Bio characterization of purified isoamylase from Rhizopus oryzae.

Extracellular isoamylase produced by Rhizopus oryzae PR7 MTCC 9642 in in Erlenmeyer flasks was purified by ultrafiltration and by two steps of Superose 6 C-10/300GL gel chromatography. The enzyme molecule was found to be a monomer with molecular weight of 68 kDa.The purified isoamylase showed optimum activity at pH 5.5 and temperature 55 °C. The catalytic activity was found to remain stable at a broad range of pH (4-8) and could show remarkable thermo resistance specially in presence of exogenous thiols. The noteworthy enhancement of activity in presence of Mn2+ indicated its role as enzyme cofactor while thermos and chemostability in presence of exogenous thiols indicated the presence of disulfide linkage at active site of the enzyme. Both in vitro study and doking analysis indicated the highest affinity of the isoamylase of R. oryzae PR7 toward glycogen and the enzyme exhibited Km and Vmax values of 0.38 mg/mL and 6.65 mM/min/mL, respectively. Purified debranching amylolytic enzyme from R. oryzae PR7 has potential for the study of glycogen and starch structure and industrial application in combination with other amylolytic enzymes. The rapid, convenient, relatively simple purification process and other functional attributes of the enzyme made it competent to be employed for industrial utilization.

Doubling Power Output of Starch Biobattery Treated by the Most Thermostable Isoamylase from an Archaeon Sulfolobus tokodaii.

Biobattery, a kind of enzymatic fuel cells, can convert organic compounds (e.g., glucose, starch) to electricity in a closed system without moving parts. Inspired by natural starch metabolism catalyzed by starch phosphorylase, isoamylase is essential to debranch alpha-1,6-glycosidic bonds of starch, yielding linear amylodextrin - the best fuel for sugar-powered biobattery. However, there is no thermostable isoamylase stable enough for simultaneous starch gelatinization and enzymatic hydrolysis, different from the case of thermostable alpha-amylase. A putative isoamylase gene was mined from megagenomic database. The open reading frame ST0928 from a hyperthermophilic archaeron Sulfolobus tokodaii was cloned and expressed in E. coli. The recombinant protein was easily purified by heat precipitation at 80 (o)C for 30 min. This enzyme was characterized and required Mg(2+) as an activator. This enzyme was the most stable isoamylase reported with a half lifetime of 200 min at 90 (o)C in the presence of 0.5 mM MgCl2, suitable for simultaneous starch gelatinization and isoamylase hydrolysis. The cuvett-based air-breathing biobattery powered by isoamylase-treated starch exhibited nearly doubled power outputs than that powered by the same concentration starch solution, suggesting more glucose 1-phosphate generated.

The heteromultimeric debranching enzyme involved in starch synthesis in Arabidopsis requires both isoamylase1 and isoamylase2 subunits for complex stability and activity.

Isoamylase-type debranching enzymes (ISAs) play an important role in determining starch structure. Amylopectin - a branched polymer of glucose - is the major component of starch granules and its architecture underlies the semi-crystalline nature of starch. Mutants of several species lacking the ISA1-subclass of isoamylase are impaired in amylopectin synthesis. Consequently, starch levels are decreased and an aberrant soluble glucan (phytoglycogen) with altered branch lengths and branching pattern accumulates. Here we use TAP (tandem affinity purification) tagging to provide direct evidence in Arabidopsis that ISA1 interacts with its homolog ISA2. No evidence for interaction with other starch biosynthetic enzymes was found. Analysis of the single mutants shows that each protein is destabilised in the absence of the other. Co-expression of both ISA1 and ISA2 Escherichia coli allowed the formation of the active recombinant enzyme and we show using site-directed mutagenesis that ISA1 is the catalytic subunit. The presence of the active isoamylase alters glycogen biosynthesis in E. coli, resulting in colonies that stain more starch-like with iodine. However, analysis of the glucans reveals that rather than producing an amylopectin like substance, cells expressing the active isoamylase still accumulate small amounts of glycogen together with a population of linear oligosaccharides that stain strongly with iodine. We conclude that for isoamylase to promote amylopectin synthesis it needs to act on a specific precursor (pre-amylopectin) generated by the combined actions of plant starch synthase and branching enzyme isoforms and when presented with an unsuitable substrate (i.e. E. coli glycogen) it simply degrades it.

Purification, characterization and cloning of a thermotolerant isoamylase produced from Bacillus sp. CICIM 304.

A novel thermostable isoamylase, IAM, was purified to homogeneity from the newly isolated thermophilic bacterium Bacillus sp. CICIM 304. The purified monomeric protein with an estimated molecular mass of 100 kDa displayed its optimal temperature and pH at 70 °C and 6.0, respectively, with excellent thermostability between 30 and 70 °C and pH values from 5.5 to 9.0. Under the conditions of temperature 50 °C and pH 6.0, the K m and V max on glycogen were 0.403 ± 0.018 mg/mg and 0.018 ± 0.001 mg/(min mg), respectively. Gene encoding IAM, BsIam was identified from genomic DNA sequence with inverse PCRs. The open reading frame of the BsIam gene was 2,655 base pairs long and encoded a polypeptide of 885 amino acids with a calculated molecular mass of 101,155 Da. The deduced amino acid sequence of IAM shared less than 40 % homology with that of microbial isoamylase ever reported, which indicated it was a novel isoamylase. This enzyme showed its obvious superiority in the industrial starch conversion process.

Isolation and partial characterization of three isoamylases of Rhyzopertha dominica F. (Coleoptera: Bostrichidae).

Three isoamylases of Rhyzopertha dominica (termed RdA70, RdA79, and RdA90 according to their relative mobility in gel electrophoresis) were isolated by ammonium sulfate fractionation and hydrophobic interaction chromatography. RdA70 and RdA79 showed an optimal pH of 7.0, whereas for RdA90 the optimal pH was 6.5. The three isoamylases remained stable at 50 degrees C for 1 h, but at 60 degrees C, all lost 50% of their activity in 20 min and were completely inactivated in 1 h. RdA70 and RdA79 were inhibited by albumin extracts from wheat samples varying widely in amylase inhibitory activity; however, RdA90 was highly resistant to inhibition. beta-Mercaptoethanol up to 30 mM increased the activity of the three isoamylases by 2.5-fold. The action pattern of the three isoamylases was typical of endoamylases; however, differences were observed on the hydrolytic efficiency rates measured as V(max)/K(m) ratio on starch, amylopectin, and amylose. The hydrolyzing action of RdA90 on starch and amylopectin (V(max)/K(m)=90.4+/-2.3 and 78.9+/-6.6, respectively) was less efficient than that on amylose (V(max)/K(m)=214+/-23.2). RdA79 efficiently hydrolyzed both amylopectin and amylose (V(max)/K(m)=260.6+/-12.9 and 326.5+/-9.4, respectively). RdA70 hydrolyzed starch and amylose at similar rates (V(max)/K(m)=202.9+/-5.5 and 215.9+/-6.2, respectively), but amylopectin was a poor substrate (V(max)/K(m)=124.2+/-7.4). The overall results suggest that RdA70 and RdA79 appear to belong to a group of saccharifying isoamylases that breaks down long fragments of oligosaccharide chains produced by the hydrolytic action of RdA90. The simultaneous action of the three isoamylases on starch, aside from the high resistance of RdA90 to wheat amylase inhibitors, might allow R. dominica to feed and reproduce successfully on the wheat kernel.

Differential chain-length specificities of two isoamylase-type starch-debranching enzymes from developing seeds of kidney bean.

Plant isoamylase-type starch-debranching enzymes (ISAs) hydrolyze alpha-1,6-linkages in alpha-1,4/alpha-1,6-linked polyglucans. Two ISAs, designated PvISA1/2 and PvISA3, were purified from developing seeds of kidney bean by ammonium sulfate fractionation and several column chromatographic procedures. The enzymes displayed different substrate specificities for polyglucans: PvISA1/2 showed broad chain-length specificities, whereas PvISA3 liberated specific chains with a DP of 2 to 4.

Biochemical characterization of wild-type and mutant isoamylases of Chlamydomonas reinhardtii supports a function of the multimeric enzyme organization in amylopectin maturation.

Chlamydomonas reinhardtii mutants of the STA8 gene produce reduced amounts of high amylose starch and phytoglycogen. In contrast to the previously described phytoglycogen-producing mutants of C. reinhardtii that contain no residual isoamylase activity, the sta8 mutants still contained 35% of the normal amount of enzyme activity. We have purified this residual isoamylase and compared it with the wild-type C. reinhardtii enzyme. We have found that the high-mass multimeric enzyme has reduced its average mass at least by one-half. This coincides with the disappearance of two out of the three activity bands that can be seen on zymogram gels. Wild-type and mutant enzymes are shown to be located within the plastid. In addition, they both act by cleaving off the outer branches of polysaccharides with no consistent difference in enzyme specificity. Because the mutant enzyme was demonstrated to digest phytoglycogen to completion in vitro, we propose that its inability to do so in vivo supports a function of the enzyme complex architecture in the processing of pre-amylopectin chains.

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.

Purification, characterization, and cDNA structure of isoamylase from developing endosperm of rice.

Isoamylase (EC 3.2.1.68) in rice (Oryza sativa L.) was efficiently purified within a day to homogeneity, as confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), from developing endosperm by sequential use of Q Sepharose HP anion-exchange chromatography, ammonium sulfate fractionation, and TSKgel G4000SWXL and G3000SWXL gel filtration chromatography. Although the protein exhibited a molecular size of ca. 83 kDa on SDS-PAGE, the apparent size of the native enzyme was approximately 340 and 490 kDa on TSKgel G3000SWXL and G4000SWXL gel filtration chromatograms, respectively, suggesting that rice isoamylase exists in a homo-tetramer to homo-hexamer form in developing endosperm. The purified rice isoamylase was able to debranch glycogen, phytoglycogen and amylopectin but could not attack pullulan. The optimum pH and temperature for isoamylase activity were found to be pH 6.5 to 7.0 and 30 degrees C, respectively. The enzyme activity was completely inhibited by HgCl2 and p-chloromercuribenzoate at 1 mM. These results indicate that rice isoamylase possesses properties which are distinct from those reported for bacterial isoamylase. Complementary-DNA clones for rice endosperm isoamylase were isolated with a polymerase-chain-reaction product as probe which was generated by primers designed from nucleotides conserved in cDNA for maize Sugary-1 isoamylase (M.G. James et al., 1995. Plant Cell 7: 417-429) and a Pseudomonas amyloderamosa gene encoding isoamylase (A. Amemura et al. 1988, J Biol Chem 263: 9271-9275). The nucleotide sequence and deduced amino acid sequence of the longest clone showed a high similarity to those of maize Surgary-1 isoamylase, but a lesser similarity to those of Pseudomonas amyloderamosa isoamylase. Southern blot analysis and gene mapping analysis indicated that the isoamylase gene exists as a single copy in the rice genome and is located on chromosome 8 of cv. Nipponbare which belongs to the Japonica rice group. Phylogenetic analysis indicated that isoamylases from maize and rice are more closely related to a number of glgX gene products of the blue green alga Synechocystis and various bacteria than to isoamylases from Pseudomonas and Flavobacterium. Hence, it is proposed that glgX proteins are classified as isoamylase-type debranching enzymes. Our tree also showed that all starch- and glycogen-debranching enzymes from plants and bacteria tested can be classified into two distinct types, an isoamylase-type and a pullulanase-type.

A mutant of Arabidopsis lacking a chloroplastic isoamylase accumulates both starch and phytoglycogen.

In this study, our goal was to evaluate the role of starch debranching enzymes in the determination of the structure of amylopectin. We screened mutant populations of Arabidopsis for plants with alterations in the structure of leaf starch by using iodine staining. The leaves of two mutant lines stained reddish brown, whereas wild-type leaves stained brownish black, indicating that a more highly branched polyglucan than amylopectin was present. The mutants were allelic, and the mutation mapped to position 18.8 on chromosome 1. One mutant line lacked the transcript for a gene with sequence similarity to higher plant debranching enzymes, and both mutants lacked a chloroplastic starch-hydrolyzing enzyme. This enzyme was identified as a debranching enzyme of the isoamylase type. The loss of this isoamylase resulted in a 90% reduction in the accumulation of starch in this mutant line when compared with the wild type and in the accumulation of the highly branched water-soluble polysaccharide phytoglycogen. Both normal starch and phytoglycogen accumulated simultaneously in the same chloroplasts in the mutant lines, suggesting that isoamylase has an indirect rather than a direct role in determining amylopectin structure.

An isoamylase with neutral pH optimum from a Flavobacterium species: cloning, characterization and expression of the iam gene.

The gene encoding an isoamylase with neutral pH optimum (iam) from a Flavobacterium species was cloned using a PCR probe generated from highly conserved regions of amylolytic enzymes. Active isoamylase was expressed from a 4.9-kb Pst I fragment in Escherichia coli, and was detected in the extracellular medium by a plate assay. The iam nucleotide sequence has an open reading frame of 2334 nucleotides (778 amino acids) with a GC content of 69%. Sequence analysis suggests that transcriptional control of the Flavobacterium sp. iam gene is mediated through the product of a malT regulatory gene. The deduced amino acid sequence of iam contained an N-terminal signal peptide of 32 amino acids, and was 61% homologous with Pseudomonas amyloderamosa isoamylase. The mature enzyme, which was engineered for overexpression in E. coli and purified to homogeneity, has a relative molecular mass of 83 kDa, a pH optimum of 6-7, and a highest rate of hydrolysis for glycogen (but did not cleave pullulan). Polyclonal antiserum generated from purified donor isoamylase cross-reacted with crude and purified recombinant isoamylase from E. coli. This is the first report of the cloning, characterization, and sequence of an novel isoamylase that has a neutral pH optimum. A comparison of the sequence of Flavobacterium sp. iam with acidic isoamylase from Pseudomonas sp. identified putative residues which may be associated with the pH for optimal activity of isoamylases.

Isoamylase determination by isoelectric focusing in pancreatic disorders. A potential clinical aid.

Isoamylase analysis by isoelectric focusing was performed in the serum of 30 healthy volunteers, 65 patients with acute or chronic pancreatic diseases, nine with acute abdomen, four with macroamylasemia, and four with duodenal duplication. In controls, up to four fractions (2 salivary, 2 pancreatic) were found; the pancreatic fractions were as a mean 44.7% (SD 8.6) of total. In chronic pancreatitis, only patients with steatorrhea showed a significant reduction of pancreatic isoamylase (p less than 0.001). In all patients with acute pancreatitis or pseudocysts, an additional fraction (similar to the so-called P3 fraction) was resolved. Moreover, additional isoenzymes were found in all patients with severe acute pancreatitis or pseudocysts, and not in controls or patients with mild forms, acute abdomen or duodenal duplication. A similar pattern was shown in a stored control serum after 10 mo at -20 degrees C. These fractions disappeared after successful surgical drainage. No specific alteration was found in pancreatic cancer. Amylase fractionation by isoelectric focusing can be used to confirm an acute pancreatitis, and to monitor patients with pancreatic pseudocysts and collections after surgical drainage.

Cloning and nucleotide sequence of the isoamylase gene from a strain of Pseudomonas sp.

A strain of Pseudomonas sp., SMP1, isolated from a soil sample collected in the Monterotondo area (Rome), secreted isoamylase activity into the culture medium. The enzyme was purified and optimal reaction and stability conditions were determined by varying pH and temperature. The chemico-physical properties of the enzyme were similar to those of the isoamylase purified in Japan more than 20 years ago from 'Pseudomonas amyloderamosa' strain SB15. A genomic library of SMP1 was prepared in Escherichia coli using pUC12 as vector. Two isoamylase-producing colonies were identified out of 6300 screened. The hybrid plasmids isolated from the two clones showed common restriction patterns. The chromosomal portion of one of these plasmids (pSM257) was completely sequenced. Comparison between the deduced amino acid sequence of the isoamylase and the published sequences of other amylolytic enzymes showed the presence of conserved domains.

Three methods compared for isoamylase separation in tissue homogenates.

Using homogenates of autopsy tissue, we compared three widely available techniques for separating amylase isoenzymes: wheat-germ inhibition (WI), and electrophoresis on cellulose acetate (CA) or agarose (AG). WI separated amylase into two isoforms, CA into seven (three pancreatic and four salivary), and AG into nine (five pancreatic and four salivary). CA and WI had similar isoamylase detection limits (8-10 U/L) and similar imprecision in measuring percent S-type vs P-type isoamylase (within-run SD 1-2%), and they demonstrated a linear response to added S or P isoamylase. In contrast, the AG method had higher detection limits (10-15 U/L), greater imprecision (within-run SD 3%), and showed a nonlinear response to added S or P isomylase. We conclude that CA and WI have essentially equivalent assay attributes, superior to AG, but that CA resolves more amylase isoforms than WI.

Metabolism of human isoamylases in the rabbit.

Human isoamylases were purified from pancreas and saliva with separation of salivary isoenzymes into glycosylated and nonglycosylated forms. After iodination, bolus injection of each purified isoamylase into conscious rabbits revealed biexponential disappearance from plasma. Glycosylated salivary amylase had a metabolic clearance (t 1/2 = 35 min) that was three to four times faster than nonglycosylated salivary (t 1/2 = 139 min) or pancreatic (t 1/2 = 111 min) amylase. In contrast to our previous studies on homologous (rabbit) isoamylases, human pancreatic isoamylase was excreted into urine as protein-bound radioactivity more readily than salivary isoamylase. No organ contained more than 18% of the injected dose of radioactivity except for a striking accumulation of radioactivity in the liver after injection of 125I-labeled glycosylated salivary amylase. We concluded that 1) human nonglycosylated salivary amylase and pancreatic amylase are cleared from the rabbit circulation at rates comparable with those reported for homologous isoamylases in the rabbit and baboon, 2) the rabbit kidney excretes human pancreatic amylase into urine more readily than human salivary isoamylases, and 3) with the notable exception of glycosylated salivary isoamylase, human isoamylases do not appear to be metabolized primarily by any single organ.

Development of an agarose gel electrophoresis technique for determining alpha-amylase isoenzymes.

Evaluation of alpha-amylase isoenzymes as a clinical diagnostic aid by previous methodologies has been either too insensitive or too cumbersome for routine clinical laboratory use. With use of an agarose gel electrophoresis system (Worthington Diagnostic Systems, Inc.) serum amylase activity can easily be resolved into at least nine isoenzymes, the resolution being comparable with that of isoelectric focusing. Samples can be analyzed in less than one working day, with use of conventional reagents.

Aging changes of pancreatic isoamylases and the appearance of "old amylase" in the serum of patients with pancreatic pseudocysts.

Human serum and pancreatic secretions contain at least three isoamylases of pancreatic origin. As determined by gel electrophoresis and saccharogenic amylase assay, P1, P2, and P3 designate isoenzymes with slow, intermediate, and rapid electrophoretic mobilities, respectively. The P1 isoamylase normally accounts fo 80-90% of total amylase activity, P2 for 10-20%, and P3 for 0-4% in both serum and pancreatic juice. When pancreatic amylase is incubated at 37 degrees C, P1 decreases, and P2 and P3 increase within hours. Whereas P2/P1 is always < 0.25 in fresh pancreatic juice, normal serum, acute pancreatitis serum, chronic pancreatitis serum, or pancreatic cancer serum, the ratio was elevated in 11 of 12 pseudocyst contents (mean P2/P1 = 0.51) and in 14 of 16 sera from patients with proven pseudocysts (mean P2/P1 = 0.43) (P < 0.001). After pseudocysts were surgically drained, the proportions of the pancreatic isoamylases in serum reverted to normal. The precise, characteristic, and predictable changes in electrophoretic mobility, presumably a result of specific spontaneous chemical alterations of the isoenzyme molecules, allow identification of "old amylase" in the serum of patients with pancreatic pseudocysts. This finding may be a useful adjunct for diagnosis, but whether the amount of "old amylase" can be used to estimate the age of a pseudocyst is not yet known.