Characterization of Pseudomonas isoamylase by its actions on amylopectin and glycogen: comparison with Aerobacter pullulanase

In situ mass spectrometry imaging reveals heterogeneous glycogen stores in human normal and cancerous tissues

Glycogen dysregulation is a hallmark of aging, and aberrant glycogen drives metabolic reprogramming and pathogenesis in multiple diseases. However, glycogen heterogeneity in healthy and diseased tissues remains largely unknown. Herein, we describe a method to define spatial glycogen architecture in mouse and human tissues using matrix-assisted laser desorption/ionization mass spectrometry imaging. This assay provides robust and sensitive spatial glycogen quantification and architecture characterization in the brain, liver, kidney, testis, lung, bladder, and even the bone. Armed with this tool, we interrogated glycogen spatial distribution and architecture in different types of human cancers. We demonstrate that glycogen stores and architecture are heterogeneous among diseases. Additionally, we observe unique hyperphosphorylated glycogen accumulation in Ewing sarcoma, a pediatric bone cancer. Using preclinical models, we correct glycogen hyperphosphorylation in Ewing sarcoma through genetic and pharmacological interventions that ablate in vivo tumor growth, demonstrating the clinical therapeutic potential of targeting glycogen in Ewing sarcoma.

Microbial starch debranching enzymes: Developments and applications

Starch debranching enzymes (SDBEs) hydrolyze the α-1,6 glycosidic bonds in polysaccharides such as starch, amylopectin, pullulan and glycogen. SDBEs are also important enzymes for the preparation of sugar syrup, resistant starch and cyclodextrin. As the synergistic catalysis of SDBEs and other starch-acting hydrolases can effectively improve the raw material utilization and production efficiency during starch processing steps such as saccharification and modification, they have attracted substantial research interest in the past decades. The substrate specificities of the two major members of SDBEs, pullulanases and isoamylases, are quite different. Pullulanases generally require at least two α-1,4 linked glucose units existing on both sugar chains linked by the α-1,6 bond, while isoamylases require at least three units of α-1,4 linked glucose. SDBEs mainly belong to glycoside hydrolase (GH) family 13 and 57. Except for GH57 type II pullulanse, GH13 pullulanases and isoamylases share plenty of similarities in sequence and structure of the core catalytic domains. However, the N-terminal domains, which might be one of the determinants contributing to the substrate binding of SDBEs, are distinct in different enzymes. In order to overcome the current defects of SDBEs in catalytic efficiency, thermostability and expression level, great efforts have been made to develop effective enzyme engineering and fermentation strategies. Herein, the diverse biochemical properties and distinct features in the sequence and structure of pullulanase and isoamylase from different sources are summarized. Up-to-date developments in the enzyme engineering, heterologous production and industrial applications of SDBEs is also reviewed. Finally, research perspective which could help understanding and broadening the applications of SDBEs are provided.

Starch nanoparticles prepared by enzymatic hydrolysis and self-assembly of short-chain glucans

Enzymatic hydrolysis and self-assembly are considered promising methods for preparation of starch nanoparticles (SNPs) because they are environmentally friendly, and time- and cost-effective. These methods are based on the self-assembly of short-chain glucans released from the α-1,6 bonds in amylopectin. Since their discovery, many studies have described the structural and physicochemical properties of self-assembled SNPs. Self-assembled SNPs can be prepared by two methods: using only the soluble portion containing the short-chain glucans, or using the whole hydrolyzate including both insoluble and soluble fractions. Although the structural and physical properties of self-assembled SNPs can be attributed to the composition of the hydrolyzates that participate in self-assembly, this aspect has not yet been discussed. This review focuses on SNPs self-assembled with only soluble short-chain glucans and addresses their characteristics, including formation mechanisms as well as structural and physicochemical properties, compared with SNPs prepared with total hydrolyzates.

Identification of Thermotoga maritima MSB8 GH57 α-amylase AmyC as a glycogen-branching enzyme with high hydrolytic activity

AmyC, a glycoside hydrolase family 57 (GH57) enzyme of Thermotoga maritima MSB8, has previously been identified as an intracellular α-amylase playing a role in either maltodextrin utilization or storage polysaccharide metabolism. However, the α-amylase specificity of AmyC is questionable as extensive phylogenetic analysis of GH57 and tertiary structural comparison suggest that AmyC could actually be a glycogen-branching enzyme (GBE), a key enzyme in the biosynthesis of glycogen. This communication presents phylogenetic and biochemical evidence that AmyC is a GBE with a relatively high hydrolytic (α-amylase) activity (up to 30% of the total activity), creating a branched α-glucan with 8.5% α-1,6-glycosidic bonds. The high hydrolytic activity is explained by the fact that AmyC has a considerably shorter catalytic loop (residues 213-220) not reaching the acceptor side. Secondly, in AmyC, the tryptophan residue (W 246) near the active site has its side chain buried in the protein interior, while the side chain is at the surface in Tk1436 and Tt1467 GBEs. The putative GBEs from three other Thermotogaceae, with very high sequence similarities to AmyC, were found to have the same structural elements as AmyC, suggesting that GH57 GBEs with relatively high hydrolytic activity may be widespread in nature.

Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin

Crystal structures of Klebsiella pneumoniae pullulanase (KPP) in complex with α-cyclodextrin (α-CD), β-cyclodextrin (β-CD) and γ-cyclodextrin (γ-CD) were refined at around 1.98–2.59 Å resolution from data collected at SPring-8. In the structures of the complexes obtained with 1 mM α-CD or γ-CD, one molecule of CD was found at carbohydrate-binding module 41 only (CBM41). In the structures of the complexes obtained with 1 mM β-CD or with 10 mM α-CD or γ-CD, two molecules of CD were found at CBM41 and in the active-site cleft, where the hydrophobic residue of Phe746 occupies the inside cavity of the CD rings. In contrast to α-CD and γ-CD, one β-CD molecule was found at the active site only in the presence of 0.1 mM β-CD. These results were coincident with the solution experiments, which showed that β-CD inhibits this enzyme more than a thousand times more potently than α-CD and γ-CD. The strong inhibition of β-CD is caused by the optimized interaction between β-CD and the side chain of Phe746. The increased K i values of the F746A mutant for β-CD supported the importance of Phe746 in the strong interaction of pullulanase with β-CD.

Understanding Starch Structure: Recent Progress

Starch is a major food supply for humanity. It is produced in seeds, rhizomes, roots and tubers in the form of semi-crystalline granules with unique properties for each plant. Though the size and morphology of the granules is specific for each plant species, their internal structures have remarkably similar architecture, consisting of growth rings, blocklets, and crystalline and amorphous lamellae. The basic components of starch granules are two polyglucans, namely amylose and amylopectin. The molecular structure of amylose is comparatively simple as it consists of glucose residues connected through α-(1,4)-linkages to long chains with a few α-(1,6)-branches. Amylopectin, which is the major component, has the same basic structure, but it has considerably shorter chains and a lot of α-(1,6)-branches. This results in a very complex, three-dimensional structure, the nature of which remains uncertain. Several models of the amylopectin structure have been suggested through the years, and in this review two models are described, namely the “cluster model” and the “building block backbone model”. The structure of the starch granules is discussed in light of both models.

Qualitative and Quantitative Analyses of Glycogen in Human Milk

Identification as well as a detailed analysis of glycogen in human milk has not been shown yet. The present study confirmed that glycogen is contained in human milk by qualitative and quantitative analyses. High-performance anion exchange chromatography (HPAEC) and high-performance size exclusion chromatography with a multiangle laser light scattering detector (HPSEC-MALLS) were used for qualitative analysis of glycogen in human milk. Quantitative analysis was carried out by using samples obtained from the individual milks. The result revealed that the concentration of human milk glycogen varied depending on the mother's condition-such as the period postpartum and inflammation. The amounts of glycogen in human milk collected at 0 and 1-2 months postpartum were higher than in milk collected at 3-14 months postpartum. In the milk from mothers with severe mastitis, the concentration of glycogen was about 40 times higher than that in normal milk.

Underpinning Starch Biology with in vitro Studies on Carbohydrate-Active Enzymes and Biosynthetic Glycomaterials

Starch makes up more than half of the calories in the human diet and is also a valuable bulk commodity that is used across the food, brewing and distilling, medicines and renewable materials sectors. Despite its importance, our understanding of how plants make starch, and what controls the deposition of this insoluble, polymeric, liquid crystalline material, remains rather limited. Advances are hampered by the challenges inherent in analyzing enzymes that operate across the solid-liquid interface. Glyconanotechnology, in the form of glucan-coated sensor chips and metal nanoparticles, present novel opportunities to address this problem. Herein, we review recent developments aimed at the bottom-up generation and self-assembly of starch-like materials, in order to better understand which enzymes are required for starch granule biogenesis and metabolism.

Expression of the isoamylase gene of Flavobacterium odoratum KU in Escherichia coli and identification of essential residues of the enzyme by site-directed mutagenesis

The isoamylase gene from Flavobacterium odoratum KU was cloned into and expressed in Escherichia coli JM109. The promoter of the gene was successful in E. coli, and the enzyme produced was excreted into the culture medium, depending on the amount of the enzyme expressed. The enzyme found in the culture medium showed almost the same M(r), heat-inactivating constant, and N-terminal sequence as those of the enzyme accumulated in the periplasmic space. This result indicated that the enzyme accumulated in an active form at the periplasm was transported out of the cell. The primary sequence of the enzyme, which was deduced from its nucleotide sequence, showed that the mature enzyme consisted of 741 amino acid residues. By changing five possible residues to Ala independently, it was found that Asp-374, Glu-422, and Asp-497 were essential. The sequences around those residues were highly conserved in isoamylases of different origins and the glycogen operon protein X, GlgX. The comparison of the distance between these essential residues with those of various amylases suggested that the bacterial and plant isoamylase but not GlgX had a longer fourth loop than the other amylases. This longer fourth loop had a possible role in accommodating the long branched chains of native glycogens and starches.

Synthesis of branched cyclomalto-oligosaccharides using Pseudomonas isoamylase

Branched cyclomalto-oligosaccharides (cyclodextrins) were synthesised from cyclomalto-oligosaccharides and maltose or maltotriose through the reverse action of Pseudomonas isoamylase. The reaction rate was greater with maltotriose than with maltose, and with increasing size of the cyclomalto-oligosaccharide (cG6 less than cG7 less than cG8). Maltotriose is effective as both a side-chain donor and acceptor, and three isomers of 6-O-alpha-maltotriosylmaltotriose (branched G6) were formed through mutual condensation, but maltose was effective only as a side-chain donor. Each branched cyclomalto-oligosaccharide and G6 was purified by liquid chromatography, and their structures were determined by chemical, enzymic, and 13C-n.m.r. spectroscopic analyses.

Molecular weight of the undegraded polypeptide chain of Pseudomonas amyloderamosa isoamylase

Crystalline isoamylase of Pseudomonas amyloderamosa was found to be contaminated with a trace of proteolytic enzyme. This contaminant digested the isoamylase under neutral or alkaline conditions, especially in the presence of sodium dodecyl sulfate (SDS). A reliable molecular weight of the enzyme was obtained by SDS-polyacrylamide gel electrophoresis and by gel filtration on Sepharose-6B in 6 M guanidine-hydrochloride after heat inactivation of the contaminant. The molecular weight of the undergraded polypeptide chain of the isoamylase was about 90 000. The lower molecular weight and the subunit structure of the enzyme reported previously are incorrect.

Multimolecular substrate reactions catalyzed by caabohydrases. Aspergillus oryzae alpha-amylase degradation of maltooligosaccharides

Aspergillus oryzae alpha-amylase degrades maltooligosaccharides by other pathways besides simple glycosidic bond scission. The utilization of the alternate pathways increases with the concentration of substrate implicating a multimolecular substrate mechanism. Reducing-end labeled and uniformly labeled maltooligosaccharides were used to elucidate these alternate degradation mechanisms. Condensation followed by hydrolysis is not a significant pathway. Transglycosylation is concluded to occur, but no single transglycosylation mechanism can account for all of the experimental data for maltotriose degradation. Rather, a combination of transglycosylations must be invoked.

Repetitive attack by Aspergillus oryzae alpha amylase

The action of Aspergillus oryzae alpha amylase on reducing-end, and uniformly radiolabeled maltotriose through maltodecaose has been studied. The enzyme is found to hydrolyze more than a single glycosidic bond during enzyme-substrate encounters. The extent of this repetitive attack is quantitated.

Structure of the polysaccharide formed by incubating glycogen with D-[14C]glucose in the presence of the glycogen debranching enzyme [amylo-(1 linked to 6)-glucosidase-4-alpha-glucanotransferase]

[14C]Glycogen has been synthetized in vitro by incubating D-[14C]glucose with rabbit-liver glycogen in the presence of a pure preparation of the glycogen debranching enzyme [amylo-(1 linked to 6)-glucosidase-4-alpha-glucanotransferase]. The course of the reaction has been monitored and 14C-products isolated after 30 min and 5 h. The distribution of D-[14C]glucose groups in the polysaccharides has been determined by debranching the molecules with a crystalline isoamylase from Pseudomonas. The quantities of unlabeled and 14C-linear unit chains containing D-[14C]glucose at their reducing ends have been determined by paper chromatography followed by enzymic degradation and analysis. In the 30-min product, between 65 and 85% of the D-[14C]glucose groups were covered by unlabeled groups because of transferase action. In the 5-h product, the extent of covering approached 100%. Extensive redistribution of unlabeled groups also was found to have occurred, even in the early stages of the reaction. It is concluded that the D-[14C]glucose incorporation assay for amylo-(1 linked to 6)-glucosidase, as ordinarily carried out, is probably not specific just for the hydrolytic action of this enzyme, but that it depends indirectly on its transferase activity as well.

Action of Pseudomonas isoamylase on various branched oligo and poly-saccharides

Pseudomonas isoamylase (EC 3.2.1.68) hydrolyzes (1 linked to 6)-alpha-D-glucosidic linkages of amylopectin, glycogen, and various branched dextrins and oligosaccharides. The detailed structural requirements for the substrate are examined qualitatively and quantitatively in this paper, in comparison with the pullulanase of Klebsiella aerogenes. As with pullulanase, Ps. isoamylase is unable to cleave D-glucosyl stubs from branched saccharides. Ps. isoamylase differs from pullulanase in the following characteristics: (1) The favored substrates for Ps. isoamylase are higher-molecular-weight polysaccharides. Most of the branched oligosaccharides examined were hydrolyzed at a lower rate, 10% or less of the rate of hydrolysis of amylopectin. (2) Maltosyl branches are hydrolyzed off by Ps. isoamylase very slowly in comparison with maltotriosyl branches. (3) Ps. isoamylase requires a minimum of three D-glucose residues in the B- or C-chain.

Purification and some properties of alkaline pullulanase from a strain of bacillus no. 202-1, an alkalophilic microorganism

Pullulanase (pullulan 6-glucanohydrolase EC 3.2.1.41) was purified about 290-fold from the culture fluid of Bacillus No. 202-1 by DEAE-cellulose adsorption, acetone fractionation, (NH4) 2SO4 precipitation and DEAE--cellulose column chromatography followed by Sephadex G-200 molecular sieve chromatography. The enzyme gave a single band of protein by disc polyacrylamide gel electrophoresis. The molecular weight was estimated as 92 000 by sodium dodecyl sulfate gel electrophoresis. The isolectric point was lower than pH 2.5. The optimum pH for enzyme action was about 8.5-9.0. The action of the enzyme on amylopectin and glycogen resulted in increase in the iodine coloration of 85% and 70%, respectively. The enzyme completely hydrolyzed 1,6-alpha-glucosidic linkages in amylopectin, glycogen and pullulan.

Formations of extracellular isoamylase and intracellular alpha-glucosidase and amylase(s) by Pseudomonas SB15 and a mutant strain

Pseudomonas SB15, which produces extracellular isoamylase, was found to produce intracellular alpha-glucosidase and amylase(s) when grown on maltose. A mutant strain (MS1) derived from it, which formed isoamylase constitutively, also produced these intracellular enzymes constitutively. The activities of the enzymes produced in the mutant strain were much greater than those induced in the parent strain.