Novel enzymatic production of trehalose from sucrose using amylosucrase and maltooligosyltrehalose synthase-trehalohydrolase

Trehalose (α-d-glucopyranosyl α-d-glucopyranoside) is an important non-reducing disaccharide used in the food industry due to its mild sweetness (45% that of sucrose), low cariogenicity, high glass transition temperature, low hygroscopicity, and protein protection properties. In this study, we accomplished the production of trehalose from sucrose as a sole substrate using a novel dual-enzyme system, in which amylosucrase (ASase) and maltooligosyltrehalose synthase-trehalohydrolase (MTSH) fusion enzyme were employed. The biotransformation of sucrose to trehalose was confirmed by high-performance anion-exchange chromatography (HPAEC) analysis. Trehalose was successfully produced by both simultaneous and sequential methods by using ASase and MTSH. A higher trehalose production yield (3.15 ± 0.83 mM trehalose/20 mM sucrose) was observed in the sequential method than the simultaneous method (1.43 ± 0.14 mM trehalose/20 mM sucrose), indicating that the production of maltooligosaccharides from sucrose by ASase was an important step in the biosynthesis of trehalose.     

Glycogen metabolism in the genus Neisseria: synthesis from sucrose by amylosucrase

Eight strains (seven species) of Neisseria were found to possess intracellular amylosucrases capable of synthesizing glycogen directly from sucrose. All eight systems were stimulated by primer glycogen, possessed similar kinetic parameters, and were competitively inhibited to similar degrees by fructose. The enzymes bound tightly to their polysaccharide products but these complexes could be readily dissociated by polyacrylamide gel electrophoresis. Some of the enzyme-product complexes appeared to be virutally free of contaminating proteins.     

Structural insights into the assembly of human translesion polymerase complexes

In addition to DNA repair pathways, cells utilize translesion DNA synthesis (TLS) to bypass DNA lesions during replication. During TLS, Y-family DNA polymerase (Polη, Polκ, Polι and Rev1) inserts specific nucleotide opposite preferred DNA lesions, and then Polζ consisting of two subunits, Rev3 and Rev7, carries out primer extension. Here, we report the complex structures of Rev3-Rev7-Rev1^CTD and Rev3-Rev7-Rev1^CTDPolκ^RIR. These two structures demonstrate that Rev1^CTD contains separate binding sites for Pol- and Rev7. Our BIAcore experiments provide additional support for the notion that the interaction between Rev3 and Rev7 increases the affinity of Rev7 and Rev1. We also verified through FRET experiment that Rev1, Rev3, Rev7 and Polκ form a stable quaternary complex in vivo, thereby suggesting an efficient switching mechanism where the “inserter” polymerase can be immediately replaced by an “extender” polymerase within the same quaternary complex.     

Crystal structures and mutagenesis of sucrose hydrolase from Xanthomonas axonopodis pv. glycines: insight into the exclusively hydrolytic amylosucrase fold

Neisseria polysaccharea amylosucrase (NpAS), a transglucosidase of glycoside hydrolase family 13, is a hydrolase and glucosyltransferase that catalyzes the synthesis of amylose-like polymer from a sucrose substrate. Recently, an NpAS homolog from Xanthomonas axonopodis pv. glycines was identified as a member of the newly defined carbohydrate utilization locus that regulates the utilization of plant sucrose in phytopathogenic bacteria. Interestingly, this enzyme is exclusively a hydrolase and not a glucosyltransferase; it is thus known as sucrose hydrolase (SUH). Here, we elucidated the novel functional features of SUH using X-ray crystallography and site-directed mutagenesis. Four different crystal structures of SUH, including the SUH-Tris and the SUH-sucrose and SUH-glucose complexes, represent structural snapshots along the catalytic reaction coordinate. These structures show that SUH is distinctly different from NpAS in that ligand-induced conformational changes in SUH cause the formation of a pocket-shaped active site and in that SUH lacks the three arginine residues found in the NpAS active site that appear to be crucial for NpAS glucosyltransferase activity. Mutation of SUH to insert these arginines failed to confer glucosyltransferase activity, providing evidence that its enzymatic activity is limited to sucrose hydrolysis by its pocket-shaped active site and the identity of residues in the vicinity of the active site.     

Structural investigation of the thermostability and product specificity of amylosucrase from the bacterium Deinococcus geothermalis

Amylosucrases are sucrose-utilizing α-transglucosidases that naturally catalyze the synthesis of α-glucans, linked exclusively through α1,4-linkages. Side products and in particular sucrose isomers such as turanose and trehalulose are also produced by these enzymes. Here, we report the first structural and biophysical characterization of the most thermostable amylosucrase identified so far, the amylosucrase from Deinoccocus geothermalis (DgAS). The three-dimensional structure revealed a homodimeric quaternary organization, never reported before for other amylosucrases. A sequence signature of dimerization was identified from the analysis of the dimer interface and sequence alignments. By rigidifying the DgAS structure, the quaternary organization is likely to participate in the enhanced thermal stability of the protein. Amylosucrase specificity with respect to sucrose isomer formation (turanose or trehalulose) was also investigated. We report the first structures of the amylosucrases from Deinococcus geothermalis and Neisseria polysaccharea in complex with turanose. In the amylosucrase from N. polysaccharea (NpAS), key residues were found to force the fructosyl moiety to bind in an open state with the O3' ideally positioned to explain the preferential formation of turanose by NpAS. Such residues are either not present or not similarly placed in DgAS. As a consequence, DgAS binds the furanoid tautomers of fructose through a weak network of interactions to enable turanose formation. Such topology at subsite +1 is likely favoring other possible fructose binding modes in agreement with the higher amount of trehalulose formed by DgAS. Our findings help to understand the inter-relationships between amylosucrase structure, flexibility, function, and stability and provide new insight for amylosucrase design.     

Crystal structure of the Glu328Gln mutant of Neisseria polysaccharea amylosucrase in complex with sucrose and maltoheptaose

Several enzymes acting on sucrose are found in glycoside hydrolase family 13 (the α–amylase family). They all transfer a glucosyl moiety from sucrose to an acceptor, but the products can be very different. The structure of a variant of one of these, the Glu328Gln mutant of Neisseria polysaccharea amylosucrase, has been determined in a ternary complex with sucrose and an oligosaccharide to 2.16 Å resolution using x-ray crystallography. Sucrose selectively binds in the active site and the oligosaccharide only binds at surface sites. When this structure is compared to structures of other enzymes acting on sucrose from glycoside hydrolase family 13, it is found that the active site residues are very similar around the glucose part of sucrose while much variation is seen around the fructose moiety.     

Structural basis for the anticoagulant activity of heparin. 2. Relationship of anticoagulant activity to the thermodynamics and fluorescence fading kinetics of acridine orange-heparin complexes.

Complexing heparin or dermatan sulfate with the fluorescent probe acridine orange provides a means of studying electrostatic as well as static and dynamic conformational aspects of these glycosaminoglycans via the thermodynamic and photochemical (fluorescence fading) properties of these complexes. The cooperative binding constants (Kq), fluorescence fading rate parameters (r'), and anticoagulant activities of heparins fractionated according to anionic density all showed qualitatively the same dependence upon anionic density. When Kq and r' were plotted against anticoagulant activity, empirical relationships were observed. Interestingly, the corresponding values for unfractionated dermatan sulfate fell on the lines defined by the heparin fractions. Temperature-dependence, studies demonstrated that differences in fading rate observed for heparins of different anionic densities are entropic in origin and reflect differences in the ability to assume a special configuration. Differences in activation entropy for fluorescence fading can be empirically correlated with anticoagulant activity. The latter correlation suggests a physical similarity in the roles played by anionic density in both fluorescence fading and anticoagulant activity.     

Cardiolipin binding in bacterial respiratory complexes: Structural and functional implications

The structural and functional integrity of biological membranes is vital to life. The interplay of lipids and membrane proteins is crucial for numerous fundamental processes ranging from respiration, photosynthesis, signal transduction, solute transport to motility. Evidence is accumulating that specific lipids play important roles in membrane proteins, but how specific lipids interact with and enable membrane proteins to achieve their full functionality remains unclear. X-ray structures of membrane proteins have revealed tight and specific binding of lipids. For instance, cardiolipin, an anionic phospholipid, has been found to be associated to a number of eukaryotic and prokaryotic respiratory complexes. Moreover, polar and septal accumulation of cardiolipin in a number of prokaryotes may ensure proper spatial segregation and/or activity of proteins. In this review, we describe current knowledge of the functions associated with cardiolipin binding to respiratory complexes in prokaryotes as a frame to discuss how specific lipid binding may tune their reactivity towards quinone and participate to supercomplex formation of both aerobic and anaerobic respiratory chains. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).     

Increased amylosucrase activity and specificity, and identification of regions important for activity, specificity and stability through molecular evolution

Amylosucrase is a transglycosidase which belongs to family 13 of the glycoside hydrolases and transglycosidases, and catalyses the formation of amylose from sucrose. Its potential use as an industrial tool for the synthesis or modification of polysaccharides is hampered by its low catalytic efficiency on sucrose alone, its low stability and the catalysis of side reactions resulting in sucrose isomer formation. Therefore, combinatorial engineering of the enzyme through random mutagenesis, gene shuffling and selective screening (directed evolution) was applied, in order to generate more efficient variants of the enzyme. This resulted in isolation of the most active amylosucrase (Asn387Asp) characterized to date, with a 60% increase in activity and a highly efficient polymerase (Glu227Gly) that produces a longer polymer than the wild-type enzyme. Furthermore, judged from the screening results, several variants are expected to be improved concerning activity and/or thermostability. Most of the amino acid substitutions observed in the totality of these improved variants are clustered around specific regions. The secondary sucrose-binding site and beta strand 7, connected to the important Asp393 residue, are found to be important for amylosucrase activity, whereas a specific loop in the B-domain is involved in amylosucrase specificity and stability.     

Structural requirements for duodenal permeability of heparin-diamine complexes.

We have compared the physico-chemical behaviors alone and in the presence of a synthetic bilayer membrane, in aqueous solution and the bioavailability after intraduodenal administration to rabbits, of the two heparin diamine salts ITF-300 and ITF-331 with those of the heparin-amine salt ITF-1175. The three salts have similar structures but different characteristics of compounds tend to form aggregates in solution, but at different critical concentrations. The compounds induce fusion of single-walled vesicles of a synthetic peptide lipid into multi-walled lamellae. The minimal concentrations of the compounds required for the formation of such lamellae differ. This behavior in solution explains the differences in absorption in the animal model. This makes it possible to correlate enhanced heparin bioavailability with the structural nature of the diamine counter-ions used to prepare heparin salts.     

The implications of using mutagenic primers in combination with Taq polymerase having proofreading activity.

Polymerases with proofreading activity provide high fidelity PCR amplifications. In this study we examined the consequences of using a Taq polymerase with proofreading activity, such as Optimase Taq polymerase, in combination with 4 different mutagenic reverse primers for the amplification of a 345-bp FII PCR product. The amplifications were performed with Optimase Taq polymerase (Transgenomic), and Taq DNA polymerase-recombinant (Invitrogen), without proofreading activity. Mutation screening was carried out by DHPLC and restriction fragment analysis. The usage of Optimase Taq polymerase results in complete reversion of the first and second mutated nucleotide introduced at the 3' end of the mutagenic reverse primer. It also partially reverses the missense nucleotide introduced in the third position of the mutagenic primer and leads to misleading DHPLC and restriction fragment analysis patterns. Nevertheless it cannot perform such an activity when an abnormal nucleotide is introduced in the fourth position.     

Structural Characterization of an Oligosaccharide Made by Neisseria sicca

Neisseria sicca 4320 expresses two carbohydrate-containing components with sodium dodecyl sulfate-polyacrylamide gel electrophoresis mobilities that resemble those of lipooligosaccharide and lipopolysaccharide. Using matrix-assisted laser desorption ionization—time of flight and electrospray ionization mass spectrometry, we characterized a disaccharide carbohydrate repeating unit expressed by this strain. Gas chromatography identified the sugars composing the unit as rhamnose and N-acetyl-d-glucosamine. Glycosidase digestion confirmed the identity of the nonreducing terminal sugar of the disaccharide and established its β-anomeric configuration. Mass spectrometry analysis and lectin binding were used to verify the linkages within the disaccharide repeat. The results revealed that the disaccharide repeat is [-4) β-l-rhamnose (1-3) β-N-acetyl-d-glucosamine (1-] with an N-acetyl-d-glucosamine nonreducing terminus. This work is the first structural characterization of a molecule that possesses rhamnose in the genus Neisseria.Commensal Neisseria strains colonize the human respiratory tract. Frequent interspecific genetic exchange between commensal Neisseria strains and the pathogens Neisseria meningitidis and Neisseria gonorrhoeae occurs (13). It is thought the commensal organisms serve as reservoirs for antibiotic resistance genes (20). The similarity between the gene complements of the commensals and pathogens suggests that the virulence of the pathogenic Neisseria spp. may not result from the genes that they possess but rather from a “genetic personality” which is a result of combinations of these genes, sequence variations that alter the function of gene products, the presence of genes for which a virulence phenotype has not yet been identified, and/or differences in the regulation of genes (25).Lipooligosaccharide (LOS) is an important neisserial virulence determinant consisting of an oligosaccharide (OS) component attached to lipid A via 3-deoxy-2-keto-d-manno-octulosonic acid (Kdo). The structures of a sufficient number of neisserial LOS molecules have been determined to form a coherent yet incomplete picture of the structural diversity of their LOS (Fig. ​(Fig.1).1). The different LOS structures have a conserved core with two Kdo molecules, two heptose (Hep) molecules, and one N-acetylhexosamine (HexNAc) molecule and vary in the composition and size of the OS attached to one Hep (HepI; α-chain variation) and in the attachment of an OS or phosphoethanolamine to the other Hep (HepII; β-chain variation) or by addition of a galactose to the N-acetylglucosamine (GlcNAc) found on HepII (γ-chain extension) (3, 6, 7, 9-11). This structural motif is different from that of lipopolysaccharide (LPS) of other types of bacteria, which contains an O antigen composed of a repeating sugar polymer, typically consisting of four to seven sugars (26). No one has reported the presence of an O antigen in pathogenic strains of Neisseria.Open in a separate windowFIG. 1.Structrual diversity of the sugar backbone of LOS isolated from pathogenic Neisseria spp. The various LOS structures that have been identified in N. gonorrhoeae or N. meningitidis are shown.A few studies have analyzed the structure of LOS produced by commensal Neisseria strains, and the data indicate that the LOS heterogeneity is greater than the heterogeneity in the gonococcus and meningococcus (21). Commensal Neisseria strains are capable of producing LOS molecules that are structurally different from the molecules in the known Neisseria repertoire in that they fail to bind monoclonal antibodies specific for LOS epitopes characteristic of the gonococcus and meningococcus (1). They also can lack some of the LOS biosynthesis genes found in N. meningitidis and N. gonorrhoeae (1, 33). These findings suggest that alternative LOS structures are present in commensal Neisseria strains. Sandlin and Stein (21) identified a strain of Neisseria sicca that expressed an unusual glycolipid that appeared based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to be analogous to LPS made by enteric bacteria. A poly-N-acetyllactosamine repeat was seen in some strains of the gonococcus (10), and we postulated that the repeating carbohydrate found in N. sicca could be a variant of this structure.A few studies have shown that both Neisseria and Haemophilus strains have the ability to extend their LOS by adding lactosamine repeats to form polylactosamine; these strains seem to possess increased virulence (4, 10, 22). When N. gonorrhoeae MS11mkC was used to inoculate healthy male volunteers, 100% of the volunteers developed urethritis, compared to an infectivity rate of 40% for strains expressing a truncated LOS (23). Fresh isolates from the volunteers who had contracted urethritis produced LOS molecules with N-acetyllactosamine repeats, whereas the isolates in the original inoculum expressed paraglobsyl and gangliosyl LOS (23, 24). However, the number of disaccharide repeats was limited to two or three (10). Analogous results were generated when the infectivity of Haemophilus ducreyi, a causative agent of genital ulcers, was studied; infectious strains made LOS with a few lactosamine repeats (4, 22).N. sicca is normally not pathogenic in healthy adults. A previous study indicated that N. sicca 4320 expressed a molecule with a repeating carbohydrate structure that appeared to be similar to the O-antigen structure (21). Because such molecules have not been found in pathogenic Neisseria strains, we analyzed the structure of the repeating carbohydrate unit and showed that it is a repeating disaccharide that is novel to the genus Neisseria.     

A DNA polymerase from Ustilago maydis. 1. Purification and properties of the polymerase activity.

A DNA polymerase from Ustilago maydis has been purified to apparent homogeneity. The native enzyme possesses a subunit structure consisting of 50000 and 55000-dalton monomers. The apparent sedimentation coefficient of the polymerase activity in the absence of salt is 8.4 S (Mr=180000-200000), that in its presence (0.6 M NaCl or 0.12 M KCl) being 6.3 S (Mr=80000-100000). Low concentrations of EDTA also converted the 8.4-S to a 6.3-S form, whereas magnesium ions catalysed the reverse association. The enzyme has an absolute requirement for both a DNA or RNA template and a DNA primer. For homopolymer templates the primer requirement was satisified by a short complementary oligodeoxynucleotide, but oligoribonucleotides were extremely inefficient primers. With the template-primer poly(dA) X (dT)12, the enzyme added an average of 50 dTMP nucleotides on to each primer molecule, whereas with poly(rA) X (dT)12, this figure was 300. The enzyme also possesses an associated deoxyribonuclease activity. No other DNA polymerase activity was detected in cell-free extracts of U. maydis.     

Structural rearrangements of sucrose phosphorylase from Bifidobacterium adolescentis during sucrose conversion

The reaction mechanism of sucrose phosphorylase from Bifidobacterium adolescentis (BiSP) was studied by site-directed mutagenesis and x-ray crystallography. An inactive mutant of BiSP (E232Q) was co-crystallized with sucrose. The structure revealed a substrate-binding mode comparable with that seen in other related sucrose-acting enzymes. Wild-type BiSP was also crystallized in the presence of sucrose. In the dimeric structure, a covalent glucosyl intermediate was formed in one molecule of the BiSP dimer, and after hydrolysis of the glucosyl intermediate, a beta-D-glucose product complex was formed in the other molecule. Although the overall structure of the BiSP-glucosyl intermediate complex is similar to that of the BiSP(E232Q)-sucrose complex, the glucose complex discloses major differences in loop conformations. Two loops (residues 336-344 and 132-137) in the proximity of the active site move up to 16 and 4 A, respectively. On the basis of these findings, we have suggested a reaction cycle that takes into account the large movements in the active-site entrance loops.