-psicose: function and its biosynthesis / 生物工程学报

As the morbidity of metabolic syndrome like obesity and diabetes increases rapidly worldwide, the issue of nutrition (functional food) and health has drawn more attention. D-psicose, a rare natural ketohexose, has become a hot topic in functional food and health-care field because of its hypoglycemic and hypolipidemic function with good sweetness. This article mainly discusses the functional properties and biosynthesis research progress of D-psicose, together with the crystal structure of ketose-3-epimerase, to provide theoretical guidance for D-psicose-producing strain screening as well as improving the thermostability and catalytic efficiency of ketose-3-epimerase for industrial application.

Presence of bound substrate in lactate dehydrogenase from carp liver.

While attempting to purify UDP-galactose 4-epimerase from carp liver extract at pH 8.0, it was observed that the preparation even after dialysis could reduce NAD to NADH, interfering epimerase assay. The NAD reduction activity and the epimerase were co-eluted in a series of chromatographic steps. Mass spectrometric analysis of semi-purified fraction revealed that carp liver lactate dehydrogenase (LDH) contained bound lactate which was converted to pyruvate in the presence of NAD. The enzyme-bound lactate and the association with epimerase stabilized LDH from trypsin digestion and thermal inactivation at 45°C by factors of 2.7 and 4.2 respectively, as compared to substrate-free LDH. LDH and epimerase do not belong to any one pathway, but are the rate-limiting enzymes of two different pathways of carbohydrate metabolism. Typically, strongly associated enzymes work in combination, such as two enzymes of the same metabolic pathway. In that background, co-purification of LDH and epimerase as reloaded in this study was an unusual phenomenon.

Generalized epimerase deficiency galactosemia.

Galactosemia is caused by inherited deficiencies in one of three enzymes involved in the metabolism of galactose: galactose- 1-phosphate uridyltransferase (GALT), galactokinase (GALK), and uridine diphosphate galactose-4-epimerase (GALE). The rarest and most poorly understood form of galactosemia is due to epimerase deficiency. We are reporting such a rarest form of galactosemia presenting with progressively increasing cholestatic jaundice and failure to thrive at one month of age. After confirmation of decreased epimerase level in RBC hemolysate, the patient was put on galactose restricted diet and vitamins supplementation, which reversed the clinical signs as well as altered liver function. Patient is on regular follow-up and now at 15 months of age he has no marked developmental delay.

A Strategy for Bioproduction of Rare Sugars: Izumoring / 中国生物工程杂志

Rare sugars were defined as monosaccharides and their derivatives that rarely exist in nature. They played an important role in food, health, medicine and etc A strategy for bioproduction of rare sugars, namely Izumoring, was described. By the Izumoring method, all monosaccharides and polyols could be linked, using enzymatic reaction with D-tagatose 3-epimerase, aldose isomerases and polyol dehydrogenases. Izumoring for hexoses, pentoses and tetroses were designed respectively. According to this strategy, the bioproduction routes of various rare sugars, using microbial and enzymatic reactions, could be obtained. In addition, the future research tendency of biotransformation of rare sugars was put forward.

Galactosemia / 한양의대학술지

Galactosemia, a term that denotes the presence of galactose in the blood, is the name of rare inborn error of galactose metabolism due to a deficiency of the enzyme galactokinase (GALK), galactose-1-phosphate uridyltransferase (GALT) and uridine diphosphate-galactose 4-epimerase (GALE). GALT deficiency is the most common and shows the most severe clinical manifestation, including hepatomegaly, cataracts, and mental retardation. The main symptom of GALT deficiency is juvenile cataracts. GALE deficiency has two different forms; benign and severe forms. The benign form has no clinical significance, however, the severe form shows the same clinical manifestations as those of GALT deficiency.

A Case of Nonaka Myopathy Confirmed by GNE Mutation

Nonaka myopathy (NM) or distal myopathy with rimmed vacuoles (DMRV) is an autosomal recessively inherited neuromuscular disorder characterized by early adult-onset weakness of distal muscles, rimmed vacuoles in muscle biopsy, and mutations in the UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE) gene. The authors describe a patient with typical clinical features of NM confirmed by GNE mutation. Mutation analysis of the GNE gene revealed that the patient was a compound heterozygous for V572L and C13S mutations.

Nonaka Myopathy: A case report

Nonaka myopathy (NM) or distal myopathy with rimmed vacuoles was an autosomal recessive muscle disease with preferential involvement of the tibialis anterior and sparing quadriceps muscles in young adulthood. Patients with NM usually showed slightly elevated serum creatine kinase (CK) levels and characteristic rimmed vacuoles in muscle biopsy. Recently, the UDP-N-acetylglucosamine-2-epimerase/N-ace-tylmannosamine kinase (GNE) gene was identified as the identified as the causative gene for NM. Here we reported a NM patient carrying homozygous mutations (V572L) of the GNE gene. To the best of our knowledge, this was the first report of genetically confirmed NM in Korea and NM should be included in the differential diagnosis of slowly progressive weakness of distal legs.

CYTOCHEMICAL OBSERVATION OF THE EPIMERASE ACTIVITIES OF BONE MARROW STROMAL CELLS IN CULTURE / 解剖学报

Fibroblasts, reticular cells and macrophages are the important components of bone marrow hemopoietic in liquid to study whether HP-Ⅱ-E(Hydroxyproli- ne-2-epimerase, EC5, 1, 1,a) is involved in the synthesis of functional proteins of stromal cells. The femoral bone of 6 to 8 week-old 615 mice were made in suspension for cell culture in vitro. DMEM medium supplied with 25% calf serum was used After one to fifteen day's attaching incubation in stationary liquid the culture cells were stained with Giemsa, nonspecific esterase and HP-Ⅱ-E at different intervals. From the third day of the incubation, reticular cells began to develop form- ing stallate cells of the bone marrow. During an earlier time, enzymatic reaction was only observed in the nuclear membrance, but after three day's culture all the enzymatic activity in the cells increased dramatically. The enzymatic reac- tive granules were abundant in the outer cytoplasma of the stallate cells and fibroblasts and the cytoplasma of the macrophages. It was observed that hyd- roxyproline was changed by epimerase,

Uridine 5'-diphosphate glucose 4-epimerase from Ehrlich ascites carcinoma cells.

Uridine 5'-diphosphate glucose 4-epimerase (EC 5.1.3.2) from Ehrlich ascites carcinoma cells was purified to apparent homogeneity using conventional procedures and NAD-hexane-agarose affinity chromatography. The protein had a molecular weight of 96,000. The ascites enzyme had an absolute requirement for exogenously added NAD (10 μM) for stability. This appears to be a unique feature of ascites epimerase since epimerase from other mammalian sources did not exhibit such a dependence. Exogenously added NAD was also needed for catalysis with an apparent Km value of 2·5 μM. NADH was a very potent competitive inhibitor (K i = 0·11 μM with respect to NAD) of the enzyme activity at pH values close to intracellular pH. The dependence of the enzyme on NAD for stability and its inhibition by NADH may have some potential significance in tumor metabolism.